Notable changes:
-
Bugfix: misassgined "properly paired" SAM flag (#60). After this fix, flag 0x2 is only applied if the primary hits land on the same chromosome. The flag for a supplementary hit follows the primary hit for consistency with bwa-mem.
-
Bugfix: unrecognized command-line options may be reported at wrong positions.
(0.7: 6 August 2027, r421)
Notable changes:
- Bugfix: option
-Iwas not working (#57 and #58)
(0.6: 30 July 2026, r416)
Notable changes:
-
Improvement: theoretically better mapping quality (mapQ) for paired-end reads. Bwa-mem overestimates mapQ in a rare case, which is an oversight. The new release fixes the issue. On real-world SNP calling, the change increases precision but reduces sensivity. See 98e89de for details.
-
New feature: option
--mmapfor loading index as memory-mapped files (#55). It reduces index loading time but may slow down mapping depending on the system. -
New feature: option
-Ito specify the insert size distribution without inferring from data (#57). -
New feature: option
--outsto skip poor hits in output or in the XA tag (#56). -
Bugfix: APIs did not support BS-seq (#53).
(0.5: 25 July 2026, r414)
Notable changes:
-
Improvement: penalize heavily clipped alignment when rescoring. Older minibwa may produce a clipped primary alignment together with an end-to-end supplementary alignment with more mismatches/gaps. While often neither alignment is correct, having them both is confusing. This happens very rarely.
-
Bugfix: subcommand name was missing from the PG-CL tag in output SAM (#46). Also fixed a few typos in command-line help messages (#48 and #49).
(0.4: 12 July 2026, r400)
Notable changes:
-
New feature: added the
memsubcommand to mimic the bwa-mem command-line interface (CLI). Most input/output options and commonly used options are retained; unsupported or incompatible bwa-mem options are silently ignored. For commonly used bwa-mem command lines, replacing "bwa mem" with "minibwa mem" often gives comparable outputs. -
New feature: added option
-Hto inject arbitrary header lines. -
New feature: added the
XAtag to encode secondary alignments if there are not too many (#25). -
Bugfix: SAM header was outputted to stdout even if an output file is specified.
-
Bugfix: seed sorting was incorrectly implemented (#39).
-
Bugfix: compiled mimalloc missed the
aligned_allocfunction in C11 (#30). -
Bugfix: methylation index was incorrectly generated under the low-memory indexing mode (#42).
(0.3: 28 June 2026, r391)
This release fixed several minor bugs:
-
Bugfix: FASTA comments not parsed correctly during indexing (#22). It is recommended to reindex the reference genome with the new release.
-
Bugfix: double TABs ahead of each MD tag (#27)
-
Bugfix: a small memory leak during index loading (#26)
-
Bugfix: compilation error on ARM Linux (#24)
(0.2: 18 June 2026, r370)
First public release.
(0.1: 15 June 2026, r363)