diff PsiCLASS-1.0.2/samtools-0.1.19/ChangeLog.old @ 0:903fc43d6227 draft default tip

Uploaded

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+++ b/PsiCLASS-1.0.2/samtools-0.1.19/ChangeLog.old	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,3875 @@
+commit db2ad3e19068cbafde72ecde75d0638bbb3598ba
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 16 14:45:17 2012 -0500
+
+    removed downsample.c
+
+commit 6c55c576903992c6fef148fe3b606fbc8bd10655
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 16 14:45:06 2012 -0500
+
+    print to output
+
+commit db1044a34e6049c87eaa63c39ed6e56f03e7d4c1
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 16 14:39:34 2012 -0500
+
+    removed sample
+    
+    Downsampling already exists in "view". View also keeps pairing while "sample" does not.
+
+commit ffdeed3e5d4a530bfdf6f9ba97fff0ba7add6cba
+Merge: 2daad7b accf026
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 16 14:22:15 2012 -0500
+
+    Merge branch 'master' of github.com:lh3/samtools
+
+commit accf0260fd1117e10047344345d40b31a9ec31bb
+Merge: 9134e0d c554160
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 16 11:21:14 2012 -0800
+
+    Merge pull request #8 from nh13/master
+    
+    Patches
+
+commit c554160df16ec7748cfdda4c7b54c641be7b809f
+Author: Nils Homer <[e-mail]>
+Date:   Thu Feb 16 14:06:52 2012 -0500
+
+    * more README.md work
+
+commit 2a81ffe349208d917666808fbc9f3041e0cb57de
+Author: Nils Homer <[e-mail]>
+Date:   Thu Feb 16 14:06:10 2012 -0500
+
+    * more README work
+
+commit fb3125f732715f62cded8685a23a002a96ce009b
+Author: Nils Homer <[e-mail]>
+Date:   Thu Feb 16 14:05:19 2012 -0500
+
+    * more README work
+
+commit 444d41002c37e1c3d0f9208b4a88126c47276386
+Author: Nils Homer <[e-mail]>
+Date:   Thu Feb 16 14:02:13 2012 -0500
+
+    * updating README
+
+commit dec53cb1043fe7efadfde75fa2fd39b76de22e54
+Author: Nils Homer <[e-mail]>
+Date:   Thu Feb 16 13:55:01 2012 -0500
+
+    updating the README for markdown syntax
+
+commit 798da18c346dca8ec6005582a0ddb1d5420b04ca
+Author: Nils Homer <[e-mail]>
+Date:   Thu Feb 16 13:48:35 2012 -0500
+
+    adding a README with the current differences between this repository and
+    the official one
+
+commit 4d22d86c0f28636662f2144a88cd168e104c4275
+Author: Nils Homer <[e-mail]>
+Date:   Thu Feb 16 13:35:03 2012 -0500
+
+    adding "samtools sample" to the main
+
+commit 893c25a37c21005dc42f45d45e9ad78ddc5f29bb
+Author: Nils Homer <[e-mail]>
+Date:   Thu Feb 16 13:33:51 2012 -0500
+
+    * removing some compile flags to work with OS X
+
+commit 7ac22f72fdc32edd5c24af6baebfa7db5faf8e7b
+Author: Jonathan Manning <[e-mail]>
+Date:   Thu Feb 16 10:47:14 2012 -0500
+
+    Check write filehandle after opening for write. tamw/tamr is a union type, so change is only semantic.
+    
+    Signed-off-by: Nils Homer <[e-mail]>
+
+commit fef53330416631690f60fdff42b6e43d764170dc
+Author: Jonathan Manning <[e-mail]>
+Date:   Thu Feb 16 10:44:59 2012 -0500
+
+    Catch and report invalid BAM header, instead of segfaulting later on.
+    
+    Signed-off-by: Nils Homer <[e-mail]>
+
+commit 5cc013fe4930bf9b6e7963aab1cd4a3c94f695bc
+Author: Jonathan Manning <[e-mail]>
+Date:   Thu Feb 16 10:44:16 2012 -0500
+
+    Add downsample to examples.
+    
+    Signed-off-by: Nils Homer <[e-mail]>
+
+commit b3fa9e7071532905a81dc7aa48eadc24b8c8846b
+Author: Jonathan Manning <[e-mail]>
+Date:   Thu Feb 16 10:43:48 2012 -0500
+
+    Adjust for leading hard clip on colorspace reads.
+    
+    Signed-off-by: Nils Homer <[e-mail]>
+
+commit 1a9296c1389469d1c1db5b8069f0e11ffcc8abb2
+Author: Jonathan Manning <[e-mail]>
+Date:   Thu Feb 16 10:42:52 2012 -0500
+
+    Add samtools sample command, contributed by Davide Cittaro <[e-mail]>.
+    
+    Signed-off-by: Nils Homer <[e-mail]>
+
+commit 2a804f3379748aeba944f1dec306dd726ff3235e
+Author: Jonathan Manning <[e-mail]>
+Date:   Thu Feb 16 10:42:07 2012 -0500
+
+    Add samtools qa command, contributed by Roman Valls Guimera <[e-mail]>.
+    
+    Signed-off-by: Nils Homer <[e-mail]>
+
+commit 0f3207fe8fd93e44d40fcf57204079c8c06d24a6
+Author: Jonathan Manning <[e-mail]>
+Date:   Thu Feb 16 10:39:08 2012 -0500
+
+    Makefile cleanup - allow CC, CFLAGS, LDFLAGS to be passed on make command line. Use LDFLAGS in samtools compile.
+    
+    Signed-off-by: Nils Homer <[e-mail]>
+
+commit 6e7df604025f6a86881bf7f4a16f30e15d31538a
+Author: Jonathan Manning <[e-mail]>
+Date:   Thu Feb 16 10:31:15 2012 -0500
+
+    Allow max_mem for sort to be specified with units.
+    
+    Signed-off-by: Nils Homer <[e-mail]>
+
+commit f12ebcaf6e60d34180a27d70e09b743cef140b98
+Author: Jonathan Manning <[e-mail]>
+Date:   Thu Feb 16 10:29:11 2012 -0500
+
+    Allow user defined [lowercase] tags in header elements.
+    
+    Signed-off-by: Nils Homer <[e-mail]>
+
+commit 50b931fa3312dc109537a4260698ddecd0f06a05
+Author: Jonathan Manning <[e-mail]>
+Date:   Thu Feb 16 10:27:11 2012 -0500
+
+    Check lowerbound in text entry box to avoid segfault in tview. Remove redundant call to bam_aux_get.
+    
+    Signed-off-by: Nils Homer <[e-mail]>
+
+commit 5e729da5190949a813d20d329eab7ddb661816bd
+Author: Nils Homer <[e-mail]>
+Date:   Thu Feb 16 10:31:48 2012 -0500
+
+    * fixing overflow/underflow in integer parsing
+
+commit fa50a4330b9abedaf07c26e13d31f05e57f1d319
+Author: Nils Homer <[e-mail]>
+Date:   Thu Feb 16 10:30:40 2012 -0500
+
+    * updating help message for samtools depth
+
+commit 79e52c9624b6dd3bdfdf439f4b4bc6f774c230a4
+Author: Nils Homer <[e-mail]>
+Date:   Thu Feb 16 10:29:32 2012 -0500
+
+    * adding support for outputting a circos histogram file in "samtools depth".  Use
+    the "-c/-B" options.
+
+commit 2daad7b52daa86561c0fb65fe366691fad9f5ed3
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 16 09:31:57 2012 -0500
+
+    bugfix: wrong SP; missing DV in the VCF hdr
+
+commit 9134e0d5047c281ef3bd53da91771d4814a5131c
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 8 11:19:12 2012 -0500
+
+    missing support of DV
+
+commit 34ebf12078c1d1015a0b8b9a9221243a60b22893
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 8 11:08:56 2012 -0500
+
+    new BCF DV format: number of variant reads
+
+commit 9589d3312fa2d076f48bdd68e2a5edd419c8070c
+Author: Heng Li <[e-mail]>
+Date:   Tue Jan 10 10:30:27 2012 -0500
+
+    scale depth to quality (hidden option)
+
+commit 704473e14668333ecaca5fb7b238af405c43e3b1
+Author: Heng Li <[e-mail]>
+Date:   Tue Jan 10 10:18:17 2012 -0500
+
+    really nothing
+
+commit 01b307fd287962372bbf07461c88b54f41636817
+Author: Heng Li <[e-mail]>
+Date:   Wed Dec 7 13:07:42 2011 -0500
+
+    added an example containing 'B'
+
+commit c678791f0451ceb9205c1ab5c52c84641863c99a
+Author: Heng Li <[e-mail]>
+Date:   Sat Dec 3 12:10:30 2011 -0500
+
+    'B' now moves backward w.r.t. the query
+
+commit 152119bc06a073933ca830e8e1407538e44626cc
+Author: Heng Li <[e-mail]>
+Date:   Fri Dec 2 10:50:12 2011 -0500
+
+    better consensus; a little more robust
+
+commit 454da4754ac503edda5b1329b67757d797e46e07
+Author: Heng Li <[e-mail]>
+Date:   Fri Dec 2 00:20:22 2011 -0500
+
+    in pileup call remove_B()
+
+commit ff2bcac1cc078ba1879f18c89cfae314439d7086
+Author: Heng Li <[e-mail]>
+Date:   Fri Dec 2 00:17:32 2011 -0500
+
+    working on a few toy examples
+
+commit 745ca7260158d6df7897b52598033ffb055a9e4f
+Author: Heng Li <[e-mail]>
+Date:   Thu Dec 1 22:55:39 2011 -0500
+
+    bam_remove_B(); not tested
+
+commit 07e4cdc7300abfcc82e03105b4689f95cab551cd
+Author: Heng Li <[e-mail]>
+Date:   Thu Nov 10 12:58:55 2011 -0500
+
+    baseQ threshold on plain pipleup; removed -E
+
+commit 322ebf2082dfa91df44b3a996d26c85357e5d5a2
+Author: Heng Li <[e-mail]>
+Date:   Wed Oct 19 09:28:04 2011 -0400
+
+    fixed two gcc warnings
+
+commit a632457b4c4adc50d833b56b5a5231feafaf8193
+Author: Heng Li <[e-mail]>
+Date:   Tue Oct 4 10:13:23 2011 -0400
+
+    change size_t to uint32_t in bam_header_t
+    
+    This may cause issues on 64-bit big-endian machines. Reported and fixed by Paolo Emilio Mazzon.
+
+commit af31bf5a78aea03baf6eb90fe50076549d499f6e
+Author: Heng Li <[e-mail]>
+Date:   Mon Sep 26 20:17:57 2011 -0400
+
+    rename pad2unpad to depad
+
+commit 77b198b73dfad1048e5d1c5a64aa75ee7b90f596
+Author: Heng Li <[e-mail]>
+Date:   Fri Sep 23 01:22:40 2011 -0400
+
+    convert padded BAM to unpadded BAM
+
+commit adb9e2342b7b7501d9527d3c23afab10469ae2c6
+Author: Heng Li <[e-mail]>
+Date:   Wed Sep 7 11:40:50 2011 -0400
+
+    generate template cigar with "fixmate"
+
+commit 46e5ab445a0fe880216cbc0daf1225725b569d7a
+Author: Heng Li <[e-mail]>
+Date:   Fri Sep 2 12:50:18 2011 -0400
+
+    update kseq.h to the latest version
+
+commit 68e9e4a73eb91405bb3e56bf0cdaf12d1b487abb
+Author: Heng Li <[e-mail]>
+Date:   Fri Sep 2 12:44:45 2011 -0400
+
+    Release samtools-0.1.18
+
+commit aa06bdadb2d109a79f927f478102f96a1f5fd258
+Author: Heng Li <[e-mail]>
+Date:   Fri Sep 2 12:14:17 2011 -0400
+
+    updated the revision number
+
+commit 267e1e1b6e54c0ab24f94cd9aee9cbd2d1923f9f
+Merge: 19ff1d3 aebab30
+Author: Heng Li <[e-mail]>
+Date:   Fri Sep 2 12:13:08 2011 -0400
+
+    Merge https://github.com/lh3/samtools into reduce
+    
+    Conflicts:
+    	bam_md.c
+    
+    Fixed a few typos in the merge
+
+commit aebab302399c24eaa6c5ab79d13d6bd5e2e9ea9a
+Merge: c2c63d0 da62663
+Author: Heng Li <[e-mail]>
+Date:   Fri Sep 2 09:03:49 2011 -0700
+
+    Merge pull request #4 from peterjc/x_equals2
+    
+    Implement basic support for =/X CIGAR operations
+
+commit 19ff1d3d7f47d7e61b121292aefe5a74bb8a18d2
+Author: Heng Li <[e-mail]>
+Date:   Thu Aug 25 16:38:12 2011 -0400
+
+    reduce BAM size (experimental)
+
+commit da626630fd98fd4e07ceb4d58c5c9a42d312a85d
+Author: peterjc <[e-mail]>
+Date:   Mon Aug 22 06:58:08 2011 +0100
+
+    Support =/X CIGAR operations (treated like M)
+
+commit 461d8003529db77a4d5ecbd108312e868b051a3d
+Author: peterjc <[e-mail]>
+Date:   Mon Aug 22 05:52:56 2011 +0100
+
+    Define CIGAR equals and X operationss (7 and 8)
+
+commit c2c63d067113baab41f3bc35fb28f4f00578accb
+Merge: 7ab3ef3 9a0ed9a
+Author: Heng Li <[e-mail]>
+Date:   Thu Aug 18 17:21:54 2011 -0700
+
+    Merge pull request #3 from peterjc/x_equals
+    
+    Accept SAM files using = in CIGAR (treats X and = as M)
+
+commit 9a0ed9a6b85c7981465f459300208dbd93e3c6f5
+Author: peterjc <[e-mail]>
+Date:   Thu Aug 18 19:28:52 2011 +0100
+
+    Accept SAM files using = in CIGAR (treats X and = as M)
+
+commit 7ab3ef388c1eb34d7912fd70cc5656c955240263
+Author: Heng Li <[e-mail]>
+Date:   Mon Aug 8 10:22:22 2011 -0400
+
+    bugfix: indexing takes huge memory
+    
+    This happens when an unmapped mate has coordinate 1. Thank Joel Martin for the fix.
