Commit 1de25c35 authored by bow's avatar bow
Browse files

Make sure WipeReads also checks for single reads when filtering + writing

parent 84a7f167
......@@ -328,6 +328,8 @@ object WipeReads extends MainCommand {
case rec: SAMRecord if rec.getReadPairedFlag =>
filteredOutSet.contains(rec.getReadName + "_" + rec.getAlignmentStart).isTrue &&
filteredOutSet.contains(rec.getReadName + "_" + rec.getMateAlignmentStart).isTrue
case rec: SAMRecord if !rec.getReadPairedFlag =>
filteredOutSet.contains(rec.getReadName + "_" + rec.getAlignmentStart).isTrue
case rec: String => filteredOutSet.contains(rec).isTrue
case _ => false
}
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment