# HG changeset patch
# User researchdx-plus91technologies
# Date 1403181832 14400
# Node ID 925f6330cd80b67b69dbba0c22bfe817f7e96dd6
# Parent  4e09cf4d692a53c7357dda70042f904855095a12
Uploaded

diff -r 4e09cf4d692a -r 925f6330cd80 README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Thu Jun 19 08:43:52 2014 -0400
@@ -0,0 +1,50 @@
+SoftSearch:
+
+ --SoftSearch is a tool that uses soft-masked reads and discordant read pairs to identify structural variants(SV) in 
+   Illumina paired-end next-generation sequencing data. 
+ --Using Soft Clipped reads in which one part of the read maps to the reference genome but the other part does not SoftSearch 
+   can identify and call SVs including deletions, insertions, translocations, inversions, and tandem duplications
+ --SoftSearch requires two inputs: a BAM file of aligned reads and fasta file of the reference genome to which the reads 
+   were aligned.
+
+ Google Code Link:
+ 
+		https://code.google.com/p/softsearch/
+		
+------------------------------------------------------------------------------------------------------------------		
+Pre-Requirement:
+
+ -Perl
+ -Bedtools  
+ -SamTools
+   Must be accessible from the PATH environment variable
+    
+------------------------------------------------------------------------------------------------------------------
+How To Select fasta file from Database (Additional Configuration):
+
+ --A fasta_indexes.loc file must be located in shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/
+   8578d978014c/softsearch/tool-data/
+
+ --open the fasta_indexes.loc file and add an entry according to the example below
+
+        <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+
+        eg: hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
+
+ --open shed_tool_data_table_conf.xml file and add the following
+
+   	<tables>
+    <table name="fasta_indexes" comment_char="#">
+      	    <columns>value, dbkey, name, path</columns>
+       	    <file path="/path/to/fasta_indexes.loc" />
+  	    </table>
+</tables>
+
+------------------------------------------------------------------------------------------------------------------
+Authors:
+
+   ResearchDx
+   http://researchdx.com
+   
+   Plus91 Technologies Private Limited
+   http://www.plus91.in/
diff -r 4e09cf4d692a -r 925f6330cd80 SoftSearch.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SoftSearch.pl	Thu Jun 19 08:43:52 2014 -0400
@@ -0,0 +1,1192 @@
+#!/usr/bin/perl
+
+####
+#### Usage: SoftSearch.pl [-lqrmsd] -b <BAM> -f <Genome.fa> -sam <samtools path> -bed <bedtools path>
+#### Created 1-30-2012 by Steven Hart, PhD
+#### hart.steven@mayo.edu
+#### Required bedtools & samtools to be in path
+
+
+use lib "/home/plus91/shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies-pvt-ltd/softsearch/e3609c8714fb/softsearch/2.4/lib" ;
+
+use Getopt::Long;
+use strict;
+use warnings;
+#use Data::Dumper;
+use LevD;
+use File::Basename;
+
+my ($INPUT_BAM,$INPUT_FASTA,$OUTPUT_FILE,$minSoft,$minSoftReads,$dist_To_Soft,$bedtools,$samtools);
+my ($minRP, $temp_output, $num_sd, $MapQ, $chrom, $unmated_pairs, $minBQ, $pair_only, $disable_RP_only);
+my ($levD_local_threshold, $levD_distl_threshold,$pe_upper_limit,$high_qual,$sv_only,$blacklist,$genome_file,$verbose);
+
+my $cmd = "";
+
+#Declare variables
+GetOptions(
+	'b=s' => \$INPUT_BAM,
+	'f=s' => \$INPUT_FASTA,
+	'o:s' => \$OUTPUT_FILE,
+	'm:i' => \$minRP,
+	'l:i' => \$minSoft,
+	'r:i' => \$minSoftReads,
+	't:i' => \$temp_output,
+	's:s' => \$num_sd,
+	'd:i' => \$dist_To_Soft,
+	'q:i' => \$MapQ,
+	'c:s' => \$chrom,
+	'u:s' => \$unmated_pairs,
+	'x:s' => \$minBQ,
+	'p' => \$pair_only,
+	'g' => \$disable_RP_only,
+	'j:s' => \$levD_local_threshold,
+	'k:s' => \$levD_distl_threshold,
+        'a:s' => \$pe_upper_limit,
+        'e:s' => \$high_qual,
+	'L' => \$sv_only,
+	'v' => \$verbose, 
+	'blacklist:s' => \$blacklist,
+	'genome_file:s' => \$genome_file,
+	"help|h|?"	=> \&usage);
+
+unless($sv_only){$sv_only=""};
+if(defined($INPUT_BAM)){$INPUT_BAM=$INPUT_BAM} else {print usage();die "Where is the BAM file?\n\n"}
+if(defined($INPUT_FASTA)){$INPUT_FASTA=$INPUT_FASTA} else {print usage();die "Where is the fasta file?\n\n"}
+my ($fn,$pathname) = fileparse($INPUT_BAM,".bam");
+my $index=`ls $pathname/$fn*bai|head -1`;
+#my $index =`ls \${INPUT_BAM%.bam}*bai`;
+#print "INDEX=$index\n";
+if(!$index){die "\n\nERROR: you need index your BAM file\n\n"}
+
+### get current time
+print "Start Time : " . &spGetCurDateTime() . "\n";
+my $now = time;
+
+#if(defined($OUTPUT_FILE)){$OUTPUT_FILE=$OUTPUT_FILE} else {$OUTPUT_FILE="output.vcf"; print "\nNo outfile specified.  Using output.vcf as default\n\n"}
+if(defined($minSoft)){$minSoft=$minSoft} else {$minSoft=5}
+if(defined($minRP)){$minRP=$minRP} else {$minRP=5}
+if(defined($minSoftReads)){$minSoftReads=$minSoftReads} else {$minSoftReads=5}
+if(defined($dist_To_Soft)){$dist_To_Soft=$dist_To_Soft} else {$dist_To_Soft=300}
+if(defined($num_sd)){$num_sd=$num_sd} else {$num_sd=6}
+if(defined($MapQ)){$MapQ=$MapQ} else {$MapQ=20}
+
+unless (defined $pe_upper_limit) { $pe_upper_limit = 10000; }
+unless (defined $levD_local_threshold) { $levD_local_threshold = 0.05; }
+unless (defined $levD_distl_threshold) { $levD_distl_threshold = 0.05; }
+#Get sample name if available
+my $SAMPLE_NAME="";
+my $OUTNAME ="";
+$SAMPLE_NAME=`samtools view -f2 -H $INPUT_BAM|awk '{if(\$1~/^\@RG/){sub("ID:","",\$2);name=\$2;print name}}'|head -1`;
+$SAMPLE_NAME=~s/\n//g;
+if (!$OUTPUT_FILE){
+	if($SAMPLE_NAME ne ""){$OUTNAME=$SAMPLE_NAME.".vcf"}
+	else {$OUTNAME="output.vcf"}
+}
+else{$OUTNAME=$OUTPUT_FILE}
+
+print "Writing results to $OUTNAME\n";
+
+
+##Make sure if submitting on SGE, to prepned the "chr".  Not all referecne FAST files require "chr", so we shouldn't force the issue.