+
+commit a3f6738593e944354a8f75306687d8b3acf08bf1
+Merge: a8bdca9 bc67ea2
+Author: Heng Li <[e-mail]>
+Date:   Mon Aug 8 09:52:26 2011 -0400
+
+    Merge branch 'master' of github.com:lh3/samtools
+
+commit bc67ea225da653f36a70b38382d6111dd494f659
+Author: Petr Danecek <[e-mail]>
+Date:   Thu Jul 28 20:03:16 2011 +0100
+
+    Variant Distance Bias
+
+commit deb578f0c49d0b7d8c3bc6be220b4d67e2e7dfdf
+Author: Petr Danecek <[e-mail]>
+Date:   Tue Jul 26 09:57:37 2011 +0100
+
+    If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but use the tag instead.
+
+commit a8bdca9cf482a637b89ee4f98469a93e0ab5e69b
+Author: Heng Li <[e-mail]>
+Date:   Mon Jul 25 10:10:55 2011 -0400
+
+    bugfix: LRT2=nan
+
+commit 0afe33137d046a3e849eeb4a54590f27cbad4228
+Author: Heng Li <[e-mail]>
+Date:   Fri Jul 22 21:55:38 2011 -0400
+
+    fixed a bug/typo
+
+commit 62d5849658c10222d40308c6b53ab4f99a448494
+Author: Heng Li <[e-mail]>
+Date:   Fri Jul 15 16:04:19 2011 -0400
+
+    allow to set see in subsampling
+
+commit 5f46243824cc9435b167973e1d51e13128794ea1
+Author: Heng Li <[e-mail]>
+Date:   Fri Jul 15 15:54:47 2011 -0400
+
+    support subsampling
+
+commit 5e55b6f34fc86cba7cf98d52ccaed405c3ffabbc
+Author: Heng Li <[e-mail]>
+Date:   Fri Jul 15 15:53:38 2011 -0400
+
+    support indels
+
+commit f31c162926d6f43e8b60171789a258d02e1f9be5
+Author: Heng Li <[e-mail]>
+Date:   Thu Jul 7 17:02:33 2011 -0400
+
+    do not count indel with "view -Y"
+
+commit e412dae587883b4c17e5fbf4b7c33f38bfa8458a
+Author: Heng Li <[e-mail]>
+Date:   Thu Jul 7 00:35:25 2011 -0400
+
+    for WIN32 compatibility
+
+commit 70a52501bcfa63824749893a5ab8ed3c38e34958
+Author: Heng Li <[e-mail]>
+Date:   Thu Jul 7 00:32:46 2011 -0400
+
+    for WIN32 compatibility
+
+commit 00438f14ed5984f08e8f7645a9b95644a812f969
+Author: Heng Li <[e-mail]>
+Date:   Wed Jul 6 23:41:45 2011 -0400
+
+    fixed an uninitialized variable
+
+commit 7609c4a01059c326544b3d0142dfe9c4229d68c6
+Author: Heng Li <[e-mail]>
+Date:   Wed Jul 6 23:39:31 2011 -0400
+
+    fixed an uninitialized variable
+
+commit cec7189a412f80ccb068a73bd28528915c16b0bf
+Author: Heng Li <[e-mail]>
+Date:   Wed Jul 6 22:53:19 2011 -0400
+
+    Release samtools-0.1.17
+
+commit 93c06a249de3bb666029bf07b66de5e8e5e314fa
+Author: Heng Li <[e-mail]>
+Date:   Wed Jul 6 09:46:09 2011 -0400
+
+    bugfix: incorrect idxstats for the last seq
+    
+    Again, this bug is caused by 3rd-party code for the sorting order checking.
+
+commit 84f6ca62db6e27b8c4c711e7b5f3ca704bf27b4f
+Author: Heng Li <[e-mail]>
+Date:   Tue Jul 5 23:30:23 2011 -0400
+
+    output mapping quality in the old pileup format
+
+commit 362e05fd670886acaede69b864903d730b9db3ca
+Author: Heng Li <[e-mail]>
+Date:   Tue Jul 5 21:59:22 2011 -0400
+
+    added a brief description of the VCF format
+
+commit e690a696468205e0cc4560016361c997660dd496
+Author: Heng Li <[e-mail]>
+Date:   Tue Jul 5 16:23:10 2011 -0400
+
+    improved samtools manual page
+
+commit 362b4a1408ef3c32311d638aa8d85ce39c1c7b2d
+Author: Heng Li <[e-mail]>
+Date:   Tue Jul 5 15:58:29 2011 -0400
+
+    merge bcftools.1 to samtools.1
+
+commit 643e0e61ba7266efbc9e5bfcb8e41f369ba2ce0a
+Author: Heng Li <[e-mail]>
+Date:   Tue Jul 5 13:39:02 2011 -0400
+
+    mpileup: when region set, set reference properly
+
+commit 613e4d67624a94f62563935fbd5cc294df69605a
+Author: Heng Li <[e-mail]>
+Date:   Mon Jul 4 23:29:02 2011 -0400
+
+    compute the min PL diff
+
+commit 5b7d5d3f52b97ca42c8500eede808dab88a46a53
+Author: Heng Li <[e-mail]>
+Date:   Mon Jul 4 22:57:48 2011 -0400
+
+    rename trio.c to mut.c
+
+commit 84fe96ad64b0365ead93a4115d1684b9bebb98fc
+Author: Heng Li <[e-mail]>
+Date:   Sun Jul 3 15:38:51 2011 -0400
+
+    added pair caller interface; not tested
+
+commit 2f2867b87b84c35319cc416d6173819d5c8a4e8c
+Author: Heng Li <[e-mail]>
+Date:   Sun Jul 3 15:24:23 2011 -0400
+
+    inital implementation of a pair caller
+
+commit e97653cf2ad653c95886933c42a2b5492ccab5ff
+Author: Heng Li <[e-mail]>
+Date:   Sun Jul 3 00:06:28 2011 -0400
+
+    convert bam to single-end fastq
+
+commit e8013e11f7a8db0a8d18c60d130169cca39bf2bd
+Author: Heng Li <[e-mail]>
+Date:   Sat Jul 2 14:39:18 2011 -0400
+
+    improve BED parsing
+
+commit 1025714325fdc636aeee47a76db8dafbbbfde64b
+Author: Heng Li <[e-mail]>
+Date:   Fri Jul 1 14:19:54 2011 -0400
+
+    update the manual page
+
+commit 8022d0039dff47b1c11b2421357d510c1f28ae15
+Author: Heng Li <[e-mail]>
+Date:   Fri Jul 1 14:17:03 2011 -0400
+
+    output the best constrained genotypes in trio
+
+commit 18c87295e12f5bebafdcae00d52000fb94c8a566
+Author: Heng Li <[e-mail]>
+Date:   Fri Jul 1 11:18:14 2011 -0400
+
+    added documentations for view -T
+
+commit daf7a8d96bd495296bf7c7d99cddb808a3ced7d5
+Author: Heng Li <[e-mail]>
+Date:   Thu Jun 30 22:45:20 2011 -0400
+
+    fixed a bug in writing SP
+
+commit e5c32bf9b28c6e3e861db88de56b5dbe11058b61
+Author: Heng Li <[e-mail]>
+Date:   Thu Jun 30 22:35:25 2011 -0400
+
+    optionally output read positions in mpileup
+
+commit 1008051155ec994c1901e18f3eb03ea32a62e5d7
+Author: Heng Li <[e-mail]>
+Date:   Thu Jun 30 22:17:25 2011 -0400
+
+    make faidx works with <2GB lines
+
+commit 2daebb63762425dd3074ddf71582ad189001e394
+Author: Heng Li <[e-mail]>
+Date:   Thu Jun 30 17:28:58 2011 -0400
+
+    fixed an issue in the trio caller and the indel caller
+
+commit 9fdd52cf0716fb342a94946433d564b28b230835
+Author: Heng Li <[e-mail]>
+Date:   Thu Jun 30 13:34:01 2011 -0400
+
+    Added trio caller; NOT tested yet
+
+commit ea22a8ed83625e9c82382b56acc42a2d9cfd17e5
+Author: Heng Li <[e-mail]>
+Date:   Thu Jun 30 11:42:29 2011 -0400
+
+    convert PL to 10-likelihood GL
+
+commit 10d7065267b0d12c2bfcb6c70204fb6944cd395d
+Author: Heng Li <[e-mail]>
+Date:   Thu Jun 30 10:49:05 2011 -0400
+
+    fix a compatibility issue with the new bcftools
+
+commit d340f01f609c61b719d38a6a55629a3fc899e1cd
+Author: Heng Li <[e-mail]>
+Date:   Sun Jun 26 23:41:20 2011 -0400
+
+    allow to ignore RG
+
+commit d6321faf98ebfe899b9409fb23c90a4aa8c6b542
+Author: Heng Li <[e-mail]>
+Date:   Sun Jun 5 23:05:21 2011 -0400
+
+    fixed a bug in SO checking due to a recent change
+
+commit bc995abf666d0c9ab4258f6c1b3518a45a89209f
+Author: Heng Li <[e-mail]>
+Date:   Fri Jun 3 14:45:36 2011 -0400
+
+    update the version number
+
+commit 9e7cd83a08383858d008e0ccb2238a2b93831d6c
+Author: Heng Li <[e-mail]>
+Date:   Fri Jun 3 14:43:12 2011 -0400
+
+    smarter way to parse a region string
+
+commit e58a90a0fde54053dac65352b34c13c3fea815fc
+Author: Heng Li <[e-mail]>
+Date:   Wed Jun 1 14:36:22 2011 -0400
+
+    output LRT2 instead of LRT1
+
+commit 08f78c9af3e5661f04f80bef424232de721dba03
+Author: Heng Li <[e-mail]>
+Date:   Wed Jun 1 14:02:28 2011 -0400
+
+    genotype test, but assuming 1-degree
+
+commit 587b852340d7e60f6f7cf474a92ef77aeab46018
+Author: Heng Li <[e-mail]>
+Date:   Wed Jun 1 12:55:19 2011 -0400
+
+    perform 2-degree test by default
+
+commit 3d38e403c5c830478b7eb157a484776997440501
+Author: Heng Li <[e-mail]>
+Date:   Wed Jun 1 12:44:34 2011 -0400
+
+    fixed a typo; but the result is still not good
+
+commit 06291624f7dcc57445676f3be25d0bc355dd7110
+Author: Heng Li <[e-mail]>
+Date:   Wed Jun 1 12:24:18 2011 -0400
+
+    fixed a typo
+
+commit 63b98aa33636b0d82a435bf49153c8c1502e7d42
+Author: Heng Li <[e-mail]>
+Date:   Wed Jun 1 12:23:37 2011 -0400
+
+    added HWE+F<0 filter
+
+commit 37d926e8999999b593d0637ab7dc379dbd3d6006
+Author: Heng Li <[e-mail]>
+Date:   Wed May 4 10:11:59 2011 -0400
+
+    improved sorting order checking in index
+    
+    Patches from Jonathan Manning
+
+commit 1c2dc6762c5f7cd946046b53346513f2f9761dbf
+Author: Heng Li <[e-mail]>
+Date:   Tue May 3 23:09:05 2011 -0400
+
+    added r^2 estimate; added Brent's method
+
+commit c2d3bcd8f98e31668b5f1321222fbc6fd6336e75
+Author: Heng Li <[e-mail]>
+Date:   Sun May 1 23:45:23 2011 -0400
+
+    combine several utilites into vcfutils.lua
+
+commit be2e7362d7593ea4d03fb33cdb6af2aa096ca6c4
+Author: Heng Li <[e-mail]>
+Date:   Wed Apr 27 21:09:22 2011 -0400
+
+    minor warning
+
+commit 683ef0443860813d743cf84fa86dda9bfaf5445a
+Author: Heng Li <[e-mail]>
+Date:   Wed Apr 27 10:10:38 2011 -0400
+
+    added versioning
+
+commit ed72f25ec85671f7646dbc92fa7b5b1dda427f7d
+Author: Heng Li <[e-mail]>
+Date:   Wed Apr 27 10:04:02 2011 -0400
+
+    Output ML allele count
+
+commit 2a9e36d2d6c405b2411ca47458f028ada8fe1000
+Author: Heng Li <[e-mail]>
+Date:   Tue Apr 26 16:14:20 2011 -0400
+
+    use ar -s
+
+commit 7a4f54e6dbcd7c94acbb3f1050a93f94b8a07949
+Author: Heng Li <[e-mail]>
+Date:   Sat Apr 23 01:22:31 2011 -0400
+
+    added another type of LRT
+
+commit b9c5e84762a4aacce3a3771b51ea80967c79a2e5
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 22 16:00:31 2011 -0400
+
+    added version
+
+commit 8fad6677c5952efd67391581d64e67e02e7f6e68
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 22 00:30:19 2011 -0400
+
+    remove the pileup command
+
+commit 3a962fb6ebf779de70f9e6effb2d8701a9aa3dd9
+Author: Heng Li <[e-mail]>
+Date:   Thu Apr 21 23:10:45 2011 -0400
+
+    Release 0.1.16 (r963:234)
+
+commit b4d683cffbd98c43f05aff8610b37d63dd7e54aa
+Author: Heng Li <[e-mail]>
+Date:   Thu Apr 21 12:44:44 2011 -0400
+
+    fixed a bug when coordinate-less reads are on the reverse strand
+
+commit c5ec45a128f409debc6a56a798024f53004037dc
+Author: Heng Li <[e-mail]>
+Date:   Wed Apr 20 11:36:52 2011 -0400
+
+    added option '-f' to merge to avoid overwritting
+
+commit 68d431531370d24907c01a27f166f2341d7c4d35
+Author: Heng Li <[e-mail]>
+Date:   Wed Apr 20 10:26:58 2011 -0400
+
+    do not print a warning
+
+commit 32922607e51ad2260c337eb022b9e4aedacb049f
+Author: Heng Li <[e-mail]>
+Date:   Wed Apr 20 10:21:06 2011 -0400
+
+    Added ldpair to compute LD between requested pairs
+
+commit b8d6fa71b91678fa02338257e0707d1e5ca098dd
+Author: Heng Li <[e-mail]>
+Date:   Sun Apr 17 21:51:43 2011 -0400
+
+    On a toy sample, type "B" seems to be accepted
+
+commit 0e7ee9a6bb4029184202aa6e6738105ba0c0510b
+Author: Heng Li <[e-mail]>
+Date:   Sun Apr 17 21:21:20 2011 -0400
+
+    added type "B"; not tested yet
+
+commit a513dfad0ac0062b03871eb6ecf26cb8d18dc895
+Author: Heng Li <[e-mail]>
+Date:   Sun Apr 17 19:25:54 2011 -0400
+
+    fixed a bug in bedidx.c: input BED not sorted
+
+commit de1e192bb0a8a762a54a6eee81d882fab01c3d32
+Author: Heng Li <[e-mail]>
+Date:   Sun Apr 17 18:51:08 2011 -0400
+
+    by default, always perform posterior chi^2
+
+commit df6e0d1099895fc6cd7a19dc89fba95ed6654d35
+Author: Heng Li <[e-mail]>
+Date:   Sat Apr 16 12:33:28 2011 -0400
+
+    added debugging
+
+commit 8ce52e024dc2ef361dbd5399c232163055057e70
+Author: Heng Li <[e-mail]>
+Date:   Sat Apr 16 00:59:05 2011 -0400
+
+    avoid a segfault given wrong input
+
+commit e66b6684fc9a397f91ec29fdeecae9f8eb986a55
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 15 19:55:39 2011 -0400
+
+    do not segfault when there is no PL
+
+commit 9ce3c584ec0cebfa45576f2ef538df4dad2b7e55
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 15 11:59:55 2011 -0400
+
+    remove another unused part
+
+commit f53a051d68bf312ac8d5865210fae7a9808c0fb9
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 15 10:41:25 2011 -0400
+
+    print G3 if HWE is small
+
+commit 4b2c08bb86ca4ed4959e4cb77a28f7d6fc19f5c9
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 15 10:04:34 2011 -0400
+
+    fixed a bug
+    
+    actually not fix, but hide it
+
+commit 088e13c32453fb533b7bb1c65a573f9b90a23625
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 15 09:48:47 2011 -0400
+
+    added LRT based permutation; not used though
+
+commit 1e3c2001afcb80b5eaa4c3f88df9da7b01b62524
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 15 09:28:55 2011 -0400
+
+    Perform posterior contrast for small LRT
+    
+    Posterior contrast is much slower than LRT. Nonetheless, posterior P-value is
+    more robust to sequencing artifacts. Thus we may combine the two to achieve a
+    balance between speed and low FPR.
