8000 Commits · jdblischak/htslib · GitHub

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Commits

Commits on Jul 8, 2024

Remove AppVeyor configuration
daviesrob
committed
Read whole lines at once in fai_retrieve()

jmarshall
authored and
whitwham
committed
Simplify SSSE3 nibble2base function

rhpvorderman
authored and
jkbonfield
committed
Speed up faidx.

jkbonfield
authored and
whitwham
committed

Commits on Jul 4, 2024

Update htscodecs to include github actions branch

jkbonfield
authored and
daviesrob
committed
Add Windows CI via github actions

jkbonfield
authored and
daviesrob
committed
Define HAVE_ATTRIBUTE_CONSTRUCTOR on ARM too for non-configure builds

jmarshall
authored and
jkbonfield
committed
Add ARM Neon nibble2base_neon() implementation

jmarshall
authored and
jkbonfield
committed
Add correctness and speed tests for nibble2base() routines

jmarshall
authored and
jkbonfield
committed
Minor improvements to Intel implementation

jmarshall
authored and
jkbonfield
committed
Move __attribute__((target)) check to configure too

jmarshall
authored and
jkbonfield
committed
Complete the refactoring of nibble2base_ssse3() as an ordinary source file

jmarshall
authored and
jkbonfield
committed
Move nibble2base_resolve() infrastructure to simd.c

daviesrob
authored and
jkbonfield
committed
Move nibble2base_ssse3() SIMD code to new simd.c source file

rhpvorderman
authored and
jkbonfield
committed

Commits on Jul 2, 2024

Protect against negative POS fields in CRAM encoder.
jkbonfield
committed

Commits on Jul 1, 2024

Fix a missing bgzf->uncompressed_address incr in bgzf_read_small
jkbonfield
committed

Commits on Jun 20, 2024

Replace assert(0) with abort()

mp15
authored and
pd3
committed

Commits on Jun 6, 2024

Add regression test for hts_itr_multi_next() OOB read

daviesrob
authored and
jkbonfield
committed
Fix possible out-of-bounds read in hts_itr_multi_next() (CRAM only)

daviesrob
authored and
jkbonfield
committed
Make BAM zero-length intervals work like CRAM

whitwham
authored and
daviesrob
committed

Commits on Jun 4, 2024

Commits on May 30, 2024

Avoid possible race when selecting nibble2base implementation

daviesrob
authored and
jkbonfield
committed

Commits on May 23, 2024

Warn if bgzf_getline() returned apparently UTF-16-encoded text

jmarshall
authored and
daviesrob
committed

Commits on May 20, 2024

Update htscodecs submodule to commit 5a2627e

daviesrob
authored and
whitwham
committed
Check that __builtin_cpu_supports("ssse3") works

daviesrob
authored and
whitwham
committed
Test for more avx512 functions

daviesrob
authored and
whitwham
committed
Add check for cpuid (for htscodecs)

daviesrob
authored and
whitwham
committed

Commits on May 9, 2024

Make sure `-h -1` does not loose the first line

pd3
authored and
whitwham
committed
Fix a memory leak

pd3
authored and
whitwham
committed
Extend annot-tsv, adding several new options

pd3
authored and
whitwham
committed
Use only _regions_add() when adding the list of contig names

jmarshall
authored and
jkbonfield
committed

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