# HG changeset patch
# User devteam
# Date 1377544474 14400
# Node ID ff1ba9b75337af771f42d10f1d23972b4eb1bda0

Uploaded tool tarball.

diff -r 000000000000 -r ff1ba9b75337 pileup_parser.pl
--- /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;
diff -r 000000000000 -r ff1ba9b75337 pileup_parser.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pileup_parser.xml	Mon Aug 26 15:14:34 2013 -0400
@@ -0,0 +1,387 @@
+<tool id="pileup_parser" name="Filter pileup" version="1.0.2">>
+  <description>on coverage and SNPs</description>
+  <command interpreter="perl">
+    #if   $pileup_type.type_select == "six"    #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 $diff $qc_base
+    #elif $pileup_type.type_select == "ten"    #pileup_parser.pl $input "3" "9" "10" "8" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 $diff $qc_base
+    #elif $pileup_type.type_select == "manual" #pileup_parser.pl $input $pileup_type.ref_base_column $pileup_type.read_bases_column $pileup_type.read_qv_column $pileup_type.cvrg_column $qv_cutoff $cvrg_cutoff $snps_only $interval $pileup_type.coord_column $out_file1 $diff $qc_base
+    #end if#
+  </command>
+  <inputs>
+    <param name="input" type="data" format="pileup" label="Select dataset"/>
+    <conditional name="pileup_type">
+        <param name="type_select" type="select" label="which contains" help="See &quot;Types of pileup datasets&quot; below for examples">
+            <option value="six" selected="true">Pileup with six columns (simple)</option>
+            <option value="ten">Pileup with ten columns (with consensus)</option>
+            <option value="manual">Set columns manually</option>
+        </param>
+        <when value="manual">
+            <param name="ref_base_column" label="Select column with reference base" type="data_column" numerical="false" data_ref="input" />
+            <param name="read_bases_column" label="Select column with read bases" type="data_column" numerical="false" data_ref="input" help="something like this: ..,a.."/>
+            <param name="read_qv_column" label="Select column with base qualities" type="data_column" numerical="false" data_ref="input" help="something like this: IIIGIAI"/>
+            <param name="cvrg_column" label="Select column with coverage" type="data_column" numerical="true" data_ref="input" />
+            <param name="coord_column" label="Select coordinate column" type="data_column" numerical="true" data_ref="input" />
+        </when>
+        <when value="six">
+        </when>
+        <when value="ten">
+        </when>
+    </conditional>
+    <param name="qv_cutoff" label="Do not consider read bases with quality lower than" type="integer" value="20" help="No variants with quality below this value will be reported"/>
+    <param name="cvrg_cutoff" label="Do not report positions with coverage lower than" type="integer" value="3" help="Pileup lines with coverage lower than this value will be skipped"/>
+    <param name="snps_only" label="Only report variants?" type="select" help="See &quot;Examples 1 and 2&quot; below for explanation">
+        <option value="No">No</option>
+        <option value="Yes" selected="true">Yes</option>
+    </param>
+    <param name="interval" label="Convert coordinates to intervals?" type="select" help="See &quot;Output format&quot; below for explanation">
+        <option value="No" selected="true">No</option>
+        <option value="Yes">Yes</option>
+    </param>
+    <param name="diff" label="Print total number of differences?" type="select" help="See &quot;Example 3&quot; below for explanation">
+        <option value="No" selected="true">No</option>
+        <option value="Yes">Yes</option>
+    </param>
+    <param name="qc_base" label="Print quality and base string?" type="select" help="See &quot;Example 4&quot; below for explanation">
+        <option value="No">No</option>
+        <option value="Yes" selected="true">Yes</option>
+    </param>
+        
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_file1">
+        <change_format>
+            <when input="interval" value="Yes" format="interval" />
+        </change_format>
+   </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="pileup_parser.6col.pileup"/>
+      <output name="out_file1" file="pileup_parser.6col.20-3-yes-yes.pileup.out"/>
+      <param name="type_select" value="six"/>
+      <param name="qv_cutoff" value="20" />
+      <param name="cvrg_cutoff" value="3" />
+      <param name="snps_only" value="Yes"/>
+      <param name="interval" value="Yes" />
+      <param name="diff" value="No" />
+      <param name="qc_base" value="Yes" />
+    </test>
+    <test>
+      <param name="input" value="pileup_parser.6col.pileup"/>
+      <output name="out_file1" file="pileup_parser.6col.20-3-yes-no.pileup.out"/>
+      <param name="type_select" value="six"/>
+      <param name="qv_cutoff" value="20" />
+      <param name="cvrg_cutoff" value="3" />
+      <param name="snps_only" value="Yes"/>
+      <param name="interval" value="No" />
+       <param name="diff" value="No" />
+      <param name="qc_base" value="Yes" />
+    </test>
+    <test>
+      <param name="input" value="pileup_parser.6col.pileup"/>
+      <output name="out_file1" file="pileup_parser.6col.20-3-no-no.pileup.out"/>
+      <param name="type_select" value="six"/>
+      <param name="qv_cutoff" value="20" />
+      <param name="cvrg_cutoff" value="3" />
+      <param name="snps_only" value="No"/>
+      <param name="interval" value="No" />
+       <param name="diff" value="No" />
+      <param name="qc_base" value="Yes" />
