BWA-0.7.18 (r1243)

Notable changes:

• Support ARM64 (#359)
• Output SAM header line (#336)
• Added the XB tag to output alignment score and mapping quality
• Fixed a compiling error with GCC 10 (#267)
• Avoid potential buffer overflow (#232)

(0.7.18: 14 April 2024, r1243)

BWA-0.7.17 (r1188)

This release adds option -q to preserve the mapping quality of split alignment
with a lower alignment score than the primary alignment. Option -5
automatically applies -q as well. BWA outputs identical alignments to the
previous version unless option -5 is used.

(0.7.17: 23 October 2017, r1188)

BWA-0.7.16a (r1181)

This release added a couple of minor features and incorporated multiple pull
requests, including:

• Added option -5, which is useful to some Hi-C pipelines.

• Fixed an error with samtools sorting (#129). Updated download link for
  GRCh38 (#123). Fixed README MarkDown formatting (#70). Addressed multiple
  issues via a collected pull request #139 by @jmarshall. Avoid malformatted
  SAM header when -R is used with TAB (#84). Output mate CIGAR (#138).

(0.7.16: 30 July 2017, r1180)

BWA-0.7.15 (r1140)

• Fixed a long existing bug which potentially leads underestimated insert size
  upper bound. This bug should have little effect in practice.
• In the ALT mapping mode, this release adds the "AH:*" header tag to SQ lines
  corresponding to alternate haplotypes.

BWA-0.7.13 (r1126)

This release fixes a few minor bugs in the previous version and adds a few
minor features. All BWA algorithms should produce identical output to 0.7.12
when there are no ALT contigs.

Detailed changes:

• Fixed a bug in "bwa-postalt.js". The old version may produce 0.5% of wrong
  bases for reads mapped to the ALT contigs.
• Fixed a potential bug in the multithreading mode. It may occur when mapping
  is much faster than file reading, which should almost never happen in
  practice.
• Changed the download URL of GRCh38.
• Removed the read overlap mode. It is not working well.
• Added the ropebwt2 algorithm as an alternative to index large genomes.
  Ropebwt2 is slower than the "bwtsw" algorithm, but it has a permissive
  license. This allows us to create an Apache2-licensed BWA (in the "Apache2"
  branch) for commercial users who are concerned with GPL.

(0.7.13: 23 Feburary 2016, r1126)