# HG changeset patch
# User ashvark
# Date 1405684534 14400
# Node ID a9636dc1e99aee939cad5b7c5f46116197f3b1c9
# Parent dd1186b11b3b6550d3e971898995e91664cc074a
Deleted selected files
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/COPYING
--- a/bwa-0.6.2/COPYING Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,674 +0,0 @@
- GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc.
- Everyone is permitted to copy and distribute verbatim copies
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- Preamble
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-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
- 17. Interpretation of Sections 15 and 16.
-
- If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
- END OF TERMS AND CONDITIONS
-
- How to Apply These Terms to Your New Programs
-
- If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-
- Copyright (C)
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
-
-Also add information on how to contact you by electronic and paper mail.
-
- If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
- Copyright (C)
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-.
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/ChangeLog
--- a/bwa-0.6.2/ChangeLog Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,3864 +0,0 @@
-------------------------------------------------------------------------
-r1605 | lh3 | 2010-12-29 20:20:20 -0500 (Wed, 29 Dec 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.9rc1-2 (r1605)
- * fixed a typo/bug in bwasw
-
-------------------------------------------------------------------------
-r1587 | lh3 | 2010-12-21 18:48:30 -0500 (Tue, 21 Dec 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
-
-a typo in the manual
-
-------------------------------------------------------------------------
-r1586 | lh3 | 2010-12-21 18:47:48 -0500 (Tue, 21 Dec 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/utils.c
- M /branches/prog/bwa/utils.h
-
- * bwa-0.5.9rc1-1 (r1586)
- * a few patches by John
-
-------------------------------------------------------------------------
-r1562 | lh3 | 2010-12-10 01:02:06 -0500 (Fri, 10 Dec 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
-
-documentation on specifying @RG
-
-------------------------------------------------------------------------
-r1561 | lh3 | 2010-12-10 00:45:40 -0500 (Fri, 10 Dec 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/main.c
-
-Release bwa-0.5.9rc1 (r1561)
-
-------------------------------------------------------------------------
-r1560 | lh3 | 2010-12-10 00:29:08 -0500 (Fri, 10 Dec 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwaseqio.c
- M /branches/prog/bwa/main.c
-
- * fixed a small memory leak caused by the BAM reader
- * fixed a memory violation, also in the BAM reader
-
-------------------------------------------------------------------------
-r1559 | lh3 | 2010-12-10 00:10:48 -0500 (Fri, 10 Dec 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/Makefile
-
-change Makefile gcc options
-
-------------------------------------------------------------------------
-r1558 | lh3 | 2010-12-10 00:09:22 -0500 (Fri, 10 Dec 2010) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.8-6 (r1557)
- * added a little more comments to BWA-SW
- * randomly choosing a mapping if there are more than one
-
-------------------------------------------------------------------------
-r1557 | lh3 | 2010-12-09 21:58:00 -0500 (Thu, 09 Dec 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwtsw2_aux.c
-
-sometimes unmapped reads may not be printed...
-
-------------------------------------------------------------------------
-r1556 | lh3 | 2010-12-09 21:50:26 -0500 (Thu, 09 Dec 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwtsw2_aux.c
-
-print unmapped reads
-
-------------------------------------------------------------------------
-r1555 | lh3 | 2010-12-09 21:17:20 -0500 (Thu, 09 Dec 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.8-5 (r1555)
- * BAM input documentation
-
-------------------------------------------------------------------------
-r1544 | lh3 | 2010-11-23 11:01:41 -0500 (Tue, 23 Nov 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.8-4 (r1544)
- * supporting adding RG tags and RG lines
-
-------------------------------------------------------------------------
-r1543 | lh3 | 2010-11-23 00:16:40 -0500 (Tue, 23 Nov 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.8-3 (r1543)
- * fixed a memory leak
-
-------------------------------------------------------------------------
-r1542 | lh3 | 2010-11-22 23:50:56 -0500 (Mon, 22 Nov 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.8-2 (r1542)
- * fixed a long existing bug in random placement of reads
-
-------------------------------------------------------------------------
-r1541 | lh3 | 2010-11-22 23:27:29 -0500 (Mon, 22 Nov 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- A /branches/prog/bwa/bamlite.c
- A /branches/prog/bwa/bamlite.h
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwaseqio.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
-preliminary BAM input support
-
-------------------------------------------------------------------------
-r1537 | lh3 | 2010-10-16 23:46:20 -0400 (Sat, 16 Oct 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/bwa.1
-
-change version number and ChangeLog
-
-------------------------------------------------------------------------
-r1536 | lh3 | 2010-10-16 23:35:10 -0400 (Sat, 16 Oct 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/stdaln.c
-
- * fixed a bug in the scoring matrix
- * release bwa-0.5.8c (r1536)
-
-------------------------------------------------------------------------
-r1451 | lh3 | 2010-06-15 09:43:52 -0400 (Tue, 15 Jun 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
-
-version change
-
-------------------------------------------------------------------------
-r1450 | lh3 | 2010-06-15 09:42:21 -0400 (Tue, 15 Jun 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/stdaln.c
-
- * bwa-0.5.8b (r1450)
- * fixed a bug in scoring matrix
-
-------------------------------------------------------------------------
-r1445 | lh3 | 2010-06-11 08:58:33 -0400 (Fri, 11 Jun 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwape.c
-
-fixed a serious bug
-
-------------------------------------------------------------------------
-r1442 | lh3 | 2010-06-08 10:22:14 -0400 (Tue, 08 Jun 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/main.c
-
-Release bwa-0.5.8 (r1442)
-
-------------------------------------------------------------------------
-r1440 | lh3 | 2010-05-19 13:43:50 -0400 (Wed, 19 May 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-r1440
- * sorry, forget to remove a debugging line
-
-------------------------------------------------------------------------
-r1439 | lh3 | 2010-05-19 13:43:08 -0400 (Wed, 19 May 2010) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-r1439
- * fixed a bug in bwasw caused by a recent modification
- * throwing insane insert size when estimating isize
-
-------------------------------------------------------------------------
-r1425 | lh3 | 2010-04-29 15:15:23 -0400 (Thu, 29 Apr 2010) | 10 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.7-7 (r1425)
- * fixed a minor bug in bwasw command-line parsing
- * When band-width is not large enough, bwasw may find two highly
- overlapping but not completely overlapping alignments. The old
- version will filter out one of them, which leads to false
- negatives. The current outputs both. This solution is obviously not
- ideal. The ideal one would be to increase the band-width and redo the
- alignment.
-
-
-------------------------------------------------------------------------
-r1399 | lh3 | 2010-04-16 09:20:49 -0400 (Fri, 16 Apr 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.7-6 (r1399)
- * fixed a typo/bug (by Vaughn Iverson)
-
-------------------------------------------------------------------------
-r1329 | lh3 | 2010-03-19 23:32:46 -0400 (Fri, 19 Mar 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
-
-small correction
-
-------------------------------------------------------------------------
-r1328 | lh3 | 2010-03-19 23:28:44 -0400 (Fri, 19 Mar 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.7-4 (r1328)
- * automatically adjust ap_prior based on alignment
-
-------------------------------------------------------------------------
-r1327 | lh3 | 2010-03-19 23:02:40 -0400 (Fri, 19 Mar 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/stdaln.c
- M /branches/prog/bwa/stdaln.h
-
- * bwa-0.5.7-3 (r1327)
- * evaluate hits obtained from SW alignment in a more proper way.
-
-------------------------------------------------------------------------
-r1320 | lh3 | 2010-03-17 15:13:22 -0400 (Wed, 17 Mar 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
-
-fixed a potential out-of-boundary error. Need more testing.
-
-------------------------------------------------------------------------
-r1319 | lh3 | 2010-03-14 22:44:46 -0400 (Sun, 14 Mar 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
-
-insert size is `weird' if the 3rd quatile larger than 100,000bp
-
-------------------------------------------------------------------------
-r1318 | lh3 | 2010-03-14 22:37:35 -0400 (Sun, 14 Mar 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.7-2 (r1318)
- * in sampe, allow to disable insert size estimate
-
-------------------------------------------------------------------------
-r1317 | lh3 | 2010-03-14 22:14:14 -0400 (Sun, 14 Mar 2010) | 5 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/solid2fastq.pl
-
- * bwa-0.5.7-1 (r1317)
- * fixed a potential bug in solid2fastq.pl
- * fixed a bug in calculating mapping quality (by Rodrigo Goya)
- * fixed a very rare bug (if ever occur) about pairing
-
-------------------------------------------------------------------------
-r1310 | lh3 | 2010-03-01 10:35:45 -0500 (Mon, 01 Mar 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/main.c
-
-Release bwa-0.5.7
-
-------------------------------------------------------------------------
-r1309 | lh3 | 2010-02-26 21:42:22 -0500 (Fri, 26 Feb 2010) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.6-2 (r1309)
- * fixed an unfixed bug (by Carol Scott)
- * fixed some tiny formatting
-
-------------------------------------------------------------------------
-r1305 | lh3 | 2010-02-25 13:47:58 -0500 (Thu, 25 Feb 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.6-1 (r1304)
- * optionally write output to a file (by Tim Fennel)
-
-------------------------------------------------------------------------
-r1303 | lh3 | 2010-02-10 23:43:48 -0500 (Wed, 10 Feb 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
-Release bwa-0.5.6
-
-------------------------------------------------------------------------
-r1302 | lh3 | 2010-02-10 11:11:49 -0500 (Wed, 10 Feb 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.5-10 (r1302)
- * improve max insert size estimate (method suggested by Gerton Lunter)
-
-------------------------------------------------------------------------
-r1301 | lh3 | 2010-02-09 16:15:28 -0500 (Tue, 09 Feb 2010) | 5 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.5-9 (r1301)
- * improve mapping quality calculation for abnomalous pairs
- * fixed a bug in multiple hits
- * SOLiD multiple hits should work now
-
-------------------------------------------------------------------------
-r1300 | lh3 | 2010-02-09 12:50:02 -0500 (Tue, 09 Feb 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.5-8 (r1300)
- * output kurtosis
-
-------------------------------------------------------------------------
-r1299 | lh3 | 2010-02-09 12:33:34 -0500 (Tue, 09 Feb 2010) | 5 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.5-7 (r1299)
- * calculate skewness in sampe
- * increase min_len in SW to 20
- * perform more SW to fix discordant pairs
-
-------------------------------------------------------------------------
-r1298 | lh3 | 2010-02-08 12:40:31 -0500 (Mon, 08 Feb 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/cs2nt.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/stdaln.h
-
- * bwa-0.5.5-6 (r1297)
- * prepare to replace all 16-bit CIGAR (patches by Rodrigo Goya)
-
-------------------------------------------------------------------------
-r1297 | lh3 | 2010-02-05 22:26:11 -0500 (Fri, 05 Feb 2010) | 2 lines
-Changed paths:
- M /branches/prog/bwa/solid2fastq.pl
-
-the old fix seems not working!
-
-------------------------------------------------------------------------
-r1296 | lh3 | 2010-02-05 21:51:03 -0500 (Fri, 05 Feb 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.5-5 (r1296)
- * fixed a minor issue that the lower bound of insert size is not correctly set.
-
-------------------------------------------------------------------------
-r1295 | lh3 | 2010-02-05 21:01:10 -0500 (Fri, 05 Feb 2010) | 5 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwaseqio.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.5-4 (r1295)
- * fixed a memory leak
- * change the behaviour of -n (samse and sampe)
- * change the default of -n
-
-------------------------------------------------------------------------
-r1294 | lh3 | 2010-02-05 17:24:06 -0500 (Fri, 05 Feb 2010) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwaseqio.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.5-3 (r1294)
- * improved multi-hit report
-
-------------------------------------------------------------------------
-r1293 | lh3 | 2010-02-05 12:57:38 -0500 (Fri, 05 Feb 2010) | 5 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/cs2nt.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/solid2fastq.pl
-
- * bwa-0.5.5-2 (r1293)
- * bugfix: truncated quality string
- * bugfix: quality -1 in solid->fastq conversion
- * bugfix: color reads on the reverse strand is not complemented
-
-------------------------------------------------------------------------
-r1279 | lh3 | 2009-11-23 22:42:34 -0500 (Mon, 23 Nov 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bntseq.h
- M /branches/prog/bwa/bwase.c
- A /branches/prog/bwa/bwase.h
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.5-1 (r1279)
- * incorporate changes from Matt Hanna for Java bindings.
-
-------------------------------------------------------------------------
-r1275 | lh3 | 2009-11-10 22:13:10 -0500 (Tue, 10 Nov 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
-
-update ChangeLog
-
-------------------------------------------------------------------------
-r1273 | lh3 | 2009-11-10 22:08:16 -0500 (Tue, 10 Nov 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/main.c
- A /branches/prog/bwa/qualfa2fq.pl
-
-Release bwa-0.5.5 (r1273)
-
-------------------------------------------------------------------------
-r1272 | lh3 | 2009-11-10 22:02:50 -0500 (Tue, 10 Nov 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.4-3 (r1272)
- * fixed another typo which may lead to incorrect single-end mapping quality
-
-------------------------------------------------------------------------
-r1271 | lh3 | 2009-11-10 21:59:47 -0500 (Tue, 10 Nov 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.4-2 (r1271)
- * fixed a serious typo/bug which does not hurt if we allow one gap open
- and work with <200bp reads, but causes segfault for long reads.
-
-------------------------------------------------------------------------
-r1270 | lh3 | 2009-11-09 23:12:42 -0500 (Mon, 09 Nov 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/cs2nt.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.4-1 (r1270)
- * fixed a bug in color alignment
-
-------------------------------------------------------------------------
-r1245 | lh3 | 2009-10-09 07:42:52 -0400 (Fri, 09 Oct 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwaseqio.c
- M /branches/prog/bwa/main.c
-
-Release bwa-0.5.4
-
-------------------------------------------------------------------------
-r1244 | lh3 | 2009-10-09 05:53:52 -0400 (Fri, 09 Oct 2009) | 5 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwaseqio.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/stdaln.c
-
- * bwa-0.5.3-4 (r1244)
- * output the clipped length in XC:i: tag
- * skip mate alignment when stdaln is buggy
- * fixed a bug in NM:i: tag
-
-------------------------------------------------------------------------
-r1243 | lh3 | 2009-10-07 08:15:04 -0400 (Wed, 07 Oct 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.3-3 (r1243)
- * sampe: fixed a bug when a read sequence is identical its reverse complement.
-
-------------------------------------------------------------------------
-r1242 | lh3 | 2009-10-07 07:49:13 -0400 (Wed, 07 Oct 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.3-2 (r1242)
- * sampe: optionall preload the full index into memory
- * aln: change the default seed length to 32bp
-
-------------------------------------------------------------------------
-r1238 | lh3 | 2009-09-26 18:38:15 -0400 (Sat, 26 Sep 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/khash.h
-
-Improve portability of khash.h
-
-------------------------------------------------------------------------
-r1228 | lh3 | 2009-09-15 09:20:22 -0400 (Tue, 15 Sep 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/main.c
-
-fixed a typo
-
-------------------------------------------------------------------------
-r1227 | lh3 | 2009-09-15 09:19:35 -0400 (Tue, 15 Sep 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.3-1 (r1226)
- * in dBWT-SW, optionall use hard clipping instead of soft clipping
-
-------------------------------------------------------------------------
-r1225 | lh3 | 2009-09-15 08:32:30 -0400 (Tue, 15 Sep 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
-Release bwa-0.5.3 (r1225)
-
-------------------------------------------------------------------------
-r1223 | lh3 | 2009-09-13 07:30:41 -0400 (Sun, 13 Sep 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/main.c
-
-Release bwa-0.5.2
-
-------------------------------------------------------------------------
-r1222 | lh3 | 2009-09-11 09:11:39 -0400 (Fri, 11 Sep 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.1-5 (r1222)
- * fixed a typo. No real change
-
-------------------------------------------------------------------------
-r1221 | lh3 | 2009-09-11 09:09:44 -0400 (Fri, 11 Sep 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwaseqio.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.1-4 (r1221)
- * trim reads before alignment
-
-------------------------------------------------------------------------
-r1216 | lh3 | 2009-09-08 17:50:15 -0400 (Tue, 08 Sep 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.1-3 (r1216)
- * fixed a bug about NM tags for gapped alignment
- * print SAM header
-
-------------------------------------------------------------------------
-r1215 | lh3 | 2009-09-08 17:14:42 -0400 (Tue, 08 Sep 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.1-2 (r1215)
- * fixed a bug when read lengths vary (by John Marshall)
-
-------------------------------------------------------------------------
-r1213 | lh3 | 2009-09-06 18:58:15 -0400 (Sun, 06 Sep 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.1-1 (r1213)
- * change default -T to 30
-
-------------------------------------------------------------------------
-r1209 | lh3 | 2009-09-02 06:06:02 -0400 (Wed, 02 Sep 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/main.c
-
-Release bwa-0.5.1
-
-------------------------------------------------------------------------
-r1208 | lh3 | 2009-09-02 05:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
-
- * ChangeLog
-
-------------------------------------------------------------------------
-r1206 | lh3 | 2009-08-30 18:27:30 -0400 (Sun, 30 Aug 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.0-6 (r1206)
- * fixed two bugs caused by previous modification
-
-------------------------------------------------------------------------
-r1205 | lh3 | 2009-08-30 17:28:36 -0400 (Sun, 30 Aug 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.0-4 (r1205)
- * reduce false coordinates and CIGAR when a query bridges two reference
- sequences, although some very rare cases may fail bwa.
-
-------------------------------------------------------------------------
-r1204 | lh3 | 2009-08-30 06:06:16 -0400 (Sun, 30 Aug 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.0-3 (r1204)
- * choose one repetitive hit to extend
-
-------------------------------------------------------------------------
-r1203 | lh3 | 2009-08-29 18:11:51 -0400 (Sat, 29 Aug 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.0-2 (r1203)
- * dBWT-SW: change a parameter in calculating mapping quality
- * fixed a bug in samse
-
-------------------------------------------------------------------------
-r1202 | lh3 | 2009-08-28 19:48:41 -0400 (Fri, 28 Aug 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.5.0-1 (r1202)
- * change default band width to 50
- * improve mapping quality a bit
-
-------------------------------------------------------------------------
-r1200 | lh3 | 2009-08-20 06:21:24 -0400 (Thu, 20 Aug 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/main.c
-
-Release bwa-0.5.0 (r1200)
-
-------------------------------------------------------------------------
-r1199 | lh3 | 2009-08-20 04:49:15 -0400 (Thu, 20 Aug 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/bwa.1
-
-Updated ChangeLog and the manual
-
-------------------------------------------------------------------------
-r1198 | lh3 | 2009-08-19 11:09:15 -0400 (Wed, 19 Aug 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-36 (r1198)
- * simplify duphits removal. The accuracy is changed a tiny bit, sometimes better, sometimes worse.
-
-------------------------------------------------------------------------
-r1197 | lh3 | 2009-08-19 08:15:05 -0400 (Wed, 19 Aug 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwtsw2_aux.c
- A /branches/prog/bwa/bwtsw2_chain.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-35 (r1197)
- * further heuristic acceleration for long queries
-
-------------------------------------------------------------------------
-r1196 | lh3 | 2009-08-18 06:54:03 -0400 (Tue, 18 Aug 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-34 (r1196)
- * updated the manual page
- * output base quality if the input is fastq
-
-------------------------------------------------------------------------
-r1195 | lh3 | 2009-08-18 06:23:00 -0400 (Tue, 18 Aug 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/simple_dp.c
-
- * bwa-0.4.9-33 (r1191)
- * fixed a bug in sampe/samse when gaps occur to the 5'-end in SW alignment
- * in dbwtsw adjust -T and -c according to -a
-
-------------------------------------------------------------------------
-r1192 | lh3 | 2009-08-13 05:37:28 -0400 (Thu, 13 Aug 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
-
-update manual
-
-------------------------------------------------------------------------
-r1191 | lh3 | 2009-08-12 19:40:51 -0400 (Wed, 12 Aug 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwtsw2_main.c
-
-update documentation
-
-------------------------------------------------------------------------
-r1190 | lh3 | 2009-08-12 08:56:10 -0400 (Wed, 12 Aug 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-32 (r1190)
- * only help messages are changed
-
-------------------------------------------------------------------------
-r1189 | lh3 | 2009-08-11 09:28:55 -0400 (Tue, 11 Aug 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-31 (r1189)
- * in bwape/bwase, print CIGAR "*" if the read is unmapped
- * improved the calculation of mapping quality
-
-------------------------------------------------------------------------
-r1181 | lh3 | 2009-08-03 12:09:41 -0400 (Mon, 03 Aug 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
-
-fflush()
-
-------------------------------------------------------------------------
-r1180 | lh3 | 2009-08-03 12:08:46 -0400 (Mon, 03 Aug 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-30 (r1180)
- * fixed a memory problem
- * multi-threading sometimes does not work...
-
-------------------------------------------------------------------------
-r1179 | lh3 | 2009-08-03 11:04:39 -0400 (Mon, 03 Aug 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-29 (r1179)
- * preliminary mutli-threading support in dbwtsw
-
-------------------------------------------------------------------------
-r1178 | lh3 | 2009-08-03 09:14:54 -0400 (Mon, 03 Aug 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-28 (r1178)
- * fixed a bug in printing repetitive hits
-
-------------------------------------------------------------------------
-r1177 | lh3 | 2009-08-03 05:03:42 -0400 (Mon, 03 Aug 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-27 (r1177)
- * bwtsw2: fixed a hidden memory leak
-
-------------------------------------------------------------------------
-r1176 | lh3 | 2009-07-31 10:58:24 -0400 (Fri, 31 Jul 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-26
- * change the way mapping quality is calculated
-
-------------------------------------------------------------------------
-r1175 | lh3 | 2009-07-31 09:15:54 -0400 (Fri, 31 Jul 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-25
- * code clean up
- * automatically adjust ->t and ->is_rev based on input
-
-------------------------------------------------------------------------
-r1174 | lh3 | 2009-07-30 08:50:25 -0400 (Thu, 30 Jul 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-24
- * fixed a bug in printing the hits
-
-------------------------------------------------------------------------
-r1173 | lh3 | 2009-07-29 18:32:43 -0400 (Wed, 29 Jul 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-23
- * allow to skip reverse alignment
- * increase opt->t to 37
-
-------------------------------------------------------------------------
-r1172 | lh3 | 2009-07-29 17:22:39 -0400 (Wed, 29 Jul 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-22
- * report if the hit is found in both directions
-
-------------------------------------------------------------------------
-r1171 | lh3 | 2009-07-29 17:12:02 -0400 (Wed, 29 Jul 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-21
- * dbwtsw: map to both forward and reverse BWT to reduce false alignment
-
-------------------------------------------------------------------------
-r1170 | lh3 | 2009-07-29 15:25:14 -0400 (Wed, 29 Jul 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
-save hits before cut_tail()
-
-------------------------------------------------------------------------
-r1169 | lh3 | 2009-07-29 08:06:01 -0400 (Wed, 29 Jul 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/stdaln.c
- M /branches/prog/bwa/stdaln.h
-
- * bwa-0.4.9-19
- * use a global memory pool to reduce the CPU time spent on malloc/free().
-
-------------------------------------------------------------------------
-r1168 | lh3 | 2009-07-29 06:13:29 -0400 (Wed, 29 Jul 2009) | 5 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-18
- * reduce unnecessary extension to the 5'-end
- * allow to use different interval size for the 2 rounds
- * change default parameters
-
-------------------------------------------------------------------------
-r1167 | lh3 | 2009-07-28 19:06:17 -0400 (Tue, 28 Jul 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-17
- * dbwtsw: fixed THE memory leak.
-
-------------------------------------------------------------------------
-r1166 | lh3 | 2009-07-28 16:31:41 -0400 (Tue, 28 Jul 2009) | 5 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/stdaln.c
-
- * bwa-0.4.9-16
- * fixed a memory leak
- * a small memory leak still occurs to bwtsw2_core(). I will work on that later.
- * changed the default parameters
-
-------------------------------------------------------------------------
-r1165 | lh3 | 2009-07-28 10:15:40 -0400 (Tue, 28 Jul 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/stdaln.c
-
- * bwa-0.4.9-15
- * generate CIGAR right before output. This saves unnecessary computation.
- * this version may be buggy as I have not tested it.
-
-------------------------------------------------------------------------
-r1164 | lh3 | 2009-07-28 09:04:14 -0400 (Tue, 28 Jul 2009) | 11 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/stdaln.c
- M /branches/prog/bwa/stdaln.h
-
- * bwa-0.4.9-14
-
- * deplete unique hits in dbwtsw and postprocess them with standard sw
-
- * in principle, this stratgy should be faster and more accurate, but I
- have not tested this point. I may switch back to the old method if
- this does not work.
-
- * the code looks quite nasty now. it needs clean up...
-
-
-------------------------------------------------------------------------
-r1163 | lh3 | 2009-07-27 17:41:10 -0400 (Mon, 27 Jul 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
-
-change a default parameter
-
-------------------------------------------------------------------------
-r1162 | lh3 | 2009-07-27 17:04:35 -0400 (Mon, 27 Jul 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-13
- * dbwtsw: switch between small and large Z-best
-
-------------------------------------------------------------------------
-r1161 | lh3 | 2009-07-27 12:17:41 -0400 (Mon, 27 Jul 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-12
- * changed the default -z to 100
- * heuristically speed up alignments for polyA reads
-
-------------------------------------------------------------------------
-r1160 | lh3 | 2009-07-27 07:50:57 -0400 (Mon, 27 Jul 2009) | 6 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-11
-
- * dbwtsw potentially generates less false alignments, although in
- practice, the modification brings no improvement.
-
-
-------------------------------------------------------------------------
-r1159 | lh3 | 2009-07-27 04:37:02 -0400 (Mon, 27 Jul 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-10
- * disabled debugging code
- * add "BAM_FMU" if both ends are unmapped
-
-------------------------------------------------------------------------
-r1158 | lh3 | 2009-07-24 09:36:52 -0400 (Fri, 24 Jul 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/main.c
-
-nothing, really
-
-------------------------------------------------------------------------
-r1157 | lh3 | 2009-07-24 09:05:44 -0400 (Fri, 24 Jul 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-9
- * bwtsw2: generate SAM output
-
-------------------------------------------------------------------------
-r1156 | lh3 | 2009-07-24 05:42:47 -0400 (Fri, 24 Jul 2009) | 6 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-8
-
- * fixed a weird deadloop which only happens to icc -O3. Thanks John
- Marshall for the fix.
-
-
-------------------------------------------------------------------------
-r1155 | lh3 | 2009-07-24 05:28:40 -0400 (Fri, 24 Jul 2009) | 8 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-7
-
- * fixed a typo in bwtsw2 alignment. Now score from the standard SW
- seems to agree with score from bwtsw2, except that in reporting
- alignments, bwtsw2 may report non-optimal segments. This is expected,
- though. I will improve in future.
-
-
-------------------------------------------------------------------------
-r1154 | lh3 | 2009-07-23 17:40:20 -0400 (Thu, 23 Jul 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/stdaln.c
- M /branches/prog/bwa/stdaln.h
-
- * aln_left_core() seems to work properly
- * aln_local_core() has a bug... AN EVER EXISTING BUG!!!!!!!!!!!
-
-------------------------------------------------------------------------
-r1153 | lh3 | 2009-07-23 17:06:09 -0400 (Thu, 23 Jul 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/stdaln.c
-
-removed debugging code...
-
-------------------------------------------------------------------------
-r1152 | lh3 | 2009-07-23 17:01:00 -0400 (Thu, 23 Jul 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/stdaln.c
-
- * radical changes failed...
- * fixed a bug
-
-------------------------------------------------------------------------
-r1151 | lh3 | 2009-07-23 14:46:35 -0400 (Thu, 23 Jul 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/stdaln.c
-
-temporary changes. Will apply some radical changes to this file...
-
-------------------------------------------------------------------------
-r1150 | lh3 | 2009-07-23 10:09:56 -0400 (Thu, 23 Jul 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/stdaln.c
-
-fixed a long-existing bug in Smith-Waterman alignment
-
-------------------------------------------------------------------------
-r1149 | lh3 | 2009-07-23 08:50:52 -0400 (Thu, 23 Jul 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/simple_dp.c
- M /branches/prog/bwa/stdaln.c
- M /branches/prog/bwa/stdaln.h
-
- * bwa-0.4.9-6
- * unexplained inconsistency still occurs, but the results largely look reasonable.
-
-------------------------------------------------------------------------
-r1148 | lh3 | 2009-07-23 08:07:29 -0400 (Thu, 23 Jul 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/stdaln.c
-
-half DP
-
-------------------------------------------------------------------------
-r1147 | lh3 | 2009-07-22 08:03:06 -0400 (Wed, 22 Jul 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
-
-a bit code clean up
-
-------------------------------------------------------------------------
-r1145 | lh3 | 2009-07-21 15:52:05 -0400 (Tue, 21 Jul 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-5
- * fixed a bug in determining sub-optimal hits
- * removed some debugging codes
-
-------------------------------------------------------------------------
-r1144 | lh3 | 2009-07-21 10:17:29 -0400 (Tue, 21 Jul 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-4
- * better cmd interface
- * faster speed
-
-------------------------------------------------------------------------
-r1143 | lh3 | 2009-07-20 16:38:18 -0400 (Mon, 20 Jul 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
-bwtsw2 (dBWT-SW) is working apparently...
-
-
-------------------------------------------------------------------------
-r1139 | lh3 | 2009-07-15 05:52:18 -0400 (Wed, 15 Jul 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.9-2
- * bwtsw2: change cut_tail() such that it is faster but more likely to
- miss true hits
-
-------------------------------------------------------------------------
-r1138 | lh3 | 2009-07-15 05:18:42 -0400 (Wed, 15 Jul 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- A /branches/prog/bwa/bwt_lite.c
- A /branches/prog/bwa/bwt_lite.h
- A /branches/prog/bwa/bwtsw2.h
- A /branches/prog/bwa/bwtsw2_aux.c
- A /branches/prog/bwa/bwtsw2_core.c
- A /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
-
- * bwa-0.4.9-1
- * added back bwtsw2
-
-------------------------------------------------------------------------
-r1075 | lh3 | 2009-05-19 05:14:50 -0400 (Tue, 19 May 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
-Release bwa-0.4.9
-
-------------------------------------------------------------------------
-r1073 | lh3 | 2009-05-18 17:13:19 -0400 (Mon, 18 May 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/main.c
-
-Release bwa-0.4.8
-
-------------------------------------------------------------------------
-r1069 | lh3 | 2009-05-14 09:54:54 -0400 (Thu, 14 May 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.7-2
- * change the default of "aln -R" to 30
-
-------------------------------------------------------------------------
-r1068 | lh3 | 2009-05-14 09:27:55 -0400 (Thu, 14 May 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.7-1
- * search for suboptimal hits if the top hit is not so repetitive
-
-------------------------------------------------------------------------
-r1066 | lh3 | 2009-05-12 15:31:31 -0400 (Tue, 12 May 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
-Release bwa-0.4.7
-
-------------------------------------------------------------------------
-r1065 | lh3 | 2009-05-12 15:20:40 -0400 (Tue, 12 May 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.6-9
- * fixed compiling errors on some Linux machines
-
-------------------------------------------------------------------------
-r1064 | lh3 | 2009-05-12 07:30:46 -0400 (Tue, 12 May 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.6-8
- * avoid compilation error on some systems.
-
-------------------------------------------------------------------------
-r1035 | lh3 | 2009-05-09 05:41:33 -0400 (Sat, 09 May 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.6-7
- * fixed an integer overflow caused by previous modifications
- * made insert size estimation more robust
-
-------------------------------------------------------------------------
-r1008 | lh3 | 2009-04-29 05:41:58 -0400 (Wed, 29 Apr 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.6-5
- * fixed a integer overflow problem which may cause seg fault in very rare cases
- * made XN tags more accurate
-
-------------------------------------------------------------------------
-r1005 | lh3 | 2009-04-27 07:37:23 -0400 (Mon, 27 Apr 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/simple_dp.c
- M /branches/prog/bwa/stdaln.c
- M /branches/prog/bwa/stdaln.h
-
- * bwa-0.4.6-4
- * heuristic rules to detect suboptimal alignment
- * stdsw: support double-strand and protein alignment
-
-------------------------------------------------------------------------
-r1003 | lh3 | 2009-04-26 12:48:19 -0400 (Sun, 26 Apr 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/simple_dp.c
- M /branches/prog/bwa/stdaln.c
- M /branches/prog/bwa/stdaln.h
-
- * bwa-0.4.6-2
- * improve the functionality of stdsw
- * allow to add a threshold on SW alignment. Hope this does not incur new bugs...
-
-------------------------------------------------------------------------
-r1002 | lh3 | 2009-04-22 03:56:15 -0400 (Wed, 22 Apr 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.6-1
- * output SM and AM tag
-
-------------------------------------------------------------------------
-r914 | lh3 | 2009-03-09 17:53:50 -0400 (Mon, 09 Mar 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/main.c
-
-Release bwa-0.4.6
-
-------------------------------------------------------------------------
-r913 | lh3 | 2009-03-09 17:23:24 -0400 (Mon, 09 Mar 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwape.c
- A /branches/prog/bwa/solid2fastq.pl
-
- * added notes to bwa
- * added a script to convert SOLiD reads
- * updated documentations
-
-------------------------------------------------------------------------
-r912 | lh3 | 2009-03-09 16:57:05 -0400 (Mon, 09 Mar 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/kstring.c
- M /branches/prog/bwa/main.c
-
-fixed a bug in kstring
-
-------------------------------------------------------------------------
-r881 | lh3 | 2009-03-02 15:36:06 -0500 (Mon, 02 Mar 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtmisc.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.5-7
- * fixed a bug in pac2cspac
-
-------------------------------------------------------------------------
-r880 | lh3 | 2009-03-01 16:34:08 -0500 (Sun, 01 Mar 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
-
-disable debugging
-
-------------------------------------------------------------------------
-r879 | lh3 | 2009-03-01 16:28:04 -0500 (Sun, 01 Mar 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/cs2nt.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.5-6
- * fixed problems with coordinates for color gapped alignment
-
-------------------------------------------------------------------------
-r878 | lh3 | 2009-03-01 13:43:09 -0500 (Sun, 01 Mar 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/cs2nt.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.5-5
- * added support for gapped color alignment
-
-------------------------------------------------------------------------
-r877 | lh3 | 2009-03-01 10:27:52 -0500 (Sun, 01 Mar 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/cs2nt.c
- M /branches/prog/bwa/main.c
-
- * convert cs read to nt read (for ungapped alignment only)
-
-------------------------------------------------------------------------
-r860 | lh3 | 2009-02-27 08:58:39 -0500 (Fri, 27 Feb 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwase.c
- A /branches/prog/bwa/cs2nt.c
-
-prepare to implement cs->nt conversion (have not yet...)
-
-------------------------------------------------------------------------
-r859 | lh3 | 2009-02-27 07:00:03 -0500 (Fri, 27 Feb 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bntseq.h
- M /branches/prog/bwa/bwtindex.c
- M /branches/prog/bwa/bwtmisc.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
-
- * bwa-0.4.5-3
- * generate color index from nucleotide fasta reference
-
-------------------------------------------------------------------------
-r857 | lh3 | 2009-02-26 10:22:58 -0500 (Thu, 26 Feb 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.5-2
- * improved mapping quality a bit if one end falls in a tandem repeat
- but the mate is unique.
-
-------------------------------------------------------------------------
-r856 | lh3 | 2009-02-26 10:02:29 -0500 (Thu, 26 Feb 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.5-1
- * make bwa work for SOLiD reads
-
-------------------------------------------------------------------------
-r828 | lh3 | 2009-02-18 17:36:41 -0500 (Wed, 18 Feb 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/main.c
-
-Release bwa-0.4.5
-
-------------------------------------------------------------------------
-r827 | lh3 | 2009-02-18 16:48:48 -0500 (Wed, 18 Feb 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/stdaln.c
- M /branches/prog/bwa/stdaln.h
-
- * bwa-0.4.4-6
- * fixed a bug in SW alignment when no residue matches
-
-------------------------------------------------------------------------
-r824 | lh3 | 2009-02-17 05:33:07 -0500 (Tue, 17 Feb 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.4-5
- * fixed that bounary bug
-
-------------------------------------------------------------------------
-r823 | lh3 | 2009-02-17 04:54:18 -0500 (Tue, 17 Feb 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/bwape.c
-
-just change some logging information
-
-------------------------------------------------------------------------
-r822 | lh3 | 2009-02-17 04:20:39 -0500 (Tue, 17 Feb 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
-
-update manual
-
-------------------------------------------------------------------------
-r821 | lh3 | 2009-02-17 04:11:14 -0500 (Tue, 17 Feb 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.4-4
- * fixed a bug on boundary check in pair_sw
-
-------------------------------------------------------------------------
-r820 | lh3 | 2009-02-16 17:43:37 -0500 (Mon, 16 Feb 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.4-3
- * allow to change mismatch penalty
-
-------------------------------------------------------------------------
-r819 | lh3 | 2009-02-16 17:40:28 -0500 (Mon, 16 Feb 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.4-2
- * remove timer
- * allow to change default gapo and gape penalty at the command line
-
-------------------------------------------------------------------------
-r818 | lh3 | 2009-02-16 09:30:51 -0500 (Mon, 16 Feb 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
-
-update benchmark
-
-------------------------------------------------------------------------
-r817 | lh3 | 2009-02-16 08:44:40 -0500 (Mon, 16 Feb 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/kvec.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.4-1
- * automatically detect insert size
- * use insert size in pairing. This may potentially improve accuracy (untested!)
-
-------------------------------------------------------------------------
-r814 | lh3 | 2009-02-15 11:10:23 -0500 (Sun, 15 Feb 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/main.c
-
-Release bwa-0.4.4
-
-------------------------------------------------------------------------
-r813 | lh3 | 2009-02-15 10:22:50 -0500 (Sun, 15 Feb 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.3-5
- * impose boundary check in refine_gapped
-
-------------------------------------------------------------------------
-r811 | lh3 | 2009-02-14 09:46:13 -0500 (Sat, 14 Feb 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.3-4
- * change MD tag to match the latest SAM specification
-
-------------------------------------------------------------------------
-r810 | lh3 | 2009-02-13 04:46:04 -0500 (Fri, 13 Feb 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
-
-update ChangeLog
-
-------------------------------------------------------------------------
-r799 | lh3 | 2009-02-05 12:01:17 -0500 (Thu, 05 Feb 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
-change MD tag to meet the latest SAM specification
-
-------------------------------------------------------------------------
-r796 | lh3 | 2009-02-05 08:35:13 -0500 (Thu, 05 Feb 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.3-2
- * fixed a bug on counting 'N'
-
-------------------------------------------------------------------------
-r795 | lh3 | 2009-02-05 07:41:27 -0500 (Thu, 05 Feb 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.3-1
- * fixed potential boundary problems
- * update benchmark result
-
-------------------------------------------------------------------------
-r791 | lh3 | 2009-01-25 05:20:47 -0500 (Sun, 25 Jan 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
-
-update some numbers
-
-------------------------------------------------------------------------
-r790 | lh3 | 2009-01-24 15:13:03 -0500 (Sat, 24 Jan 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
-
-update benchmark
-
-------------------------------------------------------------------------
-r789 | lh3 | 2009-01-22 10:18:44 -0500 (Thu, 22 Jan 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtindex.c
-
-a warning message for index
-
-------------------------------------------------------------------------
-r788 | lh3 | 2009-01-22 09:54:06 -0500 (Thu, 22 Jan 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/main.c
-
-forget to change release number
-
-------------------------------------------------------------------------
-r786 | lh3 | 2009-01-22 06:27:39 -0500 (Thu, 22 Jan 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/NEWS
-
-Release bwa-0.4.3
-
-------------------------------------------------------------------------
-r785 | lh3 | 2009-01-22 06:27:16 -0500 (Thu, 22 Jan 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
-
-Release bwa-0.4.3
-
-------------------------------------------------------------------------
-r784 | lh3 | 2009-01-22 06:19:59 -0500 (Thu, 22 Jan 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.2-10
- * update documentation
- * fixed a bug on generating MD tags for SW alignment
-
-------------------------------------------------------------------------
-r782 | lh3 | 2009-01-19 12:08:38 -0500 (Mon, 19 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.2-9
- * fixed a bug in samse -n...
-
-------------------------------------------------------------------------
-r781 | lh3 | 2009-01-19 11:26:37 -0500 (Mon, 19 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.2-8
- * given -N, the previous version would stop if the top hit is a repeat. Now changed.
-
-------------------------------------------------------------------------
-r780 | lh3 | 2009-01-19 11:20:18 -0500 (Mon, 19 Jan 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.2-7
- * use a bit-wise flag to replace some member variables in the option struct
- * allow to switch off the iterative strategy
-
-------------------------------------------------------------------------
-r779 | lh3 | 2009-01-19 10:45:57 -0500 (Mon, 19 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.2-6
- * allow to dump multiple hits from samse, in another format, though
-
-------------------------------------------------------------------------
-r778 | lh3 | 2009-01-19 06:24:29 -0500 (Mon, 19 Jan 2009) | 5 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwaseqio.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/kseq.h
- A /branches/prog/bwa/kstring.c
- A /branches/prog/bwa/kstring.h
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/simple_dp.c
-
- * bwa-0.4.2-5
- * update kseq.h to the latest version
- * generate MD tag
- * print mate coordinate if only one end is unmapped
-
-------------------------------------------------------------------------
-r775 | lh3 | 2009-01-18 05:40:35 -0500 (Sun, 18 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.2-4
- * fixed a bug for SAM format
-
-------------------------------------------------------------------------
-r774 | lh3 | 2009-01-17 13:48:52 -0500 (Sat, 17 Jan 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.2-3
- * change default fnr to 0.04
- * print max_diff for valid fnr
-
-------------------------------------------------------------------------
-r773 | lh3 | 2009-01-17 05:54:37 -0500 (Sat, 17 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.2-2
- * automatically choose max_diff
-
-------------------------------------------------------------------------
-r772 | lh3 | 2009-01-16 18:16:14 -0500 (Fri, 16 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwaseqio.c
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.2-1
- * take N as a mismatch
-
-------------------------------------------------------------------------
-r768 | lh3 | 2009-01-09 11:57:23 -0500 (Fri, 09 Jan 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/main.c
-
-Release bwa-0.4.2
-
-------------------------------------------------------------------------
-r759 | lh3 | 2009-01-07 09:55:43 -0500 (Wed, 07 Jan 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
-Release bwa-0.4.1
-
-------------------------------------------------------------------------
-r758 | lh3 | 2009-01-07 05:36:06 -0500 (Wed, 07 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.0-2
- * make mate_sw fully working
-
-------------------------------------------------------------------------
-r757 | lh3 | 2009-01-06 18:04:29 -0500 (Tue, 06 Jan 2009) | 5 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwaseqio.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.4.0-1
- * do SW alignment for unmapped mate. It is working.
- * I still need to do some extra work for SW alignment, but it is too late
- and I am getting tired... I will do tomorrow.
-
-------------------------------------------------------------------------
-r755 | lh3 | 2009-01-06 10:23:29 -0500 (Tue, 06 Jan 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/main.c
-
-Release bwa-0.4.0
-
-------------------------------------------------------------------------
-r754 | lh3 | 2009-01-06 07:45:02 -0500 (Tue, 06 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/bwtgap.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.3.0-12
- * better lock
-
-------------------------------------------------------------------------
-r753 | lh3 | 2009-01-06 06:17:21 -0500 (Tue, 06 Jan 2009) | 5 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwaseqio.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.3.0-11
- * fixed a small memory leak in bwa_seq_close()
- * fixed "uninitialized memory" from bwt_aln1_t
- * multithreading for "aln" command
-
-------------------------------------------------------------------------
-r752 | lh3 | 2009-01-05 17:34:13 -0500 (Mon, 05 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- D /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwt_gen/bwt_gen.c
- A /branches/prog/bwa/bwtmisc.c (from /branches/prog/bwa/pac2bwt.c:748)
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
- D /branches/prog/bwa/pac2bwt.c
-
- * bwa-0.3.0-10
- * a little bit code clean up
-
-------------------------------------------------------------------------
-r751 | lh3 | 2009-01-05 17:19:04 -0500 (Mon, 05 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.3.0-9
- * use 64-bit integer to speed up Occ calculate, although just a little bit
-
-------------------------------------------------------------------------
-r750 | lh3 | 2009-01-05 16:44:26 -0500 (Mon, 05 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.3.0-8
- * a little bit code cleanup
-
-------------------------------------------------------------------------
-r749 | lh3 | 2009-01-05 16:37:28 -0500 (Mon, 05 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.0-7
- * accelerate Occ calculation
-
-------------------------------------------------------------------------
-r748 | lh3 | 2009-01-05 16:12:28 -0500 (Mon, 05 Jan 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtindex.c
- M /branches/prog/bwa/bwtio.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
- M /branches/prog/bwa/pac2bwt.c
-
- * bwa-0.3.0-6
- * put occ table along with bwt to save another cache miss
- * this version is already faster than the previous and I can still improve it...
-
-------------------------------------------------------------------------
-r747 | lh3 | 2009-01-05 10:16:18 -0500 (Mon, 05 Jan 2009) | 5 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwtio.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.3.0-5
- * remove occ_major to save a cache miss; however, OCC_INTERVAL has to be
- increased to keep the same memory. As a result, the speed is a little
- slower in fact.
-
-------------------------------------------------------------------------
-r746 | lh3 | 2009-01-05 09:50:53 -0500 (Mon, 05 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.3.0-4
- * added back optimization codes (it is a pain...)
-
-------------------------------------------------------------------------
-r745 | lh3 | 2009-01-05 08:23:00 -0500 (Mon, 05 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.3.0-3
- * faster bit operations
-
-------------------------------------------------------------------------
-r744 | lh3 | 2009-01-05 05:58:46 -0500 (Mon, 05 Jan 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.3.0-2
- * removed optimization codes again...
- * use a new method to count the bits
-
-------------------------------------------------------------------------
-r743 | lh3 | 2009-01-04 17:18:38 -0500 (Sun, 04 Jan 2009) | 5 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.3.0-1
- * added back the optimization codes
- * added a new option to aln: max_entries, although this is disabled by default
- * updated benchmark
-
-------------------------------------------------------------------------
-r742 | lh3 | 2009-01-04 07:56:12 -0500 (Sun, 04 Jan 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
-
-add URL
-
-------------------------------------------------------------------------
-r740 | lh3 | 2009-01-04 07:39:43 -0500 (Sun, 04 Jan 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/main.c
-
-Release bwa-0.3.0
-
-------------------------------------------------------------------------
-r739 | lh3 | 2009-01-04 06:55:06 -0500 (Sun, 04 Jan 2009) | 2 lines
-Changed paths:
- A /branches/prog/bwa/COPYING
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bntseq.h
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwtindex.c
- M /branches/prog/bwa/utils.c
- M /branches/prog/bwa/utils.h
-
-added licensing information
-
-------------------------------------------------------------------------
-r738 | lh3 | 2009-01-04 06:18:25 -0500 (Sun, 04 Jan 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-31
- * better mapping quality
- * update benchmark
-
-------------------------------------------------------------------------
-r737 | lh3 | 2009-01-03 16:00:58 -0500 (Sat, 03 Jan 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/bwa.1
-
-update documentation
-
-------------------------------------------------------------------------
-r736 | lh3 | 2009-01-02 10:26:38 -0500 (Fri, 02 Jan 2009) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
-
-update documentation
-
-------------------------------------------------------------------------
-r735 | lh3 | 2009-01-02 07:10:20 -0500 (Fri, 02 Jan 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-30
- * reduce memory a little bit
- * update documentation
-
-------------------------------------------------------------------------
-r734 | lh3 | 2009-01-01 13:45:45 -0500 (Thu, 01 Jan 2009) | 8 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-29
- * sampe: removed -O option; changed default -o to 100000
- * sampe: fixed a bug in calculating paired mapping quality
- * aln: added an option to search for suboptimal hits even if the best is a repeat.
- This option will make sampe MUCH SLOWER.
- * sampe: set isize as zero if mapped to two different chr
- * update manual (unfinished)
-
-------------------------------------------------------------------------
-r733 | lh3 | 2009-01-01 11:01:20 -0500 (Thu, 01 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-28
- * fixed a bug in calculating paired mapping quality
-
-------------------------------------------------------------------------
-r732 | lh3 | 2009-01-01 09:27:46 -0500 (Thu, 01 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- A /branches/prog/bwa/khash.h (from /branches/prog/sclib/khash/khash.h:675)
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-27
- * accelerate sampe by storing visited large intervals
-
-------------------------------------------------------------------------
-r731 | lh3 | 2009-01-01 06:51:21 -0500 (Thu, 01 Jan 2009) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-26
- * remove the optimation codes
-
-------------------------------------------------------------------------
-r730 | lh3 | 2009-01-01 06:48:59 -0500 (Thu, 01 Jan 2009) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-25
- * accelerate OCC calculation by ~7%. However, it seems not worth doing
- this by complicate the codes. I will change back later.
-
-------------------------------------------------------------------------
-r729 | lh3 | 2008-12-31 16:43:56 -0500 (Wed, 31 Dec 2008) | 6 lines
-Changed paths:
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-24
- * change command "sai2sam_pe" to "sampe"
- * print usage for sampe command
- * in sampe: change default max_occ to 1000
- * fixed a few compiling warnings in bntseq.c
-
-------------------------------------------------------------------------
-r728 | lh3 | 2008-12-27 07:14:59 -0500 (Sat, 27 Dec 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-22
- * mating information can be printed to SAM
-
-------------------------------------------------------------------------
-r727 | lh3 | 2008-12-26 18:10:59 -0500 (Fri, 26 Dec 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwaseqio.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-21
- * implement pairing (still UNFINISHED)
- * output all reads even if full of N
-
-------------------------------------------------------------------------
-r726 | lh3 | 2008-12-26 13:31:27 -0500 (Fri, 26 Dec 2008) | 5 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- A /branches/prog/bwa/bwape.c
- M /branches/prog/bwa/bwase.c
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
-
- * bwa-0.2.0-20
- * remove "-t" from aln cmd
- * code clean up: move some functions in bwt2fmv.c to other source files
- * added sai2sam_pe cmd: *UNFINISHED*
-
-------------------------------------------------------------------------
-r725 | lh3 | 2008-12-26 07:04:11 -0500 (Fri, 26 Dec 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- A /branches/prog/bwa/bwase.c
- A /branches/prog/bwa/bwaseqio.c
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/kseq.h
- A /branches/prog/bwa/ksort.h (from /branches/prog/sclib/ksort/ksort.h:712)
- A /branches/prog/bwa/kvec.h (from /branches/prog/sclib/kvec/kvec.h:537)
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-19
- * considerable code cleanup; no actual changes
-
-------------------------------------------------------------------------
-r724 | lh3 | 2008-12-25 11:32:11 -0500 (Thu, 25 Dec 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-18
- * generate SAM output
-
-------------------------------------------------------------------------
-r723 | lh3 | 2008-12-25 10:48:31 -0500 (Thu, 25 Dec 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
-
- * bwa-0.2.0-17
- * remove bwtsw2 related codes
- * separate searching for SA interval from generating alignments
-
-------------------------------------------------------------------------
-r722 | lh3 | 2008-12-25 08:57:13 -0500 (Thu, 25 Dec 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwt2fmv.c
- D /branches/prog/bwa/bwt_lite.c
- D /branches/prog/bwa/bwt_lite.h
- M /branches/prog/bwa/bwtgap.c
- D /branches/prog/bwa/bwtsw2.h
- D /branches/prog/bwa/bwtsw2_aux.c
- D /branches/prog/bwa/bwtsw2_core.c
- D /branches/prog/bwa/bwtsw2_main.c
- D /branches/prog/bwa/khash.h
- D /branches/prog/bwa/ksort.h
- D /branches/prog/bwa/kvec.h
- M /branches/prog/bwa/main.c
-
- * added interface to "aln -t"
- * remove bwtsw2 related codes
-
-------------------------------------------------------------------------
-r666 | lh3 | 2008-11-18 18:34:29 -0500 (Tue, 18 Nov 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-16
- * allow to set max mismatches based on read length, but I do not know
- whether this really works
-
-------------------------------------------------------------------------
-r665 | lh3 | 2008-11-18 08:34:03 -0500 (Tue, 18 Nov 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-15
- * fixed a bug in sequence parser.
-
-------------------------------------------------------------------------
-r612 | lh3 | 2008-10-28 06:50:53 -0400 (Tue, 28 Oct 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bwtindex.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/utils.c
-
- * bwa-0.2.0-14
- * fixed a bug caused by the change of the FASTA/Q parser
-
-------------------------------------------------------------------------
-r611 | lh3 | 2008-10-28 06:24:56 -0400 (Tue, 28 Oct 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bntseq.h
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtsw2_core.c
- A /branches/prog/bwa/kseq.h
- D /branches/prog/bwa/seq.c
- D /branches/prog/bwa/seq.h
- M /branches/prog/bwa/simple_dp.c
- M /branches/prog/bwa/utils.c
- M /branches/prog/bwa/utils.h
-
-replace seq.* with kseq.h
-
-------------------------------------------------------------------------
-r610 | lh3 | 2008-10-27 13:00:04 -0400 (Mon, 27 Oct 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-13
- * make bwtsw2 output sub-optimal hits. not completed
-
-------------------------------------------------------------------------
-r609 | lh3 | 2008-10-24 16:52:00 -0400 (Fri, 24 Oct 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/kvec.h
-
-little...
-
-------------------------------------------------------------------------
-r532 | lh3 | 2008-09-19 05:28:45 -0400 (Fri, 19 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/khash.h
-
-improve interface of khash
-
-------------------------------------------------------------------------
-r531 | lh3 | 2008-09-18 06:52:59 -0400 (Thu, 18 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-improve minor things, which make bwtsw2 slower, but should miss less true hits
-
-------------------------------------------------------------------------
-r530 | lh3 | 2008-09-17 18:19:26 -0400 (Wed, 17 Sep 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
- * fixed a bug in calculating ->D
- * enforce band-width checking
-
-------------------------------------------------------------------------
-r529 | lh3 | 2008-09-17 18:06:49 -0400 (Wed, 17 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-delete a line of code that is never visited
-
-------------------------------------------------------------------------
-r528 | lh3 | 2008-09-17 17:58:51 -0400 (Wed, 17 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-a bit code clean up
-
-------------------------------------------------------------------------
-r527 | lh3 | 2008-09-17 10:55:45 -0400 (Wed, 17 Sep 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-12
- * max-depth can be set, although it does not help the speed at all
-
-------------------------------------------------------------------------
-r526 | lh3 | 2008-09-16 17:59:36 -0400 (Tue, 16 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-cut_tail after remove duplicate
-
-------------------------------------------------------------------------
-r525 | lh3 | 2008-09-16 17:56:11 -0400 (Tue, 16 Sep 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/khash.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-11
- * improved cut_tail()
-
-------------------------------------------------------------------------
-r524 | lh3 | 2008-09-15 16:53:22 -0400 (Mon, 15 Sep 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-10
- * fixed a bug in cut_tail()
-
-------------------------------------------------------------------------
-r518 | lh3 | 2008-09-15 04:35:59 -0400 (Mon, 15 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-a bit code clean up
-
-------------------------------------------------------------------------
-r517 | lh3 | 2008-09-14 18:18:11 -0400 (Sun, 14 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-improve speed (<1%)
-
-------------------------------------------------------------------------
-r516 | lh3 | 2008-09-14 18:08:55 -0400 (Sun, 14 Sep 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
- * fixed two potential bugs, although I have not seen their effects
- * improve speed a bit (<2%)
-
-------------------------------------------------------------------------
-r515 | lh3 | 2008-09-14 17:26:49 -0400 (Sun, 14 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
-
-nothing, really
-
-------------------------------------------------------------------------
-r514 | lh3 | 2008-09-14 17:10:13 -0400 (Sun, 14 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-disable X-drop, which has to be reimplemented in the current algorithm
-
-------------------------------------------------------------------------
-r513 | lh3 | 2008-09-14 16:49:42 -0400 (Sun, 14 Sep 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwt_lite.c
- M /branches/prog/bwa/bwt_lite.h
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
-
- * temporarily disable cut_tail()
- * calculate SA in bwt_lite.c
- * fixed a bug in reversing the sequence
-
-------------------------------------------------------------------------
-r512 | lh3 | 2008-09-13 17:35:40 -0400 (Sat, 13 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- A /branches/prog/bwa/ksort.h
-
-n-best method
-
-------------------------------------------------------------------------
-r507 | lh3 | 2008-09-13 09:06:54 -0400 (Sat, 13 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwtsw2_core.c
-
-give correct result again
-
-------------------------------------------------------------------------
-r506 | lh3 | 2008-09-13 08:12:07 -0400 (Sat, 13 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-I think I know the reason. It needs more work...
-
-------------------------------------------------------------------------
-r505 | lh3 | 2008-09-13 06:20:43 -0400 (Sat, 13 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwtsw2_core.c
-
-fixed another bug, but still have
-
-------------------------------------------------------------------------
-r504 | lh3 | 2008-09-12 18:13:37 -0400 (Fri, 12 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-fixed another bug
-
-------------------------------------------------------------------------
-r503 | lh3 | 2008-09-12 17:15:56 -0400 (Fri, 12 Sep 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/khash.h
-
- * do not segfault, but the result is WRONG!
- * prepare to remove bsw2_connectivity_check()
-
-------------------------------------------------------------------------
-r502 | lh3 | 2008-09-12 15:52:41 -0400 (Fri, 12 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/kvec.h
-
-more revisions
-
-------------------------------------------------------------------------
-r501 | lh3 | 2008-09-11 18:06:15 -0400 (Thu, 11 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-further simply codes with kvec.h
-
-------------------------------------------------------------------------
-r500 | lh3 | 2008-09-11 17:42:15 -0400 (Thu, 11 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-part of revisions... have not finished
-
-------------------------------------------------------------------------
-r499 | lh3 | 2008-09-11 17:24:15 -0400 (Thu, 11 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/khash.h
- A /branches/prog/bwa/kvec.h
-
-prepare for abrupt change
-
-------------------------------------------------------------------------
-r496 | lh3 | 2008-09-11 10:34:38 -0400 (Thu, 11 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-fixed a bug; now "bwtsw2 -d" is useless
-
-------------------------------------------------------------------------
-r495 | lh3 | 2008-09-11 09:22:03 -0400 (Thu, 11 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/simple_dp.c
- M /branches/prog/bwa/stdaln.c
- M /branches/prog/bwa/stdaln.h
-
-improve speed a little bit
-
-------------------------------------------------------------------------
-r494 | lh3 | 2008-09-11 08:28:08 -0400 (Thu, 11 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-remove debug codes
-
-------------------------------------------------------------------------
-r493 | lh3 | 2008-09-11 07:49:53 -0400 (Thu, 11 Sep 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
- * improve the speed a little bit (<5%)
- * prepare to remove BSW_DEBUG
-
-------------------------------------------------------------------------
-r492 | lh3 | 2008-09-11 06:15:56 -0400 (Thu, 11 Sep 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-9
- * support reverse strand
- * fixed a bug that causes missing hits
-
-------------------------------------------------------------------------
-r491 | lh3 | 2008-09-11 05:46:16 -0400 (Thu, 11 Sep 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-8
- * better progress report
-
-------------------------------------------------------------------------
-r490 | lh3 | 2008-09-10 17:04:49 -0400 (Wed, 10 Sep 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-7
- * avoid some missing hits
- * add maximum depth
-
-------------------------------------------------------------------------
-r489 | lh3 | 2008-09-10 11:51:13 -0400 (Wed, 10 Sep 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-6
- * bwtsw2 works although on the forward strand only for now
- * better progress information
-
-------------------------------------------------------------------------
-r488 | lh3 | 2008-09-10 10:21:53 -0400 (Wed, 10 Sep 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
- * implement memory pool
- * avoid some rehashing
-
-------------------------------------------------------------------------
-r487 | lh3 | 2008-09-10 09:23:38 -0400 (Wed, 10 Sep 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_main.c
-
- * fixed a memory leak
- * prepare to implement mempool
-
-------------------------------------------------------------------------
-r486 | lh3 | 2008-09-10 09:10:09 -0400 (Wed, 10 Sep 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/khash.h
-
- * add X-dropoff
- * remove duplicated results
- * switch to simple stack
-
-------------------------------------------------------------------------
-r485 | lh3 | 2008-09-10 06:31:20 -0400 (Wed, 10 Sep 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
-
- * check whether t-node has been visited
- * prepare to remove two-level stack
-
-------------------------------------------------------------------------
-r484 | lh3 | 2008-09-10 05:00:57 -0400 (Wed, 10 Sep 2008) | 2 lines
-Changed paths:
- A /branches/prog/bwa/khash.h
-
-khash library
-
-------------------------------------------------------------------------
-r483 | lh3 | 2008-09-10 04:22:53 -0400 (Wed, 10 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-add inline
-
-------------------------------------------------------------------------
-r482 | lh3 | 2008-09-09 16:34:57 -0400 (Tue, 09 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
-
-improve speed
-
-------------------------------------------------------------------------
-r481 | lh3 | 2008-09-09 13:13:00 -0400 (Tue, 09 Sep 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2_core.c
-
-Use a 128bit hash table to keep all (tk,tl,qk,ql). This is slow. Just
-keep a copy in case I may need this in future.
-
-
-------------------------------------------------------------------------
-r480 | lh3 | 2008-09-09 12:53:32 -0400 (Tue, 09 Sep 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_core.c
-
- * no principal modification
-
-------------------------------------------------------------------------
-r479 | lh3 | 2008-09-09 11:01:45 -0400 (Tue, 09 Sep 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwtsw2_core.c
-
- * fixed a bug which may cause duplicated matching
- * accelerate the speed a bit, although using hash in avoiding duplications
- slows the speed down in the end
-
-------------------------------------------------------------------------
-r474 | lh3 | 2008-09-03 17:22:57 -0400 (Wed, 03 Sep 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwtsw2.h
- M /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-5
- * indel seems to work on toy example
- * add band
-
-------------------------------------------------------------------------
-r469 | lh3 | 2008-09-01 09:18:45 -0400 (Mon, 01 Sep 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwt_lite.c
- M /branches/prog/bwa/bwt_lite.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/bwtsw2.h
- A /branches/prog/bwa/bwtsw2_aux.c
- M /branches/prog/bwa/bwtsw2_core.c
- M /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/is.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
- M /branches/prog/bwa/simple_dp.c
-
- * bwa-0.2.0-4
- * updated bwtsw2, which seems to work properly on toy examples
-
-------------------------------------------------------------------------
-r447 | lh3 | 2008-08-27 10:05:09 -0400 (Wed, 27 Aug 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-3
- * tune for longer gaps, but it does not really work with kilo-bp gaps...
-
-------------------------------------------------------------------------
-r446 | lh3 | 2008-08-26 13:30:41 -0400 (Tue, 26 Aug 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-2
- * changed the way to extend long deletions. Now use max_del_occ.
-
-------------------------------------------------------------------------
-r445 | lh3 | 2008-08-26 13:05:58 -0400 (Tue, 26 Aug 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwt_lite.c
- M /branches/prog/bwa/bwt_lite.h
-
-updated from bwtsw2_lite
-
-------------------------------------------------------------------------
-r436 | lh3 | 2008-08-23 12:28:44 -0400 (Sat, 23 Aug 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwt.h
- A /branches/prog/bwa/bwt_lite.c
- A /branches/prog/bwa/bwt_lite.h
- A /branches/prog/bwa/bwtsw2.h
- A /branches/prog/bwa/bwtsw2_core.c
- A /branches/prog/bwa/bwtsw2_main.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.2.0-1
- * add bwt_lite: a light-weighted version of bwt (NOT TESTED!)
- * add core codes for bwtsw2: NOT TESTED!!!
-
-------------------------------------------------------------------------
-r427 | lh3 | 2008-08-15 05:38:12 -0400 (Fri, 15 Aug 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
-Release bwa-0.2.0
-
-------------------------------------------------------------------------
-r426 | lh3 | 2008-08-14 11:26:19 -0400 (Thu, 14 Aug 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.6-7
- * change default seed length to 31
- * add incomplete support to color sequences (not tested yet!)
-
-------------------------------------------------------------------------
-r425 | lh3 | 2008-08-14 06:23:11 -0400 (Thu, 14 Aug 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.6-6
- * change default seed length to 33bp
-
-------------------------------------------------------------------------
-r424 | lh3 | 2008-08-14 05:55:33 -0400 (Thu, 14 Aug 2008) | 6 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.6-5
- * fixed a bug that may miss true alignments. this bugs exists in most
- early versions.
- * fixed a bug that yields wrong coordinates for reads mapped on the forward
- strands with gaps.
-
-------------------------------------------------------------------------
-r423 | lh3 | 2008-08-14 04:07:28 -0400 (Thu, 14 Aug 2008) | 2 lines
-Changed paths:
- D /branches/prog/bwa/Makefile.div
-
-useless
-
-------------------------------------------------------------------------
-r422 | lh3 | 2008-08-13 19:21:14 -0400 (Wed, 13 Aug 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.6-4
- * fixed one bug
- * there is another one...
-
-------------------------------------------------------------------------
-r421 | lh3 | 2008-08-13 18:23:33 -0400 (Wed, 13 Aug 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/bwtgap.h
- M /branches/prog/bwa/bwtindex.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.6-3
- * almost there, but not quite right
-
-------------------------------------------------------------------------
-r419 | lh3 | 2008-08-13 17:27:02 -0400 (Wed, 13 Aug 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/bwtgap.h
- M /branches/prog/bwa/main.c
-
- * improve the seeding method
- * prepare to load two BWTs into memory. A BIG change!
-
-------------------------------------------------------------------------
-r418 | lh3 | 2008-08-13 10:56:54 -0400 (Wed, 13 Aug 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/bwtgap.h
- M /branches/prog/bwa/main.c
-
- * added seeding
- * unfinished yet
-
-------------------------------------------------------------------------
-r413 | lh3 | 2008-08-08 11:48:35 -0400 (Fri, 08 Aug 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/main.c
-
-Release bwa-0.1.6
-
-------------------------------------------------------------------------
-r410 | lh3 | 2008-08-06 15:48:22 -0400 (Wed, 06 Aug 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/simple_dp.c
-
-sw: output alignment score
-
-------------------------------------------------------------------------
-r407 | lh3 | 2008-08-04 10:01:20 -0400 (Mon, 04 Aug 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
- A /branches/prog/bwa/simple_dp.c
- M /branches/prog/bwa/stdaln.c
- M /branches/prog/bwa/stdaln.h
-
- * bwa-0.1.5-3
- * added a simple interface to SW/NW alignment
- * stdaln-0.9.8 (see header for more details)
-
-------------------------------------------------------------------------
-r406 | lh3 | 2008-08-01 19:21:59 -0400 (Fri, 01 Aug 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
- A /branches/prog/bwa/stdaln.c
- A /branches/prog/bwa/stdaln.h
-
- * bwa-0.1.5-2
- * give accurate gap positions
-
-------------------------------------------------------------------------
-r405 | lh3 | 2008-08-01 19:06:19 -0400 (Fri, 01 Aug 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
-
-unfinished, but I am tired...
-
-------------------------------------------------------------------------
-r401 | lh3 | 2008-07-30 05:59:24 -0400 (Wed, 30 Jul 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.5-1
- * fixed a potential bug which may produce an alignment in N regions,
- although extremely rare.
-
-------------------------------------------------------------------------
-r399 | lh3 | 2008-07-27 11:41:52 -0400 (Sun, 27 Jul 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/main.c
-
-Release bwa-0.1.5
-
-------------------------------------------------------------------------
-r398 | lh3 | 2008-07-25 12:14:47 -0400 (Fri, 25 Jul 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
-
-update documentation
-
-------------------------------------------------------------------------
-r397 | lh3 | 2008-07-25 09:58:56 -0400 (Fri, 25 Jul 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- *
-
-------------------------------------------------------------------------
-r396 | lh3 | 2008-07-25 06:42:01 -0400 (Fri, 25 Jul 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.4-4
- * add timer for debugging
-
-------------------------------------------------------------------------
-r395 | lh3 | 2008-07-24 05:46:21 -0400 (Thu, 24 Jul 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.4-3
- * fixed a bug in the previous code
- * this version gives identical result to bwa-0.1.4, just 10% faster
-
-------------------------------------------------------------------------
-r394 | lh3 | 2008-07-24 05:18:53 -0400 (Thu, 24 Jul 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/bwtgap.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.4-2
- * further improve the speed
- * The result is slightly different from bwa-0.1.4 now. I need to check...
-
-------------------------------------------------------------------------
-r393 | lh3 | 2008-07-23 12:04:16 -0400 (Wed, 23 Jul 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
-
-comments only
-
-------------------------------------------------------------------------
-r392 | lh3 | 2008-07-23 10:34:03 -0400 (Wed, 23 Jul 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/main.c
-
-further improve the speed in Occ functions
-
-------------------------------------------------------------------------
-r386 | lh3 | 2008-07-22 10:03:54 -0400 (Tue, 22 Jul 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/main.c
-
-Release bwa-0.1.4
-
-------------------------------------------------------------------------
-r385 | lh3 | 2008-07-22 09:44:50 -0400 (Tue, 22 Jul 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/bwa.1
-
-update documentation and ChangeLog
-
-------------------------------------------------------------------------
-r384 | lh3 | 2008-07-22 08:50:03 -0400 (Tue, 22 Jul 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.3-2
- * fixed the bug in the last modification
- * now the alignment should be more clearly defined
-
-------------------------------------------------------------------------
-r383 | lh3 | 2008-07-21 18:32:21 -0400 (Mon, 21 Jul 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.3-1
- * this is a buggy verion!
- * i will fix the bug tomorrow. It is late...
-
-------------------------------------------------------------------------
-r381 | lh3 | 2008-07-21 06:45:32 -0400 (Mon, 21 Jul 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/main.c
-
-Release bwa-0.1.3
-
-------------------------------------------------------------------------
-r380 | lh3 | 2008-07-21 06:07:43 -0400 (Mon, 21 Jul 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.2-3
- * improve the speed for gcc on Intel Mac OS X, but not really on icc on Linux
- * aln: more command-line options
-
-------------------------------------------------------------------------
-r373 | lh3 | 2008-07-17 09:09:46 -0400 (Thu, 17 Jul 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwtio.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.2-2
- * further improve the speed
- * this version gives exactly the same result as bwa-0.1.2
-
-------------------------------------------------------------------------
-r372 | lh3 | 2008-07-17 07:51:08 -0400 (Thu, 17 Jul 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.2-1
- * speed up by about 5%
-
-------------------------------------------------------------------------
-r370 | lh3 | 2008-07-17 05:12:00 -0400 (Thu, 17 Jul 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/main.c
-
-Release bwa-0.1.2
-
-------------------------------------------------------------------------
-r368 | lh3 | 2008-07-16 08:51:25 -0400 (Wed, 16 Jul 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- D /branches/prog/bwa/bwt1away.c
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/bwtgap.h
- D /branches/prog/bwa/bwttop2.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.1-9
- * some code cleanup
- * remove 1away and top2
-
-------------------------------------------------------------------------
-r367 | lh3 | 2008-07-16 08:24:34 -0400 (Wed, 16 Jul 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/is.c
-
-Yuta Mori's implementation of IS algorithm.
-
-------------------------------------------------------------------------
-r365 | lh3 | 2008-07-16 06:58:04 -0400 (Wed, 16 Jul 2008) | 6 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/bwtgap.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.1-8
- * improve gapped alignment
- * this version will miss more gapped alignments, but the speed is much faster
- * prepare to remove top2 and 1away algorithms
- * prepare to add SAIS algorithm for bwt construction
-
-------------------------------------------------------------------------
-r358 | lh3 | 2008-06-09 06:03:04 -0400 (Mon, 09 Jun 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.1-7
- * change END_SKIP from 3 to 5, but still gaps may be wrongly added
- * change default '-g' from 5 to 3
-
-------------------------------------------------------------------------
-r357 | lh3 | 2008-06-09 05:18:36 -0400 (Mon, 09 Jun 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.1-6
- * fix a bug in nested stack
-
-------------------------------------------------------------------------
-r356 | lh3 | 2008-06-08 18:43:13 -0400 (Sun, 08 Jun 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- A /branches/prog/bwa/bwtgap.h
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.1-5
- * replace heap with nested stacks
- * there are still obvious bugs...
-
-------------------------------------------------------------------------
-r355 | lh3 | 2008-06-08 17:13:44 -0400 (Sun, 08 Jun 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
-
- * bwa-0.1.1-4
- * add interface to affine gap alignment
- * there are obvious bugs and I will fix them later
-
-------------------------------------------------------------------------
-r354 | lh3 | 2008-06-08 15:39:05 -0400 (Sun, 08 Jun 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.1-3
- * affine gap seems to work, at least partially
-
-------------------------------------------------------------------------
-r353 | lh3 | 2008-06-08 09:27:18 -0400 (Sun, 08 Jun 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- A /branches/prog/bwa/bwtgap.c
- M /branches/prog/bwa/bwttop2.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.1-2
- * initial gapped alignment. not work at the moment
-
-------------------------------------------------------------------------
-r352 | lh3 | 2008-06-06 04:37:34 -0400 (Fri, 06 Jun 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwttop2.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.1-1
- * ungap: remove a useless varible in top2_entry_t
-
-------------------------------------------------------------------------
-r348 | lh3 | 2008-06-03 09:04:12 -0400 (Tue, 03 Jun 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/ChangeLog
- A /branches/prog/bwa/NEWS
- M /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/main.c
-
-Release bwa-0.1.1
-
-------------------------------------------------------------------------
-r347 | lh3 | 2008-06-03 05:45:08 -0400 (Tue, 03 Jun 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwa.1
-
-update documentation
-
-------------------------------------------------------------------------
-r346 | lh3 | 2008-06-02 18:59:50 -0400 (Mon, 02 Jun 2008) | 5 lines
-Changed paths:
- A /branches/prog/bwa/ChangeLog
- A /branches/prog/bwa/bwa.1
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.0-11
- * improve approximating mapping qualities
- * add documentation
- * add ChangeLog
-
-------------------------------------------------------------------------
-r345 | lh3 | 2008-06-02 16:04:39 -0400 (Mon, 02 Jun 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwttop2.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.0-10
- * output a random position for repetitive reads
-
-------------------------------------------------------------------------
-r344 | lh3 | 2008-06-02 15:03:54 -0400 (Mon, 02 Jun 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/pac2bwt.c
-
- * bwa-0.1.0-9
- * fix memory leaks
- * fix a potential bug in coverting to the real coordinate
-
-------------------------------------------------------------------------
-r343 | lh3 | 2008-06-02 13:44:51 -0400 (Mon, 02 Jun 2008) | 5 lines
-Changed paths:
- M /branches/prog/bwa/Makefile.div
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwttop2.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.0-8
- * fix a bug about strand
- * update Makefile.div
- * change top2b as the default method
-
-------------------------------------------------------------------------
-r342 | lh3 | 2008-06-02 11:23:26 -0400 (Mon, 02 Jun 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt1away.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.0-7
- * use bwt_2occ() and bwt_2occ4() in other functions
-
-------------------------------------------------------------------------
-r341 | lh3 | 2008-06-02 09:31:39 -0400 (Mon, 02 Jun 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwttop2.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.0-6
- * fix a bug for missing hits
-
-------------------------------------------------------------------------
-r340 | lh3 | 2008-06-02 09:10:18 -0400 (Mon, 02 Jun 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwttop2.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.0-5
- * accelerate comparisons in heap, a bit
-
-------------------------------------------------------------------------
-r339 | lh3 | 2008-06-02 08:41:31 -0400 (Mon, 02 Jun 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwttop2.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.0-4
- * avoid marginal repeated calculation in occ
-
-------------------------------------------------------------------------
-r338 | lh3 | 2008-06-02 06:46:51 -0400 (Mon, 02 Jun 2008) | 5 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwttop2.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.0-3
- * fix a bug caused by previours change
- * fix a bug in heap
- * order the heap by more criteria
-
-------------------------------------------------------------------------
-r337 | lh3 | 2008-06-01 19:11:15 -0400 (Sun, 01 Jun 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwttop2.c
- M /branches/prog/bwa/main.c
-
- * bwa-0.1.0-2
- * also sort sa range in heapsort, in attempt to improve cache performance.