+
+commit 6f1b066270902198a7175ff6c1b05ebc8d1919be
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 15 01:36:06 2011 -0400
+
+    Added Brent's method
+
+commit 3d061e5db25b67b25f6ff87afe4162e121354232
+Author: Heng Li <[e-mail]>
+Date:   Thu Apr 14 23:30:10 2011 -0400
+
+    fixed a typo in printing
+
+commit 7fd14ceb5990bb350b8e97346ef3537d80058def
+Author: Heng Li <[e-mail]>
+Date:   Thu Apr 14 23:14:23 2011 -0400
+
+    fixed a stupid bug
+
+commit f5b2c3459ec098b3cafd9619b9077132516baf58
+Author: Heng Li <[e-mail]>
+Date:   Thu Apr 14 22:42:35 2011 -0400
+
+    separate EM and posterior
+    
+    Now, constrast is not performed unless -C is in use. EM can be invoked
+    independently with -e without computing the posterior.
+
+commit 9eefcac963697fae554789b11ae3cb2c23f224d0
+Author: Heng Li <[e-mail]>
+Date:   Thu Apr 14 22:00:19 2011 -0400
+
+    further code cleanup; prepare to add EM interface
+
+commit c2cce52355262743711e4742b0c8542bfcab1cdd
+Author: Heng Li <[e-mail]>
+Date:   Thu Apr 14 21:44:03 2011 -0400
+
+    drop EM from prob1
+
+commit 24016f04bd3bdffb7eeb50cb25854f5007feb70f
+Author: Heng Li <[e-mail]>
+Date:   Thu Apr 14 21:08:33 2011 -0400
+
+    drop posterior LRT; prepare for clean up
+
+commit 3670d8bd88c3eb22873f0a80e2a5913f64ca8c9a
+Author: Heng Li <[e-mail]>
+Date:   Thu Apr 14 20:57:43 2011 -0400
+
+    better initial values for LD
+
+commit d48a8873c060b18b57799cfe3a0e5496ba069457
+Author: Heng Li <[e-mail]>
+Date:   Thu Apr 14 20:36:25 2011 -0400
+
+    finished EM
+
+commit b101f2db476188a950c23f5c1b6185fdb7f8f40b
+Author: Heng Li <[e-mail]>
+Date:   Wed Apr 13 01:19:04 2011 -0400
+
+    genotype frequency estimate
+
+commit d79bdcbf6242ecfb8accba9ac9a22fbcbd543cf2
+Author: Heng Li <[e-mail]>
+Date:   Wed Apr 13 00:37:22 2011 -0400
+
+    prepare for code clean up
+
+commit e0ce416abfc094f0c090957080b1404fd0edf752
+Author: Heng Li <[e-mail]>
+Date:   Wed Apr 13 00:34:15 2011 -0400
+
+    rename ld.c to em.c
+
+commit 45ede3ad181f35c1be24bed5d75841e472357ab7
+Author: Heng Li <[e-mail]>
+Date:   Wed Apr 13 00:22:10 2011 -0400
+
+    implemeted EM likelihood ratio test
+    
+    The idea is learned from a brief chat with Rasmus Nielsen.
+
+commit 0454a346b60e42b75a2f742272089810279c7131
+Author: Heng Li <[e-mail]>
+Date:   Tue Apr 12 15:45:52 2011 -0400
+
+    added likelihood-ratio test (idea from Nick)
+
+commit f6287c8646c690440a1554c8958e7268f4134dc2
+Author: Heng Li <[e-mail]>
+Date:   Sun Apr 10 18:24:37 2011 -0400
+
+    Release samtools-0.1.15 (r949:203)
+
+commit de6023f38f4d652438557cf7a0ac6eec324e7416
+Author: Heng Li <[e-mail]>
+Date:   Sun Apr 10 15:54:58 2011 -0400
+
+    improved help information
+
+commit d3b337f2b7eda1e6f8f5575a19d1b5ed55cae279
+Author: Heng Li <[e-mail]>
+Date:   Sat Apr 9 16:28:01 2011 -0400
+
+    fixed a minor issue
+
+commit 82f6e4f49247e75fbd8ec08c285b8d3047b3d235
+Author: Heng Li <[e-mail]>
+Date:   Sat Apr 9 15:49:04 2011 -0400
+
+    separate QC-pass and QC-fail reads
+
+commit 8362b4a255081ee7ca0a4ca2eabc8c76758b6863
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 8 17:45:19 2011 -0400
+
+    added verbose level
+
+commit f7bf419c290462be7d289249a4a6d28f825b4c93
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 8 16:08:14 2011 -0400
+
+    fixed a bug
+
+commit 890cbb1ac93b3004fb6cf42ff47195077dcfc8ad
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 8 16:00:37 2011 -0400
+
+    drop unrelated @RG when "-R" is in use
+
+commit a62dc929c950fb51311b705f5b5bfba8e3f704d7
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 8 16:00:14 2011 -0400
+
+    skip header validation
+
+commit 39da810e2c56c8f0eff1ab726600b41f26d3d8e9
+Author: Heng Li <[e-mail]>
+Date:   Tue Apr 5 23:52:22 2011 -0400
+
+    change error message
+
+commit c0c50a34df250ef8a7a29b172058cd229be582b5
+Author: Heng Li <[e-mail]>
+Date:   Tue Apr 5 23:50:46 2011 -0400
+
+    fixed a bug caused by recent modifications
+
+commit 25226e8c468404cb5e1b5272efcea57e4193c762
+Author: Heng Li <[e-mail]>
+Date:   Tue Apr 5 13:31:19 2011 -0400
+
+    reduce the indel filtering window
+
+commit 5e18d7014437734f9dac9ab45a95e43ec2526101
+Author: Heng Li <[e-mail]>
+Date:   Mon Apr 4 13:56:20 2011 -0400
+
+    only output hwe if it is small enough
+
+commit 614941fb7dd276de662e7820eb8c7bae871a18cc
+Author: Heng Li <[e-mail]>
+Date:   Mon Apr 4 13:34:02 2011 -0400
+
+    added HWE back
+
+commit 7abe8825aa0bacccdeb38125934ae94d18f0ad4d
+Author: Heng Li <[e-mail]>
+Date:   Mon Apr 4 12:46:24 2011 -0400
+
+    EM estimate of genotype frequency
+
+commit 2bfeff9c645d177416664f1cb811e85cac3ff9e3
+Author: Heng Li <[e-mail]>
+Date:   Mon Apr 4 11:29:12 2011 -0400
+
+    minor
+
+commit 401e40647e7e3abbac6e4ec3d8bb68eb6f2d401b
+Author: Heng Li <[e-mail]>
+Date:   Mon Apr 4 11:24:04 2011 -0400
+
+    Added genotype freq estimate and association test
+
+commit 6cc226df6e3b480f1bd6e763ce8ef47f785bbb74
+Author: Heng Li <[e-mail]>
+Date:   Sun Apr 3 20:57:23 2011 -0400
+
+    minor changes
+
+commit 7e47a39630e812f09b80369f14606245976f687e
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 1 15:21:59 2011 -0400
+
+    print the grayscale
+
+commit 2f675d9c0dde3c166c99e335fa17c7873a5ae8d5
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 1 08:55:16 2011 -0400
+
+    change to comment
+
+commit 0592bb514994544ed84f51e509b233cf8821e0cf
+Author: Heng Li <[e-mail]>
+Date:   Fri Apr 1 08:54:35 2011 -0400
+
+    added base quality filtering
+
+commit fc1b47e04a7b94f6362c45856cbeb89d9d0b5ca5
+Author: Heng Li <[e-mail]>
+Date:   Thu Mar 31 23:31:14 2011 -0400
+
+    fixed a few typos in comments
+
+commit 60be79bc8f0d24656e5e8a329af7e9b5b91d4c8b
+Author: Heng Li <[e-mail]>
+Date:   Thu Mar 31 23:13:23 2011 -0400
+
+    comments
+
+commit 2432864acc25ebe5cee4217dbb0120439077a7f8
+Author: Heng Li <[e-mail]>
+Date:   Thu Mar 31 22:42:46 2011 -0400
+
+    added bam2depth.c, a demo program
+
+commit 39625f7c6bea9ccbfd9af0feb22348d52079f012
+Author: Heng Li <[e-mail]>
+Date:   Thu Mar 31 16:37:22 2011 -0400
+
+    added bgzf_check_bgzf() (used by tabix)
+
+commit 6de6bd3fb67fd22753a5f07d4cc25bf94e1b5a8c
+Author: Heng Li <[e-mail]>
+Date:   Thu Mar 31 16:37:08 2011 -0400
+
+    fixed a bug in bedidx.c
+
+commit 3b9e257d25b2e81eed1625bc5d2882ed486ef20e
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 30 13:27:15 2011 -0400
+
+    added bed support to bcftools
+
+commit 47bcce3d14ec4d205283b61e5e653803996c42e0
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 30 12:56:40 2011 -0400
+
+    Added BED support to "samtools view"
+
+commit a812386017faedfc86c0e6562adbb2138329cfeb
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 30 12:47:04 2011 -0400
+
+    support BED file
+
+commit 3052dddc929f1825e6e7f7f6f6724d9465d6cf9a
+Author: Heng Li <[e-mail]>
+Date:   Mon Mar 28 15:51:55 2011 -0400
+
+    relax RG matching; proper mismatching message
+
+commit f86d60c8fe25785523f01fae1486d2a6df4ee6ef
+Author: Heng Li <[e-mail]>
+Date:   Sat Mar 26 10:38:23 2011 -0400
+
+    Avoid reporting association when something unexpected, which I do not understand, happens.
+
+commit dd41e6b26fd9fe30218748b9a0a1f49bdb1862b9
+Author: Heng Li <[e-mail]>
+Date:   Sat Mar 26 10:38:01 2011 -0400
+
+    Added -1 to merge
+
+commit 4a0364b0d7f87f1c88d71ec5857a1f1d40710681
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 23 16:56:55 2011 -0400
+
+    plot pairwise r^2
+
+commit 452629a711582e612bec22b3b082e234bd37039b
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 23 14:31:01 2011 -0400
+
+    pairwise LD; case-control AF2
+
+commit 52862951adcaecde26ba8f0d9c1897944640a674
+Author: Heng Li <[e-mail]>
+Date:   Mon Mar 21 23:03:14 2011 -0400
+
+    Release samtools-0.1.14 (r933:170)
+
+commit 59a5a8ba8e2940f0e38238f9339f02c91a8a0ce4
+Author: Heng Li <[e-mail]>
+Date:   Mon Mar 21 13:52:55 2011 -0400
+
+    optionally skip loci with too low sample coverage
+
+commit 6434264b5c69514d4fafe62cbd30b3bbaddc1d41
+Author: Heng Li <[e-mail]>
+Date:   Sat Mar 19 14:38:25 2011 -0400
+
+    mpileup support Illumina1.3+ quality; skip non-variant sites when "view -v" is in use
+
+commit 5f59e01987e1d5eca7d6359cae64a9734b18beea
+Author: Heng Li <[e-mail]>
+Date:   Fri Mar 18 17:19:18 2011 -0400
+
+    update version to r933:167
+
+commit 4d2c3c950910aa3d2c87760c3532e458fe01c0fa
+Author: Heng Li <[e-mail]>
+Date:   Fri Mar 18 16:25:01 2011 -0400
+
+    added "-1" to the command-line help
+
+commit 55313a015a7bd6369cf5a66fed7fab2333201dc9
+Author: Heng Li <[e-mail]>
+Date:   Fri Mar 18 16:22:12 2011 -0400
+
+    added the "cat" command (by Chris Saunders)
+
+commit b670272cadf3efa4dc456ac4c76104f73477d60d
+Author: Heng Li <[e-mail]>
+Date:   Fri Mar 18 15:59:46 2011 -0400
+
+    support varying the compression level
+
+commit c5dd3c9ca5f75f880e52c8cd2beae983bcb8d3b1
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 16 14:33:45 2011 -0400
+
+    update the manual pages
+
+commit 12fb4b596dc51bccd154fc4bd0593442f7937a46
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 16 12:49:26 2011 -0400
+
+    update changelog
+
+commit e7fe4fd66e02d60a1ca7952ad1938809e77729a9
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 16 12:10:05 2011 -0400
+
+    do not call indels when the depth is very high
+
+commit 7455eeaa32b949bb3856f75810890aabf7cacb18
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 16 11:56:56 2011 -0400
+
+    code clean up
+
+commit 5f16679e54ced8e67a75d949f9175c50480b914e
+Author: Heng Li <[e-mail]>
+Date:   Tue Mar 15 14:45:24 2011 -0400
+
+    when -s is specified, change the sample order
+
+commit 7ba95adee09d3b06a7eaf797d25efef837e592f5
+Author: Heng Li <[e-mail]>
+Date:   Tue Mar 15 14:11:42 2011 -0400
+
+    compute the rank in permutation
+
+commit d219783cea7643fc7e10e1bd3a98e9b3165b4506
+Author: Heng Li <[e-mail]>
+Date:   Sun Mar 13 21:35:13 2011 -0400
+
+    I have found a SERIOUS BUG!!!
