updatehtslib against intel_mods#14

Draft

eneskuluk wants to merge 511 commits intointel_modsfrom

ek_updatehtslib

This pull request is big! We're only showing the most recent 250 commits

Commits on Feb 28, 2022

Adjusted types sam.h to avoid compiler warnings
ubuntolog
committed

Commits on Mar 1, 2022

Add stricter format string checking to a gcc CI build

daviesrob
authored and
whitwham
committed

Commits on Mar 22, 2022

Fix missing parameter in hts_log() calls
daviesrob
committed

Commits on Apr 1, 2022

Improve coordinate parsing, particularly with tabix. (PR #1411)
jkbonfield
authored
Detect and fix invalid Type=Flag && Number!=0 header definitions.

pd3
authored and
daviesrob
committed
Update to htscodecs v1.2.2
daviesrob
committed
Fix excessive memory used by multi-threaded SAM output on long reads.

jkbonfield
authored and
daviesrob
committed
Improve coordinate parsing, particularly with tabix. (PR #1411)

jkbonfield
authored and
daviesrob
committed
Detect and fix invalid Type=Flag && Number!=0 header definitions.

pd3
authored and
daviesrob
committed
Update to htscodecs v1.2.2
daviesrob
committed
NEWS updates
daviesrob
committed

Commits on Apr 5, 2022

Commits on Apr 7, 2022

Commits on Apr 13, 2022

Permit BAM headers between 2GB and 4GB in size once more.

jkbonfield
authored and
whitwham
committed
Permit MM tags containing "." and "?" suffixes.

jkbonfield
authored and
whitwham
committed

Commits on Apr 27, 2022

Commits on Apr 29, 2022

Improve support for MM .? modifiers.

jkbonfield
authored and
whitwham
committed

Commits on May 5, 2022

Switch cirrus ubuntu image to ubuntu:latest

daviesrob
authored and
jkbonfield
committed

Commits on May 18, 2022

Fix buffer overrun in bam_plp_insertion_mod.

jkbonfield
authored and
whitwham
committed

Commits on May 23, 2022

Ensure str_class is set before using it in bcf_hdr_get_hrec

daviesrob
authored and
jkbonfield
committed
Update htscodecs including associated Makefile changes

daviesrob
authored and
jkbonfield
committed
Add configure changes to enable htscodecs SIMD code

daviesrob
authored and
jkbonfield
committed
Make htscodecs SIMD code build without configure

daviesrob
authored and
jkbonfield
committed
Disable unaligned access in htscodecs if it is in HTSlib

daviesrob
authored and
jkbonfield
committed
Pull in extra htscodecs pointer aliasing fixes

daviesrob
authored and
jkbonfield
committed
Fix NEWS entry for function affected by realn_check_tag() fix
jmarshall
committed

Commits on May 25, 2022

Fix clang builds under mingw.

jkbonfield
authored and
daviesrob
committed

Commits on May 31, 2022

Fix curl type warning on Windows with gcc 12.1

daviesrob
authored and
jkbonfield
committed
Add an "sclen" expression keyword.
jkbonfield
committed

Commits on Jun 1, 2022

Add an embed_ref=2 mode which starts with ref=N and edits on the fly.

jkbonfield
authored and
whitwham
committed
Add a cF CRAM specific tag.

jkbonfield
authored and
whitwham
committed
Remove unneeded abort check in cram encoding.

jkbonfield
authored and
whitwham
committed

Commits on Jun 8, 2022

Remove limit on returned size from fai_retrieve()

daviesrob
authored and
whitwham
committed
Expose a bit more of the CRAM API.
jkbonfield
committed

Commits on Jun 9, 2022

CVE-2020-36403 affected all older versions of HTSlib

jmarshall
authored and
jkbonfield
committed

Commits on Jun 10, 2022

Cap hts_getline() return value at INT_MAX
jmarshall
committed

Commits on Jun 13, 2022

Detect ARM Neon support and only build appropriate SIMD object files

jmarshall
authored and
daviesrob
committed
Add an ARM CI test
daviesrob
committed

