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Commits on May 13, 2026

• Add a CONTRIBUTING file

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  jkbonfield

  committed
  6bb8f7e

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Commits on May 11, 2026

• Clarify how defaults work when building an index with tabix (#2002)

  daviesrob

  authored
  336c98a

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Commits on May 7, 2026

• Remove some unused variables.

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  jkbonfield

  committed
  7c89556

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• Upgrade htscodecs to remove an unused variable

  jkbonfield

  committed
  96d1b38

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Commits on Apr 30, 2026

• Add Github actions builds for Linux and Mac OS

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  daviesrob

  authored and

  jkbonfield

  committed
  2b3ddfd

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Commits on Apr 20, 2026

• Improve SQ LN field checking.

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  jkbonfield

  authored and

  daviesrob

  committed
  63076c5

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• Fix extend_ref to not change ref_end on error.

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  jkbonfield

  authored and

  daviesrob

  committed
  5298117

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Commits on Apr 13, 2026

• Ensure indirect function calls have the correct type.

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  daviesrob

  authored and

  jkbonfield

  committed
  cb88c90

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Commits on Apr 2, 2026

• Merge CRAM explicit tlen and ref_end fixes

  daviesrob

  committed
  bf93316

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• Rename arguments for extend_ref().

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  jkbonfield

  committed
  5bd8e0a

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Commits on Mar 26, 2026

• Fix c->ref_end for embedded references.

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  jkbonfield

  committed
  37f5522

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• Move misplaced NULL pointer checks

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  daviesrob

  authored and

  jkbonfield

  committed
  b13f80a

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• Fix CRAM v4.0 CRAM_FLAG_EXPLICIT_TLEN usage

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  jkbonfield

  committed
  7f7e830

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Commits on Mar 18, 2026

• Merge version number bump and NEWS file from master

  daviesrob

  committed
  b8863d7

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• Release 1.23.1

  daviesrob

  committed
  d1a2a87

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Commits on Mar 16, 2026

• Update NEWS for point release

  daviesrob

  committed
  81fb71c

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Commits on Mar 13, 2026

• Move flags test in overlap_remove() (#1990)

  daviesrob

  authored
  4f08744

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• Add autoconf check for __builtin_prefetch

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  jkbonfield

  authored and

  daviesrob

  committed
  eaa17b6

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• added prefetch and minor updates to speedup pileup

  

  vasudeva8

  authored and

  daviesrob

  committed
  3675e19

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• Add HTTP/2 error codes to retryable errors

  

  Giles Hall

  authored and

  whitwham

  committed
  e805d40

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• Log error when hts_close() fails in synced reader cleanup

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  Giles Hall

  authored and

  whitwham

  committed
  6e5a94b

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• Update copyright to Broad Institute for new test files

  

  vishnubob

  authored and

  whitwham

  committed
  ec00958

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• Skip libcurl retry tests on Windows

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  vishnubob

  authored and

  whitwham

  committed
  2c988ce

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• Add test/test_hfile_libcurl to .gitignore

  

  vishnubob

  authored and

  whitwham

  committed
  87b8e8d

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• Fix HTTP support probe to check EPROTONOSUPPORT

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  vishnubob

  authored and

  whitwham

  committed
  0398ab5

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• Fix warn_unused_result errors for hclose() in tests

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  vishnubob

  authored and

  whitwham

  committed
  390f69c

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• Fix usleep() implicit declaration on Linux

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  vishnubob

  authored and

  whitwham

  committed
  3c395b4

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• Add retry/resilience to libcurl HTTP backend

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  vishnubob

  authored and

  whitwham

  committed
  6127026

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Commits on Mar 12, 2026

• Reject CRAM blocks with an unknown compression method.

  daviesrob

  committed
  654a04a

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• Fix codecs that did not correctly handle out == NULL

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  daviesrob

  committed
  e64e68d

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• Improve handling of records where sequence was not present

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  daviesrob

  committed
  d799b54

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• Reject cram files with negative-length D, H, P or N features

  daviesrob

  committed
  2a45eb1

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• Improve check for cram features beyond the end of the sequence

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  daviesrob

  committed
  8bcc990

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• Fix checks for CRAM features accessing data beyond ref_end

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  daviesrob

  committed
  22ec523

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• Catch cram records that start before the current reference segment

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  jkbonfield

  authored and

  daviesrob

  committed
  4a5ef25

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