+if(!defined($chrom)){$chrom=""}
+if(!defined($unmated_pairs)){$unmated_pairs=0}
+
+my $badQualValue=chr($MapQ);
+if(defined($minBQ)){ $badQualValue=chr($minBQ); }
+
+if($badQualValue  eq "#"){$badQualValue="\#"}
+
+# adding and cheking for samtools and bedtools in the PATh
+## check for bedtools and samtools in the path
+$bedtools=`which intersectBed` ;
+if(!defined($bedtools)){die "\nError:\n\tno bedtools. Please install bedtools and add to the path\n";}
+#$samtools=`samtools 2>&1`;
+$samtools=`which samtools`;
+if($samtools !~ /(samtools)/i){die "\nError:\n\tno samtools. Please install samtools and add to the path\n";}
+
+print "Usage = SoftSearch.pl -l $minSoft -q $MapQ -r $minSoftReads -d $dist_To_Soft -m $minRP -s $num_sd -c $chrom -b $INPUT_BAM -f $INPUT_FASTA -o $OUTNAME \n\n";
+sub usage {
+	print "\nusage: SoftSearch.pl [-cqlrmsd] -b <BAM> -f <Genome.fa> \n";
+	print "\t-q\t\tMinimum mapping quality [20]\n";
+	print "\t-l\t\tMinimum length of soft-clipped segment [5]\n";
+	print "\t-r\t\tMinimum depth of soft-clipped reads at position [5]\n";
+	print "\t-m\t\tMinimum number of discordant read pairs [5]\n";
+	print "\t-s\t\tNumber of sd away from mean to be considered discordant [6]\n";
+	print "\t-u\t\tNumber of unmated pairs [0]\n";
+	print "\t-d\t\tMax distance between soft-clipped segments and discordant read pairs [300]\n";
+	print "\t-o\t\tOutput file name [output.vcf]\n";
+	print "\t-t\t\tPrint temp files for debugging [no|yes]\n";
+	print "\t-c\t\tuse only this chrom or chr:pos1-pos2\n";
+	print "\t-p\t\tuse paired-end mode only. In other words, don't try to find soft-clipping events!\n";
+	print "\t-g\t\tEnable paired-only seach. This will look for discordant read pairs even without soft clips.\n";
+        print "\t-a\t\tset the minimum distance for a discordant read pair without soft-clipping info [10000]\n";
+        print "\t-L\t\tFlag to print out even small deletions (low quality)\n";
+        print "\t-e\t\tdisable strict quality filtering of base qualities in soft-clipped reads [no]\n";
+        print "\t-blacklist\tareas of the genome to skip calling.  Requires -genome_file\n";
+        print "\t-genome_file\ttab seperated value of chromosome name and length.  Only used with -blacklist option\n\n";
+
+	exit 1;
+	}
+
+
+#############################################################
+# create temporary variable name
+#############################################################
+srand (time ^ $$ ^ unpack "%L*", `ps axww | gzip -f`);
+our $random_name=join "", map { ("a".."z")[rand 26] } 1..8;
+
+#############################################################
+## create green list
+##############################################################
+#
+my $new_blacklist="";
+if($blacklist){
+        if(!$genome_file){die "if using a blacklist, you must also specify the location of a genome_file
+        The format of the genome_file should be
+                chrom   size
+                chr1    249250621
+                chr2    243199373
+                ...
+
+        If using hg19, you can ge the genome file by
+                mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \"select chrom, size from hg19.chromInfo\"  > hg19.genome";}
+        
+	$cmd=join("","complementBed -i $blacklist -g $genome_file >",$random_name,".bed") ;
+	system ($cmd);
+	$new_blacklist=join(""," -L ",$random_name,".bed ");
+	}
+
+if($verbose){print "CMD=$cmd\nBlacklist is $new_blacklist\n";}
+
+
+
+
+
+#############################################################
+# Calcualte insert size distribution of properly mated reads
+#############################################################
+
+#Change for compatability with other operating systems
+#my $metrics=`samtools view -q $MapQ -f2 $INPUT_BAM $chrom|cut -f9|head -10000|awk '{if (\$1<0){\$1=-\$1}else{\$1=\$1} sum+=\$1; sumsq+=\$1*\$1} END {print sum/NR, sqrt(sumsq/NR - (sum/NR)**2)}'`;
+
+my $metrics=`samtools view -q $MapQ -f2 $INPUT_BAM $chrom|head -10000|cut -f9|awk '{if (\$1<0){\$1=-\$1}else{\$1=\$1} sum+=\$1; sumsq+=\$1*\$1} END {print sum/NR, sqrt(sumsq/NR - (sum/NR)^2)}'`;
+#my ($mean,$stdev)=split(/ /,$metrics);
+my ($mean,$stdev)=split(/\s/,$metrics);
+$stdev=~s/\n//;
+my $upper_limit=int($mean+($num_sd*$stdev));
+my $lower_limit=int($mean-($num_sd*$stdev));
+die if (!$mean);
+print qq{The mean insert size is $mean +/- $stdev (sd)
+The upper limit = $upper_limit
+The lower limit = $lower_limit\n
+};
+if($lower_limit<0){
+	print "Warning!! Given this insert size distribution, we can not call small indels.  No other data will be affected\n";
+	$lower_limit=1;
+}
+my $tmp_name=join ("",$random_name,".tmp.bam");
+my $random_file_sc = "";
+my $command = "";
+
+#############################################################
+# Make sam file that has soft clipped reads
+#############################################################
+#give file a name
+if(!defined($pair_only)){
+	$random_file_sc=join ("",$random_name,".sc.sam");
+	$command=join ("","samtools view -q $MapQ -F 1024 $INPUT_BAM $chrom $new_blacklist| awk '{OFS=\"\\t\"}{c=0;if(\$6~/S/){++c};if(c == 1){print}}' | perl -ane '\$TR=(\@F[10]=~tr/\#//);if(\$TR<2){print}' > ", $random_file_sc);
+
+	print "Making SAM file of soft-clipped reads\n";
+if($verbose){	print "$command\n";}
+	system("$command");
+
+	#############################################################
+	# Find areas that have deep enough soft-clip coverage
+	print "Identifying soft-clipped regions that are at least $minSoft bp long \n";
+	open (FILE,"$random_file_sc")||die "Can't open soft-clipped sam file $random_file_sc\n";
+
+	my $tmpfile=join("",$random_file_sc,".sc.passfilter");
+	open (OUT,">$tmpfile")||die "Can't write files here!\n";
+
+	while(<FILE>){
+		@_ = split(/\t/, $_);
+		#### parse CIGAR string and create a hash of array of each operation
+		my @CIGAR = split(/([0-9]+[SMIDNHXP])/, $_[5]);
+		my $hash;
+		map { push(@{$hash->{$2}}, $1) if (/(\d+)([SMIDNHXP])/) } @CIGAR;
+
+		#for ($i=0; $i<=$#softclip_pos; $i++)	{
+		foreach my $softclip (@{$hash->{S}}) {
+			#if	($CIGAR[$softclip_pos[$i]] > $minSoft){
+			if	($softclip > $minSoft){
+				###############Make sure base qualities don't have more than 2 bad marks
+				my $qual=$_[10];
+				my $TR=($qual=~tr/$badQualValue//);
+				if($badQualValue eq "#"){ $TR=($qual=~tr/\#//); }
+				#Skip the soft clip if there is more than 2 bad qual values
+				#next if($TR > 2);
+#				if (!$high_qual){next if($TR > 2);}
+				print OUT;
+				last;
+			}
+		}
+	}
+	close FILE;
+	close OUT;
+
+	$command=join(" ","mv",$tmpfile,$random_file_sc);
+if($verbose){	print "$command\n";}
+	system("$command");
+}
+
+#########################################################
+#Stack up SoftClips
+#########################################################
+my $random_file=join("",$random_name,".sc.direction.bed");
+if(!defined($pair_only)){
+        open (FILE,"$random_file_sc")|| die "Can't open sam file\n";
+        #$random_file=join("",$random_name,".sc.direction");
+
+        print "Calling sides of soft-clips\n";
+        #\nTMPOUT=$random_file\tINPUT=$random_file_sc\n\n";
+        open (TMPOUT,">$random_file")|| die "Can't create tmp file\n";
+
+        while (<FILE>){
+                @_ = split(/\t/, $_);