+    </test>
+    <test>
+      <param name="input" value="pileup_parser.10col.pileup"/>
+      <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes.pileup.out"/>
+      <param name="type_select" value="ten"/>
+      <param name="qv_cutoff" value="20" />
+      <param name="cvrg_cutoff" value="3" />
+      <param name="snps_only" value="Yes"/>q
+      <param name="interval" value="Yes" />
+       <param name="diff" value="No" />
+      <param name="qc_base" value="Yes" />
+    </test>
+    <test>
+      <param name="input" value="pileup_parser.10col.pileup"/>
+      <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes.pileup.out"/>
+      <param name="type_select" value="manual"/>
+      <param name="ref_base_column" value="3"/>
+      <param name="read_bases_column" value="9"/>
+      <param name="read_qv_column" value="10"/>
+      <param name="cvrg_column" value="8"/>
+      <param name="coord_column" value="2"/>
+      <param name="qv_cutoff" value="20" />
+      <param name="cvrg_cutoff" value="3" />
+      <param name="snps_only" value="Yes"/>
+      <param name="interval" value="Yes" />
+       <param name="diff" value="No" />
+      <param name="qc_base" value="Yes" />
+    </test>
+        <test>
+      <param name="input" value="pileup_parser.10col.pileup"/>
+      <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes-yes-yes.pileup.out"/>
+      <param name="type_select" value="manual"/>
+      <param name="ref_base_column" value="3"/>
+      <param name="read_bases_column" value="9"/>
+      <param name="read_qv_column" value="10"/>
+      <param name="cvrg_column" value="8"/>
+      <param name="coord_column" value="2"/>
+      <param name="qv_cutoff" value="20" />
+      <param name="cvrg_cutoff" value="3" />
+      <param name="snps_only" value="Yes"/>
+      <param name="interval" value="Yes" />
+       <param name="diff" value="Yes" />
+      <param name="qc_base" value="Yes" />
+    </test>
+    <test>
+      <param name="input" value="pileup_parser.10col.pileup"/>
+      <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes-yes-no.pileup.out"/>
+      <param name="type_select" value="manual"/>
+      <param name="ref_base_column" value="3"/>
+      <param name="read_bases_column" value="9"/>
+      <param name="read_qv_column" value="10"/>
+      <param name="cvrg_column" value="8"/>
+      <param name="coord_column" value="2"/>
+      <param name="qv_cutoff" value="20" />
+      <param name="cvrg_cutoff" value="3" />
+      <param name="snps_only" value="Yes"/>
+      <param name="interval" value="Yes" />
+       <param name="diff" value="Yes" />
+      <param name="qc_base" value="No" />
+    </test>
+
+
+ </tests>
+<help>
+
+**What it does**
+
+Allows one to find sequence variants and/or sites covered by a specified number of reads with bases above a set quality threshold. The tool works on six and ten column pileup formats produced with *samtools pileup* command. However, it also allows you to specify columns in the input file manually. The tool assumes the following:
+
+- the quality scores follow phred33 convention, where input qualities are ASCII characters equal to the Phred quality plus 33.
+- the pileup dataset was produced by the *samtools pileup* command (although you can override this by setting column assignments manually).
+
+--------
+
+**Types of pileup datasets**
+
+The descriptions of the following pileup formats are largely based on information that can be found on the SAMTools_ documentation page. The 6- and 10-column variants are described below.
+
+.. _SAMTools: http://samtools.sourceforge.net/pileup.shtml
+
+**Six column pileup**::
+
+    1    2  3  4        5        6
+ ---------------------------------   
+ chrM  412  A  2       .,       II
+ chrM  413  G  4     ..t,     IIIH
+ chrM  414  C  4     ..Ta     III2
+ chrM  415  C  4     TTTt     III7
+   
+where::
+
+  Column Definition
+ ------- ----------------------------
+       1 Chromosome
+       2 Position (1-based)
+       3 Reference base at that position
+       4 Coverage (# reads aligning over that position)
+       5 Bases within reads
+       6 Quality values (phred33 scale, see Galaxy wiki for more)
+       
+**Ten column pileup**
+
+The `ten-column`__ pileup incorporates additional consensus information generated with the *-c* option of the *samtools pileup* command::
+
+
+    1    2  3  4   5   6   7   8       9       10
+ ------------------------------------------------
+ chrM  412  A  A  75   0  25  2       .,       II
+ chrM  413  G  G  72   0  25  4     ..t,     IIIH
+ chrM  414  C  C  75   0  25  4     ..Ta     III2
+ chrM  415  C  T  75  75  25  4     TTTt     III7
+
+where::
+
+  Column Definition
+ ------- ----------------------------
+       1 Chromosome
+       2 Position (1-based)
+       3 Reference base at that position
+       4 Consensus bases
+       5 Consensus quality
+       6 SNP quality
+       7 Maximum mapping quality
+       8 Coverage (# reads aligning over that position)
+       9 Bases within reads
+      10 Quality values (phred33 scale, see Galaxy wiki for more)
+
+
+.. __: http://samtools.sourceforge.net/cns0.shtml
+
+------
+
+**The output format**
+
+The tool modifies the input dataset in two ways:
+
+1. It appends five columns to the end of every reported line:
+
+- Number of **A** variants
+- Number of **C** variants
+- Number of **G** variants
+- Number of **T** variants
+- Number of read bases covering this position, where quality is equal to or higher than the value set by **Do not consider read bases with  quality lower than** option. 
