Beta Release 0.5.9 (24 January, 2011) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes: * Feature: barcode support via the `-B' option. * Feature: Illumina 1.3+ read format support via the `-I' option. * Bugfix: RG tags are not attached to unmapped reads. * Bugfix: very rare bwasw mismappings * Recommend options for PacBio reads in bwasw help message. Also, since January 13, the BWA master repository has been moved to github: https://github.com/lh3/bwa The revision number has been reset. All recent changes will be first committed to this repository. (0.5.9: 24 January 2011, r16) Beta Release Candidate 0.5.9rc1 (10 December, 2010) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes in bwasw: * Output unmapped reads. * For a repetitive read, choose a random hit instead of a fixed one. This is not well tested. Notable changes in bwa-short: * Fixed a bug in the SW scoring system, which may lead to unexpected gaps towards the end of a read. * Fixed a bug which invalidates the randomness of repetitive reads. * Fixed a rare memory leak. * Allowed to specify the read group at the command line. * Take name-grouped BAM files as input. Changes to this release are usually safe in that they do not interfere with the key functionality. However, the release has only been tested on small samples instead of on large-scale real data. If anything weird happens, please report the bugs to the bio-bwa-help mailing list. (0.5.9rc1: 10 December 2010, r1561) Beta Release 0.5.8 (8 June, 2010) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes in bwasw: * Fixed an issue of missing alignments. This should happen rarely and only when the contig/read alignment is multi-part. Very rarely, bwasw may still miss a segment in a multi-part alignment. This is difficult to fix, although possible. Notable changes in bwa-short: * Discard the SW alignment when the best single-end alignment is much better. Such a SW alignment may caused by structural variations and forcing it to be aligned leads to false alignment. This fix has not been tested thoroughly. It would be great to receive more users feedbacks on this issue. * Fixed a typo/bug in sampe which leads to unnecessarily large memory usage in some cases. * Further reduced the chance of reporting `weird pairing'. (0.5.8: 8 June 2010, r1442) Beta Release 0.5.7 (1 March, 2010) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This release only has an effect on paired-end data with fat insert-size distribution. Users are still recommended to update as the new release improves the robustness to poor data. * The fix for `weird pairing' was not working in version 0.5.6, pointed out by Carol Scott. It should work now. * Optionally output to a normal file rather than to stdout (by Tim Fennel). (0.5.7: 1 March 2010, r1310) Beta Release 0.5.6 (10 Feburary, 2010) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes in bwa-short: * Report multiple hits in the SAM format at a new tag XA encoded as: (chr,pos,CIGAR,NM;)*. By default, if a paired or single-end read has 4 or fewer hits, they will all be reported; if a read in a anomalous pair has 11 or fewer hits, all of them will be reported. * Perform Smith-Waterman alignment also for anomalous read pairs when both ends have quality higher than 17. This reduces false positives for some SV discovery algorithms. * Do not report "weird pairing" when the insert size distribution is too fat or has a mean close to zero. * If a read is bridging two adjacent chromsomes, flag it as unmapped. * Fixed a small but long existing memory leak in paired-end mapping. * Multiple bug fixes in SOLiD mapping: a) quality "-1" can be correctly parsed by solid2fastq.pl; b) truncated quality string is resolved; c) SOLiD read mapped to the reverse strand is complemented. * Bwa now calculates skewness and kurtosis of the insert size distribution. * Deploy a Bayesian method to estimate the maximum distance for a read pair considered to be paired properly. The method is proposed by Gerton Lunter, but bwa only implements a simplified version. * Export more functions for Java bindings, by Matt Hanna (See: http://www.broadinstitute.org/gsa/wiki/index.php/Sting_BWA/C_bindings) * Abstract bwa CIGAR for further extension, by Rodrigo Goya. (0.5.6: 10 Feburary 2010, r1303) Beta Release 0.5.5 (10 November, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This is a bug fix release: * Fixed a serious bug/typo in aln which does not occur given short reads, but will lead to segfault for >500bp reads. Of course, the aln command is not recommended for reads longer than 200bp, but this is a bug anyway. * Fixed a minor bug/typo which leads to incorrect single-end mapping quality when one end is moved to meet the mate-pair requirement. * Fixed a bug in samse for mapping in the color space. This bug is caused by quality filtration added since 0.5.1. (0.5.5: 10 November 2009, r1273) Beta Release 0.5.4 (9 October, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Since this version, the default seed length used in the "aln" command is changed to 32. Notable changes in bwa-short: * Added a new tag "XC:i" which