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comparison pyPRADA_1.2/tools/bwa-0.5.7-mh/NEWS @ 0:acc2ca1a3ba4
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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1 Beta Release 0.5.7 (1 March, 2010) | |
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
3 | |
4 This release only has an effect on paired-end data with fat insert-size | |
5 distribution. Users are still recommended to update as the new release | |
6 improves the robustness to poor data. | |
7 | |
8 * The fix for `weird pairing' was not working in version 0.5.6, pointed | |
9 out by Carol Scott. It should work now. | |
10 | |
11 * Optionally output to a normal file rather than to stdout (by Tim | |
12 Fennel). | |
13 | |
14 (0.5.7: 1 March 2010, r1310) | |
15 | |
16 | |
17 | |
18 Beta Release 0.5.6 (10 Feburary, 2010) | |
19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
20 | |
21 Notable changes in bwa-short: | |
22 | |
23 * Report multiple hits in the SAM format at a new tag XA encoded as: | |
24 (chr,pos,CIGAR,NM;)*. By default, if a paired or single-end read has | |
25 4 or fewer hits, they will all be reported; if a read in a anomalous | |
26 pair has 11 or fewer hits, all of them will be reported. | |
27 | |
28 * Perform Smith-Waterman alignment also for anomalous read pairs when | |
29 both ends have quality higher than 17. This reduces false positives | |
30 for some SV discovery algorithms. | |
31 | |
32 * Do not report "weird pairing" when the insert size distribution is | |
33 too fat or has a mean close to zero. | |
34 | |
35 * If a read is bridging two adjacent chromsomes, flag it as unmapped. | |
36 | |
37 * Fixed a small but long existing memory leak in paired-end mapping. | |
38 | |
39 * Multiple bug fixes in SOLiD mapping: a) quality "-1" can be correctly | |
40 parsed by solid2fastq.pl; b) truncated quality string is resolved; c) | |
41 SOLiD read mapped to the reverse strand is complemented. | |
42 | |
43 * Bwa now calculates skewness and kurtosis of the insert size | |
44 distribution. | |
45 | |
46 * Deploy a Bayesian method to estimate the maximum distance for a read | |
47 pair considered to be paired properly. The method is proposed by | |
48 Gerton Lunter, but bwa only implements a simplified version. | |
49 | |
50 * Export more functions for Java bindings, by Matt Hanna (See: | |
51 http://www.broadinstitute.org/gsa/wiki/index.php/Sting_BWA/C_bindings) | |
52 | |
53 * Abstract bwa CIGAR for further extension, by Rodrigo Goya. | |
54 | |
55 (0.5.6: 10 Feburary 2010, r1303) | |
56 | |
57 | |
58 | |
59 Beta Release 0.5.5 (10 November, 2009) | |
60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
61 | |
62 This is a bug fix release: | |
63 | |
64 * Fixed a serious bug/typo in aln which does not occur given short | |
65 reads, but will lead to segfault for >500bp reads. Of course, the aln | |
66 command is not recommended for reads longer than 200bp, but this is a | |
67 bug anyway. | |
68 | |
69 * Fixed a minor bug/typo which leads to incorrect single-end mapping | |
70 quality when one end is moved to meet the mate-pair requirement. | |
71 | |
72 * Fixed a bug in samse for mapping in the color space. This bug is | |
73 caused by quality filtration added since 0.5.1. | |
74 | |
75 (0.5.5: 10 November 2009, r1273) | |
76 | |
77 | |
78 | |
79 Beta Release 0.5.4 (9 October, 2009) | |
80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
81 | |
82 Since this version, the default seed length used in the "aln" command is | |
83 changed to 32. | |
84 | |
85 Notable changes in bwa-short: | |
86 | |
87 * Added a new tag "XC:i" which gives the length of clipped reads. | |
88 | |
89 * In sampe, skip alignments in case of a bug in the Smith-Waterman | |
90 alignment module. | |
91 | |
92 * In sampe, fixed a bug in pairing when the read sequence is identical | |
93 to its reverse complement. | |
94 | |
95 * In sampe, optionally preload the entire FM-index into memory to | |
96 reduce disk operations. | |
97 | |
98 Notable changes in dBWT-SW/BWA-SW: | |
99 | |
100 * Changed name dBWT-SW to BWA-SW. | |
101 | |
102 * Optionally use "hard clipping" in the SAM output. | |
103 | |
104 (0.5.4: 9 October 2009, r1245) | |
105 | |
106 | |
107 | |