Commits on Jun 21, 2022

Fix breakend detection and test bcf_set_variant_type (PR #1456)
mp15
authored

Commits on Jul 1, 2022

Don't use `register` in public header file
jmarshall
committed

Commits on Jul 4, 2022

Set tab delimiter in manpage for tabix GFF3 sort (PR #1457)
cmdcolin
authored

Commits on Jul 6, 2022

Improve error message when failing to load an index.
jkbonfield
committed

Commits on Jul 7, 2022

Make hfile_s3 refresh AWS credentials on expiry

daviesrob
authored and
whitwham
committed

Commits on Jul 8, 2022

Further improve MM tag consistency checking.

jkbonfield
authored and
daviesrob
committed

Commits on Jul 14, 2022

Fix and_expr expression bug

daviesrob
authored and
jkbonfield
committed
Add truth checks to test_expr, and test empty-but-true strings

daviesrob
authored and
jkbonfield
committed
Fix unary-not on null strings in expressions

daviesrob
authored and
jkbonfield
committed
Set hts_filter_t::is_true in mul_expr() and add_expr()

daviesrob
authored and
jkbonfield
committed
Ensure is_true is propagated for null-but-true in expressions

daviesrob
authored and
jkbonfield
committed
Deprecate hts_filter_eval() in favour of hts_filter_eval2().

daviesrob
authored and
jkbonfield
committed

Commits on Jul 18, 2022

Switch to rockylinux:9

daviesrob
authored and
whitwham
committed

Commits on Jul 19, 2022

Commits on Jul 20, 2022

Support 0 coordinate in BCF
pd3
committed

Commits on Jul 21, 2022

Minimal support for CRAM files with missing @RG headers.
jkbonfield
committed

Commits on Jul 27, 2022

Fix (un)locking bug introduced in commit 9562aeba

daviesrob
authored and
whitwham
committed
Fix leak of MD5 context when entering embed_ref=2 mode

daviesrob
authored and
whitwham
committed
Add an embed_ref=2 auto-mode test

daviesrob
authored and
whitwham
committed

Commits on Jul 29, 2022

Report HTS_CFLAGS_AVX2 et al in `make print-config`
jmarshall
committed
Summer 2022 copyright corrections.

whitwham
authored and
daviesrob
committed

Commits on Aug 1, 2022

Add a mapping of Zlib to Libdeflate compression levels for BGZF.
jkbonfield
committed

Commits on Aug 2, 2022

Catch arrays of BCF_BT_NULL in bcf_record_check()

daviesrob
authored and
whitwham
committed

Commits on Aug 8, 2022

Sanitize the 3-state logic for hts_expr_t, plus added some functions.
jkbonfield
committed

Commits on Aug 9, 2022

Update to htscodecs 1.3.0

daviesrob
authored and
jkbonfield
committed

Commits on Aug 10, 2022

Commits on Aug 11, 2022

Extend VCF API to distinguish between INS and DEL variant types

pd3
authored and
jkbonfield
committed
Make values returned by bcf_get_variant_type[s] backward compatible

pd3
authored and
jkbonfield
committed
Adjust new variant type interfaces

daviesrob
authored and
jkbonfield
committed

Commits on Aug 12, 2022

Commits on Aug 15, 2022

Fix clang builds on Windows/mingw.
jkbonfield
committed
Implement endianness conversion in bcf_format_gt()

jmarshall
authored and
daviesrob
committed

Commits on Aug 16, 2022

Commits on Aug 17, 2022

Improve SIMD detection

daviesrob
authored and
jkbonfield
committed
Silence some overflow warnings on i686

daviesrob
authored and
jkbonfield
committed
Silence a gcc-10 format-truncation warning.

daviesrob
authored and
jkbonfield
committed
Fix newer clang warning of unused variable.

