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Parallel cram2bam - #2015

Merged

daviesrob merged 8 commits into

samtools:developfrom

jkbonfield:parallel-cram2bam

Jun 3, 2026

Commits on Jun 2, 2026
- WIP: bulk decode CRAM to BAM when threading.
  jkbonfield
  committed
  6db85d8
- Improve CRAM decode thread speed further
  jkbonfield
  committed
  1e5905e
- Further CRAM encode/decode bam-list work.
  jkbonfield
  committed
  4b8efa3
- Replace CRAM's bam_init1 with bam->data alloc.
  jkbonfield
  committed
  ab10e11
- Remove the bam_size call in bulk_cram_to_bam.
  jkbonfield
  committed
  438f7e4
- Replace rallocs with hts_realloc_p
  jkbonfield
  committed
  8c6a406
- Export bam_tag2cigar from sam.c and call direct from the CRAM decoder.
  jkbonfield
  committed
  4bfe6f6
- Remove some memory leaks (on realloc failure).
  jkbonfield
  committed
  2b6ddeb