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Resolved #28 #39

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2 changes: 1 addition & 1 deletion CoNVaDING.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -2285,7 +2285,7 @@ sub countFromBam {
$start=$array[1];
$stop=$array[2];
$gene=$array[3];
my $extractcov = "samtools depth -r $chr:$start-$stop -a -q 0 -Q 0 $bam | awk \'\{sum+=\$3\} END \{print sum\/NR\}\'";
my $extractcov = "samtools depth -r $chr:$start-$stop -a -a -q 0 -Q 0 $bam | awk \'\{sum+=\$3\} END \{print sum\/NR\}\'";
$regioncov = `$extractcov`;
chomp $regioncov;
if (defined $regioncov and length $regioncov) { #Check for empty variable, if true set coverage to 0
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