jkbonfield
authored and
daviesrob
committed
Add some more NEWS updates.

daviesrob
authored and
jkbonfield
committed

Commits on Aug 18, 2022

Commits on Aug 19, 2022

Update man SEE ALSO sections from .BR to .IR so the website uses URLs
jkbonfield
committed

Commits on Aug 24, 2022

Fix n-squared complexity in sample line with many adjacent tabs

daviesrob
authored and
whitwham
committed

Commits on Aug 30, 2022

Add bam_aux_first()/bam_aux_next() tagged aux field iterator API

jmarshall
authored and
jkbonfield
committed
Document that bam_aux_del()'s `s` parameter must be non-NULL (& reformat)

jmarshall
authored and
jkbonfield
committed

Commits on Sep 1, 2022

bgzip text compression mode

jkbonfield
authored and
whitwham
committed
Make the bgzip -g option less opaque.

jkbonfield
authored and
whitwham
committed

Commits on Sep 2, 2022

Commits on Sep 9, 2022

Make tabix support CSI indices with large positions.
jkbonfield
committed

Commits on Sep 15, 2022

Prevent crash when only FASTA entry has no sequence.
jkbonfield
committed

Commits on Sep 22, 2022

Use POSIX `grep`

SoapGentoo
authored and
whitwham
committed

Commits on Oct 12, 2022

Switch to building libdeflate with cmake

daviesrob
authored and
whitwham
committed

Commits on Oct 14, 2022

Fix a typo in sam.h documentation

kojix2
authored and
jkbonfield
committed

Commits on Oct 18, 2022

Adds bcf_strerror method (PR #1510)
vasudeva8
authored

Commits on Oct 20, 2022

Add an fai_line_length function.
jkbonfield
committed

Commits on Oct 25, 2022

Check for invalid BC tags in fastq output.

jkbonfield
authored and
daviesrob
committed

Commits on Oct 31, 2022

Warn if ref file is given but it doesn't contain the refs we need.

jkbonfield
authored and
whitwham
committed

Commits on Nov 3, 2022

Fix buffer read-overrun in bam_plp_insertion_mod.

jkbonfield
authored and
daviesrob
committed
Fix ref fix from c91804c
jkbonfield
committed

Commits on Nov 9, 2022

Add faidx_seq_len64() and fai_adjust_region() interfaces

daviesrob
authored and
whitwham
committed
Rework / add new faidx tests

daviesrob
authored and
whitwham
committed

Commits on Nov 28, 2022

Fix build on ancient versions of gcc

daviesrob
authored and
whitwham
committed

Commits on Dec 5, 2022

Ensure strings in config_vars.h are escaped correctly

daviesrob
authored and
jkbonfield
committed

Commits on Dec 6, 2022

Make it easier to modify shared library permissions during install

jkbonfield
authored and
daviesrob
committed

Commits on Dec 13, 2022

Switch MacOS CI tests to an ARM-based image

daviesrob
authored and
jkbonfield
committed

Commits on Dec 14, 2022

Remove variable redeclaration warnings from perl test script

pd3
authored and
daviesrob
committed
Make bcf_hdr_seqnames() work with gapped chromosome ids

pd3
authored and
daviesrob
committed

Commits on Dec 15, 2022

Cut down the number of embed_ref=2 tests that get run

daviesrob
authored and
jkbonfield
committed
draft fix

bir3
authored and
whitwham
committed
fix memory leak

bir3
authored and
whitwham
committed
exit early on error

bir3
authored and
whitwham
committed

Commits on Jan 9, 2023

Make bcf_hdr_idinfo_exists() more robust
pd3
committed

Commits on Jan 13, 2023

Add CRAM SQ/M5 header checking when specifying a fasta file. (PR #1522)
jkbonfield
authored