+                #### parse CIGAR string and create a hash of array of each operation
+                my @CIGAR = split(/([0-9]+[SMIDNHXP])/, $_[5]);
+                my $hash;
+                map { push(@{$hash->{$2}}, $1) if (/(\d+)([SMIDNHXP])/) } @CIGAR;
+
+                #### next if softclips on each end
+                next if ($_[5] =~ /^[0-9]+S.*S$/);
+
+                #### next softclip occurs in the middle
+                next if ($_[5] =~ /^[0-9]+[^S][0-9].*S.+$/);
+
+                my $softclip = $hash->{S}[0];
+
+                my $end1 = 0;
+                my $end2 = 0;
+                my $softBases = "";
+		my $right_corrected="";my $left_corrected="";
+
+        if ($softclip > $minSoft) {
+		
+                        ####If the soft clip occurs at end of read and its on the minus strand, then it's a right clip
+                        if ($_[5] =~ /^.*S$/) {
+                                $end1=$_[3]+length($_[9])-$softclip-1;
+                                $end2=$end1+1;
+next if ($end1<0);
+                                #RIGHT clip on Minus
+                                $softBases=substr($_[9], length($_[9])-$softclip, length($_[9]));
+                                #Right clips don't always get clipped correctly, so fix that
+                                # Check to see if sc base matches ref
+                                $right_corrected=baseCheck($_[2],$end2,"right",$softBases);
+                               print TMPOUT "$right_corrected\n"
+
+                        } else {
+                                #### Begins with S (left clip)
+                                $end1=$_[3]-$softclip;
+next if ($end1<0);
+
+                                $softBases=substr($_[9], 0,$softclip);#print "TMP=$softBases\n";
+        			$left_corrected=baseCheck($_[2],$end1,"left",$softBases);
+if(!$left_corrected){print "baseCheck($_[2],$end1,left,$softBases)\n";next}
+                               print TMPOUT "$left_corrected\n";
+#print "\nSEQ=$_[9]\t\n";
+
+                        }
+        }
+  }
+close FILE;
+close TMPOUT;
+}
+sub baseCheck{
+        my ($chrom,$pos,$direction,$softBases)=@_;
+        #skip if position is less than 0, which is caused by MT DNA
+        return if ($pos<0);
+        my $exit="";
+
+        while(!$exit){
+        if($direction=~/right/){
+                        my $refBase=getSeq($chrom,$pos,$INPUT_FASTA);
+                        my $softBase=substr($softBases,0,1);
+                        if ($softBase !~ /$refBase/){
+                                my $value=join("\t",$chrom,$pos,$pos+1,join("|",$softBases,$direction));
+                                $exit="STOP";
+                                return $value;
+                        }
+                        else{
+                                $pos=$pos+1;
+                                $softBases=substr($softBases, 1,length($softBases));
+                        }
+         }
+        else{
+                        my $refBase=getSeq($chrom,$pos+1,$INPUT_FASTA);
+                        my $softBase=substr($softBases,-1,1);
+                        if ($softBase !~ /$refBase/){
+                                $pos=$pos-1+length($softBases);
+                                my $value=join("\t",$chrom,$pos-1,$pos,join("|",$softBases,$direction));
+                                $exit="STOP";
+                                return $value;
+                        }
+                        else{
+                                $pos=$pos-1;
+                                $softBases=substr($softBases, 0, -1);
+                                #print "Trying again $softBases\n";
+                       }
+
+        }
+
+}
+}
+#Remove SAM files to conserve space
+unlink($random_file_sc);
+
+
+my $random_file_disc="$INPUT_BAM";
+###
+#
+######################################################
+# Transform Read pair groups into softclip equivalents
+######################################################
+#
+#
+#
+my $v="";
+#if($disable_RP_only){
+print "Running Bam2pair.pl\n";
+print "Looking for discordant read pairs without requiring soft-clipping information\n";
+	use FindBin qw($Bin);
+	my $path=$Bin;
+#	print"\n\nPATH=$path\n\n";
+if($verbose){$v="-v"}
+	my $tmp_out=join("",$random_name,"RP.out");
+	$command=join("","perl ",$path,"/Bam2pair.pl -b $random_file_disc  -o $tmp_out -isize $pe_upper_limit -winsize $dist_To_Soft -min $minRP -chrom $chrom -prefix $random_name -q $MapQ -blacklist $random_name.bed $v");
+if($verbose){	print "$command\n"};
+	system("$command");
+	$command=join("","perl -ane '\$end1=\@F[1];\$end2=\@F[3];print join(\"\\t\",\@F[0..1],\$end1,\"unknown|left\");print \"\\n\";print join(\"\\t\",\@F[2..3],\$end2,\"unknown|left\");print \"\\n\"' ", $tmp_out," >> ",$random_file);
+if($verbose){print "$command\n"};
+	system($command);
+	unlink($tmp_out);
+#}
+#
+
+
+######################################################
+unlink("$random_file","$tmp_name","$random_file","$index","$random_name","$new_blacklist") if (-z $random_file || ! -e $random_file ) ;
+if (-z $random_file || ! -e $random_file){
+	print "Softclipped file is empty($random_file).\nNo soft clipping found using desired paramters\n\n";
+	open (OUT,">$OUTNAME")||die "Can't write files here!\n";
+        &print_header();
+        close OUT;
+        exit;
+	}
+
+
+#############################################################
+#  Make sure there are enough soft-clippped supporting reads
+#############################################################
+my $outfile=join("",$random_file,".sc.merge.bed");
+#sortbed -i .sc.direction | mergeBed -nms -d 25 -i stdin > .sc.merge.bed
+$command=join(" ","sortBed -i",$random_file," | mergeBed  -nms -i stdin","|egrep \";|,\"","|awk '{OFS=\"\t\"}(NF==4)'",">",$outfile);
+
+print "$command\n" if ($verbose);
+system("$command");
+
+if (-z $outfile || ! -e $outfile){
+	unlink("$tmp_name","$random_file","$outfile","$index","$random_name","$new_blacklist"); 
+	print "mergeBed file is empty.\nNo strucutral variants found\n\n" ;
+        open (OUT,">$OUTNAME")||die "Can't write files here!\n";
+        &print_header();
+        close OUT;
+        exit;
+}
+
+print "completed mergeBed\n";
+
+###############################################################
+# If left and right are on the same line, make into 2 lines
+###############################################################
+open (INFILE,$outfile)||die "couldn't open temp file : $. \n\n";
+my $tmp2=join("",$random_name,".sc.fixed.merge.bed");
+#print "INFILE=$outfile\tOUTFILE=$tmp2\n\n";
+#INPUT FORMAT=chr9\t131467\t131473\tATGCTTATTAAAA|left;TTATTAAAAGCATA|left
+open (OUTFILE,">$tmp2")||die "couldn't create temp file : $. \n\n";
+while(<INFILE>){
+	chomp $_;
+	my $l = $_;
+
+	my @a = split(/\t/, $l);
+	my $info = $a[3];
+	my @info_arr = split(/\;/, $info);
+	my @left_arr=();
+	my @right_arr=();
+	@left_arr = grep(/left/, @info_arr);
+	@right_arr = grep(/right/, @info_arr);
+
+	#New
+	my $left = join(";", @left_arr);
+	my $right = join(";", @right_arr);
+	$info = join(";", @info_arr);
+
+	if((@left_arr) && (@right_arr)){
+		print OUTFILE "$a[0]\t$a[1]\t$a[2]\t$left\n$a[0]\t$a[1]\t$a[2]\t$right\n";
+	} else{
