# HG changeset patch
# User geert-vandeweyer
# Date 1406645435 14400
# Node ID 9a26daf268dad69c22b066aa681b0303c829cb54
# Parent  8a70110535126a427dafb21ddfd9026577c26ad9
Uploaded

diff -r 8a7011053512 -r 9a26daf268da run_cf0611.pl
--- 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`;