Commits

Branch selector

 develop

User selector

All users

All time

Commit History

Commits on Jun 6, 2024

• Add regression test for hts_itr_multi_next() OOB read

  

  daviesrob

  authored and

  jkbonfield

  committedJun 6, 2024
  5f20533

• Fix possible out-of-bounds read in hts_itr_multi_next() (CRAM only)

  

  daviesrob

  authored and

  jkbonfield

  committedJun 6, 2024
  356bfd6

• Make BAM zero-length intervals work like CRAM

  

  whitwham

  authored and

  daviesrob

  committedJun 6, 2024
  1c8c335

Commits on Jun 4, 2024

• Add tests for BAM alignment records that span BGZF blocks

  daviesrob

  committedJun 4, 2024
  11205a9

• Changes from review

  

  jkbonfield

  authored and

  daviesrob

  committedJun 4, 2024
  db34f68

• Add a bgzf_write_small function for optimising small writes.

  

  jkbonfield

  authored and

  daviesrob

  committedJun 4, 2024
  ee9a36f

• A few speed ups for bam_read1.

  

  jkbonfield

  authored and

  daviesrob

  committedJun 4, 2024
  68564b0

• Add an inline version of bgzf_read for small reads.

  

  jkbonfield

  authored and

  daviesrob

  committedJun 4, 2024
  60d7aab

Commits on May 30, 2024

• Avoid possible race when selecting nibble2base implementation

  

  daviesrob

  authored and

  jkbonfield

  committedMay 30, 2024
  5d31868

Commits on May 23, 2024

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

  

  jmarshall

  authored and

  daviesrob

  committedMay 23, 2024
  30c9c50

Commits on May 20, 2024

• Update htscodecs submodule to commit 5a2627e

  

  daviesrob

  authored and

  whitwham

  committedMay 20, 2024
  6b0a9e9

• Check that __builtin_cpu_supports("ssse3") works

  

  daviesrob

  authored and

  whitwham

  committedMay 20, 2024
  58ef9ec

• Test for more avx512 functions

  

  daviesrob

  authored and

  whitwham

  committedMay 20, 2024
  75767a3

• Add check for cpuid (for htscodecs)

  

  daviesrob

  authored and

  whitwham

  committedMay 20, 2024
  667f14f

Commits on May 9, 2024

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

  

  pd3

  authored and

  whitwham

  committedMay 9, 2024
  b204d55

• Fix a memory leak

  

  pd3

  authored and

  whitwham

  committedMay 9, 2024
  80bf6b8

• Extend annot-tsv, adding several new options

  

  pd3

  authored and

  whitwham

  committedMay 9, 2024
  02853a9

• Use only _regions_add() when adding the list of contig names

  

  jmarshall

  authored and

  jkbonfield

  committedMay 9, 2024
  9ad8270

• Improve compiler compatibility of nibble2base_ssse3

  

  rhpvorderman

  authored and

  jkbonfield

  committedMay 9, 2024
  292a35d

• Make a dynamic dispatcher function for nibble2base

  

  rhpvorderman

  authored and

  jkbonfield

  committedMay 9, 2024
  1b1b8ae

• Enable SSSE3 intrinsics for nibble parsing

  

  rhpvorderman

  authored and

  jkbonfield

  committedMay 9, 2024
  0f5719a

Commits on May 3, 2024

• Provide extra CRAM container manipulations and index queries.

  

  jkbonfield

  authored and

  whitwham

  committedMay 3, 2024
  7576aca

• Fix cram_index_query to iterate correct for ref HTS_IDX_NOCOOR.

  

  jkbonfield

  authored and

  whitwham

  committedMay 3, 2024
  ab7c09f

Commits on May 2, 2024

• Check interval start to avoid overflowing bin numbers

  

  jmarshall

  authored and

  jkbonfield

  committedMay 2, 2024
  9a99a1d

• fix fuzz integer overflow in cram encoder.

  

  jkbonfield

  authored and

  daviesrob

  committedMay 2, 2024
  1e7efc0

Commits on Apr 30, 2024

• Update htscodecs version to fix compiler void pedantry.

  jkbonfield

  committedApr 30, 2024
  c93f5a5

Commits on Apr 29, 2024

• Move address sanitizer from clang-latest to gcc-latest.

  jkbonfield

  committedApr 29, 2024
  850dc64

• Fix new clang -std=c99 -pedantic warnings about func()

  jkbonfield

  committedApr 29, 2024
  94c3c82

Commits on Apr 15, 2024

• Merge version number bump and NEWS file from master

  daviesrob

  committedApr 15, 2024
  deeb9f0

• Release 1.20

  daviesrob

  committedApr 15, 2024
  0cadce2

Commits on Apr 12, 2024

• Further recommend use of libdeflate and list OS packages

  

  jkbonfield

  authored and

  daviesrob

  committedApr 12, 2024
  a67b53c

Commits on Apr 11, 2024

• Add NEWS ready for 1.20 release

  

  daviesrob

  authored and

  whitwham

  committedApr 11, 2024
  1cdc798

Commits on Apr 5, 2024

• Spring 2024 copyright update.

  whitwham

  committedApr 5, 2024
  0cc34b3

Commits on Mar 27, 2024

• Ensure S3 redirects use TLS

  

  daviesrob

  authored and

  whitwham

  committedMar 27, 2024
  c1247f9

Commits on Mar 26, 2024

• Drop duplicate tbx_conf_t

  

  adamnovak

  authored and

  whitwham

  committedMar 26, 2024
  3cfe876

Pagination

PreviousNext