+		my $all=join("\t",@a[0..2],$info);
+		print OUTFILE "$all\n";
+	}
+}
+
+# make sure output file name is $outfile
+$command=join(" ","sed -e '/ /s//\t/g'", $tmp2,"|awk 'BEGIN{OFS=\"\\t\"}(NF==4)'", "|perl -pne 's/ /\t/g'>",$outfile);
+system("$command");
+if($verbose){print "$command\n"};
+unlink("$tmp_name","$random_file","$tmp2","$outfile","$index","random_name","$new_blacklist") if (-z $outfile || ! -e $outfile) ;
+ if (-z $outfile || ! -e $outfile){
+	print "Fixed mergeBed file is empty($outfile).\nNo strucutral variants found\n\n";
+        open (OUT,">$OUTNAME")||die "Can't write files here!\n";
+        &print_header();
+        close OUT;
+        exit;
+}
+
+print "completed fixing mergeBed\n\n";
+
+###############################################################
+# Seperate directions of soft clips
+###############################################################
+my $left_sc = join("", "left", $tmp2);
+my $right_sc = join("", "right", $tmp2);
+use FindBin qw($Bin);
+#my $path=$Bin;
+
+$command=join("","grep left ", $tmp2, " |sed -e '/left /s//left\;/g' | sed -e '/ /s//\t/g'|perl ".$path."/direction_filter.pl - >",$left_sc);
+system("$command");
+#print "$command\n";
+$command=join("","grep right ", $tmp2, " |sed -e '/right /s//right\;/g' | sed -e '/ /s//\t/g'|perl ".$path."/direction_filter.pl - >",$right_sc);
+#$command=join(" ","grep right ", $tmp2, " |sed -e '/right /s//right\;/g' | sed -e '/ /s//\t/g' >",$right_sc);
+system("$command");
+#print "$command\n";
+#die "CHECK $right_sc\n";
+
+###############################################################
+# Count the number and identify directions of soft clips
+###############################################################
+print "Count the number and identify directions of soft clips\n";
+#print "looking in $outfile\n";
+$outfile=join("",$random_name,".sc.fixed.merge.bed");
+
+open (INFILE,$outfile)||die "couldn't open temp file\n\n";
+my $tmp3 = join("", $random_file, "predSV");
+open (OUTFILE, ">$tmp3")||die "couldn't create temp file\n\n";
+while(<INFILE>){
+chomp;
+	@_=split(/\t/,$_);
+	my $count=tr/\;//;$count+=tr/\,//;
+	$count=$count+1;
+	my $left=0;
+	my $right=0;
+
+	while ($_ =~ /left/g) { $left++ } # count number of right clips
+	while ($_ =~ /right/g) { $right++ } # count number of left clips
+
+	###############################################################
+	if ($count >= $minSoftReads){
+		####get longets soft-clipped read
+		my @clips=split(/\;|,|\|/,$_[3]);
+
+		my ($max, $temp, $temp2, $temp3, $dir, $maxSclip) = (0) x 6;
+		for (my $i=0; $i<$count; $i++) {
+			my $plus1=$i+1;
+			$temp=length($clips[$i]);
+			$temp2=$clips[$plus1];
+			$temp3=$clips[$i];
+
+			if ($temp > $max){
+				$maxSclip=$temp3;
+				$max =$temp;
+				$dir=$temp2;
+			} else {
+				$max=$max;
+				$dir=$dir;
+				$maxSclip=$maxSclip;
+			}
+			$i++;
+		}
+		my $order2 = join("|", $left, $right);
+        #print join ("\t",@_[0..2],$maxSclip,$max,$dir,$count,$order2) . "\n";
+		print OUTFILE join ("\t",@_[0..2],$maxSclip,$max,$dir,$count,$order2) . "\n";
+	} elsif($_=~/unknown/){
+	print OUTFILE join ("\t",@_[0..2],"NA","NA","left","NA","NA|NA") . "\n";
+        print OUTFILE join ("\t",@_[0..2],"NA","NA","right","NA","NA|NA") . "\n";
+	}
+	####Format is Chrom,start, end,longest Soft-clip,length of longest Soft-clip, direction of longest soft-clip,#supporting softclips,#right Sclips|#left Sclips
+}
+close INFILE;
+close OUTFILE;
+
+unlink("$tmp2","$tmp_name","$random_file","$tmp3","$outfile","$index","$random_name","$right_sc","$left_sc","$new_blacklist") if (-z $tmp3 || !-e $tmp3) ;
+
+ if (-z $tmp3 || !-e $tmp3){
+	print "No structural variants found while Counting the number and identify directions of soft clips.\n" ;
+
+	open (OUT,">$OUTNAME")||die "Can't write files here!\n";
+	&print_header();
+	close OUT;
+	exit;
+
+}
+
+print "Done counting Softclipped reads\n";
+###############################################################
+#### Print header information
+###############################################################
+open (OUT,">$OUTNAME")||die "Can't write files here!\n";
+&print_header();
+close OUT;
+
+###############################################################
+###############################################################
+#### DO the bulk of the work
+###############################################################
+use List::Util qw(min max);
+open (FILE,"$tmp3")|| die "Can't open file\n";
+open (OUT,">>$OUTNAME")|| die "Can't open file\n";
+
+#print "\nusing $tmp3 and writing to $OUTPUT_FILE \n";
+while (<FILE>){
+	#If left clip {+- or -- or -+ }{+- are uninformative b/c they go upstream}
+	#If right clip {++ or -- or +-}
+	chomp $_;
+	my $line = $_;
+	my @info = split(/\t/, $_);
+
+	if($info[5] eq "left") {
+		bulk_work("left", $line, $random_file_disc);
+
+	} elsif ($info[5] eq "right") {
+		bulk_work("right", $line, $random_file_disc);
+	}
+#if($. ==6){print "THIS IS LINE 6\n$_\n";die}
+print "Completed line $.\n" if ($verbose);
+}
+close FILE;
+close OUT;
+
+###############################################################################
+###############################################################################
+#### Delete temp files
+my $meregedBed=join("",$random_name,".sc.direction.bed.sc.merge.bed");
+
+if(defined($temp_output)){$temp_output=$temp_output} else {$temp_output="no"}
+
+if ($temp_output eq "no"){
+	unlink("$tmp_name","$random_file","$tmp2",,"$tmp3","$outfile","$index","$random_name","$right_sc","$left_sc","$meregedBed","$random_name.bed");
+}
+####Sort VCF
+my $tmp=join(".",$random_name,"tmp");
+#Get header
+$cmd="grep \"#\" $OUTNAME > $tmp";
+system($cmd);
+#sort results
+$cmd="grep -v \"#\" $OUTNAME|perl -pne 's/chr//'|sort -k1,1n -k2,2n|perl -ne 'print \"chr\".\$_' >>$tmp";
+system($cmd);
+$cmd="mv $tmp $OUTNAME";
+system($cmd);
+#remove entries next to each other
+
+
+
+
+#############################################################
+##May not need this anymore since filtering on left and right
+#############################################################
+#my $tmpout=$OUTNAME;
+#$tmpout.=".tmp";
+#use FindBin qw($Bin);
+##my $path=$Bin;
+#$command="perl ".$path."/Extract_nSC.pl $OUTNAME -q nSC > $tmpout";
+##print "Command=$command\n";
+#system($command);
+#$command="perl ".$path."/reduce_redundancy.pl $tmpout $upper_limit |cut -f1-10 > $OUTNAME";
+##print "$command\n";
+#system($command);
+#system("rm $tmpout");
+########################################################
+
+
+
+
+print "Analysis Completed\n\nYou did it!!!\n";
+print "Finish Time : " . &spGetCurDateTime() . "\n";
+$now = time - $now;
+printf("\n\nTotal running time: %02d:%02d:%02d\n\n", int($now / 3600), int(($now % 3600) / 60),
+int($now % 60));
+
+exit;
+
+###############################################################################
+sub rev_comp {
+  my $dna = shift;
+  my $revcomp = reverse($dna);
+  $revcomp =~ tr/ACGTacgt/TGCAtgca/;
+
+  return $revcomp;
+}
+
+
+###############################################################################
+#### to get reference base
+sub getSeq{
+	my ($chr,$pos,$fasta)=@_;
+	#don't require chr
+	#if($chr !~ /^chr/){die "$chr is not correct\n";}
+#	die "$pos is not a number\n" if ($pos <0);