Commits on Jan 16, 2023

Cap bgzf_getline return value to INT_MAX

daviesrob
authored and
whitwham
committed
Make tbx_parse1 work for lines longer than 2Gbytes

daviesrob
authored and
whitwham
committed
Use correct type for ret in vcf_write()

daviesrob
authored and
whitwham
committed
Don't error when making an iterator on a tid not in the index

daviesrob
authored and
jkbonfield
committed

Commits on Jan 17, 2023

Happy New Year

daviesrob
authored and
jkbonfield
committed

Commits on Jan 19, 2023

Speed up load_ref_portion.

jkbonfield
authored and
daviesrob
committed

Commits on Jan 20, 2023

Expand CRAM API a bit to cope with new samtools cram_size command. (PR #1546)
jkbonfield
authored

Commits on Jan 24, 2023

Commits on Jan 31, 2023

Catch errors from bgzf_getline() in hts_readlist, hts_readlines

daviesrob
authored and
whitwham
committed

Commits on Feb 6, 2023

FIx a bug in the codec learning algorithm for TOKA

jkbonfield
authored and
daviesrob
committed
Remove a bottleneck in VCF header processing

pd3
authored and
jkbonfield
committed

Commits on Feb 8, 2023

Commits on Feb 14, 2023

Fix Cram compression container substitution matrix generation.

jkbonfield
authored and
daviesrob
committed
Tweak the CRAM_SUBST_MATRIX table.

jkbonfield
authored and
daviesrob
committed

Commits on Feb 15, 2023

Update to htscodecs v1.4.0
daviesrob
committed

Commits on Feb 16, 2023

January 2023 NEWS update.

whitwham
authored and
jkbonfield
committed
Keeping the NEWS file up-to-date.

whitwham
authored and
jkbonfield
committed
More additions and improvements.

whitwham
authored and
jkbonfield
committed
Added htscodecs update to v1.4.0

whitwham
authored and
jkbonfield
committed
More space.

whitwham
authored and
jkbonfield
committed

Commits on Feb 17, 2023

Prevent spurious and random system errors from test_bgzf.c

jkbonfield
authored and
whitwham
committed

Commits on Feb 20, 2023

Minor NEWS adjustment and additonal item

daviesrob
authored and
whitwham
committed

Commits on Feb 21, 2023

Commits on Mar 1, 2023

Switch to CURLINFO_CONTENT_LENGTH_DOWNLOAD_T for newer libcurl

daviesrob
authored and
whitwham
committed

Commits on Mar 2, 2023

Check if VCF POS column could be fully parsed

pd3
and
daviesrob
committed

Commits on Mar 6, 2023

Fix cram_index_query_last function

jkbonfield
authored and
daviesrob
committed
Avoid deeply nested containment list on old CRAM indices.

jkbonfield
authored and
daviesrob
committed

Commits on Mar 7, 2023

Fix crypt4gh redirection

daviesrob
authored and
jkbonfield
committed

Commits on Mar 8, 2023

Permit fastq output to create empty FASTQ records for seq "*".

jkbonfield
authored and
daviesrob
committed

Commits on Mar 13, 2023

Fix a couple small VCF auto-indexing bugs.

jkbonfield
authored and
daviesrob
committed
Backport attractivechaos/klib#78 to htslib.

authored and
daviesrob
committed

Commits on Mar 15, 2023

Slightly speed up various cram decoding functions (#1580)
jkbonfield
authored

Commits on Mar 21, 2023

Remove CRAM 3.1 warning.

jkbonfield
authored and
daviesrob
committed

Commits on Mar 30, 2023

Remove use of sprintf() from HTSlib source

daviesrob
authored and
jkbonfield
committed
Trivial fix to expr, removing "^".

jkbonfield
authored and
daviesrob
committed

Commits on Mar 31, 2023

Make SIMD tests work when building multiarch binaries

daviesrob
authored and
whitwham
committed
Make MacOS tests build a multiarch version of the library

daviesrob
authored and
whitwham
committed

Commits on Apr 5, 2023

Fix bug where bin number could overflow when looking for max_off

daviesrob
authored and
jkbonfield
committed

Commits on Apr 6, 2023

Add MZ:i tag as a check for base modification validity. (#1590)
jkbonfield
authored