+
+Optionally, if **Print total number of differences?** is set to **Yes**, the tool will append the sixth column with the total number of deviants (see below).
+
+2. If **Convert coordinates to intervals?** is set to **Yes**, the tool replaces the position column (typically the second column) with a pair of tab-delimited start/end values.
+
+For example, if you are calling variants with base quality above 20 on this dataset::
+
+ chrM  412  A  2       .,       II
+ chrM  413  G  4     ..t,     III2
+ chrM  414  C  4     ..Ta     III2
+ chrM  415  C  4     TTTt     III7
+
+you will get::
+
+ chrM  413  G  4  ..t,  IIIH  0  0  2  1  3
+ chrM  414  C  4  ..Ta  III2  1  1  0  1  3
+ chrM  415  C  4  TTTt  III7  0  0  0  4  4
+ 
+where::
+
+  Column Definition
+ ------- ----------------------------
+       1 Chromosome
+       2 Position (1-based)
+       3 Reference base at that position
+       4 Coverage (# reads aligning over that position)
+       5 Bases within reads where
+       6 Quality values (phred33 scale, see Galaxy wiki for more)
+       7 Number of A variants
+       8 Number of C variants
+       9 Number of G variants
+      10 Number of T variants
+      11 Quality adjusted coverage:
+      12 Number of read bases (i.e., # of reads) with quality above the set threshold
+      13 Total number of deviants (if Convert coordinates to intervals? is set to yes)
+         
+if **Print total number of differences?** is set to **Yes**, you will get::
+
+ chrM  413  G  4  ..t,  IIIH  0  0  2  1  3  1
+ chrM  414  C  4  ..Ta  III2  1  2  0  1  3  2
+ chrM  415  C  4  TTTt  III7  0  0  0  4  4  0 
+ 
+Note the additional column 13, that contains the number of deviant reads (e.g., there are two deviants, T and a, for position 414).
+
+ 
+Finally, if **Convert coordinates to intervals?** is set to **Yes**, you will get one additional column with the end coordinate::
+ 
+ chrM  412 413  G  4  ..t,  III2  0  0  2  1  3
+ chrM  414 415  C  4  ..Ta  III2  1  2  0  1  3
+ chrM  414 415  C  4  TTTt  III7  0  0  0  4  4
+ 
+where::
+
+  Column Definition
+ ------- ----------------------------
+       1 Chromosome
+       2 Start position (0-based)
+       3 End position (1-based)
+       4 Reference base at that position
+       5 Coverage (# reads aligning over that position)
+       6 Bases within reads
+       7 Quality values (phred33 scale, see Galaxy wiki for more)
+       8 Number of A variants
+       9 Number of C variants
+      10 Number of G variants
+      11 Number of T variants
+      12 Quality adjusted coverage
+      13 Total number of deviants (if Convert coordinates to intervals? is set to yes)
+
+
+Note that in this case the coordinates of SNPs were converted to intervals, where the start coordinate is 0-based and the end coordinate in 1-based using the UCSC Table Browser convention. 
+ 
+Although three positions have variants in the original file (413, 414, and 415), only 413 and 415 are reported because the quality values associated with these two SNPs are above the threshold of 20. In the case of 414 the **a** allele has a quality value of 17 ( ord("2")-33 ), and is therefore not reported. Note that five columns have been added to each of the reported lines::
+
+  chrM  413  G  4  ..t,  IIIH  0  0  2  1  3
+  
+Here, there is one variant, **t**. Because the fourth column represents **T** counts, it is incremented by 1. The last column shows that at this position, three reads have bases above the quality threshold of 20.
+
+-----
+
+**Example 1**: Just variants
+
+In this mode, the tool only outputs the lines from the input datasets where at least one read contains a sequence variant with quality above the threshold set by the **Do not consider read bases with quality lower than** option. For example, suppose one has a pileup dataset like the following::
+
+ chrM  412  A  2       .,       II
+ chrM  413  G  4     ..t,     III2
+ chrM  414  C  4     ..Ta     III2
+ chrM  415  C  4     TTTt     III7
+ 
+To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows:
+
+.. image:: ${static_path}/images/pileup_parser_help1.png 
+
+Running the tool with these parameters will return::
+
+ chrM  413  G  4  ..t,  IIIH  0  0  0  1  3
+ chrM  414  C  4  ..Ta  III2  0  2  0  1  3
+ chrM  415  C  4  TTTt  III7  0  0  0  4  4
+ 
+**Note** that position 414 is not reported because the *a* variant has associated quality value of 17 (because ord('2')-33 = 17) and is below the phred threshold of 20 set by the **Count variants with quality above this value** parameter.
+
+-----
+
+**Example 2**: Report everything
+
+In addition to calling variants, it is often useful to know the quality adjusted coverage. Running the tool with these parameters:
+
+.. image:: ${static_path}/images/pileup_parser_help2.png 
+
+will report everything from the original file::
+
+ chrM  412  A  2  .,    II    2  0  0  0  2
+ chrM  413  G  4  ..t,  III2  0  0  2  1  3
+ chrM  414  C  4  ..Ta  III2  0  2  0  1  3
+ chrM  415  C  4  TTTt  III7  0  0  0  4  4
+ 
+Here, you can see that although the total coverage at position 414 is 4 (column 4), the quality adjusted coverage is 3 (last column). This is because only three out of four reads have bases with quality above the set threshold of 20 (the actual qualities are III2 or, after conversion,  40, 40, 40, 17).
