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OceanGenomics / mudskipper

A tool for projecting genomic alignments to transcriptomic coordinates
BSD 3-Clause "New" or "Revised" License
33 stars 7 forks source link

Multiple bugfixes #17

Closed haghshenas closed 2 years ago

haghshenas commented 2 years ago

This pull request:

  1. Adds support for supplementary alignments (resolves #2)
  2. Fixes the issue of wrong pairing for PE data (resolves #3)
  3. Properly handles unmapped reads (resolves #7)
  4. Fixes the output BAM record of alignments that are projected to a reverse strand transcript (resolves #14)
  5. Fixes wrong alignment to some transcripts whose exon boundaries do not align with the splicing (resolves #12)
  6. And bunch of minor bugfixes and improvements.