+
+commit 8e20d04ecdac1a7788eef71c4bb91b8479cf7150
+Author: Heng Li <[e-mail]>
+Date:   Sun Mar 13 17:04:04 2011 -0400
+
+    optionally shuffle samples in a BCF (debugging)
+
+commit fc7b261f181f2a411427bc9ee5d586c883ca9cdc
+Author: Heng Li <[e-mail]>
+Date:   Fri Mar 11 09:34:20 2011 -0500
+
+    fixed a bug
+
+commit b3bbcc3d40994ae85705ab6fef9866ec8c142201
+Author: Heng Li <[e-mail]>
+Date:   Thu Mar 10 20:25:59 2011 -0500
+
+    use mode instead of mean
+
+commit f1161262d137098a19143b5cb0de810e5db3243e
+Author: Heng Li <[e-mail]>
+Date:   Thu Mar 10 20:09:16 2011 -0500
+
+    start from the mean instead of the mode
+
+commit 2ba56f5e99e90674855c4ffc8bf583340b932e1e
+Author: Heng Li <[e-mail]>
+Date:   Thu Mar 10 17:13:34 2011 -0500
+
+    fixed an error in Chi^2 test
+
+commit b4ce7ae400290bc43dd287240479667f99b3b11e
+Author: Heng Li <[e-mail]>
+Date:   Thu Mar 10 00:23:39 2011 -0500
+
+    minor
+
+commit 8487fa5d3a73a43443964e731ea2a4c873c9d4e5
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 9 21:33:19 2011 -0500
+
+    added -F to accept BCFs generated by old samtools
+
+commit fd51d2093f7fd775a7eaaeea57fa34716ab59ac2
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 9 17:39:09 2011 -0500
+
+    update version
+
+commit b6da54335df943015a998a934075331b467abb5b
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 9 17:37:14 2011 -0500
+
+    compute pseudo-chi2 probability
+
+commit 9f73cefdb8935421d872b989dd98fbc8e1295029
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 9 15:54:04 2011 -0500
+
+    remove a comment which is wrong
+
+commit b10b1e47ece522e97ab8ef23417bcb6454f8b9db
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 9 15:51:12 2011 -0500
+
+    clean up
+
+commit 353bfae2c6ff59205bd9223db04084cf7f507f01
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 9 15:45:29 2011 -0500
+
+    for backup
+
+commit 53915d1c6410c2537d18bfa8eb8c657a2233c35e
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 9 15:27:56 2011 -0500
+
+    having debugging code
+
+commit 0d0dbf66995b1511390d593981eae7b5d36fe17b
+Author: Heng Li <[e-mail]>
+Date:   Wed Mar 9 14:58:23 2011 -0500
+
+    temporary backup
+
+commit 5b74a174a8b637dee43b7f30250df6fb96580e12
+Author: Heng Li <[e-mail]>
+Date:   Tue Mar 8 15:46:11 2011 -0500
+
+    the output makes sense, but there may be a typo...
+
+commit d81ec654b6c0c1eef6b0625d96f14b3155cee7c6
+Author: Heng Li <[e-mail]>
+Date:   Tue Mar 8 15:19:09 2011 -0500
+
+    added contrast2(); fixed a bug in haploid mode
+
+commit 0cfd896fad5f7737cca49efa94a11892dafcd812
+Author: Heng Li <[e-mail]>
+Date:   Mon Mar 7 21:40:17 2011 -0500
+
+    fixed a bug in haploid genotyping
+
+commit ccd52155ef61273f2b42ad9c7b31ff1915f81b24
+Author: Heng Li <[e-mail]>
+Date:   Sat Mar 5 18:10:35 2011 -0500
+
+    fixed a few bugs; still not fully working
+
+commit edc3af753f96f831968ae32f2e0f915b74f31e6e
+Author: Heng Li <[e-mail]>
+Date:   Fri Mar 4 17:31:33 2011 -0500
+
+    drop HWE calculation
+
+commit 92dac194debb66ca0718c21c871822dda2dd5bc1
+Author: Heng Li <[e-mail]>
+Date:   Fri Mar 4 17:28:35 2011 -0500
+
+    implemented hap/dipoind mode; probably BUGGY!
+
+commit 7f26804bc27937e36fdc967e5c76514653ea40f5
+Author: Heng Li <[e-mail]>
+Date:   Fri Mar 4 16:01:27 2011 -0500
+
+    read ploidy
+
+commit e7b7213475b5e61a69aab77ffb02b4983c8e7678
+Author: Heng Li <[e-mail]>
+Date:   Fri Mar 4 14:12:14 2011 -0500
+
+    added math notes
+
+commit 46023e2f21321da83fc8e83e9229757a4e821acb
+Author: Heng Li <[e-mail]>
+Date:   Fri Mar 4 13:34:10 2011 -0500
+
+    update BCF spec
+
+commit 13190c49eeb006ad7013b7f1e9fc1b3beca3ae78
+Author: Heng Li <[e-mail]>
+Date:   Tue Mar 1 14:45:19 2011 -0500
+
+    Release samtools-0.1.13 (r926:134)
+
+commit be8fabbb6001d9fd5263a70a3e21ed6dfe5a9837
+Author: Heng Li <[e-mail]>
+Date:   Tue Mar 1 14:07:15 2011 -0500
+
+    prepare to finalize 0.1.13
+
+commit 1e8c753660978bed7e9289fe50becd596d9314bb
+Author: Heng Li <[e-mail]>
+Date:   Tue Mar 1 09:40:17 2011 -0500
+
+    allow to change whether to drop ambiguous reads
+
+commit 412210bfdb46606023f2e4b9086f2787f0cf1c62
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 28 22:01:29 2011 -0500
+
+    revert to the old behavior of phase
+
+commit 46035589518cf84738de8666b866e2619457c1fb
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 28 16:46:23 2011 -0500
+
+    change version number
+
+commit 7f40c33e37fc16fcb0a375ce46ae1d09cafb6d50
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 28 16:37:42 2011 -0500
+
+    bugfix in indel calling: interger overflow
+
+commit 75849470efbe30042e5ddd516f9bcbe3b9bf6062
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 28 15:35:47 2011 -0500
+
+    fixed a typo
+
+commit 9e6fb569885f906fabaab7fc2f02eae82f4bd602
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 28 15:34:09 2011 -0500
+
+    minor changes to heuristic rules
+
+commit 30a799a91f5e2c10b761aa5437f902c6649fceb3
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 28 15:20:26 2011 -0500
+
+    fixed a bug in the latest change
+
+commit e21ba9df950ea37f5c1b35c2af9ba9a4e0bba02a
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 28 12:47:06 2011 -0500
+
+    put version in bam.h
+
+commit 918b14780c1dceb39c7010638ecd61c626e17166
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 28 12:00:38 2011 -0500
+
+    frag_t::phased==0 reads are dumped to chimera.bam
+
+commit 657293c7bdba3ac69f53cd1ffa2874ed8756475e
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 28 11:05:29 2011 -0500
+
+    change default -q to 37 (previously 40)
+
+commit 33d8d3bea76e466798ea322d68d34deb8d2dff06
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 28 10:39:57 2011 -0500
+
+    fixed a minor bug in BAM reading
+
+commit daa25d426d42465d76c7317c95772bbb36bb3f47
+Author: Heng Li <[e-mail]>
+Date:   Sat Feb 26 21:07:24 2011 -0500
+
+    suppress gzopen64() warning
+
+commit 9cec4256eb9e7848d4711adb67b540659c141e32
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 22:14:52 2011 -0500
+
+    fixed a long existing bug in vcf2fq
+
+commit 304487c83067a733add71cbc3886fa8c49f7ef2a
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 16:37:40 2011 -0500
+
+    change version number
+
+commit 10ba6bf4f16692760f696f7b17f3719065786f77
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 16:34:08 2011 -0500
+
+    Change the order of PL; change SP to int32_t
+
+commit c5cc2a8036a9c3579fbfde651efec4f6763b0228
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 14:52:03 2011 -0500
+
+    claim X defined in the header
+
+commit 4ee8cb29f6092fd14a89f0cc5d3575112a204f39
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 14:40:24 2011 -0500
+
+    minor changes
+
+commit 00065e9336a2831dc53bee7da2f4719845be1a2a
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 11:39:06 2011 -0500
+
+    fixed an error in the BCF spec
+
+commit 1e2a73afcb72a02aa448718cb017c0438de89f90
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 11:36:40 2011 -0500
+
+    update BCF spec
+
+commit dbf8eedaa38a405cb2fba5b3952b85776f51d035
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 11:28:43 2011 -0500
+
+    update BCF spec
+
+commit eed1d91af9fad3c9d965333a55e623757f9c4e9d
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 09:51:39 2011 -0500
+
+    fixed a flaw in targetcut
+
+commit 59bc980bb832b92a8b0cc244cf106e6150e4db6f
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 00:54:35 2011 -0500
+
+    update manual page
+
+commit fcc4738c4abdca79e3de159e21208df1b98ac76c
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 00:45:39 2011 -0500
+
+    update version format
+
+commit 5748639ae542b7f6b853562edc2bb3faf43030e4
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 00:45:12 2011 -0500
+
+    update version number
+
+commit 06b44cc366cf27ce8976ee6a05810a0b3c48b56d
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 00:44:21 2011 -0500
+
+    update version number
+
+commit ab7f4529d12739ff66fd4c09af9d992ab59c53ef
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 25 00:42:55 2011 -0500
+
+    various help message
+
+commit a092e1f6f963272f8bb23616986ddaf604fd0f82
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 24 23:43:13 2011 -0500
+
+    disable unfinished functionality
+
+commit f00a78db72b14ee4c6689fc13f20ed31aeaecd40
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 24 10:04:56 2011 -0500
+
+    added "const" to bcf_p1_cal()
+
+commit 91049c4a8db3bf50dcc9d07506f22fa4ca5b5a96
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 23 11:53:47 2011 -0500
+
+    randomly allocate unphased reads
+
+commit f4405354a8d4cb3441141fa734573031059d7f57
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 22 15:36:07 2011 -0500
+
+    fixed a typo
+
+commit 3075e4dc5c7c9d954426aabda6a73fa788357100
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 22 15:33:40 2011 -0500
+
+    make output more informative
+
+commit 628cf3235e2815a40acf089fb1d3357be6437787
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 22 14:50:06 2011 -0500
+
+    change the scoring rule; change default k to 13
+
+commit f22fd99831e4b5c74f898719216f359dbe987bbf
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 22 14:45:15 2011 -0500
+
+    update scoring in masking
+
+commit 2f23547b81984555032aa0eefd064b8e07986fdc
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 22 14:37:17 2011 -0500
+
+    remove dropreg()
+
+commit 4d8b6b1f1f331ca9041983c66e34a857c3b8f1bb
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 22 13:10:16 2011 -0500
+
+    accept files from stdin
+
+commit 9b50c5038e6fc0185e29ca5b50fe0806a9a939b9
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 22 11:16:57 2011 -0500
+
+    fixed a bug in consensus generation
+
+commit 1332ab32fb788fdc81b2ba8653b905d106238fad
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 21 22:53:23 2011 -0500
+
+    print dropped fragments
+
+commit a288761b4ca1584e51076a71cbc4d72fe923dda1
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 21 22:37:04 2011 -0500
+
+    bugfix: singletons are not phased
+
+commit 683365f534c0223dea7d72532015ac16a45ba22b
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 21 17:27:10 2011 -0500
+
+    output singleton blocks
+
+commit 841a4609084d81f1bc81e0b00dd806002461e7d9
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 21 15:58:55 2011 -0500
+
+    fixed a bug; not working with -l right now
+
+commit fdd57ea31732b5516dc212d72174b60206952636
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 21 15:17:00 2011 -0500
+
+    skip mapQ==0 reads
+
+commit 4eb6ba75c23c1c9be5f76814fa1b93a2e304b2af
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 21 14:03:03 2011 -0500
+
+    print the "targetcut" command
+
+commit 0123d9559ba58b026c0dfd15bc26019a193cd21a
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 21 11:22:13 2011 -0500
+
+    allow to set the maximum depth
+
+commit 0f92eb248a4d06645b2c3d736a0faea8a7a9f731
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 21 09:56:41 2011 -0500
+
+    use a proper error model to call hets
+
+commit 587a01504af5aea6288740d121dccf48fb8a75f4
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 21 09:16:38 2011 -0500
+
+    phase is UNFINISHED; strip RG when merging
+
+commit 723bf3cd79e4f4a558373d4c707fa6b3db0fb357
+Author: Heng Li <[e-mail]>
+Date:   Sat Feb 19 23:38:11 2011 -0500
+
+    use a proper model to compute consensus
+
+commit 891a6b02d4a9af2ed98fbaac4915bf1f0da4f6c8
+Author: Heng Li <[e-mail]>
+Date:   Sat Feb 19 22:14:19 2011 -0500
+
+    added comment
+
+commit 8b55e0a581ecc9e4ba754d1f3c8784f3038b6e48
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 18 17:23:39 2011 -0500
+
+    change the output format
+
+commit 75c36e8c563eddd0a362ba3b38cf0aea21aafb1f
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 15 20:31:00 2011 -0500
+
+    fixed a bug in writing BAM
+
+commit bb0ce52f066cfebaa35a125d57b353bb717a5165
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 14 23:39:09 2011 -0500
+
+    skip uncovered; unknown alleles taken as X
+
+commit ba67f4d119c7d06907db3015d337d9a01a3fc9fe
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 14 23:21:19 2011 -0500
+
+    fixed a bug
+
+commit e4448d49e6129a5e1ee9c7f04f43612f12d6aad6
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 14 22:43:09 2011 -0500
+
+    prepare to read hets from a list; unfinished
+
+commit 129ea29c1f12177c0a7c3e21676f6210370fc59b
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 14 16:32:22 2011 -0500
+
+    updated khash.h to 0.2.5
+
+commit 15b44ed93bd949dffcf79ac8dbea6d9b7dfcb58c
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 14 16:15:04 2011 -0500
+
+    use the latest version of khash
+
+commit 486c05f06f44d981dfb2069bcb43e4b35fd8389c
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 14 15:04:40 2011 -0500
+
+    change the default -k to 11
+
+commit 07cf9d1e443d73cf053de38dd01671e3781f6e29
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 14 14:50:51 2011 -0500
+
+    sort fragments by vpos instead of by beg
+
+commit d0d3e7faabf5cbb7e5ff7b294f7e220da807c4c0
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 14 14:45:41 2011 -0500
+
+    shuffling the two haplotypes for better randomness
+
+commit 3be28eaf5f6033229aedf12ddb11a0084ba01cd8
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 14 14:09:17 2011 -0500
+
+    write chimeras to a separate BAM
+
+commit 80ccbc26f43918fe42be123cc1da9d3d7ce30816
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 14 13:54:13 2011 -0500
+
+    no mem leak/violation on small files; correctness is not checked
+
+commit 5c923867432fa14c26a19e3782e7f48d4080f6ac
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 14 13:50:25 2011 -0500
+
+    bam separation; at least not immediate segfault
+
+commit cea2643ec30a59735bf89b2f562b563bf7263e79
+Author: Heng Li <[e-mail]>
+Date:   Sun Feb 13 23:24:11 2011 -0500
+
+    on the way to implement BAM separation; unfinished
+
+commit 964269cd15036a470ca89e43d0952201a0825671
+Author: Heng Li <[e-mail]>
+Date:   Sun Feb 13 18:07:56 2011 -0500
+
+    keep singletons in the hash table
+
+commit 2d4aa649bd670d5e038a1acaefd33c5fe24ae0e8
+Author: Heng Li <[e-mail]>
+Date:   Sun Feb 13 17:42:24 2011 -0500
+
+    Revert "prepare to add bam separation"
+    
+    This reverts commit ed6957e5211c2c4cf684dcb8bbb661052c74df6f.