+
+One can use the last column of this dataset to filter out (using Galaxy's **Filter** tool) positions where quality adjusted coverage (last column) is below a set threshold.
+
+------
+
+**Example 3**: Report everything and print total number of differences
+
+If you set the **Print total number of differences?** to **Yes** the tool will print an additional column with the total number of reads where a devinat base is above the quality threshold. So, seetiing parametrs like this:
+
+.. image:: ${static_path}/images/pileup_parser_help3.png
+
+will produce this::
+
+ chrM  412  A  2  .,    II    2  0  0  0  2  0
+ chrM  413  G  4  ..t,  III2  0  0  2  1  3  1
+ chrM  414  C  4  ..Ta  III2  0  2  0  1  3  1
+ chrM  415  C  4  TTTt  III7  0  0  0  4  4  0
+ 
+ 
+-----
+
+**Example 4**: Report everything, print total number of differences, and ignore qualities and read bases
+
+Setting **Print quality and base string?** to **Yes** as shown here:
+
+.. image:: ${static_path}/images/pileup_parser_help4.png
+
+will produce this::
+
+ chrM  412  A  2  2  0  0  0  2  0
+ chrM  413  G  4  0  0  2  1  3  1
+ chrM  414  C  4  0  2  0  1  3  1
+ chrM  415  C  4  0  0  0  4  4  0
+
+
+
+ 
+</help>
+</tool>
diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.10col.20-3-yes-yes-yes-no.pileup.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_parser.10col.20-3-yes-yes-yes-no.pileup.out	Mon Aug 26 15:14:34 2013 -0400
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diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.10col.20-3-yes-yes-yes-yes.pileup.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_parser.10col.20-3-yes-yes-yes-yes.pileup.out	Mon Aug 26 15:14:34 2013 -0400
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diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.10col.20-3-yes-yes.pileup.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_parser.10col.20-3-yes-yes.pileup.out	Mon Aug 26 15:14:34 2013 -0400
@@ -0,0 +1,86 @@
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diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.10col.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_parser.10col.pileup	Mon Aug 26 15:14:34 2013 -0400
@@ -0,0 +1,1000 @@
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diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.6col.20-3-no-no.pileup.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_parser.6col.20-3-no-no.pileup.out	Mon Aug 26 15:14:34 2013 -0400
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diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.6col.20-3-yes-no.pileup.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_parser.6col.20-3-yes-no.pileup.out	Mon Aug 26 15:14:34 2013 -0400
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diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.6col.20-3-yes-yes.pileup.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_parser.6col.20-3-yes-yes.pileup.out	Mon Aug 26 15:14:34 2013 -0400
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diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.6col.40-3-yes-yes.pileup.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_parser.6col.40-3-yes-yes.pileup.out	Mon Aug 26 15:14:34 2013 -0400
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diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.6col.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_parser.6col.pileup	Mon Aug 26 15:14:34 2013 -0400
