GeezerVison

Download the source code here: samtools-1.25.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.)

New work and changes:

• CHANGE. samtools checksum reported version set to 2.0. Checksum calculations differed between samtools 1.24 and previous releases. In earlier releases, the --check-mate option produced incorrect checksums. This was fixed in v1.24 but made already existing checksums invalid. Therefore, the fixed checksum is now designated Checksum 2.0 while the previous one is left at Checksum 1.0 in order differentiate the versions.
  NB Samtools version 1.24 produced corrected checksums but erroneously labelled them as version 1.0. If you used this release with the --check-mate option then we advise recomputing or manually editing the version numbers in the output files.
  (PR #2365, fixes #2354. Reported by Ruben Vorderman)

• CHANGE. When the HTSlib version in use cannot be deduced from the SAMtools version, the @PG VN field now records it too, for example VN:1.24.1 (with HTSlib 1.25).
  (PR #2350. Thanks to Benjamin Demaille)

• In mpileup, added an ENDPOS field to --output-extra. Combined with POS, this gives the left and right extents on the reference for this alignment, meaning we can observe how close to either end this pileup base is.
  (PR #2351, fixes #2343. Requested by Devang Thakkar)

• Strip UR tags from header SQ lines in samtools view.
  (PR #2357, fixes #2327. Requested by Florian Plaza Oñate)

• Make samtools view --unmap and --unoutput work together.
  (PR #2358, fixes #2356. Requested by Eric Boyden)

• Make samtools import accept empty FASTQ input. This avoids halting a pipeline when one file has no data.
  (PR #2395. Thanks to Clint Valentine)

• samtools stats changed to use hts_crc32() instead of zlib's crc32() to take advantage of libdeflate (if used). Plus some minor fixes.
  (PR #2406, thanks to John Marshall)

Documentation:

• Update values in embed_ref and multi_seq_per_slice options.
  (PR #2386)

Bug fixes:

• 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 -M and -z cigar options. 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)

• In samtools stats grow the coverage ring buffer instead of wrapping around.
  (PR #2379, fixes #2378. Thanks to Cynthia Krafft)

• Fix --move-umi-to-tag in samtools markdup.
  (PR #2382, fixes #2380. Reported by mrubio-chavarria)

• Relax the --barcode-name regex in samtools markdup.
  (PR #2387, fixes #2385. Reported by fjvorhoelter)

• Make phase and targetcut work with records where seq is '*'.
  (PR #2393, fixes #2390. Reported by babayaga)

• Check the number of temporary files is above 0 in samtools collate.
  (PR #2394. Thanks to Pierre Lindenbaum)

• Fix optical duplicates being set in markdup even when read name prefixes differ.
  (PR #2400, fixes #2399. Thanks to Kris Alavattam)

• Fix samtools cat exit code when unable to use CRAM file. cram_cat() now distinguishes between failure and EOF.
  (PR #2403, fixes #2401. Reported by Matthieu Muffato)

• FIX. samtools stats counted secondary and supplementary records in reads duplicated and bases duplicated, while sequences and total length exclude them. Non-primary duplicates are now not included in the counts. Also, samtools stats counted pairs with insert size 0 (TLEN unknown) in the denominator of insert size average and insert size standard deviation, and in the mean but not in the sum of squares of the standard deviation. They are now left out of both statistics and of the -m main-bulk cut-off.
  (PR #2388. Addresses a question in #696. Thanks to Cindy Krafft)

• Fix samtools calmd when correcting MD tags that aren't aux type Z.
  (PR #2408)

Non user-visible changes and build improvements:

• Add more CI targets (various Linux releases and other operating systems). Fixed warnings that occurred on some platforms.
  (PR #2353)

• Add --norc --noprofile to bash invocations in test.pl.
  (PR #2362)

• 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)

• Various error checking and reporting changes.
  (PR #2368, PR #2369, PR #2370, PR #2371, PR #2373)

• Switch containers to ones built by samtools/c-maint. This reduces the dependence on upstream repositories.
  (PR #2381)

Download the source code here: samtools-1.25.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.)

Download the source code here: samtools-1.24.1.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.)

• This release bundles HTSlib 1.24.1, which includes many important bug fixes. Please see htslib/NEWS for details.

• 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 -M and -z cigar options. 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 phase and targetcut work 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 calmd when correcting MD tags that aren't aux type Z.
  (PR #2408)

• Various error checking and reporting changes.
  (PR #2368, PR #2369, PR #2370, PR #2371, PR #2373)

Download the source code here: samtools-1.24.1.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.)

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.

• This release bundles HTSlib 1.23.3, which includes many important bug fixes. Please see htslib/NEWS for details.

