--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2.4/script/Bam2pair.pl	Mon Jun 02 07:35:53 2014 -0400
@@ -0,0 +1,98 @@
+#!/usr/bin/perl
+#Author Steven Hart, PhD
+#11-15-2012
+#Convert and filter BAM files into merged bed 
+#Output should be 
+#chrA StartA EndA chrB StartB EndB Gene_id #supportingReads StrandA StrandB
+#chr9 1000 5000 chr9 3000 3800 bedpe_example2 100 - +
+
+use Cwd;
+use File::Basename;
+#Usage
+sub usage(){
+	print "Usage: perl Bam2Pair.pl -b <BAM> -o <outfile>\n
+		-isize [10000]\t\tThe insert size to be considered discordant\n
+		-winsize [10000]\tThe distance between mate pairs to be considered the same\n
+		-min [1]\t\tThe minimum number of reads required to support an SV event\n
+		-prefix need a random prefix so files with the same name don't get created\n\n"
+		;
+}
+$bedtools=`which intersectBed`;
+$samtools=`which samtools`;
+
+if(!defined($bedtools)){die "BEDtools must be installed\n";}
+if(!defined($samtools)){die "Samtools must be installed\n";}
+use Getopt::Long;
+#Declare variables
+GetOptions(
+	'b=s' => \$BAM_FILE,		#path to bam
+	'out=s' => \$outfile,		#path to output
+	'java:s' => \$java	,
+        'chrom:s' => \$chrom      ,
+	'isize=i' => \$isize,
+	'winsize=i' => \$winsize,
+        'prefix=s' => \$prefix,
+	'min=i' => \$minSupport,
+	'blacklist:s' => \$new_blacklist,
+	'q=s' => \$qual,
+	'v' => \$verbose
+	);
+#if(defined($picard_path)){$picard_path=$picard_path} else {die "Must specify a path to PICARD so that files can be sorted and indexed properly\n"};
+if(!defined($BAM_FILE)){die "Must specify a BAM file!\n".usage();}
+if(!defined($outfile)){die "Must specify an out filename!\n".usage();}
+if(!defined($java)){$java=$java;}else{$java=`which java`}
+if(!defined($qual)){$qual=20}
+if($new_blacklist){$new_blacklist=" -L $new_blacklist"}
+
+
+$Filter_BAM=$BAM_FILE;
+
+@bam=split("/",$Filter_BAM);
+$Filter_BAM=@bam[@bam-1];
+$Filter_BAM=~s/.bam/$prefix.bam/;
+$Filter_sam=$Filter_BAM;
+$Filter_sam=~s/.bam/.sam/;
+
+
+
+
+print "\nLooking for Discordant read pairs (and Unmated reads) without soft-clips\n";
+
+#$command=join("","samtools view -h -q 20 -f 1 -F 1804 ",$BAM_FILE," ",$chrom," ",$new_blacklist," |  awk -F\'\\t\' \'{if (\$9 > ", $isize, " || \$9 < -",$isize," || \$9 == 0 || \$1 ~ /^@/) print \$0}' > ",$Filter_sam);
+
+
+#Change command to allow reads where mate is unmapped & remove qual
+$command=join("","samtools view -h -f 1 -F 1800 -q $qual ",$BAM_FILE," ",$chrom," ",$new_blacklist," |  awk -F\'\\t\' \'{if (\$9 > ", $isize, " || \$9 < -",$isize," || \$9 == 0 || \$1 ~ /^@/) print \$0}' > ",$Filter_sam);
+
+print "$command\n" if ($verbose);
+system($command);
+$path = dirname(__FILE__);
+$Filter_cluster=$Filter_sam;
+$Filter_cluster=~s/.sam/.cluster/;
+$command=join("",$path,"/ReadCluster.pl -i=$Filter_sam -o=$Filter_cluster -m $minSupport");
+if($verbose){print "\n$command\n"};	
+
+system($command);
+
+##################################
+#Now there are 2 SAM files of filtered reads
+#.filter.cluster.inter.sam
+#.filter.cluster.intra.sam
+$result_pe=join("",$Filter_cluster,".out");
+$command=join("","cat ",$Filter_cluster,".int\*|perl -ane 'next if(\@F[0]=~/^\@/);if(\@F[6]!~/=/){print join(\"\\t\",\$F[11],\@F[2],\@F[3],\@F[6],\@F[7],\"\\n\")}else{print join(\"\\t\",\$F[11],\@F[2],\@F[3],\@F[2],\@F[7],\"\\n\")}' >",$result_pe);
+if($verbose){print $command."\n"};
+system($command);
+ #my ($sample, $chrstart, $start, $chrend, $end) 
+$command=join("","cat ",$result_pe," | ",$path,"/cluster.pair.pl ",$winsize," |awk '(\$6 >",$minSupport,")' >> ", $outfile);
+if($verbose){print $command."\n"};
+system($command);
+$filt1=join("",$Filter_cluster,".inter.sam");
+$filt2=join("",$Filter_cluster,".intra.sam");
+
+
+unlink($Filter_sam,$filt1,$filt2,$result_pe);
+
+#########################################
+#Now determine if left or righ clipping surrogate
+print "\nBam2pair.pl Done\n";
+