- Unfortunately, it does not work well at all.
-
-------------------------------------------------------------------------
-r336 | lh3 | 2008-06-01 17:45:23 -0400 (Sun, 01 Jun 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/Makefile.div
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/main.c
-
- * 0.1.0-1
- * fix a bug in calculating the real coordinate
-
-------------------------------------------------------------------------
-r335 | lh3 | 2008-06-01 16:03:09 -0400 (Sun, 01 Jun 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
-
-nothing, really
-
-------------------------------------------------------------------------
-r334 | lh3 | 2008-06-01 15:59:13 -0400 (Sun, 01 Jun 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- A /branches/prog/bwa/Makefile.div
- M /branches/prog/bwa/bwtindex.c
- M /branches/prog/bwa/pac2bwt.c
-
-use IS algorithm by default
-
-------------------------------------------------------------------------
-r333 | lh3 | 2008-06-01 15:05:15 -0400 (Sun, 01 Jun 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwtindex.c
- M /branches/prog/bwa/is.c
- M /branches/prog/bwa/pac2bwt.c
-
- * a bit code clean up in is.c
- * add IS algorithm for constructing BWT, albeit slower
-
-------------------------------------------------------------------------
-r332 | lh3 | 2008-06-01 13:23:08 -0400 (Sun, 01 Jun 2008) | 2 lines
-Changed paths:
- A /branches/prog/bwa/is.c
-
-IS linear-time algorithm for constructing SA/BWT
-
-------------------------------------------------------------------------
-r331 | lh3 | 2008-06-01 10:35:26 -0400 (Sun, 01 Jun 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bntseq.c
- A /branches/prog/bwa/bwtindex.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
-
- * fix a bug in generating .pac
- * index in one go
-
-------------------------------------------------------------------------
-r330 | lh3 | 2008-06-01 09:17:05 -0400 (Sun, 01 Jun 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bntseq.h
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwttop2.c
-
-real coordinates can be ouput
-
-------------------------------------------------------------------------
-r329 | lh3 | 2008-05-31 19:21:02 -0400 (Sat, 31 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwttop2.c
-
-add top2e which is similar to 1away
-
-------------------------------------------------------------------------
-r328 | lh3 | 2008-05-31 18:46:12 -0400 (Sat, 31 May 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwttop2.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
-
- * unified cmd-line interface for ungapped alignment
- * add two alternatives to top2 algorithm
-
-------------------------------------------------------------------------
-r327 | lh3 | 2008-05-31 18:14:46 -0400 (Sat, 31 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
-
-add cmd-line interface to alntop2
-
-------------------------------------------------------------------------
-r326 | lh3 | 2008-05-31 17:59:31 -0400 (Sat, 31 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwt1away.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- A /branches/prog/bwa/bwttop2.c
-
-top2 algorithm seems to work. I need to change interface, though
-
-------------------------------------------------------------------------
-r325 | lh3 | 2008-05-31 15:11:49 -0400 (Sat, 31 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwt1away.c
-
-change the variable in the structure
-
-------------------------------------------------------------------------
-r324 | lh3 | 2008-05-31 14:52:13 -0400 (Sat, 31 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwt1away.c
-
-set a slightly better bound on the maximum allowed mismatches
-
-------------------------------------------------------------------------
-r323 | lh3 | 2008-05-30 18:40:21 -0400 (Fri, 30 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
-
- * output time statistics
-
-------------------------------------------------------------------------
-r322 | lh3 | 2008-05-30 17:58:25 -0400 (Fri, 30 May 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- A /branches/prog/bwa/bwt1away.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
-
- * presumably better way to make use of prefix. But for the moment I do
- not know whether it is correct or not.
- * a bit code clean up: separate alignment part
-
-------------------------------------------------------------------------
-r321 | lh3 | 2008-05-30 13:57:43 -0400 (Fri, 30 May 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwt_gen/Makefile
- M /branches/prog/bwa/bwt_gen/bwt_gen.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
- M /branches/prog/bwa/pac2bwt.c
-
- * a bit code clean up
- * put bwt_gen in bwa
-
-------------------------------------------------------------------------
-r320 | lh3 | 2008-05-30 11:40:11 -0400 (Fri, 30 May 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtio.c
-
- * improve cmd-line interface
- * fix a bug in loading .sa
- * change default sa interval to 32
-
-------------------------------------------------------------------------
-r319 | lh3 | 2008-05-30 10:31:37 -0400 (Fri, 30 May 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwtaln.c
-
- * fix memory leak (I know that. Just a bit lazy)
- * change to another method to do 1-away alignment
-
-------------------------------------------------------------------------
-r318 | lh3 | 2008-05-30 09:21:49 -0400 (Fri, 30 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
-
-best unique match is partially finished
-
-------------------------------------------------------------------------
-r317 | lh3 | 2008-05-30 06:33:28 -0400 (Fri, 30 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
-
-remove "ungapped" command and related codes
-
-------------------------------------------------------------------------
-r316 | lh3 | 2008-05-30 06:05:20 -0400 (Fri, 30 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
-
-change variable name thick to width
-
-------------------------------------------------------------------------
-r315 | lh3 | 2008-05-29 19:06:13 -0400 (Thu, 29 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtio.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
- M /branches/prog/bwa/pac2bwt.c
-
-revised algorithm for ungapped alignment. the old one can still be used.
-
-------------------------------------------------------------------------
-r314 | lh3 | 2008-05-29 16:36:11 -0400 (Thu, 29 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwt_gen/bwt_gen.c
- M /branches/prog/bwa/bwtio.c
- M /branches/prog/bwa/pac2bwt.c
-
- * make commands more independent, but ungapped does not work at the moment
-
-------------------------------------------------------------------------
-r313 | lh3 | 2008-05-29 15:56:14 -0400 (Thu, 29 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwt_gen/bwt_gen.c
-
-little...
-
-------------------------------------------------------------------------
-r312 | lh3 | 2008-05-29 15:54:01 -0400 (Thu, 29 May 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt_gen/bwt_gen.c
- M /branches/prog/bwa/bwt_gen/bwt_gen.h
-
- * add CopyRight information from the original codes
- * do not dump .fmv files
-
-------------------------------------------------------------------------
-r311 | lh3 | 2008-05-29 15:44:36 -0400 (Thu, 29 May 2008) | 2 lines
-Changed paths:
- A /branches/prog/bwa/bwt_gen
- A /branches/prog/bwa/bwt_gen/Makefile
- A /branches/prog/bwa/bwt_gen/QSufSort.c
- A /branches/prog/bwa/bwt_gen/QSufSort.h
- A /branches/prog/bwa/bwt_gen/bwt_gen.c
- A /branches/prog/bwa/bwt_gen/bwt_gen.h
-
-codes from BWT-SW, for building BWT from packed file
-
-------------------------------------------------------------------------
-r310 | lh3 | 2008-05-28 17:03:35 -0400 (Wed, 28 May 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtio.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
-
- * change OCC_INTERVAL to 0x40, which makes bwa twice as fast.
- * write Occ file as ".occ" as it is using a different interval from
- .fmv, the BWT-SW correspondance of .occ
-
-------------------------------------------------------------------------
-r309 | lh3 | 2008-05-28 11:39:37 -0400 (Wed, 28 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt2fmv.c
-
-fix a bug
-
-------------------------------------------------------------------------
-r308 | lh3 | 2008-05-28 09:56:16 -0400 (Wed, 28 May 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt2fmv.c
-
-add heuristics to improve the speed, but I have not tested whether the
-results are correct or not.
-
-
-------------------------------------------------------------------------
-r307 | lh3 | 2008-05-28 06:31:34 -0400 (Wed, 28 May 2008) | 5 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/bwtaln.c
- M /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
-
- * make ungapped alignment basically works...
- * but it is very slow in comparison to others...
- * also I need to improve the interface...
- * a lot of things to keep me busy today...
-
-------------------------------------------------------------------------
-r306 | lh3 | 2008-05-27 18:41:27 -0400 (Tue, 27 May 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwtaln.c
-
- * remove recursion
- * fixed a bug in bwt_occ()
-
-------------------------------------------------------------------------
-r305 | lh3 | 2008-05-27 16:59:44 -0400 (Tue, 27 May 2008) | 5 lines
-Changed paths:
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwtaln.c
-
- * bwa now tells whether a sequenced can be mapped with maximum allowed
- mismatches. ONLY ungapped.
- * this is a recursive version. I will remove recursion later.
-
-
-------------------------------------------------------------------------
-r304 | lh3 | 2008-05-27 09:12:17 -0400 (Tue, 27 May 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwt2fmv.c
- A /branches/prog/bwa/bwtaln.c
- A /branches/prog/bwa/bwtaln.h
- M /branches/prog/bwa/bwtio.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
- M /branches/prog/bwa/utils.c
-
- * load .sa and .fmv files
- * exact alignment now works
-
-------------------------------------------------------------------------
-r303 | lh3 | 2008-05-27 06:33:38 -0400 (Tue, 27 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwtio.c
- M /branches/prog/bwa/utils.c
- M /branches/prog/bwa/utils.h
-
-add xassert and fix a bug
-
-------------------------------------------------------------------------
-r302 | lh3 | 2008-05-27 06:23:20 -0400 (Tue, 27 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwtio.c
- A /branches/prog/bwa/utils.c
- A /branches/prog/bwa/utils.h
-
-improve error message and error handling
-
-------------------------------------------------------------------------
-r301 | lh3 | 2008-05-27 05:37:51 -0400 (Tue, 27 May 2008) | 4 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwt2fmv.c
- A /branches/prog/bwa/bwtio.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
-
- * move I/O codes to bwtio.c
- * SA can be dumped and interestingly, it is identical to BWTSW
- * now, .fmv is still different from BWTSW
-
-------------------------------------------------------------------------
-r299 | lh3 | 2008-05-26 18:07:44 -0400 (Mon, 26 May 2008) | 2 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwt2fmv.c
-
-generate/retrieve SA and Occ
-
-------------------------------------------------------------------------
-r298 | lh3 | 2008-05-26 13:16:49 -0400 (Mon, 26 May 2008) | 3 lines
-Changed paths:
- M /branches/prog/bwa/bntseq.h
- M /branches/prog/bwa/bwt.c
- M /branches/prog/bwa/bwt.h
- M /branches/prog/bwa/bwt2fmv.c
-
- * retrieve occ value at any position
- * move bwt_cal_occ() to bwt.c
-
-------------------------------------------------------------------------
-r297 | lh3 | 2008-05-25 17:43:58 -0400 (Sun, 25 May 2008) | 6 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- A /branches/prog/bwa/bwt.c
- A /branches/prog/bwa/bwt.h
- A /branches/prog/bwa/bwt2fmv.c
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
- M /branches/prog/bwa/pac2bwt.c
-
- * add bwt2fmv. It works to some extend. However, I do not understand
- the purpose of some weird codes in BWT-SW. As a consequence, bwt2fmv
- could generate a file almost identical, but not exactly identical, to
- the .fmv file from BWT-SW.
-
-
-------------------------------------------------------------------------
-r296 | lh3 | 2008-05-24 18:35:02 -0400 (Sat, 24 May 2008) | 5 lines
-Changed paths:
- M /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bntseq.c
- M /branches/prog/bwa/bntseq.h
- M /branches/prog/bwa/main.c
- M /branches/prog/bwa/main.h
- A /branches/prog/bwa/pac2bwt.c
-
-Burrows-Wheeler Transform now works. At least on one example, the
-current code generates the same BWT as BWT-SW. Kind of magical, I would
-say. :)
-
-
-------------------------------------------------------------------------
-r295 | lh3 | 2008-05-24 11:25:31 -0400 (Sat, 24 May 2008) | 3 lines
-Changed paths:
- A /branches/prog/bwa/Makefile
- M /branches/prog/bwa/bntseq.c
- A /branches/prog/bwa/main.c
- A /branches/prog/bwa/main.h
-
- * add Makefile and main.*
- * improve interface to fa2bns, a bit
-
-------------------------------------------------------------------------
-r293 | lh3 | 2008-05-24 10:57:03 -0400 (Sat, 24 May 2008) | 3 lines
-Changed paths:
- A /branches/prog/bwa
- A /branches/prog/bwa/bntseq.c
- A /branches/prog/bwa/bntseq.h
- A /branches/prog/bwa/seq.c
- A /branches/prog/bwa/seq.h
-
- * Burrow-Wheeler Alignment
- * initial codes
-
-------------------------------------------------------------------------
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/Makefile
--- a/bwa-0.6.2/Makefile Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-CC= gcc
-CXX= g++
-CFLAGS= -g -Wall -O2
-CXXFLAGS= $(CFLAGS)
-AR= ar
-DFLAGS= -DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
-LOBJS= bwa.o bamlite.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o bntseq.o stdaln.o \
- bwaseqio.o bwase.o kstring.o
-AOBJS= QSufSort.o bwt_gen.o \
- is.o bwtmisc.o bwtindex.o ksw.o simple_dp.o \
- bwape.o cs2nt.o \
- bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
- bwtsw2_chain.o fastmap.o bwtsw2_pair.o
-PROG= bwa
-INCLUDES=
-LIBS= -lm -lz -lpthread
-SUBDIRS= .
-
-.SUFFIXES:.c .o .cc
-
-.c.o:
- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-.cc.o:
- $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-
-all:$(PROG)
-
-bwa:libbwa.a $(AOBJS) main.o
- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
-
-libbwa.a:$(LOBJS)
- $(AR) -csru $@ $(LOBJS)
-
-bwa.o:bwa.h
-
-QSufSort.o:QSufSort.h
-
-bwt.o:bwt.h
-bwtio.o:bwt.h
-bwtaln.o:bwt.h bwtaln.h kseq.h
-bntseq.o:bntseq.h
-bwtgap.o:bwtgap.h bwtaln.h bwt.h
-
-bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
-bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
-bwtsw2_main.o:bwtsw2.h
-
-clean:
- rm -f gmon.out *.o a.out $(PROG) *~ *.a
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/NEWS
--- a/bwa-0.6.2/NEWS Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,658 +0,0 @@
-Release 0.6.2 (19 June, 2012)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-This is largely a bug-fix release. Notable changes in BWA-short and BWA-SW:
-
- * Bugfix: BWA-SW may give bad alignments due to incorrect band width.
-
- * Bugfix: A segmentation fault due to an out-of-boundary error. The fix is a
- temporary solution. The real cause has not been identified.
-
- * Attempt to read index from prefix.64.bwt, such that the 32-bit and 64-bit
- index can coexist.
-
- * Added options '-I' and '-S' to control BWA-SW pairing.
-
-(0.6.2: 19 June 2012, r126)
-
-
-
-Release 0.6.1 (28 November, 2011)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Notable changes to BWA-short:
-
- * Bugfix: duplicated alternative hits in the XA tag.
-
- * Bugfix: when trimming enabled, bwa-aln trims 1bp less.
-
- * Disabled the color-space alignment. 0.6.x is not working with SOLiD reads at
- present.
-
-Notable changes to BWA-SW:
-
- * Bugfix: segfault due to excessive ambiguous bases.
-
- * Bugfix: incorrect mate position in the SE mode.
-
- * Bugfix: rare segfault in the PE mode
-
- * When macro _NO_SSE2 is in use, fall back to the standard Smith-Waterman
- instead of SSE2-SW.
-
- * Optionally mark split hits with lower alignment scores as secondary.
-
-Changes to fastmap:
-
- * Bugfix: infinite loop caused by ambiguous bases.
-
- * Optionally output the query sequence.
-
-(0.6.1: 28 November 2011, r104)
-
-
-
-Release 0.5.10 and 0.6.0 (12 November, 2011)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-The 0.6.0 release comes with two major changes. Firstly, the index data
-structure has been changed to support genomes longer than 4GB. The forward and
-reverse backward genome is now integrated in one index. This change speeds up
-BWA-short by about 20% and BWA-SW by 90% with the mapping acccuracy largely
-unchanged. A tradeoff is BWA requires more memory, but this is the price almost
-all mappers that index the genome have to pay.
-
-Secondly, BWA-SW in 0.6.0 now works with paired-end data. It is more accurate
-for highly unique reads and more robust to long indels and structural
-variations. However, BWA-short still has edges for reads with many suboptimal
-hits. It is yet to know which algorithm is the best for variant calling.
-
-0.5.10 is a bugfix release only and is likely to be the last release in the 0.5
-branch unless I find critical bugs in future.
-
-Other notable changes:
-
- * Added the `fastmap' command that finds super-maximal exact matches. It does
- not give the final alignment, but runs much faster. It can be a building
- block for other alignment algorithms. [0.6.0 only]
-
- * Output the timing information before BWA exits. This also tells users that
- the task has been finished instead of being killed or aborted. [0.6.0 only]
-
- * Sped up multi-threading when using many (>20) CPU cores.
-
- * Check I/O error.
-
- * Increased the maximum barcode length to 63bp.
-
- * Automatically choose the indexing algorithm.
-
- * Bugfix: very rare segfault due to an uninitialized variable. The bug also
- affects the placement of suboptimal alignments. The effect is very minor.
-
-This release involves quite a lot of tricky changes. Although it has been
-tested on a few data sets, subtle bugs may be still hidden. It is *NOT*
-recommended to use this release in a production pipeline. In future, however,
-BWA-SW may be better when reads continue to go longer. I would encourage users
-to try the 0.6 release. I would also like to hear the users' experience. Thank
-you.
-
-(0.6.0: 12 November 2011, r85)
-
-
-
-Beta Release 0.5.9 (24 January, 2011)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Notable changes:
-
- * Feature: barcode support via the `-B' option.
-
- * Feature: Illumina 1.3+ read format support via the `-I' option.
-
- * Bugfix: RG tags are not attached to unmapped reads.
-
- * Bugfix: very rare bwasw mismappings
-
- * Recommend options for PacBio reads in bwasw help message.
-
-
-Also, since January 13, the BWA master repository has been moved to github:
-
- https://github.com/lh3/bwa
-
-The revision number has been reset. All recent changes will be first
-committed to this repository.
-
-(0.5.9: 24 January 2011, r16)
-
-
-
-Beta Release Candidate 0.5.9rc1 (10 December, 2010)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Notable changes in bwasw:
-
- * Output unmapped reads.
-
- * For a repetitive read, choose a random hit instead of a fixed
- one. This is not well tested.
-
-Notable changes in bwa-short:
-
- * Fixed a bug in the SW scoring system, which may lead to unexpected
- gaps towards the end of a read.
-
- * Fixed a bug which invalidates the randomness of repetitive reads.
-
- * Fixed a rare memory leak.
-
- * Allowed to specify the read group at the command line.
-
- * Take name-grouped BAM files as input.
-
-Changes to this release are usually safe in that they do not interfere
-with the key functionality. However, the release has only been tested on
-small samples instead of on large-scale real data. If anything weird
-happens, please report the bugs to the bio-bwa-help mailing list.
-
-(0.5.9rc1: 10 December 2010, r1561)
-
-
-
-Beta Release 0.5.8 (8 June, 2010)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Notable changes in bwasw:
-
- * Fixed an issue of missing alignments. This should happen rarely and
- only when the contig/read alignment is multi-part. Very rarely, bwasw
- may still miss a segment in a multi-part alignment. This is difficult
- to fix, although possible.
-
-Notable changes in bwa-short:
-
- * Discard the SW alignment when the best single-end alignment is much
- better. Such a SW alignment may caused by structural variations and
- forcing it to be aligned leads to false alignment. This fix has not
- been tested thoroughly. It would be great to receive more users
- feedbacks on this issue.
-
- * Fixed a typo/bug in sampe which leads to unnecessarily large memory
- usage in some cases.
-
- * Further reduced the chance of reporting `weird pairing'.
-
-(0.5.8: 8 June 2010, r1442)
-
-
-
-Beta Release 0.5.7 (1 March, 2010)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-This release only has an effect on paired-end data with fat insert-size
-distribution. Users are still recommended to update as the new release
-improves the robustness to poor data.
-
- * The fix for `weird pairing' was not working in version 0.5.6, pointed
- out by Carol Scott. It should work now.
-
- * Optionally output to a normal file rather than to stdout (by Tim
- Fennel).
-
-(0.5.7: 1 March 2010, r1310)
-
-
-
-Beta Release 0.5.6 (10 Feburary, 2010)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Notable changes in bwa-short:
-
- * Report multiple hits in the SAM format at a new tag XA encoded as:
- (chr,pos,CIGAR,NM;)*. By default, if a paired or single-end read has
- 4 or fewer hits, they will all be reported; if a read in a anomalous
- pair has 11 or fewer hits, all of them will be reported.
-
- * Perform Smith-Waterman alignment also for anomalous read pairs when
- both ends have quality higher than 17. This reduces false positives
- for some SV discovery algorithms.
-
- * Do not report "weird pairing" when the insert size distribution is
- too fat or has a mean close to zero.
-
- * If a read is bridging two adjacent chromsomes, flag it as unmapped.
-
- * Fixed a small but long existing memory leak in paired-end mapping.
-
- * Multiple bug fixes in SOLiD mapping: a) quality "-1" can be correctly
- parsed by solid2fastq.pl; b) truncated quality string is resolved; c)
- SOLiD read mapped to the reverse strand is complemented.
-
- * Bwa now calculates skewness and kurtosis of the insert size
- distribution.
-
- * Deploy a Bayesian method to estimate the maximum distance for a read
- pair considered to be paired properly. The method is proposed by
- Gerton Lunter, but bwa only implements a simplified version.
-
- * Export more functions for Java bindings, by Matt Hanna (See:
- http://www.broadinstitute.org/gsa/wiki/index.php/Sting_BWA/C_bindings)
-
- * Abstract bwa CIGAR for further extension, by Rodrigo Goya.
-
-(0.5.6: 10 Feburary 2010, r1303)
-
-
-
-Beta Release 0.5.5 (10 November, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-This is a bug fix release:
-
- * Fixed a serious bug/typo in aln which does not occur given short
- reads, but will lead to segfault for >500bp reads. Of course, the aln
- command is not recommended for reads longer than 200bp, but this is a
- bug anyway.
-
- * Fixed a minor bug/typo which leads to incorrect single-end mapping
- quality when one end is moved to meet the mate-pair requirement.
-
- * Fixed a bug in samse for mapping in the color space. This bug is
- caused by quality filtration added since 0.5.1.
-
-(0.5.5: 10 November 2009, r1273)
-
-
-
-Beta Release 0.5.4 (9 October, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Since this version, the default seed length used in the "aln" command is
-changed to 32.
-
-Notable changes in bwa-short:
-
- * Added a new tag "XC:i" which gives the length of clipped reads.
-
- * In sampe, skip alignments in case of a bug in the Smith-Waterman
- alignment module.
-
- * In sampe, fixed a bug in pairing when the read sequence is identical
- to its reverse complement.
-
- * In sampe, optionally preload the entire FM-index into memory to
- reduce disk operations.
-
-Notable changes in dBWT-SW/BWA-SW:
-
- * Changed name dBWT-SW to BWA-SW.
-
- * Optionally use "hard clipping" in the SAM output.
-
-(0.5.4: 9 October 2009, r1245)
-
-
-
-Beta Release 0.5.3 (15 September, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Fixed a critical bug in bwa-short: reads mapped to the reverse strand
-are not complemented.
-
-(0.5.3: 15 September 2009, r1225)
-
-
-
-Beta Release 0.5.2 (13 September, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Notable changes in bwa-short:
-
- * Optionally trim reads before alignment. See the manual page on `aln
- -q' for detailed description.
-
- * Fixed a bug in calculating the NM tag for a gapped alignment.
-
- * Fixed a bug given a mixture of reads with some longer than the seed
- length and some shorter.
-
- * Print SAM header.
-
-Notable changes in dBWT-SW:
-
- * Changed the default value of -T to 30. As a result, the accuracy is a
- little higher for short reads at the cost of speed.
-
-(0.5.2: 13 September 2009, r1223)
-
-
-
-Beta Release 0.5.1 (2 September, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Notable changes in the short read alignment component:
-
- * Fixed a bug in samse: do not write mate coordinates.
-
-Notable changes in dBWT-SW:
-
- * Randomly choose one alignment if the read is a repetitive.
-
- * Fixed a flaw when a read is mapped across two adjacent reference
- sequences. However, wrong alignment reports may still occur rarely in
- this case.
-
- * Changed the default band width to 50. The speed is slower due to this
- change.
-
- * Improved the mapping quality a little given long query sequences.
-
-(0.5.1: 2 September 2009, r1209)
-
-
-
-Beta Release 0.5.0 (20 August, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-This release implements a novel algorithm, dBWT-SW, specifically
-designed for long reads. It is 10-50 times faster than SSAHA2, depending
-on the characteristics of the input data, and achieves comparable
-alignment accuracy while allowing chimera detection. In comparison to
-BLAT, dBWT-SW is several times faster and much more accurate especially
-when the error rate is high. Please read the manual page for more
-information.
-
-The dBWT-SW algorithm is kind of developed for future sequencing
-technologies which produce much longer reads with a little higher error
-rate. It is still at its early development stage. Some features are
-missing and it may be buggy although I have evaluated on several
-simulated and real data sets. But following the "release early"
-paradigm, I would like the users to try it first.
-
-Other notable changes in BWA are:
-
- * Fixed a rare bug in the Smith-Waterman alignment module.
-
- * Fixed a rare bug about the wrong alignment coordinate when a read is
- poorly aligned.
-
- * Fixed a bug in generating the "mate-unmap" SAM tag when both ends in
- a pair are unmapped.
-
-(0.5.0: 20 August 2009, r1200)
-
-
-
-Beta Release 0.4.9 (19 May, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Interestingly, the integer overflow bug claimed to be fixed in 0.4.7 has
-not in fact. Now I have fixed the bug. Sorry for this and thank Quan
-Long for pointing out the bug (again).
-
-(0.4.9: 19 May 2009, r1075)
-
-
-
-Beta Release 0.4.8 (18 May, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-One change to "aln -R". Now by default, if there are no more than `-R'
-equally best hits, bwa will search for suboptimal hits. This change
-affects the ability in finding SNPs in segmental duplications.
-
-I have not tested this option thoroughly, but this simple change is less
-likely to cause new bugs. Hope I am right.
-
-(0.4.8: 18 May 2009, r1073)
-
-
-
-Beta Release 0.4.7 (12 May, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Notable changes:
-
- * Output SM (single-end mapping quality) and AM (smaller mapping
- quality among the two ends) tag from sam output.
-
- * Improved the functionality of stdsw.
-
- * Made the XN tag more accurate.
-
- * Fixed a very rare segfault caused by integer overflow.
-
- * Improve the insert size estimation.
-
- * Fixed compiling errors for some Linux systems.
-
-(0.4.7: 12 May 2009, r1066)
-
-
-
-Beta Release 0.4.6 (9 March, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-This release improves the SOLiD support. First, a script for converting
-SOLiD raw data is provided. This script is adapted from solid2fastq.pl
-in the MAQ package. Second, a nucleotide reference file can be directly
-used with `bwa index'. Third, SOLiD paired-end support is
-completed. Fourth, color-space reads will be converted to nucleotides
-when SAM output is generated. Color errors are corrected in this
-process. Please note that like MAQ, BWA cannot make use of the primer
-base and the first color.
-
-In addition, the calculation of mapping quality is also improved a
-little bit, although end-users may barely observe the difference.
-
-(0.4.6: 9 March 2009, r915)
-
-
-
-Beta Release 0.4.5 (18 Feburary, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Not much happened, but I think it would be good to let the users use the
-latest version.
-
-Notable changes (Thank Bob Handsaker for catching the two bugs):
-
- * Improved bounary check. Previous version may still give incorrect
- alignment coordinates in rare cases.
-
- * Fixed a bug in SW alignment when no residue matches. This only
- affects the `sampe' command.
-
- * Robustly estimate insert size without setting the maximum on the
- command line. Since this release `sampe -a' only has an effect if
- there are not enough good pairs to infer the insert size
- distribution.
-
- * Reduced false PE alignments a little bit by using the inferred insert
- size distribution. This fix may be more important for long insert
- size libraries.
-
-(0.4.5: 18 Feburary 2009, r829)
-
-
-
-Beta Release 0.4.4 (15 Feburary, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-This is mainly a bug fix release. Notable changes are:
-
- * Imposed boundary check for extracting subsequence from the
- genome. Previously this causes memory problem in rare cases.
-
- * Fixed a bug in failing to find whether an alignment overlapping with
- N on the genome.
-
- * Changed MD tag to meet the latest SAM specification.
-
-(0.4.4: 15 Feburary 2009, r815)
-
-
-
-Beta Release 0.4.3 (22 January, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Notable changes:
-
- * Treat an ambiguous base N as a mismatch. Previous versions will not
- map reads containing any N.
-
- * Automatically choose the maximum allowed number of differences. This
- is important when reads of different lengths are mixed together.
-
- * Print mate coordinate if only one end is unmapped.
-
- * Generate MD tag. This tag encodes the mismatching positions and the
- reference bases at these positions. Deletions from the reference will
- also be printed.
-
- * Optionally dump multiple hits from samse, in another concise format
- rather than SAM.
-
- * Optionally disable iterative search. This is VERY SLOOOOW, though.
-
- * Fixed a bug in generate SAM.
-
-(0.4.3: 22 January 2009, r787)
-
-
-
-Beta Release 0.4.2 (9 January, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Aaron Quinlan found a bug in the indexer: the bwa indexer segfaults if
-there are no comment texts in the FASTA header. This is a critical
-bug. Nothing else was changed.
-
-(0.4.2: 9 January 2009, r769)
-
-
-
-Beta Release 0.4.1 (7 January, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-I am sorry for the quick updates these days. I like to set a milestone
-for BWA and this release seems to be. For paired end reads, BWA also
-does Smith-Waterman alignment for an unmapped read whose mate can be
-mapped confidently. With this strategy BWA achieves similar accuracy to
-maq. Benchmark is also updated accordingly.
-
-(0.4.1: 7 January 2009, r760)
-
-
-
-Beta Release 0.4.0 (6 January, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-In comparison to the release two days ago, this release is mainly tuned
-for performance with some tricks I learnt from Bowtie. However, as the
-indexing format has also been changed, I have to increase the version
-number to 0.4.0 to emphasize that *DATABASE MUST BE RE-INDEXED* with
-`bwa index'.
-
- * Improved the speed by about 20%.
-
- * Added multi-threading to `bwa aln'.
-
-(0.4.0: 6 January 2009, r756)
-
-
-
-Beta Release 0.3.0 (4 January, 2009)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- * Added paired-end support by separating SA calculation and alignment
- output.
-
- * Added SAM output.
-
- * Added evaluation to the documentation.
-
-(0.3.0: 4 January 2009, r741)
-
-
-
-Beta Release 0.2.0 (15 Augusst, 2008)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- * Take the subsequence at the 5'-end as seed. Seeding strategy greatly
- improves the speed for long reads, at the cost of missing a few true
- hits that contain many differences in the seed. Seeding also increase
- the memory by 800MB.
-
- * Fixed a bug which may miss some gapped alignments. Fixing the bug
- also slows the speed a little.
-
-(0.2.0: 15 August 2008, r428)
-
-
-
-Beta Release 0.1.6 (08 Augusst, 2008)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- * Give accurate CIGAR string.
-
- * Add a simple interface to SW/NW alignment
-
-(0.1.6: 08 August 2008, r414)
-
-
-
-Beta Release 0.1.5 (27 July, 2008)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- * Improve the speed. This version is expected to give the same results.
-
-(0.1.5: 27 July 2008, r400)
-
-
-
-Beta Release 0.1.4 (22 July, 2008)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- * Fixed a bug which may cause missing gapped alignments.
-
- * More clearly define what alignments can be found by BWA (See
- manual). Now BWA runs a little slower because it will visit more
- potential gapped alignments.
-
- * A bit code clean up.
-
-(0.1.4: 22 July 2008, r387)
-
-
-
-Beta Release 0.1.3 (21 July, 2008)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Improve the speed with some tricks on retrieving occurences. The results
-should be exactly the same as that of 0.1.2.
-
-(0.1.3: 21 July 2008, r382)
-
-
-
-Beta Release 0.1.2 (17 July, 2008)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Support gapped alignment. Codes for ungapped alignment has been removed.
-
-(0.1.2: 17 July 2008, r371)
-
-
-
-Beta Release 0.1.1 (03 June, 2008)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-This is the first release of BWA, Burrows-Wheeler Alignment tool. Please
-read man page for more information about this software.
-
-(0.1.1: 03 June 2008, r349)
-
-
-
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/QSufSort.c
--- a/bwa-0.6.2/QSufSort.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,405 +0,0 @@
-/* QSufSort.c
-
- Original source from qsufsort.c
-
- Copyright 1999, N. Jesper Larsson, all rights reserved.
-
- This file contains an implementation of the algorithm presented in "Faster
- Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko
- Sadakane (sada@is.s.u-tokyo.ac.jp).
-
- This software may be used freely for any purpose. However, when distributed,
- the original source must be clearly stated, and, when the source code is
- distributed, the copyright notice must be retained and any alterations in
- the code must be clearly marked. No warranty is given regarding the quality
- of this software.
-
- Modified by Wong Chi-Kwong, 2004
-
- Changes summary: - Used long variable and function names
- - Removed global variables
- - Replace pointer references with array references
- - Used insertion sort in place of selection sort and increased insertion sort threshold
- - Reconstructing suffix array from inverse becomes an option
- - Add handling where end-of-text symbol is not necessary < all characters
- - Removed codes for supporting alphabet size > number of characters
-
- No warrenty is given regarding the quality of the modifications.
-
-*/
-
-
-#include
-#include
-#include
-#include "QSufSort.h"
-
-#define min(value1, value2) ( ((value1) < (value2)) ? (value1) : (value2) )
-#define med3(a, b, c) ( ac ? b : a>c ? c : a))
-#define swap(a, b, t); t = a; a = b; b = t;
-
-// Static functions
-static void QSufSortSortSplit(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos,
- const qsint_t highestPos, const qsint_t numSortedChar);
-static qsint_t QSufSortChoosePivot(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos,
- const qsint_t highestPos, const qsint_t numSortedChar);
-static void QSufSortInsertSortSplit(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos,
- const qsint_t highestPos, const qsint_t numSortedChar);
-static void QSufSortBucketSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t alphabetSize);
-static qsint_t QSufSortTransform(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t largestInputSymbol,
- const qsint_t smallestInputSymbol, const qsint_t maxNewAlphabetSize, qsint_t *numSymbolAggregated);
-
-/* Makes suffix array p of x. x becomes inverse of p. p and x are both of size
- n+1. Contents of x[0...n-1] are integers in the range l...k-1. Original
- contents of x[n] is disregarded, the n-th symbol being regarded as
- end-of-string smaller than all other symbols.*/
-void QSufSortSuffixSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t largestInputSymbol,
- const qsint_t smallestInputSymbol, const int skipTransform)
-{
- qsint_t i, j;
- qsint_t s, negatedSortedGroupLength;
- qsint_t numSymbolAggregated;
- qsint_t maxNumInputSymbol;
- qsint_t numSortedPos = 1;
- qsint_t newAlphabetSize;
-
- maxNumInputSymbol = largestInputSymbol - smallestInputSymbol + 1;
-
- if (!skipTransform) {
- /* bucketing possible*/
- newAlphabetSize = QSufSortTransform(V, I, numChar, largestInputSymbol, smallestInputSymbol,
- numChar, &numSymbolAggregated);
- QSufSortBucketSort(V, I, numChar, newAlphabetSize);
- I[0] = -1;
- V[numChar] = 0;
- numSortedPos = numSymbolAggregated;
- }
-
- while ((qsint_t)(I[0]) >= -(qsint_t)numChar) {
- i = 0;
- negatedSortedGroupLength = 0;
- do {
- s = I[i];
- if (s < 0) {
- i -= s; /* skip over sorted group.*/
- negatedSortedGroupLength += s;
- } else {
- if (negatedSortedGroupLength) {
- I[i+negatedSortedGroupLength] = negatedSortedGroupLength; /* combine preceding sorted groups */
- negatedSortedGroupLength = 0;
- }
- j = V[s] + 1;
- QSufSortSortSplit(V, I, i, j - 1, numSortedPos);
- i = j;
- }
- } while (i <= numChar);
- if (negatedSortedGroupLength) {
- /* array ends with a sorted group.*/
- I[i+negatedSortedGroupLength] = negatedSortedGroupLength; /* combine sorted groups at end of I.*/
- }
- numSortedPos *= 2; /* double sorted-depth.*/
- }
-}
-
-void QSufSortGenerateSaFromInverse(const qsint_t* V, qsint_t* __restrict I, const qsint_t numChar)
-{
- qsint_t i;
- for (i=0; i<=numChar; i++)
- I[V[i]] = i + 1;
-}
-
-/* Sorting routine called for each unsorted group. Sorts the array of integers
- (suffix numbers) of length n starting at p. The algorithm is a ternary-split
- quicksort taken from Bentley & McIlroy, "Engineering a Sort Function",
- Software -- Practice and Experience 23(11), 1249-1265 (November 1993). This
- function is based on Program 7.*/
-static void QSufSortSortSplit(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos,
- const qsint_t highestPos, const qsint_t numSortedChar) {
-
- qsint_t a, b, c, d;
- qsint_t l, m;
- qsint_t f, v, s, t;
- qsint_t tmp;
- qsint_t numItem;
-
- numItem = highestPos - lowestPos + 1;
-
- if (numItem <= INSERT_SORT_NUM_ITEM) {
- QSufSortInsertSortSplit(V, I, lowestPos, highestPos, numSortedChar);
- return;
- }
-
- v = QSufSortChoosePivot(V, I, lowestPos, highestPos, numSortedChar);
-
- a = b = lowestPos;
- c = d = highestPos;
-
- while (1) {
- while (c >= b && (f = KEY(V, I, b, numSortedChar)) <= v) {
- if (f == v) {
- swap(I[a], I[b], tmp);
- a++;
- }
- b++;
- }
- while (c >= b && (f = KEY(V, I, c, numSortedChar)) >= v) {
- if (f == v) {
- swap(I[c], I[d], tmp);
- d--;
- }
- c--;
- }
- if (b > c)
- break;
- swap(I[b], I[c], tmp);
- b++;
- c--;
- }
-
- s = a - lowestPos;
- t = b - a;
- s = min(s, t);
- for (l = lowestPos, m = b - s; m < b; l++, m++) {
- swap(I[l], I[m], tmp);
- }
-
- s = d - c;
- t = highestPos - d;
- s = min(s, t);
- for (l = b, m = highestPos - s + 1; m <= highestPos; l++, m++) {
- swap(I[l], I[m], tmp);
- }
-
- s = b - a;
- t = d - c;
- if (s > 0)
- QSufSortSortSplit(V, I, lowestPos, lowestPos + s - 1, numSortedChar);
-
- // Update group number for equal portion
- a = lowestPos + s;
- b = highestPos - t;
- if (a == b) {
- // Sorted group
- V[I[a]] = a;
- I[a] = -1;
- } else {
- // Unsorted group
- for (c=a; c<=b; c++)
- V[I[c]] = b;
- }
-
- if (t > 0)
- QSufSortSortSplit(V, I, highestPos - t + 1, highestPos, numSortedChar);
-
-}
-
-/* Algorithm by Bentley & McIlroy.*/
-static qsint_t QSufSortChoosePivot(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos,
- const qsint_t highestPos, const qsint_t numSortedChar) {
-
- qsint_t m;
- qsint_t keyl, keym, keyn;
- qsint_t key1, key2, key3;
- qsint_t s;
- qsint_t numItem;
-
- numItem = highestPos - lowestPos + 1;
-
- m = lowestPos + numItem / 2;
-
- s = numItem / 8;
- key1 = KEY(V, I, lowestPos, numSortedChar);
- key2 = KEY(V, I, lowestPos+s, numSortedChar);
- key3 = KEY(V, I, lowestPos+2*s, numSortedChar);
- keyl = med3(key1, key2, key3);
- key1 = KEY(V, I, m-s, numSortedChar);
- key2 = KEY(V, I, m, numSortedChar);
- key3 = KEY(V, I, m+s, numSortedChar);
- keym = med3(key1, key2, key3);
- key1 = KEY(V, I, highestPos-2*s, numSortedChar);
- key2 = KEY(V, I, highestPos-s, numSortedChar);
- key3 = KEY(V, I, highestPos, numSortedChar);
- keyn = med3(key1, key2, key3);
-
- return med3(keyl, keym, keyn);
-
-
-}
-
-/* Quadratic sorting method to use for small subarrays. */
-static void QSufSortInsertSortSplit(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos,
- const qsint_t highestPos, const qsint_t numSortedChar)
-{
- qsint_t i, j;
- qsint_t tmpKey, tmpPos;
- qsint_t numItem;
- qsint_t key[INSERT_SORT_NUM_ITEM], pos[INSERT_SORT_NUM_ITEM];
- qsint_t negativeSortedLength;
- qsint_t groupNum;
-
- numItem = highestPos - lowestPos + 1;
-
- for (i=0; i0 && key[j-1] > tmpKey; j--) {
- key[j] = key[j-1];
- pos[j] = pos[j-1];
- }
- key[j] = tmpKey;
- pos[j] = tmpPos;
- }
-
- negativeSortedLength = -1;
-
- i = numItem - 1;
- groupNum = highestPos;
- while (i > 0) {
- I[i+lowestPos] = pos[i];
- V[I[i+lowestPos]] = groupNum;
- if (key[i-1] == key[i]) {
- negativeSortedLength = 0;
- } else {
- if (negativeSortedLength < 0)
- I[i+lowestPos] = negativeSortedLength;
- groupNum = i + lowestPos - 1;
- negativeSortedLength--;
- }
- i--;
- }
-
- I[lowestPos] = pos[0];
- V[I[lowestPos]] = groupNum;
- if (negativeSortedLength < 0)
- I[lowestPos] = negativeSortedLength;
-}
-
-/* Bucketsort for first iteration.
-
- Input: x[0...n-1] holds integers in the range 1...k-1, all of which appear
- at least once. x[n] is 0. (This is the corresponding output of transform.) k
- must be at most n+1. p is array of size n+1 whose contents are disregarded.
-
- Output: x is V and p is I after the initial sorting stage of the refined
- suffix sorting algorithm.*/
-
-static void QSufSortBucketSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t alphabetSize)
-{
- qsint_t i, c;
- qsint_t d;
- qsint_t groupNum;
- qsint_t currentIndex;
-
- // mark linked list empty
- for (i=0; i0; i--) {
- c = I[i-1];
- d = (qsint_t)(V[c]);
- groupNum = currentIndex;
- V[c] = groupNum;
- if (d >= 0) {
- I[currentIndex] = c;
- while (d >= 0) {
- c = d;
- d = V[c];
- V[c] = groupNum;
- currentIndex--;
- I[currentIndex] = c;
- }
- } else {
- // sorted group
- I[currentIndex] = -1;
- }
- currentIndex--;
- }
-}
-
-/* Transforms the alphabet of x by attempting to aggregate several symbols into
- one, while preserving the suffix order of x. The alphabet may also be
- compacted, so that x on output comprises all integers of the new alphabet
- with no skipped numbers.
-
- Input: x is an array of size n+1 whose first n elements are positive
- integers in the range l...k-1. p is array of size n+1, used for temporary
- storage. q controls aggregation and compaction by defining the maximum intue
- for any symbol during transformation: q must be at least k-l; if q<=n,
- compaction is guaranteed; if k-l>n, compaction is never done; if q is
- INT_MAX, the maximum number of symbols are aggregated into one.
-
- Output: Returns an integer j in the range 1...q representing the size of the
- new alphabet. If j<=n+1, the alphabet is compacted. The global variable r is
- set to the number of old symbols grouped into one. Only x[n] is 0.*/
-static qsint_t QSufSortTransform(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t largestInputSymbol,
- const qsint_t smallestInputSymbol, const qsint_t maxNewAlphabetSize, qsint_t *numSymbolAggregated)
-{
- qsint_t c, i, j;
- qsint_t a; // numSymbolAggregated
- qsint_t mask;
- qsint_t minSymbolInChunk = 0, maxSymbolInChunk = 0;
- qsint_t newAlphabetSize;
- qsint_t maxNumInputSymbol, maxNumBit, maxSymbol;
-
- maxNumInputSymbol = largestInputSymbol - smallestInputSymbol + 1;
-
- for (maxNumBit = 0, i = maxNumInputSymbol; i; i >>= 1) ++maxNumBit;
- maxSymbol = QSINT_MAX >> maxNumBit;
-
- c = maxNumInputSymbol;
- for (a = 0; a < numChar && maxSymbolInChunk <= maxSymbol && c <= maxNewAlphabetSize; a++) {
- minSymbolInChunk = (minSymbolInChunk << maxNumBit) | (V[a] - smallestInputSymbol + 1);
- maxSymbolInChunk = c;
- c = (maxSymbolInChunk << maxNumBit) | maxNumInputSymbol;
- }
-
- mask = (1 << (a-1) * maxNumBit) - 1; /* mask masks off top old symbol from chunk.*/
- V[numChar] = smallestInputSymbol - 1; /* emulate zero terminator.*/
-
- /* bucketing possible, compact alphabet.*/
- for (i=0; i<=maxSymbolInChunk; i++)
- I[i] = 0; /* zero transformation table.*/
- c = minSymbolInChunk;
- for (i=a; i<=numChar; i++) {
- I[c] = 1; /* mark used chunk symbol.*/
- c = ((c & mask) << maxNumBit) | (V[i] - smallestInputSymbol + 1); /* shift in next old symbol in chunk.*/
- }
- for (i=1; i number of characters
-
- No warrenty is given regarding the quality of the modifications.
-
-*/
-
-#ifndef __QSUFSORT_H__
-#define __QSUFSORT_H__
-
-#include
-
-#define KEY(V, I, p, h) ( V[ I[p] + h ] )
-#define INSERT_SORT_NUM_ITEM 16
-
-typedef int64_t qsint_t;
-#define QSINT_MAX INT64_MAX
-
-void QSufSortSuffixSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t largestInputSymbol,
- const qsint_t smallestInputSymbol, const int skipTransform);
-void QSufSortGenerateSaFromInverse(const qsint_t *V, qsint_t* __restrict I, const qsint_t numChar);
-
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/README
--- a/bwa-0.6.2/README Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-Released packages can be downloaded from SourceForge.net:
-
- http://sourceforge.net/projects/bio-bwa/files/
-
-Introduction and FAQ are available at:
-
- http://bio-bwa.sourceforge.net
-
-Manual page at:
-
- http://bio-bwa.sourceforge.net/bwa.shtml
-
-Mailing list:
-
- bio-bwa-help@lists.sourceforge.net
-
-To sign up:
-
- http://sourceforge.net/mail/?group_id=276243
-
-Publications (Open Access):
-
- http://www.ncbi.nlm.nih.gov/pubmed/20080505
- http://www.ncbi.nlm.nih.gov/pubmed/19451168
-
-Incomplete list of citations (via HubMed.org):
-
- http://www.hubmed.org/references.cgi?uids=20080505
- http://www.hubmed.org/references.cgi?uids=19451168
-
-Related projects:
-
- http://pbwa.sourceforge.net/
- http://www.many-core.group.cam.ac.uk/projects/lam.shtml
- http://biodoop-seal.sourceforge.net/
- http://gitorious.org/bwa-cuda
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bamlite.c
--- a/bwa-0.6.2/bamlite.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,155 +0,0 @@
-#include
-#include
-#include
-#include
-#include "bamlite.h"
-
-/*********************
- * from bam_endian.c *
- *********************/
-
-static inline int bam_is_big_endian()
-{
- long one= 1;
- return !(*((char *)(&one)));
-}
-static inline uint16_t bam_swap_endian_2(uint16_t v)
-{
- return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8));
-}
-static inline void *bam_swap_endian_2p(void *x)
-{
- *(uint16_t*)x = bam_swap_endian_2(*(uint16_t*)x);
- return x;
-}
-static inline uint32_t bam_swap_endian_4(uint32_t v)
-{
- v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
- return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
-}
-static inline void *bam_swap_endian_4p(void *x)
-{
- *(uint32_t*)x = bam_swap_endian_4(*(uint32_t*)x);
- return x;
-}
-static inline uint64_t bam_swap_endian_8(uint64_t v)
-{
- v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
- v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
- return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
-}
-static inline void *bam_swap_endian_8p(void *x)
-{
- *(uint64_t*)x = bam_swap_endian_8(*(uint64_t*)x);
- return x;
-}
-
-/**************
- * from bam.c *
- **************/
-
-int bam_is_be;
-
-bam_header_t *bam_header_init()
-{
- bam_is_be = bam_is_big_endian();
- return (bam_header_t*)calloc(1, sizeof(bam_header_t));
-}
-
-void bam_header_destroy(bam_header_t *header)
-{
- int32_t i;
- if (header == 0) return;
- if (header->target_name) {
- for (i = 0; i < header->n_targets; ++i)
- free(header->target_name[i]);
- free(header->target_name);
- free(header->target_len);
- }
- free(header->text);
- free(header);
-}
-
-bam_header_t *bam_header_read(bamFile fp)
-{
- bam_header_t *header;
- char buf[4];
- int magic_len;
- int32_t i = 1, name_len;
- // read "BAM1"
- magic_len = bam_read(fp, buf, 4);
- if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
- fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
- return 0;
- }
- header = bam_header_init();
- // read plain text and the number of reference sequences
- bam_read(fp, &header->l_text, 4);
- if (bam_is_be) bam_swap_endian_4p(&header->l_text);
- header->text = (char*)calloc(header->l_text + 1, 1);
- bam_read(fp, header->text, header->l_text);
- bam_read(fp, &header->n_targets, 4);
- if (bam_is_be) bam_swap_endian_4p(&header->n_targets);
- // read reference sequence names and lengths
- header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
- header->target_len = (uint32_t*)calloc(header->n_targets, 4);
- for (i = 0; i != header->n_targets; ++i) {
- bam_read(fp, &name_len, 4);
- if (bam_is_be) bam_swap_endian_4p(&name_len);
- header->target_name[i] = (char*)calloc(name_len, 1);
- bam_read(fp, header->target_name[i], name_len);
- bam_read(fp, &header->target_len[i], 4);
- if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
- }
- return header;
-}
-
-static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
-{
- uint8_t *s;
- uint32_t i, *cigar = (uint32_t*)(data + c->l_qname);
- s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
- for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]);
- while (s < data + data_len) {
- uint8_t type;
- s += 2; // skip key
- type = toupper(*s); ++s; // skip type
- if (type == 'C' || type == 'A') ++s;
- else if (type == 'S') { bam_swap_endian_2p(s); s += 2; }
- else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
- else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
- else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
- }
-}
-
-int bam_read1(bamFile fp, bam1_t *b)
-{
- bam1_core_t *c = &b->core;
- int32_t block_len, ret, i;
- uint32_t x[8];
-
- if ((ret = bam_read(fp, &block_len, 4)) != 4) {
- if (ret == 0) return -1; // normal end-of-file
- else return -2; // truncated
- }
- if (bam_read(fp, x, sizeof(bam1_core_t)) != sizeof(bam1_core_t)) return -3;
- if (bam_is_be) {
- bam_swap_endian_4p(&block_len);
- for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
- }
- c->tid = x[0]; c->pos = x[1];
- c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
- c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
- c->l_qseq = x[4];
- c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
- b->data_len = block_len - sizeof(bam1_core_t);
- if (b->m_data < b->data_len) {
- b->m_data = b->data_len;
- kroundup32(b->m_data);
- b->data = (uint8_t*)realloc(b->data, b->m_data);
- }
- if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4;
- b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
- if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
- return 4 + block_len;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bamlite.h
--- a/bwa-0.6.2/bamlite.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
-#ifndef BAMLITE_H_
-#define BAMLITE_H_
-
-#include
-#include
-
-typedef gzFile bamFile;
-#define bam_open(fn, mode) gzopen(fn, mode)
-#define bam_dopen(fd, mode) gzdopen(fd, mode)
-#define bam_close(fp) gzclose(fp)
-#define bam_read(fp, buf, size) gzread(fp, buf, size)
-
-typedef struct {
- int32_t n_targets;
- char **target_name;
- uint32_t *target_len;
- size_t l_text, n_text;
- char *text;
-} bam_header_t;
-
-#define BAM_FPAIRED 1
-#define BAM_FPROPER_PAIR 2
-#define BAM_FUNMAP 4
-#define BAM_FMUNMAP 8
-#define BAM_FREVERSE 16
-#define BAM_FMREVERSE 32
-#define BAM_FREAD1 64
-#define BAM_FREAD2 128
-#define BAM_FSECONDARY 256
-#define BAM_FQCFAIL 512
-#define BAM_FDUP 1024
-
-#define BAM_CIGAR_SHIFT 4
-#define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1)
-
-#define BAM_CMATCH 0
-#define BAM_CINS 1
-#define BAM_CDEL 2
-#define BAM_CREF_SKIP 3
-#define BAM_CSOFT_CLIP 4
-#define BAM_CHARD_CLIP 5
-#define BAM_CPAD 6
-
-typedef struct {
- int32_t tid;
- int32_t pos;
- uint32_t bin:16, qual:8, l_qname:8;
- uint32_t flag:16, n_cigar:16;
- int32_t l_qseq;
- int32_t mtid;
- int32_t mpos;
- int32_t isize;
-} bam1_core_t;
-
-typedef struct {
- bam1_core_t core;
- int l_aux, data_len, m_data;
- uint8_t *data;
-} bam1_t;
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-#define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
-#define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
-#define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))
-#define bam1_qname(b) ((char*)((b)->data))
-#define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname)
-#define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))
-#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
-#define bam1_aux(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (b)->core.l_qseq + ((b)->core.l_qseq + 1)/2)
-
-#define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
-#define bam_destroy1(b) do { \
- if (b) { free((b)->data); free(b); } \
- } while (0)
-
-extern int bam_is_be;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- bam_header_t *bam_header_init(void);
- void bam_header_destroy(bam_header_t *header);
- bam_header_t *bam_header_read(bamFile fp);
- int bam_read1(bamFile fp, bam1_t *b);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bntseq.c
--- a/bwa-0.6.2/bntseq.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,323 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008 Genome Research Ltd (GRL).
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-/* Contact: Heng Li */
-
-#include
-#include
-#include
-#include
-#include
-#include "bntseq.h"
-#include "main.h"
-#include "utils.h"
-
-#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
-
-unsigned char nst_nt4_table[256] = {
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
-};
-
-void bns_dump(const bntseq_t *bns, const char *prefix)
-{
- char str[1024];
- FILE *fp;
- int i;
- { // dump .ann
- strcpy(str, prefix); strcat(str, ".ann");
- fp = xopen(str, "w");
- fprintf(fp, "%lld %d %u\n", (long long)bns->l_pac, bns->n_seqs, bns->seed);
- for (i = 0; i != bns->n_seqs; ++i) {
- bntann1_t *p = bns->anns + i;
- fprintf(fp, "%d %s", p->gi, p->name);
- if (p->anno[0]) fprintf(fp, " %s\n", p->anno);
- else fprintf(fp, "\n");
- fprintf(fp, "%lld %d %d\n", (long long)p->offset, p->len, p->n_ambs);
- }
- fclose(fp);
- }
- { // dump .amb
- strcpy(str, prefix); strcat(str, ".amb");
- fp = xopen(str, "w");
- fprintf(fp, "%lld %d %u\n", (long long)bns->l_pac, bns->n_seqs, bns->n_holes);
- for (i = 0; i != bns->n_holes; ++i) {
- bntamb1_t *p = bns->ambs + i;
- fprintf(fp, "%lld %d %c\n", (long long)p->offset, p->len, p->amb);
- }
- fclose(fp);
- }
-}
-
-bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename)
-{
- char str[1024];
- FILE *fp;
- bntseq_t *bns;
- long long xx;
- int i;
- bns = (bntseq_t*)calloc(1, sizeof(bntseq_t));
- { // read .ann
- fp = xopen(ann_filename, "r");
- fscanf(fp, "%lld%d%u", &xx, &bns->n_seqs, &bns->seed);
- bns->l_pac = xx;
- bns->anns = (bntann1_t*)calloc(bns->n_seqs, sizeof(bntann1_t));
- for (i = 0; i < bns->n_seqs; ++i) {
- bntann1_t *p = bns->anns + i;
- char *q = str;
- int c;
- // read gi and sequence name
- fscanf(fp, "%u%s", &p->gi, str);
- p->name = strdup(str);
- // read fasta comments
- while ((c = fgetc(fp)) != '\n' && c != EOF) *q++ = c;
- *q = 0;
- if (q - str > 1) p->anno = strdup(str + 1); // skip leading space
- else p->anno = strdup("");
- // read the rest
- fscanf(fp, "%lld%d%d", &xx, &p->len, &p->n_ambs);
- p->offset = xx;
- }
- fclose(fp);
- }
- { // read .amb
- int64_t l_pac;
- int32_t n_seqs;
- fp = xopen(amb_filename, "r");
- fscanf(fp, "%lld%d%d", &xx, &n_seqs, &bns->n_holes);
- l_pac = xx;
- xassert(l_pac == bns->l_pac && n_seqs == bns->n_seqs, "inconsistent .ann and .amb files.");
- bns->ambs = (bntamb1_t*)calloc(bns->n_holes, sizeof(bntamb1_t));
- for (i = 0; i < bns->n_holes; ++i) {
- bntamb1_t *p = bns->ambs + i;
- fscanf(fp, "%lld%d%s", &xx, &p->len, str);
- p->offset = xx;
- p->amb = str[0];
- }
- fclose(fp);
- }
- { // open .pac
- bns->fp_pac = xopen(pac_filename, "rb");
- }
- return bns;
-}
-
-bntseq_t *bns_restore(const char *prefix)
-{
- char ann_filename[1024], amb_filename[1024], pac_filename[1024];
- strcat(strcpy(ann_filename, prefix), ".ann");
- strcat(strcpy(amb_filename, prefix), ".amb");
- strcat(strcpy(pac_filename, prefix), ".pac");
- return bns_restore_core(ann_filename, amb_filename, pac_filename);
-}
-
-void bns_destroy(bntseq_t *bns)
-{
- if (bns == 0) return;
- else {
- int i;
- if (bns->fp_pac) fclose(bns->fp_pac);
- free(bns->ambs);
- for (i = 0; i < bns->n_seqs; ++i) {
- free(bns->anns[i].name);
- free(bns->anns[i].anno);
- }
- free(bns->anns);
- free(bns);
- }
-}
-
-#define _set_pac(pac, l, c) ((pac)[(l)>>2] |= (c)<<((~(l)&3)<<1))
-#define _get_pac(pac, l) ((pac)[(l)>>2]>>((~(l)&3)<<1)&3)
-
-static uint8_t *add1(const kseq_t *seq, bntseq_t *bns, uint8_t *pac, int64_t *m_pac, int *m_seqs, int *m_holes, bntamb1_t **q)
-{
- bntann1_t *p;
- int i, lasts;
- if (bns->n_seqs == *m_seqs) {
- *m_seqs <<= 1;
- bns->anns = (bntann1_t*)realloc(bns->anns, *m_seqs * sizeof(bntann1_t));
- }
- p = bns->anns + bns->n_seqs;
- p->name = strdup((char*)seq->name.s);
- p->anno = seq->comment.s? strdup((char*)seq->comment.s) : strdup("(null)");
- p->gi = 0; p->len = seq->seq.l;
- p->offset = (bns->n_seqs == 0)? 0 : (p-1)->offset + (p-1)->len;
- p->n_ambs = 0;
- for (i = lasts = 0; i < seq->seq.l; ++i) {
- int c = nst_nt4_table[(int)seq->seq.s[i]];
- if (c >= 4) { // N
- if (lasts == seq->seq.s[i]) { // contiguous N
- ++(*q)->len;
- } else {
- if (bns->n_holes == *m_holes) {
- (*m_holes) <<= 1;
- bns->ambs = (bntamb1_t*)realloc(bns->ambs, (*m_holes) * sizeof(bntamb1_t));
- }
- *q = bns->ambs + bns->n_holes;
- (*q)->len = 1;
- (*q)->offset = p->offset + i;
- (*q)->amb = seq->seq.s[i];
- ++p->n_ambs;
- ++bns->n_holes;
- }
- }
- lasts = seq->seq.s[i];
- { // fill buffer
- if (c >= 4) c = lrand48()&3;
- if (bns->l_pac == *m_pac) { // double the pac size
- *m_pac <<= 1;
- pac = realloc(pac, *m_pac/4);
- memset(pac + bns->l_pac/4, 0, (*m_pac - bns->l_pac)/4);
- }
- _set_pac(pac, bns->l_pac, c);
- ++bns->l_pac;
- }
- }
- ++bns->n_seqs;
- return pac;
-}
-
-int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix, int for_only)
-{
- extern void seq_reverse(int len, ubyte_t *seq, int is_comp); // in bwaseqio.c
- kseq_t *seq;
- char name[1024];
- bntseq_t *bns;
- uint8_t *pac = 0;
- int32_t m_seqs, m_holes;
- int64_t ret = -1, m_pac, l;
- bntamb1_t *q;
- FILE *fp;
-
- // initialization
- seq = kseq_init(fp_fa);
- bns = (bntseq_t*)calloc(1, sizeof(bntseq_t));
- bns->seed = 11; // fixed seed for random generator
- srand48(bns->seed);
- m_seqs = m_holes = 8; m_pac = 0x10000;
- bns->anns = (bntann1_t*)calloc(m_seqs, sizeof(bntann1_t));
- bns->ambs = (bntamb1_t*)calloc(m_holes, sizeof(bntamb1_t));
- pac = calloc(m_pac/4, 1);
- q = bns->ambs;
- strcpy(name, prefix); strcat(name, ".pac");
- fp = xopen(name, "wb");
- // read sequences
- while (kseq_read(seq) >= 0) pac = add1(seq, bns, pac, &m_pac, &m_seqs, &m_holes, &q);
- if (!for_only) { // add the reverse complemented sequence
- m_pac = (bns->l_pac * 2 + 3) / 4 * 4;
- pac = realloc(pac, m_pac/4);
- memset(pac + (bns->l_pac+3)/4, 0, (m_pac - (bns->l_pac+3)/4*4) / 4);
- for (l = bns->l_pac - 1; l >= 0; --l, ++bns->l_pac)
- _set_pac(pac, bns->l_pac, 3-_get_pac(pac, l));
- }
- ret = bns->l_pac;
- { // finalize .pac file
- ubyte_t ct;
- fwrite(pac, 1, (bns->l_pac>>2) + ((bns->l_pac&3) == 0? 0 : 1), fp);
- // the following codes make the pac file size always (l_pac/4+1+1)
- if (bns->l_pac % 4 == 0) {
- ct = 0;
- fwrite(&ct, 1, 1, fp);
- }
- ct = bns->l_pac % 4;
- fwrite(&ct, 1, 1, fp);
- // close .pac file
- fclose(fp);
- }
- bns_dump(bns, prefix);
- bns_destroy(bns);
- kseq_destroy(seq);
- free(pac);
- return ret;
-}
-
-int bwa_fa2pac(int argc, char *argv[])
-{
- int c, for_only = 0;
- gzFile fp;
- while ((c = getopt(argc, argv, "f")) >= 0) {
- switch (c) {
- case 'f': for_only = 1; break;
- }
- }
- if (argc == optind) {
- fprintf(stderr, "Usage: bwa fa2pac [-f] []\n");
- return 1;
- }
- fp = xzopen(argv[optind], "r");
- bns_fasta2bntseq(fp, (optind+1 < argc)? argv[optind+1] : argv[optind], for_only);
- gzclose(fp);
- return 0;
-}
-
-int bns_cnt_ambi(const bntseq_t *bns, int64_t pos_f, int len, int *ref_id)
-{
- int left, mid, right, nn;
- if (ref_id) {
- left = 0; mid = 0; right = bns->n_seqs;
- while (left < right) {
- mid = (left + right) >> 1;
- if (pos_f >= bns->anns[mid].offset) {
- if (mid == bns->n_seqs - 1) break;
- if (pos_f < bns->anns[mid+1].offset) break; // bracketed
- left = mid + 1;
- } else right = mid;
- }
- *ref_id = mid;
- }
- left = 0; right = bns->n_holes; nn = 0;
- while (left < right) {
- mid = (left + right) >> 1;
- if (pos_f >= bns->ambs[mid].offset + bns->ambs[mid].len) left = mid + 1;
- else if (pos_f + len <= bns->ambs[mid].offset) right = mid;
- else { // overlap
- if (pos_f >= bns->ambs[mid].offset) {
- nn += bns->ambs[mid].offset + bns->ambs[mid].len < pos_f + len?
- bns->ambs[mid].offset + bns->ambs[mid].len - pos_f : len;
- } else {
- nn += bns->ambs[mid].offset + bns->ambs[mid].len < pos_f + len?
- bns->ambs[mid].len : len - (bns->ambs[mid].offset - pos_f);
- }
- break;
- }
- }
- return nn;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bntseq.h
--- a/bwa-0.6.2/bntseq.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,85 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008 Genome Research Ltd (GRL).
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-/* Contact: Heng Li */
-
-#ifndef BWT_BNTSEQ_H
-#define BWT_BNTSEQ_H
-
-#include
-#include
-
-#ifndef BWA_UBYTE
-#define BWA_UBYTE
-typedef uint8_t ubyte_t;
-#endif
-
-typedef struct {
- int64_t offset;
- int32_t len;
- int32_t n_ambs;
- uint32_t gi;
- char *name, *anno;
-} bntann1_t;
-
-typedef struct {
- int64_t offset;
- int32_t len;
- char amb;
-} bntamb1_t;
-
-typedef struct {
- int64_t l_pac;
- int32_t n_seqs;
- uint32_t seed;
- bntann1_t *anns; // n_seqs elements
- int32_t n_holes;
- bntamb1_t *ambs; // n_holes elements
- FILE *fp_pac;
-} bntseq_t;
-
-extern unsigned char nst_nt4_table[256];
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- void bns_dump(const bntseq_t *bns, const char *prefix);
- bntseq_t *bns_restore(const char *prefix);
- bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename);
- void bns_destroy(bntseq_t *bns);
- int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix, int for_only);
- int bns_cnt_ambi(const bntseq_t *bns, int64_t pos_f, int len, int *ref_id);
-
-#ifdef __cplusplus
-}
-#endif
-
-static inline int64_t bns_depos(const bntseq_t *bns, int64_t pos, int *is_rev)
-{
- return (*is_rev = (pos >= bns->l_pac))? (bns->l_pac<<1) - 1 - pos : pos;
-}
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwa.1
--- a/bwa-0.6.2/bwa.1 Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,571 +0,0 @@
-.TH bwa 1 "19 June 2012" "bwa-0.6.2" "Bioinformatics tools"
-.SH NAME
-.PP
-bwa - Burrows-Wheeler Alignment Tool
-.SH SYNOPSIS
-.PP
-bwa index -a bwtsw database.fasta
-.PP
-bwa aln database.fasta short_read.fastq > aln_sa.sai
-.PP
-bwa samse database.fasta aln_sa.sai short_read.fastq > aln.sam
-.PP
-bwa sampe database.fasta aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln.sam
-.PP
-bwa bwasw database.fasta long_read.fastq > aln.sam
-
-.SH DESCRIPTION
-.PP
-BWA is a fast light-weighted tool that aligns relatively short sequences
-(queries) to a sequence database (targe), such as the human reference
-genome. It implements two different algorithms, both based on
-Burrows-Wheeler Transform (BWT). The first algorithm is designed for
-short queries up to ~150bp with low error rate (<3%). It does gapped
-global alignment w.r.t. queries, supports paired-end reads, and is one
-of the fastest short read alignment algorithms to date while also
-visiting suboptimal hits. The second algorithm, BWA-SW, is designed for
-reads longer than 100bp with more errors. It performs a heuristic Smith-Waterman-like
-alignment to find high-scoring local hits and split hits. On
-low-error short queries, BWA-SW is a little slower and less accurate than the
-first algorithm, but on long queries, it is better.
-.PP
-For both algorithms, the database file in the FASTA format must be
-first indexed with the
-.B `index'
-command, which typically takes a few hours for a 3GB genome. The first algorithm is
-implemented via the
-.B `aln'
-command, which finds the suffix array (SA) coordinates of good hits of
-each individual read, and the
-.B `samse/sampe'
-command, which converts SA coordinates to chromosomal coordinate and
-pairs reads (for `sampe'). The second algorithm is invoked by the
-.B `bwasw'
-command. It works for single-end reads only.
-
-.SH COMMANDS AND OPTIONS
-.TP
-.B index
-bwa index [-p prefix] [-a algoType]
-
-Index database sequences in the FASTA format.
-
-.B OPTIONS:
-.RS
-.TP 10
-.B -c
-Build color-space index. The input fast should be in nucleotide space. (Disabled since 0.6.x)
-.TP
-.BI -p \ STR
-Prefix of the output database [same as db filename]
-.TP
-.BI -a \ STR
-Algorithm for constructing BWT index. Available options are:
-.RS
-.TP
-.B is
-IS linear-time algorithm for constructing suffix array. It requires
-5.37N memory where N is the size of the database. IS is moderately fast,
-but does not work with database larger than 2GB. IS is the default
-algorithm due to its simplicity. The current codes for IS algorithm are
-reimplemented by Yuta Mori.
-.TP
-.B bwtsw
-Algorithm implemented in BWT-SW. This method works with the whole human
-genome.
-.RE
-.RE
-
-.TP
-.B aln
-bwa aln [-n maxDiff] [-o maxGapO] [-e maxGapE] [-d nDelTail] [-i
-nIndelEnd] [-k maxSeedDiff] [-l seedLen] [-t nThrds] [-cRN] [-M misMsc]
-[-O gapOsc] [-E gapEsc] [-q trimQual] >
-
-
-Find the SA coordinates of the input reads. Maximum
-.I maxSeedDiff
-differences are allowed in the first
-.I seedLen
-subsequence and maximum
-.I maxDiff
-differences are allowed in the whole sequence.
-
-.B OPTIONS:
-.RS
-.TP 10
-.BI -n \ NUM
-Maximum edit distance if the value is INT, or the fraction of missing
-alignments given 2% uniform base error rate if FLOAT. In the latter
-case, the maximum edit distance is automatically chosen for different
-read lengths. [0.04]
-.TP
-.BI -o \ INT
-Maximum number of gap opens [1]
-.TP
-.BI -e \ INT
-Maximum number of gap extensions, -1 for k-difference mode (disallowing
-long gaps) [-1]
-.TP
-.BI -d \ INT
-Disallow a long deletion within INT bp towards the 3'-end [16]
-.TP
-.BI -i \ INT
-Disallow an indel within INT bp towards the ends [5]
-.TP
-.BI -l \ INT
-Take the first INT subsequence as seed. If INT is larger than the query
-sequence, seeding will be disabled. For long reads, this option is
-typically ranged from 25 to 35 for `-k 2'. [inf]
-.TP
-.BI -k \ INT
-Maximum edit distance in the seed [2]
-.TP
-.BI -t \ INT
-Number of threads (multi-threading mode) [1]
-.TP
-.BI -M \ INT
-Mismatch penalty. BWA will not search for suboptimal hits with a score
-lower than (bestScore-misMsc). [3]
-.TP
-.BI -O \ INT
-Gap open penalty [11]
-.TP
-.BI -E \ INT
-Gap extension penalty [4]
-.TP
-.BI -R \ INT
-Proceed with suboptimal alignments if there are no more than INT equally
-best hits. This option only affects paired-end mapping. Increasing this
-threshold helps to improve the pairing accuracy at the cost of speed,
-especially for short reads (~32bp).
-.TP
-.B -c
-Reverse query but not complement it, which is required for alignment in
-the color space. (Disabled since 0.6.x)
-.TP
-.B -N
-Disable iterative search. All hits with no more than
-.I maxDiff
-differences will be found. This mode is much slower than the default.
-.TP
-.BI -q \ INT
-Parameter for read trimming. BWA trims a read down to
-argmax_x{\\sum_{i=x+1}^l(INT-q_i)} if q_l 1.sai
- bwa aln ref.fa -b2 reads.bam > 2.sai
- bwa sampe ref.fa 1.sai 2.sai reads.bam reads.bam > aln.sam
-.TP
-.B -0
-When
-.B -b
-is specified, only use single-end reads in mapping.
-.TP
-.B -1
-When
-.B -b
-is specified, only use the first read in a read pair in mapping (skip
-single-end reads and the second reads).
-.TP
-.B -2
-When
-.B -b
-is specified, only use the second read in a read pair in mapping.
-.B
-.RE
-
-.TP
-.B samse
-bwa samse [-n maxOcc] >
-
-Generate alignments in the SAM format given single-end reads. Repetitive
-hits will be randomly chosen.
-
-.B OPTIONS:
-.RS
-.TP 10
-.BI -n \ INT
-Maximum number of alignments to output in the XA tag for reads paired
-properly. If a read has more than INT hits, the XA tag will not be
-written. [3]
-.TP
-.BI -r \ STR
-Specify the read group in a format like `@RG\\tID:foo\\tSM:bar'. [null]
-.RE
-
-.TP
-.B sampe
-bwa sampe [-a maxInsSize] [-o maxOcc] [-n maxHitPaired] [-N maxHitDis]
-[-P] >
-
-Generate alignments in the SAM format given paired-end reads. Repetitive
-read pairs will be placed randomly.
-
-.B OPTIONS:
-.RS
-.TP 8
-.BI -a \ INT
-Maximum insert size for a read pair to be considered being mapped
-properly. Since 0.4.5, this option is only used when there are not
-enough good alignment to infer the distribution of insert sizes. [500]
-.TP
-.BI -o \ INT
-Maximum occurrences of a read for pairing. A read with more occurrneces
-will be treated as a single-end read. Reducing this parameter helps
-faster pairing. [100000]
-.TP
-.B -P
-Load the entire FM-index into memory to reduce disk operations
-(base-space reads only). With this option, at least 1.25N bytes of
-memory are required, where N is the length of the genome.
-.TP
-.BI -n \ INT
-Maximum number of alignments to output in the XA tag for reads paired
-properly. If a read has more than INT hits, the XA tag will not be
-written. [3]
-.TP
-.BI -N \ INT
-Maximum number of alignments to output in the XA tag for disconcordant
-read pairs (excluding singletons). If a read has more than INT hits, the
-XA tag will not be written. [10]
-.TP
-.BI -r \ STR
-Specify the read group in a format like `@RG\\tID:foo\\tSM:bar'. [null]
-.RE
-
-.TP
-.B bwasw
-bwa bwasw [-a matchScore] [-b mmPen] [-q gapOpenPen] [-r gapExtPen] [-t
-nThreads] [-w bandWidth] [-T thres] [-s hspIntv] [-z zBest] [-N
-nHspRev] [-c thresCoef] [mate.fq]
-
-Align query sequences in the
-.I in.fq
-file. When
-.I mate.fq
-is present, perform paired-end alignment. The paired-end mode only works
-for reads Illumina short-insert libraries. In the paired-end mode, BWA-SW
-may still output split alignments but they are all marked as not properly
-paired; the mate positions will not be written if the mate has multiple
-local hits.
-
-.B OPTIONS:
-.RS
-.TP 10
-.BI -a \ INT
-Score of a match [1]
-.TP
-.BI -b \ INT
-Mismatch penalty [3]
-.TP
-.BI -q \ INT
-Gap open penalty [5]
-.TP
-.BI -r \ INT
-Gap extension penalty. The penalty for a contiguous gap of size k is
-q+k*r. [2]
-.TP
-.BI -t \ INT
-Number of threads in the multi-threading mode [1]
-.TP
-.BI -w \ INT
-Band width in the banded alignment [33]
-.TP
-.BI -T \ INT
-Minimum score threshold divided by a [37]
-.TP
-.BI -c \ FLOAT
-Coefficient for threshold adjustment according to query length. Given an
-l-long query, the threshold for a hit to be retained is
-a*max{T,c*log(l)}. [5.5]
-.TP
-.BI -z \ INT
-Z-best heuristics. Higher -z increases accuracy at the cost of speed. [1]
-.TP
-.BI -s \ INT
-Maximum SA interval size for initiating a seed. Higher -s increases
-accuracy at the cost of speed. [3]
-.TP
-.BI -N \ INT
-Minimum number of seeds supporting the resultant alignment to skip
-reverse alignment. [5]
-.RE
-
-.SH SAM ALIGNMENT FORMAT
-.PP
-The output of the
-.B `aln'
-command is binary and designed for BWA use only. BWA outputs the final
-alignment in the SAM (Sequence Alignment/Map) format. Each line consists
-of:
-
-.TS
-center box;
-cb | cb | cb
-n | l | l .
