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mauranolab / mapping

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Clean up nearby read clustering #116

Closed mattmaurano closed 4 years ago

mattmaurano commented 4 years ago
  1. Remove explicit loop over chromosomes: "while read main_chrom"
  2. Refactor to use bedops -m / bedmap --count
  3. Apply same code to cluster both nearby bam1 and bam2 coordinates
mattmaurano commented 4 years ago

Focus on #1-2

For #3, something along the lines of: bedmap --multidelim '|' --delim '|' --echo --echo-map regions.bed bamintersect12.bed to match on bam1 Then pipe to awk -F "|" '{split(,,"\t")}' to match on bam2