From 50a92204297a75aaaae86ce6f79b83798d93c5a9 Mon Sep 17 00:00:00 2001 From: jklughammer Date: Mon, 8 Aug 2016 07:52:54 +0200 Subject: [PATCH] fix unmapped read reporting now also unmapped reads are reported in their original (not converted) form. --- bwameth.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/bwameth.py b/bwameth.py index c0deb23..5b61d67 100755 --- a/bwameth.py +++ b/bwameth.py @@ -343,9 +343,7 @@ def handle_reads(alns, set_as_failed): assert len(aln.seq) == len(aln.qual), aln.read # don't need this any more. aln.other = [x for x in aln.other if not x.startswith('YS:Z')] - if aln.chrom == "*": # chrom - continue - + # first letter of chrom is 'f' or 'r' direction = aln.chrom[0] aln.chrom = aln.chrom.lstrip('fr')