1.23

Download the source code here: htslib-1.23.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

Updates

HTSlib 1.22 changed the VCF reader so that it stored GT prefixed phasing information, but only for files specifying fileformat=VCFv4.4 or higher. This caused problems when merging files with different versions, so the VCF reader will now store prefixed phasing information irrespective of the VCF version listed in the file headers. For files up to VCFv4.3, the first phasing bit will be set if all other alleles are phased, and cleared otherwise (following the rules for VCFv4.4 onwards where no explicit phasing symbol is present). This will also happen when reading BCF. When accessing GT data, it is no longer safe to assume that the phasing is set to zero even if the file reports a version earlier than VCFv4.4. Interfaces such as bcf_gt_allele() should always be used to access GT allele data. For compatibility, prefixed phasing will be stripped when writing VCF files with version 4.3 or earlier. (PR #1938, fixes #1932)
Add support for VCFv4.4 / VCFv4.5 "Number=" fields. (PR #1874)
Consolidate and simplify SAM header parsing. This considerably speeds up parsing files with many SQ lines. (PR #1947. PR #1953 fixes oss-fuzz issues 444492071, 444492076, 444547724, 444490034, PR #1977)
Switch from strtol to hts_str2uint in mod parsing for speed increase. (PR #1957. Thanks to Chris Wright)
Add UMI support to FASTQ input and output. See samtools/samtools#2270. (PR #1960, fixes samtools/samtools#2259. Requested by Poshi)
Removed direct access to htsFile struct members in some sample functions. (PR #1963, fixes #1961. Reported by John Marshall)
Improved operation of filters that work with header data. Filter expressions set as an HTS_OPT_FILTER on a BAM or CRAM iterator failed to return records matching on rname, mrname, rnext or library. (PR #1959)
Add Type to the INFO/FORMAT sanity check. This produces a warning on incorrect Type usage. (PR #1967, fixes #1937 and samtools/bcftools#2431. Reported by Jukka Matilainen)
S3 reading code now reads in chunks to limit the amount of data read (and therefore egress costs) from the object store when doing a range request. Also this combines the reading, writing and authorisation code into a single file. (PR #1958, fixes #1670. Reported by Stephan Drukewitz)

Build Changes

Change optimisation for -fsanitize=address,undefined test build to counter slow build and high compiler memory use. (PR #1924)
Fix compilation failure on MacOS X 10.9 (and likely other very old platforms). (PR #1945, fixes #1941. Reported by Ryan Carsten Schmidt)
Fix htslib.map update due to recent change in nm behaviour. (PR #1975, fixes #1971. Reported by John Marshall).
The htscodecs submodule is updated to v1.6.5. This includes a fix to the rANS encoder when running on x86-64 hardware with some SIMD features disabled. (Fixes samtools/samtools#2256. Reported by Ran Fan)

Bug fixes

Fix segfault on an empty valid MM tag. (PR #1939, fixes #1936. Reported by John Marshall)
Fix bam_next_basemod + HTS_MOD_REPORT_UNCHECKED flag. (PR #1946, fixes #1943)
For the VCF rlen calculation, only use SVLEN for DEL, DUP and CNV symbolic alleles. A bug is also fixed on big-endian platforms where INFO and FORMAT values were being accessed incorrectly. (PR #1942, fixes #1940)
Correct TLEN assignment in CRAM decode. Also improve decoder when dealing with multiple secondary alignments. See also samtools/hts-specs#842. (PR #1951, fixes #1948. Reported by Matt Sexton)
Make tabix skip comments (-c) wherever they occur, not just at the start of the file. (PR #1952, fixes #1950. Reported by Victor Negîrneac)
Update htscodecs for better AVX2 / AVX512 runtime detection. (PR #1954, fixes samtools/samtools#2256. Reported by Ran Fan)
Fix embed_ref=2 on SEQ * and MD:Z tag. The combination of no sequence and MD:Z with embed_ref=2 caused the slice extents to be miscalculated, causing invalid CRAM output to be written. (PR #1964, fixes samtools/samtools#2277. Reported by fo40225)
Try to ensure CSI indexes are built with valid parameters. Adjusts the min_shift and n_lvls to cover the size of the genome. This may override the user setting of min_shift (with warning) if needed. (PR #1968, fixes #1966. Reported by Marc Sturm)
Fix bug where multi-threaded CRAM iterators could drop long alignments starting significantly before, but overlapping, the region of interest. (PR #1973, fixes samtools/samtools#2285, Reported by Nick Owens)

Documentation updates

Added support information and samtools email for security issues. (PR #1956)
Fix spelling in function name in sam.h. (PR #1972. Thanks to Jack Turpitt)

Download the source code here: htslib-1.23.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

Updates

HTSlib 1.22 changed the VCF reader so that it stored GT prefixed phasing information, but only for files specifying fileformat=VCFv4.4 or higher. This caused problems when merging files with different versions, so the VCF reader will now store prefixed phasing information irrespective of the VCF version listed in the file headers. For files up to VCFv4.3, the first phasing bit will be set if all other alleles are phased, and cleared otherwise (following the rules for VCFv4.4 onwards where no explicit phasing symbol is present). This will also happen when reading BCF. When accessing GT data, it is no longer safe to assume that the phasing is set to zero even if the file reports a version earlier than VCFv4.4. Interfaces such as bcf_gt_allele() should always be used to access GT allele data. For compatibility, prefixed phasing will be stripped when writing VCF files with version 4.3 or earlier. (PR #1938, fixes #1932)

Add support for VCFv4.4 / VCFv4.5 "Number=" fields. (PR #1874)

Consolidate and simplify SAM header parsing. This considerably speeds up parsing files with many SQ lines. (PR #1947. PR #1953 fixes oss-fuzz issues 444492071, 444492076, 444547724, 444490034, PR #1977)

Switch from strtol to hts_str2uint in mod parsing for speed increase. (PR #1957. Thanks to Chris Wright)

Add UMI support to FASTQ input and output. See samtools/samtools#2270. (PR #1960, fixes samtools/samtools#2259. Requested by Poshi)

Removed direct access to htsFile struct members in some sample functions. (PR #1963, fixes #1961. Reported by John Marshall)

Improved operation of filters that work with header data. Filter expressions set as an HTS_OPT_FILTER on a BAM or CRAM iterator failed to return records matching on rname, mrname, rnext or library. (PR #1959)

Add Type to the INFO/FORMAT sanity check. This produces a warning on incorrect Type usage. (PR #1967, fixes #1937 and samtools/bcftools#2431. Reported by Jukka Matilainen)

S3 reading code now reads in chunks to limit the amount of data read (and therefore egress costs) from the object store when doing a range request. Also this combines the reading, writing and authorisation code into a single file. (PR #1958, fixes #1670. Reported by Stephan Drukewitz)

Build Changes

Change optimisation for -fsanitize=address,undefined test build to counter slow build and high compiler memory use. (PR #1924)

Fix compilation failure on MacOS X 10.9 (and likely other very old platforms). (PR #1945, fixes #1941. Reported by Ryan Carsten Schmidt)

Fix htslib.map update due to recent change in nm behaviour. (PR #1975, fixes #1971. Reported by John Marshall).

The htscodecs submodule is updated to v1.6.5. This includes a fix to the rANS encoder when running on x86-64 hardware with some SIMD features disabled. (Fixes samtools/samtools#2256. Reported by Ran Fan)

Bug fixes

Fix segfault on an empty valid MM tag. (PR #1939, fixes #1936. Reported by John Marshall)

Fix bam_next_basemod + HTS_MOD_REPORT_UNCHECKED flag. (PR #1946, fixes #1943)

For the VCF rlen calculation, only use SVLEN for DEL, DUP and CNV symbolic alleles. A bug is also fixed on big-endian platforms where INFO and FORMAT values were being accessed incorrectly. (PR #1942, fixes #1940)

Correct TLEN assignment in CRAM decode. Also improve decoder when dealing with multiple secondary alignments. See also samtools/hts-specs#842. (PR #1951, fixes #1948. Reported by Matt Sexton)

Make tabix skip comments (-c) wherever they occur, not just at the start of the file. (PR #1952, fixes #1950. Reported by Victor Negîrneac)

Update htscodecs for better AVX2 / AVX512 runtime detection. (PR #1954, fixes samtools/samtools#2256. Reported by Ran Fan)

Fix embed_ref=2 on SEQ * and MD:Z tag. The combination of no sequence and MD:Z with embed_ref=2 caused the slice extents to be miscalculated, causing invalid CRAM output to be written. (PR #1964, fixes samtools/samtools#2277. Reported by fo40225)

Try to ensure CSI indexes are built with valid parameters. Adjusts the min_shift and n_lvls to cover the size of the genome. This may override the user setting of min_shift (with warning) if needed. (PR #1968, fixes #1966. Reported by Marc Sturm)

Fix bug where multi-threaded CRAM iterators could drop long alignments starting significantly before, but overlapping, the region of interest. (PR #1973, fixes samtools/samtools#2285, Reported by Nick Owens)

Documentation updates

Added support information and samtools email for security issues. (PR #1956)

Fix spelling in function name in sam.h. (PR #1972. Thanks to Jack Turpitt)

Download the source code here: htslib-1.23.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

htslib

Updates

Build Changes

Bug fixes

Documentation updates

More C Projects

scrcpy

PowerToys

Ventoy

redis

1.23

Updates

Build Changes

Bug fixes

Documentation updates

More C Projects

scrcpy

PowerToys

Ventoy

redis