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timbitz / Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level
MIT License
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Incorrect SAM output. #37

Closed timbitz closed 7 years ago

timbitz commented 7 years ago

There seem to be several bugs related to formatting of SAM output @UBrau identified. These are a direct result of a lack of tests for SAM format in tests/runtests.jl which is clearly necessary.

  1. '+' strand introns may be off-by-one, such that downstream of splice junctions is shifted by 1 in igv browser.
  2. Genes on minus strand may be placed in mirror image coordinates.
  3. Some CIGAR strings are wrong based on one-sided soft-padding.