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+chrM	310	T	2	,.	II
+chrM	311	T	2	,.	II
+chrM	312	T	3	,.^:.	III
+chrM	313	C	3	,..	III
+chrM	314	G	3	,..	III
+chrM	315	T	3	,..	III
+chrM	316	G	3	,..	III
+chrM	317	C	3	,..	III
+chrM	318	C	3	,..	III
+chrM	319	A	3	,$..	III
+chrM	320	G	2	..	II
+chrM	321	C	2	.$.	II
+chrM	322	C	1	.	I
+chrM	323	A	1	.	I
+chrM	324	C	1	.	I
+chrM	325	C	1	.	I
+chrM	326	G	1	.	I
+chrM	327	C	1	.	I
+chrM	328	G	1	.	I
+chrM	329	G	1	.	I
+chrM	330	T	1	.	I
+chrM	331	C	1	.	I
+chrM	332	A	1	.	I
+chrM	333	T	1	.	I
+chrM	334	A	1	.	I
+chrM	335	C	1	.	I
+chrM	336	G	1	.	I
+chrM	337	A	1	.	I
+chrM	338	T	1	.	I
+chrM	339	T	1	.	I
+chrM	340	A	1	.	I
+chrM	341	A	1	.	D
+chrM	342	C	1	.	I
+chrM	343	C	1	.	I
+chrM	344	C	1	.	I
+chrM	345	A	1	.	I
+chrM	346	A	1	.	;
+chrM	347	A	1	.$	7
+chrM	360	C	1	^:.	I
+chrM	361	G	1	.	I
+chrM	362	G	1	.	I
+chrM	363	C	1	.	I
+chrM	364	G	1	.	I
+chrM	365	T	1	.	I
+chrM	366	A	1	.	I
+chrM	367	A	1	.	I
+chrM	368	A	1	.	I
+chrM	369	G	1	.	I
+chrM	370	C	1	.	I
+chrM	371	G	1	.	I
+chrM	372	T	1	.	I
+chrM	373	G	1	.	I
+chrM	374	T	1	.	I
+chrM	375	C	1	.	I
+chrM	376	A	1	.	I
+chrM	377	A	1	.	I
+chrM	378	A	1	.	I
+chrM	379	G	1	.	I
+chrM	380	A	1	.	I
+chrM	381	C	1	T	I
+chrM	382	T	1	.	I
+chrM	383	A	1	.	I
+chrM	384	A	1	.	I
+chrM	385	T	1	.	I
+chrM	386	A	1	G	I
+chrM	387	C	1	.	I
+chrM	388	C	1	.	I
+chrM	389	A	2	.^:.	II
+chrM	390	A	3	..^:.	III
+chrM	391	A	3	...	>II
+chrM	392	A	3	...	III
+chrM	393	T	3	...	III
+chrM	394	A	3	...	III
+chrM	395	A	3	.$..	III
+chrM	396	A	2	..	II
+chrM	397	G	2	..	II
+chrM	398	T	2	..	EI
+chrM	399	T	2	..	II
+chrM	400	A	3	..^:.	III
+chrM	401	A	3	...	III
+chrM	402	A	3	...	III
+chrM	403	A	3	...	III
+chrM	404	C	3	...	III
+chrM	405	C	3	...	III
+chrM	406	C	3	...	EII
+chrM	407	A	3	...	III
+chrM	408	G	3	...	III
+chrM	409	T	3	...	0II
+chrM	410	T	3	...	III
+chrM	411	A	4	...^:,	IIII
+chrM	412	A	4	...,	FIII
+chrM	413	G	4	...,	IIIH
+chrM	414	C	4	...a	III2
+chrM	415	C	4	TTTt	III7
+chrM	416	G	5	...,^:,	II?7:
+chrM	417	T	5	...,,	;IIE@
+chrM	418	A	5	...,,	IIIII
+chrM	419	A	5	...,,	IIIII
+chrM	420	A	5	...,,	FIIII
+chrM	421	A	5	...,,	IIIII
+chrM	422	A	5	...,,	>IIII
+chrM	423	G	6	...,,^:,	HII/I,
+chrM	424	C	6	.$..a,,	;II-I:
+chrM	425	T	5	.$.,,,	IIIIF
+chrM	426	A	5	.,,,^:,	III@I
+chrM	427	C	5	.,,,,	III$I
+chrM	428	A	5	.,,,,	IIIII
+chrM	429	A	5	.,,,,	IIII.
+chrM	430	C	5	.,,,a	I%I5'
+chrM	431	C	5	.,,,,	I(I5<
+chrM	432	A	5	.,,,,	IIIII
+chrM	433	A	5	.,,,,	0IIII
+chrM	434	A	5	.,,,,	=IIII
+chrM	435	G	5	.$,,,,	EIIII
+chrM	436	T	4	,,,,	III5
+chrM	437	A	4	,,,,	IIII
+chrM	438	A	4	,,,,	IIII
+chrM	439	A	4	,,,,	IIII
+chrM	440	A	4	,,,,	IIIF
+chrM	441	T	6	,,,,^:.^:.	III;II
+chrM	442	A	6	,,,,..	IIIIII
+chrM	443	G	6	,,,,..	IIIIII
+chrM	444	A	6	,,,,..	IIIIII
+chrM	445	C	6	,,,,..	IIIIII
+chrM	446	T	6	,$,,,..	IIIIII
+chrM	447	A	5	,,,..	IIIII
+chrM	448	C	5	,,,..	IIIII
+chrM	449	G	6	,,,..^:,	IIIII6
+chrM	450	A	6	,,,..,	IIIIII
+chrM	451	A	6	,$,,..,	IIIIII
+chrM	452	A	5	,,..,	IIIII
+chrM	453	G	5	,,..,	IIIII
+chrM	454	T	6	,,..,^:,	IIIIII
+chrM	455	G	6	,,..,,	IIIIII
+chrM	456	A	6	,,..,,	IIIIII
+chrM	457	C	6	,,..,,	IIIII=
+chrM	458	T	6	,$,..,,	IIIIII
+chrM	459	T	5	,..,,	IIIII
+chrM	460	T	5	,..,,	IIIII
+chrM	461	A	5	,$..,,	IIIII
+chrM	462	A	4	..,,	IIII
+chrM	463	T	4	..,,	IIIC
+chrM	464	A	4	..,,	IIII
+chrM	465	C	4	..,,	IIII
+chrM	466	C	4	..,,	IIII
+chrM	467	T	4	..,,	II>?