Commits on Apr 13, 2023

Make reg2bins faster on whole-chromosome queries

daviesrob
authored and
jkbonfield
committed
Make reg2intervals() faster on whole-chromosome queries

daviesrob
authored and
jkbonfield
committed

Commits on Apr 18, 2023

Fix typo in kh_int_hash_func2 macro.

jkbonfield
authored and
daviesrob
committed

Commits on Apr 27, 2023

Switched back to openssl for Alpine.
whitwham
committed

Commits on May 1, 2023

Mention in INSTALL that using plugins may need -rdynamic
jmarshall
committed

Commits on May 8, 2023

Fix example in docs for sam_hdr_add_line
kojix2
authored

Commits on May 9, 2023

Rename aux tag MZ to MN.

jkbonfield
authored and
whitwham
committed

Commits on May 11, 2023

Protect against overly large containers.

jkbonfield
authored and
daviesrob
committed
Don't create overly large CRAM blocks.

jkbonfield
authored and
daviesrob
committed

Commits on May 15, 2023

Add a missing break statement in cram_codec_to_id. (#1614)
jkbonfield
authored

Commits on May 16, 2023

Fix fd_seek on pipes on modern MinGW releases.

authored and
daviesrob
committed

Commits on May 23, 2023

Amalgamate multiple CIGAR ops into single entry. (#1607)
whitwham
authored

Commits on Jun 6, 2023

Update to latest htscodecs

daviesrob
authored and
jkbonfield
committed
Don't set _POSIX_C_SOURCE for htscodecs tests

daviesrob
authored and
jkbonfield
committed
Set _XOPEN_SOURCE in configure if it's not already set

authored and
jkbonfield
committed
Fix trailing space in config.h made by configure

daviesrob
authored and
jkbonfield
committed
Ignore generated config_vars.h file in copyright check

daviesrob
authored and
jkbonfield
committed
Switch to `/usr/bin/env perl` for all perl scripts

daviesrob
authored and
jkbonfield
committed
Stop the overwriting of the end value.

whitwham
authored and
jkbonfield
committed

Commits on Jun 9, 2023

Commits on Jun 11, 2023

cram/cram_external.c: fix external htscodecs include
emollier
committed

Commits on Jun 21, 2023

htslib-s3-plugin.7: fix whatis entry

emollier
authored and
whitwham
committed
Allow repeated calls of bcf_sr_set_regions (PR #1624)
pd3
authored

Commits on Jun 27, 2023

Change bounds checking in probaln_glocal

jkbonfield
authored and
daviesrob
committed
Adjust comments in probaln_glocal()
daviesrob
committed
Add support for non-standard chromosome names containing [:-] characters

pd3
authored and
jkbonfield
committed
An attempt to parse malformatted region such as {1:1}-2 should fail

pd3
authored and
jkbonfield
committed
Expand test-bcf-sr.c capabilities

daviesrob
authored and
jkbonfield
committed
Add synced reader region tests, and move no-index tests

authored and
jkbonfield
committed

Commits on Jul 6, 2023

Fix a containment bug in cram_index_last.
jkbonfield
committed

Commits on Jul 10, 2023

Migrate base modification code out of sam.c

jkbonfield
authored and
whitwham
committed
Correct base modification implicit / explicit status when mixed together.

jkbonfield
authored and
whitwham
committed
Add a bam_mods_queryi interface.

jkbonfield
authored and
whitwham
committed
Add bam_parse_basemod2 API with additional flags argument.

jkbonfield
authored and
whitwham
committed
Add more internal sam_mods.c documentation

jkbonfield
authored and
whitwham
committed
Update bam_next_basemod too to cope with HTS_MOD_REPORT_UNCHECKED.