+
+commit ed6957e5211c2c4cf684dcb8bbb661052c74df6f
+Author: Heng Li <[e-mail]>
+Date:   Sun Feb 13 00:24:28 2011 -0500
+
+    prepare to add bam separation
+
+commit d211e652d93791d2e112d334added243ffe5fc3e
+Author: Heng Li <[e-mail]>
+Date:   Sat Feb 12 18:50:20 2011 -0500
+
+    accelerate kstrtok
+
+commit 2d6af49d331ff5afe7b9e9b102e79d7d4512fdbe
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 11 21:08:21 2011 -0500
+
+    split unlinked blocks
+
+commit 68e4cd1b560b0a6fd4c77e5e51eadde9fda26ea4
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 11 10:47:58 2011 -0500
+
+    remove heading and tailing ambiguous positions
+
+commit d2b685141426a902ae76660c1fbe8020da150cf8
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 11 10:02:21 2011 -0500
+
+    code clean up for further features
+
+commit c6980e062d55928b59f287c03e599dd5a37ed509
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 11 08:00:08 2011 -0500
+
+    change /64 to >>6; the latter is faster
+
+commit 91635b9c2687f24d72ee6a8aad2050a79bb8400f
+Merge: 41d4df2 9a7e155
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 11 01:22:55 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit 9a7e155cc591c1b6c9f7f9cb939364a6becb65b2
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 11 01:21:07 2011 -0500
+
+    output an unrecognized field as '.'; autofix GL/PL
+
+commit 41d4df2e9545e9abe97151cfe5d6c763f3d00db1
+Merge: c00c41c aacce0c
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 10 23:00:14 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit aacce0ce7276f451e4fddf81832f9e5f7f65198b
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 10 22:57:53 2011 -0500
+
+    finished VCF->BCF conversion
+
+commit 0e875df643e41d848b709e2fa877de8ae53cdd4c
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 10 21:57:28 2011 -0500
+
+    fixed a bug in reading VCF files
+
+commit c00c41c2a5da69cccea64adb542a0b365e56b4fc
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 10 16:28:37 2011 -0500
+
+    suppres one-allele blocks
+
+commit 2e2354b673722e2f00d72970a043f80a66270da1
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 10 16:06:56 2011 -0500
+
+    fixed the bug in filtering
+
+commit d971e1fe24de4ecaf94055efffc5f641e2bdb563
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 10 12:24:23 2011 -0500
+
+    prepare to add filtering; buggy right now
+
+commit a0a5a3fbf504c3b02f7b9212e72315c1047cc249
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 10 11:55:02 2011 -0500
+
+    make masking optional
+
+commit 28db71ccd95054a5f8a47c2332794f8968f6a822
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 10 11:40:47 2011 -0500
+
+    routine to mask poorly called regions
+
+commit a3f6c439262bc10a4067860440f4d4dde9e0c515
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 9 17:18:33 2011 -0500
+
+    code clean up: remove globals
+
+commit 0b711978492f6ad39d459d78723c299468906818
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 9 16:52:54 2011 -0500
+
+    output more information
+
+commit f69d217ae5b691bf42ad07a97f29a7cc6456046f
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 9 16:11:54 2011 -0500
+
+    fixed another bug in flipping
+
+commit d47882d549337fbcc251597508a2c7faf1bb92e2
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 9 16:01:35 2011 -0500
+
+    fixed a stupid bug in flipping
+
+commit e33f89de499496537f5fbde396a66557f0353f1b
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 9 15:54:42 2011 -0500
+
+    fix chimeras; a little weird...
+
+commit 03d3c1d0b945245108ce0942d4772536a32212c7
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 9 13:27:35 2011 -0500
+
+    no effective change; prepare to fix chimera
+
+commit 6bc0a4676dd2252085a6e67bb06daa5ae05a554f
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 9 11:52:58 2011 -0500
+
+    better count output
+
+commit dcac515439d25f71125d6de8111da417776ab9ce
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 9 10:31:07 2011 -0500
+
+    prepare for another way of filtering
+
+commit ca7e4f1899b86d2e077994c789e8f69d699b3cd9
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 8 16:10:08 2011 -0500
+
+    fixed the bug; I can do better.
+
+commit 0733f77b98af121bdcb198cea6151d159831bb9c
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 8 15:55:38 2011 -0500
+
+    fixed two bugs; still not working...
+
+commit 80f18cba9ba73c9592380fc1ecd53c351d294782
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 8 15:42:58 2011 -0500
+
+    filter false SNPs; NOT working right now
+
+commit 69a66e2f96d5b102cd712ff1527a3802fa84c590
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 8 14:39:09 2011 -0500
+
+    write sequence in the SAM format for debugging
+
+commit b6f1c9d160822af2b713be206f37bd6dde00546a
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 7 11:51:21 2011 -0500
+
+    fixed two bugs
+
+commit 400aa5c06100af9c47cd5e4ce8b95b7deb84f54b
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 7 11:22:38 2011 -0500
+
+    Optionally apply BAQ
+
+commit 4c82e0e19682e424f5cdb8381364114c307b329e
+Author: Heng Li <[e-mail]>
+Date:   Mon Feb 7 01:23:31 2011 -0500
+
+    improved output; the result makes sense at a glance
+
+commit dc7853a581ab24bcc496e96b123ccf637e32ed1d
+Author: Heng Li <[e-mail]>
+Date:   Sun Feb 6 14:12:43 2011 -0500
+
+    process per linked block instead of per chr
+
+commit e867d9c6c2e61d9e748e78163e5481dca5697a36
+Author: Heng Li <[e-mail]>
+Date:   Sun Feb 6 00:45:46 2011 -0500
+
+    DP seems to work on toy examples
+
+commit 445ad72fc43d4354d56f5f759790e8ae0be73d02
+Author: Heng Li <[e-mail]>
+Date:   Sat Feb 5 01:24:42 2011 -0500
+
+    implemented backtrack; not tested
+
+commit ba38e180b9cd545956583b22e97e09b4bb12073e
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 4 23:55:23 2011 -0500
+
+    More "correct" DP; backtrack not implemented
+
+commit d69761fd9351273ccd37ea431b10509add91e7cf
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 4 17:22:31 2011 -0500
+
+    scratch of dynamic programming; unfinished...
+
+commit 769ffcb44e26e59300791658801d321559b33858
+Author: Heng Li <[e-mail]>
+Date:   Fri Feb 4 16:29:55 2011 -0500
+
+    UNFINISHED commit.
+
+commit 9adab9591317c3467f3d8cdf2d19ec1f65d1b5b7
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 3 16:20:59 2011 -0500
+
+    another way of counting; can be even faster
+
+commit bbafbdc01ed1ceaab44927def1ad47c4c78aeb9c
+Author: Heng Li <[e-mail]>
+Date:   Thu Feb 3 14:48:20 2011 -0500
+
+    for backup
+
+commit eba7446389cad62a19133bced1386a4334dcab79
+Merge: a44a98e f01a593
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 2 14:06:07 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit f01a5930445b5fda7e6b5b813ed63c652160ada2
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 2 11:31:54 2011 -0500
+
+    Better truncation warning when EOF is absent
+
+commit dd3ee5ed26c8bbef4a62fa5b2bfb0a75833f2c31
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 2 10:38:28 2011 -0500
+
+    fixed a typo in BCF/VCF headers
+
+commit b9d1137c55f401387113d1ad8a387489afe741db
+Author: Heng Li <[e-mail]>
+Date:   Wed Feb 2 09:13:44 2011 -0500
+
+    fixed an out-of-boundary bug (fixed by Roel Kluin)
+
+commit a44a98e16559b9672e8a3492c8f8c640074b7ee2
+Merge: ef68a14 d0443d5
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 1 21:54:48 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit d0443d5c2f648e0f69bd4c56eaac7868e501c18b
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 1 17:31:52 2011 -0500
+
+    improved sorting order checking
+
+commit ef68a14fab91399b2ecd38345936c3d6e7391cf3
+Merge: 1e597b3 1a39a2e
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 1 15:12:37 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit 1a39a2eb08a270e20a34a0983e8bed6ffb3e2008
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 1 15:12:14 2011 -0500
+
+    more precise error message
+
+commit e028e7a47c02232e06a9dd3009262c00dede1060
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 1 14:48:01 2011 -0500
+
+    improved sorting order validation in index
+
+commit 1e597b3356744e2b791b12c9187f91c8054511d5
+Author: Heng Li <[e-mail]>
+Date:   Tue Feb 1 14:44:27 2011 -0500
+
+    testing only; not working
+
+commit 5753ace1e54228822d8ee95f69943f586e42f6e8
+Author: Heng Li <[e-mail]>
+Date:   Mon Jan 31 17:37:08 2011 -0500
+
+    reduce the effect of seq errors at the cost of SN
+
+commit 6f239ce5e0abd47babee33174476d48b723260d8
+Author: Heng Li <[e-mail]>
+Date:   Mon Jan 31 17:29:34 2011 -0500
+
+    added testing code
+
+commit 3db42fe22d27d61ab5735cd2308f73d93def8ebe
+Author: Heng Li <[e-mail]>
+Date:   Mon Jan 31 14:33:21 2011 -0500
+
+    routine for phasing fosmid resequencing (incomplete)
+
+commit ed88f2797323229ae8f38fbcd107b231007956a8
+Author: Heng Li <[e-mail]>
+Date:   Mon Jan 31 10:12:53 2011 -0500
+
+    SAM output
+
+commit abc6acae28dc4794f6422255f077cf370d34e414
+Merge: f1985a9 b133dbf
+Author: Heng Li <[e-mail]>
+Date:   Sat Jan 29 22:56:10 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit b133dbf82de4e8cea5eb56e5bbf0c4b3e9368fd5
+Author: Heng Li <[e-mail]>
+Date:   Sat Jan 29 22:37:11 2011 -0500
+
+    fixed a bug in tview on big-endian by Nathan Weeks
+
+commit 9d3fdaef29f91e21dbfcb9ff0165b9573e7c1042
+Author: Heng Li <[e-mail]>
+Date:   Sat Jan 29 22:24:00 2011 -0500
+
+    update INSTALL
+
+commit 9d074a38bde53961f96157b6fb3683b6dded38d7
+Author: Heng Li <[e-mail]>
+Date:   Sat Jan 29 21:56:25 2011 -0500
+
+    avoid a segfault when network connect fails
+
+commit f1985a93f7455b3ea1b0ef9b959d50b896ccd620
+Author: Heng Li <[e-mail]>
+Date:   Sat Jan 29 21:53:18 2011 -0500
+
+    fixed a bug about bit ordering
+
+commit d09797db6fef648a6823cbe718d67664660c6ebe
+Author: Heng Li <[e-mail]>
+Date:   Thu Jan 27 16:53:19 2011 -0500
+
+    point out there are 4 or fewer free parameters
+
+commit 5fd1717650ed68ab6c55d094d1648c16a054891a
+Author: Heng Li <[e-mail]>
+Date:   Thu Jan 27 16:09:18 2011 -0500
+
+    updated .gitignore
+
+commit fccb19fbe8f9de91f59d85bb49a248683dc6266c
+Author: Heng Li <[e-mail]>
+Date:   Thu Jan 27 16:08:14 2011 -0500
+
+    fixed a bug; better scoring
+
+commit b4dcb844bde3d09eedcd9f6832186ece60ae5afd
+Merge: ffc3e89 6f502de
+Author: Heng Li <[e-mail]>
+Date:   Thu Jan 27 14:50:30 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit 6f502dec46b18dae4bb5b2319715d028b5e193d0
+Author: Heng Li <[e-mail]>
+Date:   Thu Jan 27 14:47:31 2011 -0500
+
+    skip unmapped and ref-skip reads in indel calling
+
+commit 3639f37dd8257b24560c35effcc3b6c16c3c1bcb
+Author: Heng Li <[e-mail]>
+Date:   Thu Jan 27 14:19:15 2011 -0500
+
+    fixed an out-of-boundary bug in rare cases
+
+commit ffc3e89678ab9052b84f403da1e43044b045e73f
+Author: Heng Li <[e-mail]>
+Date:   Thu Jan 27 14:00:17 2011 -0500
+
+    targetcut can be compiled, though probably buggy
+
+commit f452b3ac51306865ddde31a8d715b155d4d3e6e6
+Author: Heng Li <[e-mail]>
+Date:   Wed Jan 26 18:58:43 2011 -0500
+
+    this is for a very special application...