-Col Field Description
-_
-1 QNAME Query (pair) NAME
-2 FLAG bitwise FLAG
-3 RNAME Reference sequence NAME
-4 POS 1-based leftmost POSition/coordinate of clipped sequence
-5 MAPQ MAPping Quality (Phred-scaled)
-6 CIAGR extended CIGAR string
-7 MRNM Mate Reference sequence NaMe (`=' if same as RNAME)
-8 MPOS 1-based Mate POSistion
-9 ISIZE Inferred insert SIZE
-10 SEQ query SEQuence on the same strand as the reference
-11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
-12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
-.TE
-
-.PP
-Each bit in the FLAG field is defined as:
-
-.TS
-center box;
-cb | cb | cb
-c | l | l .
-Chr Flag Description
-_
-p 0x0001 the read is paired in sequencing
-P 0x0002 the read is mapped in a proper pair
-u 0x0004 the query sequence itself is unmapped
-U 0x0008 the mate is unmapped
-r 0x0010 strand of the query (1 for reverse)
-R 0x0020 strand of the mate
-1 0x0040 the read is the first read in a pair
-2 0x0080 the read is the second read in a pair
-s 0x0100 the alignment is not primary
-f 0x0200 QC failure
-d 0x0400 optical or PCR duplicate
-.TE
-
-.PP
-The Please check for the format
-specification and the tools for post-processing the alignment.
-
-BWA generates the following optional fields. Tags starting with `X' are
-specific to BWA.
-
-.TS
-center box;
-cb | cb
-cB | l .
-Tag Meaning
-_
-NM Edit distance
-MD Mismatching positions/bases
-AS Alignment score
-BC Barcode sequence
-_
-X0 Number of best hits
-X1 Number of suboptimal hits found by BWA
-XN Number of ambiguous bases in the referenece
-XM Number of mismatches in the alignment
-XO Number of gap opens
-XG Number of gap extentions
-XT Type: Unique/Repeat/N/Mate-sw
-XA Alternative hits; format: (chr,pos,CIGAR,NM;)*
-_
-XS Suboptimal alignment score
-XF Support from forward/reverse alignment
-XE Number of supporting seeds
-.TE
-
-.PP
-Note that XO and XG are generated by BWT search while the CIGAR string
-by Smith-Waterman alignment. These two tags may be inconsistent with the
-CIGAR string. This is not a bug.
-
-.SH NOTES ON SHORT-READ ALIGNMENT
-.SS Alignment Accuracy
-.PP
-When seeding is disabled, BWA guarantees to find an alignment
-containing maximum
-.I maxDiff
-differences including
-.I maxGapO
-gap opens which do not occur within
-.I nIndelEnd
-bp towards either end of the query. Longer gaps may be found if
-.I maxGapE
-is positive, but it is not guaranteed to find all hits. When seeding is
-enabled, BWA further requires that the first
-.I seedLen
-subsequence contains no more than
-.I maxSeedDiff
-differences.
-.PP
-When gapped alignment is disabled, BWA is expected to generate the same
-alignment as Eland version 1, the Illumina alignment program. However, as BWA
-change `N' in the database sequence to random nucleotides, hits to these
-random sequences will also be counted. As a consequence, BWA may mark a
-unique hit as a repeat, if the random sequences happen to be identical
-to the sequences which should be unqiue in the database.
-.PP
-By default, if the best hit is not highly repetitive (controlled by -R), BWA
-also finds all hits contains one more mismatch; otherwise, BWA finds all
-equally best hits only. Base quality is NOT considered in evaluating
-hits. In the paired-end mode, BWA pairs all hits it found. It further
-performs Smith-Waterman alignment for unmapped reads to rescue reads with a
-high erro rate, and for high-quality anomalous pairs to fix potential alignment
-errors.
-
-.SS Estimating Insert Size Distribution
-.PP
-BWA estimates the insert size distribution per 256*1024 read pairs. It
-first collects pairs of reads with both ends mapped with a single-end
-quality 20 or higher and then calculates median (Q2), lower and higher
-quartile (Q1 and Q3). It estimates the mean and the variance of the
-insert size distribution from pairs whose insert sizes are within
-interval [Q1-2(Q3-Q1), Q3+2(Q3-Q1)]. The maximum distance x for a pair
-considered to be properly paired (SAM flag 0x2) is calculated by solving
-equation Phi((x-mu)/sigma)=x/L*p0, where mu is the mean, sigma is the
-standard error of the insert size distribution, L is the length of the
-genome, p0 is prior of anomalous pair and Phi() is the standard
-cumulative distribution function. For mapping Illumina short-insert
-reads to the human genome, x is about 6-7 sigma away from the
-mean. Quartiles, mean, variance and x will be printed to the standard
-error output.
-
-.SS Memory Requirement
-.PP
-With bwtsw algorithm, 5GB memory is required for indexing the complete
-human genome sequences. For short reads, the
-.B aln
-command uses ~3.2GB memory and the
-.B sampe
-command uses ~5.4GB.
-
-.SS Speed
-.PP
-Indexing the human genome sequences takes 3 hours with bwtsw
-algorithm. Indexing smaller genomes with IS algorithms is
-faster, but requires more memory.
-.PP
-The speed of alignment is largely determined by the error rate of the query
-sequences (r). Firstly, BWA runs much faster for near perfect hits than
-for hits with many differences, and it stops searching for a hit with
-l+2 differences if a l-difference hit is found. This means BWA will be
-very slow if r is high because in this case BWA has to visit hits with
-many differences and looking for these hits is expensive. Secondly, the
-alignment algorithm behind makes the speed sensitive to [k log(N)/m],
-where k is the maximum allowed differences, N the size of database and m
-the length of a query. In practice, we choose k w.r.t. r and therefore r
-is the leading factor. I would not recommend to use BWA on data with
-r>0.02.
-.PP
-Pairing is slower for shorter reads. This is mainly because shorter
-reads have more spurious hits and converting SA coordinates to
-chromosomal coordinates are very costly.
-
-.SH NOTES ON LONG-READ ALIGNMENT
-.PP
-Command
-.B bwasw
-is designed for long-read alignment. BWA-SW essentially aligns the trie
-of the reference genome against the directed acyclic word graph (DAWG) of a
-read to find seeds not highly repetitive in the genome, and then performs a
-standard Smith-Waterman algorithm to extend the seeds. A key heuristic, called
-the Z-best heuristic, is that at each vertex in the DAWG, BWA-SW only keeps the
-top Z reference suffix intervals that match the vertex. BWA-SW is more accurate
-if the resultant alignment is supported by more seeds, and therefore BWA-SW
-usually performs better on long queries or queries with low divergence to the
-reference genome.
-
-BWA-SW is perhaps a better choice than BWA-short for 100bp single-end HiSeq reads
-mainly because it gives better gapped alignment. For paired-end reads, it is yet
-to know whether BWA-short or BWA-SW yield overall better results.
-
-.SH CHANGES IN BWA-0.6
-.PP
-Since version 0.6, BWA has been able to work with a reference genome longer than 4GB.
-This feature makes it possible to integrate the forward and reverse complemented
-genome in one FM-index, which speeds up both BWA-short and BWA-SW. As a tradeoff,
-BWA uses more memory because it has to keep all positions and ranks in 64-bit
-integers, twice larger than 32-bit integers used in the previous versions.
-
-The latest BWA-SW also works for paired-end reads longer than 100bp. In
-comparison to BWA-short, BWA-SW tends to be more accurate for highly unique
-reads and more robust to relative long INDELs and structural variants.
-Nonetheless, BWA-short usually has higher power to distinguish the optimal hit
-from many suboptimal hits. The choice of the mapping algorithm may depend on
-the application.
-
-.SH SEE ALSO
-BWA website , Samtools website
-
-
-.SH AUTHOR
-Heng Li at the Sanger Institute wrote the key source codes and
-integrated the following codes for BWT construction: bwtsw
-, implemented by Chi-Kwong Wong at
-the University of Hong Kong and IS
- originally proposed by Nong Ge
- at the Sun Yat-Sen University and
-implemented by Yuta Mori.
-
-.SH LICENSE AND CITATION
-.PP
-The full BWA package is distributed under GPLv3 as it uses source codes
-from BWT-SW which is covered by GPL. Sorting, hash table, BWT and IS
-libraries are distributed under the MIT license.
-.PP
-If you use the short-read alignment component, please cite the following
-paper:
-.PP
-Li H. and Durbin R. (2009) Fast and accurate short read alignment with
-Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. [PMID: 19451168]
-.PP
-If you use the long-read component (BWA-SW), please cite:
-.PP
-Li H. and Durbin R. (2010) Fast and accurate long-read alignment with
-Burrows-Wheeler transform. Bioinformatics, 26, 589-595. [PMID: 20080505]
-
-.SH HISTORY
-BWA is largely influenced by BWT-SW. It uses source codes from BWT-SW
-and mimics its binary file formats; BWA-SW resembles BWT-SW in several
-ways. The initial idea about BWT-based alignment also came from the
-group who developed BWT-SW. At the same time, BWA is different enough
-from BWT-SW. The short-read alignment algorithm bears no similarity to
-Smith-Waterman algorithm any more. While BWA-SW learns from BWT-SW, it
-introduces heuristics that can hardly be applied to the original
-algorithm. In all, BWA does not guarantee to find all local hits as what
-BWT-SW is designed to do, but it is much faster than BWT-SW on both
-short and long query sequences.
-
-I started to write the first piece of codes on 24 May 2008 and got the
-initial stable version on 02 June 2008. During this period, I was
-acquainted that Professor Tak-Wah Lam, the first author of BWT-SW paper,
-was collaborating with Beijing Genomics Institute on SOAP2, the successor
-to SOAP (Short Oligonucleotide Analysis Package). SOAP2 has come out in
-November 2008. According to the SourceForge download page, the third
-BWT-based short read aligner, bowtie, was first released in August
-2008. At the time of writing this manual, at least three more BWT-based
-short-read aligners are being implemented.
-
-The BWA-SW algorithm is a new component of BWA. It was conceived in
-November 2008 and implemented ten months later.
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwa.c
--- a/bwa-0.6.2/bwa.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,272 +0,0 @@
-#include
-#include
-#include
-#include
-#include "bwa.h"
-#include "bwt.h"
-#include "bwtgap.h"
-#include "bntseq.h"
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-extern unsigned char nst_nt4_table[256];
-extern void seq_reverse(int len, uint8_t *seq, int is_comp);
-
-bwa_opt_t bwa_def_opt = { 11, 4, -1, 1, 6, 32, 2, 0.04 };
-
-struct bwa_idx_t {
- bwt_t *bwt;
- bntseq_t *bns;
- uint8_t *pac;
-};
-
-struct bwa_buf_t {
- int max_buf;
- bwa_pestat_t pes;
- gap_stack_t *stack;
- gap_opt_t *opt;
- int *diff_tab;
- uint8_t *buf;
- int *logn;
-};
-
-bwa_idx_t *bwa_idx_load(const char *prefix)
-{
- bwa_idx_t *p;
- int l;
- char *str;
- l = strlen(prefix);
- p = calloc(1, sizeof(bwa_idx_t));
- str = malloc(l + 10);
- strcpy(str, prefix);
- p->bns = bns_restore(str);
- strcpy(str + l, ".bwt");
- p->bwt = bwt_restore_bwt(str);
- str[l] = 0;
- strcpy(str + l, ".sa");
- bwt_restore_sa(str, p->bwt);
- free(str);
- p->pac = calloc(p->bns->l_pac/4+1, 1);
- fread(p->pac, 1, p->bns->l_pac/4+1, p->bns->fp_pac);
- fclose(p->bns->fp_pac);
- p->bns->fp_pac = 0;
- return p;
-}
-
-void bwa_idx_destroy(bwa_idx_t *p)
-{
- bns_destroy(p->bns);
- bwt_destroy(p->bwt);
- free(p->pac);
- free(p);
-}
-
-bwa_buf_t *bwa_buf_init(const bwa_opt_t *opt, int max_score)
-{
- extern gap_opt_t *gap_init_opt(void);
- extern int bwa_cal_maxdiff(int l, double err, double thres);
- int i;
- bwa_buf_t *p;
- p = malloc(sizeof(bwa_buf_t));
- p->stack = gap_init_stack2(max_score);
- p->opt = gap_init_opt();
- p->opt->s_gapo = opt->s_gapo;
- p->opt->s_gape = opt->s_gape;
- p->opt->max_diff = opt->max_diff;
- p->opt->max_gapo = opt->max_gapo;
- p->opt->max_gape = opt->max_gape;
- p->opt->seed_len = opt->seed_len;
- p->opt->max_seed_diff = opt->max_seed_diff;
- p->opt->fnr = opt->fnr;
- p->diff_tab = calloc(BWA_MAX_QUERY_LEN, sizeof(int));
- for (i = 1; i < BWA_MAX_QUERY_LEN; ++i)
- p->diff_tab[i] = bwa_cal_maxdiff(i, BWA_AVG_ERR, opt->fnr);
- p->logn = calloc(256, sizeof(int));
- for (i = 1; i != 256; ++i)
- p->logn[i] = (int)(4.343 * log(i) + 0.499);
- return p;
-}
-
-void bwa_buf_destroy(bwa_buf_t *p)
-{
- gap_destroy_stack(p->stack);
- free(p->diff_tab); free(p->logn); free(p->opt);
- free(p);
-}
-
-bwa_sai_t bwa_sai(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq)
-{
- extern int bwt_cal_width(const bwt_t *bwt, int len, const ubyte_t *str, bwt_width_t *width);
- int i, seq_len, buf_len;
- bwt_width_t *w, *seed_w;
- uint8_t *s;
- gap_opt_t opt2 = *buf->opt;
- bwa_sai_t sai;
-
- seq_len = strlen(seq);
- // estimate the buffer length
- buf_len = (buf->opt->seed_len + seq_len + 1) * sizeof(bwt_width_t) + seq_len;
- if (buf_len > buf->max_buf) {
- buf->max_buf = buf_len;
- kroundup32(buf->max_buf);
- buf->buf = realloc(buf->buf, buf->max_buf);
- }
- memset(buf->buf, 0, buf_len);
- seed_w = (bwt_width_t*)buf->buf;
- w = seed_w + buf->opt->seed_len;
- s = (uint8_t*)(w + seq_len + 1);
- if (opt2.fnr > 0.) opt2.max_diff = buf->diff_tab[seq_len];
- // copy the sequence
- for (i = 0; i < seq_len; ++i)
- s[i] = nst_nt4_table[(int)seq[i]];
- seq_reverse(seq_len, s, 0);
- // mapping
- bwt_cal_width(idx->bwt, seq_len, s, w);
- if (opt2.seed_len >= seq_len) opt2.seed_len = 0x7fffffff;
- if (seq_len > buf->opt->seed_len)
- bwt_cal_width(idx->bwt, buf->opt->seed_len, s + (seq_len - buf->opt->seed_len), seed_w);
- for (i = 0; i < seq_len; ++i) // complement; I forgot why...
- s[i] = s[i] > 3? 4 : 3 - s[i];
- sai.sai = (bwa_sai1_t*)bwt_match_gap(idx->bwt, seq_len, s, w, seq_len <= buf->opt->seed_len? 0 : seed_w, &opt2, &sai.n, buf->stack);
- return sai;
-}
-
-static void compute_NM(const uint8_t *pac, uint64_t l_pac, uint8_t *seq, int64_t pos, int n_cigar, uint32_t *cigar, int *n_mm, int *n_gaps)
-{
- uint64_t x = pos, z;
- int k, y = 0;
- *n_mm = *n_gaps = 0;
- for (k = 0; k < n_cigar; ++k) {
- int l = cigar[k]>>4;
- int op = cigar[k]&0xf;
- if (op == 0) { // match/mismatch
- for (z = 0; z < l && x + z < l_pac; ++z) {
- int c = pac[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
- if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) ++(*n_mm);
- }
- }
- if (op == 1 || op == 2) (*n_gaps) += l;
- if (op == 0 || op == 2) x += l;
- if (op == 0 || op == 1 || op == 4) y += l;
- }
-}
-
-void bwa_sa2aln(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, uint64_t sa, int n_gaps, bwa_aln_t *aln)
-{
- extern bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int len, int *strand);
- extern bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const uint8_t *seq, bwtint_t *_pos, int ext, int *n_cigar, int is_end_correct);
- int strand, seq_len, i, n_gap, n_mm;
- uint64_t pos3, pac_pos;
- uint8_t *s[2];
-
- memset(aln, 0, sizeof(bwa_aln_t));
- seq_len = strlen(seq);
- if (seq_len<<1 > buf->max_buf) {
- buf->max_buf = seq_len<<1;
- kroundup32(buf->max_buf);
- buf->buf = realloc(buf->buf, buf->max_buf);
- }
- s[0] = buf->buf;
- s[1] = s[0] + seq_len;
- for (i = 0; i < seq_len; ++i)
- s[0][i] = s[1][i] = nst_nt4_table[(int)seq[i]];
- seq_reverse(seq_len, s[1], 1);
- pac_pos = bwa_sa2pos(idx->bns, idx->bwt, sa, seq_len, &strand);
- if (strand) aln->flag |= 16;
- if (n_gaps) { // only for gapped alignment
- int n_cigar;
- bwa_cigar_t *cigar16;
- cigar16 = bwa_refine_gapped_core(idx->bns->l_pac, idx->pac, seq_len, s[strand], &pac_pos, strand? n_gaps : -n_gaps, &n_cigar, 1);
- aln->n_cigar = n_cigar;
- aln->cigar = malloc(n_cigar * 4);
- for (i = 0, pos3 = pac_pos; i < n_cigar; ++i) {
- int op = cigar16[i]>>14;
- int len = cigar16[i]&0x3fff;
- if (op == 3) op = 4; // the 16-bit CIGAR is different from the 32-bit CIGAR
- aln->cigar[i] = len<<4 | op;
- if (op == 0 || op == 2) pos3 += len;
- }
- free(cigar16);
- } else { // ungapped
- aln->n_cigar = 1;
- aln->cigar = malloc(4);
- aln->cigar[0] = seq_len<<4 | 0;
- pos3 = pac_pos + seq_len;
- }
- aln->n_n = bns_cnt_ambi(idx->bns, pac_pos, pos3 - pac_pos, &aln->ref_id);
- aln->offset = pac_pos - idx->bns->anns[aln->ref_id].offset;
- if (pos3 - idx->bns->anns[aln->ref_id].offset > idx->bns->anns[aln->ref_id].len) // read mapped beyond the end of a sequence
- aln->flag |= 4; // read unmapped
- compute_NM(idx->pac, idx->bns->l_pac, s[strand], pac_pos, aln->n_cigar, aln->cigar, &n_mm, &n_gap);
- aln->n_mm = n_mm;
- aln->n_gap = n_gap;
-}
-
-/************************
- * Single-end alignment *
- ************************/
-
-bwa_one_t *bwa_se(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, int gen_cigar)
-{
- bwa_one_t *one;
- int best, cnt, i, seq_len;
-
- seq_len = strlen(seq);
- one = calloc(1, sizeof(bwa_one_t));
- one->sai = bwa_sai(idx, buf, seq);
- if (one->sai.n == 0) return one;
- // count number of hits; randomly select one alignment
- best = one->sai.sai[0].score;
- for (i = cnt = 0; i < one->sai.n; ++i) {
- bwa_sai1_t *p = &one->sai.sai[i];
- if (p->score > best) break;
- if (drand48() * (p->l - p->k + 1 + cnt) > (double)cnt) {
- one->which = p;
- one->sa = p->k + (bwtint_t)((p->l - p->k + 1) * drand48());
- }
- cnt += p->l - p->k + 1;
- }
- one->c1 = cnt;
- for (; i < one->sai.n; ++i)
- cnt += one->sai.sai[i].l - one->sai.sai[i].k + 1;
- one->c2 = cnt - one->c1;
- // estimate single-end mapping quality
- one->mapQs = -1;
- if (one->c1 == 0) one->mapQs = 23; // FIXME: is it possible?
- else if (one->c1 > 1) one->mapQs = 0;
- else {
- int diff = one->which->n_mm + one->which->n_gapo + one->which->n_gape;
- if (diff >= buf->diff_tab[seq_len]) one->mapQs = 25;
- else if (one->c2 == 0) one->mapQs = 37;
- }
- if (one->mapQs < 0) {
- cnt = (one->c2 >= 255)? 255 : one->c2;
- one->mapQs = 23 < buf->logn[cnt]? 0 : 23 - buf->logn[cnt];
- }
- one->mapQ = one->mapQs;
- // compute CIGAR on request
- one->one.ref_id = -1;
- if (gen_cigar) bwa_sa2aln(idx, buf, seq, one->sa, one->which->n_gapo + one->which->n_gape, &one->one);
- return one;
-}
-
-void bwa_one_destroy(bwa_one_t *one)
-{
- free(one->sai.sai);
- free(one->one.cigar);
- free(one);
-}
-
-/************************
- * Paired-end alignment *
- ************************/
-
-void bwa_pestat(bwa_buf_t *buf, int n, bwa_one_t **o[2])
-{
-}
-
-void bwa_pe(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq[2], bwa_one_t *o[2])
-{
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwa.h
--- a/bwa-0.6.2/bwa.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,107 +0,0 @@
-#ifndef BWA_H_
-#define BWA_H_
-
-#include
-
-#define BWA_DEF_MAX_SCORE 2048
-#define BWA_MAX_QUERY_LEN 1024
-
-// BWA index
-struct bwa_idx_t;
-typedef struct bwa_idx_t bwa_idx_t;
-
-// Buffer for BWA alignment
-struct bwa_buf_t;
-typedef struct bwa_buf_t bwa_buf_t;
-
-// BWA alignment options
-typedef struct {
- int s_gapo, s_gape; // gap open and extension penalties; the mismatch penalty is fixed at 3
- int max_diff, max_gapo, max_gape; // max differences (-1 to use fnr for length-adjusted max diff), gap opens and gap extensions
- int seed_len, max_seed_diff; // seed length and max differences allowed in the seed
- float fnr; // parameter for automatic length-adjusted max differences
-} bwa_opt_t;
-
-// default BWA alignment options
-extern bwa_opt_t bwa_def_opt; // = { 11, 4, -1, 1, 6, 32, 2, 0.04 }
-
-// an interval hit in the SA coordinate; basic unit in .sai files
-typedef struct {
- uint32_t n_mm:16, n_gapo:8, n_gape:8;
- int score;
- uint64_t k, l; // [k,l] is the SA interval; each interval has l-k+1 hits
-} bwa_sai1_t;
-
-// all interval hits in the SA coordinate
-typedef struct {
- int n; // number of interval hits
- bwa_sai1_t *sai;
-} bwa_sai_t;
-
-// an alignment
-typedef struct {
- uint32_t n_n:8, n_gap:12, n_mm:12; // number of ambiguous bases, gaps and mismatches in the alignment
- int32_t ref_id; // referece sequence index (the first seq is indexed by 0)
- uint32_t offset; // coordinate on the reference; zero-based
- uint32_t n_cigar:16, flag:16; // number of CIGAR operations; SAM flag
- uint32_t *cigar; // CIGAR in the BAM 28+4 encoding; having n_cigar operations
-} bwa_aln_t;
-
-typedef struct {
- int mapQs, mapQ, c1, c2;
- uint64_t sa;
- bwa_sai1_t *which;
- bwa_sai_t sai;
- bwa_aln_t one;
-} bwa_one_t;
-
-typedef struct {
- double avg, std, ap_prior;
- uint64_t low, high, high_bayesian;
-} bwa_pestat_t;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- // load a BWA index
- bwa_idx_t *bwa_idx_load(const char *prefix);
- void bwa_idx_destroy(bwa_idx_t *p);
-
- // allocate a BWA alignment buffer; if unsure, set opt to &bwa_def_opt and max_score to BWA_DEF_MAX_SCORE
- bwa_buf_t *bwa_buf_init(const bwa_opt_t *opt, int max_score);
- void bwa_buf_destroy(bwa_buf_t *p);
-
- /**
- * Find all the SA intervals
- *
- * @param idx BWA index; multiple threads can share the same index
- * @param buf BWA alignment buffer; each thread should have its own buffer
- * @param seq NULL terminated C string, consisting of A/C/G/T/N only
- *
- * @return SA intervals seq is matched to
- */
- bwa_sai_t bwa_sai(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq);
-
- /**
- * Construct an alignment in the base-pair coordinate
- *
- * @param idx BWA index
- * @param buf BWA alignment buffer
- * @param seq NULL terinated C string
- * @param sa Suffix array value
- * @param n_gaps Number of gaps (typically equal to bwa_sai1_t::n_gapo + bwa_sai1_t::n_gape
- *
- * @return An alignment
- */
- void bwa_sa2aln(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, uint64_t sa, int n_gaps, bwa_aln_t *aln);
-
- bwa_one_t *bwa_se(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, int gen_cigar);
-
- void bwa_one_destroy(bwa_one_t *one);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwape.c
--- a/bwa-0.6.2/bwape.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,824 +0,0 @@
-#include
-#include
-#include
-#include
-#include
-#include
-#include "bwtaln.h"
-#include "kvec.h"
-#include "bntseq.h"
-#include "utils.h"
-#include "stdaln.h"
-#include "bwase.h"
-
-typedef struct {
- int n;
- bwtint_t *a;
-} poslist_t;
-
-typedef struct {
- double avg, std, ap_prior;
- bwtint_t low, high, high_bayesian;
-} isize_info_t;
-
-typedef struct {
- uint64_t x, y;
-} b128_t;
-
-#define b128_lt(a, b) ((a).x < (b).x)
-#define b128_eq(a, b) ((a).x == (b).x && (a).y == (b).y)
-#define b128_hash(a) ((uint32_t)(a).x)
-
-#include "khash.h"
-KHASH_INIT(b128, b128_t, poslist_t, 1, b128_hash, b128_eq)
-
-#include "ksort.h"
-KSORT_INIT(b128, b128_t, b128_lt)
-KSORT_INIT_GENERIC(uint64_t)
-
-typedef struct {
- kvec_t(b128_t) arr;
- kvec_t(b128_t) pos[2];
- kvec_t(bwt_aln1_t) aln[2];
-} pe_data_t;
-
-#define MIN_HASH_WIDTH 1000
-
-extern int g_log_n[256]; // in bwase.c
-static kh_b128_t *g_hash;
-
-void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi);
-void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
-int bwa_approx_mapQ(const bwa_seq_t *p, int mm);
-void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2);
-bntseq_t *bwa_open_nt(const char *prefix);
-void bwa_print_sam_SQ(const bntseq_t *bns);
-void bwa_print_sam_PG();
-
-pe_opt_t *bwa_init_pe_opt()
-{
- pe_opt_t *po;
- po = (pe_opt_t*)calloc(1, sizeof(pe_opt_t));
- po->max_isize = 500;
- po->force_isize = 0;
- po->max_occ = 100000;
- po->n_multi = 3;
- po->N_multi = 10;
- po->type = BWA_PET_STD;
- po->is_sw = 1;
- po->ap_prior = 1e-5;
- return po;
-}
-
-static inline uint64_t hash_64(uint64_t key)
-{
- key += ~(key << 32);
- key ^= (key >> 22);
- key += ~(key << 13);
- key ^= (key >> 8);
- key += (key << 3);
- key ^= (key >> 15);
- key += ~(key << 27);
- key ^= (key >> 31);
- return key;
-}
-/*
-static double ierfc(double x) // inverse erfc(); iphi(x) = M_SQRT2 *ierfc(2 * x);
-{
- const double a = 0.140012;
- double b, c;
- b = log(x * (2 - x));
- c = 2./M_PI/a + b / 2.;
- return sqrt(sqrt(c * c - b / a) - c);
-}
-*/
-
-// for normal distribution, this is about 3std
-#define OUTLIER_BOUND 2.0
-
-static int infer_isize(int n_seqs, bwa_seq_t *seqs[2], isize_info_t *ii, double ap_prior, int64_t L)
-{
- uint64_t x, *isizes, n_ap = 0;
- int n, i, tot, p25, p75, p50, max_len = 1, tmp;
- double skewness = 0.0, kurtosis = 0.0, y;
-
- ii->avg = ii->std = -1.0;
- ii->low = ii->high = ii->high_bayesian = 0;
- isizes = (uint64_t*)calloc(n_seqs, 8);
- for (i = 0, tot = 0; i != n_seqs; ++i) {
- bwa_seq_t *p[2];
- p[0] = seqs[0] + i; p[1] = seqs[1] + i;
- if (p[0]->mapQ >= 20 && p[1]->mapQ >= 20) {
- x = (p[0]->pos < p[1]->pos)? p[1]->pos + p[1]->len - p[0]->pos : p[0]->pos + p[0]->len - p[1]->pos;
- if (x < 100000) isizes[tot++] = x;
- }
- if (p[0]->len > max_len) max_len = p[0]->len;
- if (p[1]->len > max_len) max_len = p[1]->len;
- }
- if (tot < 20) {
- fprintf(stderr, "[infer_isize] fail to infer insert size: too few good pairs\n");
- free(isizes);
- return -1;
- }
- ks_introsort(uint64_t, tot, isizes);
- p25 = isizes[(int)(tot*0.25 + 0.5)];
- p50 = isizes[(int)(tot*0.50 + 0.5)];
- p75 = isizes[(int)(tot*0.75 + 0.5)];
- tmp = (int)(p25 - OUTLIER_BOUND * (p75 - p25) + .499);
- ii->low = tmp > max_len? tmp : max_len; // ii->low is unsigned
- ii->high = (int)(p75 + OUTLIER_BOUND * (p75 - p25) + .499);
- for (i = 0, x = n = 0; i < tot; ++i)
- if (isizes[i] >= ii->low && isizes[i] <= ii->high)
- ++n, x += isizes[i];
- ii->avg = (double)x / n;
- for (i = 0; i < tot; ++i) {
- if (isizes[i] >= ii->low && isizes[i] <= ii->high) {
- double tmp = (isizes[i] - ii->avg) * (isizes[i] - ii->avg);
- ii->std += tmp;
- skewness += tmp * (isizes[i] - ii->avg);
- kurtosis += tmp * tmp;
- }
- }
- kurtosis = kurtosis/n / (ii->std / n * ii->std / n) - 3;
- ii->std = sqrt(ii->std / n); // it would be better as n-1, but n is usually very large
- skewness = skewness / n / (ii->std * ii->std * ii->std);
- for (y = 1.0; y < 10.0; y += 0.01)
- if (.5 * erfc(y / M_SQRT2) < ap_prior / L * (y * ii->std + ii->avg)) break;
- ii->high_bayesian = (bwtint_t)(y * ii->std + ii->avg + .499);
- for (i = 0; i < tot; ++i)
- if (isizes[i] > ii->high_bayesian) ++n_ap;
- ii->ap_prior = .01 * (n_ap + .01) / tot;
- if (ii->ap_prior < ap_prior) ii->ap_prior = ap_prior;
- free(isizes);
- fprintf(stderr, "[infer_isize] (25, 50, 75) percentile: (%d, %d, %d)\n", p25, p50, p75);
- if (isnan(ii->std) || p75 > 100000) {
- ii->low = ii->high = ii->high_bayesian = 0; ii->avg = ii->std = -1.0;
- fprintf(stderr, "[infer_isize] fail to infer insert size: weird pairing\n");
- return -1;
- }
- for (y = 1.0; y < 10.0; y += 0.01)
- if (.5 * erfc(y / M_SQRT2) < ap_prior / L * (y * ii->std + ii->avg)) break;
- ii->high_bayesian = (bwtint_t)(y * ii->std + ii->avg + .499);
- fprintf(stderr, "[infer_isize] low and high boundaries: %ld and %ld for estimating avg and std\n", (long)ii->low, (long)ii->high);
- fprintf(stderr, "[infer_isize] inferred external isize from %d pairs: %.3lf +/- %.3lf\n", n, ii->avg, ii->std);
- fprintf(stderr, "[infer_isize] skewness: %.3lf; kurtosis: %.3lf; ap_prior: %.2e\n", skewness, kurtosis, ii->ap_prior);
- fprintf(stderr, "[infer_isize] inferred maximum insert size: %ld (%.2lf sigma)\n", (long)ii->high_bayesian, y);
- return 0;
-}
-
-static int pairing(bwa_seq_t *p[2], pe_data_t *d, const pe_opt_t *opt, int s_mm, const isize_info_t *ii)
-{
- int i, j, o_n, subo_n, cnt_chg = 0, low_bound = ii->low, max_len;
- uint64_t o_score, subo_score;
- b128_t last_pos[2][2], o_pos[2];
- max_len = p[0]->full_len;
- if (max_len < p[1]->full_len) max_len = p[1]->full_len;
- if (low_bound < max_len) low_bound = max_len;
-
- // here v>=u. When ii is set, we check insert size with ii; otherwise with opt->max_isize
-#define __pairing_aux(u,v) do { \
- bwtint_t l = (v).x + p[(v).y&1]->len - ((u).x); \
- if ((u).x != (uint64_t)-1 && (v).x > (u).x && l >= max_len \
- && ((ii->high && l <= ii->high_bayesian) || (ii->high == 0 && l <= opt->max_isize))) \
- { \
- uint64_t s = d->aln[(v).y&1].a[(v).y>>2].score + d->aln[(u).y&1].a[(u).y>>2].score; \
- s *= 10; \
- if (ii->high) s += (int)(-4.343 * log(.5 * erfc(M_SQRT1_2 * fabs(l - ii->avg) / ii->std)) + .499); \
- s = s<<32 | (uint32_t)hash_64((u).x<<32 | (v).x); \
- if (s>>32 == o_score>>32) ++o_n; \
- else if (s>>32 < o_score>>32) { subo_n += o_n; o_n = 1; } \
- else ++subo_n; \
- if (s < o_score) subo_score = o_score, o_score = s, o_pos[(u).y&1] = (u), o_pos[(v).y&1] = (v); \
- else if (s < subo_score) subo_score = s; \
- } \
- } while (0)
-
-#define __pairing_aux2(q, w) do { \
- const bwt_aln1_t *r = d->aln[(w).y&1].a + ((w).y>>2); \
- (q)->extra_flag |= SAM_FPP; \
- if ((q)->pos != (w).x || (q)->strand != ((w).y>>1&1)) { \
- (q)->n_mm = r->n_mm; (q)->n_gapo = r->n_gapo; (q)->n_gape = r->n_gape; (q)->strand = (w).y>>1&1; \
- (q)->score = r->score; \
- (q)->pos = (w).x; \
- if ((q)->mapQ > 0) ++cnt_chg; \
- } \
- } while (0)
-
- o_score = subo_score = (uint64_t)-1;
- o_n = subo_n = 0;
- ks_introsort(b128, d->arr.n, d->arr.a);
- for (j = 0; j < 2; ++j) last_pos[j][0].x = last_pos[j][0].y = last_pos[j][1].x = last_pos[j][1].y = (uint64_t)-1;
- if (opt->type == BWA_PET_STD) {
- for (i = 0; i < d->arr.n; ++i) {
- b128_t x = d->arr.a[i];
- int strand = x.y>>1&1;
- if (strand == 1) { // reverse strand, then check
- int y = 1 - (x.y&1);
- __pairing_aux(last_pos[y][1], x);
- __pairing_aux(last_pos[y][0], x);
- } else { // forward strand, then push
- last_pos[x.y&1][0] = last_pos[x.y&1][1];
- last_pos[x.y&1][1] = x;
- }
- }
- } else if (opt->type == BWA_PET_SOLID) {
- for (i = 0; i < d->arr.n; ++i) {
- b128_t x = d->arr.a[i];
- int strand = x.y>>1&1;
- if ((strand^x.y)&1) { // push
- int y = 1 - (x.y&1);
- __pairing_aux(last_pos[y][1], x);
- __pairing_aux(last_pos[y][0], x);
- } else { // check
- last_pos[x.y&1][0] = last_pos[x.y&1][1];
- last_pos[x.y&1][1] = x;
- }
- }
- } else {
- fprintf(stderr, "[paring] not implemented yet!\n");
- exit(1);
- }
- // set pairing
- //fprintf(stderr, "[%ld, %d, %d, %d]\n", d->arr.n, (int)(o_score>>32), (int)(subo_score>>32), o_n);
- if (o_score != (uint64_t)-1) {
- int mapQ_p = 0; // this is the maximum mapping quality when one end is moved
- //fprintf(stderr, "%d, %d\n", o_n, subo_n);
- if (o_n == 1) {
- if (subo_score == (uint64_t)-1) mapQ_p = 29; // no sub-optimal pair
- else if ((subo_score>>32) - (o_score>>32) > s_mm * 10) mapQ_p = 23; // poor sub-optimal pair
- else {
- int n = subo_n > 255? 255 : subo_n;
- mapQ_p = ((subo_score>>32) - (o_score>>32)) / 2 - g_log_n[n];
- if (mapQ_p < 0) mapQ_p = 0;
- }
- }
- if ((p[0]->pos == o_pos[0].x && p[0]->strand == (o_pos[0].y>>1&1)) && (p[1]->pos == o_pos[1].x && p[1]->strand == (o_pos[1].y>>1&1))) { // both ends not moved
- if (p[0]->mapQ > 0 && p[1]->mapQ > 0) {
- int mapQ = p[0]->mapQ + p[1]->mapQ;
- if (mapQ > 60) mapQ = 60;
- p[0]->mapQ = p[1]->mapQ = mapQ;
- } else {
- if (p[0]->mapQ == 0) p[0]->mapQ = (mapQ_p + 7 < p[1]->mapQ)? mapQ_p + 7 : p[1]->mapQ;
- if (p[1]->mapQ == 0) p[1]->mapQ = (mapQ_p + 7 < p[0]->mapQ)? mapQ_p + 7 : p[0]->mapQ;
- }
- } else if (p[0]->pos == o_pos[0].x && p[0]->strand == (o_pos[0].y>>1&1)) { // [1] moved
- p[1]->seQ = 0; p[1]->mapQ = p[0]->mapQ;
- if (p[1]->mapQ > mapQ_p) p[1]->mapQ = mapQ_p;
- } else if (p[1]->pos == o_pos[1].x && p[1]->strand == (o_pos[1].y>>1&1)) { // [0] moved
- p[0]->seQ = 0; p[0]->mapQ = p[1]->mapQ;
- if (p[0]->mapQ > mapQ_p) p[0]->mapQ = mapQ_p;
- } else { // both ends moved
- p[0]->seQ = p[1]->seQ = 0;
- mapQ_p -= 20;
- if (mapQ_p < 0) mapQ_p = 0;
- p[0]->mapQ = p[1]->mapQ = mapQ_p;
- }
- __pairing_aux2(p[0], o_pos[0]);
- __pairing_aux2(p[1], o_pos[1]);
- }
- return cnt_chg;
-}
-
-typedef struct {
- kvec_t(bwt_aln1_t) aln;
-} aln_buf_t;
-
-int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bwt, int n_seqs, bwa_seq_t *seqs[2], FILE *fp_sa[2], isize_info_t *ii,
- const pe_opt_t *opt, const gap_opt_t *gopt, const isize_info_t *last_ii)
-{
- int i, j, cnt_chg = 0;
- char str[1024];
- bwt_t *bwt;
- pe_data_t *d;
- aln_buf_t *buf[2];
-
- d = (pe_data_t*)calloc(1, sizeof(pe_data_t));
- buf[0] = (aln_buf_t*)calloc(n_seqs, sizeof(aln_buf_t));
- buf[1] = (aln_buf_t*)calloc(n_seqs, sizeof(aln_buf_t));
-
- if (_bwt == 0) { // load forward SA
- strcpy(str, prefix); strcat(str, ".bwt"); bwt = bwt_restore_bwt(str);
- strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
- } else bwt = _bwt;
-
- // SE
- for (i = 0; i != n_seqs; ++i) {
- bwa_seq_t *p[2];
- for (j = 0; j < 2; ++j) {
- int n_aln;
- p[j] = seqs[j] + i;
- p[j]->n_multi = 0;
- p[j]->extra_flag |= SAM_FPD | (j == 0? SAM_FR1 : SAM_FR2);
- fread(&n_aln, 4, 1, fp_sa[j]);
- if (n_aln > kv_max(d->aln[j]))
- kv_resize(bwt_aln1_t, d->aln[j], n_aln);
- d->aln[j].n = n_aln;
- fread(d->aln[j].a, sizeof(bwt_aln1_t), n_aln, fp_sa[j]);
- kv_copy(bwt_aln1_t, buf[j][i].aln, d->aln[j]); // backup d->aln[j]
- // generate SE alignment and mapping quality
- bwa_aln2seq(n_aln, d->aln[j].a, p[j]);
- if (p[j]->type == BWA_TYPE_UNIQUE || p[j]->type == BWA_TYPE_REPEAT) {
- int strand;
- int max_diff = gopt->fnr > 0.0? bwa_cal_maxdiff(p[j]->len, BWA_AVG_ERR, gopt->fnr) : gopt->max_diff;
- p[j]->seQ = p[j]->mapQ = bwa_approx_mapQ(p[j], max_diff);
- p[j]->pos = bwa_sa2pos(bns, bwt, p[j]->sa, p[j]->len, &strand);
- p[j]->strand = strand;
- }
- }
- }
-
- // infer isize
- infer_isize(n_seqs, seqs, ii, opt->ap_prior, bwt->seq_len/2);
- if (ii->avg < 0.0 && last_ii->avg > 0.0) *ii = *last_ii;
- if (opt->force_isize) {
- fprintf(stderr, "[%s] discard insert size estimate as user's request.\n", __func__);
- ii->low = ii->high = 0; ii->avg = ii->std = -1.0;
- }
-
- // PE
- for (i = 0; i != n_seqs; ++i) {
- bwa_seq_t *p[2];
- for (j = 0; j < 2; ++j) {
- p[j] = seqs[j] + i;
- kv_copy(bwt_aln1_t, d->aln[j], buf[j][i].aln);
- }
- if ((p[0]->type == BWA_TYPE_UNIQUE || p[0]->type == BWA_TYPE_REPEAT)
- && (p[1]->type == BWA_TYPE_UNIQUE || p[1]->type == BWA_TYPE_REPEAT))
- { // only when both ends mapped
- b128_t x;
- int j, k;
- long long n_occ[2];
- for (j = 0; j < 2; ++j) {
- n_occ[j] = 0;
- for (k = 0; k < d->aln[j].n; ++k)
- n_occ[j] += d->aln[j].a[k].l - d->aln[j].a[k].k + 1;
- }
- if (n_occ[0] > opt->max_occ || n_occ[1] > opt->max_occ) continue;
- d->arr.n = 0;
- for (j = 0; j < 2; ++j) {
- for (k = 0; k < d->aln[j].n; ++k) {
- bwt_aln1_t *r = d->aln[j].a + k;
- bwtint_t l;
- if (0 && r->l - r->k + 1 >= MIN_HASH_WIDTH) { // then check hash table
- b128_t key;
- int ret;
- key.x = r->k; key.y = r->l;
- khint_t iter = kh_put(b128, g_hash, key, &ret);
- if (ret) { // not in the hash table; ret must equal 1 as we never remove elements
- poslist_t *z = &kh_val(g_hash, iter);
- z->n = r->l - r->k + 1;
- z->a = (bwtint_t*)malloc(sizeof(bwtint_t) * z->n);
- for (l = r->k; l <= r->l; ++l) {
- int strand;
- z->a[l - r->k] = bwa_sa2pos(bns, bwt, l, p[j]->len, &strand)<<1;
- z->a[l - r->k] |= strand;
- }
- }
- for (l = 0; l < kh_val(g_hash, iter).n; ++l) {
- x.x = kh_val(g_hash, iter).a[l]>>1;
- x.y = k<<2 | (kh_val(g_hash, iter).a[l]&1)<<1 | j;
- kv_push(b128_t, d->arr, x);
- }
- } else { // then calculate on the fly
- for (l = r->k; l <= r->l; ++l) {
- int strand;
- x.x = bwa_sa2pos(bns, bwt, l, p[j]->len, &strand);
- x.y = k<<2 | strand<<1 | j;
- kv_push(b128_t, d->arr, x);
- }
- }
- }
- }
- cnt_chg += pairing(p, d, opt, gopt->s_mm, ii);
- }
-
- if (opt->N_multi || opt->n_multi) {
- for (j = 0; j < 2; ++j) {
- if (p[j]->type != BWA_TYPE_NO_MATCH) {
- int k, n_multi;
- if (!(p[j]->extra_flag&SAM_FPP) && p[1-j]->type != BWA_TYPE_NO_MATCH) {
- bwa_aln2seq_core(d->aln[j].n, d->aln[j].a, p[j], 0, p[j]->c1+p[j]->c2-1 > opt->N_multi? opt->n_multi : opt->N_multi);
- } else bwa_aln2seq_core(d->aln[j].n, d->aln[j].a, p[j], 0, opt->n_multi);
- for (k = 0, n_multi = 0; k < p[j]->n_multi; ++k) {
- int strand;
- bwt_multi1_t *q = p[j]->multi + k;
- q->pos = bwa_sa2pos(bns, bwt, q->pos, p[j]->len, &strand);
- q->strand = strand;
- if (q->pos != p[j]->pos)
- p[j]->multi[n_multi++] = *q;
- }
- p[j]->n_multi = n_multi;
- }
- }
- }
- }
-
- // free
- for (i = 0; i < n_seqs; ++i) {
- kv_destroy(buf[0][i].aln);
- kv_destroy(buf[1][i].aln);
- }
- free(buf[0]); free(buf[1]);
- if (_bwt == 0) bwt_destroy(bwt);
- kv_destroy(d->arr);
- kv_destroy(d->pos[0]); kv_destroy(d->pos[1]);
- kv_destroy(d->aln[0]); kv_destroy(d->aln[1]);
- free(d);
- return cnt_chg;
-}
-
-#define SW_MIN_MATCH_LEN 20
-#define SW_MIN_MAPQ 17
-
-// cnt = n_mm<<16 | n_gapo<<8 | n_gape
-bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const ubyte_t *seq, int64_t *beg, int reglen,
- int *n_cigar, uint32_t *_cnt)
-{
- bwa_cigar_t *cigar = 0;
- ubyte_t *ref_seq;
- bwtint_t k, x, y, l;
- int path_len, ret, subo;
- AlnParam ap = aln_param_bwa;
- path_t *path, *p;
-
- // check whether there are too many N's
- if (reglen < SW_MIN_MATCH_LEN || (int64_t)l_pac - *beg < len) return 0;
- for (k = 0, x = 0; k < len; ++k)
- if (seq[k] >= 4) ++x;
- if ((float)x/len >= 0.25 || len - x < SW_MIN_MATCH_LEN) return 0;
-
- // get reference subsequence
- ref_seq = (ubyte_t*)calloc(reglen, 1);
- for (k = *beg, l = 0; l < reglen && k < l_pac; ++k)
- ref_seq[l++] = pacseq[k>>2] >> ((~k&3)<<1) & 3;
- path = (path_t*)calloc(l+len, sizeof(path_t));
-
- // do alignment
- ret = aln_local_core(ref_seq, l, (ubyte_t*)seq, len, &ap, path, &path_len, 1, &subo);
- if (ret < 0 || subo == ret) { // no hit or tandem hits
- free(path); free(cigar); free(ref_seq); *n_cigar = 0;
- return 0;
- }
- cigar = bwa_aln_path2cigar(path, path_len, n_cigar);
-
- // check whether the alignment is good enough
- for (k = 0, x = y = 0; k < *n_cigar; ++k) {
- bwa_cigar_t c = cigar[k];
- if (__cigar_op(c) == FROM_M) x += __cigar_len(c), y += __cigar_len(c);
- else if (__cigar_op(c) == FROM_D) x += __cigar_len(c);
- else y += __cigar_len(c);
- }
- if (x < SW_MIN_MATCH_LEN || y < SW_MIN_MATCH_LEN) { // not good enough
- free(path); free(cigar); free(ref_seq);
- *n_cigar = 0;
- return 0;
- }
-
- { // update cigar and coordinate;
- int start, end;
- p = path + path_len - 1;
- *beg += (p->i? p->i : 1) - 1;
- start = (p->j? p->j : 1) - 1;
- end = path->j;
- cigar = (bwa_cigar_t*)realloc(cigar, sizeof(bwa_cigar_t) * (*n_cigar + 2));
- if (start) {
- memmove(cigar + 1, cigar, sizeof(bwa_cigar_t) * (*n_cigar));
- cigar[0] = __cigar_create(3, start);
- ++(*n_cigar);
- }
- if (end < len) {
- /*cigar[*n_cigar] = 3<<14 | (len - end);*/
- cigar[*n_cigar] = __cigar_create(3, (len - end));
- ++(*n_cigar);
- }
- }
-
- { // set *cnt
- int n_mm, n_gapo, n_gape;
- n_mm = n_gapo = n_gape = 0;
- p = path + path_len - 1;
- x = p->i? p->i - 1 : 0; y = p->j? p->j - 1 : 0;
- for (k = 0; k < *n_cigar; ++k) {
- bwa_cigar_t c = cigar[k];
- if (__cigar_op(c) == FROM_M) {
- for (l = 0; l < (__cigar_len(c)); ++l)
- if (ref_seq[x+l] < 4 && seq[y+l] < 4 && ref_seq[x+l] != seq[y+l]) ++n_mm;
- x += __cigar_len(c), y += __cigar_len(c);
- } else if (__cigar_op(c) == FROM_D) {
- x += __cigar_len(c), ++n_gapo, n_gape += (__cigar_len(c)) - 1;
- } else if (__cigar_op(c) == FROM_I) {
- y += __cigar_len(c), ++n_gapo, n_gape += (__cigar_len(c)) - 1;
- }
- }
- *_cnt = (uint32_t)n_mm<<16 | n_gapo<<8 | n_gape;
- }
-
- free(ref_seq); free(path);
- return cigar;
-}
-
-ubyte_t *bwa_paired_sw(const bntseq_t *bns, const ubyte_t *_pacseq, int n_seqs, bwa_seq_t *seqs[2], const pe_opt_t *popt, const isize_info_t *ii)
-{
- ubyte_t *pacseq;
- int i;
- uint64_t n_tot[2], n_mapped[2];
-
- // load reference sequence
- if (_pacseq == 0) {
- pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
- rewind(bns->fp_pac);
- fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
- } else pacseq = (ubyte_t*)_pacseq;
- if (!popt->is_sw || ii->avg < 0.0) return pacseq;
-
- // perform mate alignment
- n_tot[0] = n_tot[1] = n_mapped[0] = n_mapped[1] = 0;
- for (i = 0; i != n_seqs; ++i) {
- bwa_seq_t *p[2];
- p[0] = seqs[0] + i; p[1] = seqs[1] + i;
- if ((p[0]->mapQ >= SW_MIN_MAPQ || p[1]->mapQ >= SW_MIN_MAPQ) && (p[0]->extra_flag&SAM_FPP) == 0) { // unpaired and one read has high mapQ
- int k, n_cigar[2], is_singleton, mapQ = 0, mq_adjust[2];
- int64_t beg[2], end[2];
- bwa_cigar_t *cigar[2];
- uint32_t cnt[2];
-
- /* In the following, _pref points to the reference read
- * which must be aligned; _pmate points to its mate which is
- * considered to be modified. */
-
-#define __set_rght_coor(_a, _b, _pref, _pmate) do { \
- (_a) = (int64_t)_pref->pos + ii->avg - 3 * ii->std - _pmate->len * 1.5; \
- (_b) = (_a) + 6 * ii->std + 2 * _pmate->len; \
- if ((_a) < (int64_t)_pref->pos + _pref->len) (_a) = _pref->pos + _pref->len; \
- if ((_b) > bns->l_pac) (_b) = bns->l_pac; \
- } while (0)
-
-#define __set_left_coor(_a, _b, _pref, _pmate) do { \
- (_a) = (int64_t)_pref->pos + _pref->len - ii->avg - 3 * ii->std - _pmate->len * 0.5; \
- (_b) = (_a) + 6 * ii->std + 2 * _pmate->len; \
- if ((_a) < 0) (_a) = 0; \
- if ((_b) > _pref->pos) (_b) = _pref->pos; \
- } while (0)
-
-#define __set_fixed(_pref, _pmate, _beg, _cnt) do { \
- _pmate->type = BWA_TYPE_MATESW; \
- _pmate->pos = _beg; \
- _pmate->seQ = _pref->seQ; \
- _pmate->strand = (popt->type == BWA_PET_STD)? 1 - _pref->strand : _pref->strand; \
- _pmate->n_mm = _cnt>>16; _pmate->n_gapo = _cnt>>8&0xff; _pmate->n_gape = _cnt&0xff; \
- _pmate->extra_flag |= SAM_FPP; \
- _pref->extra_flag |= SAM_FPP; \
- } while (0)
-
- mq_adjust[0] = mq_adjust[1] = 255; // not effective
- is_singleton = (p[0]->type == BWA_TYPE_NO_MATCH || p[1]->type == BWA_TYPE_NO_MATCH)? 1 : 0;
-
- ++n_tot[is_singleton];
- cigar[0] = cigar[1] = 0;
- n_cigar[0] = n_cigar[1] = 0;
- if (popt->type != BWA_PET_STD && popt->type != BWA_PET_SOLID) continue; // other types of pairing is not considered
- for (k = 0; k < 2; ++k) { // p[1-k] is the reference read and p[k] is the read considered to be modified
- ubyte_t *seq;
- if (p[1-k]->type == BWA_TYPE_NO_MATCH) continue; // if p[1-k] is unmapped, skip
- if (popt->type == BWA_PET_STD) {
- if (p[1-k]->strand == 0) { // then the mate is on the reverse strand and has larger coordinate
- __set_rght_coor(beg[k], end[k], p[1-k], p[k]);
- seq = p[k]->rseq;
- } else { // then the mate is on forward stand and has smaller coordinate
- __set_left_coor(beg[k], end[k], p[1-k], p[k]);
- seq = p[k]->seq;
- seq_reverse(p[k]->len, seq, 0); // because ->seq is reversed; this will reversed back shortly
- }
- } else { // BWA_PET_SOLID
- if (p[1-k]->strand == 0) { // R3-F3 pairing
- if (k == 0) __set_left_coor(beg[k], end[k], p[1-k], p[k]); // p[k] is R3
- else __set_rght_coor(beg[k], end[k], p[1-k], p[k]); // p[k] is F3
- seq = p[k]->rseq;
- seq_reverse(p[k]->len, seq, 0); // because ->seq is reversed
- } else { // F3-R3 pairing
- if (k == 0) __set_rght_coor(beg[k], end[k], p[1-k], p[k]); // p[k] is R3
- else __set_left_coor(beg[k], end[k], p[1-k], p[k]); // p[k] is F3
- seq = p[k]->seq;
- }
- }
- // perform SW alignment
- cigar[k] = bwa_sw_core(bns->l_pac, pacseq, p[k]->len, seq, &beg[k], end[k] - beg[k], &n_cigar[k], &cnt[k]);
- if (cigar[k] && p[k]->type != BWA_TYPE_NO_MATCH) { // re-evaluate cigar[k]
- int s_old, clip = 0, s_new;
- if (__cigar_op(cigar[k][0]) == 3) clip += __cigar_len(cigar[k][0]);
- if (__cigar_op(cigar[k][n_cigar[k]-1]) == 3) clip += __cigar_len(cigar[k][n_cigar[k]-1]);
- s_old = (int)((p[k]->n_mm * 9 + p[k]->n_gapo * 13 + p[k]->n_gape * 2) / 3. * 8. + .499);
- s_new = (int)(((cnt[k]>>16) * 9 + (cnt[k]>>8&0xff) * 13 + (cnt[k]&0xff) * 2 + clip * 3) / 3. * 8. + .499);
- s_old += -4.343 * log(ii->ap_prior / bns->l_pac);
- s_new += (int)(-4.343 * log(.5 * erfc(M_SQRT1_2 * 1.5) + .499)); // assume the mapped isize is 1.5\sigma
- if (s_old < s_new) { // reject SW alignment
- mq_adjust[k] = s_new - s_old;
- free(cigar[k]); cigar[k] = 0; n_cigar[k] = 0;
- } else mq_adjust[k] = s_old - s_new;
- }
- // now revserse sequence back such that p[*]->seq looks untouched
- if (popt->type == BWA_PET_STD) {
- if (p[1-k]->strand == 1) seq_reverse(p[k]->len, seq, 0);
- } else {
- if (p[1-k]->strand == 0) seq_reverse(p[k]->len, seq, 0);
- }
- }
- k = -1; // no read to be changed
- if (cigar[0] && cigar[1]) {
- k = p[0]->mapQ < p[1]->mapQ? 0 : 1; // p[k] to be fixed
- mapQ = abs(p[1]->mapQ - p[0]->mapQ);
- } else if (cigar[0]) k = 0, mapQ = p[1]->mapQ;
- else if (cigar[1]) k = 1, mapQ = p[0]->mapQ;
- if (k >= 0 && p[k]->pos != beg[k]) {
- ++n_mapped[is_singleton];
- { // recalculate mapping quality
- int tmp = (int)p[1-k]->mapQ - p[k]->mapQ/2 - 8;
- if (tmp <= 0) tmp = 1;
- if (mapQ > tmp) mapQ = tmp;
- p[k]->mapQ = p[1-k]->mapQ = mapQ;
- p[k]->seQ = p[1-k]->seQ = p[1-k]->seQ < mapQ? p[1-k]->seQ : mapQ;
- if (p[k]->mapQ > mq_adjust[k]) p[k]->mapQ = mq_adjust[k];
- if (p[k]->seQ > mq_adjust[k]) p[k]->seQ = mq_adjust[k];
- }
- // update CIGAR
- free(p[k]->cigar); p[k]->cigar = cigar[k]; cigar[k] = 0;
- p[k]->n_cigar = n_cigar[k];
- // update the rest of information
- __set_fixed(p[1-k], p[k], beg[k], cnt[k]);
- }
- free(cigar[0]); free(cigar[1]);
- }
- }
- fprintf(stderr, "[bwa_paired_sw] %lld out of %lld Q%d singletons are mated.\n",
- (long long)n_mapped[1], (long long)n_tot[1], SW_MIN_MAPQ);
- fprintf(stderr, "[bwa_paired_sw] %lld out of %lld Q%d discordant pairs are fixed.\n",
- (long long)n_mapped[0], (long long)n_tot[0], SW_MIN_MAPQ);
- return pacseq;
-}
-
-void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const fn_fa[2], pe_opt_t *popt)
-{
- extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
- int i, j, n_seqs, tot_seqs = 0;
- bwa_seq_t *seqs[2];
- bwa_seqio_t *ks[2];
- clock_t t;
- bntseq_t *bns, *ntbns = 0;
- FILE *fp_sa[2];
- gap_opt_t opt, opt0;
- khint_t iter;
- isize_info_t last_ii; // this is for the last batch of reads
- char str[1024];
- bwt_t *bwt;
- uint8_t *pac;
-
- // initialization
- bwase_initialize(); // initialize g_log_n[] in bwase.c
- pac = 0; bwt = 0;
- for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
- bns = bns_restore(prefix);
- srand48(bns->seed);
- fp_sa[0] = xopen(fn_sa[0], "r");
- fp_sa[1] = xopen(fn_sa[1], "r");
- g_hash = kh_init(b128);
- last_ii.avg = -1.0;
-
- fread(&opt, sizeof(gap_opt_t), 1, fp_sa[0]);
- ks[0] = bwa_open_reads(opt.mode, fn_fa[0]);
- opt0 = opt;
- fread(&opt, sizeof(gap_opt_t), 1, fp_sa[1]); // overwritten!
- ks[1] = bwa_open_reads(opt.mode, fn_fa[1]);
- if (!(opt.mode & BWA_MODE_COMPREAD)) {
- popt->type = BWA_PET_SOLID;
- ntbns = bwa_open_nt(prefix);
- } else { // for Illumina alignment only
- if (popt->is_preload) {
- strcpy(str, prefix); strcat(str, ".bwt"); bwt = bwt_restore_bwt(str);
- strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
- pac = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
- rewind(bns->fp_pac);
- fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
- }
- }
-
- // core loop
- bwa_print_sam_SQ(bns);
- bwa_print_sam_PG();
- while ((seqs[0] = bwa_read_seq(ks[0], 0x40000, &n_seqs, opt0.mode, opt0.trim_qual)) != 0) {
- int cnt_chg;
- isize_info_t ii;
- ubyte_t *pacseq;
-
- seqs[1] = bwa_read_seq(ks[1], 0x40000, &n_seqs, opt.mode, opt.trim_qual);
- tot_seqs += n_seqs;
- t = clock();
-
- fprintf(stderr, "[bwa_sai2sam_pe_core] convert to sequence coordinate... \n");
- cnt_chg = bwa_cal_pac_pos_pe(bns, prefix, bwt, n_seqs, seqs, fp_sa, &ii, popt, &opt, &last_ii);
- fprintf(stderr, "[bwa_sai2sam_pe_core] time elapses: %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
- fprintf(stderr, "[bwa_sai2sam_pe_core] changing coordinates of %d alignments.\n", cnt_chg);
-
- fprintf(stderr, "[bwa_sai2sam_pe_core] align unmapped mate...\n");
- pacseq = bwa_paired_sw(bns, pac, n_seqs, seqs, popt, &ii);
- fprintf(stderr, "[bwa_sai2sam_pe_core] time elapses: %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
-
- fprintf(stderr, "[bwa_sai2sam_pe_core] refine gapped alignments... ");
- for (j = 0; j < 2; ++j)
- bwa_refine_gapped(bns, n_seqs, seqs[j], pacseq, ntbns);
- fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
- if (pac == 0) free(pacseq);
-
- fprintf(stderr, "[bwa_sai2sam_pe_core] print alignments... ");
- for (i = 0; i < n_seqs; ++i) {
- bwa_seq_t *p[2];
- p[0] = seqs[0] + i; p[1] = seqs[1] + i;
- if (p[0]->bc[0] || p[1]->bc[0]) {
- strcat(p[0]->bc, p[1]->bc);
- strcpy(p[1]->bc, p[0]->bc);
- }
- bwa_print_sam1(bns, p[0], p[1], opt.mode, opt.max_top2);
- bwa_print_sam1(bns, p[1], p[0], opt.mode, opt.max_top2);
- }
- fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
-
- for (j = 0; j < 2; ++j)
- bwa_free_read_seq(n_seqs, seqs[j]);
- fprintf(stderr, "[bwa_sai2sam_pe_core] %d sequences have been processed.\n", tot_seqs);
- last_ii = ii;
- }
-
- // destroy
- bns_destroy(bns);
- if (ntbns) bns_destroy(ntbns);
- for (i = 0; i < 2; ++i) {
- bwa_seq_close(ks[i]);
- fclose(fp_sa[i]);
- }
- for (iter = kh_begin(g_hash); iter != kh_end(g_hash); ++iter)
- if (kh_exist(g_hash, iter)) free(kh_val(g_hash, iter).a);
- kh_destroy(b128, g_hash);
- if (pac) {
- free(pac); bwt_destroy(bwt);
- }
-}
-
-int bwa_sai2sam_pe(int argc, char *argv[])
-{
- extern char *bwa_rg_line, *bwa_rg_id;
- extern int bwa_set_rg(const char *s);
- extern char *bwa_infer_prefix(const char *hint);
- int c;
- pe_opt_t *popt;
- char *prefix;
-
- popt = bwa_init_pe_opt();
- while ((c = getopt(argc, argv, "a:o:sPn:N:c:f:Ar:")) >= 0) {
- switch (c) {
- case 'r':
- if (bwa_set_rg(optarg) < 0) {
- fprintf(stderr, "[%s] malformated @RG line\n", __func__);
- return 1;
- }
- break;
- case 'a': popt->max_isize = atoi(optarg); break;
- case 'o': popt->max_occ = atoi(optarg); break;
- case 's': popt->is_sw = 0; break;
- case 'P': popt->is_preload = 1; break;
- case 'n': popt->n_multi = atoi(optarg); break;
- case 'N': popt->N_multi = atoi(optarg); break;
- case 'c': popt->ap_prior = atof(optarg); break;
- case 'f': xreopen(optarg, "w", stdout); break;
- case 'A': popt->force_isize = 1; break;
- default: return 1;
- }
- }
-
- if (optind + 5 > argc) {
- fprintf(stderr, "\n");
- fprintf(stderr, "Usage: bwa sampe [options] \n\n");
- fprintf(stderr, "Options: -a INT maximum insert size [%d]\n", popt->max_isize);
- fprintf(stderr, " -o INT maximum occurrences for one end [%d]\n", popt->max_occ);
- fprintf(stderr, " -n INT maximum hits to output for paired reads [%d]\n", popt->n_multi);
- fprintf(stderr, " -N INT maximum hits to output for discordant pairs [%d]\n", popt->N_multi);
- fprintf(stderr, " -c FLOAT prior of chimeric rate (lower bound) [%.1le]\n", popt->ap_prior);
- fprintf(stderr, " -f FILE sam file to output results to [stdout]\n");
- fprintf(stderr, " -r STR read group header line such as `@RG\\tID:foo\\tSM:bar' [null]\n");
- fprintf(stderr, " -P preload index into memory (for base-space reads only)\n");
- fprintf(stderr, " -s disable Smith-Waterman for the unmapped mate\n");
- fprintf(stderr, " -A disable insert size estimate (force -s)\n\n");
- fprintf(stderr, "Notes: 1. For SOLiD reads, corresponds R3 reads and to F3.\n");
- fprintf(stderr, " 2. For reads shorter than 30bp, applying a smaller -o is recommended to\n");
- fprintf(stderr, " to get a sensible speed at the cost of pairing accuracy.\n");
- fprintf(stderr, "\n");
- return 1;
- }
- if ((prefix = bwa_infer_prefix(argv[optind])) == 0) {
- fprintf(stderr, "[%s] fail to locate the index\n", __func__);
- free(bwa_rg_line); free(bwa_rg_id);
- return 0;
- }
- bwa_sai2sam_pe_core(prefix, argv + optind + 1, argv + optind+3, popt);
- free(bwa_rg_line); free(bwa_rg_id); free(prefix);
- free(popt);
- return 0;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwase.c
--- a/bwa-0.6.2/bwase.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,683 +0,0 @@
-#include
-#include
-#include
-#include
-#include
-#include
-#include "stdaln.h"
-#include "bwase.h"
-#include "bwtaln.h"
-#include "bntseq.h"
-#include "utils.h"
-#include "kstring.h"
-
-int g_log_n[256];
-char *bwa_rg_line, *bwa_rg_id;
-
-void bwa_print_sam_PG();
-
-void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi)
-{
- int i, cnt, best;
- if (n_aln == 0) {
- s->type = BWA_TYPE_NO_MATCH;
- s->c1 = s->c2 = 0;
- return;
- }
-
- if (set_main) {
- best = aln[0].score;
- for (i = cnt = 0; i < n_aln; ++i) {
- const bwt_aln1_t *p = aln + i;
- if (p->score > best) break;
- if (drand48() * (p->l - p->k + 1 + cnt) > (double)cnt) {
- s->n_mm = p->n_mm; s->n_gapo = p->n_gapo; s->n_gape = p->n_gape;
- s->score = p->score;
- s->sa = p->k + (bwtint_t)((p->l - p->k + 1) * drand48());
- }
- cnt += p->l - p->k + 1;
- }
- s->c1 = cnt;
- for (; i < n_aln; ++i) cnt += aln[i].l - aln[i].k + 1;
- s->c2 = cnt - s->c1;
- s->type = s->c1 > 1? BWA_TYPE_REPEAT : BWA_TYPE_UNIQUE;
- }
-
- if (n_multi) {
- int k, rest, n_occ, z = 0;
- for (k = n_occ = 0; k < n_aln; ++k) {
- const bwt_aln1_t *q = aln + k;
- n_occ += q->l - q->k + 1;
- }
- if (s->multi) free(s->multi);
- if (n_occ > n_multi + 1) { // if there are too many hits, generate none of them
- s->multi = 0; s->n_multi = 0;
- return;
- }
- /* The following code is more flexible than what is required
- * here. In principle, due to the requirement above, we can
- * simply output all hits, but the following samples "rest"
- * number of random hits. */
- rest = n_occ > n_multi + 1? n_multi + 1 : n_occ; // find one additional for ->sa
- s->multi = calloc(rest, sizeof(bwt_multi1_t));
- for (k = 0; k < n_aln; ++k) {
- const bwt_aln1_t *q = aln + k;
- if (q->l - q->k + 1 <= rest) {
- bwtint_t l;
- for (l = q->k; l <= q->l; ++l) {
- s->multi[z].pos = l;
- s->multi[z].gap = q->n_gapo + q->n_gape;
- s->multi[z++].mm = q->n_mm;
- }
- rest -= q->l - q->k + 1;
- } else { // Random sampling (http://code.activestate.com/recipes/272884/). In fact, we never come here.
- int j, i, k;
- for (j = rest, i = q->l - q->k + 1, k = 0; j > 0; --j) {
- double p = 1.0, x = drand48();
- while (x < p) p -= p * j / (i--);
- s->multi[z].pos = q->l - i;
- s->multi[z].gap = q->n_gapo + q->n_gape;
- s->multi[z++].mm = q->n_mm;
- }
- rest = 0;
- break;
- }
- }
- s->n_multi = z;
- }
-}
-
-void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s)
-{
- bwa_aln2seq_core(n_aln, aln, s, 1, 0);
-}
-
-int bwa_approx_mapQ(const bwa_seq_t *p, int mm)
-{
- int n;
- if (p->c1 == 0) return 23;
- if (p->c1 > 1) return 0;
- if (p->n_mm == mm) return 25;
- if (p->c2 == 0) return 37;
- n = (p->c2 >= 255)? 255 : p->c2;
- return (23 < g_log_n[n])? 0 : 23 - g_log_n[n];
-}
-
-bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int len, int *strand)
-{
- bwtint_t pos_f;
- int is_rev;
- pos_f = bns_depos(bns, bwt_sa(bwt, sapos), &is_rev); // pos_f
- *strand = !is_rev;
- /* NB: For gapped alignment, pacpos may not be correct, which will be fixed
- * in bwa_refine_gapped_core(). This line also determines the way "x" is
- * calculated in bwa_refine_gapped_core() when (ext < 0 && is_end == 0). */
- if (is_rev) pos_f = pos_f + 1 < len? 0 : pos_f - len + 1; // mapped to the forward strand
- return pos_f; // FIXME: it is possible that pos_f < bns->anns[ref_id].offset
-}
-
-/**
- * Derive the actual position in the read from the given suffix array
- * coordinates. Note that the position will be approximate based on
- * whether indels appear in the read and whether calculations are
- * performed from the start or end of the read.
- */
-void bwa_cal_pac_pos_core(const bntseq_t *bns, const bwt_t *bwt, bwa_seq_t *seq, const int max_mm, const float fnr)
-{
- int max_diff, strand;
- if (seq->type != BWA_TYPE_UNIQUE && seq->type != BWA_TYPE_REPEAT) return;
- max_diff = fnr > 0.0? bwa_cal_maxdiff(seq->len, BWA_AVG_ERR, fnr) : max_mm;
- seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
- seq->pos = bwa_sa2pos(bns, bwt, seq->sa, seq->len, &strand);
- seq->strand = strand;
- seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
-}
-
-void bwa_cal_pac_pos(const bntseq_t *bns, const char *prefix, int n_seqs, bwa_seq_t *seqs, int max_mm, float fnr)
-{
- int i, j, strand, n_multi;
- char str[1024];
- bwt_t *bwt;
- // load forward SA
- strcpy(str, prefix); strcat(str, ".bwt"); bwt = bwt_restore_bwt(str);
- strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
- for (i = 0; i != n_seqs; ++i) {
- bwa_seq_t *p = &seqs[i];
- bwa_cal_pac_pos_core(bns, bwt, p, max_mm, fnr);
- for (j = n_multi = 0; j < p->n_multi; ++j) {
- bwt_multi1_t *q = p->multi + j;
- q->pos = bwa_sa2pos(bns, bwt, q->pos, p->len, &strand);
- q->strand = strand;
- if (q->pos != p->pos)
- p->multi[n_multi++] = *q;
- }
- p->n_multi = n_multi;
- }
- bwt_destroy(bwt);
-}
-
-/* is_end_correct == 1 if (*pos+len) gives the correct coordinate on
- * forward strand. This happens when p->pos is calculated by
- * bwa_cal_pac_pos(). is_end_correct==0 if (*pos) gives the correct
- * coordinate. This happens only for color-converted alignment. */
-bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const ubyte_t *seq, bwtint_t *_pos,
- int ext, int *n_cigar, int is_end_correct)
-{
- bwa_cigar_t *cigar = 0;
- ubyte_t *ref_seq;
- int l = 0, path_len, ref_len;
- AlnParam ap = aln_param_bwa;
- path_t *path;
- int64_t k, __pos = *_pos;
-
- ref_len = len + abs(ext);
- if (ext > 0) {
- ref_seq = (ubyte_t*)calloc(ref_len, 1);
- for (k = __pos; k < __pos + ref_len && k < l_pac; ++k)
- ref_seq[l++] = pacseq[k>>2] >> ((~k&3)<<1) & 3;
- } else {
- int64_t x = __pos + (is_end_correct? len : ref_len);
- ref_seq = (ubyte_t*)calloc(ref_len, 1);
- for (l = 0, k = x - ref_len > 0? x - ref_len : 0; k < x && k < l_pac; ++k)
- ref_seq[l++] = pacseq[k>>2] >> ((~k&3)<<1) & 3;
- }
- path = (path_t*)calloc(l+len, sizeof(path_t));
-
- aln_global_core(ref_seq, l, (ubyte_t*)seq, len, &ap, path, &path_len);
- cigar = bwa_aln_path2cigar(path, path_len, n_cigar);
-
- if (ext < 0 && is_end_correct) { // fix coordinate for reads mapped to the forward strand
- for (l = k = 0; k < *n_cigar; ++k) {
- if (__cigar_op(cigar[k]) == FROM_D) l -= __cigar_len(cigar[k]);
- else if (__cigar_op(cigar[k]) == FROM_I) l += __cigar_len(cigar[k]);
- }
- __pos += l;
- }
-
- if (__cigar_op(cigar[0]) == FROM_D) { // deletion at the 5'-end
- __pos += __cigar_len(cigar[0]);
- for (k = 0; k < *n_cigar - 1; ++k) cigar[k] = cigar[k+1];
- --(*n_cigar);
- }
- if (__cigar_op(cigar[*n_cigar-1]) == FROM_D) --(*n_cigar); // deletion at the 3'-end
-
- // change "I" at either end of the read to S. just in case. This should rarely happen...
