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osteosarc 0.14.4

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@iskandr iskandr released this 28 Sep 08:38
· 12 commits to main since this release
709cc0b

openvax-v2, the next bundle of reads the OpenVax libraries share (#71, #88); the data is the openvax-v2 release. See shared test data.

  • It has openvax-v1's 993 members, the libraries' 429 record for record, and leaves out mates with no position of their own (116 records, none of them the libraries'), so it rebuilds without reading any BAM's unplaced reads.
  • The reads it keeps bring their split alignments: 14 more records that their SA tags name. An alignment in a pileup, with more than 10,000 records at its first base, is left out.
  • SV targets say which side of each breakend they keep, where that's known, and any sequence inserted at the junction. ATP5MG--KMT2A, FOXO3--STRADA-CCDC47 and TPST1--CRCP now give theirs, and DLG5's deletion is at the junction esvee resolved, with its 24-base insertion.
  • Carrying a bundle's library records forward keeps a source's mates with no position only if one of those records lacks a position.
  • Reading past max_records, or a recovery policy's, raises RecordLimitError (an IntegrityError). For regional reads the cache remembers it: asking again, even offline, gives the same answer without reading.

openvax-v1 stays published, and the libraries move to openvax-v2 at their own pace.