CVE-2026-31966HTSlib CRAM reader has out-of-bounds read due to improper validation of input

Official description

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding CRAM records, the reference data is stored in a char array, and parts matching the alignment record sequence are copied over as necessary. Due to insufficient validation of the feature data series, it was possible to make the `cram_decode_seq()` function copy data from either before the start, or after the end of the stored reference either into the buffer used to store the output sequence for the cram record, or into the buffer used to build the SAM `MD` tag. This allowed arbitrary data to be leaked to the calling function. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt to access invalid memory. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.

Affected packages & fixed versions

Affected products (as reported)

References

• https://github.com/samtools/htslib/security/advisories/GHSA-5cj8-mj52-8vp3 x_refsource_CONFIRM
• https://github.com/samtools/htslib/commit/22ec5230ef95769ab009420da69568c7e530af28 x_refsource_MISC
• https://github.com/samtools/htslib/commit/2a45eb129d703ad27f9fabc8169f0e94d3c69fa3 x_refsource_MISC
• https://github.com/samtools/htslib/commit/4a5ef25eb1fb3d64438103316fffe423b2c3f5f4 x_refsource_MISC