- if (__cigar_op(cigar[*n_cigar-1]) == FROM_I) cigar[*n_cigar-1] = __cigar_create(3, (__cigar_len(cigar[*n_cigar-1])));
- if (__cigar_op(cigar[0]) == FROM_I) cigar[0] = __cigar_create(3, (__cigar_len(cigar[0])));
-
- *_pos = (bwtint_t)__pos;
- free(ref_seq); free(path);
- return cigar;
-}
-
-char *bwa_cal_md1(int n_cigar, bwa_cigar_t *cigar, int len, bwtint_t pos, ubyte_t *seq,
- bwtint_t l_pac, ubyte_t *pacseq, kstring_t *str, int *_nm)
-{
- bwtint_t x, y;
- int z, u, c, nm = 0;
- str->l = 0; // reset
- x = pos; y = 0;
- if (cigar) {
- int k, l;
- for (k = u = 0; k < n_cigar; ++k) {
- l = __cigar_len(cigar[k]);
- if (__cigar_op(cigar[k]) == FROM_M) {
- for (z = 0; z < l && x+z < l_pac; ++z) {
- c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
- if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
- ksprintf(str, "%d", u);
- kputc("ACGTN"[c], str);
- ++nm;
- u = 0;
- } else ++u;
- }
- x += l; y += l;
- } else if (__cigar_op(cigar[k]) == FROM_I || __cigar_op(cigar[k]) == FROM_S) {
- y += l;
- if (__cigar_op(cigar[k]) == FROM_I) nm += l;
- } else if (__cigar_op(cigar[k]) == FROM_D) {
- ksprintf(str, "%d", u);
- kputc('^', str);
- for (z = 0; z < l && x+z < l_pac; ++z)
- kputc("ACGT"[pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3], str);
- u = 0;
- x += l; nm += l;
- }
- }
- } else { // no gaps
- for (z = u = 0; z < (bwtint_t)len && x+z < l_pac; ++z) {
- c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
- if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
- ksprintf(str, "%d", u);
- kputc("ACGTN"[c], str);
- ++nm;
- u = 0;
- } else ++u;
- }
- }
- ksprintf(str, "%d", u);
- *_nm = nm;
- return strdup(str->s);
-}
-
-void bwa_correct_trimmed(bwa_seq_t *s)
-{
- if (s->len == s->full_len) return;
- if (s->strand == 0) { // forward
- if (s->cigar && __cigar_op(s->cigar[s->n_cigar-1]) == FROM_S) { // the last is S
- s->cigar[s->n_cigar-1] += s->full_len - s->len;
- } else {
- if (s->cigar == 0) {
- s->n_cigar = 2;
- s->cigar = calloc(s->n_cigar, sizeof(bwa_cigar_t));
- s->cigar[0] = __cigar_create(0, s->len);
- } else {
- ++s->n_cigar;
- s->cigar = realloc(s->cigar, s->n_cigar * sizeof(bwa_cigar_t));
- }
- s->cigar[s->n_cigar-1] = __cigar_create(3, (s->full_len - s->len));
- }
- } else { // reverse
- if (s->cigar && __cigar_op(s->cigar[0]) == FROM_S) { // the first is S
- s->cigar[0] += s->full_len - s->len;
- } else {
- if (s->cigar == 0) {
- s->n_cigar = 2;
- s->cigar = calloc(s->n_cigar, sizeof(bwa_cigar_t));
- s->cigar[1] = __cigar_create(0, s->len);
- } else {
- ++s->n_cigar;
- s->cigar = realloc(s->cigar, s->n_cigar * sizeof(bwa_cigar_t));
- memmove(s->cigar + 1, s->cigar, (s->n_cigar-1) * sizeof(bwa_cigar_t));
- }
- s->cigar[0] = __cigar_create(3, (s->full_len - s->len));
- }
- }
- s->len = s->full_len;
-}
-
-void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, bntseq_t *ntbns)
-{
- ubyte_t *pacseq, *ntpac = 0;
- int i, j;
- kstring_t *str;
-
- if (ntbns) { // in color space
- ntpac = (ubyte_t*)calloc(ntbns->l_pac/4+1, 1);
- rewind(ntbns->fp_pac);
- fread(ntpac, 1, ntbns->l_pac/4 + 1, ntbns->fp_pac);
- }
-
- if (!_pacseq) {
- pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
- rewind(bns->fp_pac);
- fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
- } else pacseq = _pacseq;
- for (i = 0; i != n_seqs; ++i) {
- bwa_seq_t *s = seqs + i;
- seq_reverse(s->len, s->seq, 0); // IMPORTANT: s->seq is reversed here!!!
- for (j = 0; j < s->n_multi; ++j) {
- bwt_multi1_t *q = s->multi + j;
- int n_cigar;
- if (q->gap == 0) continue;
- q->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, q->strand? s->rseq : s->seq, &q->pos,
- (q->strand? 1 : -1) * q->gap, &n_cigar, 1);
- q->n_cigar = n_cigar;
- }
- if (s->type == BWA_TYPE_NO_MATCH || s->type == BWA_TYPE_MATESW || s->n_gapo == 0) continue;
- s->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, s->strand? s->rseq : s->seq, &s->pos,
- (s->strand? 1 : -1) * (s->n_gapo + s->n_gape), &s->n_cigar, 1);
- }
-#if 0
- if (ntbns) { // in color space
- for (i = 0; i < n_seqs; ++i) {
- bwa_seq_t *s = seqs + i;
- bwa_cs2nt_core(s, bns->l_pac, ntpac);
- for (j = 0; j < s->n_multi; ++j) {
- bwt_multi1_t *q = s->multi + j;
- int n_cigar;
- if (q->gap == 0) continue;
- free(q->cigar);
- q->cigar = bwa_refine_gapped_core(bns->l_pac, ntpac, s->len, q->strand? s->rseq : s->seq, &q->pos,
- (q->strand? 1 : -1) * q->gap, &n_cigar, 0);
- q->n_cigar = n_cigar;
- }
- if (s->type != BWA_TYPE_NO_MATCH && s->cigar) { // update cigar again
- free(s->cigar);
- s->cigar = bwa_refine_gapped_core(bns->l_pac, ntpac, s->len, s->strand? s->rseq : s->seq, &s->pos,
- (s->strand? 1 : -1) * (s->n_gapo + s->n_gape), &s->n_cigar, 0);
- }
- }
- }
-#endif
- // generate MD tag
- str = (kstring_t*)calloc(1, sizeof(kstring_t));
- for (i = 0; i != n_seqs; ++i) {
- bwa_seq_t *s = seqs + i;
- if (s->type != BWA_TYPE_NO_MATCH) {
- int nm;
- s->md = bwa_cal_md1(s->n_cigar, s->cigar, s->len, s->pos, s->strand? s->rseq : s->seq,
- bns->l_pac, ntbns? ntpac : pacseq, str, &nm);
- s->nm = nm;
- }
- }
- free(str->s); free(str);
-
- // correct for trimmed reads
- if (!ntbns) // trimming is only enabled for Illumina reads
- for (i = 0; i < n_seqs; ++i) bwa_correct_trimmed(seqs + i);
-
- if (!_pacseq) free(pacseq);
- free(ntpac);
-}
-
-int64_t pos_end(const bwa_seq_t *p)
-{
- if (p->cigar) {
- int j;
- int64_t x = p->pos;
- for (j = 0; j != p->n_cigar; ++j) {
- int op = __cigar_op(p->cigar[j]);
- if (op == 0 || op == 2) x += __cigar_len(p->cigar[j]);
- }
- return x;
- } else return p->pos + p->len;
-}
-
-int64_t pos_end_multi(const bwt_multi1_t *p, int len) // analogy to pos_end()
-{
- if (p->cigar) {
- int j;
- int64_t x = p->pos;
- for (j = 0; j != p->n_cigar; ++j) {
- int op = __cigar_op(p->cigar[j]);
- if (op == 0 || op == 2) x += __cigar_len(p->cigar[j]);
- }
- return x;
- } else return p->pos + len;
-}
-
-static int64_t pos_5(const bwa_seq_t *p)
-{
- if (p->type != BWA_TYPE_NO_MATCH)
- return p->strand? pos_end(p) : p->pos;
- return -1;
-}
-
-void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2)
-{
- int j;
- if (p->type != BWA_TYPE_NO_MATCH || (mate && mate->type != BWA_TYPE_NO_MATCH)) {
- int seqid, nn, am = 0, flag = p->extra_flag;
- char XT;
-
- if (p->type == BWA_TYPE_NO_MATCH) {
- p->pos = mate->pos;
- p->strand = mate->strand;
- flag |= SAM_FSU;
- j = 1;
- } else j = pos_end(p) - p->pos; // j is the length of the reference in the alignment
-
- // get seqid
- nn = bns_cnt_ambi(bns, p->pos, j, &seqid);
- if (p->type != BWA_TYPE_NO_MATCH && p->pos + j - bns->anns[seqid].offset > bns->anns[seqid].len)
- flag |= SAM_FSU; // flag UNMAP as this alignment bridges two adjacent reference sequences
-
- // update flag and print it
- if (p->strand) flag |= SAM_FSR;
- if (mate) {
- if (mate->type != BWA_TYPE_NO_MATCH) {
- if (mate->strand) flag |= SAM_FMR;
- } else flag |= SAM_FMU;
- }
- err_printf("%s\t%d\t%s\t", p->name, flag, bns->anns[seqid].name);
- err_printf("%d\t%d\t", (int)(p->pos - bns->anns[seqid].offset + 1), p->mapQ);
-
- // print CIGAR
- if (p->cigar) {
- for (j = 0; j != p->n_cigar; ++j)
- err_printf("%d%c", __cigar_len(p->cigar[j]), "MIDS"[__cigar_op(p->cigar[j])]);
- } else if (p->type == BWA_TYPE_NO_MATCH) err_printf("*");
- else err_printf("%dM", p->len);
-
- // print mate coordinate
- if (mate && mate->type != BWA_TYPE_NO_MATCH) {
- int m_seqid, m_is_N;
- long long isize;
- am = mate->seQ < p->seQ? mate->seQ : p->seQ; // smaller single-end mapping quality
- // redundant calculation here, but should not matter too much
- m_is_N = bns_cnt_ambi(bns, mate->pos, mate->len, &m_seqid);
- err_printf("\t%s\t", (seqid == m_seqid)? "=" : bns->anns[m_seqid].name);
- isize = (seqid == m_seqid)? pos_5(mate) - pos_5(p) : 0;
- if (p->type == BWA_TYPE_NO_MATCH) isize = 0;
- err_printf("%d\t%lld\t", (int)(mate->pos - bns->anns[m_seqid].offset + 1), isize);
- } else if (mate) err_printf("\t=\t%d\t0\t", (int)(p->pos - bns->anns[seqid].offset + 1));
- else err_printf("\t*\t0\t0\t");
-
- // print sequence and quality
- if (p->strand == 0)
- for (j = 0; j != p->full_len; ++j) putchar("ACGTN"[(int)p->seq[j]]);
- else for (j = 0; j != p->full_len; ++j) putchar("TGCAN"[p->seq[p->full_len - 1 - j]]);
- putchar('\t');
- if (p->qual) {
- if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
- err_printf("%s", p->qual);
- } else err_printf("*");
-
- if (bwa_rg_id) err_printf("\tRG:Z:%s", bwa_rg_id);
- if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
- if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
- if (p->type != BWA_TYPE_NO_MATCH) {
- int i;
- // calculate XT tag
- XT = "NURM"[p->type];
- if (nn > 10) XT = 'N';
- // print tags
- err_printf("\tXT:A:%c\t%s:i:%d", XT, (mode & BWA_MODE_COMPREAD)? "NM" : "CM", p->nm);
- if (nn) err_printf("\tXN:i:%d", nn);
- if (mate) err_printf("\tSM:i:%d\tAM:i:%d", p->seQ, am);
- if (p->type != BWA_TYPE_MATESW) { // X0 and X1 are not available for this type of alignment
- err_printf("\tX0:i:%d", p->c1);
- if (p->c1 <= max_top2) err_printf("\tX1:i:%d", p->c2);
- }
- err_printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
- if (p->md) err_printf("\tMD:Z:%s", p->md);
- // print multiple hits
- if (p->n_multi) {
- err_printf("\tXA:Z:");
- for (i = 0; i < p->n_multi; ++i) {
- bwt_multi1_t *q = p->multi + i;
- int k;
- j = pos_end_multi(q, p->len) - q->pos;
- nn = bns_cnt_ambi(bns, q->pos, j, &seqid);
- err_printf("%s,%c%d,", bns->anns[seqid].name, q->strand? '-' : '+',
- (int)(q->pos - bns->anns[seqid].offset + 1));
- if (q->cigar) {
- for (k = 0; k < q->n_cigar; ++k)
- err_printf("%d%c", __cigar_len(q->cigar[k]), "MIDS"[__cigar_op(q->cigar[k])]);
- } else err_printf("%dM", p->len);
- err_printf(",%d;", q->gap + q->mm);
- }
- }
- }
- putchar('\n');
- } else { // this read has no match
- ubyte_t *s = p->strand? p->rseq : p->seq;
- int flag = p->extra_flag | SAM_FSU;
- if (mate && mate->type == BWA_TYPE_NO_MATCH) flag |= SAM_FMU;
- err_printf("%s\t%d\t*\t0\t0\t*\t*\t0\t0\t", p->name, flag);
- for (j = 0; j != p->len; ++j) putchar("ACGTN"[(int)s[j]]);
- putchar('\t');
- if (p->qual) {
- if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
- err_printf("%s", p->qual);
- } else err_printf("*");
- if (bwa_rg_id) err_printf("\tRG:Z:%s", bwa_rg_id);
- if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
- if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
- putchar('\n');
- }
-}
-
-bntseq_t *bwa_open_nt(const char *prefix)
-{
- bntseq_t *ntbns;
- char *str;
- str = (char*)calloc(strlen(prefix) + 10, 1);
- strcat(strcpy(str, prefix), ".nt");
- ntbns = bns_restore(str);
- free(str);
- return ntbns;
-}
-
-void bwa_print_sam_SQ(const bntseq_t *bns)
-{
- int i;
- for (i = 0; i < bns->n_seqs; ++i)
- err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
- if (bwa_rg_line) err_printf("%s\n", bwa_rg_line);
-}
-
-void bwase_initialize()
-{
- int i;
- for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
-}
-
-char *bwa_escape(char *s)
-{
- char *p, *q;
- for (p = q = s; *p; ++p) {
- if (*p == '\\') {
- ++p;
- if (*p == 't') *q++ = '\t';
- else if (*p == 'n') *q++ = '\n';
- else if (*p == 'r') *q++ = '\r';
- else if (*p == '\\') *q++ = '\\';
- } else *q++ = *p;
- }
- *q = '\0';
- return s;
-}
-
-int bwa_set_rg(const char *s)
-{
- char *p, *q, *r;
- if (strstr(s, "@RG") != s) return -1;
- if (bwa_rg_line) free(bwa_rg_line);
- if (bwa_rg_id) free(bwa_rg_id);
- bwa_rg_line = strdup(s);
- bwa_rg_id = 0;
- bwa_escape(bwa_rg_line);
- p = strstr(bwa_rg_line, "\tID:");
- if (p == 0) return -1;
- p += 4;
- for (q = p; *q && *q != '\t' && *q != '\n'; ++q);
- bwa_rg_id = calloc(q - p + 1, 1);
- for (q = p, r = bwa_rg_id; *q && *q != '\t' && *q != '\n'; ++q)
- *r++ = *q;
- return 0;
-}
-
-void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ)
-{
- extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
- int i, n_seqs, tot_seqs = 0, m_aln;
- bwt_aln1_t *aln = 0;
- bwa_seq_t *seqs;
- bwa_seqio_t *ks;
- clock_t t;
- bntseq_t *bns, *ntbns = 0;
- FILE *fp_sa;
- gap_opt_t opt;
-
- // initialization
- bwase_initialize();
- bns = bns_restore(prefix);
- srand48(bns->seed);
- fp_sa = xopen(fn_sa, "r");
-
- m_aln = 0;
- fread(&opt, sizeof(gap_opt_t), 1, fp_sa);
- if (!(opt.mode & BWA_MODE_COMPREAD)) // in color space; initialize ntpac
- ntbns = bwa_open_nt(prefix);
- bwa_print_sam_SQ(bns);
- //bwa_print_sam_PG();
- // set ks
- ks = bwa_open_reads(opt.mode, fn_fa);
- // core loop
- while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt.mode, opt.trim_qual)) != 0) {
- tot_seqs += n_seqs;
- t = clock();
-
- // read alignment
- for (i = 0; i < n_seqs; ++i) {
- bwa_seq_t *p = seqs + i;
- int n_aln;
- fread(&n_aln, 4, 1, fp_sa);
- if (n_aln > m_aln) {
- m_aln = n_aln;
- aln = (bwt_aln1_t*)realloc(aln, sizeof(bwt_aln1_t) * m_aln);
- }
- fread(aln, sizeof(bwt_aln1_t), n_aln, fp_sa);
- bwa_aln2seq_core(n_aln, aln, p, 1, n_occ);
- }
-
- fprintf(stderr, "[bwa_aln_core] convert to sequence coordinate... ");
- bwa_cal_pac_pos(bns, prefix, n_seqs, seqs, opt.max_diff, opt.fnr); // forward bwt will be destroyed here
- fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
-
- fprintf(stderr, "[bwa_aln_core] refine gapped alignments... ");
- bwa_refine_gapped(bns, n_seqs, seqs, 0, ntbns);
- fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
-
- fprintf(stderr, "[bwa_aln_core] print alignments... ");
- for (i = 0; i < n_seqs; ++i)
- bwa_print_sam1(bns, seqs + i, 0, opt.mode, opt.max_top2);
- fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
-
- bwa_free_read_seq(n_seqs, seqs);
- fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
- }
-
- // destroy
- bwa_seq_close(ks);
- if (ntbns) bns_destroy(ntbns);
- bns_destroy(bns);
- fclose(fp_sa);
- free(aln);
-}
-
-int bwa_sai2sam_se(int argc, char *argv[])
-{
- extern char *bwa_infer_prefix(const char *hint);
- int c, n_occ = 3;
- char *prefix;
- while ((c = getopt(argc, argv, "hn:f:r:")) >= 0) {
- switch (c) {
- case 'h': break;
- case 'r':
- if (bwa_set_rg(optarg) < 0) {
- fprintf(stderr, "[%s] malformated @RG line\n", __func__);
- return 1;
- }
- break;
- case 'n': n_occ = atoi(optarg); break;
- case 'f': xreopen(optarg, "w", stdout); break;
- default: return 1;
- }
- }
-
- if (optind + 3 > argc) {
- fprintf(stderr, "Usage: bwa samse [-n max_occ] [-f out.sam] [-r RG_line] \n");
- return 1;
- }
- if ((prefix = bwa_infer_prefix(argv[optind])) == 0) {
- fprintf(stderr, "[%s] fail to locate the index\n", __func__);
- free(bwa_rg_line); free(bwa_rg_id);
- return 0;
- }
- bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ);
- free(bwa_rg_line); free(bwa_rg_id);
- return 0;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwase.h
--- a/bwa-0.6.2/bwase.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-#ifndef BWASE_H
-#define BWASE_H
-
-#include "bntseq.h"
-#include "bwt.h"
-#include "bwtaln.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- // Initialize mapping tables in the bwa single-end mapper.
- void bwase_initialize();
- // Calculate the approximate position of the sequence from the specified bwt with loaded suffix array.
- void bwa_cal_pac_pos_core(const bntseq_t *bns, const bwt_t* bwt, bwa_seq_t* seq, const int max_mm, const float fnr);
- // Refine the approximate position of the sequence to an actual placement for the sequence.
- void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, bntseq_t *ntbns);
- // Backfill certain alignment properties mainly centering around number of matches.
- void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
- // Calculate the end position of a read given a certain sequence.
- int64_t pos_end(const bwa_seq_t *p);
- //
- bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int len, int *strand);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif // BWASE_H
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwaseqio.c
--- a/bwa-0.6.2/bwaseqio.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,227 +0,0 @@
-#include
-#include
-#include "bwtaln.h"
-#include "utils.h"
-#include "bamlite.h"
-
-#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
-
-extern unsigned char nst_nt4_table[256];
-static char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
-
-struct __bwa_seqio_t {
- // for BAM input
- int is_bam, which; // 1st bit: read1, 2nd bit: read2, 3rd: SE
- bamFile fp;
- // for fastq input
- kseq_t *ks;
-};
-
-bwa_seqio_t *bwa_bam_open(const char *fn, int which)
-{
- bwa_seqio_t *bs;
- bam_header_t *h;
- bs = (bwa_seqio_t*)calloc(1, sizeof(bwa_seqio_t));
- bs->is_bam = 1;
- bs->which = which;
- bs->fp = bam_open(fn, "r");
- h = bam_header_read(bs->fp);
- bam_header_destroy(h);
- return bs;
-}
-
-bwa_seqio_t *bwa_seq_open(const char *fn)
-{
- gzFile fp;
- bwa_seqio_t *bs;
- bs = (bwa_seqio_t*)calloc(1, sizeof(bwa_seqio_t));
- fp = xzopen(fn, "r");
- bs->ks = kseq_init(fp);
- return bs;
-}
-
-void bwa_seq_close(bwa_seqio_t *bs)
-{
- if (bs == 0) return;
- if (bs->is_bam) bam_close(bs->fp);
- else {
- gzclose(bs->ks->f->f);
- kseq_destroy(bs->ks);
- }
- free(bs);
-}
-
-void seq_reverse(int len, ubyte_t *seq, int is_comp)
-{
- int i;
- if (is_comp) {
- for (i = 0; i < len>>1; ++i) {
- char tmp = seq[len-1-i];
- if (tmp < 4) tmp = 3 - tmp;
- seq[len-1-i] = (seq[i] >= 4)? seq[i] : 3 - seq[i];
- seq[i] = tmp;
- }
- if (len&1) seq[i] = (seq[i] >= 4)? seq[i] : 3 - seq[i];
- } else {
- for (i = 0; i < len>>1; ++i) {
- char tmp = seq[len-1-i];
- seq[len-1-i] = seq[i]; seq[i] = tmp;
- }
- }
-}
-
-int bwa_trim_read(int trim_qual, bwa_seq_t *p)
-{
- int s = 0, l, max = 0, max_l = p->len;
- if (trim_qual < 1 || p->qual == 0) return 0;
- for (l = p->len - 1; l >= BWA_MIN_RDLEN; --l) {
- s += trim_qual - (p->qual[l] - 33);
- if (s < 0) break;
- if (s > max) max = s, max_l = l;
- }
- p->clip_len = p->len = max_l;
- return p->full_len - p->len;
-}
-
-static bwa_seq_t *bwa_read_bam(bwa_seqio_t *bs, int n_needed, int *n, int is_comp, int trim_qual)
-{
- bwa_seq_t *seqs, *p;
- int n_seqs, l, i;
- long n_trimmed = 0, n_tot = 0;
- bam1_t *b;
-
- b = bam_init1();
- n_seqs = 0;
- seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
- while (bam_read1(bs->fp, b) >= 0) {
- uint8_t *s, *q;
- int go = 0;
- if ((bs->which & 1) && (b->core.flag & BAM_FREAD1)) go = 1;
- if ((bs->which & 2) && (b->core.flag & BAM_FREAD2)) go = 1;
- if ((bs->which & 4) && !(b->core.flag& BAM_FREAD1) && !(b->core.flag& BAM_FREAD2))go = 1;
- if (go == 0) continue;
- l = b->core.l_qseq;
- p = &seqs[n_seqs++];
- p->tid = -1; // no assigned to a thread
- p->qual = 0;
- p->full_len = p->clip_len = p->len = l;
- n_tot += p->full_len;
- s = bam1_seq(b); q = bam1_qual(b);
- p->seq = (ubyte_t*)calloc(p->len + 1, 1);
- p->qual = (ubyte_t*)calloc(p->len + 1, 1);
- for (i = 0; i != p->full_len; ++i) {
- p->seq[i] = bam_nt16_nt4_table[(int)bam1_seqi(s, i)];
- p->qual[i] = q[i] + 33 < 126? q[i] + 33 : 126;
- }
- if (bam1_strand(b)) { // then reverse
- seq_reverse(p->len, p->seq, 1);
- seq_reverse(p->len, p->qual, 0);
- }
- if (trim_qual >= 1) n_trimmed += bwa_trim_read(trim_qual, p);
- p->rseq = (ubyte_t*)calloc(p->full_len, 1);
- memcpy(p->rseq, p->seq, p->len);
- seq_reverse(p->len, p->seq, 0); // *IMPORTANT*: will be reversed back in bwa_refine_gapped()
- seq_reverse(p->len, p->rseq, is_comp);
- p->name = strdup((const char*)bam1_qname(b));
- if (n_seqs == n_needed) break;
- }
- *n = n_seqs;
- if (n_seqs && trim_qual >= 1)
- fprintf(stderr, "[bwa_read_seq] %.1f%% bases are trimmed.\n", 100.0f * n_trimmed/n_tot);
- if (n_seqs == 0) {
- free(seqs);
- bam_destroy1(b);
- return 0;
- }
- bam_destroy1(b);
- return seqs;
-}
-
-#define BARCODE_LOW_QUAL 13
-
-bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int mode, int trim_qual)
-{
- bwa_seq_t *seqs, *p;
- kseq_t *seq = bs->ks;
- int n_seqs, l, i, is_comp = mode&BWA_MODE_COMPREAD, is_64 = mode&BWA_MODE_IL13, l_bc = mode>>24;
- long n_trimmed = 0, n_tot = 0;
-
- if (l_bc > BWA_MAX_BCLEN) {
- fprintf(stderr, "[%s] the maximum barcode length is %d.\n", __func__, BWA_MAX_BCLEN);
- return 0;
- }
- if (bs->is_bam) return bwa_read_bam(bs, n_needed, n, is_comp, trim_qual); // l_bc has no effect for BAM input
- n_seqs = 0;
- seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
- while ((l = kseq_read(seq)) >= 0) {
- if ((mode & BWA_MODE_CFY) && (seq->comment.l != 0)) {
- // skip reads that are marked to be filtered by Casava
- char *s = index(seq->comment.s, ':');
- if (s && *(++s) == 'Y') {
- continue;
- }
- }
- if (is_64 && seq->qual.l)
- for (i = 0; i < seq->qual.l; ++i) seq->qual.s[i] -= 31;
- if (seq->seq.l <= l_bc) continue; // sequence length equals or smaller than the barcode length
- p = &seqs[n_seqs++];
- if (l_bc) { // then trim barcode
- for (i = 0; i < l_bc; ++i)
- p->bc[i] = (seq->qual.l && seq->qual.s[i]-33 < BARCODE_LOW_QUAL)? tolower(seq->seq.s[i]) : toupper(seq->seq.s[i]);
- p->bc[i] = 0;
- for (; i < seq->seq.l; ++i)
- seq->seq.s[i - l_bc] = seq->seq.s[i];
- seq->seq.l -= l_bc; seq->seq.s[seq->seq.l] = 0;
- if (seq->qual.l) {
- for (i = l_bc; i < seq->qual.l; ++i)
- seq->qual.s[i - l_bc] = seq->qual.s[i];
- seq->qual.l -= l_bc; seq->qual.s[seq->qual.l] = 0;
- }
- l = seq->seq.l;
- } else p->bc[0] = 0;
- p->tid = -1; // no assigned to a thread
- p->qual = 0;
- p->full_len = p->clip_len = p->len = l;
- n_tot += p->full_len;
- p->seq = (ubyte_t*)calloc(p->len, 1);
- for (i = 0; i != p->full_len; ++i)
- p->seq[i] = nst_nt4_table[(int)seq->seq.s[i]];
- if (seq->qual.l) { // copy quality
- p->qual = (ubyte_t*)strdup((char*)seq->qual.s);
- if (trim_qual >= 1) n_trimmed += bwa_trim_read(trim_qual, p);
- }
- p->rseq = (ubyte_t*)calloc(p->full_len, 1);
- memcpy(p->rseq, p->seq, p->len);
- seq_reverse(p->len, p->seq, 0); // *IMPORTANT*: will be reversed back in bwa_refine_gapped()
- seq_reverse(p->len, p->rseq, is_comp);
- p->name = strdup((const char*)seq->name.s);
- { // trim /[12]$
- int t = strlen(p->name);
- if (t > 2 && p->name[t-2] == '/' && (p->name[t-1] == '1' || p->name[t-1] == '2')) p->name[t-2] = '\0';
- }
- if (n_seqs == n_needed) break;
- }
- *n = n_seqs;
- if (n_seqs && trim_qual >= 1)
- fprintf(stderr, "[bwa_read_seq] %.1f%% bases are trimmed.\n", 100.0f * n_trimmed/n_tot);
- if (n_seqs == 0) {
- free(seqs);
- return 0;
- }
- return seqs;
-}
-
-void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs)
-{
- int i, j;
- for (i = 0; i != n_seqs; ++i) {
- bwa_seq_t *p = seqs + i;
- for (j = 0; j < p->n_multi; ++j)
- if (p->multi[j].cigar) free(p->multi[j].cigar);
- free(p->name);
- free(p->seq); free(p->rseq); free(p->qual); free(p->aln); free(p->md); free(p->multi);
- free(p->cigar);
- }
- free(seqs);
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwt.c
--- a/bwa-0.6.2/bwt.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,339 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008 Genome Research Ltd (GRL).
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-/* Contact: Heng Li */
-
-#include
-#include
-#include
-#include
-#include
-#include "utils.h"
-#include "bwt.h"
-#include "kvec.h"
-
-void bwt_gen_cnt_table(bwt_t *bwt)
-{
- int i, j;
- for (i = 0; i != 256; ++i) {
- uint32_t x = 0;
- for (j = 0; j != 4; ++j)
- x |= (((i&3) == j) + ((i>>2&3) == j) + ((i>>4&3) == j) + (i>>6 == j)) << (j<<3);
- bwt->cnt_table[i] = x;
- }
-}
-
-// bwt->bwt and bwt->occ must be precalculated
-void bwt_cal_sa(bwt_t *bwt, int intv)
-{
- bwtint_t isa, sa, i; // S(isa) = sa
- int intv_round = intv;
-
- kv_roundup32(intv_round);
- xassert(intv_round == intv, "SA sample interval is not a power of 2.");
- xassert(bwt->bwt, "bwt_t::bwt is not initialized.");
-
- if (bwt->sa) free(bwt->sa);
- bwt->sa_intv = intv;
- bwt->n_sa = (bwt->seq_len + intv) / intv;
- bwt->sa = (bwtint_t*)calloc(bwt->n_sa, sizeof(bwtint_t));
- if (bwt->sa == 0) {
- fprintf(stderr, "[%s] Fail to allocate %.3fMB memory. Abort!\n", __func__, bwt->n_sa * sizeof(bwtint_t) / 1024.0/1024.0);
- abort();
- }
- // calculate SA value
- isa = 0; sa = bwt->seq_len;
- for (i = 0; i < bwt->seq_len; ++i) {
- if (isa % intv == 0) bwt->sa[isa/intv] = sa;
- --sa;
- isa = bwt_invPsi(bwt, isa);
- }
- if (isa % intv == 0) bwt->sa[isa/intv] = sa;
- bwt->sa[0] = (bwtint_t)-1; // before this line, bwt->sa[0] = bwt->seq_len
-}
-
-bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k)
-{
- bwtint_t sa = 0, mask = bwt->sa_intv - 1;
- while (k & mask) {
- ++sa;
- k = bwt_invPsi(bwt, k);
- }
- /* without setting bwt->sa[0] = -1, the following line should be
- changed to (sa + bwt->sa[k/bwt->sa_intv]) % (bwt->seq_len + 1) */
- return sa + bwt->sa[k/bwt->sa_intv];
-}
-
-static inline int __occ_aux(uint64_t y, int c)
-{
- // reduce nucleotide counting to bits counting
- y = ((c&2)? y : ~y) >> 1 & ((c&1)? y : ~y) & 0x5555555555555555ull;
- // count the number of 1s in y
- y = (y & 0x3333333333333333ull) + (y >> 2 & 0x3333333333333333ull);
- return ((y + (y >> 4)) & 0xf0f0f0f0f0f0f0full) * 0x101010101010101ull >> 56;
-}
-
-inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c)
-{
- bwtint_t n, l, j;
- uint32_t *p;
-
- if (k == bwt->seq_len) return bwt->L2[c+1] - bwt->L2[c];
- if (k == (bwtint_t)(-1)) return 0;
- if (k >= bwt->primary) --k; // because $ is not in bwt
-
- // retrieve Occ at k/OCC_INTERVAL
- n = ((bwtint_t*)(p = bwt_occ_intv(bwt, k)))[c];
- p += sizeof(bwtint_t); // jump to the start of the first BWT cell
-
- // calculate Occ up to the last k/32
- j = k >> 5 << 5;
- for (l = k/OCC_INTERVAL*OCC_INTERVAL; l < j; l += 32, p += 2)
- n += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
-
- // calculate Occ
- n += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~k&31)<<1)) - 1), c);
- if (c == 0) n -= ~k&31; // corrected for the masked bits
-
- return n;
-}
-
-// an analogy to bwt_occ() but more efficient, requiring k <= l
-inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol)
-{
- bwtint_t _k, _l;
- _k = (k >= bwt->primary)? k-1 : k;
- _l = (l >= bwt->primary)? l-1 : l;
- if (_l/OCC_INTERVAL != _k/OCC_INTERVAL || k == (bwtint_t)(-1) || l == (bwtint_t)(-1)) {
- *ok = bwt_occ(bwt, k, c);
- *ol = bwt_occ(bwt, l, c);
- } else {
- bwtint_t m, n, i, j;
- uint32_t *p;
- if (k >= bwt->primary) --k;
- if (l >= bwt->primary) --l;
- n = ((bwtint_t*)(p = bwt_occ_intv(bwt, k)))[c];
- p += sizeof(bwtint_t);
- // calculate *ok
- j = k >> 5 << 5;
- for (i = k/OCC_INTERVAL*OCC_INTERVAL; i < j; i += 32, p += 2)
- n += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
- m = n;
- n += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~k&31)<<1)) - 1), c);
- if (c == 0) n -= ~k&31; // corrected for the masked bits
- *ok = n;
- // calculate *ol
- j = l >> 5 << 5;
- for (; i < j; i += 32, p += 2)
- m += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
- m += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~l&31)<<1)) - 1), c);
- if (c == 0) m -= ~l&31; // corrected for the masked bits
- *ol = m;
- }
-}
-
-#define __occ_aux4(bwt, b) \
- ((bwt)->cnt_table[(b)&0xff] + (bwt)->cnt_table[(b)>>8&0xff] \
- + (bwt)->cnt_table[(b)>>16&0xff] + (bwt)->cnt_table[(b)>>24])
-
-inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
-{
- bwtint_t l, j, x;
- uint32_t *p;
- if (k == (bwtint_t)(-1)) {
- memset(cnt, 0, 4 * sizeof(bwtint_t));
- return;
- }
- if (k >= bwt->primary) --k; // because $ is not in bwt
- p = bwt_occ_intv(bwt, k);
- memcpy(cnt, p, 4 * sizeof(bwtint_t));
- p += sizeof(bwtint_t);
- j = k >> 4 << 4;
- for (l = k / OCC_INTERVAL * OCC_INTERVAL, x = 0; l < j; l += 16, ++p)
- x += __occ_aux4(bwt, *p);
- x += __occ_aux4(bwt, *p & ~((1U<<((~k&15)<<1)) - 1)) - (~k&15);
- cnt[0] += x&0xff; cnt[1] += x>>8&0xff; cnt[2] += x>>16&0xff; cnt[3] += x>>24;
-}
-
-// an analogy to bwt_occ4() but more efficient, requiring k <= l
-inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4])
-{
- bwtint_t _k, _l;
- _k = (k >= bwt->primary)? k-1 : k;
- _l = (l >= bwt->primary)? l-1 : l;
- if (_l/OCC_INTERVAL != _k/OCC_INTERVAL || k == (bwtint_t)(-1) || l == (bwtint_t)(-1)) {
- bwt_occ4(bwt, k, cntk);
- bwt_occ4(bwt, l, cntl);
- } else {
- bwtint_t i, j, x, y;
- uint32_t *p;
- if (k >= bwt->primary) --k; // because $ is not in bwt
- if (l >= bwt->primary) --l;
- p = bwt_occ_intv(bwt, k);
- memcpy(cntk, p, 4 * sizeof(bwtint_t));
- p += sizeof(bwtint_t);
- // prepare cntk[]
- j = k >> 4 << 4;
- for (i = k / OCC_INTERVAL * OCC_INTERVAL, x = 0; i < j; i += 16, ++p)
- x += __occ_aux4(bwt, *p);
- y = x;
- x += __occ_aux4(bwt, *p & ~((1U<<((~k&15)<<1)) - 1)) - (~k&15);
- // calculate cntl[] and finalize cntk[]
- j = l >> 4 << 4;
- for (; i < j; i += 16, ++p) y += __occ_aux4(bwt, *p);
- y += __occ_aux4(bwt, *p & ~((1U<<((~l&15)<<1)) - 1)) - (~l&15);
- memcpy(cntl, cntk, 4 * sizeof(bwtint_t));
- cntk[0] += x&0xff; cntk[1] += x>>8&0xff; cntk[2] += x>>16&0xff; cntk[3] += x>>24;
- cntl[0] += y&0xff; cntl[1] += y>>8&0xff; cntl[2] += y>>16&0xff; cntl[3] += y>>24;
- }
-}
-
-int bwt_match_exact(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *sa_begin, bwtint_t *sa_end)
-{
- bwtint_t k, l, ok, ol;
- int i;
- k = 0; l = bwt->seq_len;
- for (i = len - 1; i >= 0; --i) {
- ubyte_t c = str[i];
- if (c > 3) return 0; // no match
- bwt_2occ(bwt, k - 1, l, c, &ok, &ol);
- k = bwt->L2[c] + ok + 1;
- l = bwt->L2[c] + ol;
- if (k > l) break; // no match
- }
- if (k > l) return 0; // no match
- if (sa_begin) *sa_begin = k;
- if (sa_end) *sa_end = l;
- return l - k + 1;
-}
-
-int bwt_match_exact_alt(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *k0, bwtint_t *l0)
-{
- int i;
- bwtint_t k, l, ok, ol;
- k = *k0; l = *l0;
- for (i = len - 1; i >= 0; --i) {
- ubyte_t c = str[i];
- if (c > 3) return 0; // there is an N here. no match
- bwt_2occ(bwt, k - 1, l, c, &ok, &ol);
- k = bwt->L2[c] + ok + 1;
- l = bwt->L2[c] + ol;
- if (k > l) return 0; // no match
- }
- *k0 = k; *l0 = l;
- return l - k + 1;
-}
-
-/*********************
- * Bidirectional BWT *
- *********************/
-
-void bwt_extend(const bwt_t *bwt, const bwtintv_t *ik, bwtintv_t ok[4], int is_back)
-{
- bwtint_t tk[4], tl[4];
- int i;
- bwt_2occ4(bwt, ik->x[!is_back] - 1, ik->x[!is_back] - 1 + ik->x[2], tk, tl);
- for (i = 0; i != 4; ++i) {
- ok[i].x[!is_back] = bwt->L2[i] + 1 + tk[i];
- ok[i].x[2] = tl[i] - tk[i];
- }
- ok[3].x[is_back] = ik->x[is_back] + (ik->x[!is_back] <= bwt->primary && ik->x[!is_back] + ik->x[2] - 1 >= bwt->primary);
- ok[2].x[is_back] = ok[3].x[is_back] + ok[3].x[2];
- ok[1].x[is_back] = ok[2].x[is_back] + ok[2].x[2];
- ok[0].x[is_back] = ok[1].x[is_back] + ok[1].x[2];
-}
-
-static void bwt_reverse_intvs(bwtintv_v *p)
-{
- if (p->n > 1) {
- int j;
- for (j = 0; j < p->n>>1; ++j) {
- bwtintv_t tmp = p->a[p->n - 1 - j];
- p->a[p->n - 1 - j] = p->a[j];
- p->a[j] = tmp;
- }
- }
-}
-
-int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, bwtintv_v *mem, bwtintv_v *tmpvec[2])
-{
- int i, j, c, ret;
- bwtintv_t ik, ok[4];
- bwtintv_v a[2], *prev, *curr, *swap;
-
- mem->n = 0;
- if (q[x] > 3) return x + 1;
- kv_init(a[0]); kv_init(a[1]);
- prev = tmpvec[0]? tmpvec[0] : &a[0];
- curr = tmpvec[1]? tmpvec[1] : &a[1];
- bwt_set_intv(bwt, q[x], ik);
- ik.info = x + 1;
-
- for (i = x + 1, curr->n = 0; i < len; ++i) { // forward search
- if (q[i] < 4) {
- c = 3 - q[i];
- bwt_extend(bwt, &ik, ok, 0);
- if (ok[c].x[2] != ik.x[2]) // change of the interval size
- kv_push(bwtintv_t, *curr, ik);
- if (ok[c].x[2] == 0) break; // cannot be extended
- ik = ok[c]; ik.info = i + 1;
- } else { // an ambiguous base
- kv_push(bwtintv_t, *curr, ik);
- break; // cannot be extended; in this case, ia[0].info; // this will be the returned value
- swap = curr; curr = prev; prev = swap;
-
- for (i = x - 1; i >= -1; --i) { // backward search for MEMs
- if (q[i] > 3) break;
- c = i < 0? 0 : q[i];
- for (j = 0, curr->n = 0; j < prev->n; ++j) {
- bwtintv_t *p = &prev->a[j];
- bwt_extend(bwt, p, ok, 1);
- if (ok[c].x[2] == 0 || i == -1) { // keep the hit if reaching the beginning or not extended further
- if (curr->n == 0) { // curr->n to make sure there is no longer matches
- if (mem->n == 0 || i + 1 < mem->a[mem->n-1].info>>32) { // skip contained matches
- ik = *p; ik.info |= (uint64_t)(i + 1)<<32;
- kv_push(bwtintv_t, *mem, ik);
- }
- } // otherwise the match is contained in another longer match
- }
- if (ok[c].x[2] && (curr->n == 0 || ok[c].x[2] != curr->a[curr->n-1].x[2])) {
- ok[c].info = p->info;
- kv_push(bwtintv_t, *curr, ok[c]);
- }
- }
- if (curr->n == 0) break;
- swap = curr; curr = prev; prev = swap;
- }
- bwt_reverse_intvs(mem); // s.t. sorted by the start coordinate
-
- if (tmpvec[0] == 0) free(a[0].a);
- if (tmpvec[1] == 0) free(a[1].a);
- return ret;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwt.h
--- a/bwa-0.6.2/bwt.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,130 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008 Genome Research Ltd (GRL).
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-/* Contact: Heng Li */
-
-#ifndef BWA_BWT_H
-#define BWA_BWT_H
-
-#include
-
-// requirement: (OCC_INTERVAL%16 == 0); please DO NOT change this line
-#define OCC_INTERVAL 0x80
-
-#ifndef BWA_UBYTE
-#define BWA_UBYTE
-typedef unsigned char ubyte_t;
-#endif
-
-typedef uint64_t bwtint_t;
-
-typedef struct {
- bwtint_t primary; // S^{-1}(0), or the primary index of BWT
- bwtint_t L2[5]; // C(), cumulative count
- bwtint_t seq_len; // sequence length
- bwtint_t bwt_size; // size of bwt, about seq_len/4
- uint32_t *bwt; // BWT
- // occurance array, separated to two parts
- uint32_t cnt_table[256];
- // suffix array
- int sa_intv;
- bwtint_t n_sa;
- bwtint_t *sa;
-} bwt_t;
-
-typedef struct {
- bwtint_t x[3], info;
-} bwtintv_t;
-
-typedef struct { size_t n, m; bwtintv_t *a; } bwtintv_v;
-
-/* For general OCC_INTERVAL, the following is correct:
-#define bwt_bwt(b, k) ((b)->bwt[(k)/OCC_INTERVAL * (OCC_INTERVAL/(sizeof(uint32_t)*8/2) + sizeof(bwtint_t)/4*4) + sizeof(bwtint_t)/4*4 + (k)%OCC_INTERVAL/16])
-#define bwt_occ_intv(b, k) ((b)->bwt + (k)/OCC_INTERVAL * (OCC_INTERVAL/(sizeof(uint32_t)*8/2) + sizeof(bwtint_t)/4*4)
-*/
-
-// The following two lines are ONLY correct when OCC_INTERVAL==0x80
-#define bwt_bwt(b, k) ((b)->bwt[((k)>>7<<4) + sizeof(bwtint_t) + (((k)&0x7f)>>4)])
-#define bwt_occ_intv(b, k) ((b)->bwt + ((k)>>7<<4))
-
-/* retrieve a character from the $-removed BWT string. Note that
- * bwt_t::bwt is not exactly the BWT string and therefore this macro is
- * called bwt_B0 instead of bwt_B */
-#define bwt_B0(b, k) (bwt_bwt(b, k)>>((~(k)&0xf)<<1)&3)
-
-// inverse Psi function
-#define bwt_invPsi(bwt, k) \
- (((k) == (bwt)->primary)? 0 : \
- ((k) < (bwt)->primary)? \
- (bwt)->L2[bwt_B0(bwt, k)] + bwt_occ(bwt, k, bwt_B0(bwt, k)) \
- : (bwt)->L2[bwt_B0(bwt, (k)-1)] + bwt_occ(bwt, k, bwt_B0(bwt, (k)-1)))
-
-#define bwt_set_intv(bwt, c, ik) ((ik).x[0] = (bwt)->L2[(int)(c)]+1, (ik).x[2] = (bwt)->L2[(int)(c)+1]-(bwt)->L2[(int)(c)], (ik).x[1] = (bwt)->L2[3-(c)]+1, (ik).info = 0)
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- void bwt_dump_bwt(const char *fn, const bwt_t *bwt);
- void bwt_dump_sa(const char *fn, const bwt_t *bwt);
-
- bwt_t *bwt_restore_bwt(const char *fn);
- void bwt_restore_sa(const char *fn, bwt_t *bwt);
-
- void bwt_destroy(bwt_t *bwt);
-
- void bwt_bwtgen(const char *fn_pac, const char *fn_bwt); // from BWT-SW
- void bwt_cal_sa(bwt_t *bwt, int intv);
-
- void bwt_bwtupdate_core(bwt_t *bwt);
-
- inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
- inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
- bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k);
-
- // more efficient version of bwt_occ/bwt_occ4 for retrieving two close Occ values
- void bwt_gen_cnt_table(bwt_t *bwt);
- inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
- inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
-
- int bwt_match_exact(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *sa_begin, bwtint_t *sa_end);
- int bwt_match_exact_alt(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *k0, bwtint_t *l0);
-
- /**
- * Extend bi-SA-interval _ik_
- */
- void bwt_extend(const bwt_t *bwt, const bwtintv_t *ik, bwtintv_t ok[4], int is_back);
-
- /**
- * Given a query _q_, collect potential SMEMs covering position _x_ and store them in _mem_.
- * Return the end of the longest exact match starting from _x_.
- */
- int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, bwtintv_v *mem, bwtintv_v *tmpvec[2]);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwt_gen.c
--- a/bwa-0.6.2/bwt_gen.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1566 +0,0 @@
-/*
-
- BWTConstruct.c BWT-Index Construction
-
- This module constructs BWT and auxiliary data structures.
-
- Copyright (C) 2004, Wong Chi Kwong.
-
- This program is free software; you can redistribute it and/or
- modify it under the terms of the GNU General Public License
- as published by the Free Software Foundation; either version 2
- of the License, or (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-*/
-
-#include
-#include
-#include
-#include
-#include
-#include "QSufSort.h"
-
-typedef uint64_t bgint_t;
-typedef int64_t sbgint_t;
-
-#define ALPHABET_SIZE 4
-#define BIT_PER_CHAR 2
-#define CHAR_PER_WORD 16
-#define CHAR_PER_BYTE 4
-
-#define BITS_IN_WORD 32
-#define BITS_IN_BYTE 8
-#define BYTES_IN_WORD 4
-
-#define ALL_ONE_MASK 0xFFFFFFFF
-#define DNA_OCC_CNT_TABLE_SIZE_IN_WORD 65536
-
-#define BITS_PER_OCC_VALUE 16
-#define OCC_VALUE_PER_WORD 2
-#define OCC_INTERVAL 256
-#define OCC_INTERVAL_MAJOR 65536
-
-#define TRUE 1
-#define FALSE 0
-
-#define BWTINC_INSERT_SORT_NUM_ITEM 7
-
-#define MIN_AVAILABLE_WORD 0x10000
-
-#define average(value1, value2) ( ((value1) & (value2)) + ((value1) ^ (value2)) / 2 )
-#define min(value1, value2) ( ((value1) < (value2)) ? (value1) : (value2) )
-#define max(value1, value2) ( ((value1) > (value2)) ? (value1) : (value2) )
-#define med3(a, b, c) ( ac ? b : a>c ? c : a))
-#define swap(a, b, t); t = a; a = b; b = t;
-#define truncateLeft(value, offset) ( (value) << (offset) >> (offset) )
-#define truncateRight(value, offset) ( (value) >> (offset) << (offset) )
-#define DNA_OCC_SUM_EXCEPTION(sum) ((sum & 0xfefefeff) == 0)
-
-typedef struct BWT {
- bgint_t textLength; // length of the text
- bgint_t inverseSa0; // SA-1[0]
- bgint_t *cumulativeFreq; // cumulative frequency
- unsigned int *bwtCode; // BWT code
- unsigned int *occValue; // Occurrence values stored explicitly
- bgint_t *occValueMajor; // Occurrence values stored explicitly
- unsigned int *decodeTable; // For decoding BWT by table lookup
- bgint_t bwtSizeInWord; // Temporary variable to hold the memory allocated
- bgint_t occSizeInWord; // Temporary variable to hold the memory allocated
- bgint_t occMajorSizeInWord; // Temporary variable to hold the memory allocated
-} BWT;
-
-typedef struct BWTInc {
- BWT *bwt;
- unsigned int numberOfIterationDone;
- bgint_t *cumulativeCountInCurrentBuild;
- bgint_t availableWord;
- bgint_t buildSize;
- bgint_t initialMaxBuildSize;
- bgint_t incMaxBuildSize;
- unsigned int firstCharInLastIteration;
- unsigned int *workingMemory;
- unsigned int *packedText;
- unsigned char *textBuffer;
- unsigned int *packedShift;
-} BWTInc;
-
-static bgint_t TextLengthFromBytePacked(bgint_t bytePackedLength, unsigned int bitPerChar,
- unsigned int lastByteLength)
-{
- return (bytePackedLength - 1) * (BITS_IN_BYTE / bitPerChar) + lastByteLength;
-}
-
-static void initializeVAL(unsigned int *startAddr, const bgint_t length, const unsigned int initValue)
-{
- bgint_t i;
- for (i=0; i>= 2;
- }
- }
-
-}
-// for BWTIncCreate()
-static bgint_t BWTOccValueMajorSizeInWord(const bgint_t numChar)
-{
- bgint_t numOfOccValue;
- unsigned numOfOccIntervalPerMajor;
- numOfOccValue = (numChar + OCC_INTERVAL - 1) / OCC_INTERVAL + 1; // Value at both end for bi-directional encoding
- numOfOccIntervalPerMajor = OCC_INTERVAL_MAJOR / OCC_INTERVAL;
- return (numOfOccValue + numOfOccIntervalPerMajor - 1) / numOfOccIntervalPerMajor * ALPHABET_SIZE;
-}
-// for BWTIncCreate()
-static bgint_t BWTOccValueMinorSizeInWord(const bgint_t numChar)
-{
- bgint_t numOfOccValue;
- numOfOccValue = (numChar + OCC_INTERVAL - 1) / OCC_INTERVAL + 1; // Value at both end for bi-directional encoding
- return (numOfOccValue + OCC_VALUE_PER_WORD - 1) / OCC_VALUE_PER_WORD * ALPHABET_SIZE;
-}
-// for BWTIncCreate()
-static bgint_t BWTResidentSizeInWord(const bgint_t numChar) {
-
- bgint_t numCharRoundUpToOccInterval;
-
- // The $ in BWT at the position of inverseSa0 is not encoded
- numCharRoundUpToOccInterval = (numChar + OCC_INTERVAL - 1) / OCC_INTERVAL * OCC_INTERVAL;
-
- return (numCharRoundUpToOccInterval + CHAR_PER_WORD - 1) / CHAR_PER_WORD;
-
-}
-
-static void BWTIncSetBuildSizeAndTextAddr(BWTInc *bwtInc)
-{
- bgint_t maxBuildSize;
-
- if (bwtInc->bwt->textLength == 0) {
- // initial build
- // Minus 2 because n+1 entries of seq and rank needed for n char
- maxBuildSize = (bwtInc->availableWord - (2 + OCC_INTERVAL / CHAR_PER_WORD) * (sizeof(bgint_t) / 4))
- / (2 * CHAR_PER_WORD + 1) * CHAR_PER_WORD / (sizeof(bgint_t) / 4);
- if (bwtInc->initialMaxBuildSize > 0) {
- bwtInc->buildSize = min(bwtInc->initialMaxBuildSize, maxBuildSize);
- } else {
- bwtInc->buildSize = maxBuildSize;
- }
- } else {
- // Minus 3 because n+1 entries of sorted rank, seq and rank needed for n char
- // Minus numberOfIterationDone because bwt slightly shift to left in each iteration
- maxBuildSize = (bwtInc->availableWord - bwtInc->bwt->bwtSizeInWord - bwtInc->bwt->occSizeInWord
- - (3 + bwtInc->numberOfIterationDone * OCC_INTERVAL / BIT_PER_CHAR) * (sizeof(bgint_t) / 4))
- / 3 / (sizeof(bgint_t) / 4);
- if (maxBuildSize < CHAR_PER_WORD) {
- fprintf(stderr, "BWTIncSetBuildSizeAndTextAddr(): Not enough space allocated to continue construction!\n");
- exit(1);
- }
- if (bwtInc->incMaxBuildSize > 0) {
- bwtInc->buildSize = min(bwtInc->incMaxBuildSize, maxBuildSize);
- } else {
- bwtInc->buildSize = maxBuildSize;
- }
- if (bwtInc->buildSize < CHAR_PER_WORD)
- bwtInc->buildSize = CHAR_PER_WORD;
- }
-
- if (bwtInc->buildSize < CHAR_PER_WORD) {
- fprintf(stderr, "BWTIncSetBuildSizeAndTextAddr(): Not enough space allocated to continue construction!\n");
- exit(1);
- }
-
- bwtInc->buildSize = bwtInc->buildSize / CHAR_PER_WORD * CHAR_PER_WORD;
-
- bwtInc->packedText = bwtInc->workingMemory + 2 * (bwtInc->buildSize + 1) * (sizeof(bgint_t) / 4);
- bwtInc->textBuffer = (unsigned char*)(bwtInc->workingMemory + (bwtInc->buildSize + 1) * (sizeof(bgint_t) / 4));
-}
-
-// for ceilLog2()
-unsigned int leadingZero(const unsigned int input)
-{
- unsigned int l;
- const static unsigned int leadingZero8bit[256] = {8,7,6,6,5,5,5,5,4,4,4,4,4,4,4,4,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,
- 2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,
- 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
- 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
- 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};
-
- if (input & 0xFFFF0000) {
- if (input & 0xFF000000) {
- l = leadingZero8bit[input >> 24];
- } else {
- l = 8 + leadingZero8bit[input >> 16];
- }
- } else {
- if (input & 0x0000FF00) {
- l = 16 + leadingZero8bit[input >> 8];
- } else {
- l = 24 + leadingZero8bit[input];
- }
- }
- return l;
-
-}
-// for BitPerBytePackedChar()
-static unsigned int ceilLog2(const unsigned int input)
-{
- if (input <= 1) return 0;
- return BITS_IN_WORD - leadingZero(input - 1);
-
-}
-// for ConvertBytePackedToWordPacked()
-static unsigned int BitPerBytePackedChar(const unsigned int alphabetSize)
-{
- unsigned int bitPerChar;
- bitPerChar = ceilLog2(alphabetSize);
- // Return the largest number of bit that does not affect packing efficiency
- if (BITS_IN_BYTE / (BITS_IN_BYTE / bitPerChar) > bitPerChar)
- bitPerChar = BITS_IN_BYTE / (BITS_IN_BYTE / bitPerChar);
- return bitPerChar;
-}
-// for ConvertBytePackedToWordPacked()
-static unsigned int BitPerWordPackedChar(const unsigned int alphabetSize)
-{
- return ceilLog2(alphabetSize);
-}
-
-static void ConvertBytePackedToWordPacked(const unsigned char *input, unsigned int *output, const unsigned int alphabetSize,
- const bgint_t textLength)
-{
- bgint_t i;
- unsigned int j, k, c;
- unsigned int bitPerBytePackedChar;
- unsigned int bitPerWordPackedChar;
- unsigned int charPerWord;
- unsigned int charPerByte;
- unsigned int bytePerIteration;
- bgint_t byteProcessed = 0;
- bgint_t wordProcessed = 0;
- unsigned int mask, shift;
-
- unsigned int buffer[BITS_IN_WORD];
-
- bitPerBytePackedChar = BitPerBytePackedChar(alphabetSize);
- bitPerWordPackedChar = BitPerWordPackedChar(alphabetSize);
- charPerByte = BITS_IN_BYTE / bitPerBytePackedChar;
- charPerWord = BITS_IN_WORD / bitPerWordPackedChar;
-
- bytePerIteration = charPerWord / charPerByte;
- mask = truncateRight(ALL_ONE_MASK, BITS_IN_WORD - bitPerWordPackedChar);
- shift = BITS_IN_WORD - BITS_IN_BYTE + bitPerBytePackedChar - bitPerWordPackedChar;
-
- while ((wordProcessed + 1) * charPerWord < textLength) {
-
- k = 0;
- for (i=0; i> bitPerWordPackedChar * i;
- }
- output[wordProcessed] = c;
- wordProcessed++;
-
- }
-
- k = 0;
- for (i=0; i < (textLength - wordProcessed * charPerWord - 1) / charPerByte + 1; i++) {
- c = (unsigned int)input[byteProcessed] << shift;
- for (j=0; j> bitPerWordPackedChar * i;
- }
- output[wordProcessed] = c;
-}
-
-BWT *BWTCreate(const bgint_t textLength, unsigned int *decodeTable)
-{
- BWT *bwt;
-
- bwt = (BWT*)calloc(1, sizeof(BWT));
-
- bwt->textLength = 0;
-
- bwt->cumulativeFreq = (bgint_t*)calloc((ALPHABET_SIZE + 1), sizeof(bgint_t));
- initializeVAL_bg(bwt->cumulativeFreq, ALPHABET_SIZE + 1, 0);
-
- bwt->bwtSizeInWord = 0;
-
- // Generate decode tables
- if (decodeTable == NULL) {
- bwt->decodeTable = (unsigned*)calloc(DNA_OCC_CNT_TABLE_SIZE_IN_WORD, sizeof(unsigned int));
- GenerateDNAOccCountTable(bwt->decodeTable);
- } else {
- bwt->decodeTable = decodeTable;
- }
-
- bwt->occMajorSizeInWord = BWTOccValueMajorSizeInWord(textLength);
- bwt->occValueMajor = (bgint_t*)calloc(bwt->occMajorSizeInWord, sizeof(bgint_t));
-
- bwt->occSizeInWord = 0;
- bwt->occValue = NULL;
-
- return bwt;
-}
-
-BWTInc *BWTIncCreate(const bgint_t textLength, unsigned int initialMaxBuildSize, unsigned int incMaxBuildSize)
-{
- BWTInc *bwtInc;
- unsigned int i, n_iter;
-
- if (textLength < incMaxBuildSize) incMaxBuildSize = textLength;
- if (textLength < initialMaxBuildSize) initialMaxBuildSize = textLength;
-
- bwtInc = (BWTInc*)calloc(1, sizeof(BWTInc));
- bwtInc->numberOfIterationDone = 0;
- bwtInc->bwt = BWTCreate(textLength, NULL);
- bwtInc->initialMaxBuildSize = initialMaxBuildSize;
- bwtInc->incMaxBuildSize = incMaxBuildSize;
- bwtInc->cumulativeCountInCurrentBuild = (bgint_t*)calloc((ALPHABET_SIZE + 1), sizeof(bgint_t));
- initializeVAL_bg(bwtInc->cumulativeCountInCurrentBuild, ALPHABET_SIZE + 1, 0);
-
- // Build frequently accessed data
- bwtInc->packedShift = (unsigned*)calloc(CHAR_PER_WORD, sizeof(unsigned int));
- for (i=0; ipackedShift[i] = BITS_IN_WORD - (i+1) * BIT_PER_CHAR;
-
- n_iter = (textLength - initialMaxBuildSize) / incMaxBuildSize + 1;
- bwtInc->availableWord = BWTResidentSizeInWord(textLength) + BWTOccValueMinorSizeInWord(textLength) // minimal memory requirement
- + OCC_INTERVAL / BIT_PER_CHAR * n_iter * 2 * (sizeof(bgint_t) / 4) // buffer at the end of occ array
- + incMaxBuildSize/5 * 3 * (sizeof(bgint_t) / 4); // space for the 3 temporary arrays in each iteration
- if (bwtInc->availableWord < MIN_AVAILABLE_WORD) bwtInc->availableWord = MIN_AVAILABLE_WORD; // lh3: otherwise segfaul when availableWord is too small
- fprintf(stderr, "[%s] textLength=%ld, availableWord=%ld\n", __func__, (long)textLength, (long)bwtInc->availableWord);
- bwtInc->workingMemory = (unsigned*)calloc(bwtInc->availableWord, BYTES_IN_WORD);
-
- return bwtInc;
-}
-// for BWTIncConstruct()
-static void BWTIncPutPackedTextToRank(const unsigned int *packedText, bgint_t* __restrict rank,
- bgint_t* __restrict cumulativeCount, const bgint_t numChar)
-{
- bgint_t i;
- unsigned int j;
- unsigned int c, t;
- unsigned int packedMask;
- bgint_t rankIndex;
- bgint_t lastWord;
- unsigned int numCharInLastWord;
-
- lastWord = (numChar - 1) / CHAR_PER_WORD;
- numCharInLastWord = numChar - lastWord * CHAR_PER_WORD;
-
- packedMask = ALL_ONE_MASK >> (BITS_IN_WORD - BIT_PER_CHAR);
- rankIndex = numChar - 1;
-
- t = packedText[lastWord] >> (BITS_IN_WORD - numCharInLastWord * BIT_PER_CHAR);
- for (i=0; i>= BIT_PER_CHAR;
- }
-
- for (i=lastWord; i--;) { // loop from lastWord - 1 to 0
- t = packedText[i];
- for (j=0; j>= BIT_PER_CHAR;
- }
- }
-
- // Convert occurrence to cumulativeCount
- cumulativeCount[2] += cumulativeCount[1];
- cumulativeCount[3] += cumulativeCount[2];
- cumulativeCount[4] += cumulativeCount[3];
-}
-
-
-static void ForwardDNAAllOccCountNoLimit(const unsigned int* dna, const bgint_t index,
- bgint_t* __restrict occCount, const unsigned int* dnaDecodeTable)
-{
- static const unsigned int truncateRightMask[16] = { 0x00000000, 0xC0000000, 0xF0000000, 0xFC000000,
- 0xFF000000, 0xFFC00000, 0xFFF00000, 0xFFFC0000,
- 0xFFFF0000, 0xFFFFC000, 0xFFFFF000, 0xFFFFFC00,
- 0xFFFFFF00, 0xFFFFFFC0, 0xFFFFFFF0, 0xFFFFFFFC };
-
- bgint_t iteration, i;
- unsigned int wordToCount, charToCount;
- unsigned int j, c, sum;
-
- occCount[0] = 0;
- occCount[1] = 0;
- occCount[2] = 0;
- occCount[3] = 0;
-
- iteration = index / 256;
- wordToCount = (index - iteration * 256) / 16;
- charToCount = index - iteration * 256 - wordToCount * 16;
-
- for (i=0; i> 16];
- sum += dnaDecodeTable[*dna & 0x0000FFFF];
- dna++;
- }
- if (!DNA_OCC_SUM_EXCEPTION(sum)) {
- occCount[0] += sum & 0x000000FF; sum >>= 8;
- occCount[1] += sum & 0x000000FF; sum >>= 8;
- occCount[2] += sum & 0x000000FF; sum >>= 8;
- occCount[3] += sum;
- } else {
- // only some or all of the 3 bits are on
- // in reality, only one of the four cases are possible
- if (sum == 0x00000100) {
- occCount[0] += 256;
- } else if (sum == 0x00010000) {
- occCount[1] += 256;
- } else if (sum == 0x01000000) {
- occCount[2] += 256;
- } else if (sum == 0x00000000) {
- occCount[3] += 256;
- } else {
- fprintf(stderr, "ForwardDNAAllOccCountNoLimit(): DNA occ sum exception!\n");
- exit(1);
- }
- }
-
- }
-
- sum = 0;
- for (j=0; j> 16];
- sum += dnaDecodeTable[*dna & 0x0000FFFF];
- dna++;
- }
-
- if (charToCount > 0) {
- c = *dna & truncateRightMask[charToCount]; // increase count of 'a' by 16 - c;
- sum += dnaDecodeTable[c >> 16];
- sum += dnaDecodeTable[c & 0xFFFF];
- sum += charToCount - 16; // decrease count of 'a' by 16 - positionToProcess
- }
-
- occCount[0] += sum & 0x000000FF; sum >>= 8;
- occCount[1] += sum & 0x000000FF; sum >>= 8;
- occCount[2] += sum & 0x000000FF; sum >>= 8;
- occCount[3] += sum;
-}
-
-static void BWTIncBuildPackedBwt(const bgint_t *relativeRank, unsigned int* __restrict bwt, const bgint_t numChar,
- const bgint_t *cumulativeCount, const unsigned int *packedShift) {
-
- bgint_t i, r;
- unsigned int c;
- bgint_t previousRank, currentRank;
- bgint_t wordIndex, charIndex;
- bgint_t inverseSa0;
-
- inverseSa0 = previousRank = relativeRank[0];
-
- for (i=1; i<=numChar; i++) {
- currentRank = relativeRank[i];
- // previousRank > cumulativeCount[c] because $ is one of the char
- c = (previousRank > cumulativeCount[1]) + (previousRank > cumulativeCount[2])
- + (previousRank > cumulativeCount[3]);
- // set bwt for currentRank
- if (c > 0) {
- // c <> 'a'
- r = currentRank;
- if (r > inverseSa0) {
- // - 1 because $ at inverseSa0 is not encoded
- r--;
- }
- wordIndex = r / CHAR_PER_WORD;
- charIndex = r - wordIndex * CHAR_PER_WORD;
- bwt[wordIndex] |= c << packedShift[charIndex];
- }
- previousRank = currentRank;
- }
-}
-
-static inline bgint_t BWTOccValueExplicit(const BWT *bwt, const bgint_t occIndexExplicit,
- const unsigned int character)
-{
- bgint_t occIndexMajor;
-
- occIndexMajor = occIndexExplicit * OCC_INTERVAL / OCC_INTERVAL_MAJOR;
-
- if (occIndexExplicit % OCC_VALUE_PER_WORD == 0) {
- return bwt->occValueMajor[occIndexMajor * ALPHABET_SIZE + character] +
- (bwt->occValue[occIndexExplicit / OCC_VALUE_PER_WORD * ALPHABET_SIZE + character] >> 16);
-
- } else {
- return bwt->occValueMajor[occIndexMajor * ALPHABET_SIZE + character] +
- (bwt->occValue[occIndexExplicit / OCC_VALUE_PER_WORD * ALPHABET_SIZE + character] & 0x0000FFFF);
- }
-}
-
-
-static unsigned int ForwardDNAOccCount(const unsigned int* dna, const unsigned int index, const unsigned int character,
- const unsigned int* dnaDecodeTable)
-{
- static const unsigned int truncateRightMask[16] = { 0x00000000, 0xC0000000, 0xF0000000, 0xFC000000,
- 0xFF000000, 0xFFC00000, 0xFFF00000, 0xFFFC0000,
- 0xFFFF0000, 0xFFFFC000, 0xFFFFF000, 0xFFFFFC00,
- 0xFFFFFF00, 0xFFFFFFC0, 0xFFFFFFF0, 0xFFFFFFFC };
-
- unsigned int wordToCount, charToCount;
- unsigned int i, c;
- unsigned int sum = 0;
-
- wordToCount = index / 16;
- charToCount = index - wordToCount * 16;
-
- for (i=0; i> 16];
- sum += dnaDecodeTable[dna[i] & 0x0000FFFF];
- }
-
- if (charToCount > 0) {
- c = dna[i] & truncateRightMask[charToCount]; // increase count of 'a' by 16 - c;
- sum += dnaDecodeTable[c >> 16];
- sum += dnaDecodeTable[c & 0xFFFF];
- sum += charToCount - 16; // decrease count of 'a' by 16 - positionToProcess
- }
-
- return (sum >> (character * 8)) & 0x000000FF;
-
-}
-
-static unsigned int BackwardDNAOccCount(const unsigned int* dna, const unsigned int index, const unsigned int character,
- const unsigned int* dnaDecodeTable)
-{
- static const unsigned int truncateLeftMask[16] = { 0x00000000, 0x00000003, 0x0000000F, 0x0000003F,
- 0x000000FF, 0x000003FF, 0x00000FFF, 0x00003FFF,
- 0x0000FFFF, 0x0003FFFF, 0x000FFFFF, 0x003FFFFF,
- 0x00FFFFFF, 0x03FFFFFF, 0x0FFFFFFF, 0x3FFFFFFF };
-
- unsigned int wordToCount, charToCount;
- unsigned int i, c;
- unsigned int sum = 0;
-
- wordToCount = index / 16;
- charToCount = index - wordToCount * 16;
-
- dna -= wordToCount + 1;
-
- if (charToCount > 0) {
- c = *dna & truncateLeftMask[charToCount]; // increase count of 'a' by 16 - c;
- sum += dnaDecodeTable[c >> 16];
- sum += dnaDecodeTable[c & 0xFFFF];
- sum += charToCount - 16; // decrease count of 'a' by 16 - positionToProcess
- }
-
- for (i=0; i> 16];
- sum += dnaDecodeTable[*dna & 0x0000FFFF];
- }
-
- return (sum >> (character * 8)) & 0x000000FF;
-
-}
-
-bgint_t BWTOccValue(const BWT *bwt, bgint_t index, const unsigned int character)
-{
- bgint_t occValue;
- bgint_t occExplicitIndex, occIndex;
-
- // $ is supposed to be positioned at inverseSa0 but it is not encoded
- // therefore index is subtracted by 1 for adjustment
- if (index > bwt->inverseSa0)
- index--;
-
- occExplicitIndex = (index + OCC_INTERVAL / 2 - 1) / OCC_INTERVAL; // Bidirectional encoding
- occIndex = occExplicitIndex * OCC_INTERVAL;
- occValue = BWTOccValueExplicit(bwt, occExplicitIndex, character);
-
- if (occIndex == index)
- return occValue;
-
- if (occIndex < index) {
- return occValue + ForwardDNAOccCount(bwt->bwtCode + occIndex / CHAR_PER_WORD, index - occIndex, character, bwt->decodeTable);
- } else {
- return occValue - BackwardDNAOccCount(bwt->bwtCode + occIndex / CHAR_PER_WORD, occIndex - index, character, bwt->decodeTable);
- }
-}
-
-static bgint_t BWTIncGetAbsoluteRank(BWT *bwt, bgint_t* __restrict absoluteRank, bgint_t* __restrict seq,
- const unsigned int *packedText, const bgint_t numChar,
- const bgint_t* cumulativeCount, const unsigned int firstCharInLastIteration)
-{
- bgint_t saIndex;
- bgint_t lastWord;
- unsigned int packedMask;
- bgint_t i;
- unsigned int c, t, j;
- bgint_t rankIndex;
- unsigned int shift;
- bgint_t seqIndexFromStart[ALPHABET_SIZE];
- bgint_t seqIndexFromEnd[ALPHABET_SIZE];
-
- for (i=0; i> shift;
- saIndex = bwt->inverseSa0;
- rankIndex = numChar - 1;
-
- lastWord = numChar / CHAR_PER_WORD;
- for (i=lastWord; i--;) { // loop from lastWord - 1 to 0
- t = packedText[i];
- for (j=0; jcumulativeFreq[c] + BWTOccValue(bwt, saIndex, c) + 1;
- // A counting sort using the first character of suffix is done here
- // If rank > inverseSa0 -> fill seq from end, otherwise fill seq from start -> to leave the right entry for inverseSa0
- if (saIndex > bwt->inverseSa0) {
- seq[seqIndexFromEnd[c]] = rankIndex;
- absoluteRank[seqIndexFromEnd[c]] = saIndex;
- seqIndexFromEnd[c]--;
- } else {
- seq[seqIndexFromStart[c]] = rankIndex;
- absoluteRank[seqIndexFromStart[c]] = saIndex;
- seqIndexFromStart[c]++;
- }
- rankIndex--;
- t >>= BIT_PER_CHAR;
- }
- }
-
- absoluteRank[seqIndexFromStart[firstCharInLastIteration]] = bwt->inverseSa0; // representing the substring of all preceding characters
- seq[seqIndexFromStart[firstCharInLastIteration]] = numChar;
-
- return seqIndexFromStart[firstCharInLastIteration];
-}
-
-static void BWTIncSortKey(bgint_t* __restrict key, bgint_t* __restrict seq, const bgint_t numItem)
-{
- #define EQUAL_KEY_THRESHOLD 4 // Partition for equal key if data array size / the number of data with equal value with pivot < EQUAL_KEY_THRESHOLD
-
- int64_t lowIndex, highIndex, midIndex;
- int64_t lowPartitionIndex, highPartitionIndex;
- int64_t lowStack[32], highStack[32];
- int stackDepth;
- int64_t i, j;
- bgint_t tempSeq, tempKey;
- int64_t numberOfEqualKey;
-
- if (numItem < 2) return;
-
- stackDepth = 0;
-
- lowIndex = 0;
- highIndex = numItem - 1;
-
- for (;;) {
-
- for (;;) {
-
- // Sort small array of data
- if (highIndex - lowIndex < BWTINC_INSERT_SORT_NUM_ITEM) { // Insertion sort on smallest arrays
- for (i=lowIndex+1; i<=highIndex; i++) {
- tempSeq = seq[i];
- tempKey = key[i];
- for (j = i; j > lowIndex && key[j-1] > tempKey; j--) {
- seq[j] = seq[j-1];
- key[j] = key[j-1];
- }
- if (j != i) {
- seq[j] = tempSeq;
- key[j] = tempKey;
- }
- }
- break;
- }
-
- // Choose pivot as median of the lowest, middle, and highest data; sort the three data
-
- midIndex = average(lowIndex, highIndex);
- if (key[lowIndex] > key[midIndex]) {
- tempSeq = seq[lowIndex];
- tempKey = key[lowIndex];
- seq[lowIndex] = seq[midIndex];
- key[lowIndex] = key[midIndex];
- seq[midIndex] = tempSeq;
- key[midIndex] = tempKey;
- }
- if (key[lowIndex] > key[highIndex]) {
- tempSeq = seq[lowIndex];
- tempKey = key[lowIndex];
- seq[lowIndex] = seq[highIndex];
- key[lowIndex] = key[highIndex];
- seq[highIndex] = tempSeq;
- key[highIndex] = tempKey;
- }
- if (key[midIndex] > key[highIndex]) {
- tempSeq = seq[midIndex];
- tempKey = key[midIndex];
- seq[midIndex] = seq[highIndex];
- key[midIndex] = key[highIndex];
- seq[highIndex] = tempSeq;
- key[highIndex] = tempKey;
- }
-
- // Partition data
-
- numberOfEqualKey = 0;
-
- lowPartitionIndex = lowIndex + 1;
- highPartitionIndex = highIndex - 1;
-
- for (;;) {
- while (lowPartitionIndex <= highPartitionIndex && key[lowPartitionIndex] <= key[midIndex]) {
- numberOfEqualKey += (key[lowPartitionIndex] == key[midIndex]);
- lowPartitionIndex++;
- }
- while (lowPartitionIndex < highPartitionIndex) {
- if (key[midIndex] >= key[highPartitionIndex]) {
- numberOfEqualKey += (key[midIndex] == key[highPartitionIndex]);
- break;
- }
- highPartitionIndex--;
- }
- if (lowPartitionIndex >= highPartitionIndex) {
- break;
- }
- tempSeq = seq[lowPartitionIndex];
- tempKey = key[lowPartitionIndex];
- seq[lowPartitionIndex] = seq[highPartitionIndex];
- key[lowPartitionIndex] = key[highPartitionIndex];