108 Beta Release 0.5.3 (15 September, 2009) | |
109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
110 | |
111 Fixed a critical bug in bwa-short: reads mapped to the reverse strand | |
112 are not complemented. | |
113 | |
114 (0.5.3: 15 September 2009, r1225) | |
115 | |
116 | |
117 | |
118 Beta Release 0.5.2 (13 September, 2009) | |
119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
120 | |
121 Notable changes in bwa-short: | |
122 | |
123 * Optionally trim reads before alignment. See the manual page on `aln | |
124 -q' for detailed description. | |
125 | |
126 * Fixed a bug in calculating the NM tag for a gapped alignment. | |
127 | |
128 * Fixed a bug given a mixture of reads with some longer than the seed | |
129 length and some shorter. | |
130 | |
131 * Print SAM header. | |
132 | |
133 Notable changes in dBWT-SW: | |
134 | |
135 * Changed the default value of -T to 30. As a result, the accuracy is a | |
136 little higher for short reads at the cost of speed. | |
137 | |
138 (0.5.2: 13 September 2009, r1223) | |
139 | |
140 | |
141 | |
142 Beta Release 0.5.1 (2 September, 2009) | |
143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
144 | |
145 Notable changes in the short read alignment component: | |
146 | |
147 * Fixed a bug in samse: do not write mate coordinates. | |
148 | |
149 Notable changes in dBWT-SW: | |
150 | |
151 * Randomly choose one alignment if the read is a repetitive. | |
152 | |
153 * Fixed a flaw when a read is mapped across two adjacent reference | |
154 sequences. However, wrong alignment reports may still occur rarely in | |
155 this case. | |
156 | |
157 * Changed the default band width to 50. The speed is slower due to this | |
158 change. | |
159 | |
160 * Improved the mapping quality a little given long query sequences. | |
161 | |
162 (0.5.1: 2 September 2009, r1209) | |
163 | |
164 | |
165 | |
166 Beta Release 0.5.0 (20 August, 2009) | |
167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
168 | |
169 This release implements a novel algorithm, dBWT-SW, specifically | |
170 designed for long reads. It is 10-50 times faster than SSAHA2, depending | |
171 on the characteristics of the input data, and achieves comparable | |
172 alignment accuracy while allowing chimera detection. In comparison to | |
173 BLAT, dBWT-SW is several times faster and much more accurate especially | |
174 when the error rate is high. Please read the manual page for more | |
175 information. | |
176 | |
177 The dBWT-SW algorithm is kind of developed for future sequencing | |
178 technologies which produce much longer reads with a little higher error | |
179 rate. It is still at its early development stage. Some features are | |
180 missing and it may be buggy although I have evaluated on several | |
181 simulated and real data sets. But following the "release early" | |
182 paradigm, I would like the users to try it first. | |
183 | |
184 Other notable changes in BWA are: | |
185 | |
186 * Fixed a rare bug in the Smith-Waterman alignment module. | |
187 | |
188 * Fixed a rare bug about the wrong alignment coordinate when a read is | |
189 poorly aligned. | |
190 | |
191 * Fixed a bug in generating the "mate-unmap" SAM tag when both ends in | |
192 a pair are unmapped. | |
193 | |
194 (0.5.0: 20 August 2009, r1200) | |
195 | |
196 | |
197 | |
198 Beta Release 0.4.9 (19 May, 2009) | |
199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
200 | |
201 Interestingly, the integer overflow bug claimed to be fixed in 0.4.7 has | |
202 not in fact. Now I have fixed the bug. Sorry for this and thank Quan | |
203 Long for pointing out the bug (again). | |
204 | |
205 (0.4.9: 19 May 2009, r1075) | |
206 | |
207 | |
208 | |
209 Beta Release 0.4.8 (18 May, 2009) | |
210 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
211 | |
212 One change to "aln -R". Now by default, if there are no more than `-R' | |
213 equally best hits, bwa will search for suboptimal hits. This change | |
214 affects the ability in finding SNPs in segmental duplications. | |
215 | |
216 I have not tested this option thoroughly, but this simple change is less | |
217 likely to cause new bugs. Hope I am right. | |
218 | |
219 (0.4.8: 18 May 2009, r1073) | |
220 | |
221 | |
222 | |
