HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. In the `cram_decode_slice()` function called while reading CRAM records, the value of the mate reference id field was not validated. Later use of this value, for example when converting the data to SAM format, could result in the out of bounds array reads when looking up the corresponding reference name. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. 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.
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History
Wed, 18 Mar 2026 20:15:00 +0000
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Wed, 18 Mar 2026 19:30:00 +0000
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| Description | HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. In the `cram_decode_slice()` function called while reading CRAM records, the value of the mate reference id field was not validated. Later use of this value, for example when converting the data to SAM format, could result in the out of bounds array reads when looking up the corresponding reference name. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. 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. | |
| Title | HTSlib CRAM reader has out-of-bounds read due to improper validation of input | |
| Weaknesses | CWE-125 CWE-129 |
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cvssV4_0
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Status: PUBLISHED
Assigner: GitHub_M
Published:
Updated: 2026-03-18T19:58:55.083Z
Reserved: 2026-03-10T15:40:10.485Z
Link: CVE-2026-31967
Updated: 2026-03-18T19:58:51.581Z
Status : Received
Published: 2026-03-18T20:16:21.280
Modified: 2026-03-18T20:16:21.280
Link: CVE-2026-31967
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OpenCVE Enrichment
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