- seq[highPartitionIndex] = tempSeq;
- key[highPartitionIndex] = tempKey;
- if (highPartitionIndex == midIndex) {
- // partition key has been moved
- midIndex = lowPartitionIndex;
- }
- lowPartitionIndex++;
- highPartitionIndex--;
- }
-
- // Adjust the partition index
- highPartitionIndex = lowPartitionIndex;
- lowPartitionIndex--;
-
- // move the partition key to end of low partition
- tempSeq = seq[midIndex];
- tempKey = key[midIndex];
- seq[midIndex] = seq[lowPartitionIndex];
- key[midIndex] = key[lowPartitionIndex];
- seq[lowPartitionIndex] = tempSeq;
- key[lowPartitionIndex] = tempKey;
-
- if (highIndex - lowIndex + BWTINC_INSERT_SORT_NUM_ITEM <= EQUAL_KEY_THRESHOLD * numberOfEqualKey) {
-
- // Many keys = partition key; separate the equal key data from the lower partition
-
- midIndex = lowIndex;
-
- for (;;) {
- while (midIndex < lowPartitionIndex && key[midIndex] < key[lowPartitionIndex]) {
- midIndex++;
- }
- while (midIndex < lowPartitionIndex && key[lowPartitionIndex] == key[lowPartitionIndex - 1]) {
- lowPartitionIndex--;
- }
- if (midIndex >= lowPartitionIndex) {
- break;
- }
- tempSeq = seq[midIndex];
- tempKey = key[midIndex];
- seq[midIndex] = seq[lowPartitionIndex - 1];
- key[midIndex] = key[lowPartitionIndex - 1];
- seq[lowPartitionIndex - 1] = tempSeq;
- key[lowPartitionIndex - 1] = tempKey;
- midIndex++;
- lowPartitionIndex--;
- }
-
- }
-
- if (lowPartitionIndex - lowIndex > highIndex - highPartitionIndex) {
- // put the larger partition to stack
- lowStack[stackDepth] = lowIndex;
- highStack[stackDepth] = lowPartitionIndex - 1;
- stackDepth++;
- // sort the smaller partition first
- lowIndex = highPartitionIndex;
- } else {
- // put the larger partition to stack
- lowStack[stackDepth] = highPartitionIndex;
- highStack[stackDepth] = highIndex;
- stackDepth++;
- // sort the smaller partition first
- if (lowPartitionIndex > lowIndex) {
- highIndex = lowPartitionIndex - 1;
- } else {
- // all keys in the partition equals to the partition key
- break;
- }
- }
- continue;
- }
-
- // Pop a range from stack
- if (stackDepth > 0) {
- stackDepth--;
- lowIndex = lowStack[stackDepth];
- highIndex = highStack[stackDepth];
- continue;
- } else return;
- }
-}
-
-
-static void BWTIncBuildRelativeRank(bgint_t* __restrict sortedRank, bgint_t* __restrict seq,
- bgint_t* __restrict relativeRank, const bgint_t numItem,
- bgint_t oldInverseSa0, const bgint_t *cumulativeCount)
-{
- bgint_t i, c;
- bgint_t s, r;
- bgint_t lastRank, lastIndex;
- bgint_t oldInverseSa0RelativeRank = 0;
- bgint_t freq;
-
- lastIndex = numItem;
- lastRank = sortedRank[numItem];
- if (lastRank > oldInverseSa0) {
- sortedRank[numItem]--; // to prepare for merging; $ is not encoded in bwt
- }
- s = seq[numItem];
- relativeRank[s] = numItem;
- if (lastRank == oldInverseSa0) {
- oldInverseSa0RelativeRank = numItem;
- oldInverseSa0++; // so that this segment of code is not run again
- lastRank++; // so that oldInverseSa0 become a sorted group with 1 item
- }
-
- c = ALPHABET_SIZE - 1;
- freq = cumulativeCount[c];
-
- for (i=numItem; i--;) { // from numItem - 1 to 0
- r = sortedRank[i];
- if (r > oldInverseSa0)
- sortedRank[i]--; // to prepare for merging; $ is not encoded in bwt
- s = seq[i];
- if (i < freq) {
- if (lastIndex >= freq)
- lastRank++; // to trigger the group across alphabet boundary to be split
- c--;
- freq = cumulativeCount[c];
- }
- if (r == lastRank) {
- relativeRank[s] = lastIndex;
- } else {
- if (i == lastIndex - 1) {
- if (lastIndex < numItem && (sbgint_t)seq[lastIndex + 1] < 0) {
- seq[lastIndex] = seq[lastIndex + 1] - 1;
- } else {
- seq[lastIndex] = (bgint_t)-1;
- }
- }
- lastIndex = i;
- lastRank = r;
- relativeRank[s] = i;
- if (r == oldInverseSa0) {
- oldInverseSa0RelativeRank = i;
- oldInverseSa0++; // so that this segment of code is not run again
- lastRank++; // so that oldInverseSa0 become a sorted group with 1 item
- }
- }
- }
-
-}
-
-static void BWTIncBuildBwt(unsigned int* insertBwt, const bgint_t *relativeRank, const bgint_t numChar,
- const bgint_t *cumulativeCount)
-{
- unsigned int c;
- bgint_t i;
- bgint_t previousRank, currentRank;
-
- previousRank = relativeRank[0];
-
- for (i=1; i<=numChar; i++) {
- currentRank = relativeRank[i];
- c = (previousRank >= cumulativeCount[1]) + (previousRank >= cumulativeCount[2])
- + (previousRank >= cumulativeCount[3]);
- insertBwt[currentRank] = c;
- previousRank = currentRank;
- }
-}
-
-static void BWTIncMergeBwt(const bgint_t *sortedRank, const unsigned int* oldBwt, const unsigned int *insertBwt,
- unsigned int* __restrict mergedBwt, const bgint_t numOldBwt, const bgint_t numInsertBwt)
-{
- unsigned int bitsInWordMinusBitPerChar;
- bgint_t leftShift, rightShift;
- bgint_t o;
- bgint_t oIndex, iIndex, mIndex;
- bgint_t mWord, mChar, oWord, oChar;
- bgint_t numInsert;
-
- bitsInWordMinusBitPerChar = BITS_IN_WORD - BIT_PER_CHAR;
-
- oIndex = 0;
- iIndex = 0;
- mIndex = 0;
-
- mWord = 0;
- mChar = 0;
-
- mergedBwt[0] = 0; // this can be cleared as merged Bwt slightly shift to the left in each iteration
-
- while (oIndex < numOldBwt) {
-
- // copy from insertBwt
- while (iIndex <= numInsertBwt && sortedRank[iIndex] <= oIndex) {
- if (sortedRank[iIndex] != 0) { // special value to indicate that this is for new inverseSa0
- mergedBwt[mWord] |= insertBwt[iIndex] << (BITS_IN_WORD - (mChar + 1) * BIT_PER_CHAR);
- mIndex++;
- mChar++;
- if (mChar == CHAR_PER_WORD) {
- mChar = 0;
- mWord++;
- mergedBwt[mWord] = 0; // no need to worry about crossing mergedBwt boundary
- }
- }
- iIndex++;
- }
-
- // Copy from oldBwt to mergedBwt
- if (iIndex <= numInsertBwt) {
- o = sortedRank[iIndex];
- } else {
- o = numOldBwt;
- }
- numInsert = o - oIndex;
-
- oWord = oIndex / CHAR_PER_WORD;
- oChar = oIndex - oWord * CHAR_PER_WORD;
- if (oChar > mChar) {
- leftShift = (oChar - mChar) * BIT_PER_CHAR;
- rightShift = (CHAR_PER_WORD + mChar - oChar) * BIT_PER_CHAR;
- mergedBwt[mWord] = mergedBwt[mWord]
- | (oldBwt[oWord] << (oChar * BIT_PER_CHAR) >> (mChar * BIT_PER_CHAR))
- | (oldBwt[oWord+1] >> rightShift);
- oIndex += min(numInsert, CHAR_PER_WORD - mChar);
- while (o > oIndex) {
- oWord++;
- mWord++;
- mergedBwt[mWord] = (oldBwt[oWord] << leftShift) | (oldBwt[oWord+1] >> rightShift);
- oIndex += CHAR_PER_WORD;
- }
- } else if (oChar < mChar) {
- rightShift = (mChar - oChar) * BIT_PER_CHAR;
- leftShift = (CHAR_PER_WORD + oChar - mChar) * BIT_PER_CHAR;
- mergedBwt[mWord] = mergedBwt[mWord]
- | (oldBwt[oWord] << (oChar * BIT_PER_CHAR) >> (mChar * BIT_PER_CHAR));
- oIndex += min(numInsert, CHAR_PER_WORD - mChar);
- while (o > oIndex) {
- oWord++;
- mWord++;
- mergedBwt[mWord] = (oldBwt[oWord-1] << leftShift) | (oldBwt[oWord] >> rightShift);
- oIndex += CHAR_PER_WORD;
- }
- } else { // oChar == mChar
- mergedBwt[mWord] = mergedBwt[mWord] | truncateLeft(oldBwt[oWord], mChar * BIT_PER_CHAR);
- oIndex += min(numInsert, CHAR_PER_WORD - mChar);
- while (o > oIndex) {
- oWord++;
- mWord++;
- mergedBwt[mWord] = oldBwt[oWord];
- oIndex += CHAR_PER_WORD;
- }
- }
- oIndex = o;
- mIndex += numInsert;
-
- // Clear the trailing garbage in mergedBwt
- mWord = mIndex / CHAR_PER_WORD;
- mChar = mIndex - mWord * CHAR_PER_WORD;
- if (mChar == 0) {
- mergedBwt[mWord] = 0;
- } else {
- mergedBwt[mWord] = truncateRight(mergedBwt[mWord], (BITS_IN_WORD - mChar * BIT_PER_CHAR));
- }
-
- }
-
- // copy from insertBwt
- while (iIndex <= numInsertBwt) {
- if (sortedRank[iIndex] != 0) {
- mergedBwt[mWord] |= insertBwt[iIndex] << (BITS_IN_WORD - (mChar + 1) * BIT_PER_CHAR);
- mIndex++;
- mChar++;
- if (mChar == CHAR_PER_WORD) {
- mChar = 0;
- mWord++;
- mergedBwt[mWord] = 0; // no need to worry about crossing mergedBwt boundary
- }
- }
- iIndex++;
- }
-}
-
-void BWTClearTrailingBwtCode(BWT *bwt)
-{
- bgint_t bwtResidentSizeInWord;
- bgint_t wordIndex, offset;
- bgint_t i;
-
- bwtResidentSizeInWord = BWTResidentSizeInWord(bwt->textLength);
-
- wordIndex = bwt->textLength / CHAR_PER_WORD;
- offset = (bwt->textLength - wordIndex * CHAR_PER_WORD) * BIT_PER_CHAR;
- if (offset > 0) {
- bwt->bwtCode[wordIndex] = truncateRight(bwt->bwtCode[wordIndex], BITS_IN_WORD - offset);
- } else {
- if (wordIndex < bwtResidentSizeInWord) {
- bwt->bwtCode[wordIndex] = 0;
- }
- }
-
- for (i=wordIndex+1; ibwtCode[i] = 0;
- }
-}
-
-
-void BWTGenerateOccValueFromBwt(const unsigned int* bwt, unsigned int* __restrict occValue,
- bgint_t* __restrict occValueMajor,
- const bgint_t textLength, const unsigned int* decodeTable)
-{
- bgint_t numberOfOccValueMajor, numberOfOccValue;
- unsigned int wordBetweenOccValue;
- bgint_t numberOfOccIntervalPerMajor;
- unsigned int c;
- bgint_t i, j;
- bgint_t occMajorIndex;
- bgint_t occIndex, bwtIndex;
- bgint_t sum; // perhaps unsigned is big enough
- bgint_t tempOccValue0[ALPHABET_SIZE], tempOccValue1[ALPHABET_SIZE];
-
- wordBetweenOccValue = OCC_INTERVAL / CHAR_PER_WORD;
-
- // Calculate occValue
- numberOfOccValue = (textLength + OCC_INTERVAL - 1) / OCC_INTERVAL + 1; // Value at both end for bi-directional encoding
- numberOfOccIntervalPerMajor = OCC_INTERVAL_MAJOR / OCC_INTERVAL;
- numberOfOccValueMajor = (numberOfOccValue + numberOfOccIntervalPerMajor - 1) / numberOfOccIntervalPerMajor;
-
- tempOccValue0[0] = 0;
- tempOccValue0[1] = 0;
- tempOccValue0[2] = 0;
- tempOccValue0[3] = 0;
- occValueMajor[0] = 0;
- occValueMajor[1] = 0;
- occValueMajor[2] = 0;
- occValueMajor[3] = 0;
-
- occIndex = 0;
- bwtIndex = 0;
- for (occMajorIndex=1; occMajorIndex> 16];
- sum += decodeTable[c & 0x0000FFFF];
- bwtIndex++;
- }
- if (!DNA_OCC_SUM_EXCEPTION(sum)) {
- tempOccValue1[0] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue1[1] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue1[2] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue1[3] += sum;
- } else {
- if (sum == 0x00000100) {
- tempOccValue1[0] += 256;
- } else if (sum == 0x00010000) {
- tempOccValue1[1] += 256;
- } else if (sum == 0x01000000) {
- tempOccValue1[2] += 256;
- } else {
- tempOccValue1[3] += 256;
- }
- }
- occValue[occIndex * 4 + 0] = (tempOccValue0[0] << 16) | tempOccValue1[0];
- occValue[occIndex * 4 + 1] = (tempOccValue0[1] << 16) | tempOccValue1[1];
- occValue[occIndex * 4 + 2] = (tempOccValue0[2] << 16) | tempOccValue1[2];
- occValue[occIndex * 4 + 3] = (tempOccValue0[3] << 16) | tempOccValue1[3];
- tempOccValue0[0] = tempOccValue1[0];
- tempOccValue0[1] = tempOccValue1[1];
- tempOccValue0[2] = tempOccValue1[2];
- tempOccValue0[3] = tempOccValue1[3];
- sum = 0;
-
- occIndex++;
-
- for (j=0; j> 16];
- sum += decodeTable[c & 0x0000FFFF];
- bwtIndex++;
- }
- if (!DNA_OCC_SUM_EXCEPTION(sum)) {
- tempOccValue0[0] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue0[1] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue0[2] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue0[3] += sum;
- } else {
- if (sum == 0x00000100) {
- tempOccValue0[0] += 256;
- } else if (sum == 0x00010000) {
- tempOccValue0[1] += 256;
- } else if (sum == 0x01000000) {
- tempOccValue0[2] += 256;
- } else {
- tempOccValue0[3] += 256;
- }
- }
- }
-
- occValueMajor[occMajorIndex * 4 + 0] = occValueMajor[(occMajorIndex - 1) * 4 + 0] + tempOccValue0[0];
- occValueMajor[occMajorIndex * 4 + 1] = occValueMajor[(occMajorIndex - 1) * 4 + 1] + tempOccValue0[1];
- occValueMajor[occMajorIndex * 4 + 2] = occValueMajor[(occMajorIndex - 1) * 4 + 2] + tempOccValue0[2];
- occValueMajor[occMajorIndex * 4 + 3] = occValueMajor[(occMajorIndex - 1) * 4 + 3] + tempOccValue0[3];
- tempOccValue0[0] = 0;
- tempOccValue0[1] = 0;
- tempOccValue0[2] = 0;
- tempOccValue0[3] = 0;
-
- }
-
- while (occIndex < (numberOfOccValue-1)/2) {
- sum = 0;
- tempOccValue1[0] = tempOccValue0[0];
- tempOccValue1[1] = tempOccValue0[1];
- tempOccValue1[2] = tempOccValue0[2];
- tempOccValue1[3] = tempOccValue0[3];
- for (j=0; j> 16];
- sum += decodeTable[c & 0x0000FFFF];
- bwtIndex++;
- }
- if (!DNA_OCC_SUM_EXCEPTION(sum)) {
- tempOccValue1[0] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue1[1] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue1[2] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue1[3] += sum;
- } else {
- if (sum == 0x00000100) {
- tempOccValue1[0] += 256;
- } else if (sum == 0x00010000) {
- tempOccValue1[1] += 256;
- } else if (sum == 0x01000000) {
- tempOccValue1[2] += 256;
- } else {
- tempOccValue1[3] += 256;
- }
- }
- occValue[occIndex * 4 + 0] = (tempOccValue0[0] << 16) | tempOccValue1[0];
- occValue[occIndex * 4 + 1] = (tempOccValue0[1] << 16) | tempOccValue1[1];
- occValue[occIndex * 4 + 2] = (tempOccValue0[2] << 16) | tempOccValue1[2];
- occValue[occIndex * 4 + 3] = (tempOccValue0[3] << 16) | tempOccValue1[3];
- tempOccValue0[0] = tempOccValue1[0];
- tempOccValue0[1] = tempOccValue1[1];
- tempOccValue0[2] = tempOccValue1[2];
- tempOccValue0[3] = tempOccValue1[3];
- sum = 0;
- occIndex++;
-
- for (j=0; j> 16];
- sum += decodeTable[c & 0x0000FFFF];
- bwtIndex++;
- }
- if (!DNA_OCC_SUM_EXCEPTION(sum)) {
- tempOccValue0[0] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue0[1] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue0[2] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue0[3] += sum;
- } else {
- if (sum == 0x00000100) {
- tempOccValue0[0] += 256;
- } else if (sum == 0x00010000) {
- tempOccValue0[1] += 256;
- } else if (sum == 0x01000000) {
- tempOccValue0[2] += 256;
- } else {
- tempOccValue0[3] += 256;
- }
- }
- }
-
- sum = 0;
- tempOccValue1[0] = tempOccValue0[0];
- tempOccValue1[1] = tempOccValue0[1];
- tempOccValue1[2] = tempOccValue0[2];
- tempOccValue1[3] = tempOccValue0[3];
-
- if (occIndex * 2 < numberOfOccValue - 1) {
- for (j=0; j> 16];
- sum += decodeTable[c & 0x0000FFFF];
- bwtIndex++;
- }
- if (!DNA_OCC_SUM_EXCEPTION(sum)) {
- tempOccValue1[0] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue1[1] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue1[2] += (sum & 0x000000FF); sum >>= 8;
- tempOccValue1[3] += sum;
- } else {
- if (sum == 0x00000100) {
- tempOccValue1[0] += 256;
- } else if (sum == 0x00010000) {
- tempOccValue1[1] += 256;
- } else if (sum == 0x01000000) {
- tempOccValue1[2] += 256;
- } else {
- tempOccValue1[3] += 256;
- }
- }
- }
-
- occValue[occIndex * 4 + 0] = (tempOccValue0[0] << 16) | tempOccValue1[0];
- occValue[occIndex * 4 + 1] = (tempOccValue0[1] << 16) | tempOccValue1[1];
- occValue[occIndex * 4 + 2] = (tempOccValue0[2] << 16) | tempOccValue1[2];
- occValue[occIndex * 4 + 3] = (tempOccValue0[3] << 16) | tempOccValue1[3];
-
-}
-
-static void BWTIncConstruct(BWTInc *bwtInc, const bgint_t numChar)
-{
- unsigned int i;
- bgint_t mergedBwtSizeInWord, mergedOccSizeInWord;
- unsigned int firstCharInThisIteration;
-
- bgint_t *relativeRank, *seq, *sortedRank;
- unsigned int *insertBwt, *mergedBwt;
- bgint_t newInverseSa0RelativeRank, oldInverseSa0RelativeRank, newInverseSa0;
-
- mergedBwtSizeInWord = BWTResidentSizeInWord(bwtInc->bwt->textLength + numChar);
- mergedOccSizeInWord = BWTOccValueMinorSizeInWord(bwtInc->bwt->textLength + numChar);
-
- initializeVAL_bg(bwtInc->cumulativeCountInCurrentBuild, ALPHABET_SIZE + 1, 0);
-
- if (bwtInc->bwt->textLength == 0) { // Initial build
-
- // Set address
- seq = (bgint_t*)bwtInc->workingMemory;
- relativeRank = seq + bwtInc->buildSize + 1;
- // mergedBwt and packedTex may share memory
- mergedBwt = insertBwt = bwtInc->workingMemory + bwtInc->availableWord - mergedBwtSizeInWord; // build in place
-
- assert((void*)(relativeRank + bwtInc->buildSize + 1) <= (void*)bwtInc->packedText);
- assert((void*)(relativeRank + bwtInc->buildSize + 1) <= (void*)mergedBwt);
-
- // ->packedText is not used any more and may be overwritten by mergedBwt
- BWTIncPutPackedTextToRank(bwtInc->packedText, relativeRank, bwtInc->cumulativeCountInCurrentBuild, numChar);
-
- firstCharInThisIteration = relativeRank[0];
- relativeRank[numChar] = 0;
-
- // Sort suffix
- QSufSortSuffixSort((qsint_t*)relativeRank, (qsint_t*)seq, (qsint_t)numChar, (qsint_t)ALPHABET_SIZE - 1, 0, FALSE);
- newInverseSa0 = relativeRank[0];
-
- // Clear BWT area
- initializeVAL(insertBwt, mergedBwtSizeInWord, 0);
-
- // Build BWT
- BWTIncBuildPackedBwt(relativeRank, insertBwt, numChar, bwtInc->cumulativeCountInCurrentBuild, bwtInc->packedShift);
-
- // so that the cumulativeCount is not deducted
- bwtInc->firstCharInLastIteration = ALPHABET_SIZE;
-
- } else { // Incremental build
- // Set address
- sortedRank = (bgint_t*)bwtInc->workingMemory;
- seq = sortedRank + bwtInc->buildSize + 1;
- insertBwt = (unsigned*)seq; // insertBwt and seq share memory
- // relativeRank and ->packedText may share memory
- relativeRank = seq + bwtInc->buildSize + 1;
-
- assert((void*)relativeRank <= (void*)bwtInc->packedText);
-
- // Store the first character of this iteration
- firstCharInThisIteration = bwtInc->packedText[0] >> (BITS_IN_WORD - BIT_PER_CHAR);
-
- // Count occurrence of input text
- ForwardDNAAllOccCountNoLimit(bwtInc->packedText, numChar, bwtInc->cumulativeCountInCurrentBuild + 1, bwtInc->bwt->decodeTable);
- // Add the first character of the previous iteration to represent the inverseSa0 of the previous iteration
- bwtInc->cumulativeCountInCurrentBuild[bwtInc->firstCharInLastIteration + 1]++;
- bwtInc->cumulativeCountInCurrentBuild[2] += bwtInc->cumulativeCountInCurrentBuild[1];
- bwtInc->cumulativeCountInCurrentBuild[3] += bwtInc->cumulativeCountInCurrentBuild[2];
- bwtInc->cumulativeCountInCurrentBuild[4] += bwtInc->cumulativeCountInCurrentBuild[3];
-
- // Get rank of new suffix among processed suffix
- // The seq array is built into ALPHABET_SIZE + 2 groups; ALPHABET_SIZE groups + 1 group divided into 2 by inverseSa0 + inverseSa0 as 1 group
- // ->packedText is not used any more and will be overwritten by relativeRank
- oldInverseSa0RelativeRank = BWTIncGetAbsoluteRank(bwtInc->bwt, sortedRank, seq, bwtInc->packedText,
- numChar, bwtInc->cumulativeCountInCurrentBuild, bwtInc->firstCharInLastIteration);
-
- // Sort rank by ALPHABET_SIZE + 2 groups (or ALPHABET_SIZE + 1 groups when inverseSa0 sit on the border of a group)
- for (i=0; icumulativeCountInCurrentBuild[i] > oldInverseSa0RelativeRank ||
- bwtInc->cumulativeCountInCurrentBuild[i+1] <= oldInverseSa0RelativeRank) {
- BWTIncSortKey(sortedRank + bwtInc->cumulativeCountInCurrentBuild[i], seq + bwtInc->cumulativeCountInCurrentBuild[i], bwtInc->cumulativeCountInCurrentBuild[i+1] - bwtInc->cumulativeCountInCurrentBuild[i]);
- } else {
- if (bwtInc->cumulativeCountInCurrentBuild[i] < oldInverseSa0RelativeRank) {
- BWTIncSortKey(sortedRank + bwtInc->cumulativeCountInCurrentBuild[i], seq + bwtInc->cumulativeCountInCurrentBuild[i], oldInverseSa0RelativeRank - bwtInc->cumulativeCountInCurrentBuild[i]);
- }
- if (bwtInc->cumulativeCountInCurrentBuild[i+1] > oldInverseSa0RelativeRank + 1) {
- BWTIncSortKey(sortedRank + oldInverseSa0RelativeRank + 1, seq + oldInverseSa0RelativeRank + 1, bwtInc->cumulativeCountInCurrentBuild[i+1] - oldInverseSa0RelativeRank - 1);
- }
- }
- }
-
- // build relative rank; sortedRank is updated for merging to cater for the fact that $ is not encoded in bwt
- // the cumulative freq information is used to make sure that inverseSa0 and suffix beginning with different characters are kept in different unsorted groups)
- BWTIncBuildRelativeRank(sortedRank, seq, relativeRank, numChar, bwtInc->bwt->inverseSa0, bwtInc->cumulativeCountInCurrentBuild);
- assert(relativeRank[numChar] == oldInverseSa0RelativeRank);
-
- // Sort suffix
- QSufSortSuffixSort((qsint_t*)relativeRank, (qsint_t*)seq, (qsint_t)numChar, (qsint_t)numChar, 1, TRUE);
-
- newInverseSa0RelativeRank = relativeRank[0];
- newInverseSa0 = sortedRank[newInverseSa0RelativeRank] + newInverseSa0RelativeRank;
-
- sortedRank[newInverseSa0RelativeRank] = 0; // a special value so that this is skipped in the merged bwt
-
- // Build BWT; seq is overwritten by insertBwt
- BWTIncBuildBwt(insertBwt, relativeRank, numChar, bwtInc->cumulativeCountInCurrentBuild);
-
- // Merge BWT; relativeRank may be overwritten by mergedBwt
- mergedBwt = bwtInc->workingMemory + bwtInc->availableWord - mergedBwtSizeInWord
- - bwtInc->numberOfIterationDone * OCC_INTERVAL / BIT_PER_CHAR * (sizeof(bgint_t) / 4); // minus numberOfIteration * occInterval to create a buffer for merging
- assert(mergedBwt >= insertBwt + numChar);
- BWTIncMergeBwt(sortedRank, bwtInc->bwt->bwtCode, insertBwt, mergedBwt, bwtInc->bwt->textLength, numChar);
- }
-
- // Build auxiliary structure and update info and pointers in BWT
- bwtInc->bwt->textLength += numChar;
- bwtInc->bwt->bwtCode = mergedBwt;
- bwtInc->bwt->bwtSizeInWord = mergedBwtSizeInWord;
- bwtInc->bwt->occSizeInWord = mergedOccSizeInWord;
- assert(mergedBwt >= bwtInc->workingMemory + mergedOccSizeInWord);
-
- bwtInc->bwt->occValue = mergedBwt - mergedOccSizeInWord;
-
- BWTClearTrailingBwtCode(bwtInc->bwt);
- BWTGenerateOccValueFromBwt(bwtInc->bwt->bwtCode, bwtInc->bwt->occValue, bwtInc->bwt->occValueMajor,
- bwtInc->bwt->textLength, bwtInc->bwt->decodeTable);
-
- bwtInc->bwt->inverseSa0 = newInverseSa0;
-
- bwtInc->bwt->cumulativeFreq[1] += bwtInc->cumulativeCountInCurrentBuild[1] - (bwtInc->firstCharInLastIteration <= 0);
- bwtInc->bwt->cumulativeFreq[2] += bwtInc->cumulativeCountInCurrentBuild[2] - (bwtInc->firstCharInLastIteration <= 1);
- bwtInc->bwt->cumulativeFreq[3] += bwtInc->cumulativeCountInCurrentBuild[3] - (bwtInc->firstCharInLastIteration <= 2);
- bwtInc->bwt->cumulativeFreq[4] += bwtInc->cumulativeCountInCurrentBuild[4] - (bwtInc->firstCharInLastIteration <= 3);
-
- bwtInc->firstCharInLastIteration = firstCharInThisIteration;
-
- // Set build size and text address for the next build
- BWTIncSetBuildSizeAndTextAddr(bwtInc);
- bwtInc->numberOfIterationDone++;
-
-}
-
-BWTInc *BWTIncConstructFromPacked(const char *inputFileName, bgint_t initialMaxBuildSize, bgint_t incMaxBuildSize)
-{
-
- FILE *packedFile;
- bgint_t packedFileLen;
- bgint_t totalTextLength;
- bgint_t textToLoad, textSizeInByte;
- bgint_t processedTextLength;
- unsigned char lastByteLength;
-
- BWTInc *bwtInc;
-
- packedFile = (FILE*)fopen(inputFileName, "rb");
-
- if (packedFile == NULL) {
- fprintf(stderr, "BWTIncConstructFromPacked() : Cannot open inputFileName!\n");
- exit(1);
- }
-
- fseek(packedFile, -1, SEEK_END);
- packedFileLen = ftell(packedFile);
- fread(&lastByteLength, sizeof(unsigned char), 1, packedFile);
- totalTextLength = TextLengthFromBytePacked(packedFileLen, BIT_PER_CHAR, lastByteLength);
-
- bwtInc = BWTIncCreate(totalTextLength, initialMaxBuildSize, incMaxBuildSize);
-
- BWTIncSetBuildSizeAndTextAddr(bwtInc);
-
- if (bwtInc->buildSize > totalTextLength) {
- textToLoad = totalTextLength;
- } else {
- textToLoad = totalTextLength - ((totalTextLength - bwtInc->buildSize + CHAR_PER_WORD - 1) / CHAR_PER_WORD * CHAR_PER_WORD);
- }
- textSizeInByte = textToLoad / CHAR_PER_BYTE; // excluded the odd byte
-
- fseek(packedFile, -2, SEEK_CUR);
- fseek(packedFile, -((long)textSizeInByte), SEEK_CUR);
- fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte + 1, packedFile);
- fseek(packedFile, -((long)textSizeInByte + 1), SEEK_CUR);
-
- ConvertBytePackedToWordPacked(bwtInc->textBuffer, bwtInc->packedText, ALPHABET_SIZE, textToLoad);
- BWTIncConstruct(bwtInc, textToLoad);
-
- processedTextLength = textToLoad;
-
- while (processedTextLength < totalTextLength) {
- textToLoad = bwtInc->buildSize / CHAR_PER_WORD * CHAR_PER_WORD;
- if (textToLoad > totalTextLength - processedTextLength) {
- textToLoad = totalTextLength - processedTextLength;
- }
- textSizeInByte = textToLoad / CHAR_PER_BYTE;
- fseek(packedFile, -((long)textSizeInByte), SEEK_CUR);
- fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte, packedFile);
- fseek(packedFile, -((long)textSizeInByte), SEEK_CUR);
- ConvertBytePackedToWordPacked(bwtInc->textBuffer, bwtInc->packedText, ALPHABET_SIZE, textToLoad);
- BWTIncConstruct(bwtInc, textToLoad);
- processedTextLength += textToLoad;
- if (bwtInc->numberOfIterationDone % 10 == 0) {
- fprintf(stderr, "[BWTIncConstructFromPacked] %lu iterations done. %lu characters processed.\n",
- (long)bwtInc->numberOfIterationDone, (long)processedTextLength);
- }
- }
- return bwtInc;
-}
-
-void BWTFree(BWT *bwt)
-{
- if (bwt == 0) return;
- free(bwt->cumulativeFreq);
- free(bwt->bwtCode);
- free(bwt->occValue);
- free(bwt->occValueMajor);
- free(bwt->decodeTable);
- free(bwt);
-}
-
-void BWTIncFree(BWTInc *bwtInc)
-{
- if (bwtInc == 0) return;
- free(bwtInc->bwt);
- free(bwtInc->workingMemory);
- free(bwtInc);
-}
-
-static bgint_t BWTFileSizeInWord(const bgint_t numChar)
-{
- // The $ in BWT at the position of inverseSa0 is not encoded
- return (numChar + CHAR_PER_WORD - 1) / CHAR_PER_WORD;
-}
-
-void BWTSaveBwtCodeAndOcc(const BWT *bwt, const char *bwtFileName, const char *occValueFileName)
-{
- FILE *bwtFile;
-/* FILE *occValueFile; */
- bgint_t bwtLength;
-
- bwtFile = (FILE*)fopen(bwtFileName, "wb");
- if (bwtFile == NULL) {
- fprintf(stderr, "BWTSaveBwtCodeAndOcc(): Cannot open BWT code file!\n");
- exit(1);
- }
-
- fwrite(&bwt->inverseSa0, sizeof(bgint_t), 1, bwtFile);
- fwrite(bwt->cumulativeFreq + 1, sizeof(bgint_t), ALPHABET_SIZE, bwtFile);
- bwtLength = BWTFileSizeInWord(bwt->textLength);
- fwrite(bwt->bwtCode, sizeof(unsigned int), bwtLength, bwtFile);
- fclose(bwtFile);
-}
-
-void bwt_bwtgen(const char *fn_pac, const char *fn_bwt)
-{
- BWTInc *bwtInc;
- bwtInc = BWTIncConstructFromPacked(fn_pac, 10000000, 10000000);
- printf("[bwt_gen] Finished constructing BWT in %u iterations.\n", bwtInc->numberOfIterationDone);
- BWTSaveBwtCodeAndOcc(bwtInc->bwt, fn_bwt, 0);
- BWTIncFree(bwtInc);
-}
-
-int bwt_bwtgen_main(int argc, char *argv[])
-{
- if (argc < 3) {
- fprintf(stderr, "Usage: bwtgen \n");
- return 1;
- }
- bwt_bwtgen(argv[1], argv[2]);
- return 0;
-}
-
-#ifdef MAIN_BWT_GEN
-
-int main(int argc, char *argv[])
-{
- return bwt_bwtgen_main(argc, argv);
-}
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwt_lite.c
--- a/bwa-0.6.2/bwt_lite.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
-#include
-#include
-#include
-#include "bwt_lite.h"
-
-int is_sa(const uint8_t *T, uint32_t *SA, int n);
-int is_bwt(uint8_t *T, int n);
-
-bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq)
-{
- bwtl_t *b;
- int i;
- b = (bwtl_t*)calloc(1, sizeof(bwtl_t));
- b->seq_len = len;
-
- { // calculate b->bwt
- uint8_t *s;
- b->sa = (uint32_t*)calloc(len + 1, 4);
- is_sa(seq, b->sa, len);
- s = (uint8_t*)calloc(len + 1, 1);
- for (i = 0; i <= len; ++i) {
- if (b->sa[i] == 0) b->primary = i;
- else s[i] = seq[b->sa[i] - 1];
- }
- for (i = b->primary; i < len; ++i) s[i] = s[i + 1];
- b->bwt_size = (len + 15) / 16;
- b->bwt = (uint32_t*)calloc(b->bwt_size, 4);
- for (i = 0; i < len; ++i)
- b->bwt[i>>4] |= s[i] << ((15 - (i&15)) << 1);
- free(s);
- }
- { // calculate b->occ
- uint32_t c[4];
- b->n_occ = (len + 15) / 16 * 4;
- b->occ = (uint32_t*)calloc(b->n_occ, 4);
- memset(c, 0, 16);
- for (i = 0; i < len; ++i) {
- if (i % 16 == 0)
- memcpy(b->occ + (i/16) * 4, c, 16);
- ++c[bwtl_B0(b, i)];
- }
- memcpy(b->L2+1, c, 16);
- for (i = 2; i < 5; ++i) b->L2[i] += b->L2[i-1];
- }
- { // generate cnt_table
- for (i = 0; i != 256; ++i) {
- u_int32_t j, x = 0;
- for (j = 0; j != 4; ++j)
- x |= (((i&3) == j) + ((i>>2&3) == j) + ((i>>4&3) == j) + (i>>6 == j)) << (j<<3);
- b->cnt_table[i] = x;
- }
- }
- return b;
-}
-inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c)
-{
- uint32_t n, b;
- if (k == bwt->seq_len) return bwt->L2[c+1] - bwt->L2[c];
- if (k == (uint32_t)(-1)) return 0;
- if (k >= bwt->primary) --k; // because $ is not in bwt
- n = bwt->occ[k/16<<2|c];
- b = bwt->bwt[k/16] & ~((1U<<((15-(k&15))<<1)) - 1);
- n += (bwt->cnt_table[b&0xff] + bwt->cnt_table[b>>8&0xff]
- + bwt->cnt_table[b>>16&0xff] + bwt->cnt_table[b>>24]) >> (c<<3) & 0xff;
- if (c == 0) n -= 15 - (k&15); // corrected for the masked bits
- return n;
-}
-inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4])
-{
- uint32_t x, b;
- if (k == (uint32_t)(-1)) {
- memset(cnt, 0, 16);
- return;
- }
- if (k >= bwt->primary) --k; // because $ is not in bwt
- memcpy(cnt, bwt->occ + (k>>4<<2), 16);
- b = bwt->bwt[k>>4] & ~((1U<<((~k&15)<<1)) - 1);
- x = bwt->cnt_table[b&0xff] + bwt->cnt_table[b>>8&0xff]
- + bwt->cnt_table[b>>16&0xff] + bwt->cnt_table[b>>24];
- x -= 15 - (k&15);
- cnt[0] += x&0xff; cnt[1] += x>>8&0xff; cnt[2] += x>>16&0xff; cnt[3] += x>>24;
-}
-inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4])
-{
- bwtl_occ4(bwt, k, cntk);
- bwtl_occ4(bwt, l, cntl);
-}
-void bwtl_destroy(bwtl_t *bwt)
-{
- if (bwt) {
- free(bwt->occ); free(bwt->bwt); free(bwt->sa);
- free(bwt);
- }
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwt_lite.h
--- a/bwa-0.6.2/bwt_lite.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-#ifndef BWT_LITE_H_
-#define BWT_LITE_H_
-
-#include
-
-typedef struct {
- uint32_t seq_len, bwt_size, n_occ;
- uint32_t primary;
- uint32_t *bwt, *occ, *sa, L2[5];
- uint32_t cnt_table[256];
-} bwtl_t;
-
-#define bwtl_B0(b, k) ((b)->bwt[(k)>>4]>>((~(k)&0xf)<<1)&3)
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq);
- inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c);
- inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]);
- inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]);
- void bwtl_destroy(bwtl_t *bwt);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwtaln.c
--- a/bwa-0.6.2/bwtaln.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,356 +0,0 @@
-#include
-#include
-#include
-#include
-#include
-#include
-#include
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
-#include "bwtaln.h"
-#include "bwtgap.h"
-#include "utils.h"
-
-#ifdef HAVE_PTHREAD
-#include
-#endif
-
-gap_opt_t *gap_init_opt()
-{
- gap_opt_t *o;
- o = (gap_opt_t*)calloc(1, sizeof(gap_opt_t));
- /* IMPORTANT: s_mm*10 should be about the average base error
- rate. Voilating this requirement will break pairing! */
- o->s_mm = 3; o->s_gapo = 11; o->s_gape = 4;
- o->max_diff = -1; o->max_gapo = 1; o->max_gape = 6;
- o->indel_end_skip = 5; o->max_del_occ = 10; o->max_entries = 2000000;
- o->mode = BWA_MODE_GAPE | BWA_MODE_COMPREAD;
- o->seed_len = 32; o->max_seed_diff = 2;
- o->fnr = 0.04;
- o->n_threads = 1;
- o->max_top2 = 30;
- o->trim_qual = 0;
- return o;
-}
-
-int bwa_cal_maxdiff(int l, double err, double thres)
-{
- double elambda = exp(-l * err);
- double sum, y = 1.0;
- int k, x = 1;
- for (k = 1, sum = elambda; k < 1000; ++k) {
- y *= l * err;
- x *= k;
- sum += elambda * y / x;
- if (1.0 - sum < thres) return k;
- }
- return 2;
-}
-
-// width must be filled as zero
-int bwt_cal_width(const bwt_t *bwt, int len, const ubyte_t *str, bwt_width_t *width)
-{
- bwtint_t k, l, ok, ol;
- int i, bid;
- bid = 0;
- k = 0; l = bwt->seq_len;
- for (i = 0; i < len; ++i) {
- ubyte_t c = str[i];
- if (c < 4) {
- bwt_2occ(bwt, k - 1, l, c, &ok, &ol);
- k = bwt->L2[c] + ok + 1;
- l = bwt->L2[c] + ol;
- }
- if (k > l || c > 3) { // then restart
- k = 0;
- l = bwt->seq_len;
- ++bid;
- }
- width[i].w = l - k + 1;
- width[i].bid = bid;
- }
- width[len].w = 0;
- width[len].bid = ++bid;
- return bid;
-}
-
-void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt, int n_seqs, bwa_seq_t *seqs, const gap_opt_t *opt)
-{
- int i, j, max_l = 0, max_len;
- gap_stack_t *stack;
- bwt_width_t *w, *seed_w;
- gap_opt_t local_opt = *opt;
-
- // initiate priority stack
- for (i = max_len = 0; i != n_seqs; ++i)
- if (seqs[i].len > max_len) max_len = seqs[i].len;
- if (opt->fnr > 0.0) local_opt.max_diff = bwa_cal_maxdiff(max_len, BWA_AVG_ERR, opt->fnr);
- if (local_opt.max_diff < local_opt.max_gapo) local_opt.max_gapo = local_opt.max_diff;
- stack = gap_init_stack(local_opt.max_diff, local_opt.max_gapo, local_opt.max_gape, &local_opt);
-
- seed_w = (bwt_width_t*)calloc(opt->seed_len+1, sizeof(bwt_width_t));
- w = 0;
- for (i = 0; i != n_seqs; ++i) {
- bwa_seq_t *p = seqs + i;
-#ifdef HAVE_PTHREAD
- if (i % opt->n_threads != tid) continue;
-#endif
- p->sa = 0; p->type = BWA_TYPE_NO_MATCH; p->c1 = p->c2 = 0; p->n_aln = 0; p->aln = 0;
- if (max_l < p->len) {
- max_l = p->len;
- w = (bwt_width_t*)realloc(w, (max_l + 1) * sizeof(bwt_width_t));
- memset(w, 0, (max_l + 1) * sizeof(bwt_width_t));
- }
- bwt_cal_width(bwt, p->len, p->seq, w);
- if (opt->fnr > 0.0) local_opt.max_diff = bwa_cal_maxdiff(p->len, BWA_AVG_ERR, opt->fnr);
- local_opt.seed_len = opt->seed_len < p->len? opt->seed_len : 0x7fffffff;
- if (p->len > opt->seed_len)
- bwt_cal_width(bwt, opt->seed_len, p->seq + (p->len - opt->seed_len), seed_w);
- // core function
- for (j = 0; j < p->len; ++j) // we need to complement
- p->seq[j] = p->seq[j] > 3? 4 : 3 - p->seq[j];
- p->aln = bwt_match_gap(bwt, p->len, p->seq, w, p->len <= opt->seed_len? 0 : seed_w, &local_opt, &p->n_aln, stack);
- // clean up the unused data in the record
- free(p->name); free(p->seq); free(p->rseq); free(p->qual);
- p->name = 0; p->seq = p->rseq = p->qual = 0;
- }
- free(seed_w); free(w);
- gap_destroy_stack(stack);
-}
-
-#ifdef HAVE_PTHREAD
-typedef struct {
- int tid;
- bwt_t *bwt;
- int n_seqs;
- bwa_seq_t *seqs;
- const gap_opt_t *opt;
-} thread_aux_t;
-
-static void *worker(void *data)
-{
- thread_aux_t *d = (thread_aux_t*)data;
- bwa_cal_sa_reg_gap(d->tid, d->bwt, d->n_seqs, d->seqs, d->opt);
- return 0;
-}
-#endif
-
-bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa)
-{
- bwa_seqio_t *ks;
- if (mode & BWA_MODE_BAM) { // open BAM
- int which = 0;
- if (mode & BWA_MODE_BAM_SE) which |= 4;
- if (mode & BWA_MODE_BAM_READ1) which |= 1;
- if (mode & BWA_MODE_BAM_READ2) which |= 2;
- if (which == 0) which = 7; // then read all reads
- ks = bwa_bam_open(fn_fa, which);
- } else ks = bwa_seq_open(fn_fa);
- return ks;
-}
-
-void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
-{
- int i, n_seqs, tot_seqs = 0;
- bwa_seq_t *seqs;
- bwa_seqio_t *ks;
- clock_t t;
- bwt_t *bwt;
-
- // initialization
- ks = bwa_open_reads(opt->mode, fn_fa);
-
- { // load BWT
- char *str = (char*)calloc(strlen(prefix) + 10, 1);
- strcpy(str, prefix); strcat(str, ".bwt"); bwt = bwt_restore_bwt(str);
- free(str);
- }
-
- // core loop
- err_fwrite(opt, sizeof(gap_opt_t), 1, stdout);
- while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt->mode, opt->trim_qual)) != 0) {
- tot_seqs += n_seqs;
- t = clock();
-
- fprintf(stderr, "[bwa_aln_core] calculate SA coordinate... ");
-
-#ifdef HAVE_PTHREAD
- if (opt->n_threads <= 1) { // no multi-threading at all
- bwa_cal_sa_reg_gap(0, bwt, n_seqs, seqs, opt);
- } else {
- pthread_t *tid;
- pthread_attr_t attr;
- thread_aux_t *data;
- int j;
- pthread_attr_init(&attr);
- pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
- data = (thread_aux_t*)calloc(opt->n_threads, sizeof(thread_aux_t));
- tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
- for (j = 0; j < opt->n_threads; ++j) {
- data[j].tid = j; data[j].bwt = bwt;
- data[j].n_seqs = n_seqs; data[j].seqs = seqs; data[j].opt = opt;
- pthread_create(&tid[j], &attr, worker, data + j);
- }
- for (j = 0; j < opt->n_threads; ++j) pthread_join(tid[j], 0);
- free(data); free(tid);
- }
-#else
- bwa_cal_sa_reg_gap(0, bwt, n_seqs, seqs, opt);
-#endif
-
- fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
-
- t = clock();
- fprintf(stderr, "[bwa_aln_core] write to the disk... ");
- for (i = 0; i < n_seqs; ++i) {
- bwa_seq_t *p = seqs + i;
- err_fwrite(&p->n_aln, 4, 1, stdout);
- if (p->n_aln) err_fwrite(p->aln, sizeof(bwt_aln1_t), p->n_aln, stdout);
- }
- fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
-
- bwa_free_read_seq(n_seqs, seqs);
- fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
- }
-
- // destroy
- bwt_destroy(bwt);
- bwa_seq_close(ks);
-}
-
-char *bwa_infer_prefix(const char *hint)
-{
- char *prefix;
- int l_hint;
- FILE *fp;
- l_hint = strlen(hint);
- prefix = malloc(l_hint + 3 + 4 + 1);
- strcpy(prefix, hint);
- strcpy(prefix + l_hint, ".64.bwt");
- if ((fp = fopen(prefix, "rb")) != 0) {
- fclose(fp);
- prefix[l_hint + 3] = 0;
- return prefix;
- } else {
- strcpy(prefix + l_hint, ".bwt");
- if ((fp = fopen(prefix, "rb")) == 0) {
- free(prefix);
- return 0;
- } else {
- fclose(fp);
- prefix[l_hint] = 0;
- return prefix;
- }
- }
-}
-
-int bwa_aln(int argc, char *argv[])
-{
- int c, opte = -1;
- gap_opt_t *opt;
- char *prefix;
-
- opt = gap_init_opt();
- while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:cLR:m:t:NM:O:E:q:f:b012IYB:")) >= 0) {
- switch (c) {
- case 'n':
- if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1;
- else opt->max_diff = atoi(optarg), opt->fnr = -1.0;
- break;
- case 'o': opt->max_gapo = atoi(optarg); break;
- case 'e': opte = atoi(optarg); break;
- case 'M': opt->s_mm = atoi(optarg); break;
- case 'O': opt->s_gapo = atoi(optarg); break;
- case 'E': opt->s_gape = atoi(optarg); break;
- case 'd': opt->max_del_occ = atoi(optarg); break;
- case 'i': opt->indel_end_skip = atoi(optarg); break;
- case 'l': opt->seed_len = atoi(optarg); break;
- case 'k': opt->max_seed_diff = atoi(optarg); break;
- case 'm': opt->max_entries = atoi(optarg); break;
- case 't': opt->n_threads = atoi(optarg); break;
- case 'L': opt->mode |= BWA_MODE_LOGGAP; break;
- case 'R': opt->max_top2 = atoi(optarg); break;
- case 'q': opt->trim_qual = atoi(optarg); break;
- case 'c': opt->mode &= ~BWA_MODE_COMPREAD; break;
- case 'N': opt->mode |= BWA_MODE_NONSTOP; opt->max_top2 = 0x7fffffff; break;
- case 'f': xreopen(optarg, "wb", stdout); break;
- case 'b': opt->mode |= BWA_MODE_BAM; break;
- case '0': opt->mode |= BWA_MODE_BAM_SE; break;
- case '1': opt->mode |= BWA_MODE_BAM_READ1; break;
- case '2': opt->mode |= BWA_MODE_BAM_READ2; break;
- case 'I': opt->mode |= BWA_MODE_IL13; break;
- case 'Y': opt->mode |= BWA_MODE_CFY; break;
- case 'B': opt->mode |= atoi(optarg) << 24; break;
- default: return 1;
- }
- }
- if (opte > 0) {
- opt->max_gape = opte;
- opt->mode &= ~BWA_MODE_GAPE;
- }
-
- if (optind + 2 > argc) {
- fprintf(stderr, "\n");
- fprintf(stderr, "Usage: bwa aln [options] \n\n");
- fprintf(stderr, "Options: -n NUM max #diff (int) or missing prob under %.2f err rate (float) [%.2f]\n",
- BWA_AVG_ERR, opt->fnr);
- fprintf(stderr, " -o INT maximum number or fraction of gap opens [%d]\n", opt->max_gapo);
- fprintf(stderr, " -e INT maximum number of gap extensions, -1 for disabling long gaps [-1]\n");
- fprintf(stderr, " -i INT do not put an indel within INT bp towards the ends [%d]\n", opt->indel_end_skip);
- fprintf(stderr, " -d INT maximum occurrences for extending a long deletion [%d]\n", opt->max_del_occ);
- fprintf(stderr, " -l INT seed length [%d]\n", opt->seed_len);
- fprintf(stderr, " -k INT maximum differences in the seed [%d]\n", opt->max_seed_diff);
- fprintf(stderr, " -m INT maximum entries in the queue [%d]\n", opt->max_entries);
- fprintf(stderr, " -t INT number of threads [%d]\n", opt->n_threads);
- fprintf(stderr, " -M INT mismatch penalty [%d]\n", opt->s_mm);
- fprintf(stderr, " -O INT gap open penalty [%d]\n", opt->s_gapo);
- fprintf(stderr, " -E INT gap extension penalty [%d]\n", opt->s_gape);
- fprintf(stderr, " -R INT stop searching when there are >INT equally best hits [%d]\n", opt->max_top2);
- fprintf(stderr, " -q INT quality threshold for read trimming down to %dbp [%d]\n", BWA_MIN_RDLEN, opt->trim_qual);
- fprintf(stderr, " -f FILE file to write output to instead of stdout\n");
- fprintf(stderr, " -B INT length of barcode\n");
-// fprintf(stderr, " -c input sequences are in the color space\n");
- fprintf(stderr, " -L log-scaled gap penalty for long deletions\n");
- fprintf(stderr, " -N non-iterative mode: search for all n-difference hits (slooow)\n");
- fprintf(stderr, " -I the input is in the Illumina 1.3+ FASTQ-like format\n");
- fprintf(stderr, " -b the input read file is in the BAM format\n");
- fprintf(stderr, " -0 use single-end reads only (effective with -b)\n");
- fprintf(stderr, " -1 use the 1st read in a pair (effective with -b)\n");
- fprintf(stderr, " -2 use the 2nd read in a pair (effective with -b)\n");
- fprintf(stderr, " -Y filter Casava-filtered sequences\n");
- fprintf(stderr, "\n");
- return 1;
- }
- if (opt->fnr > 0.0) {
- int i, k;
- for (i = 17, k = 0; i <= 250; ++i) {
- int l = bwa_cal_maxdiff(i, BWA_AVG_ERR, opt->fnr);
- if (l != k) fprintf(stderr, "[bwa_aln] %dbp reads: max_diff = %d\n", i, l);
- k = l;
- }
- }
- if ((prefix = bwa_infer_prefix(argv[optind])) == 0) {
- fprintf(stderr, "[%s] fail to locate the index\n", __func__);
- free(opt);
- return 0;
- }
- bwa_aln_core(prefix, argv[optind+1], opt);
- free(opt); free(prefix);
- return 0;
-}
-
-/* rgoya: Temporary clone of aln_path2cigar to accomodate for bwa_cigar_t,
-__cigar_op and __cigar_len while keeping stdaln stand alone */
-bwa_cigar_t *bwa_aln_path2cigar(const path_t *path, int path_len, int *n_cigar)
-{
- uint32_t *cigar32;
- bwa_cigar_t *cigar;
- int i;
- cigar32 = aln_path2cigar32((path_t*) path, path_len, n_cigar);
- cigar = (bwa_cigar_t*)cigar32;
- for (i = 0; i < *n_cigar; ++i)
- cigar[i] = __cigar_create( (cigar32[i]&0xf), (cigar32[i]>>4) );
- return cigar;
-}
-
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwtaln.h
--- a/bwa-0.6.2/bwtaln.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,153 +0,0 @@
-#ifndef BWTALN_H
-#define BWTALN_H
-
-#include
-#include "bwt.h"
-
-#define BWA_TYPE_NO_MATCH 0
-#define BWA_TYPE_UNIQUE 1
-#define BWA_TYPE_REPEAT 2
-#define BWA_TYPE_MATESW 3
-
-#define SAM_FPD 1 // paired
-#define SAM_FPP 2 // properly paired
-#define SAM_FSU 4 // self-unmapped
-#define SAM_FMU 8 // mate-unmapped
-#define SAM_FSR 16 // self on the reverse strand
-#define SAM_FMR 32 // mate on the reverse strand
-#define SAM_FR1 64 // this is read one
-#define SAM_FR2 128 // this is read two
-#define SAM_FSC 256 // secondary alignment
-
-#define BWA_AVG_ERR 0.02
-#define BWA_MIN_RDLEN 35 // for read trimming
-
-#define BWA_MAX_BCLEN 63 // maximum barcode length; 127 is the maximum
-
-#ifndef bns_pac
-#define bns_pac(pac, k) ((pac)[(k)>>2] >> ((~(k)&3)<<1) & 3)
-#endif
-
-typedef struct {
- bwtint_t w;
- int bid;
-} bwt_width_t;
-
-typedef struct {
- uint32_t n_mm:16, n_gapo:8, n_gape:8;
- int score;
- bwtint_t k, l;
-} bwt_aln1_t;
-
-typedef uint16_t bwa_cigar_t;
-/* rgoya: If changing order of bytes, beware of operations like:
- * s->cigar[0] += s->full_len - s->len;
- */
-#define CIGAR_OP_SHIFT 14
-#define CIGAR_LN_MASK 0x3fff
-
-#define __cigar_op(__cigar) ((__cigar)>>CIGAR_OP_SHIFT)
-#define __cigar_len(__cigar) ((__cigar)&CIGAR_LN_MASK)
-#define __cigar_create(__op, __len) ((__op)<
-#include
-#include
-#include "bwtgap.h"
-#include "bwtaln.h"
-
-#define STATE_M 0
-#define STATE_I 1
-#define STATE_D 2
-
-#define aln_score(m,o,e,p) ((m)*(p)->s_mm + (o)*(p)->s_gapo + (e)*(p)->s_gape)
-
-gap_stack_t *gap_init_stack2(int max_score)
-{
- gap_stack_t *stack;
- stack = (gap_stack_t*)calloc(1, sizeof(gap_stack_t));
- stack->n_stacks = max_score;
- stack->stacks = (gap_stack1_t*)calloc(stack->n_stacks, sizeof(gap_stack1_t));
- return stack;
-}
-
-gap_stack_t *gap_init_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt)
-{
- return gap_init_stack2(aln_score(max_mm+1, max_gapo+1, max_gape+1, opt));
-}
-
-void gap_destroy_stack(gap_stack_t *stack)
-{
- int i;
- for (i = 0; i != stack->n_stacks; ++i) free(stack->stacks[i].stack);
- free(stack->stacks);
- free(stack);
-}
-
-static void gap_reset_stack(gap_stack_t *stack)
-{
- int i;
- for (i = 0; i != stack->n_stacks; ++i)
- stack->stacks[i].n_entries = 0;
- stack->best = stack->n_stacks;
- stack->n_entries = 0;
-}
-
-static inline void gap_push(gap_stack_t *stack, int i, bwtint_t k, bwtint_t l, int n_mm, int n_gapo, int n_gape,
- int state, int is_diff, const gap_opt_t *opt)
-{
- int score;
- gap_entry_t *p;
- gap_stack1_t *q;
- score = aln_score(n_mm, n_gapo, n_gape, opt);
- q = stack->stacks + score;
- if (q->n_entries == q->m_entries) {
- q->m_entries = q->m_entries? q->m_entries<<1 : 4;
- q->stack = (gap_entry_t*)realloc(q->stack, sizeof(gap_entry_t) * q->m_entries);
- }
- p = q->stack + q->n_entries;
- p->info = (u_int32_t)score<<21 | i; p->k = k; p->l = l;
- p->n_mm = n_mm; p->n_gapo = n_gapo; p->n_gape = n_gape; p->state = state;
- p->last_diff_pos = is_diff? i : 0;
- ++(q->n_entries);
- ++(stack->n_entries);
- if (stack->best > score) stack->best = score;
-}
-
-static inline void gap_pop(gap_stack_t *stack, gap_entry_t *e)
-{
- gap_stack1_t *q;
- q = stack->stacks + stack->best;
- *e = q->stack[q->n_entries - 1];
- --(q->n_entries);
- --(stack->n_entries);
- if (q->n_entries == 0 && stack->n_entries) { // reset best
- int i;
- for (i = stack->best + 1; i < stack->n_stacks; ++i)
- if (stack->stacks[i].n_entries != 0) break;
- stack->best = i;
- } else if (stack->n_entries == 0) stack->best = stack->n_stacks;
-}
-
-static inline void gap_shadow(int x, int len, bwtint_t max, int last_diff_pos, bwt_width_t *w)
-{
- int i, j;
- for (i = j = 0; i < last_diff_pos; ++i) {
- if (w[i].w > x) w[i].w -= x;
- else if (w[i].w == x) {
- w[i].bid = 1;
- w[i].w = max - (++j);
- } // else should not happen
- }
-}
-
-static inline int int_log2(uint32_t v)
-{
- int c = 0;
- if (v & 0xffff0000u) { v >>= 16; c |= 16; }
- if (v & 0xff00) { v >>= 8; c |= 8; }
- if (v & 0xf0) { v >>= 4; c |= 4; }
- if (v & 0xc) { v >>= 2; c |= 2; }
- if (v & 0x2) c |= 1;
- return c;
-}
-
-bwt_aln1_t *bwt_match_gap(bwt_t *const bwt, int len, const ubyte_t *seq, bwt_width_t *width,
- bwt_width_t *seed_width, const gap_opt_t *opt, int *_n_aln, gap_stack_t *stack)
-{
- int best_score = aln_score(opt->max_diff+1, opt->max_gapo+1, opt->max_gape+1, opt);
- int best_diff = opt->max_diff + 1, max_diff = opt->max_diff;
- int best_cnt = 0;
- int max_entries = 0, j, _j, n_aln, m_aln;
- bwt_aln1_t *aln;
-
- m_aln = 4; n_aln = 0;
- aln = (bwt_aln1_t*)calloc(m_aln, sizeof(bwt_aln1_t));
-
- // check whether there are too many N
- for (j = _j = 0; j < len; ++j)
- if (seq[j] > 3) ++_j;
- if (_j > max_diff) {
- *_n_aln = n_aln;
- return aln;
- }
-
- //for (j = 0; j != len; ++j) printf("#0 %d: [%d,%u]\t[%d,%u]\n", j, w[0][j].bid, w[0][j].w, w[1][j].bid, w[1][j].w);
- gap_reset_stack(stack); // reset stack
- gap_push(stack, len, 0, bwt->seq_len, 0, 0, 0, 0, 0, opt);
-
- while (stack->n_entries) {
- gap_entry_t e;
- int i, m, m_seed = 0, hit_found, allow_diff, allow_M, tmp;
- bwtint_t k, l, cnt_k[4], cnt_l[4], occ;
-
- if (max_entries < stack->n_entries) max_entries = stack->n_entries;
- if (stack->n_entries > opt->max_entries) break;
- gap_pop(stack, &e); // get the best entry
- k = e.k; l = e.l; // SA interval
- i = e.info&0xffff; // length
- if (!(opt->mode & BWA_MODE_NONSTOP) && e.info>>21 > best_score + opt->s_mm) break; // no need to proceed
-
- m = max_diff - (e.n_mm + e.n_gapo);
- if (opt->mode & BWA_MODE_GAPE) m -= e.n_gape;
- if (m < 0) continue;
- if (seed_width) { // apply seeding
- m_seed = opt->max_seed_diff - (e.n_mm + e.n_gapo);
- if (opt->mode & BWA_MODE_GAPE) m_seed -= e.n_gape;
- }
- //printf("#1\t[%d,%d,%d,%c]\t[%d,%d,%d]\t[%u,%u]\t[%u,%u]\t%d\n", stack->n_entries, a, i, "MID"[e.state], e.n_mm, e.n_gapo, e.n_gape, width[i-1].bid, width[i-1].w, k, l, e.last_diff_pos);
- if (i > 0 && m < width[i-1].bid) continue;
-
- // check whether a hit is found
- hit_found = 0;
- if (i == 0) hit_found = 1;
- else if (m == 0 && (e.state == STATE_M || (opt->mode&BWA_MODE_GAPE) || e.n_gape == opt->max_gape)) { // no diff allowed
- if (bwt_match_exact_alt(bwt, i, seq, &k, &l)) hit_found = 1;
- else continue; // no hit, skip
- }
-
- if (hit_found) { // action for found hits
- int score = aln_score(e.n_mm, e.n_gapo, e.n_gape, opt);
- int do_add = 1;
- //printf("#2 hits found: %d:(%u,%u)\n", e.n_mm+e.n_gapo, k, l);
- if (n_aln == 0) {
- best_score = score;
- best_diff = e.n_mm + e.n_gapo;
- if (opt->mode & BWA_MODE_GAPE) best_diff += e.n_gape;
- if (!(opt->mode & BWA_MODE_NONSTOP))
- max_diff = (best_diff + 1 > opt->max_diff)? opt->max_diff : best_diff + 1; // top2 behaviour
- }
- if (score == best_score) best_cnt += l - k + 1;
- else if (best_cnt > opt->max_top2) break; // top2b behaviour
- if (e.n_gapo) { // check whether the hit has been found. this may happen when a gap occurs in a tandem repeat
- for (j = 0; j != n_aln; ++j)
- if (aln[j].k == k && aln[j].l == l) break;
- if (j < n_aln) do_add = 0;
- }
- if (do_add) { // append
- bwt_aln1_t *p;
- gap_shadow(l - k + 1, len, bwt->seq_len, e.last_diff_pos, width);
- if (n_aln == m_aln) {
- m_aln <<= 1;
- aln = (bwt_aln1_t*)realloc(aln, m_aln * sizeof(bwt_aln1_t));
- memset(aln + m_aln/2, 0, m_aln/2*sizeof(bwt_aln1_t));
- }
- p = aln + n_aln;
- p->n_mm = e.n_mm; p->n_gapo = e.n_gapo; p->n_gape = e.n_gape;
- p->k = k; p->l = l;
- p->score = score;
- ++n_aln;
- }
- continue;
- }
-
- --i;
- bwt_2occ4(bwt, k - 1, l, cnt_k, cnt_l); // retrieve Occ values
- occ = l - k + 1;
- // test whether diff is allowed
- allow_diff = allow_M = 1;
- if (i > 0) {
- int ii = i - (len - opt->seed_len);
- if (width[i-1].bid > m-1) allow_diff = 0;
- else if (width[i-1].bid == m-1 && width[i].bid == m-1 && width[i-1].w == width[i].w) allow_M = 0;
- if (seed_width && ii > 0) {
- if (seed_width[ii-1].bid > m_seed-1) allow_diff = 0;
- else if (seed_width[ii-1].bid == m_seed-1 && seed_width[ii].bid == m_seed-1
- && seed_width[ii-1].w == seed_width[ii].w) allow_M = 0;
- }
- }
- // indels
- tmp = (opt->mode & BWA_MODE_LOGGAP)? int_log2(e.n_gape + e.n_gapo)/2+1 : e.n_gapo + e.n_gape;
- if (allow_diff && i >= opt->indel_end_skip + tmp && len - i >= opt->indel_end_skip + tmp) {
- if (e.state == STATE_M) { // gap open
- if (e.n_gapo < opt->max_gapo) { // gap open is allowed
- // insertion
- gap_push(stack, i, k, l, e.n_mm, e.n_gapo + 1, e.n_gape, STATE_I, 1, opt);
- // deletion
- for (j = 0; j != 4; ++j) {
- k = bwt->L2[j] + cnt_k[j] + 1;
- l = bwt->L2[j] + cnt_l[j];
- if (k <= l) gap_push(stack, i + 1, k, l, e.n_mm, e.n_gapo + 1, e.n_gape, STATE_D, 1, opt);
- }
- }
- } else if (e.state == STATE_I) { // extention of an insertion
- if (e.n_gape < opt->max_gape) // gap extention is allowed
- gap_push(stack, i, k, l, e.n_mm, e.n_gapo, e.n_gape + 1, STATE_I, 1, opt);
- } else if (e.state == STATE_D) { // extention of a deletion
- if (e.n_gape < opt->max_gape) { // gap extention is allowed
- if (e.n_gape + e.n_gapo < max_diff || occ < opt->max_del_occ) {
- for (j = 0; j != 4; ++j) {
- k = bwt->L2[j] + cnt_k[j] + 1;
- l = bwt->L2[j] + cnt_l[j];
- if (k <= l) gap_push(stack, i + 1, k, l, e.n_mm, e.n_gapo, e.n_gape + 1, STATE_D, 1, opt);
- }
- }
- }
- }
- }
- // mismatches
- if (allow_diff && allow_M) { // mismatch is allowed
- for (j = 1; j <= 4; ++j) {
- int c = (seq[i] + j) & 3;
- int is_mm = (j != 4 || seq[i] > 3);
- k = bwt->L2[c] + cnt_k[c] + 1;
- l = bwt->L2[c] + cnt_l[c];
- if (k <= l) gap_push(stack, i, k, l, e.n_mm + is_mm, e.n_gapo, e.n_gape, STATE_M, is_mm, opt);
- }
- } else if (seq[i] < 4) { // try exact match only
- int c = seq[i] & 3;
- k = bwt->L2[c] + cnt_k[c] + 1;
- l = bwt->L2[c] + cnt_l[c];
- if (k <= l) gap_push(stack, i, k, l, e.n_mm, e.n_gapo, e.n_gape, STATE_M, 0, opt);
- }
- }
-
- *_n_aln = n_aln;
- //fprintf(stderr, "max_entries = %d\n", max_entries);
- return aln;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwtgap.h
--- a/bwa-0.6.2/bwtgap.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-#ifndef BWTGAP_H_
-#define BWTGAP_H_
-
-#include "bwt.h"
-#include "bwtaln.h"
-
-typedef struct { // recursion stack
- u_int32_t info; // score<<21 | i
- u_int32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
- bwtint_t k, l; // (k,l) is the SA region of [i,n-1]
- int last_diff_pos;
-} gap_entry_t;
-
-typedef struct {
- int n_entries, m_entries;
- gap_entry_t *stack;
-} gap_stack1_t;
-
-typedef struct {
- int n_stacks, best, n_entries;
- gap_stack1_t *stacks;
-} gap_stack_t;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- gap_stack_t *gap_init_stack2(int max_score);
- gap_stack_t *gap_init_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt);
- void gap_destroy_stack(gap_stack_t *stack);
- bwt_aln1_t *bwt_match_gap(bwt_t *const bwt, int len, const ubyte_t *seq, bwt_width_t *w,
- bwt_width_t *seed_w, const gap_opt_t *opt, int *_n_aln, gap_stack_t *stack);
- void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwtindex.c
--- a/bwa-0.6.2/bwtindex.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,158 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008 Genome Research Ltd (GRL).
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-/* Contact: Heng Li */
-
-#include
-#include
-#include
-#include
-#include
-#include
-#include "bntseq.h"
-#include "bwt.h"
-#include "main.h"
-#include "utils.h"
-
-bwt_t *bwt_pac2bwt(const char *fn_pac, int use_is);
-void bwa_pac_rev_core(const char *fn, const char *fn_rev);
-
-int bwa_index(int argc, char *argv[])
-{
- char *prefix = 0, *str, *str2, *str3;
- int c, algo_type = 0, is_color = 0, is_64 = 0;
- clock_t t;
- int64_t l_pac;
-
- while ((c = getopt(argc, argv, "6ca:p:")) >= 0) {
- switch (c) {
- case 'a': // if -a is not set, algo_type will be determined later
- if (strcmp(optarg, "div") == 0) algo_type = 1;
- else if (strcmp(optarg, "bwtsw") == 0) algo_type = 2;
- else if (strcmp(optarg, "is") == 0) algo_type = 3;
- else err_fatal(__func__, "unknown algorithm: '%s'.", optarg);
- break;
- case 'p': prefix = strdup(optarg); break;
- case 'c': is_color = 1; break;
- case '6': is_64 = 1; break;
- default: return 1;
- }
- }
-
- if (optind + 1 > argc) {
- fprintf(stderr, "\n");
- fprintf(stderr, "Usage: bwa index [-a bwtsw|is] [-c] \n\n");
- fprintf(stderr, "Options: -a STR BWT construction algorithm: bwtsw or is [auto]\n");
- fprintf(stderr, " -p STR prefix of the index [same as fasta name]\n");
- fprintf(stderr, " -6 index files named as .64.* instead of .* \n");
-// fprintf(stderr, " -c build color-space index\n");
- fprintf(stderr, "\n");
- fprintf(stderr, "Warning: `-a bwtsw' does not work for short genomes, while `-a is' and\n");
- fprintf(stderr, " `-a div' do not work not for long genomes. Please choose `-a'\n");
- fprintf(stderr, " according to the length of the genome.\n\n");
- return 1;
- }
- if (prefix == 0) {
- prefix = malloc(strlen(argv[optind]) + 4);
- strcpy(prefix, argv[optind]);
- if (is_64) strcat(prefix, ".64");
- }
- str = (char*)calloc(strlen(prefix) + 10, 1);
- str2 = (char*)calloc(strlen(prefix) + 10, 1);
- str3 = (char*)calloc(strlen(prefix) + 10, 1);
-
- if (is_color == 0) { // nucleotide indexing
- gzFile fp = xzopen(argv[optind], "r");
- t = clock();
- fprintf(stderr, "[bwa_index] Pack FASTA... ");
- l_pac = bns_fasta2bntseq(fp, prefix, 0);
- fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- gzclose(fp);
- } else { // color indexing
- gzFile fp = xzopen(argv[optind], "r");
- strcat(strcpy(str, prefix), ".nt");
- t = clock();
- fprintf(stderr, "[bwa_index] Pack nucleotide FASTA... ");
- l_pac = bns_fasta2bntseq(fp, str, 0);
- fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- gzclose(fp);
- {
- char *tmp_argv[3];
- tmp_argv[0] = argv[0]; tmp_argv[1] = str; tmp_argv[2] = prefix;
- t = clock();
- fprintf(stderr, "[bwa_index] Convert nucleotide PAC to color PAC... ");
- bwa_pac2cspac(3, tmp_argv);
- fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- }
- }
- if (algo_type == 0) algo_type = l_pac > 50000000? 2 : 3; // set the algorithm for generating BWT
- {
- strcpy(str, prefix); strcat(str, ".pac");
- strcpy(str2, prefix); strcat(str2, ".bwt");
- t = clock();
- fprintf(stderr, "[bwa_index] Construct BWT for the packed sequence...\n");
- if (algo_type == 2) bwt_bwtgen(str, str2);
- else if (algo_type == 1 || algo_type == 3) {
- bwt_t *bwt;
- bwt = bwt_pac2bwt(str, algo_type == 3);
- bwt_dump_bwt(str2, bwt);
- bwt_destroy(bwt);
- }
- fprintf(stderr, "[bwa_index] %.2f seconds elapse.\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- }
- {
- bwt_t *bwt;
- strcpy(str, prefix); strcat(str, ".bwt");
- t = clock();
- fprintf(stderr, "[bwa_index] Update BWT... ");
- bwt = bwt_restore_bwt(str);
- bwt_bwtupdate_core(bwt);
- bwt_dump_bwt(str, bwt);
- bwt_destroy(bwt);
- fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- }
- {
- gzFile fp = xzopen(argv[optind], "r");
- t = clock();
- fprintf(stderr, "[bwa_index] Pack forward-only FASTA... ");
- l_pac = bns_fasta2bntseq(fp, prefix, 1);
- fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- gzclose(fp);
- }
- {
- bwt_t *bwt;
- strcpy(str, prefix); strcat(str, ".bwt");
- strcpy(str3, prefix); strcat(str3, ".sa");
- t = clock();
- fprintf(stderr, "[bwa_index] Construct SA from BWT and Occ... ");
- bwt = bwt_restore_bwt(str);
- bwt_cal_sa(bwt, 32);
- bwt_dump_sa(str3, bwt);
- bwt_destroy(bwt);
- fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
- }
- free(str3); free(str2); free(str); free(prefix);
- return 0;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwtio.c
--- a/bwa-0.6.2/bwtio.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,77 +0,0 @@
-#include
-#include
-#include
-#include "bwt.h"
-#include "utils.h"
-
-void bwt_dump_bwt(const char *fn, const bwt_t *bwt)
-{
- FILE *fp;
- fp = xopen(fn, "wb");
- fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
- fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
- fwrite(bwt->bwt, 4, bwt->bwt_size, fp);
- fclose(fp);
-}
-
-void bwt_dump_sa(const char *fn, const bwt_t *bwt)
-{
- FILE *fp;
- fp = xopen(fn, "wb");
- fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
- fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
- fwrite(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
- fwrite(&bwt->seq_len, sizeof(bwtint_t), 1, fp);
- fwrite(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
- fclose(fp);
-}
-
-void bwt_restore_sa(const char *fn, bwt_t *bwt)
-{
- char skipped[256];
- FILE *fp;
- bwtint_t primary;
-
- fp = xopen(fn, "rb");
- fread(&primary, sizeof(bwtint_t), 1, fp);
- xassert(primary == bwt->primary, "SA-BWT inconsistency: primary is not the same.");
- fread(skipped, sizeof(bwtint_t), 4, fp); // skip
- fread(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
- fread(&primary, sizeof(bwtint_t), 1, fp);
- xassert(primary == bwt->seq_len, "SA-BWT inconsistency: seq_len is not the same.");
-
- bwt->n_sa = (bwt->seq_len + bwt->sa_intv) / bwt->sa_intv;
- bwt->sa = (bwtint_t*)calloc(bwt->n_sa, sizeof(bwtint_t));
- bwt->sa[0] = -1;
-
- fread(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
- fclose(fp);
-}
-
-bwt_t *bwt_restore_bwt(const char *fn)
-{
- bwt_t *bwt;
- FILE *fp;
-
- bwt = (bwt_t*)calloc(1, sizeof(bwt_t));
- fp = xopen(fn, "rb");
- fseek(fp, 0, SEEK_END);
- bwt->bwt_size = (ftell(fp) - sizeof(bwtint_t) * 5) >> 2;
- bwt->bwt = (uint32_t*)calloc(bwt->bwt_size, 4);
- fseek(fp, 0, SEEK_SET);
- fread(&bwt->primary, sizeof(bwtint_t), 1, fp);
- fread(bwt->L2+1, sizeof(bwtint_t), 4, fp);
- fread(bwt->bwt, 4, bwt->bwt_size, fp);
- bwt->seq_len = bwt->L2[4];
- fclose(fp);
- bwt_gen_cnt_table(bwt);
-
- return bwt;
-}
-
-void bwt_destroy(bwt_t *bwt)
-{
- if (bwt == 0) return;
- free(bwt->sa); free(bwt->bwt);
- free(bwt);
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwtmisc.c
--- a/bwa-0.6.2/bwtmisc.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,230 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008 Genome Research Ltd (GRL).