223 Beta Release 0.4.7 (12 May, 2009) | |
224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
225 | |
226 Notable changes: | |
227 | |
228 * Output SM (single-end mapping quality) and AM (smaller mapping | |
229 quality among the two ends) tag from sam output. | |
230 | |
231 * Improved the functionality of stdsw. | |
232 | |
233 * Made the XN tag more accurate. | |
234 | |
235 * Fixed a very rare segfault caused by integer overflow. | |
236 | |
237 * Improve the insert size estimation. | |
238 | |
239 * Fixed compiling errors for some Linux systems. | |
240 | |
241 (0.4.7: 12 May 2009, r1066) | |
242 | |
243 | |
244 | |
245 Beta Release 0.4.6 (9 March, 2009) | |
246 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
247 | |
248 This release improves the SOLiD support. First, a script for converting | |
249 SOLiD raw data is provided. This script is adapted from solid2fastq.pl | |
250 in the MAQ package. Second, a nucleotide reference file can be directly | |
251 used with `bwa index'. Third, SOLiD paired-end support is | |
252 completed. Fourth, color-space reads will be converted to nucleotides | |
253 when SAM output is generated. Color errors are corrected in this | |
254 process. Please note that like MAQ, BWA cannot make use of the primer | |
255 base and the first color. | |
256 | |
257 In addition, the calculation of mapping quality is also improved a | |
258 little bit, although end-users may barely observe the difference. | |
259 | |
260 (0.4.6: 9 March 2009, r915) | |
261 | |
262 | |
263 | |
264 Beta Release 0.4.5 (18 Feburary, 2009) | |
265 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
266 | |
267 Not much happened, but I think it would be good to let the users use the | |
268 latest version. | |
269 | |
270 Notable changes (Thank Bob Handsaker for catching the two bugs): | |
271 | |
272 * Improved bounary check. Previous version may still give incorrect | |
273 alignment coordinates in rare cases. | |
274 | |
275 * Fixed a bug in SW alignment when no residue matches. This only | |
276 affects the `sampe' command. | |
277 | |
278 * Robustly estimate insert size without setting the maximum on the | |
279 command line. Since this release `sampe -a' only has an effect if | |
280 there are not enough good pairs to infer the insert size | |
281 distribution. | |
282 | |
283 * Reduced false PE alignments a little bit by using the inferred insert | |
284 size distribution. This fix may be more important for long insert | |
285 size libraries. | |
286 | |
287 (0.4.5: 18 Feburary 2009, r829) | |
288 | |
289 | |
290 | |
291 Beta Release 0.4.4 (15 Feburary, 2009) | |
292 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
293 | |
294 This is mainly a bug fix release. Notable changes are: | |
295 | |
296 * Imposed boundary check for extracting subsequence from the | |
297 genome. Previously this causes memory problem in rare cases. | |
298 | |
299 * Fixed a bug in failing to find whether an alignment overlapping with | |
300 N on the genome. | |
301 | |
302 * Changed MD tag to meet the latest SAM specification. | |
303 | |
304 (0.4.4: 15 Feburary 2009, r815) | |
305 | |
306 | |
307 | |
308 Beta Release 0.4.3 (22 January, 2009) | |
309 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
310 | |
311 Notable changes: | |
312 | |
313 * Treat an ambiguous base N as a mismatch. Previous versions will not | |
314 map reads containing any N. | |
315 | |
316 * Automatically choose the maximum allowed number of differences. This | |
317 is important when reads of different lengths are mixed together. | |
318 | |
319 * Print mate coordinate if only one end is unmapped. | |
320 | |
321 * Generate MD tag. This tag encodes the mismatching positions and the | |
322 reference bases at these positions. Deletions from the reference will | |
323 also be printed. | |
324 | |
325 * Optionally dump multiple hits from samse, in another concise format | |
326 rather than SAM. | |
327 | |
328 * Optionally disable iterative search. This is VERY SLOOOOW, though. | |
329 | |
330 * Fixed a bug in generate SAM. | |
331 | |
332 (0.4.3: 22 January 2009, r787) | |
333 | |
334 | |
335 | |
336 Beta Release 0.4.2 (9 January, 2009) | |
337 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
338 | |
