Mercurial > repos > geert-vandeweyer > coverage_report
changeset 25:6cb012c8497a draft
Added BED format check before collapsing regions.
| author | geert-vandeweyer |
|---|---|
| date | Thu, 12 Feb 2015 09:54:03 -0500 |
| parents | fd788f9db899 |
| children | 859999cb135b |
| files | CoverageReport.pl |
| diffstat | 1 files changed, 7 insertions(+), 0 deletions(-) [+] |
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--- a/CoverageReport.pl Thu Feb 12 08:51:37 2015 -0500 +++ b/CoverageReport.pl Thu Feb 12 09:54:03 2015 -0500 @@ -78,6 +78,13 @@ ## 0. Collapse overlapping target regions. if (defined($opts{'T'})) { + ## check BED format. Must have 6 cols if using this. + my $head = `head -n 1 $opts{'t'}`; + chomp; + my @c = split(/\t/,$head); + if (scalar(@c) < 6) { + die("Targets BED file must be in 6-column format for collapsings. See tool documentation for more info.\n"); + } my $targets = $opts{'t'}; my $tmptargets = "$wd/collapsedtargets.bed"; system("sort -k1,1 -k2,2n $targets > $wd/sorted.targets.bed");