[Bio-bwa-help] BWA-0.7.6 released

[lh3 <lh...@sa...>]

 

Release 0.7.6 (31 Januaray, 2014)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Changes in BWA-MEM:

 * Changed the way mapping quality is estimated. The new method tends to
give
 the same alignment a higher mapping quality. On paired-end reads, the
change
 is minor as with pairing, the mapping quality is usually high. For
short
 single-end reads, the difference is considerable.

 * Improved load balance when many threads are spawned. However, bwa-mem
is
 still not very thread efficient, probably due to the frequent heap
memory
 allocation. Further improvement is a little difficult and may affect
the
 code stability.

 * Allow to use different clipping penalties for 5'- and 3'-ends. This
helps
 when we do not want to clip one end.

 * Print the @PG line, including the command line options.

 * Improved the band width estimate: a) fixed a bug causing the band
 width extimated from extension not used in the final global alignment;
b)
 try doubled band width if the global alignment score is smaller.
 Insufficient band width leads to wrong CIGAR and spurious
mismatches/indels.

 * Added a new option -D to fine tune a heuristic on dropping suboptimal
hits.
 Reducing -D increases accuracy but decreases the mapping speed. If
unsure,
 leave it to the default.

 * Bugfix: for a repetitive single-end read, the reported hit is not
randomly
 distributed among equally best hits.

 * Bugfix: missing paired-end hits due to unsorted list of SE hits.

 * Bugfix: incorrect CIGAR caused by a defect in the global alignment.

 * Bugfix: incorrect CIGAR caused by failed SW rescue.

 * Bugfix: alignments largely mapped to the same position are regarded
to be
 distinct from each other, which leads to underestimated mapping
quality.

 * Added the MD tag.

There are no changes to BWA-backtrack in this release. However, it has a
few
known issues yet to be fixed. If you prefer BWA-track, It is still
advised to
use bwa-0.6.x.

While I developed BWA-MEM, I also found a few issues with BWA-SW. It is
now
possible to improve BWA-SW with the lessons learned from BWA-MEM.
However, as
BWA-MEM is usually better, I will not improve BWA-SW until I find
applications
where BWA-SW may excel.

(0.7.6: 31 January 2014, r432)

 


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