+
+commit ca1451c6406c7ee757cb31349ea0b8de70db0656
+Author: Heng Li <[e-mail]>
+Date:   Wed Jan 26 18:48:09 2011 -0500
+
+    fixed compiling errors
+
+commit 085b87a7642865f17239fb6a436e626e25417838
+Author: Heng Li <[e-mail]>
+Date:   Wed Jan 26 18:45:09 2011 -0500
+
+    This script was put in a wrong place...
+
+commit 090d360828622520de60385af4928ce1aebe0e48
+Author: Heng Li <[e-mail]>
+Date:   Wed Jan 26 18:33:58 2011 -0500
+
+    Imported from samtools-r902
+------------------------------------------------------------------------
+r108 | lh3lh3 | 2009-01-20 11:56:45 +0000 (Tue, 20 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/examples/Makefile
+
+made it a little more convenient
+
+------------------------------------------------------------------------
+r107 | lh3lh3 | 2009-01-20 11:53:30 +0000 (Tue, 20 Jan 2009) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/examples/Makefile
+
+added a Makefile
+
+------------------------------------------------------------------------
+r106 | lh3lh3 | 2009-01-20 11:25:05 +0000 (Tue, 20 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/maq2sam.c
+
+support RG tag
+
+------------------------------------------------------------------------
+r105 | lh3lh3 | 2009-01-18 17:37:20 +0000 (Sun, 18 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/ChangeLog
+
+update changelog
+
+------------------------------------------------------------------------
+r104 | lh3lh3 | 2009-01-18 17:31:21 +0000 (Sun, 18 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_lpileup.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-18
+ * fixed a bug in bam_lpileup.c: segment start and end are not correctly recognized
+
+------------------------------------------------------------------------
+r103 | lh3lh3 | 2009-01-18 16:34:03 +0000 (Sun, 18 Jan 2009) | 5 lines
+Changed paths:
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-17
+ * fixed a bug when there are reads without coordinates
+ * also recognize type 'c' as 'A'	
+ * found a bug in bam_lpileup.c; NOT fixed yet
+
+------------------------------------------------------------------------
+r102 | lh3lh3 | 2009-01-17 19:46:49 +0000 (Sat, 17 Jan 2009) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/INSTALL
+
+Instruction for compilation
+
+------------------------------------------------------------------------
+r101 | lh3lh3 | 2009-01-17 19:31:36 +0000 (Sat, 17 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   A /branches/dev/samtools/Makefile.lite
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/faidx.c
+   M /branches/dev/samtools/misc/Makefile
+   M /branches/dev/samtools/razf.c
+
+ * replaced HAVE_RAZF with _NO_RAZF
+ * added Makefile.lite for people who have trouble with razf.c
+
+------------------------------------------------------------------------
+r100 | lh3lh3 | 2009-01-16 10:03:37 +0000 (Fri, 16 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_mate.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/misc/wgsim.c
+
+ * samtools-0.1.1-15
+ * fixed another bug in fixmate: unmapped pair has non-zero isize
+
+------------------------------------------------------------------------
+r99 | lh3lh3 | 2009-01-16 09:13:36 +0000 (Fri, 16 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/ChangeLog
+   M /branches/dev/samtools/bam_mate.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-14
+ * fixed a bug in fixmate: isize not equal to zero if two ends mapped to
+   different chr
+
+------------------------------------------------------------------------
+r98 | lh3lh3 | 2009-01-15 16:47:41 +0000 (Thu, 15 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-13
+ * fixed the prior for hom indels (Richard pointed this out)
+
+------------------------------------------------------------------------
+r97 | lh3lh3 | 2009-01-15 16:38:47 +0000 (Thu, 15 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/COPYING
+   M /branches/dev/samtools/bam_sort.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/source.dot
+
+ * samtools-0.1.1-12
+ * fixed a bug in sort
+ * update source file graph and copyright information
+
+------------------------------------------------------------------------
+r96 | lh3lh3 | 2009-01-14 21:46:14 +0000 (Wed, 14 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/glf.c
+
+fixed a typo
+
+------------------------------------------------------------------------
+r95 | lh3lh3 | 2009-01-14 21:44:53 +0000 (Wed, 14 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/glf.c
+
+added a main function for glf.c
+
+------------------------------------------------------------------------
+r94 | lh3lh3 | 2009-01-14 17:14:59 +0000 (Wed, 14 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/bgzf.h
+   A /branches/dev/samtools/glf.c
+   M /branches/dev/samtools/glf.h
+
+ * samtools-0.1.1-11
+ * generate binary GLFv2
+ * added glfview command to dump GLFv2 binary file
+
+------------------------------------------------------------------------
+r93 | lh3lh3 | 2009-01-14 15:07:44 +0000 (Wed, 14 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_rmdup.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/glf.h
+
+ * samtools-0.1.1-10
+ * fixed several bugs in rmdup
+ * prepare to generate GLF2
+
+------------------------------------------------------------------------
+r92 | lh3lh3 | 2009-01-14 13:27:44 +0000 (Wed, 14 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_import.c
+   A /branches/dev/samtools/bam_rmdup.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-9
+ * implemented rmdup; NOT tested yet
+
+------------------------------------------------------------------------
+r91 | lh3lh3 | 2009-01-13 20:15:43 +0000 (Tue, 13 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/examples/00README.txt
+
+update README for typos
+
+------------------------------------------------------------------------
+r90 | lh3lh3 | 2009-01-13 19:57:50 +0000 (Tue, 13 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/examples/ex1.sam.gz
+
+update example
+
+------------------------------------------------------------------------
+r89 | lh3lh3 | 2009-01-13 17:21:38 +0000 (Tue, 13 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam.c
+   A /branches/dev/samtools/bam_mate.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-8
+ * added fixmate command
+
+------------------------------------------------------------------------
+r88 | lh3lh3 | 2009-01-13 10:48:23 +0000 (Tue, 13 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-7
+ * change the reported indel position to the previous way
+
+------------------------------------------------------------------------
+r87 | lh3lh3 | 2009-01-12 22:12:12 +0000 (Mon, 12 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-6
+ * addd glt output
+ * allow to change indel calling parameters at the command line
+
+------------------------------------------------------------------------
+r86 | lh3lh3 | 2009-01-12 21:16:48 +0000 (Mon, 12 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_pileup.c
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-5
+ * added two more flags
+ * allowed to select reads shown in pileup with a mask
+
+------------------------------------------------------------------------
+r85 | lh3lh3 | 2009-01-12 20:47:51 +0000 (Mon, 12 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-4
+ * fixed a bug in indexing (linear index)
+ * prepare to add glt output from pileup
+
+------------------------------------------------------------------------
+r84 | lh3lh3 | 2009-01-12 09:22:35 +0000 (Mon, 12 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-3
+ * fixed a bug in outputing the coordinate of an indel
+
+------------------------------------------------------------------------
+r83 | lh3lh3 | 2009-01-11 15:18:01 +0000 (Sun, 11 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-2
+ * pileup: allows to output indel sites only
+
+------------------------------------------------------------------------
+r82 | lh3lh3 | 2009-01-10 23:34:31 +0000 (Sat, 10 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bam_maqcns.h
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-1
+ * implemented a Bayesian indel caller
+
+------------------------------------------------------------------------
+r81 | lh3lh3 | 2009-01-09 09:54:28 +0000 (Fri, 09 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/examples/00README.txt
+   D /branches/dev/samtools/examples/ex1.fa.fai
+
+Let users generate ex1.fa.fai.
+
+------------------------------------------------------------------------
+r80 | lh3lh3 | 2009-01-08 16:10:08 +0000 (Thu, 08 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/bowtie2sam.pl
+
+make the bowtie converter works for "-k 2"
+
+------------------------------------------------------------------------
+r78 | lh3lh3 | 2009-01-03 17:25:24 +0000 (Sat, 03 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/export2sam.pl
+
+fixed a bug for "QC" reads
+
+------------------------------------------------------------------------
+r77 | lh3lh3 | 2009-01-01 18:32:06 +0000 (Thu, 01 Jan 2009) | 3 lines
+Changed paths:
+   A /branches/dev/samtools/misc/bowtie2sam.pl
+   M /branches/dev/samtools/misc/soap2sam.pl
+
+ * soap2sam.pl: added NM tag
+ * bowtie2sam.pl: converter for bowtie
+
+------------------------------------------------------------------------
+r76 | lh3lh3 | 2008-12-31 23:24:24 +0000 (Wed, 31 Dec 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/misc/soap2sam.pl
+
+soap2sam.pl: convert soap output to SAM
+
+------------------------------------------------------------------------
+r75 | lh3lh3 | 2008-12-31 17:54:32 +0000 (Wed, 31 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/misc/wgsim_eval.pl
+
+ * wgsim_eval.pl-0.1.1
+ * fixed a bug for a contig name like "NT_012345"
+
+------------------------------------------------------------------------
+r74 | lh3lh3 | 2008-12-31 16:38:21 +0000 (Wed, 31 Dec 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/misc/wgsim_eval.pl
+
+ * evaluate alignment for reads generated by wgsim
+
+------------------------------------------------------------------------
+r73 | lh3lh3 | 2008-12-31 15:11:22 +0000 (Wed, 31 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/Makefile
+   M /branches/dev/samtools/misc/wgsim.c
+
+fixed compiling warnings for wgsim
+
+------------------------------------------------------------------------
+r72 | lh3lh3 | 2008-12-31 13:40:51 +0000 (Wed, 31 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/bam_tview.c
+
+remove an unused variable (a compiler warning only)
+
+------------------------------------------------------------------------
+r71 | lh3lh3 | 2008-12-31 13:37:16 +0000 (Wed, 31 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/Makefile
+   A /branches/dev/samtools/misc/wgsim.c
+
+wgsim: Paired-end reads simulator
+
+------------------------------------------------------------------------
+r70 | bhandsaker | 2008-12-29 20:27:16 +0000 (Mon, 29 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bam_tview.c
+
+Move definition of bam_nt16_nt4_table so we can build without curses.
+
+------------------------------------------------------------------------
+r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/NEWS
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/samtools.1
+
+Release samtools-0.1.1
+
+------------------------------------------------------------------------
+r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
+Changed paths:
+   M /branches/dev/samtools/bam_aux.c
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bam_tview.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/razf.c
+   M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-66
+ * fixed a bug in razf.c: reset z_eof when razf_seek() is called
+ * fixed a memory leak in parsing a region
+ * changed pileup a little bit when -s is in use: output ^ and $
+ * when a bam is not indexed, output more meaningful error message
+ * fixed a bug in indexing for small alignment
+ * fixed a bug in the viewer when we come to the end of a reference file
+ * updated documentation
+ * prepare to release 0.1.1
+
+------------------------------------------------------------------------
+r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/examples
+   A /branches/dev/samtools/examples/00README.txt
+   A /branches/dev/samtools/examples/ex1.fa
+   A /branches/dev/samtools/examples/ex1.fa.fai
+   A /branches/dev/samtools/examples/ex1.sam.gz
+
+example
+
+------------------------------------------------------------------------
+r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/ChangeLog
+
+update ChangeLog
+
+------------------------------------------------------------------------
+r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/misc/export2sam.pl
+
+ * added comments
+ * fixed several bugs 
+
+------------------------------------------------------------------------
+r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/misc/export2sam.pl
+
+convert Export format to SAM; not thoroughly tested
+
+------------------------------------------------------------------------
+r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
+Changed paths:
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bam_tview.c
+   M /branches/dev/samtools/bamtk.c
+   A /branches/dev/samtools/source.dot
+
+ * samtools-0.1.0-65
+ * pileup: generate maq-like simple output
+ * pileup: allow to output pileup at required sites
+ * source.dot: source file relationship graph
+ * tview: fixed a minor bug
+
+------------------------------------------------------------------------
+r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
+Changed paths:
+   D /branches/dev/samtools/misc/all2sam.pl
+
+remove all2sam.pl
+
+------------------------------------------------------------------------
+r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/COPYING
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/faidx.h
+   M /branches/dev/samtools/khash.h
+   M /branches/dev/samtools/kseq.h
+   M /branches/dev/samtools/ksort.h
+   M /branches/dev/samtools/samtools.1
+
+Added copyright information and a bit more documentation. No code change.