+chrM	468	C	4	..,,	IIII
+chrM	469	T	4	..,,	IIIG
+chrM	470	G	4	..,,	%III
+chrM	471	A	4	..,,	4;II
+chrM	472	C	4	..,,	II3I
+chrM	473	T	4	..,,	IIII
+chrM	474	A	4	..,,	;III
+chrM	475	C	4	..,,	IIII
+chrM	476	A	4	.$.$,,	32II
+chrM	477	C	2	,,	II
+chrM	478	G	2	,,	II
+chrM	479	A	2	,,	II
+chrM	480	T	3	,,^:.	III
+chrM	481	A	3	,,.	III
+chrM	482	G	3	,,.	III
+chrM	483	C	4	,,.^:,	IIIE
+chrM	484	T	4	,$,.,	III9
+chrM	485	A	3	,.,	III
+chrM	486	A	3	,.,	III
+chrM	487	G	3	,.,	III
+chrM	488	A	3	,.,	III
+chrM	489	C	3	,$.,	III
+chrM	490	C	2	.,	II
+chrM	491	C	2	.,	II
+chrM	492	A	2	.,	II
+chrM	493	A	2	.,	II
+chrM	494	A	2	.,	II
+chrM	495	C	2	.,	II
+chrM	496	T	2	.,	I2
+chrM	497	G	2	.,	II
+chrM	498	G	2	.,	II
+chrM	499	G	2	.,	II
+chrM	500	A	2	.,	II
+chrM	501	T	2	.,	II
+chrM	502	T	2	.,	II
+chrM	503	A	2	.,	II
+chrM	504	G	2	.,	II
+chrM	505	A	2	.,	GI
+chrM	506	T	2	.,	II
+chrM	507	A	2	.,	II
+chrM	508	C	2	.,	II
+chrM	509	C	2	.,	II
+chrM	510	C	3	.,^:.	III
+chrM	511	C	3	.,.	III
+chrM	512	A	3	.,.	6II
+chrM	513	C	3	.,.	III
+chrM	514	T	3	.,.	III
+chrM	515	A	3	.$,.	III
+chrM	516	T	2	,.	II
+chrM	517	G	2	,.	II
+chrM	518	C	3	,$.^:.	III
+chrM	519	T	2	..	II
+chrM	520	T	3	..^:,	III
+chrM	521	A	3	..,	III
+chrM	522	G	3	..,	II,
+chrM	523	C	3	..,	III
+chrM	524	C	3	..,	II7
+chrM	525	C	3	..,	III
+chrM	526	T	3	..,	II?
+chrM	527	A	3	..,	III
+chrM	528	A	3	..,	III
+chrM	529	A	3	..,	FII
+chrM	530	C	3	..,	II+
+chrM	531	T	3	..,	III
+chrM	532	A	3	..,	:II
+chrM	533	A	3	..,	DGI
+chrM	534	A	3	..,	III
+chrM	535	A	3	..,	?CI
+chrM	536	T	3	..,	III
+chrM	537	A	3	..,	9II
+chrM	538	G	3	..,	III
+chrM	539	C	3	..,	III
+chrM	540	T	3	..,	III
+chrM	541	T	3	..,	III
+chrM	542	A	4	..,^:.	IIII
+chrM	543	C	4	..,.	IIII
+chrM	544	C	4	..,.	IIII
+chrM	545	A	4	N$.,.	"III
+chrM	546	C	3	.,.	III
+chrM	547	A	3	.,.	DII
+chrM	548	A	3	.,.	EII
+chrM	549	C	3	.,.	III
+chrM	550	A	3	.,.	III
+chrM	551	A	3	.,.	6II
+chrM	552	A	3	.,.	GII
+chrM	553	G	3	.$,.	?II
+chrM	554	C	2	,.	I<
+chrM	555	T	2	,$.	II
+chrM	556	A	2	.^:.	II
+chrM	557	T	2	..	II
+chrM	558	T	2	..	II
+chrM	559	C	2	..	II
+chrM	560	G	2	..	II
+chrM	561	C	2	..	II
+chrM	562	C	2	..	II
+chrM	563	A	2	..	CI
+chrM	564	G	2	..	II
+chrM	565	A	2	..	GI
+chrM	566	G	2	..	II
+chrM	567	T	2	..	/I
+chrM	568	A	2	..	DI
+chrM	569	C	2	..	II
+chrM	570	T	2	..	II
+chrM	571	A	2	..	II
+chrM	572	C	2	..	FI
+chrM	573	T	2	..	9I
+chrM	574	A	2	..	II
+chrM	575	G	2	..	II
+chrM	576	C	2	..	II
+chrM	577	A	3	.$.^:.	III
+chrM	578	A	2	..	II
+chrM	579	C	2	..	II
+chrM	580	A	3	..^:,	III
+chrM	581	G	3	..,	III
+chrM	582	C	3	..,	II?
