--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pileup_parser.pl	Mon Aug 26 15:14:34 2013 -0400
@@ -0,0 +1,121 @@
+#! /usr/bin/perl -w
+
+use strict;
+use POSIX;
+
+
+die "Usage: pileup_parser.pl <in_file> <ref_base_column> <read_bases_column> <base_quality_column> <coverage column> <qv cutoff> <coverage cutoff> <SNPs only?> <output bed?> <coord_column> <out_file> <total_diff> <print_qual_bases>\n" unless @ARGV == 13;
+
+my $in_file = $ARGV[0];
+my $ref_base_column = $ARGV[1]-1; # 1 based
+my $read_bases_column = $ARGV[2]-1; # 1 based
+my $base_quality_column = $ARGV[3]-1; # 1 based
+my $cvrg_column = $ARGV[4]-1; # 1 based
+my $quality_cutoff = $ARGV[5]; # phred scale integer
+my $cvrg_cutoff = $ARGV[6]; # unsigned integer
+my $SNPs_only = $ARGV[7]; # set to "Yes" to print only positions with SNPs; set to "No" to pring everything
+my $bed = $ARGV[8]; #set to "Yes" to convert coordinates to bed format (0-based start, 1-based end); set to "No" to leave as is
+my $coord_column = $ARGV[9]-1; #1 based 
+my $out_file = $ARGV[10];
+my $total_diff = $ARGV[11]; # set to "Yes" to print total number of deviant based
+my $print_qual_bases = $ARGV[12]; #set to "Yes" to print quality and read base columns
+
+my $invalid_line_counter = 0;
+my $first_skipped_line = "";
+my %SNPs = ('A',0,'T',0,'C',0,'G',0);
+my $above_qv_bases = 0;
+my $SNPs_exist = 0;
+my $out_string = "";
+my $diff_count = 0;
+
+open (IN, "<$in_file") or die "Cannot open $in_file $!\n";
+open (OUT, ">$out_file") or die "Cannot open $out_file $!\n";
+
+while (<IN>) {
+	chop;
+	next if m/^\#/;
+	my @fields = split /\t/;
+	next if $fields[ $ref_base_column ] eq "*"; # skip indel lines
+ 	my $read_bases   = $fields[ $read_bases_column ];
+ 	die "Coverage column" . ($cvrg_column+1) . " contains non-numeric values. Check your input parameters as well as format of input dataset." if ( not isdigit $fields[ $cvrg_column ] );
+    next if $fields[ $cvrg_column ] < $cvrg_cutoff;
+	my $base_quality = $fields[ $base_quality_column ];
+	if ($read_bases =~ m/[\$\^\+-]/) {
+		$read_bases =~ s/\^.//g; #removing the start of the read segement mark
+		$read_bases =~ s/\$//g; #removing end of the read segment mark
+		while ($read_bases =~ m/[\+-]{1}(\d+)/g) {
+			my $indel_len = $1;
+			$read_bases =~ s/[\+-]{1}$indel_len.{$indel_len}//; # remove indel info from read base field
+		}
+	}
+	if ( length($read_bases) != length($base_quality) ) {
+        $first_skipped_line = $. if $first_skipped_line eq "";
+        ++$invalid_line_counter;
+        next;
+	}
+	# after removing read block and indel data the length of read_base 
+	# field should identical to the length of base_quality field
+	
+	my @bases = split //, $read_bases;
+	my @qv    = split //, $base_quality;
+	
+	for my $base ( 0 .. @bases - 1 ) {
+		if ( ord( $qv[ $base ] ) - 33 >= $quality_cutoff and $bases[ $base ] ne '*')
+		{
+			++$above_qv_bases;
+			
+			if ( $bases[ $base ] =~ m/[ATGC]/i )
+			{
+				$SNPs_exist = 1;	
+				$SNPs{ uc( $bases[ $base ] ) } += 1;
+				$diff_count += 1;
+			} elsif ( $bases[ $base ] =~ m/[\.,]/ ) {
+			    $SNPs{ uc( $fields[ $ref_base_column ] ) } += 1;
+		    }		 	
+		}
+	} 
+	
+	if ($bed eq "Yes") {
+	       my $start = $fields[ $coord_column ] - 1;
+	       my $end   = $fields[ $coord_column ];
+	       $fields[ $coord_column ] = "$start\t$end";
+	} 
+	
+	if ($print_qual_bases ne "Yes") {
+	       $fields[ $base_quality_column ] = "";
+	       $fields[ $read_bases_column ] = "";
+	}
+	       
+	
+	$out_string = join("\t", @fields); # \t$read_bases\t$base_quality";
+	foreach my $SNP (sort keys %SNPs) {
+			$out_string .= "\t$SNPs{$SNP}";
+	}
+	
+	if ($total_diff eq "Yes") {
+	   $out_string .= "\t$above_qv_bases\t$diff_count\n";
+	} else {
+	   $out_string .= "\t$above_qv_bases\n";
+	}	
+	
+	$out_string =~ s/\t+/\t/g;
+	
+	if ( $SNPs_only eq "Yes" ) {
+		print OUT $out_string if $SNPs_exist == 1;
+	} else {
+		print OUT $out_string;
+	}
+
+		
+	%SNPs = ();
+	%SNPs = ('A',0,'T',0,'C',0,'G',0);
+	$above_qv_bases = 0;
+	$SNPs_exist = 0;
+	$diff_count = 0;
+	
+
+}
+
+print "Skipped $invalid_line_counter invalid line(s) beginning with line $first_skipped_line\n" if $invalid_line_counter > 0;
+close IN;
+close OUT;