Download the source code here: samtools-1.23.3.tar.bz2. (The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)
Note: Some updates from the 1.24 release were inadvertantlyincluded in version 1.23.2. These have been reverted,if you need them, please use version 1.24 or later.
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This release bundles HTSlib 1.23.3, which includes many important bug fixes. Please see htslib/NEWS for details.
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Improve sanity checking on numeric command-line parameters.
(PR #2292. Thanks to Stephen Tanner) -
Fix reuse-after-free in bam_plcmd ref cache.
(PR #2364, fixes #2363. Reported by James Smagala. GHSA-xj7m-w8mc-xvf2 GHSA-vh3p-9c59-j3hv) -
Check string aux tag types before accessing data.
(PR #2366 GHSA-3j6q-r48h-wvm3) -
Fix
samtools fixmates-Mand-z cigaroptions. Fixing base modifications failed on reads without base modifications tags. Trimming CIGAR strings to the length of the reference sequence failed on strings containing 0M.
(PR #2407 GHSA-f423-v554-fwqr) -
Make
phaseandtargetcutwork with records where seq is '*'.
(PR #2393, fixes #2390. Reported by babayaga) -
Fixed compiler warnings that occurred on some platforms.
(PR #2353) -
Remove unnecessary
strdup(optarg)calls in CLI parsing.
(PR #2361) -
Fix memory leaks when samtools view CLI bails. Minimal impact but helps with enabling memory leak detection in fuzzing.
(PR #2372) -
Fix
samtools calmdwhen correcting MD tags that aren't aux typeZ.
(PR #2408) -
Various error checking and reporting changes.
(PR #2368, PR #2369, PR #2370, PR #2371, PR #2373)
Download the source code here: samtools-1.23.3.tar.bz2. (The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)