+my @result=();
+        if ($pos <0){print "$pos is not a valid position (likely caused by circular MT chromosome)\n";return;}
+
+	@result = `samtools faidx $fasta $chr:$pos-$pos`;
+	if($result[1]){chomp($result[1]);
+	return uc($result[1]);
+	}
+	return("NA");
+	#### after return will not be printed
+	####print "RESULTS=@result\n";
+}
+
+sub getBases{
+        my ($chr,$pos1,$pos2,$fasta)=@_;
+        #don't require chr
+        #if($chr !~ /^chr/){die "$chr is not correct\n";}
+my @result=();
+        if ($pos1 <0){print "$pos1 is not a valid position (likely caused by circular MT chromosome)\n";return;};
+
+        @result = `samtools faidx $fasta $chr:$pos1-$pos2`;
+	if(!$result[1]){$result[1]="NA"};
+        chomp($result[1]);
+        return uc($result[1]);
+
+        #### after return will not be printed
+        ####print "RESULTS=@result\n";
+}
+###############################################################################
+#### to get time
+sub spGetCurDateTime {
+	my ($sec, $min, $hour, $mday, $mon, $year) = localtime();
+	my $curDateTime = sprintf "%4d-%02d-%02d %02d:%02d:%02d",
+	$year+1900, $mon+1, $mday, $hour, $min, $sec;
+	return ($curDateTime);
+}
+
+
+###############################################################################
+#### print header
+sub print_header {
+	my $date=&spGetCurDateTime();
+	my $header = qq{##fileformat=VCFv4.1
+##fileDate=$date
+##source=SoftSearch.pl
+##reference=$INPUT_FASTA
+##Usage= SoftSearch.pl -l $minSoft -q $MapQ -r $minSoftReads -d $dist_To_Soft -m $minRP -u $unmated_pairs -s $num_sd -b $INPUT_BAM -f $INPUT_FASTA -o $OUTNAME
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
+##INFO=<ID=ISIZE,Number=.,Type=String,Description="Size of the SV">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##FORMAT=<ID=lSC,Number=1,Type=Integer,Description="Length of the longest soft clips supporting the BND">
+##FORMAT=<ID=nSC,Number=1,Type=Integer,Description="Number of supporting soft-clips\">
+##FORMAT=<ID=uRP,Number=1,Type=Integer,Description="Number of unmated read pairs nearby Soft-Clips">
+##FORMAT=<ID=levD_local,Number=1,Type=Float,Description="Levenstein distance between soft-clipped bases and the area around the original soft-clipped site">
+##FORMAT=<ID=levD_distl,Number=1,Type=Float,Description="Levenstein distance between the soft-clipped bases and mate location">
+##FORMAT=<ID=CTX,Number=1,Type=Integer,Description="Number of chromosomal translocations">
+##FORMAT=<ID=DEL,Number=1,Type=Integer,Description="Number of reads supporting Large Deletions">
+##FORMAT=<ID=INS,Number=1,Type=Integer,Description="Number of reads supporting Large insertions">
+##FORMAT=<ID=NOV_INS,Number=1,Type=Integer,Description="Number of reads supporting novel sequence insertion">
+##FORMAT=<ID=TDUP,Number=1,Type=Integer,Description="Number of reads supporting a tandem duplication">
+##FORMAT=<ID=INV,Number=1,Type=Integer,Description="Number of reads supporting inversions">
+##FORMAT=<ID=sDEL,Number=1,Type=Integer,Description="Number of reads supporting novel sequence insertion">
+##INFO=<ID=NO_MATE_SC,Number=1,Type=Flag,Description="When there is no softclipping of the mate read location, an appromiate position is used">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Dummy value for maintaining VCF-Spec">
+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t$SAMPLE_NAME\n};
+
+	print OUT $header;
+}
+
+
+###############################################################################
+sub bulk_work {
+print "#####################################@_\n" if ($verbose);
+	my ($side, $line, $file) = @_;
+	my $local_levD = 0;
+	my $distl_levD = 0;
+
+	#my @info = split(/\t/, $line);
+	my @plus_Reads = split(/\t/, $line);
+	$plus_Reads[7] =~ s/\n//g;
+
+	#### softclip length and softclip size.
+	my $lSC = $plus_Reads[4];
+	my $nSC = $plus_Reads[6];
+
+
+	#Get all types of compatible reads
+	#Get improperly paired reads (@ max distance)
+
+	#### default value for left SIDE.
+	#If left-clip, then look downstream for match of softclipped reads to define a deletion, but look for DRPs upstream
+	my $sv_type = "SVTYPE=BND";
+	my $start_local=0; my $end_local=0;my $target_local="";my $target_drp="";my $start_drp="";my $end_drp="";
+	if ($side =~ /left/) {
+		$start_local = $plus_Reads[1]-$dist_To_Soft;
+		$end_local = $plus_Reads[2];
+                $start_drp = $plus_Reads[1];
+                $end_drp = $plus_Reads[1]+$dist_To_Soft;
+	
+	}
+	else{                
+                $start_local = $plus_Reads[1];
+                $end_local = $plus_Reads[1]+$dist_To_Soft;
+                $start_drp = $plus_Reads[1]-$dist_To_Soft;
+                $end_drp = $plus_Reads[1];
+        }
+	
+	$target_local=join("", $plus_Reads[0], ":", $start_local, "-", $end_local);
+	$target_drp=join("", $plus_Reads[0], ":", $start_drp, "-", $end_drp);
+	my $num_unmapped_pairs="";
+	if ($side =~ /right/) {
+		$num_unmapped_pairs=`samtools view $new_blacklist -q $MapQ -f8 -F 1536 -c $INPUT_BAM $target_drp`;
+	} else {
+        $num_unmapped_pairs=`samtools view $new_blacklist -q $MapQ -f24 -F 1536 -c $INPUT_BAM $target_drp`;
+	}
+if($verbose){print "samtools view $new_blacklist -q $MapQ -f24 -F 1536 -c $INPUT_BAM $target_drp\n";}
+
+	$num_unmapped_pairs=~s/\n//;
+if($verbose){print "NUM UNMAPPED PAIRS= $num_unmapped_pairs\n";}
+	my $REF1_base = "";
+	my $REF2_base = "";
+	my $INFO_1 = "";
+	my $INFO_2 = "";
+	my $ALT_1 = "";
+	my $ALT_2 = "";
+	my $isize = 0;
+	my $QUAL = "";
+	my $FORMAT = "GT:";
+
+	#### get 8 bit rand id
+	my $BND1_name = join "", map { ("a".."z")[rand 26] } 1..8;
+	my $BND2_name = join "", map { ("a".."z")[rand 26] } 1..8;
+	$BND1_name=join "_","BND",$BND1_name;
+	$BND2_name=join "_","BND",$BND2_name;
+
+	my $counts = {CTX => 0, DEL => 0, INS => 0, INV => 0, TDUP => 0, NOV_INS => 0 };
+	my $event_mate_info = {CTX => "", DEL => "", INS => "", INV => "", TDUP => "", NOV_INS => "" };
+
+	#### get mate pair info and counts per event
+	foreach my $e (sort keys %{$counts}) {
+		my $h = get_counts_n_info($e, $side, $MapQ, $file, $dist_To_Soft, $target_drp, $upper_limit, $lower_limit);
+
+		$counts->{$e} = $h->{count};
+		$event_mate_info->{$e} = $h->{info};
+	}
+#print Dumper($counts);
+
+	my $max = 0;
+	my $type = "UNKNOWN";
+	my $nRP = 0;
+	my $mate_info = "NA\tNA\tNA\tNA";
+	my $summary = "GT:";
+
+	#### find max count of events and set type, nRP and info to corresponding
+	#### max count event.
+	#### also create a summary string of all counts to be added to VCF file.
+	foreach my $e (sort keys %{$counts}){
+#		if ($counts->{$e} >=i $max){
+		if ($counts->{$e} > $max){		
+			$type = $e .",". $counts->{$e};
+			$nRP = $counts->{$e};
+
+			$max = $counts->{$e};
+
+			if (length($event_mate_info->{$e})) {
+				$mate_info = $event_mate_info->{$e};
+			}
+		}
+
+		$summary .= $e .",". $counts->{$e} .":";
+	}
+#	print "done with Summary\n";
+	#### remove last colon ":" from
+	$summary =~ s/:$//;
+ if (($minRP > $max)&&(!$disable_RP_only )){if ($verbose){print "FAILED BECAUSE ($minRP > $max)&&(!$disable_RP_only )"};return};
+
+	#### Run Levenstein distance on softclip in target region to find out if its a small deletion/insetion
+	#### passing 1: clip_seq, 2: chr, 3: start, 4: end, 5: ref file.