+chrM	583	C	3	..a	II-
+chrM	584	T	3	..,	IIH
+chrM	585	A	3	..,	III
+chrM	586	A	3	..,	III
+chrM	587	A	4	..,^:,	IIII
+chrM	588	A	4	..,,	IIII
+chrM	589	C	4	..,,	IIII
+chrM	590	T	4	..,,	II.5
+chrM	591	C	4	.$.,,	II<I
+chrM	592	A	3	.,,	III
+chrM	593	A	3	.,,	III
+chrM	594	A	3	.,,	III
+chrM	595	G	3	.,,	III
+chrM	596	G	3	.,,	III
+chrM	597	A	3	.,,	:EI
+chrM	598	C	3	.,,	III
+chrM	599	T	4	.,,^:.	II@I
+chrM	600	T	4	.,,.	IIII
+chrM	601	G	4	.,,.	IIII
+chrM	602	G	4	.,,.	IIII
+chrM	603	C	4	.,,.	IIII
+chrM	604	G	4	.,,.	IIII
+chrM	605	G	4	.,,.	IIII
+chrM	606	T	4	.,,.	5III
+chrM	607	G	4	.,,.	IIII
+chrM	608	C	4	.,,.	*III
+chrM	609	T	5	.,,.^:,	?IIII
+chrM	610	T	5	.,,.,	IIII8
+chrM	611	T	5	.,,.,	IIIII
+chrM	612	A	5	T$,,.,	3IIII
+chrM	613	C	4	,,.,	III)
+chrM	614	A	4	,,.,	IIII
+chrM	615	T	4	,$,.,	IIII
+chrM	616	C	3	,.,	III
+chrM	617	C	3	,.,	III
+chrM	618	C	3	,.,	III
+chrM	619	T	3	,.,	IF9
+chrM	620	C	3	,.,	II7
+chrM	621	T	3	,.,	III
+chrM	622	A	3	,$.,	I7I
+chrM	623	G	2	.,	II
+chrM	624	A	2	.,	9I
+chrM	625	G	2	.,	II
+chrM	626	G	2	.,	II
+chrM	627	A	2	.,	2I
+chrM	628	G	2	.,	II
+chrM	629	C	2	.,	II
+chrM	630	C	2	.,	II
+chrM	631	T	2	.,	II
+chrM	632	G	2	.,	II
+chrM	633	T	2	.,	II
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+chrM	635	C	1	,	I
+chrM	636	C	1	,	I
+chrM	637	A	1	,	I
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+chrM	639	A	1	,	I
+chrM	640	A	1	,	I
+chrM	641	T	1	,	I
+chrM	642	C	1	,	I
+chrM	643	G	1	,	I
+chrM	644	A	1	,$	I
+chrM	646	A	1	^:.	I
+chrM	647	A	1	.	I
+chrM	648	A	1	.	I
+chrM	649	C	2	.^:,	II
+chrM	650	C	2	.,	II
+chrM	651	C	2	.,	II
+chrM	652	C	3	.,^:,	II)
+chrM	653	G	3	.,,	II2
+chrM	654	A	3	.,,	III
+chrM	655	T	4	.,,^:.	II*I
+chrM	656	A	4	.,,.	IIII
+chrM	657	A	4	.,,.	IIII
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+chrM	662	C	4	.,,.	IIFI
+chrM	663	A	4	.,,.	=IDI
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+chrM	665	C	5	.,,.^:,	IIIII
+chrM	666	A	5	.,,.,	BIIII
+chrM	667	T	5	.,,.,	II5I+
+chrM	668	C	5	.,,.,	IIIII
+chrM	669	C	5	.,,.,	IIIII
+chrM	670	C	5	.,a.,	II.II
+chrM	671	T	5	.,,.,	IIIIA
+chrM	672	T	6	.,,.,^:.	FI9I.I
+chrM	673	G	6	.,,.,.	IIIIII
+chrM	674	C	6	.,,.,.	IIIIII
+chrM	675	T	6	.,,.,.	IIIIII
+chrM	676	A	6	.,,.,.	,IIEII
+chrM	677	A	7	.,,.,.^:.	3II;III
+chrM	678	T	7	.,,.,..	IIIIDII
+chrM	679	T	7	.,,.,..	CIIIIII
+chrM	680	C	7	.,,.,..	IIIIIII
+chrM	681	A	7	.$,,.,..	9IIIIII
+chrM	682	G	6	,,.,..	II$III
+chrM	683	C	6	,,.,..	IIIIII
+chrM	684	C	6	,$,.,..	IIIIII
+chrM	685	T	5	,.,..	IIIII
+chrM	686	A	5	,.,..	IIIII
+chrM	687	T	5	,$.,..	IIIII
+chrM	688	A	4	.,..	IIII
+chrM	689	T	4	.,..	IIII
+chrM	690	A	4	.$,..	IIII
+chrM	691	C	3	,..	III
+chrM	692	C	3	,..	III
+chrM	693	G	4	,..^:,	IIII
+chrM	694	C	4	,..,	IIII
+chrM	695	C	4	,..,	IIII
+chrM	696	A	4	,..,	IIII
+chrM	697	T	4	,..,	IIII
+chrM	698	C	4	,..,	IIII
+chrM	699	T	4	,..,	IIII
+chrM	700	T	4	,$..,	IIII
+chrM	701	C	3	..,	III
+chrM	702	A	3	..,	III
+chrM	703	G	3	..,	2II
+chrM	704	C	3	..,	III
+chrM	705	A	3	N.,	"II
+chrM	706	A	3	..,	I5I
+chrM	707	A	3	.$.,	GII
+chrM	708	C	2	.,	II
+chrM	709	C	2	.,	II
+chrM	710	C	2	.,	II
+chrM	711	T	2	.,	II
+chrM	712	A	2	.$,	II
+chrM	713	A	1	,	I
+chrM	714	A	1	,	I
