8000 Commits · retestpop/htslib · GitHub

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Commits

Commits on Jan 4, 2022

Make repeated seeks possible

pd3
authored and
daviesrob
committed

Commits on Dec 14, 2021

Make public API `-Wdouble-promotion` clean

SoapGentoo
authored and
jkbonfield
committed

Commits on Nov 17, 2021

Add pathA##idx##pathB support for CRAM indices.
jkbonfield
committed

Commits on Nov 12, 2021

Fix indexing bug with "placed" unmapped reads.

jkbonfield
authored and
daviesrob
committed

Commits on Nov 10, 2021

Make bcf_remove_allele_set() set work on unpacked records (#1358)
pd3
authored
Update to latest htscodecs

daviesrob
authored and
jkbonfield
committed

Commits on Nov 9, 2021

Update cirrus-ci macos from Catalina to Monterey.
jkbonfield
committed

Commits on Nov 3, 2021

Add hts_detect_format2() that also considers filename extensions

jmarshall
authored and
whitwham
committed

Commits on Nov 2, 2021

Fill in cr->rg when writing CRAM v1

jmarshall
authored and
jkbonfield
committed

Commits on Oct 22, 2021

Commits on Oct 15, 2021

Resolve icc 2021 warning about HTS_DEPRECATED_ENUM.
jkbonfield
committed

Commits on Oct 12, 2021

NEWS updates for autumn 2021 release

daviesrob
authored and
whitwham
committed

Commits on Oct 7, 2021

Print diagnostic for SAM input corrupted by aligner log messages

jmarshall
authored and
jkbonfield
committed
Autumn 2021 Release Copyright Update

whitwham
authored and
daviesrob
committed
Add the new field as integer, not as bit field

pd3
authored and
whitwham
committed

Commits on Oct 6, 2021

Fix a filter expression bug for flag.read2

jkbonfield
authored and
whitwham
committed
Add basic recognition of D4 quantitative interval format

jmarshall
authored and
jkbonfield
committed
Fix lzma_mem_inflate() error handling memory leak

jmarshall
authored and
jkbonfield
committed
Partially recognise XZ- and Zstd-compressed data

jmarshall
authored and
jkbonfield
committed
Ensure decompress_peek() errors are propagated

jmarshall
authored and
jkbonfield
committed

Commits on Sep 29, 2021

Warn if spaces instead of tabs are detected to prevent confusion such as in https://github.com/samtools/bcftools/issues/1575

pd3
authored and
jkbonfield
committed

Commits on Sep 27, 2021

Fix clang-13 unused variable messages.
whitwham
committed

Commits on Sep 23, 2021

Add the ability to handle no credentials.

whitwham
authored and
daviesrob
committed

Commits on Sep 22, 2021

Add fastq_name2 option tests
daviesrob
committed
Add FASTQ_OPT_NAME2 option for parsing of SRA data.

jkbonfield
authored and
daviesrob
committed

Commits on Sep 9, 2021

Look for untracked files in CI builds

daviesrob
authored and
whitwham
committed
Make version.sh work on shallow git checkouts.

daviesrob
authored and
whitwham
committed
Finer control of --regions vs --targets overlap

pd3
authored and
whitwham
committed

Commits on Sep 1, 2021

Add hts_flush() to flush buffered htsFile output data
jmarshall
committed

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