+	my $levD = new LevD;
+########################################################
+########################################################
+########################################################
+
+	#### redefine start and end location for LevD calc.
+#	$start = $plus_Reads[1]-$dist_To_Soft;
+#	$end = $plus_Reads[2];
+	my $num_bases_to_loc=0;
+	my $new_start=0;
+	my $new_end=0;
+	my $del_seq="";
+        my $start = $start_local;
+        my $end = $end_local;
+	if ($lSC=~/NA/){$lSC=0}
+
+	if ($side =~ /right/) {
+	        $levD->search($plus_Reads[3], $plus_Reads[0], $start, $end, $INPUT_FASTA);
+		$local_levD = sprintf("%.2f", $levD->{relative_edit_dist});
+	        $num_bases_to_loc=$levD->{index};
+		$new_start = $plus_Reads[2];
+                if ($plus_Reads[2]=~/^[0-9]/){$new_end=$plus_Reads[2]+$lSC};
+	}
+	else{
+		$levD->search($plus_Reads[3], $plus_Reads[0], $start, $end, $INPUT_FASTA);
+		$local_levD = sprintf("%.2f", $levD->{relative_edit_dist});
+		$num_bases_to_loc=$levD->{index};
+		if ($plus_Reads[2]=~/^[0-9]/){$new_start=$plus_Reads[2]-$lSC};
+                $new_end = $plus_Reads[2];
+	}
+	if((!$new_start)||(!$new_end)||($new_start<0)){print "FAILED AT ((!$new_start)||(!$new_end)||($new_start<0))\n";return};
+	
+	$del_seq=getBases($plus_Reads[0], $new_start,$new_end,$INPUT_FASTA);
+##############################################################################
+#	#If there is a match, where is the start position of the match?
+#
+##############################################################################
+
+
+	#if $plus_Reads[3] eq "NA", then it was found without soft-clipped reads
+	if($plus_Reads[3] !~  /NA/){
+			if (($local_levD < $levD_local_threshold)) {
+				return if (!$sv_only);
+				#### add value to summary to be written to vcf file.
+				$summary = "GT:sDel," . $plus_Reads[6];
+				$type = "sDEL";
+				###########################################################################
+				##### Printing output
+
+				#########################################
+				##### Get DNA info
+				#########################################
+				#$REF1_base = getSeq($plus_Reads[0], $plus_Reads[1], $INPUT_FASTA);
+				$REF1_base = substr($del_seq, 0, 1);
+
+				#### this is alt ref. for softclip its $plus_Reads[3]
+				$REF2_base = $del_seq;
+				$QUAL = 1/($local_levD + 0.001);
+				$QUAL = sprintf("%.2f",$QUAL);
+				$isize = length($del_seq);
+
+				#### svtype = none for sDEL
+				#### isize = length($info[3]);
+				#### nRP = NA
+				#### mate_id = NA
+				#### CTX,:DEL,:....sDEL,##
+				$INFO_1=join(";", "SVTYPE=NA", "EVENT=$type", "ISIZE=$isize");
+
+				#Add Sample infomration
+				my $FORMAT="GT:sDEL";
+				$FORMAT .= ":lSC:nSC:uRP:levD_local";
+				my $SAMPLE= "0/1:";
+				$SAMPLE .= "$plus_Reads[6]:$lSC:$nSC:$num_unmapped_pairs:$local_levD";
+
+				#### remove any white spaces.
+				$INFO_1=~s/\s//g;
+				$INFO_2=~s/\s//g;
+
+				$BND1_name =~ s/^BND/LEVD/;
+				# If left, then the start position is plus_Reads[1]-isize
+				my $start_pos=0;
+				#Make sure Ref1 and Ref2 bases are different
+				if($REF2_base eq $REF1_base){$REF1_base="NA"}
+				if($side=~/left/){$start_pos=$plus_Reads[1]-$isize}else{$start_pos=$plus_Reads[1]};		
+				print OUT join ("\t", $plus_Reads[0], $start_pos, $BND1_name, $REF2_base, $REF1_base, $QUAL, "PASS", $INFO_1,$FORMAT,$SAMPLE, "\n");
+				if ($verbose){print "No Softclipped reads here!\n"}
+				return;
+			}
+		}
+
+		#### Otherwise, look for DRP mate info
+	#if($nRP=~/NA/){print "MATE_INFO=$mate_info\tSide=$side\tline=$line\n";}
+		my @mate_info_arr = split(/\t/, $mate_info);
+		$nRP = $mate_info_arr[3];
+		my $mate_chr=$mate_info_arr[0];
+
+			if((! defined $nRP) || ($nRP =~ /na/i) || ($mate_chr =~ /NA/) ){
+			#PRINT UNKNOWN
+	if ($nRP =~ /na/i){print "Can't find SC reads\n" if ($verbose);return};
+	if ($verbose){print "There is an unknown\nNRP=$nRP Mate_CHR=$mate_chr minRP=$minRP\n"}
+				$summary .= ":unknown," . $plus_Reads[6];
+				$type = "unknown";
+				$REF1_base = getSeq($plus_Reads[0], $plus_Reads[1], $INPUT_FASTA);
+				$REF2_base = $plus_Reads[3];
+				$BND1_name =~ s/^BND/UNKNOWN/;
+				$QUAL = 1/($local_levD + 0.001);
+				$QUAL = sprintf("%.2f",$QUAL);
+				$INFO_1=join(";", "SVTYPE=unknown", "EVENT=unknown", "ISIZE=unknown");
+				#Add Sample infomration
+				my $FORMAT="GT:sDEL";
+				$FORMAT .= ":lSC:nSC:uRP:levD_local";
+				my $SAMPLE = "0/1:";
+				$SAMPLE .= "$plus_Reads[6]:$lSC:$nSC:$num_unmapped_pairs:$local_levD";
+				$SAMPLE=~s/NA/0/g;
+				#### remove any white spaces.
+				$INFO_1=~s/\s//g;
+			       #print join ("\t", $plus_Reads[0], $plus_Reads[1],  $REF2_base, $REF1_base, $QUAL, "PASS", $INFO_1,$FORMAT,$SAMPLE, "\n");
+
+				print OUT join ("\t", $plus_Reads[0], $plus_Reads[1], $BND1_name, $REF1_base, $REF2_base, $QUAL, "PASS", $INFO_1,$FORMAT,$SAMPLE, "\n");
+				return;
+
+		}
+		#### end if there is no mate info or nRP+uRP<minRP
+		if (($nRP<$minRP)&&($unmated_pairs > ($num_unmapped_pairs+$nRP))){
+			print "Something failed here\nif (($nRP<$minRP)&&($unmated_pairs > ($num_unmapped_pairs+$nRP)))\n";
+		return}
+
+		##################################################################################
+		# Find out if mates have nearby soft-clips (to refine the breakpoints)
+		##################################################################################
+		#Look for evidence of soft-clipping near mate
+		my @mate_soft_arr = ();
+		my $mate_start = 0;
+		my $mate_soft = "";
+
+		@mate_info_arr = split(/\t/, $mate_info);
+
+		#### mate start and end locations.
+		my $filename = $right_sc;
+
+		$start = $mate_info_arr[1] - $dist_To_Soft;
+		$end = $mate_info_arr[1];
+
+		if ($side =~ /right/) {
+			$start = $mate_info_arr[2];
+			$end = $mate_info_arr[2] + $dist_To_Soft;
+
+			$filename = $left_sc;
+		}
+
+		#### add levenstein distance to Summary
+	#print "Calc distal Levd\n";
+		$levD->search(rev_comp($plus_Reads[3]), $mate_info_arr[0], $start, $end, $INPUT_FASTA);
+		$distl_levD = sprintf("%.2f", $levD->{relative_edit_dist});
+	$distl_levD = "NA" if($plus_Reads[3] =~ /NA/);
+	#If there is no softclips to string match, then give 0 as quality value
+       if ($plus_Reads[3] !~ /NA/){
+			$QUAL=1/($distl_levD + 0.001);
+		}
+		else	{
+			$QUAL=0;
+		};
+	$QUAL=sprintf("%.2f",$QUAL);
+	#### looking for softclips to refine break point
+	#### if left look in right and vice-versa.