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-/* Contact: Heng Li */
-
-#include
-#include
-#include
-#include
-#include "bntseq.h"
-#include "utils.h"
-#include "main.h"
-#include "bwt.h"
-
-#ifdef _DIVBWT
-#include "divsufsort.h"
-#endif
-
-int is_bwt(ubyte_t *T, int n);
-
-int64_t bwa_seq_len(const char *fn_pac)
-{
- FILE *fp;
- int64_t pac_len;
- ubyte_t c;
- fp = xopen(fn_pac, "rb");
- fseek(fp, -1, SEEK_END);
- pac_len = ftell(fp);
- fread(&c, 1, 1, fp);
- fclose(fp);
- return (pac_len - 1) * 4 + (int)c;
-}
-
-bwt_t *bwt_pac2bwt(const char *fn_pac, int use_is)
-{
- bwt_t *bwt;
- ubyte_t *buf, *buf2;
- int i, pac_size;
- FILE *fp;
-
- // initialization
- bwt = (bwt_t*)calloc(1, sizeof(bwt_t));
- bwt->seq_len = bwa_seq_len(fn_pac);
- bwt->bwt_size = (bwt->seq_len + 15) >> 4;
- fp = xopen(fn_pac, "rb");
-
- // prepare sequence
- pac_size = (bwt->seq_len>>2) + ((bwt->seq_len&3) == 0? 0 : 1);
- buf2 = (ubyte_t*)calloc(pac_size, 1);
- fread(buf2, 1, pac_size, fp);
- fclose(fp);
- memset(bwt->L2, 0, 5 * 4);
- buf = (ubyte_t*)calloc(bwt->seq_len + 1, 1);
- for (i = 0; i < bwt->seq_len; ++i) {
- buf[i] = buf2[i>>2] >> ((3 - (i&3)) << 1) & 3;
- ++bwt->L2[1+buf[i]];
- }
- for (i = 2; i <= 4; ++i) bwt->L2[i] += bwt->L2[i-1];
- free(buf2);
-
- // Burrows-Wheeler Transform
- if (use_is) {
- bwt->primary = is_bwt(buf, bwt->seq_len);
- } else {
-#ifdef _DIVBWT
- bwt->primary = divbwt(buf, buf, 0, bwt->seq_len);
-#else
- err_fatal_simple("libdivsufsort is not compiled in.");
-#endif
- }
- bwt->bwt = (u_int32_t*)calloc(bwt->bwt_size, 4);
- for (i = 0; i < bwt->seq_len; ++i)
- bwt->bwt[i>>4] |= buf[i] << ((15 - (i&15)) << 1);
- free(buf);
- return bwt;
-}
-
-int bwa_pac2bwt(int argc, char *argv[])
-{
- bwt_t *bwt;
- int c, use_is = 1;
- while ((c = getopt(argc, argv, "d")) >= 0) {
- switch (c) {
- case 'd': use_is = 0; break;
- default: return 1;
- }
- }
- if (optind + 2 > argc) {
- fprintf(stderr, "Usage: bwa pac2bwt [-d] \n");
- return 1;
- }
- bwt = bwt_pac2bwt(argv[optind], use_is);
- bwt_dump_bwt(argv[optind+1], bwt);
- bwt_destroy(bwt);
- return 0;
-}
-
-#define bwt_B00(b, k) ((b)->bwt[(k)>>4]>>((~(k)&0xf)<<1)&3)
-
-void bwt_bwtupdate_core(bwt_t *bwt)
-{
- bwtint_t i, k, c[4], n_occ;
- uint32_t *buf;
-
- n_occ = (bwt->seq_len + OCC_INTERVAL - 1) / OCC_INTERVAL + 1;
- bwt->bwt_size += n_occ * sizeof(bwtint_t); // the new size
- buf = (uint32_t*)calloc(bwt->bwt_size, 4); // will be the new bwt
- c[0] = c[1] = c[2] = c[3] = 0;
- for (i = k = 0; i < bwt->seq_len; ++i) {
- if (i % OCC_INTERVAL == 0) {
- memcpy(buf + k, c, sizeof(bwtint_t) * 4);
- k += sizeof(bwtint_t); // in fact: sizeof(bwtint_t)=4*(sizeof(bwtint_t)/4)
- }
- if (i % 16 == 0) buf[k++] = bwt->bwt[i/16]; // 16 == sizeof(uint32_t)/2
- ++c[bwt_B00(bwt, i)];
- }
- // the last element
- memcpy(buf + k, c, sizeof(bwtint_t) * 4);
- xassert(k + sizeof(bwtint_t) == bwt->bwt_size, "inconsistent bwt_size");
- // update bwt
- free(bwt->bwt); bwt->bwt = buf;
-}
-
-int bwa_bwtupdate(int argc, char *argv[])
-{
- bwt_t *bwt;
- if (argc < 2) {
- fprintf(stderr, "Usage: bwa bwtupdate \n");
- return 1;
- }
- bwt = bwt_restore_bwt(argv[1]);
- bwt_bwtupdate_core(bwt);
- bwt_dump_bwt(argv[1], bwt);
- bwt_destroy(bwt);
- return 0;
-}
-
-const int nst_color_space_table[] = { 4, 0, 0, 1, 0, 2, 3, 4, 0, 3, 2, 4, 1, 4, 4, 4};
-
-/* this function is not memory efficient, but this will make life easier
- Ideally we should also change .amb files as one 'N' in the nucleotide
- sequence leads to two ambiguous colors. I may do this later... */
-uint8_t *bwa_pac2cspac_core(const bntseq_t *bns)
-{
- uint8_t *pac, *cspac;
- bwtint_t i;
- int c1, c2;
- pac = (uint8_t*)calloc(bns->l_pac/4 + 1, 1);
- cspac = (uint8_t*)calloc(bns->l_pac/4 + 1, 1);
- fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
- rewind(bns->fp_pac);
- c1 = pac[0]>>6; cspac[0] = c1<<6;
- for (i = 1; i < bns->l_pac; ++i) {
- c2 = pac[i>>2] >> (~i&3)*2 & 3;
- cspac[i>>2] |= nst_color_space_table[(1< \n");
- return 1;
- }
- bns = bns_restore(argv[1]);
- cspac = bwa_pac2cspac_core(bns);
- bns_dump(bns, argv[2]);
- // now write cspac
- str = (char*)calloc(strlen(argv[2]) + 5, 1);
- strcat(strcpy(str, argv[2]), ".pac");
- fp = xopen(str, "wb");
- fwrite(cspac, 1, bns->l_pac/4 + 1, fp);
- ct = bns->l_pac % 4;
- fwrite(&ct, 1, 1, fp);
- fclose(fp);
- bns_destroy(bns);
- free(cspac);
- return 0;
-}
-
-int bwa_bwt2sa(int argc, char *argv[])
-{
- bwt_t *bwt;
- int c, sa_intv = 32;
- while ((c = getopt(argc, argv, "i:")) >= 0) {
- switch (c) {
- case 'i': sa_intv = atoi(optarg); break;
- default: return 1;
- }
- }
- if (optind + 2 > argc) {
- fprintf(stderr, "Usage: bwa bwt2sa [-i %d] \n", sa_intv);
- return 1;
- }
- bwt = bwt_restore_bwt(argv[optind]);
- bwt_cal_sa(bwt, sa_intv);
- bwt_dump_sa(argv[optind+1], bwt);
- bwt_destroy(bwt);
- return 0;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwtsw2.h
--- a/bwa-0.6.2/bwtsw2.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,69 +0,0 @@
-#ifndef LH3_BWTSW2_H
-#define LH3_BWTSW2_H
-
-#include
-#include "bntseq.h"
-#include "bwt_lite.h"
-#include "bwt.h"
-
-#define BSW2_FLAG_MATESW 0x100
-#define BSW2_FLAG_TANDEM 0x200
-#define BSW2_FLAG_MOVED 0x400
-#define BSW2_FLAG_RESCUED 0x800
-
-typedef struct {
- int skip_sw:16, hard_clip:16;
- int a, b, q, r, t, qr, bw, max_ins;
- int z, is, t_seeds, multi_2nd;
- float mask_level, coef;
- int n_threads, chunk_size;
-} bsw2opt_t;
-
-typedef struct {
- bwtint_t k, l;
- uint32_t flag:18, n_seeds:13, is_rev:1;
- int len, G, G2;
- int beg, end;
-} bsw2hit_t;
-
-typedef struct {
- int flag, nn, n_cigar, chr, pos, qual, mchr, mpos, pqual, isize, nm;
- uint32_t *cigar;
-} bsw2aux_t;
-
-typedef struct {
- int n, max;
- bsw2hit_t *hits;
- bsw2aux_t *aux;
-} bwtsw2_t;
-
-typedef struct {
- void *stack;
- int max_l;
- uint8_t *aln_mem;
-} bsw2global_t;
-
-typedef struct {
- int l, tid;
- char *name, *seq, *qual, *sam;
-} bsw2seq1_t;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- bsw2opt_t *bsw2_init_opt();
- bwtsw2_t **bsw2_core(const bntseq_t *bns, const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool);
- void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target, const char *fn, const char *fn2);
- void bsw2_destroy(bwtsw2_t *b);
-
- bsw2global_t *bsw2_global_init();
- void bsw2_global_destroy(bsw2global_t *_pool);
-
- void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, bsw2seq1_t *seq, bwtsw2_t **hit);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwtsw2_aux.c
--- a/bwa-0.6.2/bwtsw2_aux.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,821 +0,0 @@
-#include
-#include
-#include
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
-#ifdef HAVE_PTHREAD
-#include
-#endif
-#include "bntseq.h"
-#include "bwt_lite.h"
-#include "utils.h"
-#include "bwtsw2.h"
-#include "stdaln.h"
-#include "kstring.h"
-
-#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
-
-#include "ksort.h"
-#define __left_lt(a, b) ((a).end > (b).end)
-KSORT_INIT(hit, bsw2hit_t, __left_lt)
-
-extern unsigned char nst_nt4_table[256];
-
-unsigned char nt_comp_table[256] = {
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','T','V','G', 'H','N','N','C', 'D','N','N','M', 'N','K','N','N',
- 'N','N','Y','S', 'A','N','B','W', 'X','R','N','N', 'N','N','N','N',
- 'n','t','v','g', 'h','n','n','c', 'd','n','n','m', 'n','k','n','n',
- 'n','n','y','s', 'a','n','b','w', 'x','r','n','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N'
-};
-
-extern int bsw2_resolve_duphits(const bntseq_t *bns, const bwt_t *bwt, bwtsw2_t *b, int IS);
-extern int bsw2_resolve_query_overlaps(bwtsw2_t *b, float mask_level);
-
-bsw2opt_t *bsw2_init_opt()
-{
- bsw2opt_t *o = (bsw2opt_t*)calloc(1, sizeof(bsw2opt_t));
- o->a = 1; o->b = 3; o->q = 5; o->r = 2; o->t = 30;
- o->bw = 50;
- o->max_ins = 20000;
- o->z = 1; o->is = 3; o->t_seeds = 5; o->hard_clip = 0; o->skip_sw = 0;
- o->mask_level = 0.50f; o->coef = 5.5f;
- o->qr = o->q + o->r; o->n_threads = 1; o->chunk_size = 10000000;
- return o;
-}
-
-void bsw2_destroy(bwtsw2_t *b)
-{
- int i;
- if (b == 0) return;
- if (b->aux)
- for (i = 0; i < b->n; ++i) free(b->aux[i].cigar);
- free(b->aux); free(b->hits);
- free(b);
-}
-
-bwtsw2_t *bsw2_dup_no_cigar(const bwtsw2_t *b)
-{
- bwtsw2_t *p;
- p = calloc(1, sizeof(bwtsw2_t));
- p->max = p->n = b->n;
- if (b->n) {
- kroundup32(p->max);
- p->hits = calloc(p->max, sizeof(bsw2hit_t));
- memcpy(p->hits, b->hits, p->n * sizeof(bsw2hit_t));
- }
- return p;
-}
-
-#define __gen_ap(par, opt) do { \
- int i; \
- for (i = 0; i < 25; ++i) (par).matrix[i] = -(opt)->b; \
- for (i = 0; i < 4; ++i) (par).matrix[i*5+i] = (opt)->a; \
- (par).gap_open = (opt)->q; (par).gap_ext = (opt)->r; \
- (par).gap_end = (opt)->r; \
- (par).row = 5; (par).band_width = opt->bw; \
- } while (0)
-
-void bsw2_extend_left(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *_query, int lq, uint8_t *pac, bwtint_t l_pac, uint8_t *_mem)
-{
- int i, matrix[25];
- bwtint_t k;
- uint8_t *target = 0, *query;
- AlnParam par;
-
- par.matrix = matrix;
- __gen_ap(par, opt);
- query = calloc(lq, 1);
- // sort according to the descending order of query end
- ks_introsort(hit, b->n, b->hits);
- target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1);
- // reverse _query
- for (i = 0; i < lq; ++i) query[lq - i - 1] = _query[i];
- // core loop
- for (i = 0; i < b->n; ++i) {
- bsw2hit_t *p = b->hits + i;
- int lt = ((p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq;
- int score, j;
- path_t path;
- p->n_seeds = 1;
- if (p->l || p->k == 0) continue;
- for (j = score = 0; j < i; ++j) {
- bsw2hit_t *q = b->hits + j;
- if (q->beg <= p->beg && q->k <= p->k && q->k + q->len >= p->k + p->len) {
- if (q->n_seeds < (1<<13) - 2) ++q->n_seeds;
- ++score;
- }
- }
- if (score) continue;
- if (lt > p->k) lt = p->k;
- for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered!
- target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
- lt = j;
- score = aln_extend_core(target, lt, query + lq - p->beg, p->beg, &par, &path, 0, p->G, _mem);
- if (score > p->G) { // extensible
- p->G = score;
- p->len += path.i;
- p->beg -= path.j;
- p->k -= path.i;
- }
- }
- free(query); free(target);
-}
-
-void bsw2_extend_rght(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *query, int lq, uint8_t *pac, bwtint_t l_pac, uint8_t *_mem)
-{
- int i, matrix[25];
- bwtint_t k;
- uint8_t *target;
- AlnParam par;
-
- par.matrix = matrix;
- __gen_ap(par, opt);
- target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1);
- for (i = 0; i < b->n; ++i) {
- bsw2hit_t *p = b->hits + i;
- int lt = ((lq - p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq;
- int j, score;
- path_t path;
- if (p->l) continue;
- for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k)
- target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
- lt = j;
- score = aln_extend_core(target, lt, query + p->beg, lq - p->beg, &par, &path, 0, 1, _mem);
-// if (score < p->G) fprintf(stderr, "[bsw2_extend_hits] %d < %d\n", score, p->G);
- if (score >= p->G) {
- p->G = score;
- p->len = path.i;
- p->end = path.j + p->beg;
- }
- }
- free(target);
-}
-
-/* generate CIGAR array(s) in b->cigar[] */
-static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], const uint8_t *pac, bwtsw2_t *b, const char *name)
-{
- uint8_t *target;
- int i, matrix[25];
- AlnParam par;
- path_t *path;
-
- par.matrix = matrix;
- __gen_ap(par, opt);
- i = ((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq; // maximum possible target length
- target = calloc(i, 1);
- path = calloc(i + lq, sizeof(path_t));
- // generate CIGAR
- for (i = 0; i < b->n; ++i) {
- bsw2hit_t *p = b->hits + i;
- bsw2aux_t *q = b->aux + i;
- uint8_t *query;
- bwtint_t k;
- int score, path_len, beg, end;
- if (p->l) continue;
- beg = (p->flag & 0x10)? lq - p->end : p->beg;
- end = (p->flag & 0x10)? lq - p->beg : p->end;
- query = seq[(p->flag & 0x10)? 1 : 0] + beg;
- for (k = p->k; k < p->k + p->len; ++k) // in principle, no out-of-boundary here
- target[k - p->k] = pac[k>>2] >> (~k&3)*2 & 0x3;
- score = aln_global_core(target, p->len, query, end - beg, &par, path, &path_len);
- q->cigar = aln_path2cigar32(path, path_len, &q->n_cigar);
-#if 0
- if (name && score != p->G) { // debugging only
- int j, glen = 0;
- for (j = 0; j < q->n_cigar; ++j)
- if ((q->cigar[j]&0xf) == 1 || (q->cigar[j]&0xf) == 2)
- glen += q->cigar[j]>>4;
- fprintf(stderr, "[E::%s] %s - unequal score: %d != %d; (qlen, aqlen, arlen, glen, bw) = (%d, %d, %d, %d, %d)\n",
- __func__, name, score, p->G, lq, end - beg, p->len, glen, opt->bw);
- }
-#endif
- if (beg != 0 || end < lq) { // write soft clipping
- q->cigar = realloc(q->cigar, 4 * (q->n_cigar + 2));
- if (beg != 0) {
- memmove(q->cigar + 1, q->cigar, q->n_cigar * 4);
- q->cigar[0] = beg<<4 | 4;
- ++q->n_cigar;
- }
- if (end < lq) {
- q->cigar[q->n_cigar] = (lq - end)<<4 | 4;
- ++q->n_cigar;
- }
- }
- }
- free(target); free(path);
-}
-
-/* this is for the debugging purpose only */
-void bsw2_debug_hits(const bwtsw2_t *b)
-{
- int i;
- printf("# raw hits: %d\n", b->n);
- for (i = 0; i < b->n; ++i) {
- bsw2hit_t *p = b->hits + i;
- if (p->G > 0)
- printf("G=%d, len=%d, [%d,%d), k=%lu, l=%lu, #seeds=%d, is_rev=%d\n", p->G, p->len, p->beg, p->end, (long)p->k, (long)p->l, p->n_seeds, p->is_rev);
- }
-}
-
-static void merge_hits(bwtsw2_t *b[2], int l, int is_reverse)
-{
- int i;
- if (b[0]->n + b[1]->n > b[0]->max) {
- b[0]->max = b[0]->n + b[1]->n;
- b[0]->hits = realloc(b[0]->hits, b[0]->max * sizeof(bsw2hit_t));
- }
- for (i = 0; i < b[1]->n; ++i) {
- bsw2hit_t *p = b[0]->hits + b[0]->n + i;
- *p = b[1]->hits[i];
- if (is_reverse) {
- int x = p->beg;
- p->beg = l - p->end;
- p->end = l - x;
- p->flag |= 0x10;
- }
- }
- b[0]->n += b[1]->n;
- bsw2_destroy(b[1]);
- b[1] = 0;
-}
-/* seq[0] is the forward sequence and seq[1] is the reverse complement. */
-static bwtsw2_t *bsw2_aln1_core(const bsw2opt_t *opt, const bntseq_t *bns, uint8_t *pac, const bwt_t *target,
- int l, uint8_t *seq[2], bsw2global_t *pool)
-{
- extern void bsw2_chain_filter(const bsw2opt_t *opt, int len, bwtsw2_t *b[2]);
- bwtsw2_t *b[2], **bb[2], **_b, *p;
- int k, j;
- bwtl_t *query;
- query = bwtl_seq2bwtl(l, seq[0]);
- _b = bsw2_core(bns, opt, query, target, pool);
- bwtl_destroy(query);
- for (k = 0; k < 2; ++k) {
- bb[k] = calloc(2, sizeof(void*));
- bb[k][0] = calloc(1, sizeof(bwtsw2_t));
- bb[k][1] = calloc(1, sizeof(bwtsw2_t));
- }
- for (k = 0; k < 2; ++k) { // separate _b into bb[2] based on the strand
- for (j = 0; j < _b[k]->n; ++j) {
- bsw2hit_t *q;
- p = bb[_b[k]->hits[j].is_rev][k];
- if (p->n == p->max) {
- p->max = p->max? p->max<<1 : 8;
- p->hits = realloc(p->hits, p->max * sizeof(bsw2hit_t));
- }
- q = &p->hits[p->n++];
- *q = _b[k]->hits[j];
- if (_b[k]->hits[j].is_rev) {
- int x = q->beg;
- q->beg = l - q->end;
- q->end = l - x;
- }
- }
- }
- b[0] = bb[0][1]; b[1] = bb[1][1]; // bb[*][1] are "narrow SA hits"
- bsw2_chain_filter(opt, l, b);
- for (k = 0; k < 2; ++k) {
- bsw2_extend_left(opt, bb[k][1], seq[k], l, pac, bns->l_pac, pool->aln_mem);
- merge_hits(bb[k], l, 0); // bb[k][1] is merged to bb[k][0] here
- bsw2_resolve_duphits(0, 0, bb[k][0], 0);
- bsw2_extend_rght(opt, bb[k][0], seq[k], l, pac, bns->l_pac, pool->aln_mem);
- b[k] = bb[k][0];
- free(bb[k]);
- }
- merge_hits(b, l, 1); // again, b[1] is merged to b[0]
- bsw2_resolve_query_overlaps(b[0], opt->mask_level);
- bsw2_destroy(_b[0]); bsw2_destroy(_b[1]); free(_b);
- return b[0];
-}
-
-/* set ->flag to records the origin of the hit (to forward bwt or reverse bwt) */
-static void flag_fr(bwtsw2_t *b[2])
-{
- int i, j;
- for (i = 0; i < b[0]->n; ++i) {
- bsw2hit_t *p = b[0]->hits + i;
- p->flag |= 0x10000;
- }
- for (i = 0; i < b[1]->n; ++i) {
- bsw2hit_t *p = b[1]->hits + i;
- p->flag |= 0x20000;
- }
- for (i = 0; i < b[0]->n; ++i) {
- bsw2hit_t *p = b[0]->hits + i;
- for (j = 0; j < b[1]->n; ++j) {
- bsw2hit_t *q = b[1]->hits + j;
- if (q->beg == p->beg && q->end == p->end && q->k == p->k && q->len == p->len && q->G == p->G) {
- q->flag |= 0x30000; p->flag |= 0x30000;
- break;
- }
- }
- }
-}
-
-typedef struct {
- int n, max;
- bsw2seq1_t *seq;
-} bsw2seq_t;
-
-static int fix_cigar(const bntseq_t *bns, bsw2hit_t *p, int n_cigar, uint32_t *cigar)
-{
- // FIXME: this routine does not work if the query bridge three reference sequences
- int32_t coor, refl, lq;
- int x, y, i, seqid;
- bns_cnt_ambi(bns, p->k, p->len, &seqid);
- coor = p->k - bns->anns[seqid].offset;
- refl = bns->anns[seqid].len;
- x = coor; y = 0;
- // test if the alignment goes beyond the boundary
- for (i = 0; i < n_cigar; ++i) {
- int op = cigar[i]&0xf, ln = cigar[i]>>4;
- if (op == 1 || op == 4 || op == 5) y += ln;
- else if (op == 2) x += ln;
- else x += ln, y += ln;
- }
- lq = y; // length of the query sequence
- if (x > refl) { // then fix it
- int j, nc, mq[2], nlen[2];
- uint32_t *cn;
- bwtint_t kk = 0;
- nc = mq[0] = mq[1] = nlen[0] = nlen[1] = 0;
- cn = calloc(n_cigar + 3, 4);
- x = coor; y = 0;
- for (i = j = 0; i < n_cigar; ++i) {
- int op = cigar[i]&0xf, ln = cigar[i]>>4;
- if (op == 4 || op == 5 || op == 1) { // ins or clipping
- y += ln;
- cn[j++] = cigar[i];
- } else if (op == 2) { // del
- if (x + ln >= refl && nc == 0) {
- cn[j++] = (uint32_t)(lq - y)<<4 | 4;
- nc = j;
- cn[j++] = (uint32_t)y<<4 | 4;
- kk = p->k + (x + ln - refl);
- nlen[0] = x - coor;
- nlen[1] = p->len - nlen[0] - ln;
- } else cn[j++] = cigar[i];
- x += ln;
- } else if (op == 0) { // match
- if (x + ln >= refl && nc == 0) {
- // FIXME: not consider a special case where a split right between M and I
- cn[j++] = (uint32_t)(refl - x)<<4 | 0; // write M
- cn[j++] = (uint32_t)(lq - y - (refl - x))<<4 | 4; // write S
- nc = j;
- mq[0] += refl - x;
- cn[j++] = (uint32_t)(y + (refl - x))<<4 | 4;
- if (x + ln - refl) cn[j++] = (uint32_t)(x + ln - refl)<<4 | 0;
- mq[1] += x + ln - refl;
- kk = bns->anns[seqid].offset + refl;
- nlen[0] = refl - coor;
- nlen[1] = p->len - nlen[0];
- } else {
- cn[j++] = cigar[i];
- mq[nc?1:0] += ln;
- }
- x += ln; y += ln;
- }
- }
- if (mq[0] > mq[1]) { // then take the first alignment
- n_cigar = nc;
- memcpy(cigar, cn, 4 * nc);
- p->len = nlen[0];
- } else {
- p->k = kk; p->len = nlen[1];
- n_cigar = j - nc;
- memcpy(cigar, cn + nc, 4 * (j - nc));
- }
- free(cn);
- }
- return n_cigar;
-}
-
-static int compute_nm(bsw2hit_t *p, int n_cigar, const uint32_t *cigar, const uint8_t *pac, const uint8_t *seq)
-{
- int k, x, n_mm = 0, i, n_gap = 0;
- bwtint_t y;
- x = 0; y = p->k;
- for (k = 0; k < n_cigar; ++k) {
- int op = cigar[k]&0xf;
- int len = cigar[k]>>4;
- if (op == 0) { // match
- for (i = 0; i < len; ++i) {
- int ref = pac[(y+i)>>2] >> (~(y+i)&3)*2 & 0x3;
- if (seq[x + i] != ref) ++n_mm;
- }
- x += len; y += len;
- } else if (op == 1) x += len, n_gap += len;
- else if (op == 2) y += len, n_gap += len;
- else if (op == 4) x += len;
- }
- return n_mm + n_gap;
-}
-
-static void write_aux(const bsw2opt_t *opt, const bntseq_t *bns, int qlen, uint8_t *seq[2], const uint8_t *pac, bwtsw2_t *b, const char *name)
-{
- int i;
- // allocate for b->aux
- if (b->n<<1 < b->max) {
- b->max = b->n;
- kroundup32(b->max);
- b->hits = realloc(b->hits, b->max * sizeof(bsw2hit_t));
- }
- b->aux = calloc(b->n, sizeof(bsw2aux_t));
- // generate CIGAR
- gen_cigar(opt, qlen, seq, pac, b, name);
- // fix CIGAR, generate mapQ, and write chromosomal position
- for (i = 0; i < b->n; ++i) {
- bsw2hit_t *p = &b->hits[i];
- bsw2aux_t *q = &b->aux[i];
- q->flag = p->flag & 0xfe;
- q->isize = 0;
- if (p->l == 0) { // unique hit
- float c = 1.0;
- int subo;
- // fix out-of-boundary CIGAR
- q->n_cigar = fix_cigar(bns, p, q->n_cigar, q->cigar);
- // compute the NM tag
- q->nm = compute_nm(p, q->n_cigar, q->cigar, pac, seq[p->is_rev]);
- // compute mapQ
- subo = p->G2 > opt->t? p->G2 : opt->t;
- if (p->flag>>16 == 1 || p->flag>>16 == 2) c *= .5;
- if (p->n_seeds < 2) c *= .2;
- q->qual = (int)(c * (p->G - subo) * (250.0 / p->G + 0.03 / opt->a) + .499);
- if (q->qual > 250) q->qual = 250;
- if (q->qual < 0) q->qual = 0;
- if (p->flag&1) q->qual = 0; // this is a random hit
- q->pqual = q->qual; // set the paired qual as qual
- // get the chromosomal position
- q->nn = bns_cnt_ambi(bns, p->k, p->len, &q->chr);
- q->pos = p->k - bns->anns[q->chr].offset;
- } else q->qual = 0, q->n_cigar = 0, q->chr = q->pos = -1, q->nn = 0;
- }
-}
-
-static void update_mate_aux(bwtsw2_t *b, const bwtsw2_t *m)
-{
- int i;
- if (m == 0) return;
- // update flag, mchr and mpos
- for (i = 0; i < b->n; ++i) {
- bsw2aux_t *q = &b->aux[i];
- q->flag |= 1; // paired
- if (m->n == 0) q->flag |= 8; // mate unmapped
- if (m->n == 1) {
- q->mchr = m->aux[0].chr;
- q->mpos = m->aux[0].pos;
- if (m->aux[0].flag&0x10) q->flag |= 0x20; // mate reverse strand
- if (q->chr == q->mchr) { // set insert size
- if (q->mpos + m->hits[0].len > q->pos)
- q->isize = q->mpos + m->hits[0].len - q->pos;
- else q->isize = q->mpos - q->pos - b->hits[0].len;
- } else q->isize = 0;
- } else q->mchr = q->mpos = -1;
- }
- // update mapping quality
- if (b->n == 1 && m->n == 1) {
- bsw2hit_t *p = &b->hits[0];
- if (p->flag & BSW2_FLAG_MATESW) { // this alignment is found by Smith-Waterman
- if (!(p->flag & BSW2_FLAG_TANDEM) && b->aux[0].pqual < 20)
- b->aux[0].pqual = 20;
- if (b->aux[0].pqual >= m->aux[0].qual) b->aux[0].pqual = m->aux[0].qual;
- } else if ((p->flag & 2) && !(m->hits[0].flag & BSW2_FLAG_MATESW)) { // properly paired
- if (!(p->flag & BSW2_FLAG_TANDEM)) { // pqual is bounded by [b->aux[0].qual,m->aux[0].qual]
- b->aux[0].pqual += 20;
- if (b->aux[0].pqual > m->aux[0].qual) b->aux[0].pqual = m->aux[0].qual;
- if (b->aux[0].pqual < b->aux[0].qual) b->aux[0].pqual = b->aux[0].qual;
- }
- }
- }
-}
-
-/* generate SAM lines for a sequence in ks with alignment stored in
- * b. ks->name and ks->seq will be freed and set to NULL in the end. */
-static void print_hits(const bntseq_t *bns, const bsw2opt_t *opt, bsw2seq1_t *ks, bwtsw2_t *b, int is_pe, bwtsw2_t *bmate)
-{
- int i, k;
- kstring_t str;
- memset(&str, 0, sizeof(kstring_t));
- if (b == 0 || b->n == 0) { // no hits
- ksprintf(&str, "%s\t4\t*\t0\t0\t*\t*\t0\t0\t", ks->name);
- for (i = 0; i < ks->l; ++i) kputc(ks->seq[i], &str);
- if (ks->qual) {
- kputc('\t', &str);
- for (i = 0; i < ks->l; ++i) kputc(ks->qual[i], &str);
- } else kputs("\t*", &str);
- kputc('\n', &str);
- }
- for (i = 0; b && i < b->n; ++i) {
- bsw2hit_t *p = b->hits + i;
- bsw2aux_t *q = b->aux + i;
- int j, beg, end, type = 0;
- // print mandatory fields before SEQ
- ksprintf(&str, "%s\t%d", ks->name, q->flag | (opt->multi_2nd && i? 0x100 : 0));
- ksprintf(&str, "\t%s\t%ld", q->chr>=0? bns->anns[q->chr].name : "*", (long)q->pos + 1);
- if (p->l == 0) { // not a repetitive hit
- ksprintf(&str, "\t%d\t", q->pqual);
- for (k = 0; k < q->n_cigar; ++k)
- ksprintf(&str, "%d%c", q->cigar[k]>>4, (opt->hard_clip? "MIDNHHP" : "MIDNSHP")[q->cigar[k]&0xf]);
- } else ksprintf(&str, "\t0\t*");
- if (!is_pe) kputs("\t*\t0\t0\t", &str);
- else ksprintf(&str, "\t%s\t%d\t%d\t", q->mchr==q->chr? "=" : (q->mchr<0? "*" : bns->anns[q->mchr].name), q->mpos+1, q->isize);
- // get the sequence begin and end
- beg = 0; end = ks->l;
- if (opt->hard_clip) {
- if ((q->cigar[0]&0xf) == 4) beg += q->cigar[0]>>4;
- if ((q->cigar[q->n_cigar-1]&0xf) == 4) end -= q->cigar[q->n_cigar-1]>>4;
- }
- for (j = beg; j < end; ++j) {
- if (p->flag&0x10) kputc(nt_comp_table[(int)ks->seq[ks->l - 1 - j]], &str);
- else kputc(ks->seq[j], &str);
- }
- // print base quality if present
- if (ks->qual) {
- kputc('\t', &str);
- for (j = beg; j < end; ++j) {
- if (p->flag&0x10) kputc(ks->qual[ks->l - 1 - j], &str);
- else kputc(ks->qual[j], &str);
- }
- } else ksprintf(&str, "\t*");
- // print optional tags
- ksprintf(&str, "\tAS:i:%d\tXS:i:%d\tXF:i:%d\tXE:i:%d\tNM:i:%d", p->G, p->G2, p->flag>>16, p->n_seeds, q->nm);
- if (q->nn) ksprintf(&str, "\tXN:i:%d", q->nn);
- if (p->l) ksprintf(&str, "\tXI:i:%d", p->l - p->k + 1);
- if (p->flag&BSW2_FLAG_MATESW) type |= 1;
- if (p->flag&BSW2_FLAG_TANDEM) type |= 2;
- if (type) ksprintf(&str, "\tXT:i:%d", type);
- kputc('\n', &str);
- }
- ks->sam = str.s;
- free(ks->seq); ks->seq = 0;
- free(ks->qual); ks->qual = 0;
- free(ks->name); ks->name = 0;
-}
-
-static void update_opt(bsw2opt_t *dst, const bsw2opt_t *src, int qlen)
-{
- double ll = log(qlen);
- int i, k;
- *dst = *src;
- if (dst->t < ll * dst->coef) dst->t = (int)(ll * dst->coef + .499);
- // set band width: the query length sets a boundary on the maximum band width
- k = (qlen * dst->a - 2 * dst->q) / (2 * dst->r + dst->a);
- i = (qlen * dst->a - dst->a - dst->t) / dst->r;
- if (k > i) k = i;
- if (k < 1) k = 1; // I do not know if k==0 causes troubles
- dst->bw = src->bw < k? src->bw : k;
-}
-
-/* Core routine to align reads in _seq. It is separated from
- * process_seqs() to realize multi-threading */
-static void bsw2_aln_core(bsw2seq_t *_seq, const bsw2opt_t *_opt, const bntseq_t *bns, uint8_t *pac, const bwt_t *target, int is_pe)
-{
- int x;
- bsw2opt_t opt;
- bsw2global_t *pool = bsw2_global_init();
- bwtsw2_t **buf;
- buf = calloc(_seq->n, sizeof(void*));
- for (x = 0; x < _seq->n; ++x) {
- bsw2seq1_t *p = _seq->seq + x;
- uint8_t *seq[2], *rseq[2];
- int i, l, k;
- bwtsw2_t *b[2];
- l = p->l;
- update_opt(&opt, _opt, p->l);
- if (pool->max_l < l) { // then enlarge working space for aln_extend_core()
- int tmp = ((l + 1) / 2 * opt.a + opt.r) / opt.r + l;
- pool->max_l = l;
- pool->aln_mem = realloc(pool->aln_mem, (tmp + 2) * 24);
- }
- // set seq[2] and rseq[2]
- seq[0] = calloc(l * 4, 1);
- seq[1] = seq[0] + l;
- rseq[0] = seq[1] + l; rseq[1] = rseq[0] + l;
- // convert sequences to 2-bit representation
- for (i = k = 0; i < l; ++i) {
- int c = nst_nt4_table[(int)p->seq[i]];
- if (c >= 4) { c = (int)(drand48() * 4); ++k; } // FIXME: ambiguous bases are not properly handled
- seq[0][i] = c;
- seq[1][l-1-i] = 3 - c;
- rseq[0][l-1-i] = 3 - c;
- rseq[1][i] = c;
- }
- if (l - k < opt.t) { // too few unambiguous bases
- buf[x] = calloc(1, sizeof(bwtsw2_t));
- free(seq[0]); continue;
- }
- // alignment
- b[0] = bsw2_aln1_core(&opt, bns, pac, target, l, seq, pool);
- for (k = 0; k < b[0]->n; ++k)
- if (b[0]->hits[k].n_seeds < opt.t_seeds) break;
- if (k < b[0]->n) {
- b[1] = bsw2_aln1_core(&opt, bns, pac, target, l, rseq, pool);
- for (i = 0; i < b[1]->n; ++i) {
- bsw2hit_t *p = &b[1]->hits[i];
- int x = p->beg;
- p->flag ^= 0x10, p->is_rev ^= 1; // flip the strand
- p->beg = l - p->end;
- p->end = l - x;
- }
- flag_fr(b);
- merge_hits(b, l, 0);
- bsw2_resolve_duphits(0, 0, b[0], 0);
- bsw2_resolve_query_overlaps(b[0], opt.mask_level);
- } else b[1] = 0;
- // generate CIGAR and print SAM
- buf[x] = bsw2_dup_no_cigar(b[0]);
- // free
- free(seq[0]);
- bsw2_destroy(b[0]);
- }
- if (is_pe) bsw2_pair(&opt, bns->l_pac, pac, _seq->n, _seq->seq, buf);
- for (x = 0; x < _seq->n; ++x) {
- bsw2seq1_t *p = _seq->seq + x;
- uint8_t *seq[2];
- int i;
- seq[0] = malloc(p->l * 2); seq[1] = seq[0] + p->l;
- for (i = 0; i < p->l; ++i) {
- int c = nst_nt4_table[(int)p->seq[i]];
- if (c >= 4) c = (int)(drand48() * 4);
- seq[0][i] = c;
- seq[1][p->l-1-i] = 3 - c;
- }
- update_opt(&opt, _opt, p->l);
- write_aux(&opt, bns, p->l, seq, pac, buf[x], _seq->seq[x].name);
- free(seq[0]);
- }
- for (x = 0; x < _seq->n; ++x) {
- if (is_pe) update_mate_aux(buf[x], buf[x^1]);
- print_hits(bns, &opt, &_seq->seq[x], buf[x], is_pe, buf[x^1]);
- }
- for (x = 0; x < _seq->n; ++x) bsw2_destroy(buf[x]);
- free(buf);
- bsw2_global_destroy(pool);
-}
-
-#ifdef HAVE_PTHREAD
-typedef struct {
- int tid, is_pe;
- bsw2seq_t *_seq;
- const bsw2opt_t *_opt;
- const bntseq_t *bns;
- uint8_t *pac;
- const bwt_t *target;
-} thread_aux_t;
-
-/* another interface to bsw2_aln_core() to facilitate pthread_create() */
-static void *worker(void *data)
-{
- thread_aux_t *p = (thread_aux_t*)data;
- bsw2_aln_core(p->_seq, p->_opt, p->bns, p->pac, p->target, p->is_pe);
- return 0;
-}
-#endif
-
-/* process sequences stored in _seq, generate SAM lines for these
- * sequences and reset _seq afterwards. */
-static void process_seqs(bsw2seq_t *_seq, const bsw2opt_t *opt, const bntseq_t *bns, uint8_t *pac, const bwt_t *target, int is_pe)
-{
- int i;
- is_pe = is_pe? 1 : 0;
-
-#ifdef HAVE_PTHREAD
- if (opt->n_threads <= 1) {
- bsw2_aln_core(_seq, opt, bns, pac, target, is_pe);
- } else {
- pthread_t *tid;
- pthread_attr_t attr;
- thread_aux_t *data;
- int j;
- pthread_attr_init(&attr);
- pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
- data = (thread_aux_t*)calloc(opt->n_threads, sizeof(thread_aux_t));
- tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
- for (j = 0; j < opt->n_threads; ++j) {
- thread_aux_t *p = data + j;
- p->tid = j; p->_opt = opt; p->bns = bns; p->is_pe = is_pe;
- p->pac = pac; p->target = target;
- p->_seq = calloc(1, sizeof(bsw2seq_t));
- p->_seq->max = (_seq->n + opt->n_threads - 1) / opt->n_threads + 1;
- p->_seq->n = 0;
- p->_seq->seq = calloc(p->_seq->max, sizeof(bsw2seq1_t));
- }
- for (i = 0; i < _seq->n; ++i) { // assign sequences to each thread
- bsw2seq_t *p = data[(i>>is_pe)%opt->n_threads]._seq;
- p->seq[p->n++] = _seq->seq[i];
- }
- for (j = 0; j < opt->n_threads; ++j) pthread_create(&tid[j], &attr, worker, &data[j]);
- for (j = 0; j < opt->n_threads; ++j) pthread_join(tid[j], 0);
- for (j = 0; j < opt->n_threads; ++j) data[j]._seq->n = 0;
- for (i = 0; i < _seq->n; ++i) { // copy the result from each thread back
- bsw2seq_t *p = data[(i>>is_pe)%opt->n_threads]._seq;
- _seq->seq[i] = p->seq[p->n++];
- }
- for (j = 0; j < opt->n_threads; ++j) {
- thread_aux_t *p = data + j;
- free(p->_seq->seq);
- free(p->_seq);
- }
- free(data); free(tid);
- }
-#else
- bsw2_aln_core(_seq, opt, bns, pac, target, is_pe);
-#endif
-
- // print and reset
- for (i = 0; i < _seq->n; ++i) {
- bsw2seq1_t *p = _seq->seq + i;
- if (p->sam) printf("%s", p->sam);
- free(p->name); free(p->seq); free(p->qual); free(p->sam);
- p->tid = -1; p->l = 0;
- p->name = p->seq = p->qual = p->sam = 0;
- }
- fflush(stdout);
- _seq->n = 0;
-}
-
-static void kseq_to_bsw2seq(const kseq_t *ks, bsw2seq1_t *p)
-{
- p->tid = -1;
- p->l = ks->seq.l;
- p->name = strdup(ks->name.s);
- p->seq = strdup(ks->seq.s);
- p->qual = ks->qual.l? strdup(ks->qual.s) : 0;
- p->sam = 0;
-}
-
-void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target, const char *fn, const char *fn2)
-{
- gzFile fp, fp2;
- kseq_t *ks, *ks2;
- int l, size = 0, is_pe = 0;
- uint8_t *pac;
- bsw2seq_t *_seq;
-
- pac = calloc(bns->l_pac/4+1, 1);
- if (pac == 0) {
- fprintf(stderr, "[bsw2_aln] insufficient memory!\n");
- return;
- }
- for (l = 0; l < bns->n_seqs; ++l)
- printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[l].name, bns->anns[l].len);
- fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
- fp = xzopen(fn, "r");
- ks = kseq_init(fp);
- _seq = calloc(1, sizeof(bsw2seq_t));
- if (fn2) {
- fp2 = xzopen(fn2, "r");
- ks2 = kseq_init(fp2);
- is_pe = 1;
- } else fp2 = 0, ks2 = 0, is_pe = 0;
- while (kseq_read(ks) >= 0) {
- if (ks->name.l > 2 && ks->name.s[ks->name.l-2] == '/')
- ks->name.l -= 2, ks->name.s[ks->name.l] = 0;
- if (_seq->n == _seq->max) {
- _seq->max = _seq->max? _seq->max<<1 : 1024;
- _seq->seq = realloc(_seq->seq, _seq->max * sizeof(bsw2seq1_t));
- }
- kseq_to_bsw2seq(ks, &_seq->seq[_seq->n++]);
- size += ks->seq.l;
- if (ks2) {
- if (kseq_read(ks2) >= 0) {
- if (ks2->name.l > 2 && ks2->name.s[ks2->name.l-2] == '/')
- ks2->name.l -= 2, ks2->name.s[ks2->name.l] = 0;
- kseq_to_bsw2seq(ks2, &_seq->seq[_seq->n++]); // for PE, _seq->n here must be odd and we do not need to enlarge
- size += ks->seq.l;
- } else {
- fprintf(stderr, "[%s] The second query file has fewer reads. Switched to the single-end mode for the following batches.\n", __func__);
- is_pe = 0;
- }
- }
- if (size > opt->chunk_size * opt->n_threads) {
- fprintf(stderr, "[bsw2_aln] read %d sequences/pairs (%d bp)...\n", _seq->n, size);
- process_seqs(_seq, opt, bns, pac, target, is_pe);
- size = 0;
- }
- }
- fprintf(stderr, "[bsw2_aln] read %d sequences/pairs (%d bp)...\n", _seq->n, size);
- process_seqs(_seq, opt, bns, pac, target, is_pe);
- // free
- free(pac);
- free(_seq->seq); free(_seq);
- kseq_destroy(ks);
- gzclose(fp);
- if (fn2) {
- kseq_destroy(ks2);
- gzclose(fp2);
- }
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwtsw2_chain.c
--- a/bwa-0.6.2/bwtsw2_chain.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,107 +0,0 @@
-#include
-#include "bwtsw2.h"
-
-typedef struct {
- uint32_t tbeg, tend;
- int qbeg, qend;
- uint32_t flag:1, idx:31;
- int chain; // also reuse as a counter
-} hsaip_t;
-
-#define _hsaip_lt(a, b) ((a).qbeg < (b).qbeg)
-
-#include "ksort.h"
-KSORT_INIT(hsaip, hsaip_t, _hsaip_lt)
-
-static int chaining(const bsw2opt_t *opt, int shift, int n, hsaip_t *z, hsaip_t *chain)
-{
- int j, k, m = 0;
- ks_introsort(hsaip, n, z);
- for (j = 0; j < n; ++j) {
- hsaip_t *p = z + j;
- for (k = m - 1; k >= 0; --k) {
- hsaip_t *q = chain + k;
- int x = p->qbeg - q->qbeg; // always positive
- int y = p->tbeg - q->tbeg;
- if (y > 0 && x - y <= opt->bw && y - x <= opt->bw) {
- if (p->qend > q->qend) q->qend = p->qend;
- if (p->tend > q->tend) q->tend = p->tend;
- ++q->chain;
- p->chain = shift + k;
- break;
- }
- }
- if (k < 0) {
- chain[m] = *p;
- chain[m].chain = 1;
- chain[m].idx = p->chain = shift + m;
- ++m;
- }
- }
- return m;
-}
-
-void bsw2_chain_filter(const bsw2opt_t *opt, int len, bwtsw2_t *b[2])
-{
- hsaip_t *z[2], *chain[2];
- int i, j, k, n[2], m[2];
- char *flag;
- // initialization
- n[0] = b[0]->n; n[1] = b[1]->n;
- z[0] = calloc(n[0] + n[1], sizeof(hsaip_t));
- z[1] = z[0] + n[0];
- chain[0] = calloc(n[0] + n[1], sizeof(hsaip_t));
- for (k = j = 0; k < 2; ++k) {
- for (i = 0; i < b[k]->n; ++i) {
- bsw2hit_t *p = b[k]->hits + i;
- hsaip_t *q = z[k] + i;
- q->flag = k; q->idx = i;
- q->tbeg = p->k; q->tend = p->k + p->len;
- q->chain = -1;
- q->qbeg = p->beg; q->qend = p->end;
- }
- }
- // chaining
- m[0] = chaining(opt, 0, n[0], z[0], chain[0]);
- chain[1] = chain[0] + m[0];
- m[1] = chaining(opt, m[0], n[1], z[1], chain[1]);
- // change query coordinate on the reverse strand
- for (k = 0; k < m[1]; ++k) {
- hsaip_t *p = chain[1] + k;
- int tmp = p->qbeg;
- p->qbeg = len - p->qend; p->qend = len - tmp;
- }
- // filtering
- flag = calloc(m[0] + m[1], 1);
- ks_introsort(hsaip, m[0] + m[1], chain[0]);
- for (k = 1; k < m[0] + m[1]; ++k) {
- hsaip_t *p = chain[0] + k;
- for (j = 0; j < k; ++j) {
- hsaip_t *q = chain[0] + j;
- if (flag[q->idx]) continue;
- if (q->qend >= p->qend && q->chain > p->chain * opt->t_seeds * 2) {
- flag[p->idx] = 1;
- break;
- }
- }
- }
- for (k = 0; k < n[0] + n[1]; ++k) {
- hsaip_t *p = z[0] + k;
- if (flag[p->chain])
- b[p->flag]->hits[p->idx].G = 0;
- }
- free(flag);
- // squeeze out filtered elements in b[2]
- for (k = 0; k < 2; ++k) {
- for (j = i = 0; j < n[k]; ++j) {
- bsw2hit_t *p = b[k]->hits + j;
- if (p->G) {
- if (i != j) b[k]->hits[i++] = *p;
- else ++i;
- }
- }
- b[k]->n = i;
- }
- // free
- free(z[0]); free(chain[0]);
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwtsw2_core.c
--- a/bwa-0.6.2/bwtsw2_core.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,615 +0,0 @@
-#include
-#include
-#include
-#include
-#include
-#include "bwt_lite.h"
-#include "bwtsw2.h"
-#include "bwt.h"
-#include "kvec.h"
-
-typedef struct {
- bwtint_t k, l;
-} qintv_t;
-
-#define qintv_eq(a, b) ((a).k == (b).k && (a).l == (b).l)
-#define qintv_hash(a) ((a).k>>7^(a).l<<17)
-
-#include "khash.h"
-KHASH_INIT(qintv, qintv_t, uint64_t, 1, qintv_hash, qintv_eq)
-KHASH_MAP_INIT_INT64(64, uint64_t)
-
-#define MINUS_INF -0x3fffffff
-#define MASK_LEVEL 0.90f
-
-struct __mempool_t;
-static void mp_destroy(struct __mempool_t*);
-typedef struct {
- bwtint_t qk, ql;
- int I, D, G;
- uint32_t pj:2, qlen:30;
- int tlen;
- int ppos, upos;
- int cpos[4];
-} bsw2cell_t;
-
-#include "ksort.h"
-KSORT_INIT_GENERIC(int)
-#define __hitG_lt(a, b) (((a).G + ((int)(a).n_seeds<<2)) > (b).G + ((int)(b).n_seeds<<2))
-KSORT_INIT(hitG, bsw2hit_t, __hitG_lt)
-
-static const bsw2cell_t g_default_cell = { 0, 0, MINUS_INF, MINUS_INF, MINUS_INF, 0, 0, 0, -1, -1, {-1, -1, -1, -1} };
-
-typedef struct {
- int n, max;
- uint32_t tk, tl; // this is fine
- bsw2cell_t *array;
-} bsw2entry_t, *bsw2entry_p;
-
-/* --- BEGIN: Stack operations --- */
-typedef struct {
- int n_pending;
- kvec_t(bsw2entry_p) stack0, pending;
- struct __mempool_t *pool;
-} bsw2stack_t;
-
-#define stack_isempty(s) (kv_size(s->stack0) == 0 && s->n_pending == 0)
-static void stack_destroy(bsw2stack_t *s) { mp_destroy(s->pool); kv_destroy(s->stack0); kv_destroy(s->pending); free(s); }
-inline static void stack_push0(bsw2stack_t *s, bsw2entry_p e) { kv_push(bsw2entry_p, s->stack0, e); }
-inline static bsw2entry_p stack_pop(bsw2stack_t *s)
-{
- assert(!(kv_size(s->stack0) == 0 && s->n_pending != 0));
- return kv_pop(s->stack0);
-}
-/* --- END: Stack operations --- */
-
-/* --- BEGIN: memory pool --- */
-typedef struct __mempool_t {
- int cnt; // if cnt!=0, then there must be memory leak
- kvec_t(bsw2entry_p) pool;
-} mempool_t;
-inline static bsw2entry_p mp_alloc(mempool_t *mp)
-{
- ++mp->cnt;
- if (kv_size(mp->pool) == 0) return (bsw2entry_t*)calloc(1, sizeof(bsw2entry_t));
- else return kv_pop(mp->pool);
-}
-inline static void mp_free(mempool_t *mp, bsw2entry_p e)
-{
- --mp->cnt; e->n = 0;
- kv_push(bsw2entry_p, mp->pool, e);
-}
-static void mp_destroy(struct __mempool_t *mp)
-{
- int i;
- for (i = 0; i != kv_size(mp->pool); ++i) {
- free(kv_A(mp->pool, i)->array);
- free(kv_A(mp->pool, i));
- }
- kv_destroy(mp->pool);
- free(mp);
-}
-/* --- END: memory pool --- */
-
-/* --- BEGIN: utilities --- */
-static khash_t(64) *bsw2_connectivity(const bwtl_t *b)
-{
- khash_t(64) *h;
- uint32_t k, l, cntk[4], cntl[4]; // this is fine
- uint64_t x;
- khiter_t iter;
- int j, ret;
- kvec_t(uint64_t) stack;
-
- kv_init(stack);
- h = kh_init(64);
- kh_resize(64, h, b->seq_len * 4);
- x = b->seq_len;
- kv_push(uint64_t, stack, x);
- while (kv_size(stack)) {
- x = kv_pop(stack);
- k = x>>32; l = (uint32_t)x;
- bwtl_2occ4(b, k-1, l, cntk, cntl);
- for (j = 0; j != 4; ++j) {
- k = b->L2[j] + cntk[j] + 1;
- l = b->L2[j] + cntl[j];
- if (k > l) continue;
- x = (uint64_t)k << 32 | l;
- iter = kh_put(64, h, x, &ret);
- if (ret) { // if not present
- kh_value(h, iter) = 1;
- kv_push(uint64_t, stack, x);
- } else ++kh_value(h, iter);
- }
- }
- kv_destroy(stack);
- //fprintf(stderr, "[bsw2_connectivity] %u nodes in the DAG\n", kh_size(h));
- return h;
-}
-// pick up top T matches at a node
-static void cut_tail(bsw2entry_t *u, int T, bsw2entry_t *aux)
-{
- int i, *a, n, x;
- if (u->n <= T) return;
- if (aux->max < u->n) {
- aux->max = u->n;
- aux->array = (bsw2cell_t*)realloc(aux->array, aux->max * sizeof(bsw2cell_t));
- }
- a = (int*)aux->array;
- for (i = n = 0; i != u->n; ++i)
- if (u->array[i].ql && u->array[i].G > 0)
- a[n++] = -u->array[i].G;
- if (n <= T) return;
- x = -ks_ksmall(int, n, a, T);
- n = 0;
- for (i = 0; i < u->n; ++i) {
- bsw2cell_t *p = u->array + i;
- if (p->G == x) ++n;
- if (p->G < x || (p->G == x && n >= T)) {
- p->qk = p->ql = 0; p->G = 0;
- if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -1;
- }
- }
-}
-// remove duplicated cells
-static inline void remove_duplicate(bsw2entry_t *u, khash_t(qintv) *hash)
-{
- int i, ret, j;
- khiter_t k;
- qintv_t key;
- kh_clear(qintv, hash);
- for (i = 0; i != u->n; ++i) {
- bsw2cell_t *p = u->array + i;
- if (p->ql == 0) continue;
- key.k = p->qk; key.l = p->ql;
- k = kh_put(qintv, hash, key, &ret);
- j = -1;
- if (ret == 0) {
- if ((uint32_t)kh_value(hash, k) >= p->G) j = i;
- else {
- j = kh_value(hash, k)>>32;
- kh_value(hash, k) = (uint64_t)i<<32 | p->G;
- }
- } else kh_value(hash, k) = (uint64_t)i<<32 | p->G;
- if (j >= 0) {
- p = u->array + j;
- p->qk = p->ql = 0; p->G = 0;
- if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -3;
- }
- }
-}
-// merge two entries
-static void merge_entry(const bsw2opt_t * __restrict opt, bsw2entry_t *u, bsw2entry_t *v, bwtsw2_t *b)
-{
- int i;
- if (u->n + v->n >= u->max) {
- u->max = u->n + v->n;
- u->array = (bsw2cell_t*)realloc(u->array, u->max * sizeof(bsw2cell_t));
- }
- for (i = 0; i != v->n; ++i) {
- bsw2cell_t *p = v->array + i;
- if (p->ppos >= 0) p->ppos += u->n;
- if (p->cpos[0] >= 0) p->cpos[0] += u->n;
- if (p->cpos[1] >= 0) p->cpos[1] += u->n;
- if (p->cpos[2] >= 0) p->cpos[2] += u->n;
- if (p->cpos[3] >= 0) p->cpos[3] += u->n;
- }
- memcpy(u->array + u->n, v->array, v->n * sizeof(bsw2cell_t));
- u->n += v->n;
-}
-
-static inline bsw2cell_t *push_array_p(bsw2entry_t *e)
-{
- if (e->n == e->max) {
- e->max = e->max? e->max<<1 : 256;
- e->array = (bsw2cell_t*)realloc(e->array, sizeof(bsw2cell_t) * e->max);
- }
- return e->array + e->n;
-}
-
-static inline double time_elapse(const struct rusage *curr, const struct rusage *last)
-{
- long t1 = (curr->ru_utime.tv_sec - last->ru_utime.tv_sec) + (curr->ru_stime.tv_sec - last->ru_stime.tv_sec);
- long t2 = (curr->ru_utime.tv_usec - last->ru_utime.tv_usec) + (curr->ru_stime.tv_usec - last->ru_stime.tv_usec);
- return (double)t1 + t2 * 1e-6;
-}
-/* --- END: utilities --- */
-
-/* --- BEGIN: processing partial hits --- */
-static void save_hits(const bwtl_t *bwt, int thres, bsw2hit_t *hits, bsw2entry_t *u)
-{
- int i;
- uint32_t k; // this is fine
- for (i = 0; i < u->n; ++i) {
- bsw2cell_t *p = u->array + i;
- if (p->G < thres) continue;
- for (k = u->tk; k <= u->tl; ++k) {
- int beg, end;
- bsw2hit_t *q = 0;
- beg = bwt->sa[k]; end = beg + p->tlen;
- if (p->G > hits[beg*2].G) {
- hits[beg*2+1] = hits[beg*2];
- q = hits + beg * 2;
- } else if (p->G > hits[beg*2+1].G) q = hits + beg * 2 + 1;
- if (q) {
- q->k = p->qk; q->l = p->ql; q->len = p->qlen; q->G = p->G;
- q->beg = beg; q->end = end; q->G2 = q->k == q->l? 0 : q->G;
- q->flag = q->n_seeds = 0;
- }
- }
- }
-}
-/* "narrow hits" are node-to-node hits that have a high score and
- * are not so repetitive (|SA interval|<=IS). */
-static void save_narrow_hits(const bwtl_t *bwtl, bsw2entry_t *u, bwtsw2_t *b1, int t, int IS)
-{
- int i;
- for (i = 0; i < u->n; ++i) {
- bsw2hit_t *q;
- bsw2cell_t *p = u->array + i;
- if (p->G >= t && p->ql - p->qk + 1 <= IS) { // good narrow hit
- if (b1->max == b1->n) {
- b1->max = b1->max? b1->max<<1 : 4;
- b1->hits = realloc(b1->hits, b1->max * sizeof(bsw2hit_t));
- }
- q = &b1->hits[b1->n++];
- q->k = p->qk; q->l = p->ql;
- q->len = p->qlen;
- q->G = p->G; q->G2 = 0;
- q->beg = bwtl->sa[u->tk]; q->end = q->beg + p->tlen;
- q->flag = 0;
- // delete p
- p->qk = p->ql = 0; p->G = 0;
- if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -3;
- }
- }
-}
-/* after this, "narrow SA hits" will be expanded and the coordinates
- * will be obtained and stored in b->hits[*].k. */
-int bsw2_resolve_duphits(const bntseq_t *bns, const bwt_t *bwt, bwtsw2_t *b, int IS)
-{
- int i, j, n, is_rev;
- if (b->n == 0) return 0;
- if (bwt && bns) { // convert to chromosomal coordinates if requested
- int old_n = b->n;
- bsw2hit_t *old_hits = b->hits;
- for (i = n = 0; i < b->n; ++i) { // compute the memory to allocated
- bsw2hit_t *p = old_hits + i;
- if (p->l - p->k + 1 <= IS) n += p->l - p->k + 1;
- else if (p->G > 0) ++n;
- }
- b->n = b->max = n;
- b->hits = calloc(b->max, sizeof(bsw2hit_t));
- for (i = j = 0; i < old_n; ++i) {
- bsw2hit_t *p = old_hits + i;
- if (p->l - p->k + 1 <= IS) { // the hit is no so repetitive
- bwtint_t k;
- if (p->G == 0 && p->k == 0 && p->l == 0 && p->len == 0) continue;
- for (k = p->k; k <= p->l; ++k) {
- b->hits[j] = *p;
- b->hits[j].k = bns_depos(bns, bwt_sa(bwt, k), &is_rev);
- b->hits[j].l = 0;
- b->hits[j].is_rev = is_rev;
- if (is_rev) b->hits[j].k -= p->len - 1;
- ++j;
- }
- } else if (p->G > 0) {
- b->hits[j] = *p;
- b->hits[j].k = bns_depos(bns, bwt_sa(bwt, p->k), &is_rev);
- b->hits[j].l = 0;
- b->hits[j].flag |= 1;
- b->hits[j].is_rev = is_rev;
- if (is_rev) b->hits[j].k -= p->len - 1;
- ++j;
- }
- }
- free(old_hits);
- }
- for (i = j = 0; i < b->n; ++i) // squeeze out empty elements
- if (b->hits[i].G) b->hits[j++] = b->hits[i];
- b->n = j;
- ks_introsort(hitG, b->n, b->hits);
- for (i = 1; i < b->n; ++i) {
- bsw2hit_t *p = b->hits + i;
- for (j = 0; j < i; ++j) {
- bsw2hit_t *q = b->hits + j;
- int compatible = 1;
- if (p->is_rev != q->is_rev) continue; // hits from opposite strands are not duplicates
- if (p->l == 0 && q->l == 0) {
- int qol = (p->end < q->end? p->end : q->end) - (p->beg > q->beg? p->beg : q->beg); // length of query overlap
- if (qol < 0) qol = 0;
- if ((float)qol / (p->end - p->beg) > MASK_LEVEL || (float)qol / (q->end - q->beg) > MASK_LEVEL) {
- int64_t tol = (int64_t)(p->k + p->len < q->k + q->len? p->k + p->len : q->k + q->len)
- - (int64_t)(p->k > q->k? p->k : q->k); // length of target overlap
- if ((double)tol / p->len > MASK_LEVEL || (double)tol / q->len > MASK_LEVEL)
- compatible = 0;
- }
- }
- if (!compatible) {
- p->G = 0;
- if (q->G2 < p->G2) q->G2 = p->G2;
- break;
- }
- }
- }
- n = i;
- for (i = j = 0; i < n; ++i) {
- if (b->hits[i].G == 0) continue;
- if (i != j) b->hits[j++] = b->hits[i];
- else ++j;
- }
- b->n = j;
- return b->n;
-}
-
-int bsw2_resolve_query_overlaps(bwtsw2_t *b, float mask_level)
-{
- int i, j, n;
- if (b->n == 0) return 0;
- ks_introsort(hitG, b->n, b->hits);
- { // choose a random one
- int G0 = b->hits[0].G;
- for (i = 1; i < b->n; ++i)
- if (b->hits[i].G != G0) break;
- j = (int)(i * drand48());
- if (j) {
- bsw2hit_t tmp;
- tmp = b->hits[0]; b->hits[0] = b->hits[j]; b->hits[j] = tmp;
- }
- }
- for (i = 1; i < b->n; ++i) {
- bsw2hit_t *p = b->hits + i;
- int all_compatible = 1;
- if (p->G == 0) break;
- for (j = 0; j < i; ++j) {
- bsw2hit_t *q = b->hits + j;
- int64_t tol = 0;
- int qol, compatible = 0;
- float fol;
- if (q->G == 0) continue;
- qol = (p->end < q->end? p->end : q->end) - (p->beg > q->beg? p->beg : q->beg);
- if (qol < 0) qol = 0;
- if (p->l == 0 && q->l == 0) {
- tol = (int64_t)(p->k + p->len < q->k + q->len? p->k + p->len : q->k + q->len)
- - (p->k > q->k? p->k : q->k);
- if (tol < 0) tol = 0;
- }
- fol = (float)qol / (p->end - p->beg < q->end - q->beg? p->end - p->beg : q->end - q->beg);
- if (fol < mask_level || (tol > 0 && qol < p->end - p->beg && qol < q->end - q->beg)) compatible = 1;
- if (!compatible) {
- if (q->G2 < p->G) q->G2 = p->G;
- all_compatible = 0;
- }
- }
- if (!all_compatible) p->G = 0;
- }
- n = i;
- for (i = j = 0; i < n; ++i) {
- if (b->hits[i].G == 0) continue;
- if (i != j) b->hits[j++] = b->hits[i];
- else ++j;
- }
- b->n = j;
- return j;
-}
-/* --- END: processing partial hits --- */
-
-/* --- BEGIN: global mem pool --- */
-bsw2global_t *bsw2_global_init()
-{
- bsw2global_t *pool;
- bsw2stack_t *stack;
- pool = calloc(1, sizeof(bsw2global_t));
- stack = calloc(1, sizeof(bsw2stack_t));
- stack->pool = (mempool_t*)calloc(1, sizeof(mempool_t));
- pool->stack = (void*)stack;
- return pool;
-}
-
-void bsw2_global_destroy(bsw2global_t *pool)
-{
- stack_destroy((bsw2stack_t*)pool->stack);
- free(pool->aln_mem);
- free(pool);
-}
-/* --- END: global mem pool --- */
-
-static inline int fill_cell(const bsw2opt_t *o, int match_score, bsw2cell_t *c[4])
-{
- int G = c[3]? c[3]->G + match_score : MINUS_INF;
- if (c[1]) {
- c[0]->I = c[1]->I > c[1]->G - o->q? c[1]->I - o->r : c[1]->G - o->qr;
- if (c[0]->I > G) G = c[0]->I;
- } else c[0]->I = MINUS_INF;
- if (c[2]) {
- c[0]->D = c[2]->D > c[2]->G - o->q? c[2]->D - o->r : c[2]->G - o->qr;
- if (c[0]->D > G) G = c[0]->D;
- } else c[0]->D = MINUS_INF;
- return(c[0]->G = G);
-}
-
-static void init_bwtsw2(const bwtl_t *target, const bwt_t *query, bsw2stack_t *s)
-{
- bsw2entry_t *u;
- bsw2cell_t *x;
-
- u = mp_alloc(s->pool);
- u->tk = 0; u->tl = target->seq_len;
- x = push_array_p(u);
- *x = g_default_cell;
- x->G = 0; x->qk = 0; x->ql = query->seq_len;
- u->n++;
- stack_push0(s, u);
-}
-/* On return, ret[1] keeps not-so-repetitive hits (narrow SA hits); ret[0] keeps all hits (right?) */
-bwtsw2_t **bsw2_core(const bntseq_t *bns, const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool)
-{
- bsw2stack_t *stack = (bsw2stack_t*)pool->stack;
- bwtsw2_t *b, *b1, **b_ret;
- int i, j, score_mat[16], *heap, heap_size, n_tot = 0;
- struct rusage curr, last;
- khash_t(qintv) *rhash;
- khash_t(64) *chash;
-
- // initialize connectivity hash (chash)
- chash = bsw2_connectivity(target);
- // calculate score matrix
- for (i = 0; i != 4; ++i)
- for (j = 0; j != 4; ++j)
- score_mat[i<<2|j] = (i == j)? opt->a : -opt->b;
- // initialize other variables
- rhash = kh_init(qintv);
- init_bwtsw2(target, query, stack);
- heap_size = opt->z;
- heap = calloc(heap_size, sizeof(int));
- // initialize the return struct
- b = (bwtsw2_t*)calloc(1, sizeof(bwtsw2_t));
- b->n = b->max = target->seq_len * 2;
- b->hits = calloc(b->max, sizeof(bsw2hit_t));
- b1 = (bwtsw2_t*)calloc(1, sizeof(bwtsw2_t));
- b_ret = calloc(2, sizeof(void*));
- b_ret[0] = b; b_ret[1] = b1;
- // initialize timer
- getrusage(0, &last);
- // the main loop: traversal of the DAG
- while (!stack_isempty(stack)) {
- int old_n, tj;
- bsw2entry_t *v;
- uint32_t tcntk[4], tcntl[4];
- bwtint_t k, l;
-
- v = stack_pop(stack); old_n = v->n;
- n_tot += v->n;
-
- for (i = 0; i < v->n; ++i) { // test max depth and band width
- bsw2cell_t *p = v->array + i;
- if (p->ql == 0) continue;
- if (p->tlen - (int)p->qlen > opt->bw || (int)p->qlen - p->tlen > opt->bw) {
- p->qk = p->ql = 0;
- if (p->ppos >= 0) v->array[p->ppos].cpos[p->pj] = -5;
- }
- }
-
- // get Occ for the DAG
- bwtl_2occ4(target, v->tk - 1, v->tl, tcntk, tcntl);
- for (tj = 0; tj != 4; ++tj) { // descend to the children
- bwtint_t qcntk[4], qcntl[4];
- int qj, *curr_score_mat = score_mat + tj * 4;
- khiter_t iter;
- bsw2entry_t *u;
-
- k = target->L2[tj] + tcntk[tj] + 1;
- l = target->L2[tj] + tcntl[tj];
- if (k > l) continue;
- // update counter
- iter = kh_get(64, chash, (uint64_t)k<<32 | l);
- --kh_value(chash, iter);
- // initialization
- u = mp_alloc(stack->pool);
- u->tk = k; u->tl = l;
- memset(heap, 0, sizeof(int) * opt->z);
- // loop through all the nodes in v
- for (i = 0; i < v->n; ++i) {
- bsw2cell_t *p = v->array + i, *x, *c[4]; // c[0]=>current, c[1]=>I, c[2]=>D, c[3]=>G
- int is_added = 0;
- if (p->ql == 0) continue; // deleted node
- c[0] = x = push_array_p(u);
- x->G = MINUS_INF;
- p->upos = x->upos = -1;
- if (p->ppos >= 0) { // parent has been visited
- c[1] = (v->array[p->ppos].upos >= 0)? u->array + v->array[p->ppos].upos : 0;
- c[3] = v->array + p->ppos; c[2] = p;
- if (fill_cell(opt, curr_score_mat[p->pj], c) > 0) { // then update topology at p and x
- x->ppos = v->array[p->ppos].upos; // the parent pos in u
- p->upos = u->n++; // the current pos in u
- if (x->ppos >= 0) u->array[x->ppos].cpos[p->pj] = p->upos; // the child pos of its parent in u
- is_added = 1;
- }
- } else {
- x->D = p->D > p->G - opt->q? p->D - opt->r : p->G - opt->qr;
- if (x->D > 0) {
- x->G = x->D;
- x->I = MINUS_INF; x->ppos = -1;
- p->upos = u->n++;
- is_added = 1;
- }
- }
- if (is_added) { // x has been added to u->array. fill the remaining variables
- x->cpos[0] = x->cpos[1] = x->cpos[2] = x->cpos[3] = -1;
- x->pj = p->pj; x->qk = p->qk; x->ql = p->ql; x->qlen = p->qlen; x->tlen = p->tlen + 1;
- if (x->G > -heap[0]) {
- heap[0] = -x->G;
- ks_heapadjust(int, 0, heap_size, heap);
- }
- }
- if ((x->G > opt->qr && x->G >= -heap[0]) || i < old_n) { // good node in u, or in v
- if (p->cpos[0] == -1 || p->cpos[1] == -1 || p->cpos[2] == -1 || p->cpos[3] == -1) {
- bwt_2occ4(query, p->qk - 1, p->ql, qcntk, qcntl);
- for (qj = 0; qj != 4; ++qj) { // descend to the prefix trie
- if (p->cpos[qj] != -1) continue; // this node will be visited later
- k = query->L2[qj] + qcntk[qj] + 1;
- l = query->L2[qj] + qcntl[qj];
- if (k > l) { p->cpos[qj] = -2; continue; }
- x = push_array_p(v);
- p = v->array + i; // p may not point to the correct position after realloc
- x->G = x->I = x->D = MINUS_INF;
- x->qk = k; x->ql = l; x->pj = qj; x->qlen = p->qlen + 1; x->ppos = i; x->tlen = p->tlen;
- x->cpos[0] = x->cpos[1] = x->cpos[2] = x->cpos[3] = -1;
- p->cpos[qj] = v->n++;
- } // ~for(qj)
- } // ~if(p->cpos[])
- } // ~if
- } // ~for(i)
- if (u->n) save_hits(target, opt->t, b->hits, u);
- { // push u to the stack (or to the pending array)
- uint32_t cnt, pos;
- cnt = (uint32_t)kh_value(chash, iter);
- pos = kh_value(chash, iter)>>32;
- if (pos) { // something in the pending array, then merge
- bsw2entry_t *w = kv_A(stack->pending, pos-1);
- if (u->n) {
- if (w->n < u->n) { // swap
- w = u; u = kv_A(stack->pending, pos-1); kv_A(stack->pending, pos-1) = w;
- }
- merge_entry(opt, w, u, b);
- }
- if (cnt == 0) { // move from pending to stack0
- remove_duplicate(w, rhash);
- save_narrow_hits(target, w, b1, opt->t, opt->is);
- cut_tail(w, opt->z, u);
- stack_push0(stack, w);
- kv_A(stack->pending, pos-1) = 0;
- --stack->n_pending;
- }
- mp_free(stack->pool, u);
- } else if (cnt) { // the first time
- if (u->n) { // push to the pending queue
- ++stack->n_pending;
- kv_push(bsw2entry_p, stack->pending, u);
- kh_value(chash, iter) = (uint64_t)kv_size(stack->pending)<<32 | cnt;
- } else mp_free(stack->pool, u);
- } else { // cnt == 0, then push to the stack
- bsw2entry_t *w = mp_alloc(stack->pool);
- save_narrow_hits(target, u, b1, opt->t, opt->is);
- cut_tail(u, opt->z, w);
- mp_free(stack->pool, w);
- stack_push0(stack, u);
- }
- }
- } // ~for(tj)
- mp_free(stack->pool, v);
- } // while(top)
- getrusage(0, &curr);
- for (i = 0; i < 2; ++i)
- for (j = 0; j < b_ret[i]->n; ++j)
- b_ret[i]->hits[j].n_seeds = 0;
- bsw2_resolve_duphits(bns, query, b, opt->is);
- bsw2_resolve_duphits(bns, query, b1, opt->is);
- //fprintf(stderr, "stats: %.3lf sec; %d elems\n", time_elapse(&curr, &last), n_tot);
- // free
- free(heap);
- kh_destroy(qintv, rhash);
- kh_destroy(64, chash);
- stack->pending.n = stack->stack0.n = 0;
- return b_ret;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwtsw2_main.c
--- a/bwa-0.6.2/bwtsw2_main.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,95 +0,0 @@
-#include
-#include
-#include
-#include
-#include
-#include "bwt.h"
-#include "bwtsw2.h"
-#include "utils.h"
-
-int bwa_bwtsw2(int argc, char *argv[])
-{
- extern char *bwa_infer_prefix(const char *hint);
- bsw2opt_t *opt;
- bwt_t *target;
- char buf[1024], *prefix;
- bntseq_t *bns;
- int c;
-
- opt = bsw2_init_opt();
- srand48(11);
- while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:s:c:N:Hf:MI:S")) >= 0) {
- switch (c) {
- case 'q': opt->q = atoi(optarg); break;
- case 'r': opt->r = atoi(optarg); break;
- case 'a': opt->a = atoi(optarg); break;
- case 'b': opt->b = atoi(optarg); break;
- case 'w': opt->bw = atoi(optarg); break;
- case 'T': opt->t = atoi(optarg); break;
- case 't': opt->n_threads = atoi(optarg); break;
- case 'z': opt->z = atoi(optarg); break;
- case 's': opt->is = atoi(optarg); break;
- case 'm': opt->mask_level = atof(optarg); break;
- case 'c': opt->coef = atof(optarg); break;
- case 'N': opt->t_seeds = atoi(optarg); break;
- case 'M': opt->multi_2nd = 1; break;
- case 'H': opt->hard_clip = 1; break;
- case 'f': xreopen(optarg, "w", stdout); break;
- case 'I': opt->max_ins = atoi(optarg); break;
- case 'S': opt->skip_sw = 1; break;
- }
- }
- opt->qr = opt->q + opt->r;
-
- if (optind + 2 > argc) {
- fprintf(stderr, "\n");
- fprintf(stderr, "Usage: bwa bwasw [options] [query2.fa]\n\n");
- fprintf(stderr, "Options: -a INT score for a match [%d]\n", opt->a);
- fprintf(stderr, " -b INT mismatch penalty [%d]\n", opt->b);
- fprintf(stderr, " -q INT gap open penalty [%d]\n", opt->q);
- fprintf(stderr, " -r INT gap extension penalty [%d]\n", opt->r);
- fprintf(stderr, " -w INT band width [%d]\n", opt->bw);
- fprintf(stderr, " -m FLOAT mask level [%.2f]\n", opt->mask_level);
- fprintf(stderr, "\n");
- fprintf(stderr, " -t INT number of threads [%d]\n", opt->n_threads);
- fprintf(stderr, " -f FILE file to output results to instead of stdout\n");
- fprintf(stderr, " -H in SAM output, use hard clipping instead of soft clipping\n");
- fprintf(stderr, " -M mark multi-part alignments as secondary\n");
- fprintf(stderr, " -S skip Smith-Waterman read pairing\n");
- fprintf(stderr, " -I INT ignore pairs with insert >=INT for inferring the size distr [%d]\n", opt->max_ins);
- fprintf(stderr, "\n");
- fprintf(stderr, " -T INT score threshold divided by a [%d]\n", opt->t);
- fprintf(stderr, " -c FLOAT coefficient of length-threshold adjustment [%.1f]\n", opt->coef);
- fprintf(stderr, " -z INT Z-best [%d]\n", opt->z);
- fprintf(stderr, " -s INT maximum seeding interval size [%d]\n", opt->is);
- fprintf(stderr, " -N INT # seeds to trigger reverse alignment [%d]\n", opt->t_seeds);
- fprintf(stderr, "\n");
- fprintf(stderr, "Note: For long Illumina, 454 and Sanger reads, assembly contigs, fosmids and\n");
- fprintf(stderr, " BACs, the default setting usually works well. For the current PacBio\n");
- fprintf(stderr, " reads (end of 2010), '-b5 -q2 -r1 -z10' is recommended. One may also\n");
- fprintf(stderr, " increase '-z' for better sensitivity.\n");
- fprintf(stderr, "\n");
-
- return 1;
- }
-
- // adjust opt for opt->a
- opt->t *= opt->a;
- opt->coef *= opt->a;
-
- if ((prefix = bwa_infer_prefix(argv[optind])) == 0) {
- fprintf(stderr, "[%s] fail to locate the index\n", __func__);
- return 0;
- }
- strcpy(buf, prefix); target = bwt_restore_bwt(strcat(buf, ".bwt"));
- strcpy(buf, prefix); bwt_restore_sa(strcat(buf, ".sa"), target);
- bns = bns_restore(prefix);
-
- bsw2_aln(opt, bns, target, argv[optind+1], optind+2 < argc? argv[optind+2] : 0);
-
- bns_destroy(bns);
- bwt_destroy(target);
- free(opt); free(prefix);
-
- return 0;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/bwtsw2_pair.c
--- a/bwa-0.6.2/bwtsw2_pair.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,291 +0,0 @@
-#include
-#include
-#include
-#include
-#include "bwt.h"
-#include "bntseq.h"
-#include "bwtsw2.h"
-#include "kstring.h"
-#ifndef _NO_SSE2
-#include "ksw.h"
-#else
-#include "stdaln.h"
-#endif
-
-#define MIN_RATIO 0.8
-#define OUTLIER_BOUND 2.0
-#define MAX_STDDEV 4.0
-#define EXT_STDDEV 4.0
-
-typedef struct {
- int low, high, failed;
- double avg, std;
-} bsw2pestat_t;
-
-bsw2pestat_t bsw2_stat(int n, bwtsw2_t **buf, kstring_t *msg, int max_ins)
-{
- extern void ks_introsort_uint64_t(size_t n, uint64_t *a);
- int i, k, x, p25, p50, p75, tmp, max_len = 0;
- uint64_t *isize;
- bsw2pestat_t r;
-
- memset(&r, 0, sizeof(bsw2pestat_t));
- isize = calloc(n, 8);
- for (i = k = 0; i < n; i += 2) {
- bsw2hit_t *t[2];
- int l;
- if (buf[i] == 0 || buf[i]->n != 1 || buf[i+1]->n != 1) continue; // more than 1 hits
- t[0] = &buf[i]->hits[0]; t[1] = &buf[i+1]->hits[0];
- if (t[0]->G2 > 0.8 * t[0]->G) continue; // the best hit is not good enough
- if (t[1]->G2 > 0.8 * t[1]->G) continue; // the best hit is not good enough
- l = t[0]->k > t[1]->k? t[0]->k - t[1]->k + t[1]->len : t[1]->k - t[0]->k + t[0]->len;
- if (l >= max_ins) continue; // skip pairs with excessively large insert
- max_len = max_len > t[0]->end - t[0]->beg? max_len : t[0]->end - t[0]->beg;
- max_len = max_len > t[1]->end - t[1]->beg? max_len : t[1]->end - t[1]->beg;
- isize[k++] = l;
- }
- ks_introsort_uint64_t(k, isize);
- p25 = isize[(int)(.25 * k + .499)];
- p50 = isize[(int)(.50 * k + .499)];
- p75 = isize[(int)(.75 * k + .499)];
- ksprintf(msg, "[%s] infer the insert size distribution from %d high-quality pairs.\n", __func__, k);
- if (k < 8) {
- ksprintf(msg, "[%s] fail to infer the insert size distribution.\n", __func__);
- free(isize);
- r.failed = 1;
- return r;
- }
- tmp = (int)(p25 - OUTLIER_BOUND * (p75 - p25) + .499);
- r.low = tmp > max_len? tmp : max_len;
- if (r.low < 1) r.low = 1;
- r.high = (int)(p75 + OUTLIER_BOUND * (p75 - p25) + .499);
- ksprintf(msg, "[%s] (25, 50, 75) percentile: (%d, %d, %d)\n", __func__, p25, p50, p75);
- ksprintf(msg, "[%s] low and high boundaries for computing mean and std.dev: (%d, %d)\n", __func__, r.low, r.high);
- for (i = x = 0, r.avg = 0; i < k; ++i)
- if (isize[i] >= r.low && isize[i] <= r.high)
- r.avg += isize[i], ++x;
- r.avg /= x;
- for (i = 0, r.std = 0; i < k; ++i)
- if (isize[i] >= r.low && isize[i] <= r.high)
- r.std += (isize[i] - r.avg) * (isize[i] - r.avg);
- r.std = sqrt(r.std / x);
- ksprintf(msg, "[%s] mean and std.dev: (%.2f, %.2f)\n", __func__, r.avg, r.std);
- tmp = (int)(p25 - 3. * (p75 - p25) + .499);
- r.low = tmp > max_len? tmp : max_len;
- if (r.low < 1) r.low = 1;
- r.high = (int)(p75 + 3. * (p75 - p25) + .499);
- if (r.low > r.avg - MAX_STDDEV * 4.) r.low = (int)(r.avg - MAX_STDDEV * 4. + .499);
- r.low = tmp > max_len? tmp : max_len;
- if (r.high < r.avg - MAX_STDDEV * 4.) r.high = (int)(r.avg + MAX_STDDEV * 4. + .499);
- ksprintf(msg, "[%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r.low, r.high);
- free(isize);
- return r;
-}
-
-typedef struct {
- int n_cigar, beg, end, len;
- int64_t pos;
- uint32_t *cigar;
-} pairaux_t;
-
-extern unsigned char nst_nt4_table[256];
-
-void bsw2_pair1(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, const bsw2pestat_t *st, const bsw2hit_t *h, int l_mseq, const char *mseq, bsw2hit_t *a, int8_t g_mat[25])
-{
- extern void seq_reverse(int len, ubyte_t *seq, int is_comp);
- int64_t k, beg, end;
- uint8_t *seq, *ref;
- int i;
- // compute the region start and end
- a->n_seeds = 1; a->flag |= BSW2_FLAG_MATESW; // before calling this routine, *a has been cleared with memset(0); the flag is set with 1<<6/7
- if (h->is_rev == 0) {
- beg = (int64_t)(h->k + st->avg - EXT_STDDEV * st->std - l_mseq + .499);
- if (beg < h->k) beg = h->k;
- end = (int64_t)(h->k + st->avg + EXT_STDDEV * st->std + .499);
- a->is_rev = 1; a->flag |= 16;
- } else {
- beg = (int64_t)(h->k + h->end - h->beg - st->avg - EXT_STDDEV * st->std + .499);
- end = (int64_t)(h->k + h->end - h->beg - st->avg + EXT_STDDEV * st->std + l_mseq + .499);
- if (end > h->k + (h->end - h->beg)) end = h->k + (h->end - h->beg);
- a->is_rev = 0;
- }
- if (beg < 1) beg = 1;
- if (end > l_pac) end = l_pac;
- if (end - beg < l_mseq) return;
- // generate the sequence
- seq = malloc(l_mseq + (end - beg));
- ref = seq + l_mseq;
- for (k = beg; k < end; ++k)
- ref[k - beg] = pac[k>>2] >> ((~k&3)<<1) & 0x3;
- if (h->is_rev == 0) {
- for (i = 0; i < l_mseq; ++i) { // on the reverse strand
- int c = nst_nt4_table[(int)mseq[i]];
- seq[l_mseq - 1 - i] = c > 3? 4 : 3 - c;
- }
- } else {
- for (i = 0; i < l_mseq; ++i) // on the forward strand
- seq[i] = nst_nt4_table[(int)mseq[i]];
- }
-#ifndef _NO_SSE2
- {
- ksw_query_t *q;
- ksw_aux_t aux[2];
- // forward Smith-Waterman
- aux[0].T = opt->t; aux[0].gapo = opt->q; aux[0].gape = opt->r; aux[1] = aux[0];
- q = ksw_qinit(l_mseq * g_mat[0] < 250? 1 : 2, l_mseq, seq, 5, g_mat);
- ksw_sse2(q, end - beg, ref, &aux[0]);
- free(q);
- if (aux[0].score < opt->t) {
- free(seq);
- return;
- }
- ++aux[0].qe; ++aux[0].te;
- // reverse Smith-Waterman
- seq_reverse(aux[0].qe, seq, 0);
- seq_reverse(aux[0].te, ref, 0);
- q = ksw_qinit(aux[0].qe * g_mat[0] < 250? 1 : 2, aux[0].qe, seq, 5, g_mat);
- ksw_sse2(q, aux[0].te, ref, &aux[1]);
- free(q);
- ++aux[1].qe; ++aux[1].te;
- // write output
- a->G = aux[0].score;
- a->G2 = aux[0].score2 > aux[1].score2? aux[0].score2 : aux[1].score2;
- if (a->G2 < opt->t) a->G2 = 0;
- if (a->G2) a->flag |= BSW2_FLAG_TANDEM;
- a->k = beg + (aux[0].te - aux[1].te);
- a->len = aux[1].te;
- a->beg = aux[0].qe - aux[1].qe;
- a->end = aux[0].qe;
- }
-#else
- {
- AlnParam ap;
- path_t path[2];
- int matrix[25];
- for (i = 0; i < 25; ++i) matrix[i] = g_mat[i];
- ap.gap_open = opt->q; ap.gap_ext = opt->r; ap.gap_end = opt->r;
- ap.matrix = matrix; ap.row = 5; ap.band_width = 50;
- a->G = aln_local_core(ref, end - beg, seq, l_mseq, &ap, path, 0, opt->t, &a->G2);
- if (a->G < opt->t) a->G = 0;
- if (a->G2 < opt->t) a->G2 = 0;
- a->k = beg + path[0].i - 1;
- a->len = path[1].i - path[0].i + 1;
- a->beg = path[0].j - 1;
- a->end = path[1].j;
- }
-#endif
- if (a->is_rev) i = a->beg, a->beg = l_mseq - a->end, a->end = l_mseq - i;
- free(seq);
-}
-
-void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, bsw2seq1_t *seq, bwtsw2_t **hits)
-{
- extern int bsw2_resolve_duphits(const bntseq_t *bns, const bwt_t *bwt, bwtsw2_t *b, int IS);
- bsw2pestat_t pes;
- int i, j, k, n_rescued = 0, n_moved = 0, n_fixed = 0;
- int8_t g_mat[25];
- kstring_t msg;
- memset(&msg, 0, sizeof(kstring_t));
- pes = bsw2_stat(n, hits, &msg, opt->max_ins);
- for (i = k = 0; i < 5; ++i) {
- for (j = 0; j < 4; ++j)
- g_mat[k++] = i == j? opt->a : -opt->b;
- g_mat[k++] = 0;
- }
- for (i = 0; i < n; i += 2) {
- bsw2hit_t a[2];
- memset(&a, 0, sizeof(bsw2hit_t) * 2);
- a[0].flag = 1<<6; a[1].flag = 1<<7;
- for (j = 0; j < 2; ++j) { // set the read1/2 flag
- if (hits[i+j] == 0) continue;
- for (k = 0; k < hits[i+j]->n; ++k) {
- bsw2hit_t *p = &hits[i+j]->hits[k];
- p->flag |= 1<<(6+j);
- }
- }
- if (pes.failed) continue;
- if (hits[i] == 0 || hits[i+1] == 0) continue; // one end has excessive N
- if (hits[i]->n != 1 && hits[i+1]->n != 1) continue; // no end has exactly one hit
- if (hits[i]->n > 1 || hits[i+1]->n > 1) continue; // one read has more than one hit
- if (!opt->skip_sw) {
- if (hits[i+0]->n == 1) bsw2_pair1(opt, l_pac, pac, &pes, &hits[i+0]->hits[0], seq[i+1].l, seq[i+1].seq, &a[1], g_mat);
- if (hits[i+1]->n == 1) bsw2_pair1(opt, l_pac, pac, &pes, &hits[i+1]->hits[0], seq[i+0].l, seq[i+0].seq, &a[0], g_mat);
- } // else a[0].G == a[1].G == a[0].G2 == a[1].G2 == 0
- // the following enumerate all possibilities. It is tedious but necessary...
