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samtools / htslib Public

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Fork 461
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Improve CRAM reader input validation#1991

Merged

daviesrob merged 10 commits intosamtools:developsamtools/htslib:developfrom

daviesrob:cram-workdaviesrob/htslib:cram-workCopy head branch name to clipboard

Mar 18, 2026

Conversation Commits10 (10)Checks Files changed

Merged

Improve CRAM reader input validation#1991
daviesrob merged 10 commits intosamtools:developfrom
daviesrob:cram-work

Commits

Commits on Mar 12, 2026

Fix byte_array_stop out-of-data checks
daviesrob
committed
Improve option checking for varint and const codecs
daviesrob
committed
Add more checks for valid CRAM ref id and mate ref id
daviesrob
committed
Catch cram records that start before the current reference segment

jkbonfield
authored and
daviesrob
committed
Fix checks for CRAM features accessing data beyond ref_end
daviesrob
committed
Improve check for cram features beyond the end of the sequence
daviesrob
committed
Reject cram files with negative-length D, H, P or N features
daviesrob
committed
Improve handling of records where sequence was not present
daviesrob
committed
Fix codecs that did not correctly handle out == NULL
daviesrob
committed
Reject CRAM blocks with an unknown compression method.
daviesrob
committed

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