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@tfenne tfenne released this 03 Oct 01:34
· 151 commits to master since this release
5.0.2
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htsjdk 5.0.2 Release Notes

A patch release on the 5.0 line that fixes CRAM reference lookups when a ReferenceSource is shared between threads. It is a drop-in replacement for 5.0.1: there is no API change.

🐛 Bug fixes

  • A CRAM ReferenceSource shared between threads no longer returns another contig's bases (#1643). It cached the most recent contig's bases and that contig's index in two fields, written without a lock from getReferenceBasesByRegion, so two threads asking for different contigs could leave one contig's bases labelled as the other's. The pair is now published as one immutable object, so a caller can no longer silently get the wrong reference bases and encode or decode CRAM records against them (#1868, a backport of #1792).

📥 How to upgrade

Change the version from 5.0.1 to 5.0.2. Nothing else is needed.

Full Changelog: 5.0.1...5.0.2

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