- if (hits[i]->n + hits[i+1]->n == 1) { // one end mapped; the other not;
- bwtsw2_t *p[2];
- int which;
- if (hits[i]->n == 1) p[0] = hits[i], p[1] = hits[i+1], which = 1;
- else p[0] = hits[i+1], p[1] = hits[i], which = 0;
- if (a[which].G == 0) continue;
- a[which].flag |= BSW2_FLAG_RESCUED;
- if (p[1]->max == 0) {
- p[1]->max = 1;
- p[1]->hits = malloc(sizeof(bsw2hit_t));
- }
- p[1]->hits[0] = a[which];
- p[1]->n = 1;
- p[0]->hits[0].flag |= 2;
- p[1]->hits[0].flag |= 2;
- ++n_rescued;
- } else { // then both ends mapped
- int is_fixed = 0;
- //fprintf(stderr, "%d; %lld,%lld; %d,%d\n", a[0].is_rev, hits[i]->hits[0].k, a[0].k, hits[i]->hits[0].end, a[0].end);
- for (j = 0; j < 2; ++j) { // fix wrong mappings and wrong suboptimal alignment score
- bsw2hit_t *p = &hits[i+j]->hits[0];
- if (p->G < a[j].G) { // the orginal mapping is suboptimal
- a[j].G2 = a[j].G2 > p->G? a[j].G2 : p->G; // FIXME: reset BSW2_FLAG_TANDEM?
- *p = a[j];
- ++n_fixed;
- is_fixed = 1;
- } else if (p->k != a[j].k && p->G2 < a[j].G) {
- p->G2 = a[j].G;
- } else if (p->k == a[j].k && p->G2 < a[j].G2) {
- p->G2 = a[j].G2;
- }
- }
- if (hits[i]->hits[0].k == a[0].k && hits[i+1]->hits[0].k == a[1].k) { // properly paired and no ends need to be moved
- for (j = 0; j < 2; ++j)
- hits[i+j]->hits[0].flag |= 2 | (a[j].flag & BSW2_FLAG_TANDEM);
- } else if (hits[i]->hits[0].k == a[0].k || hits[i+1]->hits[0].k == a[1].k) { // a tandem match
- for (j = 0; j < 2; ++j) {
- hits[i+j]->hits[0].flag |= 2;
- if (hits[i+j]->hits[0].k != a[j].k)
- hits[i+j]->hits[0].flag |= BSW2_FLAG_TANDEM;
- }
- } else if (!is_fixed && (a[0].G || a[1].G)) { // it is possible to move one end
- if (a[0].G && a[1].G) { // now we have two "proper pairs"
- int G[2];
- double diff;
- G[0] = hits[i]->hits[0].G + a[1].G;
- G[1] = hits[i+1]->hits[0].G + a[0].G;
- diff = fabs(G[0] - G[1]) / (opt->a + opt->b) / ((hits[i]->hits[0].len + a[1].len + hits[i+1]->hits[0].len + a[0].len) / 2.);
- if (diff > 0.05) a[G[0] > G[1]? 0 : 1].G = 0;
- }
- if (a[0].G == 0 || a[1].G == 0) { // one proper pair only
- bsw2hit_t *p[2]; // p[0] points the unchanged hit; p[1] to the hit to be moved
- int which, isize;
- double dev, diff;
- if (a[0].G) p[0] = &hits[i+1]->hits[0], p[1] = &hits[i]->hits[0], which = 0;
- else p[0] = &hits[i]->hits[0], p[1] = &hits[i+1]->hits[0], which = 1;
- isize = p[0]->is_rev? p[0]->k + p[0]->len - a[which].k : a[which].k + a[which].len - p[0]->k;
- dev = fabs(isize - pes.avg) / pes.std;
- diff = (double)(p[1]->G - a[which].G) / (opt->a + opt->b) / (p[1]->end - p[1]->beg) * 100.0;
- if (diff < dev * 2.) { // then move (heuristic)
- a[which].G2 = a[which].G;
- p[1][0] = a[which];
- p[1]->flag |= BSW2_FLAG_MOVED | 2;
- p[0]->flag |= 2;
- ++n_moved;
- }
- }
- } else if (is_fixed) {
- hits[i+0]->hits[0].flag |= 2;
- hits[i+1]->hits[0].flag |= 2;
- }
- }
- }
- ksprintf(&msg, "[%s] #fixed=%d, #rescued=%d, #moved=%d\n", __func__, n_fixed, n_rescued, n_moved);
- fputs(msg.s, stderr);
- free(msg.s);
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/cs2nt.c
--- a/bwa-0.6.2/cs2nt.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,191 +0,0 @@
-#include
-#include
-#include
-#include "bwtaln.h"
-#include "stdaln.h"
-
-/*
- Here is a delicate example. ref_nt=ATTAAC(RBRBG), read_cs=RBBOG. If we
- decode as ATTGAC(RBGOG), there are one color change and one nt change;
- if we decode as ATTAAC(RBRBG), there are two color changes.
-
- In DP, if color quality is smaller than COLOR_MM, we will use COLOR_MM
- as the penalty; otherwise, we will use color quality as the
- penalty. This means we always prefer two consistent color changes over
- a nt change, but if a color has high quality, we may prefer one nt
- change.
-
- In the above example, the penalties of the two types of decoding are
- q(B)+25 and q(B)+q(O), respectively. If q(O)>25, we prefer the first;
- otherwise the second. Note that no matter what we choose, the fourth
- base will get a low nt quality.
- */
-
-#define COLOR_MM 19
-#define NUCL_MM 25
-
-static const int nst_ntnt2cs_table[] = { 4, 0, 0, 1, 0, 2, 3, 4, 0, 3, 2, 4, 1, 4, 4, 4 };
-
-/*
- {A,C,G,T,N} -> {0,1,2,3,4}
- nt_ref[0..size]: nucleotide reference: 0/1/2/3/4
- cs_read[0..size-1]: color read+qual sequence: base<<6|qual; qual==63 for N
- nt_read[0..size]: nucleotide read sequence: 0/1/2/3 (returned)
- btarray[0..4*size]: backtrack array (working space)
- */
-void cs2nt_DP(int size, const uint8_t *nt_ref, const uint8_t *cs_read, uint8_t *nt_read, uint8_t *btarray)
-{
- int h[8], curr, last;
- int x, y, xmin, hmin, k;
-
- // h[0..3] and h[4..7] are the current and last best score array, depending on curr and last
-
- // recursion: initial value
- if (nt_ref[0] >= 4) memset(h, 0, sizeof(int) << 2);
- else {
- for (x = 0; x != 4; ++x) h[x] = NUCL_MM;
- h[nt_ref[0]] = 0;
- }
- // recursion: main loop
- curr = 1; last = 0;
- for (k = 1; k <= size; ++k) {
- for (x = 0; x != 4; ++x) {
- int min = 0x7fffffff, ymin = 0;
- for (y = 0; y != 4; ++y) {
- int s = h[last<<2|y];
- if ((cs_read[k-1]&0x3f) != 63 && cs_read[k-1]>>6 != nst_ntnt2cs_table[1<= 0; --k)
- nt_read[k] = btarray[(k+1)<<2 | nt_read[k+1]];
-}
-/*
- nt_read[0..size]: nucleotide read sequence: 0/1/2/3
- cs_read[0..size-1]: color read+qual sequence: base<<6|qual; qual==63 for N
- tarray[0..size*2-1]: temporary array
- */
-uint8_t *cs2nt_nt_qual(int size, const uint8_t *nt_read, const uint8_t *cs_read, uint8_t *tarray)
-{
- int k, c1, c2;
- uint8_t *t2array = tarray + size;
- // get the color sequence of nt_read
- c1 = nt_read[0];
- for (k = 1; k <= size; ++k) {
- c2 = nt_read[k]; // in principle, there is no 'N' in nt_read[]; just in case
- tarray[k-1] = (c1 >= 4 || c2 >= 4)? 4 : nst_ntnt2cs_table[1<>6 && tarray[k] == cs_read[k]>>6) {
- q = (int)(cs_read[k-1]&0x3f) + (int)(cs_read[k]&0x3f) + 10;
- } else if (tarray[k-1] == cs_read[k-1]>>6) {
- q = (int)(cs_read[k-1]&0x3f) - (int)(cs_read[k]&0x3f);
- } else if (tarray[k] == cs_read[k]>>6) {
- q = (int)(cs_read[k]&0x3f) - (int)(cs_read[k-1]&0x3f);
- } // else, q = 0
- if (q < 0) q = 0;
- if (q > 60) q = 60;
- t2array[k] = nt_read[k]<<6 | q;
- if ((cs_read[k-1]&0x3f) == 63 || (cs_read[k]&0x3f) == 63) t2array[k] = 0;
- }
- return t2array + 1; // of size-2
-}
-
-// this function will be called when p->seq has been reversed by refine_gapped()
-void bwa_cs2nt_core(bwa_seq_t *p, bwtint_t l_pac, ubyte_t *pac)
-{
- uint8_t *ta, *nt_read, *btarray, *tarray, *nt_ref, *cs_read, *new_nt_read;
- int i, len;
- uint8_t *seq;
-
- // set temporary arrays
- if (p->type == BWA_TYPE_NO_MATCH) return;
- len = p->len + p->n_gapo + p->n_gape + 100; // leave enough space
- ta = (uint8_t*)malloc(len * 7);
- nt_ref = ta;
- cs_read = nt_ref + len;
- nt_read = cs_read + len;
- btarray = nt_read + len;
- tarray = nt_read + len;
-
-#define __gen_csbase(_cs, _i, _seq) do { \
- int q = p->qual[p->strand? p->len - 1 - (_i) : (_i)] - 33; \
- if (q > 60) q = 60; \
- if (_seq[_i] > 3) q = 63; \
- (_cs) = _seq[_i]<<6 | q; \
- } while (0)
-
- // generate len, nt_ref[] and cs_read
- seq = p->strand? p->rseq : p->seq;
- nt_ref[0] = p->pos? bns_pac(pac, p->pos-1) : 4;
- if (p->cigar == 0) { // no gap or clipping
- len = p->len;
- for (i = 0; i < p->len; ++i) {
- __gen_csbase(cs_read[i], i, seq);
- nt_ref[i+1] = bns_pac(pac, p->pos + i);
- }
- } else {
- int k, z;
- bwtint_t x, y;
- x = p->pos; y = 0;
- for (k = z = 0; k < p->n_cigar; ++k) {
- int l = __cigar_len(p->cigar[k]);
- if (__cigar_op(p->cigar[k]) == FROM_M) {
- for (i = 0; i < l; ++i, ++x, ++y) {
- __gen_csbase(cs_read[z], y, seq);
- nt_ref[z+1] = bns_pac(pac, x);
- ++z;
- }
- } else if (__cigar_op(p->cigar[k]) == FROM_I) {
- for (i = 0; i < l; ++i, ++y) {
- __gen_csbase(cs_read[z], y, seq);
- nt_ref[z+1] = 4;
- ++z;
- }
- } else if (__cigar_op(p->cigar[k]) == FROM_S) y += l;
- else x += l;
- }
- len = z;
- }
-
- cs2nt_DP(len, nt_ref, cs_read, nt_read, btarray);
- new_nt_read = cs2nt_nt_qual(len, nt_read, cs_read, tarray);
-
- // update p
- p->len = p->full_len = len - 1;
- for (i = 0; i < p->len; ++i) {
- if ((new_nt_read[i]&0x3f) == 63) {
- p->qual[i] = 33; seq[i] = 4;
- } else {
- p->qual[i] = (new_nt_read[i]&0x3f) + 33;
- seq[i] = new_nt_read[i]>>6;
- }
- }
- p->qual[p->len] = seq[p->len] = 0;
- if (p->strand) {
- memcpy(p->seq, seq, p->len);
- seq_reverse(p->len, p->seq, 1);
- seq_reverse(p->len, p->qual, 0);
- } else {
- memcpy(p->rseq, seq, p->len);
- seq_reverse(p->len, p->rseq, 1);
- }
- free(ta);
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/fastmap.c
--- a/bwa-0.6.2/fastmap.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,127 +0,0 @@
-#include
-#include
-#include
-#include
-#include "bntseq.h"
-#include "bwt.h"
-#include "kvec.h"
-#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
-
-extern unsigned char nst_nt4_table[256];
-
-typedef struct {
- const bwt_t *bwt;
- const uint8_t *query;
- int start, len;
- bwtintv_v *tmpvec[2], *matches;
-} smem_i;
-
-smem_i *smem_iter_init(const bwt_t *bwt)
-{
- smem_i *iter;
- iter = calloc(1, sizeof(smem_i));
- iter->bwt = bwt;
- iter->tmpvec[0] = calloc(1, sizeof(bwtintv_v));
- iter->tmpvec[1] = calloc(1, sizeof(bwtintv_v));
- iter->matches = calloc(1, sizeof(bwtintv_v));
- return iter;
-}
-
-void smem_iter_destroy(smem_i *iter)
-{
- free(iter->tmpvec[0]->a);
- free(iter->tmpvec[1]->a);
- free(iter->matches->a);
- free(iter);
-}
-
-void smem_set_query(smem_i *iter, int len, const uint8_t *query)
-{
- iter->query = query;
- iter->start = 0;
- iter->len = len;
-}
-
-int smem_next(smem_i *iter)
-{
- iter->tmpvec[0]->n = iter->tmpvec[1]->n = iter->matches->n = 0;
- if (iter->start >= iter->len || iter->start < 0) return -1;
- while (iter->start < iter->len && iter->query[iter->start] > 3) ++iter->start; // skip ambiguous bases
- if (iter->start == iter->len) return -1;
- iter->start = bwt_smem1(iter->bwt, iter->len, iter->query, iter->start, iter->matches, iter->tmpvec);
- return iter->start;
-}
-
-int main_fastmap(int argc, char *argv[])
-{
- int c, i, min_iwidth = 20, min_len = 17, print_seq = 0;
- kseq_t *seq;
- bwtint_t k;
- gzFile fp;
- bwt_t *bwt;
- bntseq_t *bns;
- smem_i *iter;
-
- while ((c = getopt(argc, argv, "w:l:s")) >= 0) {
- switch (c) {
- case 's': print_seq = 1; break;
- case 'w': min_iwidth = atoi(optarg); break;
- case 'l': min_len = atoi(optarg); break;
- }
- }
- if (optind + 1 >= argc) {
- fprintf(stderr, "Usage: bwa fastmap [-s] [-l minLen=%d] [-w maxSaSize=%d] \n", min_len, min_iwidth);
- return 1;
- }
-
- fp = gzopen(argv[optind + 1], "r");
- seq = kseq_init(fp);
- { // load the packed sequences, BWT and SA
- char *tmp = calloc(strlen(argv[optind]) + 5, 1);
- strcat(strcpy(tmp, argv[optind]), ".bwt");
- bwt = bwt_restore_bwt(tmp);
- strcat(strcpy(tmp, argv[optind]), ".sa");
- bwt_restore_sa(tmp, bwt);
- free(tmp);
- bns = bns_restore(argv[optind]);
- }
- iter = smem_iter_init(bwt);
- while (kseq_read(seq) >= 0) {
- printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l);
- if (print_seq) {
- putchar('\t');
- puts(seq->seq.s);
- } else putchar('\n');
- for (i = 0; i < seq->seq.l; ++i)
- seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
- smem_set_query(iter, seq->seq.l, (uint8_t*)seq->seq.s);
- while (smem_next(iter) > 0) {
- for (i = 0; i < iter->matches->n; ++i) {
- bwtintv_t *p = &iter->matches->a[i];
- if ((uint32_t)p->info - (p->info>>32) < min_len) continue;
- printf("EM\t%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
- if (p->x[2] <= min_iwidth) {
- for (k = 0; k < p->x[2]; ++k) {
- bwtint_t pos;
- int len, is_rev, ref_id;
- len = (uint32_t)p->info - (p->info>>32);
- pos = bns_depos(bns, bwt_sa(bwt, p->x[0] + k), &is_rev);
- if (is_rev) pos -= len - 1;
- bns_cnt_ambi(bns, pos, len, &ref_id);
- printf("\t%s:%c%ld", bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - bns->anns[ref_id].offset) + 1);
- }
- } else fputs("\t*", stdout);
- putchar('\n');
- }
- }
- puts("//");
- }
-
- smem_iter_destroy(iter);
- bns_destroy(bns);
- bwt_destroy(bwt);
- kseq_destroy(seq);
- gzclose(fp);
- return 0;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/is.c
--- a/bwa-0.6.2/is.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,218 +0,0 @@
-/*
- * sais.c for sais-lite
- * Copyright (c) 2008 Yuta Mori All Rights Reserved.
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-#include
-
-typedef unsigned char ubyte_t;
-#define chr(i) (cs == sizeof(int) ? ((const int *)T)[i]:((const unsigned char *)T)[i])
-
-/* find the start or end of each bucket */
-static void getCounts(const unsigned char *T, int *C, int n, int k, int cs)
-{
- int i;
- for (i = 0; i < k; ++i) C[i] = 0;
- for (i = 0; i < n; ++i) ++C[chr(i)];
-}
-static void getBuckets(const int *C, int *B, int k, int end)
-{
- int i, sum = 0;
- if (end) {
- for (i = 0; i < k; ++i) {
- sum += C[i];
- B[i] = sum;
- }
- } else {
- for (i = 0; i < k; ++i) {
- sum += C[i];
- B[i] = sum - C[i];
- }
- }
-}
-
-/* compute SA */
-static void induceSA(const unsigned char *T, int *SA, int *C, int *B, int n, int k, int cs)
-{
- int *b, i, j;
- int c0, c1;
- /* compute SAl */
- if (C == B) getCounts(T, C, n, k, cs);
- getBuckets(C, B, k, 0); /* find starts of buckets */
- j = n - 1;
- b = SA + B[c1 = chr(j)];
- *b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j;
- for (i = 0; i < n; ++i) {
- j = SA[i], SA[i] = ~j;
- if (0 < j) {
- --j;
- if ((c0 = chr(j)) != c1) {
- B[c1] = b - SA;
- b = SA + B[c1 = c0];
- }
- *b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j;
- }
- }
- /* compute SAs */
- if (C == B) getCounts(T, C, n, k, cs);
- getBuckets(C, B, k, 1); /* find ends of buckets */
- for (i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
- if (0 < (j = SA[i])) {
- --j;
- if ((c0 = chr(j)) != c1) {
- B[c1] = b - SA;
- b = SA + B[c1 = c0];
- }
- *--b = ((j == 0) || (chr(j - 1) > c1)) ? ~j : j;
- } else SA[i] = ~j;
- }
-}
-
-/*
- * find the suffix array SA of T[0..n-1] in {0..k-1}^n use a working
- * space (excluding T and SA) of at most 2n+O(1) for a constant alphabet
- */
-static int sais_main(const unsigned char *T, int *SA, int fs, int n, int k, int cs)
-{
- int *C, *B, *RA;
- int i, j, c, m, p, q, plen, qlen, name;
- int c0, c1;
- int diff;
-
- /* stage 1: reduce the problem by at least 1/2 sort all the
- * S-substrings */
- if (k <= fs) {
- C = SA + n;
- B = (k <= (fs - k)) ? C + k : C;
- } else if ((C = B = (int *) malloc(k * sizeof(int))) == NULL) return -2;
- getCounts(T, C, n, k, cs);
- getBuckets(C, B, k, 1); /* find ends of buckets */
- for (i = 0; i < n; ++i) SA[i] = 0;
- for (i = n - 2, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
- if ((c0 = chr(i)) < (c1 + c)) c = 1;
- else if (c != 0) SA[--B[c1]] = i + 1, c = 0;
- }
- induceSA(T, SA, C, B, n, k, cs);
- if (fs < k) free(C);
- /* compact all the sorted substrings into the first m items of SA
- * 2*m must be not larger than n (proveable) */
- for (i = 0, m = 0; i < n; ++i) {
- p = SA[i];
- if ((0 < p) && (chr(p - 1) > (c0 = chr(p)))) {
- for (j = p + 1; (j < n) && (c0 == (c1 = chr(j))); ++j);
- if ((j < n) && (c0 < c1)) SA[m++] = p;
- }
- }
- for (i = m; i < n; ++i) SA[i] = 0; /* init the name array buffer */
- /* store the length of all substrings */
- for (i = n - 2, j = n, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
- if ((c0 = chr(i)) < (c1 + c)) c = 1;
- else if (c != 0) {
- SA[m + ((i + 1) >> 1)] = j - i - 1;
- j = i + 1;
- c = 0;
- }
- }
- /* find the lexicographic names of all substrings */
- for (i = 0, name = 0, q = n, qlen = 0; i < m; ++i) {
- p = SA[i], plen = SA[m + (p >> 1)], diff = 1;
- if (plen == qlen) {
- for (j = 0; (j < plen) && (chr(p + j) == chr(q + j)); j++);
- if (j == plen) diff = 0;
- }
- if (diff != 0) ++name, q = p, qlen = plen;
- SA[m + (p >> 1)] = name;
- }
-
- /* stage 2: solve the reduced problem recurse if names are not yet
- * unique */
- if (name < m) {
- RA = SA + n + fs - m;
- for (i = n - 1, j = m - 1; m <= i; --i) {
- if (SA[i] != 0) RA[j--] = SA[i] - 1;
- }
- if (sais_main((unsigned char *) RA, SA, fs + n - m * 2, m, name, sizeof(int)) != 0) return -2;
- for (i = n - 2, j = m - 1, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
- if ((c0 = chr(i)) < (c1 + c)) c = 1;
- else if (c != 0) RA[j--] = i + 1, c = 0; /* get p1 */
- }
- for (i = 0; i < m; ++i) SA[i] = RA[SA[i]]; /* get index */
- }
- /* stage 3: induce the result for the original problem */
- if (k <= fs) {
- C = SA + n;
- B = (k <= (fs - k)) ? C + k : C;
- } else if ((C = B = (int *) malloc(k * sizeof(int))) == NULL) return -2;
- /* put all left-most S characters into their buckets */
- getCounts(T, C, n, k, cs);
- getBuckets(C, B, k, 1); /* find ends of buckets */
- for (i = m; i < n; ++i) SA[i] = 0; /* init SA[m..n-1] */
- for (i = m - 1; 0 <= i; --i) {
- j = SA[i], SA[i] = 0;
- SA[--B[chr(j)]] = j;
- }
- induceSA(T, SA, C, B, n, k, cs);
- if (fs < k) free(C);
- return 0;
-}
-
-/**
- * Constructs the suffix array of a given string.
- * @param T[0..n-1] The input string.
- * @param SA[0..n] The output array of suffixes.
- * @param n The length of the given string.
- * @return 0 if no error occurred
- */
-int is_sa(const ubyte_t *T, int *SA, int n)
-{
- if ((T == NULL) || (SA == NULL) || (n < 0)) return -1;
- SA[0] = n;
- if (n <= 1) {
- if (n == 1) SA[1] = 0;
- return 0;
- }
- return sais_main(T, SA+1, 0, n, 256, 1);
-}
-
-/**
- * Constructs the burrows-wheeler transformed string of a given string.
- * @param T[0..n-1] The input string.
- * @param n The length of the given string.
- * @return The primary index if no error occurred, -1 or -2 otherwise.
- */
-int is_bwt(ubyte_t *T, int n)
-{
- int *SA, i, primary = 0;
- SA = (int*)calloc(n+1, sizeof(int));
- is_sa(T, SA, n);
-
- for (i = 0; i <= n; ++i) {
- if (SA[i] == 0) primary = i;
- else SA[i] = T[SA[i] - 1];
- }
- for (i = 0; i < primary; ++i) T[i] = SA[i];
- for (; i < n; ++i) T[i] = SA[i + 1];
- free(SA);
- return primary;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/khash.h
--- a/bwa-0.6.2/khash.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,506 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008, 2009 by attractor
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-/*
- An example:
-
-#include "khash.h"
-KHASH_MAP_INIT_INT(32, char)
-int main() {
- int ret, is_missing;
- khiter_t k;
- khash_t(32) *h = kh_init(32);
- k = kh_put(32, h, 5, &ret);
- if (!ret) kh_del(32, h, k);
- kh_value(h, k) = 10;
- k = kh_get(32, h, 10);
- is_missing = (k == kh_end(h));
- k = kh_get(32, h, 5);
- kh_del(32, h, k);
- for (k = kh_begin(h); k != kh_end(h); ++k)
- if (kh_exist(h, k)) kh_value(h, k) = 1;
- kh_destroy(32, h);
- return 0;
-}
-*/
-
-/*
- 2009-09-26 (0.2.4):
-
- * Improve portability
-
- 2008-09-19 (0.2.3):
-
- * Corrected the example
- * Improved interfaces
-
- 2008-09-11 (0.2.2):
-
- * Improved speed a little in kh_put()
-
- 2008-09-10 (0.2.1):
-
- * Added kh_clear()
- * Fixed a compiling error
-
- 2008-09-02 (0.2.0):
-
- * Changed to token concatenation which increases flexibility.
-
- 2008-08-31 (0.1.2):
-
- * Fixed a bug in kh_get(), which has not been tested previously.
-
- 2008-08-31 (0.1.1):
-
- * Added destructor
-*/
-
-
-#ifndef __AC_KHASH_H
-#define __AC_KHASH_H
-
-/*!
- @header
-
- Generic hash table library.
-
- @copyright Heng Li
- */
-
-#define AC_VERSION_KHASH_H "0.2.4"
-
-#include
-#include
-#include
-
-/* compipler specific configuration */
-
-#if UINT_MAX == 0xffffffffu
-typedef unsigned int khint32_t;
-#elif ULONG_MAX == 0xffffffffu
-typedef unsigned long khint32_t;
-#endif
-
-#if ULONG_MAX == ULLONG_MAX
-typedef unsigned long khint64_t;
-#else
-typedef unsigned long long khint64_t;
-#endif
-
-#ifdef _MSC_VER
-#define inline __inline
-#endif
-
-typedef khint32_t khint_t;
-typedef khint_t khiter_t;
-
-#define __ac_HASH_PRIME_SIZE 32
-static const khint32_t __ac_prime_list[__ac_HASH_PRIME_SIZE] =
-{
- 0ul, 3ul, 11ul, 23ul, 53ul,
- 97ul, 193ul, 389ul, 769ul, 1543ul,
- 3079ul, 6151ul, 12289ul, 24593ul, 49157ul,
- 98317ul, 196613ul, 393241ul, 786433ul, 1572869ul,
- 3145739ul, 6291469ul, 12582917ul, 25165843ul, 50331653ul,
- 100663319ul, 201326611ul, 402653189ul, 805306457ul, 1610612741ul,
- 3221225473ul, 4294967291ul
-};
-
-#define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2)
-#define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1)
-#define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3)
-#define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1)))
-#define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1)))
-#define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1)))
-#define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1))
-
-static const double __ac_HASH_UPPER = 0.77;
-
-#define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
- typedef struct { \
- khint_t n_buckets, size, n_occupied, upper_bound; \
- khint32_t *flags; \
- khkey_t *keys; \
- khval_t *vals; \
- } kh_##name##_t; \
- static inline kh_##name##_t *kh_init_##name() { \
- return (kh_##name##_t*)calloc(1, sizeof(kh_##name##_t)); \
- } \
- static inline void kh_destroy_##name(kh_##name##_t *h) \
- { \
- if (h) { \
- free(h->keys); free(h->flags); \
- free(h->vals); \
- free(h); \
- } \
- } \
- static inline void kh_clear_##name(kh_##name##_t *h) \
- { \
- if (h && h->flags) { \
- memset(h->flags, 0xaa, ((h->n_buckets>>4) + 1) * sizeof(khint32_t)); \
- h->size = h->n_occupied = 0; \
- } \
- } \
- static inline khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
- { \
- if (h->n_buckets) { \
- khint_t inc, k, i, last; \
- k = __hash_func(key); i = k % h->n_buckets; \
- inc = 1 + k % (h->n_buckets - 1); last = i; \
- while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
- if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \
- else i += inc; \
- if (i == last) return h->n_buckets; \
- } \
- return __ac_iseither(h->flags, i)? h->n_buckets : i; \
- } else return 0; \
- } \
- static inline void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \
- { \
- khint32_t *new_flags = 0; \
- khint_t j = 1; \
- { \
- khint_t t = __ac_HASH_PRIME_SIZE - 1; \
- while (__ac_prime_list[t] > new_n_buckets) --t; \
- new_n_buckets = __ac_prime_list[t+1]; \
- if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0; \
- else { \
- new_flags = (khint32_t*)malloc(((new_n_buckets>>4) + 1) * sizeof(khint32_t)); \
- memset(new_flags, 0xaa, ((new_n_buckets>>4) + 1) * sizeof(khint32_t)); \
- if (h->n_buckets < new_n_buckets) { \
- h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \
- if (kh_is_map) \
- h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \
- } \
- } \
- } \
- if (j) { \
- for (j = 0; j != h->n_buckets; ++j) { \
- if (__ac_iseither(h->flags, j) == 0) { \
- khkey_t key = h->keys[j]; \
- khval_t val; \
- if (kh_is_map) val = h->vals[j]; \
- __ac_set_isdel_true(h->flags, j); \
- while (1) { \
- khint_t inc, k, i; \
- k = __hash_func(key); \
- i = k % new_n_buckets; \
- inc = 1 + k % (new_n_buckets - 1); \
- while (!__ac_isempty(new_flags, i)) { \
- if (i + inc >= new_n_buckets) i = i + inc - new_n_buckets; \
- else i += inc; \
- } \
- __ac_set_isempty_false(new_flags, i); \
- if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { \
- { khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \
- if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \
- __ac_set_isdel_true(h->flags, i); \
- } else { \
- h->keys[i] = key; \
- if (kh_is_map) h->vals[i] = val; \
- break; \
- } \
- } \
- } \
- } \
- if (h->n_buckets > new_n_buckets) { \
- h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \
- if (kh_is_map) \
- h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \
- } \
- free(h->flags); \
- h->flags = new_flags; \
- h->n_buckets = new_n_buckets; \
- h->n_occupied = h->size; \
- h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \
- } \
- } \
- static inline khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
- { \
- khint_t x; \
- if (h->n_occupied >= h->upper_bound) { \
- if (h->n_buckets > (h->size<<1)) kh_resize_##name(h, h->n_buckets - 1); \
- else kh_resize_##name(h, h->n_buckets + 1); \
- } \
- { \
- khint_t inc, k, i, site, last; \
- x = site = h->n_buckets; k = __hash_func(key); i = k % h->n_buckets; \
- if (__ac_isempty(h->flags, i)) x = i; \
- else { \
- inc = 1 + k % (h->n_buckets - 1); last = i; \
- while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
- if (__ac_isdel(h->flags, i)) site = i; \
- if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \
- else i += inc; \
- if (i == last) { x = site; break; } \
- } \
- if (x == h->n_buckets) { \
- if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \
- else x = i; \
- } \
- } \
- } \
- if (__ac_isempty(h->flags, x)) { \
- h->keys[x] = key; \
- __ac_set_isboth_false(h->flags, x); \
- ++h->size; ++h->n_occupied; \
- *ret = 1; \
- } else if (__ac_isdel(h->flags, x)) { \
- h->keys[x] = key; \
- __ac_set_isboth_false(h->flags, x); \
- ++h->size; \
- *ret = 2; \
- } else *ret = 0; \
- return x; \
- } \
- static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \
- { \
- if (x != h->n_buckets && !__ac_iseither(h->flags, x)) { \
- __ac_set_isdel_true(h->flags, x); \
- --h->size; \
- } \
- }
-
-/* --- BEGIN OF HASH FUNCTIONS --- */
-
-/*! @function
- @abstract Integer hash function
- @param key The integer [khint32_t]
- @return The hash value [khint_t]
- */
-#define kh_int_hash_func(key) (khint32_t)(key)
-/*! @function
- @abstract Integer comparison function
- */
-#define kh_int_hash_equal(a, b) ((a) == (b))
-/*! @function
- @abstract 64-bit integer hash function
- @param key The integer [khint64_t]
- @return The hash value [khint_t]
- */
-#define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11)
-/*! @function
- @abstract 64-bit integer comparison function
- */
-#define kh_int64_hash_equal(a, b) ((a) == (b))
-/*! @function
- @abstract const char* hash function
- @param s Pointer to a null terminated string
- @return The hash value
- */
-static inline khint_t __ac_X31_hash_string(const char *s)
-{
- khint_t h = *s;
- if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
- return h;
-}
-/*! @function
- @abstract Another interface to const char* hash function
- @param key Pointer to a null terminated string [const char*]
- @return The hash value [khint_t]
- */
-#define kh_str_hash_func(key) __ac_X31_hash_string(key)
-/*! @function
- @abstract Const char* comparison function
- */
-#define kh_str_hash_equal(a, b) (strcmp(a, b) == 0)
-
-/* --- END OF HASH FUNCTIONS --- */
-
-/* Other necessary macros... */
-
-/*!
- @abstract Type of the hash table.
- @param name Name of the hash table [symbol]
- */
-#define khash_t(name) kh_##name##_t
-
-/*! @function
- @abstract Initiate a hash table.
- @param name Name of the hash table [symbol]
- @return Pointer to the hash table [khash_t(name)*]
- */
-#define kh_init(name) kh_init_##name()
-
-/*! @function
- @abstract Destroy a hash table.
- @param name Name of the hash table [symbol]
- @param h Pointer to the hash table [khash_t(name)*]
- */
-#define kh_destroy(name, h) kh_destroy_##name(h)
-
-/*! @function
- @abstract Reset a hash table without deallocating memory.
- @param name Name of the hash table [symbol]
- @param h Pointer to the hash table [khash_t(name)*]
- */
-#define kh_clear(name, h) kh_clear_##name(h)
-
-/*! @function
- @abstract Resize a hash table.
- @param name Name of the hash table [symbol]
- @param h Pointer to the hash table [khash_t(name)*]
- @param s New size [khint_t]
- */
-#define kh_resize(name, h, s) kh_resize_##name(h, s)
-
-/*! @function
- @abstract Insert a key to the hash table.
- @param name Name of the hash table [symbol]
- @param h Pointer to the hash table [khash_t(name)*]
- @param k Key [type of keys]
- @param r Extra return code: 0 if the key is present in the hash table;
- 1 if the bucket is empty (never used); 2 if the element in
- the bucket has been deleted [int*]
- @return Iterator to the inserted element [khint_t]
- */
-#define kh_put(name, h, k, r) kh_put_##name(h, k, r)
-
-/*! @function
- @abstract Retrieve a key from the hash table.
- @param name Name of the hash table [symbol]
- @param h Pointer to the hash table [khash_t(name)*]
- @param k Key [type of keys]
- @return Iterator to the found element, or kh_end(h) is the element is absent [khint_t]
- */
-#define kh_get(name, h, k) kh_get_##name(h, k)
-
-/*! @function
- @abstract Remove a key from the hash table.
- @param name Name of the hash table [symbol]
- @param h Pointer to the hash table [khash_t(name)*]
- @param k Iterator to the element to be deleted [khint_t]
- */
-#define kh_del(name, h, k) kh_del_##name(h, k)
-
-
-/*! @function
- @abstract Test whether a bucket contains data.
- @param h Pointer to the hash table [khash_t(name)*]
- @param x Iterator to the bucket [khint_t]
- @return 1 if containing data; 0 otherwise [int]
- */
-#define kh_exist(h, x) (!__ac_iseither((h)->flags, (x)))
-
-/*! @function
- @abstract Get key given an iterator
- @param h Pointer to the hash table [khash_t(name)*]
- @param x Iterator to the bucket [khint_t]
- @return Key [type of keys]
- */
-#define kh_key(h, x) ((h)->keys[x])
-
-/*! @function
- @abstract Get value given an iterator
- @param h Pointer to the hash table [khash_t(name)*]
- @param x Iterator to the bucket [khint_t]
- @return Value [type of values]
- @discussion For hash sets, calling this results in segfault.
- */
-#define kh_val(h, x) ((h)->vals[x])
-
-/*! @function
- @abstract Alias of kh_val()
- */
-#define kh_value(h, x) ((h)->vals[x])
-
-/*! @function
- @abstract Get the start iterator
- @param h Pointer to the hash table [khash_t(name)*]
- @return The start iterator [khint_t]
- */
-#define kh_begin(h) (khint_t)(0)
-
-/*! @function
- @abstract Get the end iterator
- @param h Pointer to the hash table [khash_t(name)*]
- @return The end iterator [khint_t]
- */
-#define kh_end(h) ((h)->n_buckets)
-
-/*! @function
- @abstract Get the number of elements in the hash table
- @param h Pointer to the hash table [khash_t(name)*]
- @return Number of elements in the hash table [khint_t]
- */
-#define kh_size(h) ((h)->size)
-
-/*! @function
- @abstract Get the number of buckets in the hash table
- @param h Pointer to the hash table [khash_t(name)*]
- @return Number of buckets in the hash table [khint_t]
- */
-#define kh_n_buckets(h) ((h)->n_buckets)
-
-/* More conenient interfaces */
-
-/*! @function
- @abstract Instantiate a hash set containing integer keys
- @param name Name of the hash table [symbol]
- */
-#define KHASH_SET_INIT_INT(name) \
- KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal)
-
-/*! @function
- @abstract Instantiate a hash map containing integer keys
- @param name Name of the hash table [symbol]
- @param khval_t Type of values [type]
- */
-#define KHASH_MAP_INIT_INT(name, khval_t) \
- KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
-
-/*! @function
- @abstract Instantiate a hash map containing 64-bit integer keys
- @param name Name of the hash table [symbol]
- */
-#define KHASH_SET_INIT_INT64(name) \
- KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
-
-/*! @function
- @abstract Instantiate a hash map containing 64-bit integer keys
- @param name Name of the hash table [symbol]
- @param khval_t Type of values [type]
- */
-#define KHASH_MAP_INIT_INT64(name, khval_t) \
- KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
-
-typedef const char *kh_cstr_t;
-/*! @function
- @abstract Instantiate a hash map containing const char* keys
- @param name Name of the hash table [symbol]
- */
-#define KHASH_SET_INIT_STR(name) \
- KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
-
-/*! @function
- @abstract Instantiate a hash map containing const char* keys
- @param name Name of the hash table [symbol]
- @param khval_t Type of values [type]
- */
-#define KHASH_MAP_INIT_STR(name, khval_t) \
- KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
-
-#endif /* __AC_KHASH_H */
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/kseq.h
--- a/bwa-0.6.2/kseq.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,208 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008, by Heng Li
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-#ifndef AC_KSEQ_H
-#define AC_KSEQ_H
-
-#include
-#include
-#include
-
-#define __KS_TYPE(type_t) \
- typedef struct __kstream_t { \
- char *buf; \
- int begin, end, is_eof; \
- type_t f; \
- } kstream_t;
-
-#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
-#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
-
-#define __KS_BASIC(type_t, __bufsize) \
- static inline kstream_t *ks_init(type_t f) \
- { \
- kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
- ks->f = f; \
- ks->buf = (char*)malloc(__bufsize); \
- return ks; \
- } \
- static inline void ks_destroy(kstream_t *ks) \
- { \
- if (ks) { \
- free(ks->buf); \
- free(ks); \
- } \
- }
-
-#define __KS_GETC(__read, __bufsize) \
- static inline int ks_getc(kstream_t *ks) \
- { \
- if (ks->is_eof && ks->begin >= ks->end) return -1; \
- if (ks->begin >= ks->end) { \
- ks->begin = 0; \
- ks->end = __read(ks->f, ks->buf, __bufsize); \
- if (ks->end < __bufsize) ks->is_eof = 1; \
- if (ks->end == 0) return -1; \
- } \
- return (int)ks->buf[ks->begin++]; \
- }
-
-#ifndef KSTRING_T
-#define KSTRING_T kstring_t
-typedef struct __kstring_t {
- size_t l, m;
- char *s;
-} kstring_t;
-#endif
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-#define __KS_GETUNTIL(__read, __bufsize) \
- static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
- { \
- if (dret) *dret = 0; \
- str->l = 0; \
- if (ks->begin >= ks->end && ks->is_eof) return -1; \
- for (;;) { \
- int i; \
- if (ks->begin >= ks->end) { \
- if (!ks->is_eof) { \
- ks->begin = 0; \
- ks->end = __read(ks->f, ks->buf, __bufsize); \
- if (ks->end < __bufsize) ks->is_eof = 1; \
- if (ks->end == 0) break; \
- } else break; \
- } \
- if (delimiter) { \
- for (i = ks->begin; i < ks->end; ++i) \
- if (ks->buf[i] == delimiter) break; \
- } else { \
- for (i = ks->begin; i < ks->end; ++i) \
- if (isspace(ks->buf[i])) break; \
- } \
- if (str->m - str->l < i - ks->begin + 1) { \
- str->m = str->l + (i - ks->begin) + 1; \
- kroundup32(str->m); \
- str->s = (char*)realloc(str->s, str->m); \
- } \
- memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
- str->l = str->l + (i - ks->begin); \
- ks->begin = i + 1; \
- if (i < ks->end) { \
- if (dret) *dret = ks->buf[i]; \
- break; \
- } \
- } \
- str->s[str->l] = '\0'; \
- return str->l; \
- }
-
-#define KSTREAM_INIT(type_t, __read, __bufsize) \
- __KS_TYPE(type_t) \
- __KS_BASIC(type_t, __bufsize) \
- __KS_GETC(__read, __bufsize) \
- __KS_GETUNTIL(__read, __bufsize)
-
-#define __KSEQ_BASIC(type_t) \
- static inline kseq_t *kseq_init(type_t fd) \
- { \
- kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
- s->f = ks_init(fd); \
- return s; \
- } \
- static inline void kseq_rewind(kseq_t *ks) \
- { \
- ks->last_char = 0; \
- ks->f->is_eof = ks->f->begin = ks->f->end = 0; \
- } \
- static inline void kseq_destroy(kseq_t *ks) \
- { \
- if (!ks) return; \
- free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \
- ks_destroy(ks->f); \
- free(ks); \
- }
-
-/* Return value:
- >=0 length of the sequence (normal)
- -1 end-of-file
- -2 truncated quality string
- */
-#define __KSEQ_READ \
- static int kseq_read(kseq_t *seq) \
- { \
- int c; \
- kstream_t *ks = seq->f; \
- if (seq->last_char == 0) { /* then jump to the next header line */ \
- while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
- if (c == -1) return -1; /* end of file */ \
- seq->last_char = c; \
- } /* the first header char has been read */ \
- seq->comment.l = seq->seq.l = seq->qual.l = 0; \
- if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; \
- if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); \
- while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
- if (isgraph(c)) { /* printable non-space character */ \
- if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \
- seq->seq.m = seq->seq.l + 2; \
- kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \
- seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
- } \
- seq->seq.s[seq->seq.l++] = (char)c; \
- } \
- } \
- if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
- seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
- if (c != '+') return seq->seq.l; /* FASTA */ \
- if (seq->qual.m < seq->seq.m) { /* allocate enough memory */ \
- seq->qual.m = seq->seq.m; \
- seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
- } \
- while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
- if (c == -1) return -2; /* we should not stop here */ \
- while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l) \
- if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c; \
- seq->qual.s[seq->qual.l] = 0; /* null terminated string */ \
- seq->last_char = 0; /* we have not come to the next header line */ \
- if (seq->seq.l != seq->qual.l) return -2; /* qual string is shorter than seq string */ \
- return seq->seq.l; \
- }
-
-#define __KSEQ_TYPE(type_t) \
- typedef struct { \
- kstring_t name, comment, seq, qual; \
- int last_char; \
- kstream_t *f; \
- } kseq_t;
-
-#define KSEQ_INIT(type_t, __read) \
- KSTREAM_INIT(type_t, __read, 4096) \
- __KSEQ_TYPE(type_t) \
- __KSEQ_BASIC(type_t) \
- __KSEQ_READ
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/ksort.h
--- a/bwa-0.6.2/ksort.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,269 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008, by Attractive Chaos
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-/*
- 2008-11-16 (0.1.4):
-
- * Fixed a bug in introsort() that happens in rare cases.
-
- 2008-11-05 (0.1.3):
-
- * Fixed a bug in introsort() for complex comparisons.
-
- * Fixed a bug in mergesort(). The previous version is not stable.
-
- 2008-09-15 (0.1.2):
-
- * Accelerated introsort. On my Mac (not on another Linux machine),
- my implementation is as fast as std::sort on random input.
-
- * Added combsort and in introsort, switch to combsort if the
- recursion is too deep.
-
- 2008-09-13 (0.1.1):
-
- * Added k-small algorithm
-
- 2008-09-05 (0.1.0):
-
- * Initial version
-
-*/
-
-#ifndef AC_KSORT_H
-#define AC_KSORT_H
-
-#include
-#include
-
-typedef struct {
- void *left, *right;
- int depth;
-} ks_isort_stack_t;
-
-#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
-
-#define KSORT_INIT(name, type_t, __sort_lt) \
- void ks_mergesort_##name(size_t n, type_t array[], type_t temp[]) \
- { \
- type_t *a2[2], *a, *b; \
- int curr, shift; \
- \
- a2[0] = array; \
- a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n); \
- for (curr = 0, shift = 0; (1ul<> 1) - 1; i != (size_t)(-1); --i) \
- ks_heapadjust_##name(i, lsize, l); \
- } \
- void ks_heapsort_##name(size_t lsize, type_t l[]) \
- { \
- size_t i; \
- for (i = lsize - 1; i > 0; --i) { \
- type_t tmp; \
- tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \
- } \
- } \
- inline void __ks_insertsort_##name(type_t *s, type_t *t) \
- { \
- type_t *i, *j, swap_tmp; \
- for (i = s + 1; i < t; ++i) \
- for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \
- swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp; \
- } \
- } \
- void ks_combsort_##name(size_t n, type_t a[]) \
- { \
- const double shrink_factor = 1.2473309501039786540366528676643; \
- int do_swap; \
- size_t gap = n; \
- type_t tmp, *i, *j; \
- do { \
- if (gap > 2) { \
- gap = (size_t)(gap / shrink_factor); \
- if (gap == 9 || gap == 10) gap = 11; \
- } \
- do_swap = 0; \
- for (i = a; i < a + n - gap; ++i) { \
- j = i + gap; \
- if (__sort_lt(*j, *i)) { \
- tmp = *i; *i = *j; *j = tmp; \
- do_swap = 1; \
- } \
- } \
- } while (do_swap || gap > 2); \
- if (gap != 1) __ks_insertsort_##name(a, a + n); \
- } \
- void ks_introsort_##name(size_t n, type_t a[]) \
- { \
- int d; \
- ks_isort_stack_t *top, *stack; \
- type_t rp, swap_tmp; \
- type_t *s, *t, *i, *j, *k; \
- \
- if (n < 1) return; \
- else if (n == 2) { \
- if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \
- return; \
- } \
- for (d = 2; 1ul<>1) + 1; \
- if (__sort_lt(*k, *i)) { \
- if (__sort_lt(*k, *j)) k = j; \
- } else k = __sort_lt(*j, *i)? i : j; \
- rp = *k; \
- if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; } \
- for (;;) { \
- do ++i; while (__sort_lt(*i, rp)); \
- do --j; while (i <= j && __sort_lt(rp, *j)); \
- if (j <= i) break; \
- swap_tmp = *i; *i = *j; *j = swap_tmp; \
- } \
- swap_tmp = *i; *i = *t; *t = swap_tmp; \
- if (i-s > t-i) { \
- if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \
- s = t-i > 16? i+1 : t; \
- } else { \
- if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \
- t = i-s > 16? i-1 : s; \
- } \
- } else { \
- if (top == stack) { \
- free(stack); \
- __ks_insertsort_##name(a, a+n); \
- return; \
- } else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \
- } \
- } \
- } \
- /* This function is adapted from: http://ndevilla.free.fr/median/ */ \
- /* 0 <= kk < n */ \
- type_t ks_ksmall_##name(size_t n, type_t arr[], size_t kk) \
- { \
- type_t *low, *high, *k, *ll, *hh, *mid; \
- low = arr; high = arr + n - 1; k = arr + kk; \
- for (;;) { \
- if (high <= low) return *k; \
- if (high == low + 1) { \
- if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
- return *k; \
- } \
- mid = low + (high - low) / 2; \
- if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
- if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
- if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \
- KSORT_SWAP(type_t, *mid, *(low+1)); \
- ll = low + 1; hh = high; \
- for (;;) { \
- do ++ll; while (__sort_lt(*ll, *low)); \
- do --hh; while (__sort_lt(*low, *hh)); \
- if (hh < ll) break; \
- KSORT_SWAP(type_t, *ll, *hh); \
- } \
- KSORT_SWAP(type_t, *low, *hh); \
- if (hh <= k) low = ll; \
- if (hh >= k) high = hh - 1; \
- } \
- }
-
-#define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t)
-#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
-#define ks_combsort(name, n, a) ks_combsort_##name(n, a)
-#define ks_heapsort(name, n, a) ks_heapsort_##name(n, a)
-#define ks_heapmake(name, n, a) ks_heapmake_##name(n, a)
-#define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a)
-#define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k)
-
-#define ks_lt_generic(a, b) ((a) < (b))
-#define ks_lt_str(a, b) (strcmp((a), (b)) < 0)
-
-typedef const char *ksstr_t;
-
-#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
-#define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str)
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/kstring.c
--- a/bwa-0.6.2/kstring.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-#include
-#include
-#include "kstring.h"
-
-int ksprintf(kstring_t *s, const char *fmt, ...)
-{
- va_list ap;
- int l;
- va_start(ap, fmt);
- l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
- va_end(ap);
- if (l + 1 > s->m - s->l) {
- s->m = s->l + l + 2;
- kroundup32(s->m);
- s->s = (char*)realloc(s->s, s->m);
- va_start(ap, fmt);
- l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
- }
- va_end(ap);
- s->l += l;
- return l;
-}
-
-#ifdef KSTRING_MAIN
-#include
-int main()
-{
- kstring_t *s;
- s = (kstring_t*)calloc(1, sizeof(kstring_t));
- ksprintf(s, "abcdefg: %d", 100);
- printf("%s\n", s->s);
- free(s);
- return 0;
-}
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/kstring.h
--- a/bwa-0.6.2/kstring.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-#ifndef KSTRING_H
-#define KSTRING_H
-
-#include
-#include
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-#ifndef KSTRING_T
-#define KSTRING_T kstring_t
-typedef struct __kstring_t {
- size_t l, m;
- char *s;
-} kstring_t;
-#endif
-
-static inline int kputs(const char *p, kstring_t *s)
-{
- int l = strlen(p);
- if (s->l + l + 1 >= s->m) {
- s->m = s->l + l + 2;
- kroundup32(s->m);
- s->s = (char*)realloc(s->s, s->m);
- }
- strcpy(s->s + s->l, p);
- s->l += l;
- return l;
-}
-
-static inline int kputc(int c, kstring_t *s)
-{
- if (s->l + 1 >= s->m) {
- s->m = s->l + 2;
- kroundup32(s->m);
- s->s = (char*)realloc(s->s, s->m);
- }
- s->s[s->l++] = c;
- s->s[s->l] = 0;
- return c;
-}
-
-int ksprintf(kstring_t *s, const char *fmt, ...);
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/ksw.c
--- a/bwa-0.6.2/ksw.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,401 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2011 by Attractive Chaos
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-#ifndef _NO_SSE2
-#include
-#include
-#include
-#include "ksw.h"
-
-#ifdef __GNUC__
-#define LIKELY(x) __builtin_expect((x),1)
-#define UNLIKELY(x) __builtin_expect((x),0)
-#else
-#define LIKELY(x) (x)
-#define UNLIKELY(x) (x)
-#endif
-
-struct _ksw_query_t {
- int qlen, slen;
- uint8_t shift, mdiff, max, size;
- __m128i *qp, *H0, *H1, *E, *Hmax;
-};
-
-ksw_query_t *ksw_qinit(int size, int qlen, const uint8_t *query, int m, const int8_t *mat)
-{
- ksw_query_t *q;
- int slen, a, tmp, p;
-
- size = size > 1? 2 : 1;
- p = 8 * (3 - size); // # values per __m128i
- slen = (qlen + p - 1) / p; // segmented length
- q = malloc(sizeof(ksw_query_t) + 256 + 16 * slen * (m + 4)); // a single block of memory
- q->qp = (__m128i*)(((size_t)q + sizeof(ksw_query_t) + 15) >> 4 << 4); // align memory
- q->H0 = q->qp + slen * m;
- q->H1 = q->H0 + slen;
- q->E = q->H1 + slen;
- q->Hmax = q->E + slen;
- q->slen = slen; q->qlen = qlen; q->size = size;
- // compute shift
- tmp = m * m;
- for (a = 0, q->shift = 127, q->mdiff = 0; a < tmp; ++a) { // find the minimum and maximum score
- if (mat[a] < (int8_t)q->shift) q->shift = mat[a];
- if (mat[a] > (int8_t)q->mdiff) q->mdiff = mat[a];
- }
- q->max = q->mdiff;
- q->shift = 256 - q->shift; // NB: q->shift is uint8_t
- q->mdiff += q->shift; // this is the difference between the min and max scores
- // An example: p=8, qlen=19, slen=3 and segmentation:
- // {{0,3,6,9,12,15,18,-1},{1,4,7,10,13,16,-1,-1},{2,5,8,11,14,17,-1,-1}}
- if (size == 1) {
- int8_t *t = (int8_t*)q->qp;
- for (a = 0; a < m; ++a) {
- int i, k, nlen = slen * p;
- const int8_t *ma = mat + a * m;
- for (i = 0; i < slen; ++i)
- for (k = i; k < nlen; k += slen) // p iterations
- *t++ = (k >= qlen? 0 : ma[query[k]]) + q->shift;
- }
- } else {
- int16_t *t = (int16_t*)q->qp;
- for (a = 0; a < m; ++a) {
- int i, k, nlen = slen * p;
- const int8_t *ma = mat + a * m;
- for (i = 0; i < slen; ++i)
- for (k = i; k < nlen; k += slen) // p iterations
- *t++ = (k >= qlen? 0 : ma[query[k]]);
- }
- }
- return q;
-}
-
-int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, ksw_aux_t *a) // the first gap costs -(_o+_e)
-{
- int slen, i, m_b, n_b, te = -1, gmax = 0;
- uint64_t *b;
- __m128i zero, gapoe, gape, shift, *H0, *H1, *E, *Hmax;
-
-#define __max_16(ret, xx) do { \
- (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 8)); \
- (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 4)); \
- (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 2)); \
- (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 1)); \
- (ret) = _mm_extract_epi16((xx), 0) & 0x00ff; \
- } while (0)
-
- // initialization
- m_b = n_b = 0; b = 0;
- zero = _mm_set1_epi32(0);
- gapoe = _mm_set1_epi8(a->gapo + a->gape);
- gape = _mm_set1_epi8(a->gape);
- shift = _mm_set1_epi8(q->shift);
- H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
- slen = q->slen;
- for (i = 0; i < slen; ++i) {
- _mm_store_si128(E + i, zero);
- _mm_store_si128(H0 + i, zero);
- _mm_store_si128(Hmax + i, zero);
- }
- // the core loop
- for (i = 0; i < tlen; ++i) {
- int j, k, cmp, imax;
- __m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
- h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
- h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x64 is little-endian
- for (j = 0; LIKELY(j < slen); ++j) {
- /* SW cells are computed in the following order:
- * H(i,j) = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
- * E(i+1,j) = max{H(i,j)-q, E(i,j)-r}
- * F(i,j+1) = max{H(i,j)-q, F(i,j)-r}
- */
- // compute H'(i,j); note that at the beginning, h=H'(i-1,j-1)
- h = _mm_adds_epu8(h, _mm_load_si128(S + j));
- h = _mm_subs_epu8(h, shift); // h=H'(i-1,j-1)+S(i,j)
- e = _mm_load_si128(E + j); // e=E'(i,j)
- h = _mm_max_epu8(h, e);
- h = _mm_max_epu8(h, f); // h=H'(i,j)
- max = _mm_max_epu8(max, h); // set max
- _mm_store_si128(H1 + j, h); // save to H'(i,j)
- // now compute E'(i+1,j)
- h = _mm_subs_epu8(h, gapoe); // h=H'(i,j)-gapo
- e = _mm_subs_epu8(e, gape); // e=E'(i,j)-gape
- e = _mm_max_epu8(e, h); // e=E'(i+1,j)
- _mm_store_si128(E + j, e); // save to E'(i+1,j)
- // now compute F'(i,j+1)
- f = _mm_subs_epu8(f, gape);
- f = _mm_max_epu8(f, h);
- // get H'(i-1,j) and prepare for the next j
- h = _mm_load_si128(H0 + j); // h=H'(i-1,j)
- }
- // NB: we do not need to set E(i,j) as we disallow adjecent insertion and then deletion
- for (k = 0; LIKELY(k < 16); ++k) { // this block mimics SWPS3; NB: H(i,j) updated in the lazy-F loop cannot exceed max
- f = _mm_slli_si128(f, 1);
- for (j = 0; LIKELY(j < slen); ++j) {
- h = _mm_load_si128(H1 + j);
- h = _mm_max_epu8(h, f); // h=H'(i,j)
- _mm_store_si128(H1 + j, h);
- h = _mm_subs_epu8(h, gapoe);
- f = _mm_subs_epu8(f, gape);
- cmp = _mm_movemask_epi8(_mm_cmpeq_epi8(_mm_subs_epu8(f, h), zero));
- if (UNLIKELY(cmp == 0xffff)) goto end_loop16;
- }
- }
-end_loop16:
- //int k;for (k=0;k<16;++k)printf("%d ", ((uint8_t*)&max)[k]);printf("\n");
- __max_16(imax, max); // imax is the maximum number in max
- if (imax >= a->T) { // write the b array; this condition adds branching unfornately
- if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) { // then append
- if (n_b == m_b) {
- m_b = m_b? m_b<<1 : 8;
- b = realloc(b, 8 * m_b);
- }
- b[n_b++] = (uint64_t)imax<<32 | i;
- } else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last
- }
- if (imax > gmax) {
- gmax = imax; te = i; // te is the end position on the target
- for (j = 0; LIKELY(j < slen); ++j) // keep the H1 vector
- _mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
- if (gmax + q->shift >= 255) break;
- }
- S = H1; H1 = H0; H0 = S; // swap H0 and H1
- }
- a->score = gmax; a->te = te;
- { // get a->qe, the end of query match; find the 2nd best score
- int max = -1, low, high, qlen = slen * 16;
- uint8_t *t = (uint8_t*)Hmax;
- for (i = 0, a->qe = -1; i < qlen; ++i, ++t)
- if ((int)*t > max) max = *t, a->qe = i / 16 + i % 16 * slen;
- //printf("%d,%d\n", max, gmax);
- i = (a->score + q->max - 1) / q->max;
- low = te - i; high = te + i;
- for (i = 0, a->score2 = 0; i < n_b; ++i) {
- int e = (int32_t)b[i];
- if ((e < low || e > high) && b[i]>>32 > (uint32_t)a->score2)
- a->score2 = b[i]>>32, a->te2 = e;
- }
- }
- free(b);
- return a->score + q->shift >= 255? 255 : a->score;
-}
-
-int ksw_sse2_8(ksw_query_t *q, int tlen, const uint8_t *target, ksw_aux_t *a) // the first gap costs -(_o+_e)
-{
- int slen, i, m_b, n_b, te = -1, gmax = 0;
- uint64_t *b;
- __m128i zero, gapoe, gape, *H0, *H1, *E, *Hmax;
-
-#define __max_8(ret, xx) do { \
- (xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 8)); \
- (xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 4)); \
- (xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 2)); \
- (ret) = _mm_extract_epi16((xx), 0); \
- } while (0)
-
- // initialization
- m_b = n_b = 0; b = 0;
- zero = _mm_set1_epi32(0);
- gapoe = _mm_set1_epi16(a->gapo + a->gape);
- gape = _mm_set1_epi16(a->gape);
- H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
- slen = q->slen;
- for (i = 0; i < slen; ++i) {
- _mm_store_si128(E + i, zero);
- _mm_store_si128(H0 + i, zero);
- _mm_store_si128(Hmax + i, zero);
- }
- // the core loop
- for (i = 0; i < tlen; ++i) {
- int j, k, imax;
- __m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
- h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
- h = _mm_slli_si128(h, 2);
- for (j = 0; LIKELY(j < slen); ++j) {
- h = _mm_adds_epi16(h, *S++);
- e = _mm_load_si128(E + j);
- h = _mm_max_epi16(h, e);
- h = _mm_max_epi16(h, f);
- max = _mm_max_epi16(max, h);
- _mm_store_si128(H1 + j, h);
- h = _mm_subs_epu16(h, gapoe);
- e = _mm_subs_epu16(e, gape);
- e = _mm_max_epi16(e, h);
- _mm_store_si128(E + j, e);
- f = _mm_subs_epu16(f, gape);
- f = _mm_max_epi16(f, h);
- h = _mm_load_si128(H0 + j);
- }
- for (k = 0; LIKELY(k < 16); ++k) {
- f = _mm_slli_si128(f, 2);
- for (j = 0; LIKELY(j < slen); ++j) {
- h = _mm_load_si128(H1 + j);
- h = _mm_max_epi16(h, f);
- _mm_store_si128(H1 + j, h);
- h = _mm_subs_epu16(h, gapoe);
- f = _mm_subs_epu16(f, gape);
- if(UNLIKELY(!_mm_movemask_epi8(_mm_cmpgt_epi16(f, h)))) goto end_loop8;
- }
- }
-end_loop8:
- __max_8(imax, max);
- if (imax >= a->T) {
- if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) {
- if (n_b == m_b) {
- m_b = m_b? m_b<<1 : 8;
- b = realloc(b, 8 * m_b);
- }
- b[n_b++] = (uint64_t)imax<<32 | i;
- } else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last
- }
- if (imax > gmax) {
- gmax = imax; te = i;
- for (j = 0; LIKELY(j < slen); ++j)
- _mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
- }
- S = H1; H1 = H0; H0 = S;
- }
- a->score = gmax; a->te = te;
- {
- int max = -1, low, high, qlen = slen * 8;
- uint16_t *t = (uint16_t*)Hmax;
- for (i = 0, a->qe = -1; i < qlen; ++i, ++t)
- if ((int)*t > max) max = *t, a->qe = i / 8 + i % 8 * slen;
- i = (a->score + q->max - 1) / q->max;
- low = te - i; high = te + i;
- for (i = 0, a->score2 = 0; i < n_b; ++i) {
- int e = (int32_t)b[i];
- if ((e < low || e > high) && b[i]>>32 > (uint32_t)a->score2)
- a->score2 = b[i]>>32, a->te2 = e;
- }
- }
- free(b);
- return a->score;
-}
-
-int ksw_sse2(ksw_query_t *q, int tlen, const uint8_t *target, ksw_aux_t *a)
-{
- if (q->size == 1) return ksw_sse2_16(q, tlen, target, a);
- else return ksw_sse2_8(q, tlen, target, a);
-}
-
-/*******************************************
- * Main function (not compiled by default) *
- *******************************************/
-
-#ifdef _KSW_MAIN
-
-#include
-#include
-#include
-#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
-
-unsigned char seq_nt4_table[256] = {
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
-};
-
-int main(int argc, char *argv[])
-{
- int c, sa = 1, sb = 3, i, j, k, forward_only = 0, size = 2;
- int8_t mat[25];
- ksw_aux_t a;
- gzFile fpt, fpq;
- kseq_t *kst, *ksq;
- // parse command line
- a.gapo = 5; a.gape = 2; a.T = 10;
- while ((c = getopt(argc, argv, "a:b:q:r:ft:s:")) >= 0) {
- switch (c) {
- case 'a': sa = atoi(optarg); break;
- case 'b': sb = atoi(optarg); break;
- case 'q': a.gapo = atoi(optarg); break;
- case 'r': a.gape = atoi(optarg); break;
- case 't': a.T = atoi(optarg); break;
- case 'f': forward_only = 1; break;
- case 's': size = atoi(optarg); break;
- }
- }
- if (optind + 2 > argc) {
- fprintf(stderr, "Usage: ksw [-s%d] [-a%d] [-b%d] [-q%d] [-r%d] \n", size, sa, sb, a.gapo, a.gape);
- return 1;
- }
- // initialize scoring matrix
- for (i = k = 0; i < 5; ++i) {
- for (j = 0; j < 4; ++j)
- mat[k++] = i == j? sa : -sb;
- mat[k++] = 0; // ambiguous base
- }
- for (j = 0; j < 5; ++j) mat[k++] = 0;
- // open file
- fpt = gzopen(argv[optind], "r"); kst = kseq_init(fpt);
- fpq = gzopen(argv[optind+1], "r"); ksq = kseq_init(fpq);
- // all-pair alignment
- while (kseq_read(ksq) > 0) {
- ksw_query_t *q[2];
- for (i = 0; i < ksq->seq.l; ++i) ksq->seq.s[i] = seq_nt4_table[(int)ksq->seq.s[i]];
- q[0] = ksw_qinit(size, ksq->seq.l, (uint8_t*)ksq->seq.s, 5, mat);
- if (!forward_only) { // reverse
- for (i = 0; i < ksq->seq.l/2; ++i) {
- int t = ksq->seq.s[i];
- ksq->seq.s[i] = ksq->seq.s[ksq->seq.l-1-i];
- ksq->seq.s[ksq->seq.l-1-i] = t;
- }
- for (i = 0; i < ksq->seq.l; ++i)
- ksq->seq.s[i] = ksq->seq.s[i] == 4? 4 : 3 - ksq->seq.s[i];
- q[1] = ksw_qinit(size, ksq->seq.l, (uint8_t*)ksq->seq.s, 5, mat);
- } else q[1] = 0;
- gzrewind(fpt); kseq_rewind(kst);
- while (kseq_read(kst) > 0) {
- int s;
- for (i = 0; i < kst->seq.l; ++i) kst->seq.s[i] = seq_nt4_table[(int)kst->seq.s[i]];
- s = ksw_sse2(q[0], kst->seq.l, (uint8_t*)kst->seq.s, &a);
- printf("%s\t%s\t+\t%d\t%d\t%d\n", ksq->name.s, kst->name.s, s, a.te+1, a.qe+1);
- if (q[1]) {
- s = ksw_sse2(q[1], kst->seq.l, (uint8_t*)kst->seq.s, &a);
- printf("%s\t%s\t-\t%d\t%d\t%d\n", ksq->name.s, kst->name.s, s, a.te+1, a.qe+1);
- }
- }
- free(q[0]); free(q[1]);
- }
- kseq_destroy(kst); gzclose(fpt);
- kseq_destroy(ksq); gzclose(fpq);
- return 0;
-}
-#endif // _KSW_MAIN
-#endif // _NO_SSE2
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/ksw.h
--- a/bwa-0.6.2/ksw.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-#ifndef __AC_KSW_H
-#define __AC_KSW_H
-
-struct _ksw_query_t;
-typedef struct _ksw_query_t ksw_query_t;
-
-typedef struct {
- // input
- unsigned gapo, gape; // the first gap costs gapo+gape
- unsigned T; // threshold
- // output
- int score, te, qe, score2, te2;
-} ksw_aux_t;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- /**
- * Initialize the query data structure
- *
- * @param size Number of bytes used to store a score; valid valures are 1 or 2
- * @param qlen Length of the query sequence
- * @param query Query sequence
- * @param m Size of the alphabet
- * @param mat Scoring matrix in a one-dimension array
- *
- * @return Query data structure
- */
- ksw_query_t *ksw_qinit(int size, int qlen, const uint8_t *query, int m, const int8_t *mat); // to free, simply call free()
-
- /**
- * Compute the maximum local score for queries initialized with ksw_qinit(1, ...)
