--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2.4/src/SoftSearch_Filter.pl	Mon Jun 02 07:35:53 2014 -0400
@@ -0,0 +1,137 @@
+#!/usr/bin/perl -s
+open (FILE,"$ARGV[0]")||usage();#die "Not using the right Parameters!\n\n";
+use Getopt::Long;
+#Declare variables
+my ($lsc,$minDist,$skip,$nSC,$nRP,$isize,$answer);
+GetOptions(
+	'dist:s' => \$minDist,		#minimum distance between events
+	'lsc:i' => \$lsc,		#minimum somatic score
+	'nsc:i' => \$nsc, 	#minimum depth of coverage in normal
+	'nRP:i' => \$nRP,	#minimum number of times it can be seen in tumor
+	'isize:i' => \$isize,	
+	'sv:s' => \$sv,		#whether or not to skip small deletions
+	'q:s' => \$answer,		#useful for plotting histograms
+	'skip:s' => \$skip
+	);
+if(defined($lsc)){$lsc=$lsc} else {$lsc=0};
+if(defined($nsc)){$nsc=$nsc} else {$nsc=0};
+if(defined($nRP)){$nRP=$nRP} else {$nRP=0};
+if(defined($minDist)){$minDist=$minDist} else {$minDist=0};
+if(!$isize){$isize=0};
+if(!$uRP){$uRP=0};
+
+if($answer eq "yes"){$answer=$answer} else {$answer="no"};
+
+if ($answer eq "yes"){
+open(lsc,">lsc.out")||die;
+open(nsc,">nsc.out")||die;
+open(nRP,">nRP.out")||die;
+}
+
+
+#Remove hits if they are within $minDist
+$chr="chr1";$pos=0;
+while (<FILE>){
+	if ($_=~/^#/){
+		print; 
+		next
+	};
+	if ($skip){next if $_=~/$skip/}
+	@_=split(/\t/,$_);
+	#Get ISIZE from INFO field
+	my @info=split(/;/,$_[7]);
+       	my $k = 0;
+	my $v = 0; 
+	my $infoHash;
+	for (my $i=0;$i<=@info;$i++){
+        	my @tmp=split(/=/,$info[$i]);
+		$k=shift(@tmp);
+		$v=shift(@tmp);
+		$infoHash{$k}=$v;
+	}
+
+	#Get the value of TYPE to find out how many reads support the event
+        my $counts = {CTX => 0, DEL => 0, INS => 0, INV => 0, TDUP => 0, NOV_INS => 0, lSC => 0, nSC => 0,uRP =>0,sDEL => 0,levD_local=>0,distl_levD => 0 };
+	#Get Complete Hash
+	#@_[8] is format
+	#@_[9] is values
+	my @format=split(/:/, $_[8]);
+	my @sample=split(/:/,$_[9]);
+	my %hash; 
+	@hash{@format}=@sample;
+	#Subset has to get proper type of variants
+	my $max_val = 0;
+	my $max_type = "NA";
+	
+	#Get TYPEOF HASH 
+	my %type;
+	%type = %hash ;
+	delete $type{'lSC'};
+        delete $type{'nSC'};
+        delete $type{'uRP'};
+        delete $type{'levD_local'};
+        delete $type{'distl_levD'};
+
+ 	while (my ($key,$val)=each(%type)){
+		if($val > $max_val){$max_val=$val;$max_type=$key}
+		}
+
+
+#######################################################################################################
+        #Start applying filters
+	
+	#Remove hits if they are within $minDist
+	$chrom=$_[0];$position=$_[1];
+
+	#next if chroms are same and distance is less than X
+	$difference=abs($pos-$position);
+	if(($chrom eq $chr)&&($difference < $minDist)){
+		$pos=$position;$chr=$chrom;;
+		next}
+	$pos=$position;$chr=$chrom;	
+	$EVENT_SIZE=$infoHash{'ISIZE'};
+	$EVENT_TYPE=$max_type;
+	$EVENT_SUPPORT=$max_val;
+	$length_of_softClips=$hash{'lSC'};
+	$number_of_softclips=$hash{'nSC'};
+        $number_of_unmated=$hash{'uRP'};
+	
+	########################################################################
+	#Print if all fileds are ok
+	next if($EVENT_SIZE < $isize);
+        next if($EVENT_SUPPORT < $nRP);
+        next if($length_of_softClips < $lsc);
+        next if($number_of_softclips < $nsc);
+        next if($number_of_unmated < $uRP);
+	next if (($sv)&&($EVENT_TYPE=~/sDEL/));
+	print;
+
+
+	if ($answer eq "yes"){
+	print lsc $length_of_softClips."\n";
+	print nsc $number_of_softclips."\n";
+	print nRP $EVENT_SUPPORT."\n";
+	}
+}
+
+
+sub usage{
+print "\nUsage: Soft_SearchFilter.pl <VCF>\n
+	-dist	#minimum distance between events [0]
+	-lsc	#minimum length soft-clip [0]
+	-nsc	#minimum number of soft-clip [0]
+	-nRP	#minimum number of discordant read pairs [0]
+	-isize	#minimum size [0]
+	-sv	#skip small deletions [no|yes]
+	-skip	#pipe-delimited list of strings to skip (e.g. chrM|chY|chrGL)
+	\n"
+}
+
+#R
+# lsc<-read.table("lsc.out")
+# nsc<-read.table("nsc.out")
+# nRP<-read.table("nRP.out")
+# par(mfrow=c(2,2))
+# hist(lsc$V1,breaks=100)
+# hist(nsc$V1,breaks=100)
+# hist(nRP$V1,breaks=100)