Mercurial > repos > geert-vandeweyer > clusterfast
changeset 22:9a26daf268da draft
Uploaded
author | geert-vandeweyer |
---|---|
date | Tue, 29 Jul 2014 10:50:35 -0400 |
parents | 8a7011053512 |
children | 42439d29305d |
files | run_cf0611.pl |
diffstat | 1 files changed, 6 insertions(+), 2 deletions(-) [+] |
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--- a/run_cf0611.pl Tue Jul 29 10:49:51 2014 -0400 +++ b/run_cf0611.pl Tue Jul 29 10:50:35 2014 -0400 @@ -21,12 +21,14 @@ use Cwd 'abs_path'; use File::Basename; -my ($inbam, $outdir, $targets, $minct1, $minct2, $dist, $novoindex, $rmtmp, $FASTA,$twobit,$refpaths,$bp1,$bp2,$contigs); +my ($inbam, $outdir, $targets, $minct1, $minct2, $dist, $novoindex, $rmtmp, $FASTA,$twobit,$refpaths,$bp1,$bp2,$contigs,$insert,$sdinsert); $minct1=2; $minct2=1; $dist=50000; $rmtmp=1; +$insert=230; +$sdinsert=140; my $known_partners=0; my $partnerfile=''; @@ -71,6 +73,8 @@ "c|contigs=s"=>\$contigs, "y|bp1=s"=>\$bp1, "z|bp2=s"=>\$bp2, + "i|insert=i"=>\$insert, + "s|sdinsert=i"=>\$sdinsert, ) or die "Usage: run_cf_0611.pl -b inbam -o outdir -f fasta -t targets -d distance -i novoindex -r rmtmp -m1 min_pairs -m2 min_splits -t genome.2bit\n"; if($help) { @@ -151,7 +155,7 @@ $r = int(rand(100)); } -$cmd="${NOVOALIGN}novoalign -o SAM -i 230 140 -r all -e 999 -c2 -d $novoindex -F STDFQ -f toRemap1.fq toRemap2.fq > novoout.2.sam 2>/tmp/na.stderr.$r"; +$cmd="${NOVOALIGN}novoalign -o SAM -i $insert $sdinsert -r all -e 999 -c2 -d $novoindex -F STDFQ -f toRemap1.fq toRemap2.fq > novoout.2.sam 2>/tmp/na.stderr.$r"; print STDOUT "$cmd\n"; system($cmd); my $na = `cat /tmp/na.stderr.$r`;