- *
- * @param q Query data structure returned by ksw_qinit(1, ...)
- * @param tlen Length of the target sequence
- * @param target Target sequence
- * @param a Auxiliary data structure (see ksw.h)
- *
- * @return The maximum local score; if the returned value equals 255, the SW may not be finished
- */
- int ksw_sse2_8(ksw_query_t *q, int tlen, const uint8_t *target, ksw_aux_t *a);
-
- /** Compute the maximum local score for queries initialized with ksw_qinit(2, ...) */
- int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, ksw_aux_t *a);
-
- /** Unified interface for ksw_sse2_8() and ksw_sse2_16() */
- int ksw_sse2(ksw_query_t *q, int tlen, const uint8_t *target, ksw_aux_t *a);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/kvec.h
--- a/bwa-0.6.2/kvec.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008, by Attractive Chaos
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-/*
- An example:
-
-#include "kvec.h"
-int main() {
- kvec_t(int) array;
- kv_init(array);
- kv_push(int, array, 10); // append
- kv_a(int, array, 20) = 5; // dynamic
- kv_A(array, 20) = 4; // static
- kv_destroy(array);
- return 0;
-}
-*/
-
-/*
- 2008-09-22 (0.1.0):
-
- * The initial version.
-
-*/
-
-#ifndef AC_KVEC_H
-#define AC_KVEC_H
-
-#include
-
-#define kv_roundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-
-#define kvec_t(type) struct { size_t n, m; type *a; }
-#define kv_init(v) ((v).n = (v).m = 0, (v).a = 0)
-#define kv_destroy(v) free((v).a)
-#define kv_A(v, i) ((v).a[(i)])
-#define kv_pop(v) ((v).a[--(v).n])
-#define kv_size(v) ((v).n)
-#define kv_max(v) ((v).m)
-
-#define kv_resize(type, v, s) ((v).m = (s), (v).a = (type*)realloc((v).a, sizeof(type) * (v).m))
-
-#define kv_copy(type, v1, v0) do { \
- if ((v1).m < (v0).n) kv_resize(type, v1, (v0).n); \
- (v1).n = (v0).n; \
- memcpy((v1).a, (v0).a, sizeof(type) * (v0).n); \
- } while (0) \
-
-#define kv_push(type, v, x) do { \
- if ((v).n == (v).m) { \
- (v).m = (v).m? (v).m<<1 : 2; \
- (v).a = (type*)realloc((v).a, sizeof(type) * (v).m); \
- } \
- (v).a[(v).n++] = (x); \
- } while (0)
-
-#define kv_pushp(type, v) (((v).n == (v).m)? \
- ((v).m = ((v).m? (v).m<<1 : 2), \
- (v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0) \
- : 0), ((v).a + ((v).n++))
-
-#define kv_a(type, v, i) ((v).m <= (size_t)(i)? \
- ((v).m = (v).n = (i) + 1, kv_roundup32((v).m), \
- (v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0) \
- : (v).n <= (size_t)(i)? (v).n = (i) \
- : 0), (v).a[(i)]
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/main.c
--- a/bwa-0.6.2/main.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-#include
-#include
-#include "main.h"
-#include "utils.h"
-
-#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.6.2-r126"
-#endif
-
-static int usage()
-{
- fprintf(stderr, "\n");
- fprintf(stderr, "Program: bwa (alignment via Burrows-Wheeler transformation)\n");
- fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
- fprintf(stderr, "Contact: Heng Li \n\n");
- fprintf(stderr, "Usage: bwa [options]\n\n");
- fprintf(stderr, "Command: index index sequences in the FASTA format\n");
- fprintf(stderr, " aln gapped/ungapped alignment\n");
- fprintf(stderr, " samse generate alignment (single ended)\n");
- fprintf(stderr, " sampe generate alignment (paired ended)\n");
- fprintf(stderr, " bwasw BWA-SW for long queries\n");
- fprintf(stderr, " fastmap identify super-maximal exact matches\n");
- fprintf(stderr, "\n");
- fprintf(stderr, " fa2pac convert FASTA to PAC format\n");
- fprintf(stderr, " pac2bwt generate BWT from PAC\n");
- fprintf(stderr, " pac2bwtgen alternative algorithm for generating BWT\n");
- fprintf(stderr, " bwtupdate update .bwt to the new format\n");
- fprintf(stderr, " bwt2sa generate SA from BWT and Occ\n");
- fprintf(stderr, " pac2cspac convert PAC to color-space PAC\n");
- fprintf(stderr, " stdsw standard SW/NW alignment\n");
- fprintf(stderr, "\n");
- return 1;
-}
-
-void bwa_print_sam_PG()
-{
- printf("@PG\tID:bwa\tPN:bwa\tVN:%s\n", PACKAGE_VERSION);
-}
-
-int main(int argc, char *argv[])
-{
- int i, ret;
- double t_real;
- t_real = realtime();
- if (argc < 2) return usage();
- if (strcmp(argv[1], "fa2pac") == 0) ret = bwa_fa2pac(argc-1, argv+1);
- else if (strcmp(argv[1], "pac2bwt") == 0) ret = bwa_pac2bwt(argc-1, argv+1);
- else if (strcmp(argv[1], "pac2bwtgen") == 0) ret = bwt_bwtgen_main(argc-1, argv+1);
- else if (strcmp(argv[1], "bwtupdate") == 0) ret = bwa_bwtupdate(argc-1, argv+1);
- else if (strcmp(argv[1], "bwt2sa") == 0) ret = bwa_bwt2sa(argc-1, argv+1);
- else if (strcmp(argv[1], "index") == 0) ret = bwa_index(argc-1, argv+1);
- else if (strcmp(argv[1], "aln") == 0) ret = bwa_aln(argc-1, argv+1);
- else if (strcmp(argv[1], "sw") == 0) ret = bwa_stdsw(argc-1, argv+1);
- else if (strcmp(argv[1], "samse") == 0) ret = bwa_sai2sam_se(argc-1, argv+1);
- else if (strcmp(argv[1], "sampe") == 0) ret = bwa_sai2sam_pe(argc-1, argv+1);
- else if (strcmp(argv[1], "pac2cspac") == 0) ret = bwa_pac2cspac(argc-1, argv+1);
- else if (strcmp(argv[1], "stdsw") == 0) ret = bwa_stdsw(argc-1, argv+1);
- else if (strcmp(argv[1], "bwtsw2") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
- else if (strcmp(argv[1], "dbwtsw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
- else if (strcmp(argv[1], "bwasw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
- else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1);
- else {
- fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
- return 1;
- }
- err_fflush(stdout);
- err_fclose(stdout);
- if (ret == 0) {
- fprintf(stderr, "[%s] Version: %s\n", __func__, PACKAGE_VERSION);
- fprintf(stderr, "[%s] CMD:", __func__);
- for (i = 0; i < argc; ++i)
- fprintf(stderr, " %s", argv[i]);
- fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime());
- }
- return 0;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/main.h
--- a/bwa-0.6.2/main.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-#ifndef BWA_MAIN_H
-#define BWA_MAIN_H
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- int bwa_fa2pac(int argc, char *argv[]);
- int bwa_pac2cspac(int argc, char *argv[]);
- int bwa_pac2bwt(int argc, char *argv[]);
- int bwa_bwtupdate(int argc, char *argv[]);
- int bwa_bwt2sa(int argc, char *argv[]);
- int bwa_index(int argc, char *argv[]);
- int bwa_aln(int argc, char *argv[]);
- int bwt_bwtgen_main(int argc, char *argv[]);
-
- int bwa_sai2sam_se(int argc, char *argv[]);
- int bwa_sai2sam_pe(int argc, char *argv[]);
-
- int bwa_stdsw(int argc, char *argv[]);
-
- int bwa_bwtsw2(int argc, char *argv[]);
-
- int main_fastmap(int argc, char *argv[]);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/qualfa2fq.pl
--- a/bwa-0.6.2/qualfa2fq.pl Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-#!/usr/bin/perl -w
-
-use strict;
-use warnings;
-
-die("Usage: qualfa2fq.pl \n") if (@ARGV != 2);
-
-my ($fhs, $fhq, $q);
-open($fhs, ($ARGV[0] =~ /\.gz$/)? "gzip -dc $ARGV[0] |" : $ARGV[0]) || die;
-open($fhq, ($ARGV[1] =~ /\.gz$/)? "gzip -dc $ARGV[1] |" : $ARGV[1]) || die;
-
-$/ = ">"; <$fhs>; <$fhq>; $/ = "\n";
-while (<$fhs>) {
- $q = <$fhq>;
- print "\@$_";
- $/ = ">";
- $_ = <$fhs>; $q = <$fhq>;
- chomp; chomp($q);
- $q =~ s/\s*(\d+)\s*/chr($1+33)/eg;
- print $_, "+\n";
- for (my $i = 0; $i < length($q); $i += 60) {
- print substr($q, $i, 60), "\n";
- }
- $/ = "\n";
-}
-
-close($fhs); close($fhq);
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/simple_dp.c
--- a/bwa-0.6.2/simple_dp.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,162 +0,0 @@
-#include
-#include
-#include
-#include
-#include
-#include
-#include "stdaln.h"
-#include "utils.h"
-
-#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
-
-typedef struct {
- int l;
- unsigned char *s;
- char *n;
-} seq1_t;
-
-typedef struct {
- int n_seqs, m_seqs;
- seq1_t *seqs;
-} seqs_t;
-
-unsigned char aln_rev_table[256] = {
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','T','V','G', 'H','N','N','C', 'D','N','N','M', 'N','K','N','N',
- 'N','N','Y','S', 'A','N','B','W', 'X','R','N','N', 'N','N','N','N',
- 'N','t','v','g', 'h','N','N','c', 'd','N','N','m', 'N','k','N','N',
- 'N','N','y','s', 'a','N','b','w', 'x','r','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
- 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N'
-};
-
-static int g_is_global = 0, g_thres = 1, g_strand = 0, g_aa = 0;
-static AlnParam g_aln_param;
-
-static void revseq(int len, uint8_t *seq)
-{
- int i;
- for (i = 0; i < len>>1; ++i) {
- uint8_t tmp = aln_rev_table[seq[len-1-i]];
- seq[len-1-i] = aln_rev_table[seq[i]];
- seq[i] = tmp;
- }
- if (len&1) seq[i] = aln_rev_table[seq[i]];
-}
-
-static seqs_t *load_seqs(const char *fn)
-{
- seqs_t *s;
- seq1_t *p;
- gzFile fp;
- int l;
- kseq_t *seq;
-
- fp = xzopen(fn, "r");
- seq = kseq_init(fp);
- s = (seqs_t*)calloc(1, sizeof(seqs_t));
- s->m_seqs = 256;
- s->seqs = (seq1_t*)calloc(s->m_seqs, sizeof(seq1_t));
- while ((l = kseq_read(seq)) >= 0) {
- if (s->n_seqs == s->m_seqs) {
- s->m_seqs <<= 1;
- s->seqs = (seq1_t*)realloc(s->seqs, s->m_seqs * sizeof(seq1_t));
- }
- p = s->seqs + (s->n_seqs++);
- p->l = seq->seq.l;
- p->s = (unsigned char*)malloc(p->l + 1);
- memcpy(p->s, seq->seq.s, p->l);
- p->s[p->l] = 0;
- p->n = strdup((const char*)seq->name.s);
- }
- kseq_destroy(seq);
- gzclose(fp);
- fprintf(stderr, "[load_seqs] %d sequences are loaded.\n", s->n_seqs);
- return s;
-}
-
-static void aln_1seq(const seqs_t *ss, const char *name, int l, const char *s, char strand)
-{
- int i;
- for (i = 0; i < ss->n_seqs; ++i) {
- AlnAln *aa;
- seq1_t *p = ss->seqs + i;
- g_aln_param.band_width = l + p->l;
- aa = aln_stdaln_aux(s, (const char*)p->s, &g_aln_param, g_is_global, g_thres, l, p->l);
- if (aa->score >= g_thres || g_is_global) {
- printf(">%s\t%d\t%d\t%s\t%c\t%d\t%d\t%d\t%d\t", p->n, aa->start1? aa->start1 : 1, aa->end1, name, strand,
- aa->start2? aa->start2 : 1, aa->end2, aa->score, aa->subo);
- // NB: I put the short sequence as the first sequence in SW, an insertion to
- // the reference becomes a deletion from the short sequence. Therefore, I use
- // "MDI" here rather than "MID", and print ->out2 first rather than ->out1.
- for (i = 0; i != aa->n_cigar; ++i)
- printf("%d%c", aa->cigar32[i]>>4, "MDI"[aa->cigar32[i]&0xf]);
- printf("\n%s\n%s\n%s\n", aa->out2, aa->outm, aa->out1);
- }
- aln_free_AlnAln(aa);
- }
-}
-
-static void aln_seqs(const seqs_t *ss, const char *fn)
-{
- gzFile fp;
- kseq_t *seq;
- int l;
-
- fp = xzopen(fn, "r");
- seq = kseq_init(fp);
- while ((l = kseq_read(seq)) >= 0) {
- if (g_strand&1) aln_1seq(ss, (char*)seq->name.s, l, seq->seq.s, '+');
- if (g_strand&2) {
- revseq(l, (uint8_t*)seq->seq.s);
- aln_1seq(ss, (char*)seq->name.s, l, seq->seq.s, '-');
- }
- }
- kseq_destroy(seq);
- gzclose(fp);
-}
-
-int bwa_stdsw(int argc, char *argv[])
-{
- int c;
- seqs_t *ss;
-
- while ((c = getopt(argc, argv, "gT:frp")) >= 0) {
- switch (c) {
- case 'g': g_is_global = 1; break;
- case 'T': g_thres = atoi(optarg); break;
- case 'f': g_strand |= 1; break;
- case 'r': g_strand |= 2; break;
- case 'p': g_aa = 1; break;
- }
- }
- if (g_strand == 0) g_strand = 3;
- if (g_aa) g_strand = 1;
- if (optind + 1 >= argc) {
- fprintf(stderr, "\nUsage: bwa stdsw [options] \n\n");
- fprintf(stderr, "Options: -T INT minimum score [%d]\n", g_thres);
- fprintf(stderr, " -p protein alignment (suppressing -r)\n");
- fprintf(stderr, " -f forward strand only\n");
- fprintf(stderr, " -r reverse strand only\n");
- fprintf(stderr, " -g global alignment\n\n");
- fprintf(stderr, "Note: This program is specifically designed for alignment between multiple short\n");
- fprintf(stderr, " sequences and ONE long sequence. It outputs the suboptimal score on the long\n");
- fprintf(stderr, " sequence.\n\n");
- return 1;
- }
- g_aln_param = g_aa? aln_param_aa2aa : aln_param_blast;
- g_aln_param.gap_end = 0;
- ss = load_seqs(argv[optind]);
- aln_seqs(ss, argv[optind+1]);
- return 0;
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/solid2fastq.pl
--- a/bwa-0.6.2/solid2fastq.pl Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,111 +0,0 @@
-#!/usr/bin/perl -w
-
-# Author: lh3
-# Note: Ideally, this script should be written in C. It is a bit slow at present.
-# Also note that this script is different from the one contained in MAQ.
-
-use strict;
-use warnings;
-use Getopt::Std;
-
-my %opts;
-my $version = '0.1.4';
-my $usage = qq{
-Usage: solid2fastq.pl
-
-Note: is the string showed in the `# Title:' line of a
- ".csfasta" read file. Then F3.csfasta is read sequence
- file and F3_QV.qual is the quality file. If
- R3.csfasta is present, this script assumes reads are
- paired; otherwise reads will be regarded as single-end.
-
- The read name will be :panel_x_y/[12] with `1' for R3
- tag and `2' for F3. Usually you may want to use short
- to save diskspace. Long also causes troubles to maq.
-
-};
-
-getopts('', \%opts);
-die($usage) if (@ARGV != 2);
-my ($title, $pre) = @ARGV;
-my (@fhr, @fhw);
-my @fn_suff = ('F3.csfasta', 'F3_QV.qual', 'R3.csfasta', 'R3_QV.qual');
-my $is_paired = (-f "$title$fn_suff[2]" || -f "$title$fn_suff[2].gz")? 1 : 0;
-if ($is_paired) { # paired end
- for (0 .. 3) {
- my $fn = "$title$fn_suff[$_]";
- $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
- open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
- }
- open($fhw[0], "|gzip >$pre.read2.fastq.gz") || die; # this is NOT a typo
- open($fhw[1], "|gzip >$pre.read1.fastq.gz") || die;
- open($fhw[2], "|gzip >$pre.single.fastq.gz") || die;
- my (@df, @dr);
- @df = &read1(1); @dr = &read1(2);
- while (@df && @dr) {
- if ($df[0] eq $dr[0]) { # mate pair
- print {$fhw[0]} $df[1]; print {$fhw[1]} $dr[1];
- @df = &read1(1); @dr = &read1(2);
- } else {
- if ($df[0] le $dr[0]) {
- print {$fhw[2]} $df[1];
- @df = &read1(1);
- } else {
- print {$fhw[2]} $dr[1];
- @dr = &read1(2);
- }
- }
- }
- if (@df) {
- print {$fhw[2]} $df[1];
- while (@df = &read1(1, $fhr[0], $fhr[1])) {
- print {$fhw[2]} $df[1];
- }
- }
- if (@dr) {
- print {$fhw[2]} $dr[1];
- while (@dr = &read1(2, $fhr[2], $fhr[3])) {
- print {$fhw[2]} $dr[1];
- }
- }
- close($fhr[$_]) for (0 .. $#fhr);
- close($fhw[$_]) for (0 .. $#fhw);
-} else { # single end
- for (0 .. 1) {
- my $fn = "$title$fn_suff[$_]";
- $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
- open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
- }
- open($fhw[2], "|gzip >$pre.single.fastq.gz") || die;
- my @df;
- while (@df = &read1(1, $fhr[0], $fhr[1])) {
- print {$fhw[2]} $df[1];
- }
- close($fhr[$_]) for (0 .. $#fhr);
- close($fhw[2]);
-}
-
-sub read1 {
- my $i = shift(@_);
- my $j = ($i-1)<<1;
- my ($key, $seq);
- my ($fhs, $fhq) = ($fhr[$j], $fhr[$j|1]);
- while (<$fhs>) {
- my $t = <$fhq>;
- if (/^>(\d+)_(\d+)_(\d+)_[FR]3/) {
- $key = sprintf("%.4d_%.4d_%.4d", $1, $2, $3); # this line could be improved on 64-bit machines
- die(qq/** unmatched read name: '$_' != '$_'\n/) unless ($_ eq $t);
- my $name = "$pre:$1_$2_$3/$i";
- $_ = substr(<$fhs>, 2);
- tr/0123./ACGTN/;
- my $s = $_;
- $_ = <$fhq>;
- s/-1\b/0/eg;
- s/^(\d+)\s*//;
- s/(\d+)\s*/chr($1+33)/eg;
- $seq = qq/\@$name\n$s+\n$_\n/;
- last;
- }
- }
- return defined($seq)? ($key, $seq) : ();
-}
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/stdaln.c
--- a/bwa-0.6.2/stdaln.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1072 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2003-2006, 2008, 2009, by Heng Li
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-#include
-#include
-#include
-#include
-#include "stdaln.h"
-
-/* char -> 17 (=16+1) nucleotides */
-unsigned char aln_nt16_table[256] = {
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,16 /*'-'*/,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15, 1,14, 4, 11,15,15, 2, 13,15,15,10, 15, 5,15,15,
- 15,15, 3, 6, 8,15, 7, 9, 0,12,15,15, 15,15,15,15,
- 15, 1,14, 4, 11,15,15, 2, 13,15,15,10, 15, 5,15,15,
- 15,15, 3, 6, 8,15, 7, 9, 0,12,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
-};
-char *aln_nt16_rev_table = "XAGRCMSVTWKDYHBN-";
-
-/* char -> 5 (=4+1) nucleotides */
-unsigned char aln_nt4_table[256] = {
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 0, 4, 2, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 0, 4, 2, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
-};
-char *aln_nt4_rev_table = "AGCTN-";
-
-/* char -> 22 (=20+1+1) amino acids */
-unsigned char aln_aa_table[256] = {
- 21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
- 21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
- 21,21,21,21, 21,21,21,21, 21,21,20,21, 21,22 /*'-'*/,21,21,
- 21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
- 21, 0,21, 4, 3, 6,13, 7, 8, 9,21,11, 10,12, 2,21,
- 14, 5, 1,15, 16,21,19,17, 21,18,21,21, 21,21,21,21,
- 21, 0,21, 4, 3, 6,13, 7, 8, 9,21,11, 10,12, 2,21,
- 14, 5, 1,15, 16,21,19,17, 21,18,21,21, 21,21,21,21,
- 21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
- 21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
- 21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
- 21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
- 21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
- 21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
- 21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
- 21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21
-};
-char *aln_aa_rev_table = "ARNDCQEGHILKMFPSTWYV*X-";
- /* 01234567890123456789012 */
-
-/* translation table. They are useless in stdaln.c, but when you realize you need it, you need not write the table again. */
-unsigned char aln_trans_table_eu[66] = {
- 11,11, 2, 2, 1, 1,15,15, 16,16,16,16, 9,12, 9, 9,
- 6, 6, 3, 3, 7, 7, 7, 7, 0, 0, 0, 0, 19,19,19,19,
- 5, 5, 8, 8, 1, 1, 1, 1, 14,14,14,14, 10,10,10,10,
- 20,20,18,18, 20,17, 4, 4, 15,15,15,15, 10,10,13,13, 21, 22
-};
-char *aln_trans_table_eu_char = "KKNNRRSSTTTTIMIIEEDDGGGGAAAAVVVVQQHHRRRRPPPPLLLL**YY*WCCSSSSLLFFX";
- /* 01234567890123456789012345678901234567890123456789012345678901234 */
-int aln_sm_blosum62[] = {
-/* A R N D C Q E G H I L K M F P S T W Y V * X */
- 4,-1,-2,-2, 0,-1,-1, 0,-2,-1,-1,-1,-1,-2,-1, 1, 0,-3,-2, 0,-4, 0,
- -1, 5, 0,-2,-3, 1, 0,-2, 0,-3,-2, 2,-1,-3,-2,-1,-1,-3,-2,-3,-4,-1,
- -2, 0, 6, 1,-3, 0, 0, 0, 1,-3,-3, 0,-2,-3,-2, 1, 0,-4,-2,-3,-4,-1,
- -2,-2, 1, 6,-3, 0, 2,-1,-1,-3,-4,-1,-3,-3,-1, 0,-1,-4,-3,-3,-4,-1,
- 0,-3,-3,-3, 9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-4,-2,
- -1, 1, 0, 0,-3, 5, 2,-2, 0,-3,-2, 1, 0,-3,-1, 0,-1,-2,-1,-2,-4,-1,
- -1, 0, 0, 2,-4, 2, 5,-2, 0,-3,-3, 1,-2,-3,-1, 0,-1,-3,-2,-2,-4,-1,
- 0,-2, 0,-1,-3,-2,-2, 6,-2,-4,-4,-2,-3,-3,-2, 0,-2,-2,-3,-3,-4,-1,
- -2, 0, 1,-1,-3, 0, 0,-2, 8,-3,-3,-1,-2,-1,-2,-1,-2,-2, 2,-3,-4,-1,
- -1,-3,-3,-3,-1,-3,-3,-4,-3, 4, 2,-3, 1, 0,-3,-2,-1,-3,-1, 3,-4,-1,
- -1,-2,-3,-4,-1,-2,-3,-4,-3, 2, 4,-2, 2, 0,-3,-2,-1,-2,-1, 1,-4,-1,
- -1, 2, 0,-1,-3, 1, 1,-2,-1,-3,-2, 5,-1,-3,-1, 0,-1,-3,-2,-2,-4,-1,
- -1,-1,-2,-3,-1, 0,-2,-3,-2, 1, 2,-1, 5, 0,-2,-1,-1,-1,-1, 1,-4,-1,
- -2,-3,-3,-3,-2,-3,-3,-3,-1, 0, 0,-3, 0, 6,-4,-2,-2, 1, 3,-1,-4,-1,
- -1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4, 7,-1,-1,-4,-3,-2,-4,-2,
- 1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-2, 0,-1,-2,-1, 4, 1,-3,-2,-2,-4, 0,
- 0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 1, 5,-2,-2, 0,-4, 0,
- -3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, 1,-4,-3,-2,11, 2,-3,-4,-2,
- -2,-2,-2,-3,-2,-1,-2,-3, 2,-1,-1,-2,-1, 3,-3,-2,-2, 2, 7,-1,-4,-1,
- 0,-3,-3,-3,-1,-2,-2,-3,-3, 3, 1,-2, 1,-1,-2,-2, 0,-3,-1, 4,-4,-1,
- -4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4, 1,-4,
- 0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2, 0, 0,-2,-1,-1,-4,-1
-};
-
-int aln_sm_blosum45[] = {
-/* A R N D C Q E G H I L K M F P S T W Y V * X */
- 5,-2,-1,-2,-1,-1,-1, 0,-2,-1,-1,-1,-1,-2,-1, 1, 0,-2,-2, 0,-5, 0,
- -2, 7, 0,-1,-3, 1, 0,-2, 0,-3,-2, 3,-1,-2,-2,-1,-1,-2,-1,-2,-5,-1,
- -1, 0, 6, 2,-2, 0, 0, 0, 1,-2,-3, 0,-2,-2,-2, 1, 0,-4,-2,-3,-5,-1,
- -2,-1, 2, 7,-3, 0, 2,-1, 0,-4,-3, 0,-3,-4,-1, 0,-1,-4,-2,-3,-5,-1,
- -1,-3,-2,-3,12,-3,-3,-3,-3,-3,-2,-3,-2,-2,-4,-1,-1,-5,-3,-1,-5,-2,
- -1, 1, 0, 0,-3, 6, 2,-2, 1,-2,-2, 1, 0,-4,-1, 0,-1,-2,-1,-3,-5,-1,
- -1, 0, 0, 2,-3, 2, 6,-2, 0,-3,-2, 1,-2,-3, 0, 0,-1,-3,-2,-3,-5,-1,
- 0,-2, 0,-1,-3,-2,-2, 7,-2,-4,-3,-2,-2,-3,-2, 0,-2,-2,-3,-3,-5,-1,
- -2, 0, 1, 0,-3, 1, 0,-2,10,-3,-2,-1, 0,-2,-2,-1,-2,-3, 2,-3,-5,-1,
- -1,-3,-2,-4,-3,-2,-3,-4,-3, 5, 2,-3, 2, 0,-2,-2,-1,-2, 0, 3,-5,-1,
- -1,-2,-3,-3,-2,-2,-2,-3,-2, 2, 5,-3, 2, 1,-3,-3,-1,-2, 0, 1,-5,-1,
- -1, 3, 0, 0,-3, 1, 1,-2,-1,-3,-3, 5,-1,-3,-1,-1,-1,-2,-1,-2,-5,-1,
- -1,-1,-2,-3,-2, 0,-2,-2, 0, 2, 2,-1, 6, 0,-2,-2,-1,-2, 0, 1,-5,-1,
- -2,-2,-2,-4,-2,-4,-3,-3,-2, 0, 1,-3, 0, 8,-3,-2,-1, 1, 3, 0,-5,-1,
- -1,-2,-2,-1,-4,-1, 0,-2,-2,-2,-3,-1,-2,-3, 9,-1,-1,-3,-3,-3,-5,-1,
- 1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-3,-1,-2,-2,-1, 4, 2,-4,-2,-1,-5, 0,
- 0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-1,-1, 2, 5,-3,-1, 0,-5, 0,
- -2,-2,-4,-4,-5,-2,-3,-2,-3,-2,-2,-2,-2, 1,-3,-4,-3,15, 3,-3,-5,-2,
- -2,-1,-2,-2,-3,-1,-2,-3, 2, 0, 0,-1, 0, 3,-3,-2,-1, 3, 8,-1,-5,-1,
- 0,-2,-3,-3,-1,-3,-3,-3,-3, 3, 1,-2, 1, 0,-3,-1, 0,-3,-1, 5,-5,-1,
- -5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5, 1,-5,
- 0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1, 0, 0,-2,-1,-1,-5,-1
-};
-
-int aln_sm_nt[] = {
-/* X A G R C M S V T W K D Y H B N */
- -2,-2,-2,-2,-2,-2,-2,-2,-2,-2,-2,-2,-2,-2,-2,-2,
- -2, 2,-1, 1,-2, 1,-2, 0,-2, 1,-2, 0,-2, 0,-2, 0,
- -2,-1, 2, 1,-2,-2, 1, 0,-2,-2, 1, 0,-2,-2, 0, 0,
- -2, 1, 1, 1,-2,-1,-1, 0,-2,-1,-1, 0,-2, 0, 0, 0,
- -2,-2,-2,-2, 2, 1, 1, 0,-1,-2,-2,-2, 1, 0, 0, 0,
- -2, 1,-2,-1, 1, 1,-1, 0,-2,-1,-2, 0,-1, 0, 0, 0,
- -2,-2, 1,-1, 1,-1, 1, 0,-2,-2,-1, 0,-1, 0, 0, 0,
- -2, 0, 0, 0, 0, 0, 0, 0,-2, 0, 0, 0, 0, 0, 0, 0,
- -2,-2,-2,-2,-1,-2,-2,-2, 2, 1, 1, 0, 1, 0, 0, 0,
- -2, 1,-2,-1,-2,-1,-2, 0, 1, 1,-1, 0,-1, 0, 0, 0,
- -2,-2, 1,-1,-2,-2,-1, 0, 1,-1, 1, 0,-1, 0, 0, 0,
- -2, 0, 0, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- -2,-2,-2,-2, 1,-1,-1, 0, 1,-1,-1, 0, 1, 0, 0, 0,
- -2, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- -2,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
-};
-
-int aln_sm_read[] = {
-/* X A G R C M S V T W K D Y H B N */
- -17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,
- -17, 2,-17, 1,-17, 1,-17, 0,-17, 1,-17, 0,-17, 0,-17, 0,
- -17,-17, 2, 1,-17,-17, 1, 0,-17,-17, 1, 0,-17,-17, 0, 0,
- -17, 1, 1, 1,-17,-17,-17, 0,-17,-17,-17, 0,-17, 0, 0, 0,
- -17,-17,-17,-17, 2, 1, 1, 0,-17,-17,-17,-17, 1, 0, 0, 0,
- -17, 1,-17,-17, 1, 1,-17, 0,-17,-17,-17, 0,-17, 0, 0, 0,
- -17,-17, 1,-17, 1,-17, 1, 0,-17,-17,-17, 0,-17, 0, 0, 0,
- -17, 0, 0, 0, 0, 0, 0, 0,-17, 0, 0, 0, 0, 0, 0, 0,
- -17,-17,-17,-17,-17,-17,-17,-17, 2, 1, 1, 0, 1, 0, 0, 0,
- -17, 1,-17,-17,-17,-17,-17, 0, 1, 1,-17, 0,-17, 0, 0, 0,
- -17,-17, 1,-17,-17,-17,-17, 0, 1,-17, 1, 0,-17, 0, 0, 0,
- -17, 0, 0, 0,-17, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- -17,-17,-17,-17, 1,-17,-17, 0, 1,-17,-17, 0, 1, 0, 0, 0,
- -17, 0,-17, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- -17,-17, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- -17, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
-};
-
-int aln_sm_hs[] = {
-/* A G C T N */
- 91, -31,-114,-123, -44,
- -31, 100,-125,-114, -42,
- -123,-125, 100, -31, -42,
- -114,-114, -31, 91, -42,
- -44, -42, -42, -42, -43
-};
-
-int aln_sm_maq[] = {
- 11, -19, -19, -19, -13,
- -19, 11, -19, -19, -13,
- -19, -19, 11, -19, -13,
- -19, -19, -19, 11, -13,
- -13, -13, -13, -13, -13
-};
-
-int aln_sm_blast[] = {
- 1, -3, -3, -3, -2,
- -3, 1, -3, -3, -2,
- -3, -3, 1, -3, -2,
- -3, -3, -3, 1, -2,
- -2, -2, -2, -2, -2
-};
-
-/********************/
-/* START OF align.c */
-/********************/
-
-AlnParam aln_param_blast = { 5, 2, 2, aln_sm_blast, 5, 50 };
-AlnParam aln_param_bwa = { 26, 9, 5, aln_sm_maq, 5, 50 };
-AlnParam aln_param_nt2nt = { 8, 2, 2, aln_sm_nt, 16, 75 };
-AlnParam aln_param_rd2rd = { 1, 19, 19, aln_sm_read, 16, 75 };
-AlnParam aln_param_aa2aa = { 10, 2, 2, aln_sm_blosum62, 22, 50 };
-
-AlnAln *aln_init_AlnAln()
-{
- AlnAln *aa;
- aa = (AlnAln*)malloc(sizeof(AlnAln));
- aa->path = 0;
- aa->out1 = aa->out2 = aa->outm = 0;
- aa->path_len = 0;
- return aa;
-}
-void aln_free_AlnAln(AlnAln *aa)
-{
- free(aa->path); free(aa->cigar32);
- free(aa->out1); free(aa->out2); free(aa->outm);
- free(aa);
-}
-
-/***************************/
-/* START OF common_align.c */
-/***************************/
-
-#define LOCAL_OVERFLOW_THRESHOLD 32000
-#define LOCAL_OVERFLOW_REDUCE 16000
-#define NT_LOCAL_SCORE int
-#define NT_LOCAL_SHIFT 16
-#define NT_LOCAL_MASK 0xffff
-
-#define SET_INF(s) (s).M = (s).I = (s).D = MINOR_INF;
-
-#define set_M(MM, cur, p, sc) \
-{ \
- if ((p)->M >= (p)->I) { \
- if ((p)->M >= (p)->D) { \
- (MM) = (p)->M + (sc); (cur)->Mt = FROM_M; \
- } else { \
- (MM) = (p)->D + (sc); (cur)->Mt = FROM_D; \
- } \
- } else { \
- if ((p)->I > (p)->D) { \
- (MM) = (p)->I + (sc); (cur)->Mt = FROM_I; \
- } else { \
- (MM) = (p)->D + (sc); (cur)->Mt = FROM_D; \
- } \
- } \
-}
-#define set_I(II, cur, p) \
-{ \
- if ((p)->M - gap_open > (p)->I) { \
- (cur)->It = FROM_M; \
- (II) = (p)->M - gap_open - gap_ext; \
- } else { \
- (cur)->It = FROM_I; \
- (II) = (p)->I - gap_ext; \
- } \
-}
-#define set_end_I(II, cur, p) \
-{ \
- if (gap_end >= 0) { \
- if ((p)->M - gap_open > (p)->I) { \
- (cur)->It = FROM_M; \
- (II) = (p)->M - gap_open - gap_end; \
- } else { \
- (cur)->It = FROM_I; \
- (II) = (p)->I - gap_end; \
- } \
- } else set_I(II, cur, p); \
-}
-#define set_D(DD, cur, p) \
-{ \
- if ((p)->M - gap_open > (p)->D) { \
- (cur)->Dt = FROM_M; \
- (DD) = (p)->M - gap_open - gap_ext; \
- } else { \
- (cur)->Dt = FROM_D; \
- (DD) = (p)->D - gap_ext; \
- } \
-}
-#define set_end_D(DD, cur, p) \
-{ \
- if (gap_end >= 0) { \
- if ((p)->M - gap_open > (p)->D) { \
- (cur)->Dt = FROM_M; \
- (DD) = (p)->M - gap_open - gap_end; \
- } else { \
- (cur)->Dt = FROM_D; \
- (DD) = (p)->D - gap_end; \
- } \
- } else set_D(DD, cur, p); \
-}
-
-typedef struct
-{
- unsigned char Mt:3, It:2, Dt:2;
-} dpcell_t;
-
-typedef struct
-{
- int M, I, D;
-} dpscore_t;
-
-/* build score profile for accelerating alignment, in theory */
-void aln_init_score_array(unsigned char *seq, int len, int row, int *score_matrix, int **s_array)
-{
- int *tmp, *tmp2, i, k;
- for (i = 0; i != row; ++i) {
- tmp = score_matrix + i * row;
- tmp2 = s_array[i];
- for (k = 0; k != len; ++k)
- tmp2[k] = tmp[seq[k]];
- }
-}
-/***************************
- * banded global alignment *
- ***************************/
-int aln_global_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
- path_t *path, int *path_len)
-{
- register int i, j;
- dpcell_t **dpcell, *q;
- dpscore_t *curr, *last, *s;
- path_t *p;
- int b1, b2, tmp_end;
- int *mat, end, max;
- unsigned char type, ctype;
-
- int gap_open, gap_ext, gap_end, b;
- int *score_matrix, N_MATRIX_ROW;
-
- /* initialize some align-related parameters. just for compatibility */
- gap_open = ap->gap_open;
- gap_ext = ap->gap_ext;
- gap_end = ap->gap_end;
- b = ap->band_width;
- score_matrix = ap->matrix;
- N_MATRIX_ROW = ap->row;
-
- if (len1 == 0 || len2 == 0) {
- *path_len = 0;
- return 0;
- }
- /* calculate b1 and b2 */
- if (len1 > len2) {
- b1 = len1 - len2 + b;
- b2 = b;
- } else {
- b1 = b;
- b2 = len2 - len1 + b;
- }
- if (b1 > len1) b1 = len1;
- if (b2 > len2) b2 = len2;
- --seq1; --seq2;
-
- /* allocate memory */
- end = (b1 + b2 <= len1)? (b1 + b2 + 1) : (len1 + 1);
- dpcell = (dpcell_t**)malloc(sizeof(dpcell_t*) * (len2 + 1));
- for (j = 0; j <= len2; ++j)
- dpcell[j] = (dpcell_t*)malloc(sizeof(dpcell_t) * end);
- for (j = b2 + 1; j <= len2; ++j)
- dpcell[j] -= j - b2;
- curr = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1));
- last = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1));
-
- /* set first row */
- SET_INF(*curr); curr->M = 0;
- for (i = 1, s = curr + 1; i < b1; ++i, ++s) {
- SET_INF(*s);
- set_end_D(s->D, dpcell[0] + i, s - 1);
- }
- s = curr; curr = last; last = s;
-
- /* core dynamic programming, part 1 */
- tmp_end = (b2 < len2)? b2 : len2 - 1;
- for (j = 1; j <= tmp_end; ++j) {
- q = dpcell[j]; s = curr; SET_INF(*s);
- set_end_I(s->I, q, last);
- end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1;
- mat = score_matrix + seq2[j] * N_MATRIX_ROW;
- ++s; ++q;
- for (i = 1; i != end; ++i, ++s, ++q) {
- set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */
- set_I(s->I, q, last + i);
- set_D(s->D, q, s - 1);
- }
- set_M(s->M, q, last + i - 1, mat[seq1[i]]);
- set_D(s->D, q, s - 1);
- if (j + b1 - 1 > len1) { /* bug fixed, 040227 */
- set_end_I(s->I, q, last + i);
- } else s->I = MINOR_INF;
- s = curr; curr = last; last = s;
- }
- /* last row for part 1, use set_end_D() instead of set_D() */
- if (j == len2 && b2 != len2 - 1) {
- q = dpcell[j]; s = curr; SET_INF(*s);
- set_end_I(s->I, q, last);
- end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1;
- mat = score_matrix + seq2[j] * N_MATRIX_ROW;
- ++s; ++q;
- for (i = 1; i != end; ++i, ++s, ++q) {
- set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */
- set_I(s->I, q, last + i);
- set_end_D(s->D, q, s - 1);
- }
- set_M(s->M, q, last + i - 1, mat[seq1[i]]);
- set_end_D(s->D, q, s - 1);
- if (j + b1 - 1 > len1) { /* bug fixed, 040227 */
- set_end_I(s->I, q, last + i);
- } else s->I = MINOR_INF;
- s = curr; curr = last; last = s;
- ++j;
- }
-
- /* core dynamic programming, part 2 */
- for (; j <= len2 - b2 + 1; ++j) {
- SET_INF(curr[j - b2]);
- mat = score_matrix + seq2[j] * N_MATRIX_ROW;
- end = j + b1 - 1;
- for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i != end; ++i, ++s, ++q) {
- set_M(s->M, q, last + i - 1, mat[seq1[i]]);
- set_I(s->I, q, last + i);
- set_D(s->D, q, s - 1);
- }
- set_M(s->M, q, last + i - 1, mat[seq1[i]]);
- set_D(s->D, q, s - 1);
- s->I = MINOR_INF;
- s = curr; curr = last; last = s;
- }
-
- /* core dynamic programming, part 3 */
- for (; j < len2; ++j) {
- SET_INF(curr[j - b2]);
- mat = score_matrix + seq2[j] * N_MATRIX_ROW;
- for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) {
- set_M(s->M, q, last + i - 1, mat[seq1[i]]);
- set_I(s->I, q, last + i);
- set_D(s->D, q, s - 1);
- }
- set_M(s->M, q, last + len1 - 1, mat[seq1[i]]);
- set_end_I(s->I, q, last + i);
- set_D(s->D, q, s - 1);
- s = curr; curr = last; last = s;
- }
- /* last row */
- if (j == len2) {
- SET_INF(curr[j - b2]);
- mat = score_matrix + seq2[j] * N_MATRIX_ROW;
- for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) {
- set_M(s->M, q, last + i - 1, mat[seq1[i]]);
- set_I(s->I, q, last + i);
- set_end_D(s->D, q, s - 1);
- }
- set_M(s->M, q, last + len1 - 1, mat[seq1[i]]);
- set_end_I(s->I, q, last + i);
- set_end_D(s->D, q, s - 1);
- s = curr; curr = last; last = s;
- }
-
- /* backtrace */
- i = len1; j = len2;
- q = dpcell[j] + i;
- s = last + len1;
- max = s->M; type = q->Mt; ctype = FROM_M;
- if (s->I > max) { max = s->I; type = q->It; ctype = FROM_I; }
- if (s->D > max) { max = s->D; type = q->Dt; ctype = FROM_D; }
-
- p = path;
- p->ctype = ctype; p->i = i; p->j = j; /* bug fixed 040408 */
- ++p;
- do {
- switch (ctype) {
- case FROM_M: --i; --j; break;
- case FROM_I: --j; break;
- case FROM_D: --i; break;
- }
- q = dpcell[j] + i;
- ctype = type;
- switch (type) {
- case FROM_M: type = q->Mt; break;
- case FROM_I: type = q->It; break;
- case FROM_D: type = q->Dt; break;
- }
- p->ctype = ctype; p->i = i; p->j = j;
- ++p;
- } while (i || j);
- *path_len = p - path - 1;
-
- /* free memory */
- for (j = b2 + 1; j <= len2; ++j)
- dpcell[j] += j - b2;
- for (j = 0; j <= len2; ++j)
- free(dpcell[j]);
- free(dpcell);
- free(curr); free(last);
-
- return max;
-}
-/*************************************************
- * local alignment combined with banded strategy *
- *************************************************/
-int aln_local_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
- path_t *path, int *path_len, int _thres, int *_subo)
-{
- register NT_LOCAL_SCORE *s;
- register int i;
- int q, r, qr, tmp_len, qr_shift;
- int **s_array, *score_array;
- int e, f;
- int is_overflow, of_base;
- NT_LOCAL_SCORE *eh, curr_h, last_h, curr_last_h;
- int j, start_i, start_j, end_i, end_j;
- path_t *p;
- int score_f, score_r, score_g;
- int start, end, max_score;
- int thres, *suba, *ss;
-
- int gap_open, gap_ext, b;
- int *score_matrix, N_MATRIX_ROW;
-
- /* initialize some align-related parameters. just for compatibility */
- gap_open = ap->gap_open;
- gap_ext = ap->gap_ext;
- b = ap->band_width;
- score_matrix = ap->matrix;
- N_MATRIX_ROW = ap->row;
- thres = _thres > 0? _thres : -_thres;
-
- if (len1 == 0 || len2 == 0) return -1;
-
- /* allocate memory */
- suba = (int*)malloc(sizeof(int) * (len2 + 1));
- eh = (NT_LOCAL_SCORE*)malloc(sizeof(NT_LOCAL_SCORE) * (len1 + 1));
- s_array = (int**)malloc(sizeof(int*) * N_MATRIX_ROW);
- for (i = 0; i != N_MATRIX_ROW; ++i)
- s_array[i] = (int*)malloc(sizeof(int) * len1);
- /* initialization */
- aln_init_score_array(seq1, len1, N_MATRIX_ROW, score_matrix, s_array);
- q = gap_open;
- r = gap_ext;
- qr = q + r;
- qr_shift = (qr+1) << NT_LOCAL_SHIFT;
- tmp_len = len1 + 1;
- start_i = start_j = end_i = end_j = 0;
- for (i = 0, max_score = 0; i != N_MATRIX_ROW * N_MATRIX_ROW; ++i)
- if (max_score < score_matrix[i]) max_score = score_matrix[i];
- /* convert the coordinate */
- --seq1; --seq2;
- for (i = 0; i != N_MATRIX_ROW; ++i) --s_array[i];
-
- /* forward dynamic programming */
- for (i = 0, s = eh; i != tmp_len; ++i, ++s) *s = 0;
- score_f = 0;
- is_overflow = of_base = 0;
- suba[0] = 0;
- for (j = 1, ss = suba + 1; j <= len2; ++j, ++ss) {
- int subo = 0;
- last_h = f = 0;
- score_array = s_array[seq2[j]];
- if (is_overflow) { /* adjust eh[] array if overflow occurs. */
- /* If LOCAL_OVERFLOW_REDUCE is too small, optimal alignment might be missed.
- * If it is too large, this block will be excuted frequently and therefore
- * slow down the whole program.
- * Acually, smaller LOCAL_OVERFLOW_REDUCE might also help to reduce the
- * number of assignments because it sets some cells to zero when overflow
- * happens. */
- int tmp, tmp2;
- score_f -= LOCAL_OVERFLOW_REDUCE;
- of_base += LOCAL_OVERFLOW_REDUCE;
- is_overflow = 0;
- for (i = 1, s = eh; i <= tmp_len; ++i, ++s) {
- tmp = *s >> NT_LOCAL_SHIFT; tmp2 = *s & NT_LOCAL_MASK;
- if (tmp2 < LOCAL_OVERFLOW_REDUCE) tmp2 = 0;
- else tmp2 -= LOCAL_OVERFLOW_REDUCE;
- if (tmp < LOCAL_OVERFLOW_REDUCE) tmp = 0;
- else tmp -= LOCAL_OVERFLOW_REDUCE;
- *s = (tmp << NT_LOCAL_SHIFT) | tmp2;
- }
- }
- for (i = 1, s = eh; i != tmp_len; ++i, ++s) {
- /* prepare for calculate current h */
- curr_h = (*s >> NT_LOCAL_SHIFT) + score_array[i];
- if (curr_h < 0) curr_h = 0;
- if (last_h > 0) { /* initialize f */
- f = (f > last_h - q)? f - r : last_h - qr;
- if (curr_h < f) curr_h = f;
- }
- if (*(s+1) >= qr_shift) { /* initialize e */
- curr_last_h = *(s+1) >> NT_LOCAL_SHIFT;
- e = ((*s & NT_LOCAL_MASK) > curr_last_h - q)? (*s & NT_LOCAL_MASK) - r : curr_last_h - qr;
- if (curr_h < e) curr_h = e;
- *s = (last_h << NT_LOCAL_SHIFT) | e;
- } else *s = last_h << NT_LOCAL_SHIFT; /* e = 0 */
- last_h = curr_h;
- if (subo < curr_h) subo = curr_h;
- if (score_f < curr_h) {
- score_f = curr_h; end_i = i; end_j = j;
- if (score_f > LOCAL_OVERFLOW_THRESHOLD) is_overflow = 1;
- }
- }
- *s = last_h << NT_LOCAL_SHIFT;
- *ss = subo + of_base;
- }
- score_f += of_base;
-
- if (score_f < thres) { /* no matching residue at all, 090218 */
- if (path_len) *path_len = 0;
- goto end_func;
- }
- if (path == 0) goto end_func; /* skip path-filling */
-
- /* reverse dynamic programming */
- for (i = end_i, s = eh + end_i; i >= 0; --i, --s) *s = 0;
- if (end_i == 0 || end_j == 0) goto end_func; /* no local match */
- score_r = score_matrix[seq1[end_i] * N_MATRIX_ROW + seq2[end_j]];
- is_overflow = of_base = 0;
- start_i = end_i; start_j = end_j;
- eh[end_i] = ((NT_LOCAL_SCORE)(qr + score_r)) << NT_LOCAL_SHIFT; /* in order to initialize f and e, 040408 */
- start = end_i - 1;
- end = end_i - 3;
- if (end <= 0) end = 0;
-
- /* second pass DP can be done in a band, speed will thus be enhanced */
- for (j = end_j - 1; j != 0; --j) {
- last_h = f = 0;
- score_array = s_array[seq2[j]];
- if (is_overflow) { /* adjust eh[] array if overflow occurs. */
- int tmp, tmp2;
- score_r -= LOCAL_OVERFLOW_REDUCE;
- of_base += LOCAL_OVERFLOW_REDUCE;
- is_overflow = 0;
- for (i = start, s = eh + start + 1; i >= end; --i, --s) {
- tmp = *s >> NT_LOCAL_SHIFT; tmp2 = *s & NT_LOCAL_MASK;
- if (tmp2 < LOCAL_OVERFLOW_REDUCE) tmp2 = 0;
- else tmp2 -= LOCAL_OVERFLOW_REDUCE;
- if (tmp < LOCAL_OVERFLOW_REDUCE) tmp = 0;
- else tmp -= LOCAL_OVERFLOW_REDUCE;
- *s = (tmp << NT_LOCAL_SHIFT) | tmp2;
- }
- }
- for (i = start, s = eh + start + 1; i != end; --i, --s) {
- /* prepare for calculate current h */
- curr_h = (*s >> NT_LOCAL_SHIFT) + score_array[i];
- if (curr_h < 0) curr_h = 0;
- if (last_h > 0) { /* initialize f */
- f = (f > last_h - q)? f - r : last_h - qr;
- if (curr_h < f) curr_h = f;
- }
- curr_last_h = *(s-1) >> NT_LOCAL_SHIFT;
- e = ((*s & NT_LOCAL_MASK) > curr_last_h - q)? (*s & NT_LOCAL_MASK) - r : curr_last_h - qr;
- if (e < 0) e = 0;
- if (curr_h < e) curr_h = e;
- *s = (last_h << NT_LOCAL_SHIFT) | e;
- last_h = curr_h;
- if (score_r < curr_h) {
- score_r = curr_h; start_i = i; start_j = j;
- if (score_r + of_base - qr == score_f) {
- j = 1; break;
- }
- if (score_r > LOCAL_OVERFLOW_THRESHOLD) is_overflow = 1;
- }
- }
- *s = last_h << NT_LOCAL_SHIFT;
- /* recalculate start and end, the boundaries of the band */
- if ((eh[start] >> NT_LOCAL_SHIFT) <= qr) --start;
- if (start <= 0) start = 0;
- end = start_i - (start_j - j) - (score_r + of_base + (start_j - j) * max_score) / r - 1;
- if (end <= 0) end = 0;
- }
-
- if (_subo) {
- int tmp2 = 0, tmp = (int)(start_j - .33 * (end_j - start_j) + .499);
- for (j = 1; j <= tmp; ++j)
- if (tmp2 < suba[j]) tmp2 = suba[j];
- tmp = (int)(end_j + .33 * (end_j - start_j) + .499);
- for (j = tmp; j <= len2; ++j)
- if (tmp2 < suba[j]) tmp2 = suba[j];
- *_subo = tmp2;
- }
-
- if (path_len == 0) {
- path[0].i = start_i; path[0].j = start_j;
- path[1].i = end_i; path[1].j = end_j;
- goto end_func;
- }
-
- score_r += of_base;
- score_r -= qr;
-
-#ifdef DEBUG
- /* this seems not a bug */
- if (score_f != score_r)
- fprintf(stderr, "[aln_local_core] unknown flaw occurs: score_f(%d) != score_r(%d)\n", score_f, score_r);
-#endif
-
- if (_thres > 0) { /* call global alignment to fill the path */
- score_g = 0;
- j = (end_i - start_i > end_j - start_j)? end_i - start_i : end_j - start_j;
- ++j; /* j is the maximum band_width */
- for (i = ap->band_width;; i <<= 1) {
- AlnParam ap_real = *ap;
- ap_real.gap_end = -1;
- ap_real.band_width = i;
- score_g = aln_global_core(seq1 + start_i, end_i - start_i + 1, seq2 + start_j,
- end_j - start_j + 1, &ap_real, path, path_len);
- if (score_g == score_r || score_f == score_g) break;
- if (i > j) break;
- }
- if (score_r > score_g && score_f > score_g) {
- fprintf(stderr, "[aln_local_core] Potential bug: (%d,%d) > %d\n", score_f, score_r, score_g);
- score_f = score_r = -1;
- } else score_f = score_g;
-
- /* convert coordinate */
- for (p = path + *path_len - 1; p >= path; --p) {
- p->i += start_i - 1;
- p->j += start_j - 1;
- }
- } else { /* just store the start and end */
- *path_len = 2;
- path[1].i = start_i; path[1].j = start_j;
- path->i = end_i; path->j = end_j;
- }
-
-end_func:
- /* free */
- free(eh); free(suba);
- for (i = 0; i != N_MATRIX_ROW; ++i) {
- ++s_array[i];
- free(s_array[i]);
- }
- free(s_array);
- return score_f;
-}
-AlnAln *aln_stdaln_aux(const char *seq1, const char *seq2, const AlnParam *ap,
- int type, int thres, int len1, int len2)
-{
- unsigned char *seq11, *seq22;
- int score;
- int i, j, l;
- path_t *p;
- char *out1, *out2, *outm;
- AlnAln *aa;
-
- if (len1 < 0) len1 = strlen(seq1);
- if (len2 < 0) len2 = strlen(seq2);
-
- aa = aln_init_AlnAln();
- seq11 = (unsigned char*)malloc(sizeof(unsigned char) * len1);
- seq22 = (unsigned char*)malloc(sizeof(unsigned char) * len2);
- aa->path = (path_t*)malloc(sizeof(path_t) * (len1 + len2 + 1));
-
- if (ap->row < 10) { /* 4-nucleotide alignment */
- for (i = 0; i < len1; ++i)
- seq11[i] = aln_nt4_table[(int)seq1[i]];
- for (j = 0; j < len2; ++j)
- seq22[j] = aln_nt4_table[(int)seq2[j]];
- } else if (ap->row < 20) { /* 16-nucleotide alignment */
- for (i = 0; i < len1; ++i)
- seq11[i] = aln_nt16_table[(int)seq1[i]];
- for (j = 0; j < len2; ++j)
- seq22[j] = aln_nt16_table[(int)seq2[j]];
- } else { /* amino acids */
- for (i = 0; i < len1; ++i)
- seq11[i] = aln_aa_table[(int)seq1[i]];
- for (j = 0; j < len2; ++j)
- seq22[j] = aln_aa_table[(int)seq2[j]];
- }
-
- if (type == ALN_TYPE_GLOBAL) score = aln_global_core(seq11, len1, seq22, len2, ap, aa->path, &aa->path_len);
- else if (type == ALN_TYPE_LOCAL) score = aln_local_core(seq11, len1, seq22, len2, ap, aa->path, &aa->path_len, thres, &aa->subo);
- else if (type == ALN_TYPE_EXTEND) score = aln_extend_core(seq11, len1, seq22, len2, ap, aa->path, &aa->path_len, 1, 0);
- else {
- free(seq11); free(seq22); free(aa->path);
- aln_free_AlnAln(aa);
- return 0;
- }
- aa->score = score;
-
- if (thres > 0) {
- out1 = aa->out1 = (char*)malloc(sizeof(char) * (aa->path_len + 1));
- out2 = aa->out2 = (char*)malloc(sizeof(char) * (aa->path_len + 1));
- outm = aa->outm = (char*)malloc(sizeof(char) * (aa->path_len + 1));
-
- --seq1; --seq2;
- --seq11; --seq22;
-
- p = aa->path + aa->path_len - 1;
-
- for (l = 0; p >= aa->path; --p, ++l) {
- switch (p->ctype) {
- case FROM_M: out1[l] = seq1[p->i]; out2[l] = seq2[p->j];
- outm[l] = (seq11[p->i] == seq22[p->j] && seq11[p->i] != ap->row)? '|' : ' ';
- break;
- case FROM_I: out1[l] = '-'; out2[l] = seq2[p->j]; outm[l] = ' '; break;
- case FROM_D: out1[l] = seq1[p->i]; out2[l] = '-'; outm[l] = ' '; break;
- }
- }
- out1[l] = out2[l] = outm[l] = '\0';
- ++seq11; ++seq22;
- }
-
- free(seq11);
- free(seq22);
-
- p = aa->path + aa->path_len - 1;
- aa->start1 = p->i? p->i : 1;
- aa->end1 = aa->path->i;
- aa->start2 = p->j? p->j : 1;
- aa->end2 = aa->path->j;
- aa->cigar32 = aln_path2cigar32(aa->path, aa->path_len, &aa->n_cigar);
-
- return aa;
-}
-AlnAln *aln_stdaln(const char *seq1, const char *seq2, const AlnParam *ap, int type, int thres)
-{
- return aln_stdaln_aux(seq1, seq2, ap, type, thres, -1, -1);
-}
-
-/* for backward compatibility */
-uint16_t *aln_path2cigar(const path_t *path, int path_len, int *n_cigar)
-{
- uint32_t *cigar32;
- uint16_t *cigar;
- int i;
- cigar32 = aln_path2cigar32(path, path_len, n_cigar);
- cigar = (uint16_t*)cigar32;
- for (i = 0; i < *n_cigar; ++i)
- cigar[i] = (cigar32[i]&0xf)<<14 | (cigar32[i]>>4&0x3fff);
- return cigar;
-}
-
-/* newly added functions (2009-07-21) */
-
-int aln_extend_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
- path_t *path, int *path_len, int G0, uint8_t *_mem)
-{
- int q, r, qr, tmp_len;
- int32_t **s_array, *score_array;
- int is_overflow, of_base;
- uint32_t *eh;
- int i, j, end_i, end_j;
- int score, start, end;
- int *score_matrix, N_MATRIX_ROW;
- uint8_t *mem, *_p;
-
- /* initialize some align-related parameters. just for compatibility */
- q = ap->gap_open;
- r = ap->gap_ext;
- qr = q + r;
- score_matrix = ap->matrix;
- N_MATRIX_ROW = ap->row;
-
- if (len1 == 0 || len2 == 0) return -1;
-
- /* allocate memory */
- mem = _mem? _mem : calloc((len1 + 2) * (N_MATRIX_ROW + 1), 4);
- _p = mem;
- eh = (uint32_t*)_p, _p += 4 * (len1 + 2);
- s_array = calloc(N_MATRIX_ROW, sizeof(void*));
- for (i = 0; i != N_MATRIX_ROW; ++i)
- s_array[i] = (int32_t*)_p, _p += 4 * len1;
- /* initialization */
- aln_init_score_array(seq1, len1, N_MATRIX_ROW, score_matrix, s_array);
- tmp_len = len1 + 1;
- start = 1; end = 2;
- end_i = end_j = 0;
- score = 0;
- is_overflow = of_base = 0;
- /* convert the coordinate */
- --seq1; --seq2;
- for (i = 0; i != N_MATRIX_ROW; ++i) --s_array[i];
-
- /* dynamic programming */
- memset(eh, 0, 4 * (len1 + 2));
- eh[1] = (uint32_t)G0<<16;
- for (j = 1; j <= len2; ++j) {
- int _start, _end;
- int h1 = 0, f = 0;
- score_array = s_array[seq2[j]];
- /* set start and end */
- _start = j - ap->band_width;
- if (_start < 1) _start = 1;
- if (_start > start) start = _start;
- _end = j + ap->band_width;
- if (_end > len1 + 1) _end = len1 + 1;
- if (_end < end) end = _end;
- if (start == end) break;
- /* adjust eh[] array if overflow occurs. */
- if (is_overflow) {
- int tmp, tmp2;
- score -= LOCAL_OVERFLOW_REDUCE;
- of_base += LOCAL_OVERFLOW_REDUCE;
- is_overflow = 0;
- for (i = start; i <= end; ++i) {
- uint32_t *s = &eh[i];
- tmp = *s >> 16; tmp2 = *s & 0xffff;
- if (tmp2 < LOCAL_OVERFLOW_REDUCE) tmp2 = 0;
- else tmp2 -= LOCAL_OVERFLOW_REDUCE;
- if (tmp < LOCAL_OVERFLOW_REDUCE) tmp = 0;
- else tmp -= LOCAL_OVERFLOW_REDUCE;
- *s = (tmp << 16) | tmp2;
- }
- }
- _start = _end = 0;
- /* the inner loop */
- for (i = start; i < end; ++i) {
- /* At the beginning of each cycle:
- eh[i] -> h[j-1,i-1]<<16 | e[j,i]
- f -> f[j,i]
- h1 -> h[j,i-1]
- */
- uint32_t *s = &eh[i];
- int h = (int)(*s >> 16);
- int e = *s & 0xffff; /* this is e[j,i] */
- *s = (uint32_t)h1 << 16; /* eh[i] now stores h[j,i-1]<<16 */
- h += h? score_array[i] : 0; /* this is left_core() specific */
- /* calculate h[j,i]; don't need to test 0, as {e,f}>=0 */
- h = h > e? h : e;
- h = h > f? h : f; /* h now is h[j,i] */
- h1 = h;
- if (h > 0) {
- if (_start == 0) _start = i;
- _end = i;
- if (score < h) {
- score = h; end_i = i; end_j = j;
- if (score > LOCAL_OVERFLOW_THRESHOLD) is_overflow = 1;
- }
- }
- /* calculate e[j+1,i] and f[j,i+1] */
- h -= qr;
- h = h > 0? h : 0;
- e -= r;
- e = e > h? e : h;
- f -= r;
- f = f > h? f : h;
- *s |= e;
- }
- eh[end] = h1 << 16;
- /* recalculate start and end, the boundaries of the band */
- if (_end <= 0) break; /* no cell in this row has a positive score */
- start = _start;
- end = _end + 3;
- }
-
- score += of_base - 1;
- if (score <= 0) {
- if (path_len) *path_len = 0;
- goto end_left_func;
- }
-
- if (path == 0) goto end_left_func;
-
- if (path_len == 0) {
- path[0].i = end_i; path[0].j = end_j;
- goto end_left_func;
- }
-
- { /* call global alignment to fill the path */
- int score_g = 0;
- j = (end_i - 1 > end_j - 1)? end_i - 1 : end_j - 1;
- ++j; /* j is the maximum band_width */
- for (i = ap->band_width;; i <<= 1) {
- AlnParam ap_real = *ap;
- ap_real.gap_end = -1;
- ap_real.band_width = i;
- score_g = aln_global_core(seq1 + 1, end_i, seq2 + 1, end_j, &ap_real, path, path_len);
- if (score == score_g) break;
- if (i > j) break;
- }
- if (score > score_g)
- fprintf(stderr, "[aln_left_core] no suitable bandwidth: %d < %d\n", score_g, score);
- score = score_g;
- }
-
-end_left_func:
- /* free */
- free(s_array);
- if (!_mem) free(mem);
- return score;
-}
-
-uint32_t *aln_path2cigar32(const path_t *path, int path_len, int *n_cigar)
-{
- int i, n;
- uint32_t *cigar;
- unsigned char last_type;
-
- if (path_len == 0 || path == 0) {
- *n_cigar = 0;
- return 0;
- }
-
- last_type = path->ctype;
- for (i = n = 1; i < path_len; ++i) {
- if (last_type != path[i].ctype) ++n;
- last_type = path[i].ctype;
- }
- *n_cigar = n;
- cigar = (uint32_t*)malloc(*n_cigar * 4);
-
- cigar[0] = 1u << 4 | path[path_len-1].ctype;
- last_type = path[path_len-1].ctype;
- for (i = path_len - 2, n = 0; i >= 0; --i) {
- if (path[i].ctype == last_type) cigar[n] += 1u << 4;
- else {
- cigar[++n] = 1u << 4 | path[i].ctype;
- last_type = path[i].ctype;
- }
- }
-
- return cigar;
-}
-
-#ifdef STDALN_MAIN
-int main()
-{
- AlnAln *aln_local, *aln_global, *aln_left;
- int i;
-
- aln_local = aln_stdaln("CGTGCGATGCactgCATACGGCTCGCCTAGATCA", "AAGGGATGCTCTGCATCgCTCGGCTAGCTGT", &aln_param_blast, 0, 1);
- aln_global = aln_stdaln("CGTGCGATGCactgCATACGGCTCGCCTAGATCA", "AAGGGATGCTCTGCATCGgCTCGGCTAGCTGT", &aln_param_blast, 1, 1);
-// aln_left = aln_stdaln( "GATGCACTGCATACGGCTCGCCTAGATCA", "GATGCTCTGCATCGgCTCGGCTAGCTGT", &aln_param_blast, 2, 1);
- aln_left = aln_stdaln("CACCTTCGACTCACGTCTCATTCTCGGAGTCGAGTGGACGGTCCCTCATACACGAACAGGTTC",
- "CACCTTCGACTTTCACCTCTCATTCTCGGACTCGAGTGGACGGTCCCTCATCCAAGAACAGGGTCTGTGAAA", &aln_param_blast, 2, 1);
-
- printf(">%d,%d\t%d,%d\n", aln_local->start1, aln_local->end1, aln_local->start2, aln_local->end2);
- printf("%s\n%s\n%s\n", aln_local->out1, aln_local->outm, aln_local->out2);
-
- printf(">%d,%d\t%d,%d\t", aln_global->start1, aln_global->end1, aln_global->start2, aln_global->end2);
- for (i = 0; i != aln_global->n_cigar; ++i)
- printf("%d%c", aln_global->cigar32[i]>>4, "MID"[aln_global->cigar32[i]&0xf]);
- printf("\n%s\n%s\n%s\n", aln_global->out1, aln_global->outm, aln_global->out2);
-
- printf(">%d\t%d,%d\t%d,%d\t", aln_left->score, aln_left->start1, aln_left->end1, aln_left->start2, aln_left->end2);
- for (i = 0; i != aln_left->n_cigar; ++i)
- printf("%d%c", aln_left->cigar32[i]>>4, "MID"[aln_left->cigar32[i]&0xf]);
- printf("\n%s\n%s\n%s\n", aln_left->out1, aln_left->outm, aln_left->out2);
-
- aln_free_AlnAln(aln_local);
- aln_free_AlnAln(aln_global);
- aln_free_AlnAln(aln_left);
- return 0;
-}
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/stdaln.h
--- a/bwa-0.6.2/stdaln.h Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,162 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2003-2006, 2008, by Heng Li
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-/*
- 2009-07-23, 0.10.0
-
- - Use 32-bit to store CIGAR
-
- - Report suboptimal aligments
-
- - Implemented half-fixed-half-open DP
-
- 2009-04-26, 0.9.10
-
- - Allow to set a threshold for local alignment
-
- 2009-02-18, 0.9.9
-
- - Fixed a bug when no residue matches
-
- 2008-08-04, 0.9.8
-
- - Fixed the wrong declaration of aln_stdaln_aux()
-
- - Avoid 0 coordinate for global alignment
-
- 2008-08-01, 0.9.7
-
- - Change gap_end penalty to 5 in aln_param_bwa
-
- - Add function to convert path_t to the CIGAR format
-
- 2008-08-01, 0.9.6
-
- - The first gap now costs (gap_open+gap_ext), instead of
- gap_open. Scoring systems are modified accordingly.
-
- - Gap end is now correctly handled. Previously it is not correct.
-
- - Change license to MIT.
-
- */
-
-#ifndef LH3_STDALN_H_
-#define LH3_STDALN_H_
-
-
-#define STDALN_VERSION 0.11.0
-
-#include
-
-#define FROM_M 0
-#define FROM_I 1
-#define FROM_D 2
-#define FROM_S 3
-
-#define ALN_TYPE_LOCAL 0
-#define ALN_TYPE_GLOBAL 1
-#define ALN_TYPE_EXTEND 2
-
-/* This is the smallest integer. It might be CPU-dependent in very RARE cases. */
-#define MINOR_INF -1073741823
-
-typedef struct
-{
- int gap_open;
- int gap_ext;
- int gap_end;
-
- int *matrix;
- int row;
- int band_width;
-} AlnParam;
-
-typedef struct
-{
- int i, j;
- unsigned char ctype;
-} path_t;
-
-typedef struct
-{
- path_t *path; /* for advanced users... :-) */
- int path_len; /* for advanced users... :-) */
- int start1, end1; /* start and end of the first sequence, coordinations are 1-based */
- int start2, end2; /* start and end of the second sequence, coordinations are 1-based */
- int score, subo; /* score */
-
- char *out1, *out2; /* print them, and then you will know */
- char *outm;
-
- int n_cigar;
- uint32_t *cigar32;
-} AlnAln;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- AlnAln *aln_stdaln_aux(const char *seq1, const char *seq2, const AlnParam *ap,
- int type, int do_align, int len1, int len2);
- AlnAln *aln_stdaln(const char *seq1, const char *seq2, const AlnParam *ap, int type, int do_align);
- void aln_free_AlnAln(AlnAln *aa);
-
- int aln_global_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
- path_t *path, int *path_len);
- int aln_local_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
- path_t *path, int *path_len, int _thres, int *_subo);
- int aln_extend_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
- path_t *path, int *path_len, int G0, uint8_t *_mem);
- uint16_t *aln_path2cigar(const path_t *path, int path_len, int *n_cigar);
- uint32_t *aln_path2cigar32(const path_t *path, int path_len, int *n_cigar);
-
-#ifdef __cplusplus
-}
-#endif
-
-/********************
- * global variables *
- ********************/
-
-extern AlnParam aln_param_bwa; /* = { 37, 9, 0, aln_sm_maq, 5, 50 }; */
-extern AlnParam aln_param_blast; /* = { 5, 2, 2, aln_sm_blast, 5, 50 }; */
-extern AlnParam aln_param_nt2nt; /* = { 10, 2, 2, aln_sm_nt, 16, 75 }; */
-extern AlnParam aln_param_aa2aa; /* = { 20, 19, 19, aln_sm_read, 16, 75 }; */
-extern AlnParam aln_param_rd2rd; /* = { 12, 2, 2, aln_sm_blosum62, 22, 50 }; */
-
-/* common nucleotide score matrix for 16 bases */
-extern int aln_sm_nt[], aln_sm_bwa[];
-
-/* BLOSUM62 and BLOSUM45 */
-extern int aln_sm_blosum62[], aln_sm_blosum45[];
-
-/* common read for 16 bases. note that read alignment is quite different from common nucleotide alignment */
-extern int aln_sm_read[];
-
-/* human-mouse score matrix for 4 bases */
-extern int aln_sm_hs[];
-
-#endif
diff -r dd1186b11b3b -r a9636dc1e99a bwa-0.6.2/utils.c
--- a/bwa-0.6.2/utils.c Fri Jul 18 07:55:14 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,164 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008 Genome Research Ltd (GRL).
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-/* Contact: Heng Li