Mercurial > repos > geert-vandeweyer > coverage_report
changeset 24:fd788f9db899 draft
Added (default) option to collapse repetitive bed files
| author | geert-vandeweyer |
|---|---|
| date | Thu, 12 Feb 2015 08:51:37 -0500 |
| parents | a718420c834e |
| children | 6cb012c8497a |
| files | CoverageReport.pl |
| diffstat | 1 files changed, 11 insertions(+), 1 deletions(-) [+] |
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--- a/CoverageReport.pl Thu Feb 12 08:51:06 2015 -0500 +++ b/CoverageReport.pl Thu Feb 12 08:51:37 2015 -0500 @@ -28,12 +28,13 @@ # n : sample (n)ame. -getopts('b:t:o:z:rsSALm:n:f:', \%opts) ; +getopts('b:t:o:z:rsSALm:n:f:T', \%opts) ; # make output directory in (tmp) working dir our $wd = "/tmp/Coverage.".int(rand(1000)); while (-d $wd) { $wd = "/tmp/Coverage.".int(rand(1000)); + } system("mkdir $wd"); @@ -75,6 +76,15 @@ $tarfile = "$wd/Results.tar.gz"; } +## 0. Collapse overlapping target regions. +if (defined($opts{'T'})) { + my $targets = $opts{'t'}; + my $tmptargets = "$wd/collapsedtargets.bed"; + system("sort -k1,1 -k2,2n $targets > $wd/sorted.targets.bed"); + system("bedtools merge -s -scores max -nms -i $wd/sorted.targets.bed > $tmptargets"); + $opts{'t'} = $tmptargets; +} + # 1. Global Summary => default &GlobalSummary($opts{'b'}, $opts{'t'});