details: http://www.bx.psu.edu/hg/galaxy/rev/3d8a7da23e46 changeset: 3650:3d8a7da23e46 user: Anton Nekrutenko anton@bx.psu.edu date: Wed Apr 14 13:52:35 2010 -0400 description: Fixed indel calling in pileup wrapper. TO DO: Write a separate wrapper for indels only.
diffstat:
tools/samtools/pileup_parser.pl | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-)
diffs (12 lines):
diff -r cffa627364bb -r 3d8a7da23e46 tools/samtools/pileup_parser.pl --- a/tools/samtools/pileup_parser.pl Wed Apr 14 11:27:15 2010 -0400 +++ b/tools/samtools/pileup_parser.pl Wed Apr 14 13:52:35 2010 -0400 @@ -60,7 +60,7 @@ my @qv = split //, $base_quality; for my $base ( 0 .. @bases - 1 ) { - if ( ord( $qv[ $base ] ) - 33 >= $quality_cutoff ) + if ( ord( $qv[ $base ] ) - 33 >= $quality_cutoff and $bases[ $base ] ne '*') { ++$above_qv_bases;