jkbonfield
authored and
whitwham
committed

Commits on Jul 13, 2023

Commits on Jul 14, 2023

Ensure number of modifications is always set in bam_parse_basemod2()

daviesrob
authored and
jkbonfield
committed

Commits on Jul 18, 2023

Fix to 2e672f33 decompress_peek_gz change.

jkbonfield
authored and
daviesrob
committed

Commits on Jul 19, 2023

Ensure simple_test_driver.sh cleans up its temporary files

daviesrob
authored and
jkbonfield
committed
Ensure base mod test result is noticed by the Makefile

daviesrob
authored and
jkbonfield
committed
Improve test/test_mod.c

daviesrob
authored and
jkbonfield
committed
Add missing Makefile dependencies [minor]

jmarshall
authored and
jkbonfield
committed
Make last_in a pointer to const [minor]

jmarshall
authored and
jkbonfield
committed

Commits on Jul 20, 2023

Switch to htscodecs 1.5.1

daviesrob
authored and
jkbonfield
committed
Add fai_thread_pool interface.

jkbonfield
authored and
whitwham
committed
Summer 2023 copyright update.
whitwham
committed

Commits on Jul 21, 2023

Demonstration of htslib/sam api usage.

vasudeva8
authored and
jkbonfield
committed
NEWS updates for pending release

jkbonfield
and
daviesrob
committed
formatting update

vasudeva8
authored and
jkbonfield
committed

Commits on Jul 25, 2023

Commits on Jul 31, 2023

Makes bam_parse_cigar able to modify existing BAM records rather than

jkbonfield
authored and
whitwham
committed
Fix cut and paste errors in bam_aux2f documentation

jkbonfield
authored and
whitwham
committed
Add "uncompressed" in hts_format_description() where appropriate

jmarshall
authored and
whitwham
committed

Commits on Aug 7, 2023

Commits on Aug 9, 2023

Revert most of the vcf_parse_info improvements.
jkbonfield
committed

Commits on Aug 15, 2023

Add an hclen SAM filter function.

jkbonfield
authored and
daviesrob
committed

Commits on Aug 16, 2023

Speed up removal of lines in large headers.

whitwham
authored and
jkbonfield
committed

Commits on Aug 25, 2023

Skip CRC checks when fuzzing

daviesrob
authored and
whitwham
committed
Prevent out-of-memory reports when fuzzing

daviesrob
authored and
whitwham
committed
Add missing dependency on libhts.a for hts_open_fuzzer

daviesrob
authored and
whitwham
committed
Apply the packed attribute to uint*_u types for Clang

MaskRay
authored and
daviesrob
committed

Commits on Aug 28, 2023

Commits on Aug 31, 2023

Add hclose()-doesn't-close-fd option and use it for hopen("-")

jmarshall
authored and
jkbonfield
committed
Take advantage of shared hopen("-") in htsfile.c

jmarshall
authored and
jkbonfield
committed
Explicitly fclose(stdout) in test/test_view.c too

jmarshall
authored and
jkbonfield
committed

Commits on Sep 1, 2023

bgzf_useek fails when offset is above block limits

vasudeva8
authored and
whitwham
committed

Commits on Sep 13, 2023

Fix a minor memory leak in malformed CRAM EXTERNAL blocks. (#1671)
jkbonfield
authored

Commits on Sep 14, 2023

Add support for multiple files to bgzip

vasudeva8
authored and
jkbonfield
committed

Commits on Sep 15, 2023

Enable auto-vectorisation in CRAM 3.1 codecs.

jkbonfield
authored and
whitwham
committed

Commits on Sep 18, 2023

Merge branch 'masterpull' into ek_updatehtslib
eneskuluk
committed

Commits on Sep 22, 2023

revert precision change and minor fix in faidx.c
eneskuluk
committed

Commits on Sep 25, 2023

address some of the comments
eneskuluk
committed