gives the length of clipped reads. * In sampe, skip alignments in case of a bug in the Smith-Waterman alignment module. * In sampe, fixed a bug in pairing when the read sequence is identical to its reverse complement. * In sampe, optionally preload the entire FM-index into memory to reduce disk operations. Notable changes in dBWT-SW/BWA-SW: * Changed name dBWT-SW to BWA-SW. * Optionally use "hard clipping" in the SAM output. (0.5.4: 9 October 2009, r1245) Beta Release 0.5.3 (15 September, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fixed a critical bug in bwa-short: reads mapped to the reverse strand are not complemented. (0.5.3: 15 September 2009, r1225) Beta Release 0.5.2 (13 September, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes in bwa-short: * Optionally trim reads before alignment. See the manual page on `aln -q' for detailed description. * Fixed a bug in calculating the NM tag for a gapped alignment. * Fixed a bug given a mixture of reads with some longer than the seed length and some shorter. * Print SAM header. Notable changes in dBWT-SW: * Changed the default value of -T to 30. As a result, the accuracy is a little higher for short reads at the cost of speed. (0.5.2: 13 September 2009, r1223) Beta Release 0.5.1 (2 September, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes in the short read alignment component: * Fixed a bug in samse: do not write mate coordinates. Notable changes in dBWT-SW: * Randomly choose one alignment if the read is a repetitive. * Fixed a flaw when a read is mapped across two adjacent reference sequences. However, wrong alignment reports may still occur rarely in this case. * Changed the default band width to 50. The speed is slower due to this change. * Improved the mapping quality a little given long query sequences. (0.5.1: 2 September 2009, r1209) Beta Release 0.5.0 (20 August, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This release implements a novel algorithm, dBWT-SW, specifically designed for long reads. It is 10-50 times faster than SSAHA2, depending on the characteristics of the input data, and achieves comparable alignment accuracy while allowing chimera detection. In comparison to BLAT, dBWT-SW is several times faster and much more accurate especially when the error rate is high. Please read the manual page for more information. The dBWT-SW algorithm is kind of developed for future sequencing technologies which produce much longer reads with a little higher error rate. It is still at its early development stage. Some features are missing and it may be buggy although I have evaluated on several simulated and real data sets. But following the "release early" paradigm, I would like the users to try it first. Other notable changes in BWA are: * Fixed a rare bug in the Smith-Waterman alignment module. * Fixed a rare bug about the wrong alignment coordinate when a read is poorly aligned. * Fixed a bug in generating the "mate-unmap" SAM tag when both ends in a pair are unmapped. (0.5.0: 20 August 2009, r1200) Beta Release 0.4.9 (19 May, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Interestingly, the integer overflow bug claimed to be fixed in 0.4.7 has not in fact. Now I have fixed the bug. Sorry for this and thank Quan Long for pointing out the bug (again). (0.4.9: 19 May 2009, r1075) Beta Release 0.4.8 (18 May, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ One change to "aln -R". Now by default, if there are no more than `-R' equally best hits, bwa will search for suboptimal hits. This change affects the ability in finding SNPs in segmental duplications. I have not tested this option thoroughly, but this simple change is less likely to cause new bugs. Hope I am right. (0.4.8: 18 May 2009, r1073) Beta Release 0.4.7 (12 May, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes: * Output SM (single-end mapping quality) and AM (smaller mapping quality among the two ends) tag from sam output. * Improved the functionality of stdsw. * Made the XN tag more accurate. * Fixed a very rare segfault caused by integer overflow. * Improve the insert size estimation. * Fixed compiling errors for some Linux systems. (0.4.7: 12 May 2009, r1066) Beta Release 0.4.6 (9 March, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This release improves the SOLiD support. First, a script for converting SOLiD raw data is provided. This script is adapted from solid2fastq.pl in the MAQ package. Second, a nucleotide reference file can be directly used with `bwa index'. Third, SOLiD paired-end support is completed. Fourth, color-space reads will be converted to nucleotides when SAM output is generated. Color errors are corrected in this process. Please note that like MAQ, BWA cannot make use of the primer base and the first color. In addition, the calculation of mapping quality is also improved a little bit, although end-users may barely observe the difference. (0.4.6: 9 March 2009, r915) Beta Release 0.4.5 (18 Feburary, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Not much happened, but I think it would be good to let the users use the latest version. Notable changes (Thank Bob Handsaker for catching the two bugs): * Improved bounary check. Previous version may still give incorrect alignment coordinates in rare cases. * Fixed a bug in SW alignment when no residue matches. This only affects the `sampe' command. * Robustly estimate insert size without setting the maximum on the command line. Since this release `sampe -a' only has an effect if there are not enough good pairs to infer the insert size distribution. * Reduced false PE alignments a little bit by using the inferred insert size distribution. This fix may be more important for long insert size libraries. (0.4.5: 18 Feburary 2009, r829) Beta Release 0.4.4 (15 Feburary, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This is mainly a bug fix release. Notable changes are: * Imposed boundary check for extracting subsequence from the genome. Previously this causes memory problem in rare cases. * Fixed a bug in failing to find whether an alignment overlapping with N on the genome. * Changed MD tag to meet the latest SAM specification. (0.4.4: 15 Feburary 2009, r815) Beta Release 0.4.3 (22 January, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes: * Treat an ambiguous base N as a mismatch. Previous versions will not map reads containing any N. * Automatically choose the maximum allowed number of differences. This is important when reads of different lengths are mixed together. * Print mate coordinate if only one end is unmapped. * Generate MD tag. This tag encodes the mismatching positions and the reference bases at these positions. Deletions from the reference will also be printed. * Optionally dump multiple hits from samse, in another concise format rather than SAM. * Optionally disable iterative search. This is VERY SLOOOOW, though. * Fixed a bug in generate SAM. (0.4.3: 22 January 2009, r787) Beta Release 0.4.2 (9 January, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Aaron Quinlan found a bug in the indexer: the bwa indexer segfaults if there are no comment texts in the FASTA header. This is a critical bug. Nothing else was changed. (0.4.2: 9 January 2009, r769) Beta Release 0.4.1 (7 January, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ I am sorry for the quick updates these days. I like to set a milestone for BWA and this release seems to be. For paired end reads, BWA also does Smith-Waterman alignment for an unmapped read whose mate can be mapped confidently. With this strategy BWA achieves similar accuracy to maq. Benchmark is also updated accordingly. (0.4.1: 7 January 2009, r760) Beta Release 0.4.0 (6 January, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In comparison to the release two days ago, this release is mainly tuned for performance with some tricks I learnt from Bowtie. However, as the indexing format has also been changed, I have to increase the version number to 0.4.0 to emphasize that *DATABASE MUST BE RE-INDEXED* with `bwa index'. * Improved the speed by about 20%. * Added multi-threading to `bwa aln'. (0.4.0: 6 January 2009, r756) Beta Release 0.3.0 (4 January, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * Added paired-end support by separating SA calculation and alignment output. * Added SAM output. * Added evaluation to the documentation. (0.3.0: 4 January 2009, r741) Beta Release 0.2.0 (15 Augusst, 2008) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * Take the subsequence at the 5'-end as seed. Seeding strategy greatly improves the speed for long reads, at the cost of missing a few true hits that contain many differences in the seed. Seeding also increase the memory by 800MB. * Fixed a bug which may miss some gapped alignments. Fixing the bug also slows the speed a little. (0.2.0: 15 August 2008, r428) Beta Release 0.1.6 (08 Augusst, 2008) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * Give accurate CIGAR string. * Add a simple interface to SW/NW alignment (0.1.6: 08 August 2008, r414) Beta Release 0.1.5 (27 July, 2008) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * Improve the speed. This version is expected to give the same results. (0.1.5: 27 July 2008, r400) Beta Release 0.1.4 (22 July, 2008) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * Fixed a bug which may cause missing gapped alignments. * More clearly define what alignments can be found by BWA (See manual). Now BWA runs a little slower because it will visit more potential gapped alignments. * A bit code clean up. (0.1.4: 22 July 2008, r387) Beta Release 0.1.3 (21 July, 2008) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Improve the speed with some tricks on retrieving occurences. The results should be exactly the same as that of 0.1.2. (0.1.3: 21 July 2008, r382) Beta Release 0.1.2 (17 July, 2008) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Support gapped alignment. Codes for ungapped alignment has been removed. (0.1.2: 17 July 2008, r371) Beta Release 0.1.1 (03 June, 2008) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This is the first release of BWA, Burrows-Wheeler Alignment tool. Please read man page for more information about this software. (0.1.1: 03 June 2008, r349)