--- a/varscan_somatic.pl	Tue Mar 11 06:11:19 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,173 +0,0 @@
-#!/usr/bin/perl
-
-
-use strict;
-use Cwd;
-
-die qq(
-Bad numbr of inputs
-
-) if(!@ARGV);
-
-my $options ="";
-my $normal="";
-my $command="";
-my $tumor="";
-my $tumorbam = "";
-my $output="";
-my $snp="";
-my $indel="";
-my $working_dir = cwd();
-my $log = '';
-
-foreach my $input (@ARGV) 
-{
-	my @tmp = split "::", $input;
-	if($tmp[0] eq "COMMAND") 
-	{
-		$command = $tmp[1];
-	} 
-	elsif($tmp[0] eq "NORMAL") 
-	{
-		$normal = $tmp[1];
-	} 
-	elsif($tmp[0] eq "TUMOR") 
-	{
-		$tumor = $tmp[1];
-	}
-	elsif($tmp[0] eq "TUMORBAM")
-	{
-		$tumorbam = $tmp[1];
-	}
-	elsif($tmp[0] eq "OPTION") 
-	{
-		my @p = split(/\s+/,$tmp[1]);
-		if ($p[0] =~ m/validation|strand-filter|output-vcf/ && $p[1] == 0) {
-			next;
-		}
-		$options = "$options ${tmp[1]}";
-	}
-	elsif($tmp[0] eq "OUTPUT") 
-	{
-		$output = $tmp[1];
-	}
-	elsif($tmp[0] eq "SNP") 
-	{
-		$snp = $tmp[1];
-	}
-	elsif($tmp[0] eq "INDEL") 
-	{
-		$indel = $tmp[1];
-	}
-
-	elsif($tmp[0] eq "LOG")
-        {
-                $log = $tmp[1];
-        }
-	
-	else 
-	{
-		die("Unknown Input: $input\n");
-	}
-}
-
-## VCF OUTPUT 
-if ($output ne '') {
-	system ("$command $normal $tumor $options --output-snp $working_dir/out.snp --output-indel $working_dir/out.indel 2>$log");
-	my $indels = "$working_dir/out.indel.vcf";
-	my $snps = "$working_dir/out.snp.vcf";
-	
-	system("grep -v '^\#' $indels | grep -v '^chrom position' >> $snps");
-	my @chr_ord = chromosome_order($tumorbam);
-
-	vs2vcf($snps, $output,\@chr_ord);
-}
-## SNP/INDEL OUTPUT
-else {
-	system  ("$command $normal $tumor $options --output-snp $snp --output-indel $indel 2>$log");
-}
-
-sub vs2vcf 
-{
-
-	#
-	# G l o b a l     v a r i a b l e s 
-	#
-	my $version = '0.1';
-
-	#
-	# Read in file
-	#
-	my $input = shift;
-	my $output = shift;
-	my $chr_ord = shift;
-	open(IN, $input) or die "Can't open $input': $!\n";
-	open(OUT, ">$output") or die "Can't create $output': $!\n";
-	my %output;
-
-	while ( <IN> )
-	{
-		if ( /^#/ )
-		{
-			print OUT;
-			next;
-		}
-		chomp;
-		my $line = $_;
-
-		my @flds = split ( "\t", $line );
-		my $ref = $flds[3];
-		my $alt = $flds[4];
-		#
-		# Deletion of bases
-		#
-		if ( $alt =~ /^\-/ )
-		{
-			($flds[3], $flds[4]) = ($ref.substr($alt,1), $ref);
-		}
-
-		#
-		# Insertion of bases
-		#
-		if ( $alt =~ /^\+/ )
-		{
-			$flds[4] = $ref.substr($alt,1);
-		}
-		## insert dot for reference positions.
-		if ($flds[4] eq '') {
-			$flds[4] = '.';
-		}
-		print OUT join( "\t", @flds),"\n" unless defined $chr_ord;
-		$output{$flds[0]}{$flds[1]} = join( "\t", @flds)."\n" if defined $chr_ord;
-	}
-	close(IN);
-	# if chromosome order given return in sorted order
-	if(defined $chr_ord) 
-	{
-		for my $chrom (@{ $chr_ord }) 
-		{
-			for my $pos (sort {$a<=>$b} keys %{ $output{$chrom} }) 
-			{
-				print OUT $output{$chrom}{$pos};
-			}
-		}
-	}
-	close(OUT);
-}
-
-
-sub chromosome_order 
-{
-	my $input = shift;
-	# calculate flagstats
-	my $COMM = "samtools view -H $input | grep '^\@SQ'";
-	my @SQ = `$COMM`;
-	chomp @SQ;
-	for(my $i = 0; $i <= $#SQ; $i++) 
-	{
-		$SQ[$i] =~ s/^\@SQ\tSN:(.*?)\tLN:\d+$/$1/;
-	} 
-	return(@SQ);
-}
-
-