+	$cmd = qq{echo -e "$mate_info_arr[0]\t$start\t$end"};
+	$cmd .= qq{ | awk -F'\t' 'NF==3' | intersectBed -a stdin -b $filename | head -1};
+print "$cmd\n" if $verbose;
+	$mate_soft = `$cmd`;
+
+	$mate_soft =~ s/\n//g;
+	@mate_soft_arr = split(/\s/, $mate_soft);
+my $NO_MATE_SC="";
+	if(@mate_soft_arr){
+		$mate_chr = $mate_soft_arr[0];
+		$mate_start = $mate_soft_arr[1];
+                $NO_MATE_SC="APPROXIMATE";
+
+	} else{
+		@mate_info_arr = split(/\s/,$mate_info);
+		$mate_chr = $mate_info_arr[0];
+		$mate_start = $mate_info_arr[1];
+	}
+
+	#end if there is no mate info
+	return if ($mate_chr eq "");
+	#end if there is no mate info and !disable_RP_only
+	return if (($lSC =~/NA/)&&(!$disable_RP_only));
+	
+	
+	###########################################################################
+	##### Printing output
+
+	#########################################
+	# Get DNA info
+	#########################################
+	#print "PLUS_READS=$plus_Reads[0],$plus_Reads[1]\nMATE=$mate_chr,$mate_start,$INPUT_FASTA\n";
+	$REF1_base = getSeq($plus_Reads[0], $plus_Reads[1], $INPUT_FASTA);
+
+	### this is alt ref. for softclip its $plus_Reads[3]
+	$REF2_base = getSeq($mate_chr, $mate_start, $INPUT_FASTA);
+
+	#########################################
+	# print in VCF format
+	#########################################
+
+	#### abs value to account for left and right reads.
+	$isize = abs($plus_Reads[1]-$mate_start);
+	
+	my $event_type=$type;
+	$event_type=~ s/,|[0-9]//g;
+	$INFO_1=join(";", "$sv_type", "EVENT=$event_type","END=$mate_start", "ISIZE=$isize","MATEID=$BND2_name");
+	$INFO_2=join(";", "$sv_type", "EVENT=$event_type","END=$plus_Reads[1]", "ISIZE=$isize","MATEID=$BND1_name");
+
+	#### remove any white spaces.
+	#### ask: did you mean to remove space from ends? eg. trim()
+	$INFO_1=~s/\s//g;
+	$INFO_2=~s/\s//g;
+
+	$FORMAT=$summary;
+ 	$FORMAT=~ s/,|[0-9]//g;
+        $FORMAT .= ":lSC:nSC:uRP:distl_levD";
+	if($NO_MATE_SC){$INFO_2 .= ":NO_MATE_SC"}
+	my $SAMPLE="0/1:";	
+	$SAMPLE .=$summary;
+#        if($NO_MATE_SC){$SAMPLE.= ":$NO_MATE_SC"}
+
+	$SAMPLE=~s/[A-Z|,|_]//g;
+        my $MATE_SAMPLE=$SAMPLE;
+        $SAMPLE .= ":$lSC:$nSC:$num_unmapped_pairs:$distl_levD";
+	$MATE_SAMPLE .=":NA:NA:NA:NA";
+	$SAMPLE=~s/::/:/g;
+	$MATE_SAMPLE=~s/::/:/g;
+	$MATE_SAMPLE=~s/NA/0/g;
+	$SAMPLE=~s/NA/0/g;
+ 
+	if($type !~ /INV/){
+		$ALT_1 = join("","]",$mate_chr,":",$mate_start,"]",$REF1_base);
+		$ALT_2 = join("",$REF2_base,"[",$plus_Reads[0],":",$plus_Reads[1],"[");
+		#		2      321682 bnd_V  T   ]13:123456]T  6    PASS SVTYPE=BND
+		#		13     123456 bnd_U  C   C[2:321682[   6    PASS SVTYPE=BND
+	} else {
+		$ALT_1 = join("", "]", $plus_Reads[0], ":", $plus_Reads[1], "]", $REF2_base);
+		$ALT_2 = join("", $REF1_base, "[", $mate_chr, ":", $mate_start, "[");
+	}
+
+	if(($mate_chr) && ($plus_Reads[0])){
+		print OUT join ("\t", $plus_Reads[0], $plus_Reads[1], $BND1_name, $REF1_base, $ALT_1, $QUAL,"PASS", $INFO_1, $FORMAT,$SAMPLE,"\n");
+		print OUT join ("\t", $mate_chr, $mate_start, $BND2_name, $REF2_base, $ALT_2, $QUAL, "PASS", $INFO_2, $FORMAT,$MATE_SAMPLE,"\n");
+	}
+}
+
+###############################################################################
+###############################################################################
+sub get_counts_n_info {
+        my ($event, $side, $mapQ, $file, $dist, $target, $upL, $lwL) = @_;
+
+        my $mate_info = "";
+        my $cmd = "";
+
+        if ($event =~ /^CTX$/i) {
+                #print "CTX side $side\n";
+                if ($side =~ /right/i) {
+                        $cmd = qq{samtools view $new_blacklist -q $mapQ -f 32 -F 1536 $file $target};
+                        $cmd .= qq{ | perl -ane 'if(\$F[6] ne "="){\$end=\$F[7]+1; print join ("\\t",\$F[6],\$F[7],\$end,"\\n")}'};
+                        $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1};
+#if($verbose){print "$cmd\n"}
+                        $mate_info=`$cmd`;
+                } else {
+                        $cmd = qq{ samtools view $new_blacklist -q $mapQ -f 16 -F 1536 $file $target};
+                        $cmd .= qq{ | perl -ane 'if(\$F[6] ne "="){\$end=\$F[7]+1; print join ("\\t",\$F[6],\$F[7],\$end,"\\n")}'};
+                        $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1};
+#if($verbose){print "$cmd\n"}
+                        $mate_info=`$cmd`;
+                }
+        } elsif ($event =~ /^DEL$/i) {
+                #print "DEL side $side\n";
+                if ($side =~ /right/i) {
+                        $cmd = qq{samtools view $new_blacklist -q $mapQ  -f 32 -F 1552 $file $target};
+                        $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$9>$upL)){end=\$8+1;print \$3,\$8,end}}'};
+                        $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1};
+#if($verbose){print "$cmd\n"}
+                        $mate_info=`$cmd`;
+                } else {
+                        $cmd = qq{samtools view $new_blacklist -q $mapQ -F 1568 -f 16 $file $target};
+                        $cmd .= qq{ | awk '{OFS="\\t"} {if((\$7 ~ /=/)&&(\$9<-$upL)){end=\$8+1;print \$3,\$8,end}}'};
+                        $cmd .= qq{ | sortBed | mergeBed -d $dist_To_Soft -n | sort -k4nr | head -1};
+#if($verbose){print "$cmd\n"}
+
+                        $mate_info=`$cmd`;
+                }
+        } elsif ($event =~ /^INS$/i) {
+                #print "INS side $side\n";
+                if ($side =~ /right/i) {
+                        $cmd = qq{samtools view $new_blacklist -q $mapQ -f 32 -F 1552 $file $target};
+                        $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$9<$lwL && \$9 > 0 )){end=\$8+1;print \$3,\$8,end}}'};
+                        $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1};
+#if($verbose){print "$cmd\n"}
+                        $mate_info = `$cmd`;
+                } else {
+                        $cmd = qq {samtools view $new_blacklist -q $mapQ -f 16 -F 1568 $file $target};
+                        $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$9>-$lwL && \$9 < 0 )){end=\$8+1;print \$3,\$8,end}}'};
+                        $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1};
+#if($verbose){print "$cmd\n"}
+                        $mate_info = `$cmd`;
+                }
+        } elsif ($event =~ /^INV$/i) {
+                #print "INV side $side\n";
+                if ($side =~ /right/i) {
+                        $cmd = qq{samtools view $new_blacklist -q $mapQ  -F 1596 $file $target};
+                        $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)){end=\$8+1;print \$3,\$8,end}}'};
+                        $cmd .= qq{ | sortBed | mergeBed -d $dist_To_Soft -n | sort -k4nr | head -1};
+#if($verbose){print "$cmd\n"}
+                        $mate_info = `$cmd`;
+                } else {
+                        $cmd = qq{samtools view $new_blacklist -q $mapQ -f 48 -F 1548 $file $target};
+                        $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)){end=\$8+1;print \$3,\$8,end}}'};
+                        $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1};
+#if($verbose){print "$cmd\n"}
+                        $mate_info = `$cmd`;
+                }
+        } elsif ($event =~ /^TDUP$/i) {
+                #print "TDUP side $side\n";
+                if ($side =~ /right/i) {
+                        $cmd = qq{samtools view $new_blacklist -q $mapQ -f 32 -F 1552 $file $target};
+#			$cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$9>$upL)){end=\$8+1;print \$3,\$8,end}}'};
+			$cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$4>\$8)&&(\$9<0)&& (\$9>$upL)){end=\$8+1;print \$3,\$8,end}}'};