+
+------------------------------------------------------------------------
+r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam.c
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-64
+ * improved efficiency of the indel caller for spliced alignments
+
+------------------------------------------------------------------------
+r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam.c
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_aux.c
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-63
+ * a bit code cleanup: reduce the dependency between source files
+
+------------------------------------------------------------------------
+r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-62
+ * fixed a memory leak
+
+------------------------------------------------------------------------
+r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/ChangeLog
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/samtools.1
+
+update documentation, ChangeLog and a comment
+
+------------------------------------------------------------------------
+r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bam_maqcns.h
+   M /branches/dev/samtools/bam_pileup.c
+   A /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-61
+ * moved pileup command to a separate source file
+ * added indel caller
+ * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
+ * updated documentation
+
+------------------------------------------------------------------------
+r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-60
+ * fixed another bug in maqcns when there is a nearby deletion
+
+------------------------------------------------------------------------
+r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bam_pileup.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-59
+ * pileup: outputing consensus is now optional
+ * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
+   I am not quite sure why the previous version may have problem.
+
+------------------------------------------------------------------------
+r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
+Changed paths:
+   M /branches/dev/samtools/bam_pileup.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-58
+ * add maq consensus to pileup. However, I will move this part to a new
+   command as strictly speaking, consensus callin is not part of pileup,
+   and imposing it would make it harder to generate for other language
+   bindings.
+
+------------------------------------------------------------------------
+r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/bgzf.c
+
+Fix bug in tell() after reads that consume to the exact end of a block.
+
+------------------------------------------------------------------------
+r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/samtools.1
+
+update manual
+
+------------------------------------------------------------------------
+r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-57
+ * fixed a bug in parser when there is auxiliary fields
+ * made the parser a bit more robust
+
+------------------------------------------------------------------------
+r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
+Changed paths:
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/bgzf.c
+
+ * samtools-0.1.0-56
+ * fixed a bug in bgzf (only reading is affected)
+ * fixed a typo in bam_index.c
+ * in bam_index.c, check potential bugs in the underlying I/O library
+
+------------------------------------------------------------------------
+r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/samtools.1
+
+update manual
+
+------------------------------------------------------------------------
+r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
+Changed paths:
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_pileup.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-55
+ * tried to make pileup work with clipping (previously not), though NOT tested
+ * removed -v from pileup
+ * made pileup take the reference sequence
+
+------------------------------------------------------------------------
+r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-54
+ * in parser, recognize "=", rather than ",", as a match
+ * in parser, correctl parse "=" at the MRNM field.
+
+------------------------------------------------------------------------
+r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/maq2sam.c
+
+fixed a bug in handling maq flag 64 and 192
+
+------------------------------------------------------------------------
+r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/md5fa.c
+
+also calculate unordered md5sum check
+
+------------------------------------------------------------------------
+r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/md5fa.c
+
+fixed a minor bug when there are space in the sequence
+
+------------------------------------------------------------------------
+r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/md5fa.c
+
+fixed a potential memory leak
+
+------------------------------------------------------------------------
+r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bamtk.c
+
+ * fixed a bug in import: bin is wrongly calculated
+
+------------------------------------------------------------------------
+r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/all2sam.pl
+
+nothing, really
+
+------------------------------------------------------------------------
+r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/kseq.h
+   M /branches/dev/samtools/misc/Makefile
+   A /branches/dev/samtools/misc/md5.c
+   A /branches/dev/samtools/misc/md5.h
+   A /branches/dev/samtools/misc/md5fa.c
+
+ * fixed two warnings in kseq.h
+ * added md5sum utilities
+
+------------------------------------------------------------------------
+r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bamtk.c
+   A /branches/dev/samtools/kseq.h
+   D /branches/dev/samtools/kstream.h
+
+ * samtools-0.1.0-52
+ * replace kstream with kseq. kseq is a superset of kstream. I need the
+   extra functions in kseq.h.
+ * also compile stand-alone faidx
+
+------------------------------------------------------------------------
+r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_sort.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-51
+ * sorting by read names is available
+
+------------------------------------------------------------------------
+r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam.c
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bam_pileup.c
+   M /branches/dev/samtools/bam_sort.c
+   M /branches/dev/samtools/bam_tview.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/misc/maq2sam.c
+
+ * samtools-0.1.0-50
+ * format change to meet the latest specification
+
+------------------------------------------------------------------------
+r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/misc/maq2sam.c
+
+ * minor change in maqcns: special care when n==0
+ * change maq2sam to meet the latest specification
+
+------------------------------------------------------------------------
+r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/razf.c
+   M /branches/dev/samtools/razf.h
+
+considerable code clean up in razf
+
+------------------------------------------------------------------------
+r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/ChangeLog
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/faidx.c
+
+make RAZF optional in faidx.c
+
+------------------------------------------------------------------------
+r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_aux.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-49
+ * added routines for retrieving aux data, NOT TESTED YET!
+
+------------------------------------------------------------------------
+r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
+Changed paths:
+   M /branches/dev/samtools/bam.c
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/bgzf.c
+   M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-48
+ * bgzf: fixed a potential integer overflow on 32-it machines
+ * maqcns: set the minimum combined quality as 0
+ * supporting hex strings
+
+------------------------------------------------------------------------
+r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-47
+ * fixed the bug in maqcns
+
+------------------------------------------------------------------------
+r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam.h
+   A /branches/dev/samtools/bam_maqcns.c
+   A /branches/dev/samtools/bam_maqcns.h
+   M /branches/dev/samtools/bam_tview.c
+   M /branches/dev/samtools/bamtk.c
+   A /branches/dev/samtools/glf.h
+
+ * samtools-0.1.0-46
+ * add MAQ consensus caller, currently BUGGY!
+
+------------------------------------------------------------------------
+r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_pileup.c
+   M /branches/dev/samtools/bam_tview.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-45
+ * tview: display padded alignment (but not P operation)
+ * better coordinates and reference sequence
+
+------------------------------------------------------------------------
+r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/ChangeLog
+
+new ChangeLog
+
+------------------------------------------------------------------------
+r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
+Changed paths:
+   D /branches/dev/samtools/ChangeLog
+   A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
+
+Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
+the log of my personal SVN repository.
+
+------------------------------------------------------------------------
+r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/bgzf.c
+
+ * samtools-0.1.0-44
+ * declare fseeko and ftello as some Linux may not do this by default and
+   missing these declarations will make bgzf buggy
+ * get rid of some harmless warings
+ * use BGZF by default, now
+
+------------------------------------------------------------------------
+r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/razf.c
+
+ * samtools-0.1.0-43
+ * fixed a bug in razf_read()
+ * give more warnings when the file is truncated (or due to bugs in I/O library)
+
+------------------------------------------------------------------------
+r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/bgzf.c
+
+fixed a bug in bgzf.c at the end of the file
+
+------------------------------------------------------------------------
+r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-42
+ * a lot happened to RAZF, although samtools itself is untouched. Better
+   also update the version number anyway to avoid confusion
+
+------------------------------------------------------------------------
+r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/razf.c
+
+a change from Jue, but I think it should not matter
+
+------------------------------------------------------------------------
+r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/razf.c
+
+fixed a potential bug in razf. However, it seems still buggy, just
+rarely happens, very rarely.
+
+------------------------------------------------------------------------
+r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/razf.c
+
+fixed a bug in razf, with the help of Jue
+
+------------------------------------------------------------------------
+r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/bam_index.c
+
+remove a comment
+
+------------------------------------------------------------------------
+r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/razf.c
+   M /branches/dev/samtools/razf.h
+
+ * Jue has updated razf to realize Bob's scheme
+
+------------------------------------------------------------------------
+r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/samtools.1
+
+the manual page
+
+------------------------------------------------------------------------
+r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
+Changed paths:
+   A /branches/dev/samtools/ChangeLog
+   A /branches/dev/samtools/Makefile
+   A /branches/dev/samtools/bam.c
+   A /branches/dev/samtools/bam.h
+   A /branches/dev/samtools/bam_aux.c
+   A /branches/dev/samtools/bam_endian.h
+   A /branches/dev/samtools/bam_import.c
+   A /branches/dev/samtools/bam_index.c
+   A /branches/dev/samtools/bam_lpileup.c
+   A /branches/dev/samtools/bam_pileup.c
+   A /branches/dev/samtools/bam_sort.c
+   A /branches/dev/samtools/bam_tview.c
+   A /branches/dev/samtools/bamtk.c
+   A /branches/dev/samtools/bgzf.c
+   A /branches/dev/samtools/bgzf.h
+   A /branches/dev/samtools/bgzip.c
+   A /branches/dev/samtools/faidx.c
+   A /branches/dev/samtools/faidx.h
+   A /branches/dev/samtools/khash.h
+   A /branches/dev/samtools/ksort.h
+   A /branches/dev/samtools/kstream.h
+   A /branches/dev/samtools/misc
+   A /branches/dev/samtools/misc/Makefile
+   A /branches/dev/samtools/misc/all2sam.pl
+   A /branches/dev/samtools/misc/maq2sam.c
+   A /branches/dev/samtools/razf.c
+   A /branches/dev/samtools/razf.h
+   A /branches/dev/samtools/razip.c
+   A /branches/dev/samtools/zutil.h
+
+The initial version of samtools, replicated from my local SVN repository.
+The current version is: 0.1.0-42. All future development will happen here.
+
+------------------------------------------------------------------------
+r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools
+
+samtools (C version)
+
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+r703 | lh3 | 2008-11-25 20:20:02 +0000 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/samtools.1
+
+rename bamtk to samtools
+
+------------------------------------------------------------------------
+r702 | lh3 | 2008-11-25 20:15:09 +0000 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+   D /branches/prog/bam/bamtk.1
+   A /branches/prog/bam/samtools.1 (from /branches/prog/bam/bamtk.1:679)
+
+rename bamtk.1 to samtools.1
+
+------------------------------------------------------------------------
+r701 | lh3 | 2008-11-25 13:29:10 +0000 (Tue, 25 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam.c
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/misc/Makefile
+
+ * samtools-0.1.0-41
+ * small (but a bit dangerous) changes to meet the latest specification
+
+------------------------------------------------------------------------
+r700 | lh3 | 2008-11-25 13:15:11 +0000 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/prog/bam/misc/all2sam.pl (from /branches/prog/bam/misc/all2tam.pl:649)
+   D /branches/prog/bam/misc/all2tam.pl
+   A /branches/prog/bam/misc/maq2sam.c (from /branches/prog/bam/misc/maq2tam.c:699)
+   D /branches/prog/bam/misc/maq2tam.c
+
+rename tam to sam
+
+------------------------------------------------------------------------
+r699 | lh3 | 2008-11-25 13:14:49 +0000 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/misc/maq2tam.c
+
+change for the new specification
+
+------------------------------------------------------------------------
+r698 | lh3 | 2008-11-24 13:15:20 +0000 (Mon, 24 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/razf.c
+   M /branches/prog/bam/razf.h
+
+ * add a fake BGZF mode to razf. It is fake in that it loads razf index into
+   memory but gives BGZF like virtual offset
+
+------------------------------------------------------------------------
+r697 | lh3 | 2008-11-24 09:53:44 +0000 (Mon, 24 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/prog/bam/ChangeLog
+
+change log
+
+------------------------------------------------------------------------
+r696 | lh3 | 2008-11-24 09:53:23 +0000 (Mon, 24 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bgzf.c
+
+updated bgzf, on behalf of Bob
+
+------------------------------------------------------------------------
+r695 | lh3 | 2008-11-23 11:40:31 +0000 (Sun, 23 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/razf.c
+
+fixed a bug in razf
+
+------------------------------------------------------------------------
+r694 | lh3 | 2008-11-22 16:23:52 +0000 (Sat, 22 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_lpileup.c
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bam-0.1.0-40
+ * fixed two small memory leaks
+ * fixed a memory problem when seek outside the length of the sequence
+
+------------------------------------------------------------------------
+r693 | lh3 | 2008-11-22 16:10:04 +0000 (Sat, 22 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bamtk.c
+
+ * bam-0.1.0-39
+ * fixed an uninitialized warning. This does not matter in fact
+
+------------------------------------------------------------------------
+r692 | lh3 | 2008-11-22 15:44:05 +0000 (Sat, 22 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/razf.c
+   M /branches/prog/bam/razf.h
+
+Jue's new razf
+
+------------------------------------------------------------------------
+r691 | lh3 | 2008-11-21 21:30:39 +0000 (Fri, 21 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/bgzip.c
+
+ * bam-0.1.0-38
+ * get rid of some warings in bgzip.c
+ * potentially improve performance in indexing for BGZF
+
+------------------------------------------------------------------------
+r690 | lh3 | 2008-11-21 21:15:51 +0000 (Fri, 21 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bgzf.c
+
+I think I have fixed the bug in bgzf
+
+------------------------------------------------------------------------
+r689 | lh3 | 2008-11-21 20:48:56 +0000 (Fri, 21 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bgzf.c
+
+bug fix by Bob
+
+------------------------------------------------------------------------
+r688 | lh3 | 2008-11-21 20:37:27 +0000 (Fri, 21 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+