339 Aaron Quinlan found a bug in the indexer: the bwa indexer segfaults if | |
340 there are no comment texts in the FASTA header. This is a critical | |
341 bug. Nothing else was changed. | |
342 | |
343 (0.4.2: 9 January 2009, r769) | |
344 | |
345 | |
346 | |
347 Beta Release 0.4.1 (7 January, 2009) | |
348 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
349 | |
350 I am sorry for the quick updates these days. I like to set a milestone | |
351 for BWA and this release seems to be. For paired end reads, BWA also | |
352 does Smith-Waterman alignment for an unmapped read whose mate can be | |
353 mapped confidently. With this strategy BWA achieves similar accuracy to | |
354 maq. Benchmark is also updated accordingly. | |
355 | |
356 (0.4.1: 7 January 2009, r760) | |
357 | |
358 | |
359 | |
360 Beta Release 0.4.0 (6 January, 2009) | |
361 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
362 | |
363 In comparison to the release two days ago, this release is mainly tuned | |
364 for performance with some tricks I learnt from Bowtie. However, as the | |
365 indexing format has also been changed, I have to increase the version | |
366 number to 0.4.0 to emphasize that *DATABASE MUST BE RE-INDEXED* with | |
367 `bwa index'. | |
368 | |
369 * Improved the speed by about 20%. | |
370 | |
371 * Added multi-threading to `bwa aln'. | |
372 | |
373 (0.4.0: 6 January 2009, r756) | |
374 | |
375 | |
376 | |
377 Beta Release 0.3.0 (4 January, 2009) | |
378 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
379 | |
380 * Added paired-end support by separating SA calculation and alignment | |
381 output. | |
382 | |
383 * Added SAM output. | |
384 | |
385 * Added evaluation to the documentation. | |
386 | |
387 (0.3.0: 4 January 2009, r741) | |
388 | |
389 | |
390 | |
391 Beta Release 0.2.0 (15 Augusst, 2008) | |
392 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
393 | |
394 * Take the subsequence at the 5'-end as seed. Seeding strategy greatly | |
395 improves the speed for long reads, at the cost of missing a few true | |
396 hits that contain many differences in the seed. Seeding also increase | |
397 the memory by 800MB. | |
398 | |
399 * Fixed a bug which may miss some gapped alignments. Fixing the bug | |
400 also slows the speed a little. | |
401 | |
402 (0.2.0: 15 August 2008, r428) | |
403 | |
404 | |
405 | |
406 Beta Release 0.1.6 (08 Augusst, 2008) | |
407 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
408 | |
409 * Give accurate CIGAR string. | |
410 | |
411 * Add a simple interface to SW/NW alignment | |
412 | |
413 (0.1.6: 08 August 2008, r414) | |
414 | |
415 | |
416 | |
417 Beta Release 0.1.5 (27 July, 2008) | |
418 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
419 | |
420 * Improve the speed. This version is expected to give the same results. | |
421 | |
422 (0.1.5: 27 July 2008, r400) | |
423 | |
424 | |
425 | |
426 Beta Release 0.1.4 (22 July, 2008) | |
427 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
428 | |
429 * Fixed a bug which may cause missing gapped alignments. | |
430 | |
431 * More clearly define what alignments can be found by BWA (See | |
432 manual). Now BWA runs a little slower because it will visit more | |
433 potential gapped alignments. | |
434 | |
435 * A bit code clean up. | |
436 | |
437 (0.1.4: 22 July 2008, r387) | |
438 | |
439 | |
440 | |
441 Beta Release 0.1.3 (21 July, 2008) | |
442 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
443 | |
444 Improve the speed with some tricks on retrieving occurences. The results | |
445 should be exactly the same as that of 0.1.2. | |
446 | |
447 (0.1.3: 21 July 2008, r382) | |
448 | |
449 | |
450 | |
451 Beta Release 0.1.2 (17 July, 2008) | |
452 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
453 | |
454 Support gapped alignment. Codes for ungapped alignment has been removed. | |
455 | |
456 (0.1.2: 17 July 2008, r371) | |
457 | |
458 | |
459 | |
460 Beta Release 0.1.1 (03 June, 2008) | |
461 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
462 | |
463 This is the first release of BWA, Burrows-Wheeler Alignment tool. Please | |
464 read man page for more information about this software. | |
465 | |
466 (0.1.1: 03 June 2008, r349) | |
467 | |
468 | |
469 |