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osteosarc 0.14.0

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@iskandr iskandr released this 27 Sep 14:21
· 16 commits to main since this release
v0.14.0
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Learn about vigilant mode.

Fast test data with no options (#84).

  • Mates with no position are left out by default. make_bundle, osteosarc test-data make and osteosarc reads --fetch-pairs leave out mates that didn't align and have no position of their own, as STAR stores them. Finding those means reading every unplaced read of each BAM.
    • test-data make for one variant from T2_tumor's three RNA-seq BAMs took 15 s instead of 91 s, and for another 12 s instead of 19 minutes.
    • make_bundle(..., unplaced_mates=True), or --unplaced-mates, keeps them. It replaces 0.13.2's --placed-mates.
    • extract_reads(fetch_pairs=True) still fetches every mate, so existing recipes, such as openvax-v1's, rebuild the same.
  • Removed osteosarc.legacy_fixtures (#72), which no OpenVax library imports. osteosarc.cohort_bundle stays.

The OpenVax libraries can widen their pin to <0.15 with no code changes.

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