• 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 -M and -z cigar options. 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 phase and targetcut work 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 calmd when correcting MD tags that aren't aux type Z.
  (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.)

Download the source code here: samtools-1.22.4.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.)

• This release bundles HTSlib 1.22.4, which includes many important bug fixes. Please see htslib/NEWS for details.

• 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 -M and -z cigar options. 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 phase and targetcut work 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 calmd when correcting MD tags that aren't aux type Z.
  (PR #2408)

• Various error checking and reporting changes.
  (PR #2368, PR #2369, PR #2370, PR #2371, PR #2373)

Download the source code here: samtools-1.22.4.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.)

Download the source code here: samtools-1.21.3.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.)

• This release bundles HTSlib 1.21.3, which includes many important bug fixes. Please see htslib/NEWS for details.

• 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 -M and -z cigar options. 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 phase and targetcut work 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 calmd when correcting MD tags that aren't aux type Z.
  (PR #2408)

• Various error checking and reporting changes.
  (PR #2368, PR #2369, PR #2370, PR #2371, PR #2373)

Download the source code here: samtools-1.21.3.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.)

Download the source code here: samtools-1.24.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.)

New work and changes:

• NEW. Contribution guidelines, Including sections on complexity, completeness, signing and our AI policy. (PR #2335)

• CHANGE. The default seed for samtools view --subsample is now based on the input file header and not zero. This means that repeated subsampling of the same file will work as expected. The previous behaviour can be replicated by setting the seed to zero. (PR #2320, fixes #1201. Thanks to Tim Fennell. Reported by Stathis)

• Add --move-umi-to-tag option to samtools markdup to extract UMI from QNAME and add to RX tag. (PR #2316, fixes #2181. Thanks to Matthias De Smet)

• Ensure indirect function calls have the correct type. This uses the new HTSlib interface introduced in samtools/htslib#1994. (PR #2322)

• Changes to make checksum merging compatible with biobambam2 checksums. (PR #2329, fixes #2323. Reported by Keith James)

• Speed improvement for samtools stats. (PR #2326)

• Changed --customized-index-file to --customized-index in samtools stats to match other subcommands. As this option had never worked (see #2315) this should not cause any compatibility problems. (PR #2334, fixes #2333. Thanks to Alexis Lucattini)

• Fill in mate information on supplementary alignments in samtools fixmate. Takes mate information from the primary and adds it to the supplementary alignment. Does not affect secondary alignments. (PR #2347. Thanks to Nils Homer)

Bug fixes:

• Various option fixes. Removed the mistaken required argument from --customized-index-file in stats. Also removed some unused and undocumented options from bam_plcmd.c. (PR #2317, fixes #2315. Reported by Alexis Lucattini)

• For samtools stats check before and after region with --target-regions. Previously doing only one or the other. (PR #2328, fixes #2303. Reported by Yuan Tian)

Non user-visible changes and build improvements:

• Add Github actions builds for Linux and Mac OS. This replaces the Cirrus CI tests that were discontinued. (PR #2330)

• Ensure PACKAGE_VERSION is set in the Makefile. (PR #2342, fixes #2337. Reported by James Ferguson)

• Make version.sh work when .git is present but the git executable is not. (PR #2345)

• Adjust tail commands so they work on Solaris. (PR #2346)

Download the source code here: samtools-1.24.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.)

Download the source code here: samtools-1.23.2.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.)

This release bundles HTSlib 1.23.2, which includes many important bug fixes. There are no changes to SAMtools. Please see htslib/NEWS for details.

Download the source code here: samtools-1.22.3.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.)

This release bundles HTSlib 1.22.3, which includes many important bug fixes. There are no changes to SAMtools. Please see htslib/NEWS for details.

Download the source code here: samtools-1.21.2.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.)

This release bundles HTSlib 1.21.2, which includes many important bug fixes. There are no changes to SAMtools. Please see htslib/NEWS for details.

Download the source code here: samtools-1.23.1.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.)

Bug fixes:

• This release bundles HTSlib 1.23.1, which includes many important bug fixes. Please see htslib/NEWS for details.

• Fix incorrect variable expansion in seq_cache_populate.py (PR #2291. Thanks to Ruben Vorderman)

• Don't try to write out empty strings in threaded consensus pileup mode. (PR #2305)

• Wrap ctype.h functions to avoid array subscript warnings, and add casts to prevent sign extension where arrays are indexed with char values. (PR #2306)

• Make samtools cram-size exit cleanly instead of crashing if it reads an invalid CRAM header. (CVE-2026-31973) (PR #2313)

Build changes:

• Reordered options for grep commands in tests so the input file is at the end. (PR #2311)

• Limit memory used by samtools sort in tests. (PR #2312)

Download the source code here: samtools-1.23.1.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.)