+                        $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1};
+#if($verbose){print "$cmd\n"}
+                        $mate_info = `$cmd`;
+                } else {
+                        $cmd = qq{samtools view $new_blacklist -q $mapQ -f 16 -F 1568 $file $target};
+#                        $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$9<-$upL )){end=\$8+1;print \$3,\$8,end}}'};
+                        $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$4<\$8)&&(\$9>0)&&(\$9>$upL)){end=\$8+1;print \$3,\$8,end}}'};
+                        $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1};
+#if($verbose){print "$cmd\n"}
+                        $mate_info = `$cmd`;
+                }
+        } elsif ($event =~ /^NOV_INS$/i) {
+                #print "NOV_INS side $side\n";
+                if ($side =~ /right/i) {
+                        $cmd = qq{samtools view $new_blacklist -q $mapQ -f 8 -F 1552 $file $target};
+                        $cmd .= qq{ | awk '{OFS="\\t"}{end=\$8+1;print \$3,\$8,end}'};
+                        $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1};
+#if($verbose){print "$cmd\n"}
+                        $mate_info = `$cmd`;
+                } else {
+                        $cmd = qq{samtools view $new_blacklist -q $mapQ  -f 24 -F 1536 $file $target};
+                        $cmd .= qq{ | awk '{OFS="\\t"}{end=\$8+1;print \$3,\$8,end}'};
+                        $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1};
+#if($verbose){print "$cmd\n"}
+                        $mate_info = `$cmd`;
+                }
+        }
+
+        $mate_info=~s/\n//g;
+        my @tmp=split(/\t/, $mate_info);
+
+        my $counts = 0;
+
+        if (defined $tmp[3]) {
+                $tmp[3] =~ s/\n//g;
+
+                $counts = $tmp[3] if (length($tmp[3]));
+        }
+        return ({count=>$counts, info=>$mate_info});                                                                                                                                
+}
diff -r 4e09cf4d692a -r 925f6330cd80 softsearch_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/softsearch_wrapper.xml	Thu Jun 19 08:43:52 2014 -0400
@@ -0,0 +1,56 @@
+<?xml version="1.0"?>
+<tool id="Softsearch" name="softsearch" version="0.6">
+  <requirements>
+	    	<requirement type="package" version="0.6">softsearch</requirement>
+  </requirements>
+  <description>for structure variation</description>
+  <command>#if $source.index_source=="history" 
+	        samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.history_fasta_file -o $out_file1
+	    #else
+		samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.ref_fasta.fields.path -o $out_file1
+	    #end if		
+ </command>
+  <inputs>
+      <param name="bam_file" type="data"   format="bam" label="BAM Files" />
+	 <conditional name="source">
+            <param name="index_source" type="select" label="Choose the source for the reference list">
+                <option value="cached">Locally cached</option>
+                <option value="history">History</option>
+            </param>
+            <when value="history">
+                <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/>
+            </when>
+            <when value="cached">
+                  <param name="ref_fasta" type="select" >
+                    <options from_data_table="fasta_indexes">
+                    <validator type="no_options" message="No Fasta file is available" />
+                    </options>
+                  </param>
+            </when>
+        </conditional>
+      <param name="inc" type="hidden" value="n=$RANDOM" />
+     	<param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" /> 
+        <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" /> 	
+	<param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" /> 
+	<param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" /> 
+	<param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" />       
+  </inputs>
+  <outputs>
+      <data format="vcf" name="out_file1" />
+  </outputs>
+  <help>
+  </help>
+</tool>
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 4e09cf4d692a -r 925f6330cd80 tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Thu Jun 19 08:43:52 2014 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 4e09cf4d692a -r 925f6330cd80 tool-data/tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tool_data_table_conf.xml.sample	Thu Jun 19 08:43:52 2014 -0400
@@ -0,0 +1,82 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    <!-- Locations of indexes in the BFAST mapper format -->
+    <table name="bfast_indexes" comment_char="#">
+        <columns>value, dbkey, formats, name, path</columns>
+        <file path="tool-data/bfast_indexes.loc" />
+    </table>
+    <!-- Locations of nucleotide (mega)blast databases -->
+    <table name="blastdb" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/blastdb.loc" />
+    </table>
+    <!-- Locations of protein (mega)blast databases -->
+    <table name="blastdb_p" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/blastdb_p.loc" />
+    </table>
+    <!-- Locations of indexes in the BWA mapper format -->
+    <table name="bwa_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bwa_index.loc" />
+    </table>
+    <!-- Locations of indexes in the BWA color-space mapper format -->
+    <table name="bwa_indexes_color" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bwa_index_color.loc" />
+    </table>
+    <!-- Locations of MAF files that have been indexed with bx-python -->
+    <table name="indexed_maf_files">
+        <columns>name, value, dbkey, species</columns>
+        <file path="tool-data/maf_index.loc" />
+    </table>
+    <!-- Locations of fasta files appropriate for NGS simulation -->
+    <table name="ngs_sim_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/ngs_sim_fasta.loc" />
+    </table>
+    <!-- Locations of PerM base index files -->
+    <table name="perm_base_indexes" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/perm_base_index.loc" />
+    </table>
+    <!-- Locations of PerM color-space index files -->
+    <table name="perm_color_indexes" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/perm_color_index.loc" />
+    </table>
+    <!-- Location of Picard dict file and other files -->
+    <table name="picard_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/picard_index.loc" />
+    </table>
+    <!-- Location of Picard dict files valid for GATK -->
+    <table name="gatk_picard_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/gatk_sorted_picard_index.loc" />
+    </table>
+    <!-- Available of GATK references -->
+    <table name="gatk_annotations" comment_char="#">
+        <columns>value, name, gatk_value, tools_valid_for</columns>
+        <file path="tool-data/gatk_annotations.txt" />
+    </table>
+    <!-- Location of SRMA dict file and other files -->
+    <table name="srma_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/picard_index.loc" />
+    </table>
+    <!-- Location of Mosaik files -->
+    <table name="mosaik_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/mosaik_index.loc" />
+    </table>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>
diff -r 4e09cf4d692a -r 925f6330cd80 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jun 19 08:43:52 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+   	<package name="softsearch" version="0.6">
+       <repository changeset_revision="1f22f71328fa" name="softsearch_dependency" owner="researchdx-plus91technologies" toolshed="http://toolshed.g2.bx.psu.edu"/>
+   </package>	
+</tool_dependency>