+fixed a bug due to the name change in _IOLIB
+
+------------------------------------------------------------------------
+r687 | lh3 | 2008-11-21 14:42:56 +0000 (Fri, 21 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bgzf.c
+
+fix small things
+
+------------------------------------------------------------------------
+r686 | lh3 | 2008-11-21 14:37:59 +0000 (Fri, 21 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/prog/bam/bgzf.c
+   A /branches/prog/bam/bgzf.h
+   A /branches/prog/bam/bgzip.c
+
+Bob's BGZF format, although currently buggy
+
+------------------------------------------------------------------------
+r685 | lh3 | 2008-11-21 09:48:20 +0000 (Fri, 21 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bam-0.1.0-37
+ * improve interface a little bit
+
+------------------------------------------------------------------------
+r684 | lh3 | 2008-11-21 09:30:18 +0000 (Fri, 21 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bam-0.1.0-36
+ * improve the interface of tview, a little bit
+
+------------------------------------------------------------------------
+r683 | lh3 | 2008-11-20 22:33:54 +0000 (Thu, 20 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam_tview.c
+
+a little better viewer
+
+------------------------------------------------------------------------
+r682 | lh3 | 2008-11-20 22:27:01 +0000 (Thu, 20 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-35
+ * better viewer
+
+------------------------------------------------------------------------
+r681 | lh3 | 2008-11-20 20:51:16 +0000 (Thu, 20 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-34
+ * tview is now a component of bamtk
+
+------------------------------------------------------------------------
+r680 | lh3 | 2008-11-20 19:17:30 +0000 (Thu, 20 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/prog/bam/bam_tview.c
+
+text alignment viewer
+
+------------------------------------------------------------------------
+r679 | lh3 | 2008-11-20 19:17:15 +0000 (Thu, 20 Nov 2008) | 5 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_lpileup.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.1
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/faidx.c
+
+ * bamtk-0.1.0-33
+ * added routines to reset pileup bufferes
+ * fixed a bug in faidx
+ * add text alignment viewer
+
+------------------------------------------------------------------------
+r678 | lh3 | 2008-11-20 11:05:02 +0000 (Thu, 20 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   A /branches/prog/bam/bam_lpileup.c (from /branches/prog/bam/bam_tview.c:668)
+   D /branches/prog/bam/bam_tview.c
+
+rename tview as lpileup
+
+------------------------------------------------------------------------
+r677 | lh3 | 2008-11-20 10:08:52 +0000 (Thu, 20 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/razf.c
+
+fixed a bug in razf
+
+------------------------------------------------------------------------
+r676 | lh3 | 2008-11-19 22:52:20 +0000 (Wed, 19 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/faidx.h
+
+add documentations
+
+------------------------------------------------------------------------
+r674 | lh3 | 2008-11-19 21:39:17 +0000 (Wed, 19 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bamtk.1
+   M /branches/prog/bam/faidx.h
+
+update documentation
+
+------------------------------------------------------------------------
+r673 | lh3 | 2008-11-19 21:19:03 +0000 (Wed, 19 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/prog/bam/bamtk.1
+
+add manual page
+
+------------------------------------------------------------------------
+r672 | lh3 | 2008-11-19 16:40:49 +0000 (Wed, 19 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/faidx.c
+
+ * bamtk-0.1.0-32
+ * make faidx more error resistant
+
+------------------------------------------------------------------------
+r671 | lh3 | 2008-11-19 16:09:55 +0000 (Wed, 19 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/faidx.h
+
+add index
+
+------------------------------------------------------------------------
+r670 | lh3 | 2008-11-19 16:02:39 +0000 (Wed, 19 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/faidx.c
+
+ * bamtk-0.1.0-31
+ * show reference sequence in pileup -v (not in the default pileup)
+
+------------------------------------------------------------------------
+r669 | lh3 | 2008-11-19 14:51:17 +0000 (Wed, 19 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/faidx.c
+
+ * bamtk-0.1.0-30
+ * put faidx in bamtk and remove faidx_main.c
+
+------------------------------------------------------------------------
+r668 | lh3 | 2008-11-19 14:15:05 +0000 (Wed, 19 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+   A /branches/prog/bam/faidx.c
+   A /branches/prog/bam/faidx.h
+   M /branches/prog/bam/razf.c
+
+ * bamtk-0.1.0-29
+ * fixed a bug in tview.c
+ * prepare to add faidx
+
+------------------------------------------------------------------------
+r667 | lh3 | 2008-11-19 10:20:45 +0000 (Wed, 19 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/razf.c
+   M /branches/prog/bam/razf.h
+
+gzip-compatible razf
+
+------------------------------------------------------------------------
+r664 | lh3 | 2008-11-18 12:50:23 +0000 (Tue, 18 Nov 2008) | 5 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-28
+ * fetch: fixed a bug at an array boundary
+ * fetch: fixed a bug when the whole chromosome is retrieved
+ * add linear index
+
+------------------------------------------------------------------------
+r663 | lh3 | 2008-11-17 21:29:22 +0000 (Mon, 17 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam.c
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-27
+ * put l_qseq into core and move l_aux to bam1_t
+
+------------------------------------------------------------------------
+r662 | lh3 | 2008-11-17 20:55:16 +0000 (Mon, 17 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam.c
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-26
+ * save seq and qual separately
+
+------------------------------------------------------------------------
+r661 | lh3 | 2008-11-17 13:09:37 +0000 (Mon, 17 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+
+little
+
+------------------------------------------------------------------------
+r660 | lh3 | 2008-11-17 13:06:14 +0000 (Mon, 17 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+
+more documentations
+
+------------------------------------------------------------------------
+r659 | lh3 | 2008-11-17 12:55:08 +0000 (Mon, 17 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-25
+ * make tview work for TAM
+
+------------------------------------------------------------------------
+r658 | lh3 | 2008-11-17 12:50:21 +0000 (Mon, 17 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-24
+ * make tview as an independent module
+
+------------------------------------------------------------------------
+r657 | lh3 | 2008-11-17 11:26:06 +0000 (Mon, 17 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_pileup.c
+
+change little
+
+------------------------------------------------------------------------
+r656 | lh3 | 2008-11-16 21:33:19 +0000 (Sun, 16 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-23
+ * also add tview for TAM
+
+------------------------------------------------------------------------
+r655 | lh3 | 2008-11-16 21:29:46 +0000 (Sun, 16 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-22
+ * make tview more efficient for deep depth
+
+------------------------------------------------------------------------
+r654 | lh3 | 2008-11-16 20:52:19 +0000 (Sun, 16 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bam_pileup.c
+   A /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-21
+ * fixed bug in the TAM parser: lowercase not recognized
+ * unfinished function to leveled pileup (tview)
+
+------------------------------------------------------------------------
+r653 | lh3 | 2008-11-15 12:58:36 +0000 (Sat, 15 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-20
+ * pileup now display deleted bases as '*'
+
+------------------------------------------------------------------------
+r652 | lh3 | 2008-11-15 09:58:39 +0000 (Sat, 15 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-19
+ * fixed a bug in fetch()
+ * reduce memory in indexing
+
+------------------------------------------------------------------------
+r651 | lh3 | 2008-11-14 21:56:05 +0000 (Fri, 14 Nov 2008) | 5 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-18
+ * important changes are made to index: the index size is increased, but
+   now we have no limit on file sizes and the new method potentially
+   works with BGZF, Bob's new compression format.
+
+------------------------------------------------------------------------
+r650 | lh3 | 2008-11-14 16:03:22 +0000 (Fri, 14 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-17
+ * more comments in bam.h
+ * fixed a bug in bam_index.c
+
+------------------------------------------------------------------------
+r649 | lh3 | 2008-11-13 16:04:18 +0000 (Thu, 13 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/bam.c
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bam_sort.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-16
+ * use macros to retrieve pointers from bam1_t and thus reduce the size
+   of bam1_t struct.
+
+------------------------------------------------------------------------
+r648 | lh3 | 2008-11-13 13:21:39 +0000 (Thu, 13 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_sort.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-15
+ * make more things work over pipe
+
+------------------------------------------------------------------------
+r647 | lh3 | 2008-11-13 12:49:28 +0000 (Thu, 13 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/misc/maq2tam.c
+
+fixed a bug in maq2tam
+
+------------------------------------------------------------------------
+r646 | lh3 | 2008-11-13 11:46:59 +0000 (Thu, 13 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/misc/Makefile
+   M /branches/prog/bam/misc/maq2tam.c
+
+ * bug fix in maq2tam.c
+ * improve Makefile
+
+------------------------------------------------------------------------
+r645 | lh3 | 2008-11-13 11:39:46 +0000 (Thu, 13 Nov 2008) | 3 lines
+Changed paths:
+   A /branches/prog/bam/misc/Makefile
+   M /branches/prog/bam/misc/maq2tam.c
+
+ * corrected maq2tam
+ * add Makefile
+
+------------------------------------------------------------------------
+r644 | lh3 | 2008-11-13 11:25:45 +0000 (Thu, 13 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/razf.c
+
+fixed the bug in buffered write (on behalf of Jue)
+
+------------------------------------------------------------------------
+r643 | lh3 | 2008-11-13 10:53:42 +0000 (Thu, 13 Nov 2008) | 2 lines
+Changed paths:
+   D /branches/prog/bam/all2tam.pl
+   A /branches/prog/bam/misc/all2tam.pl (from /branches/prog/bam/all2tam.pl:642)
+
+move to misc
+
+------------------------------------------------------------------------
+r642 | lh3 | 2008-11-13 10:53:23 +0000 (Thu, 13 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/all2tam.pl
+
+change tag
+
+------------------------------------------------------------------------
+r641 | lh3 | 2008-11-13 10:53:12 +0000 (Thu, 13 Nov 2008) | 2 lines
+Changed paths:
+   D /branches/prog/bam/utils
+
+has been renamed
+
+------------------------------------------------------------------------
+r640 | lh3 | 2008-11-13 10:52:50 +0000 (Thu, 13 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/prog/bam/misc (from /branches/prog/bam/utils:639)
+
+rename
+
+------------------------------------------------------------------------
+r639 | lh3 | 2008-11-13 10:52:35 +0000 (Thu, 13 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/prog/bam/utils
+   A /branches/prog/bam/utils/maq2tam.c
+
+utilities (converters and so on)
+
+------------------------------------------------------------------------
+r638 | lh3 | 2008-11-12 22:24:22 +0000 (Wed, 12 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/bam.c
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-14
+ * copy the text header to BAM
+ * add BAM1 header flag
+
+------------------------------------------------------------------------
+r637 | lh3 | 2008-11-12 14:56:08 +0000 (Wed, 12 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/razf.c
+
+ * bamtk-0.1.0-13
+ * fixed a bug in razf
+ * improved and fixed potential bugs in index
+
+------------------------------------------------------------------------
+r636 | lh3 | 2008-11-12 11:57:13 +0000 (Wed, 12 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+
+update documentation in the HeaderDOC format
+
+------------------------------------------------------------------------
+r635 | lh3 | 2008-11-12 10:08:38 +0000 (Wed, 12 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/bam.c
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-12
+ * more documentations
+ * rename baf1_core_t as bam1_core_t
+
+------------------------------------------------------------------------
+r634 | lh3 | 2008-11-11 23:00:35 +0000 (Tue, 11 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_pileup.c
+
+documentation
+
+------------------------------------------------------------------------
+r633 | lh3 | 2008-11-11 21:23:49 +0000 (Tue, 11 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-11
+ * give up regional pileup. We can now use pipe to mimic that.
+ * for index file, change suffix .idx to .bmi
+
+------------------------------------------------------------------------
+r632 | lh3 | 2008-11-11 21:00:11 +0000 (Tue, 11 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/razf.c
+
+ * bamtk-0.1.0-10
+ * make pileup work on TAM
+
+------------------------------------------------------------------------
+r631 | lh3 | 2008-11-11 09:20:29 +0000 (Tue, 11 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/razf.c
+   M /branches/prog/bam/razf.h
+   M /branches/prog/bam/razip.c
+
+ * bamtk-0.1.0-9
+ * razf now supports streaming
+ * prepare to improve pileup (have not yet)
+
+------------------------------------------------------------------------
+r630 | lh3 | 2008-11-10 18:34:40 +0000 (Mon, 10 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-8
+ * improve the interface of TAM parser
+
+------------------------------------------------------------------------
+r629 | lh3 | 2008-11-10 13:06:13 +0000 (Mon, 10 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-7
+ * almost nothing
+
+------------------------------------------------------------------------
+r628 | lh3 | 2008-11-10 12:56:36 +0000 (Mon, 10 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam.c
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-6
+ * fixed a bug in bam_pileup.c
+
+------------------------------------------------------------------------
+r627 | lh3 | 2008-11-10 11:32:46 +0000 (Mon, 10 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/razf.c
+
+ * bamtk-0.1.0-5
+ * fixed a bug in razf.c, caused by my modifications
+ * improve the interface of pileup. Now it will be slower but more flexible
+
+------------------------------------------------------------------------
+r626 | lh3 | 2008-11-09 20:51:04 +0000 (Sun, 09 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-4
+ * view: dumping binary output
+
+------------------------------------------------------------------------
+r625 | lh3 | 2008-11-09 20:31:54 +0000 (Sun, 09 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam.c
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bam_sort.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-3
+ * rename functions
+
+------------------------------------------------------------------------
+r624 | lh3 | 2008-11-09 15:07:32 +0000 (Sun, 09 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+
+add comments
+
+------------------------------------------------------------------------
+r623 | lh3 | 2008-11-08 22:32:49 +0000 (Sat, 08 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-2
+ * improve indexing for a mixture of long and short reads, although currently
+   I do not know whether it really works...
+
+------------------------------------------------------------------------
+r622 | lh3 | 2008-11-08 22:13:58 +0000 (Sat, 08 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-1
+ * prepare for improving indexing algorithm
+
+------------------------------------------------------------------------
+r621 | lh3 | 2008-11-08 20:28:09 +0000 (Sat, 08 Nov 2008) | 4 lines
+Changed paths:
+   A /branches/prog/bam/all2tam.pl
+   M /branches/prog/bam/bam.c
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bamtk.c
+   D /branches/prog/bam/tam_utils.pl
+
+ * bamtk-0.1.0
+ * smarter integers
+ * rename tam_utils.pl to all2tam.pl
+
+------------------------------------------------------------------------
+r620 | lh3 | 2008-11-08 17:17:22 +0000 (Sat, 08 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/prog/bam
+   A /branches/prog/bam/Makefile
+   A /branches/prog/bam/bam.c
+   A /branches/prog/bam/bam.h
+   A /branches/prog/bam/bam_endian.h
+   A /branches/prog/bam/bam_import.c
+   A /branches/prog/bam/bam_index.c
+   A /branches/prog/bam/bam_pileup.c
+   A /branches/prog/bam/bam_sort.c
+   A /branches/prog/bam/bamtk.c
+   A /branches/prog/bam/khash.h
+   A /branches/prog/bam/ksort.h
+   A /branches/prog/bam/kstream.h
+   A /branches/prog/bam/razf.c
+   A /branches/prog/bam/razf.h
+   A /branches/prog/bam/razip.c
+   A /branches/prog/bam/tam_utils.pl
+   A /branches/prog/bam/zutil.h
+
+The Binary Alignment/Mapping format.
+
+------------------------------------------------------------------------