+chrM	715	C	1	,	I
+chrM	716	A	1	,	I
+chrM	717	A	1	,	I
+chrM	718	G	1	,	I
+chrM	719	G	2	,^:,	I&
+chrM	720	T	2	,g	I$
+chrM	721	A	2	,,	I3
+chrM	722	C	2	,,	I$
+chrM	723	C	2	,t	I&
+chrM	724	G	2	,,	I)
+chrM	725	A	2	,,	II
+chrM	726	A	3	,,^:.	III
+chrM	727	G	3	,,.	III
+chrM	728	T	3	,$,.	III
+chrM	729	A	2	,.	II
+chrM	730	A	2	n.	"I
+chrM	731	G	2	,.	II
+chrM	732	C	3	a.^:.	$II
+chrM	733	A	3	,..	III
+chrM	734	C	3	,..	%II
+chrM	735	A	3	,..	III
+chrM	736	A	3	,..	*II
+chrM	737	A	3	,..	III
+chrM	738	T	3	,..	III
+chrM	739	A	3	,..	III
+chrM	740	T	3	,..	III
+chrM	741	C	3	,..	III
+chrM	742	C	3	,..	III
+chrM	743	A	3	,..	III
+chrM	744	A	3	,..	III
+chrM	745	C	3	,..	III
+chrM	746	A	3	,..	IIE
+chrM	747	T	3	,..	III
+chrM	748	A	3	,..	III
+chrM	749	A	3	,..	III
+chrM	750	A	3	,..	III
+chrM	751	A	3	,..	IAI
+chrM	752	A	3	,..	III
+chrM	753	C	3	,..	III
+chrM	754	G	3	,$..	III
+chrM	755	T	2	..	II
+chrM	756	T	3	..^:,	III
+chrM	757	A	3	..,	III
+chrM	758	G	3	..,	III
+chrM	759	G	3	..,	III
+chrM	760	T	3	..,	=II
+chrM	761	C	3	.$.,	IID
+chrM	762	A	2	.,	=I
+chrM	763	A	2	.,	EI
+chrM	764	G	2	.,	II
+chrM	765	G	2	.,	II
+chrM	766	T	2	.,	:I
+chrM	767	G	3	.$,^:,	III
+chrM	768	T	2	,,	I>
+chrM	769	A	3	,,^:,	III
+chrM	770	G	3	,,,	III
+chrM	771	C	3	,,,	IHI
+chrM	772	C	3	,a,	I)/
+chrM	773	C	3	,,,	I7I
+chrM	774	A	4	,,,^:.	II:I
+chrM	775	T	4	,,,.	IH.I
+chrM	776	G	4	,,,.	IIII
+chrM	777	G	4	,,,.	IIII
+chrM	778	G	4	,,,.	IIII
+chrM	779	A	4	,,,.	IIAI
+chrM	780	T	4	,,,.	IIGI
+chrM	781	G	4	,,,.	IIII
+chrM	782	G	4	,,,.	IIII
+chrM	783	A	4	,,,.	IIII
+chrM	784	G	4	,,,.	IIII
+chrM	785	A	4	,,,.	IIII
+chrM	786	G	4	,,,.	IIII
+chrM	787	A	4	,,,.	IIII
+chrM	788	A	4	,,,.	IIII
+chrM	789	A	4	,,,.	IIII
+chrM	790	T	5	,,,.^:.	IIIII
+chrM	791	G	5	,$,,..	IIIII
+chrM	792	G	4	,,..	IIII
+chrM	793	G	4	,,..	IIII
+chrM	794	C	4	,,..	IIII
+chrM	795	T	4	,,..	IIII
+chrM	796	A	4	,,..	IIII
+chrM	797	C	4	,,..	IIII
+chrM	798	A	4	,,..	IIII
+chrM	799	T	4	,,..	IIII
+chrM	800	T	4	,,..	IIII
+chrM	801	T	4	,,..	IIII
+chrM	802	T	4	,$,..	IIII
+chrM	803	C	3	,..	III
+chrM	804	T	3	,$..	III
+chrM	805	A	2	..	II
+chrM	806	C	3	..^:.	III
+chrM	807	C	3	...	III
+chrM	808	C	3	...	III
+chrM	809	T	3	.$..	III
+chrM	810	A	3	..^:,	III
+chrM	811	A	3	..,	III
+chrM	812	G	3	..,	II7
+chrM	813	A	3	..,	III
+chrM	814	A	3	..,	III
+chrM	815	C	3	..,	III
+chrM	816	A	3	..,	III
+chrM	817	A	3	..,	III
+chrM	818	G	3	..,	III
+chrM	819	A	3	..,	III
+chrM	820	A	3	..,	&II
+chrM	821	C	3	..,	III
+chrM	822	T	3	..,	III
+chrM	823	T	3	..n	II"
+chrM	824	T	3	..,	III
+chrM	825	A	3	.$.,	III
+chrM	826	A	3	.,^:.	III
+chrM	827	C	3	.,.	III
+chrM	828	C	3	.,.	III
+chrM	829	C	4	.,.^:,	IIII
+chrM	830	G	4	.,.,	IIII
+chrM	831	G	4	.,.,	IIII
+chrM	832	A	4	.,.,	IIII
+chrM	833	C	4	.,.,	IIII
+chrM	834	G	4	.,.,	IIII
+chrM	835	A	4	.,.,	IIII
+chrM	836	A	4	.,.,	8III
+chrM	837	A	4	.,.,	IIII
+chrM	838	G	4	.,.,	IIII
+chrM	839	T	5	.,.,^:,	4:IIG
+chrM	840	C	5	.,.,,	IIIII
+chrM	841	T	5	.$,.,,	IIIII
+chrM	842	C	4	,.,,	IIII
+chrM	843	C	4	,.,,	IIII
+chrM	844	A	4	,.,,	IIII
+chrM	845	T	4	,$.,,	IIII
+chrM	846	G	3	.,,	@II
+chrM	847	A	3	.,,	III
+chrM	848	A	3	.,,	III
+chrM	849	A	3	.,,	III
+chrM	850	C	3	.,,	III
+chrM	851	T	3	.,,	III
+chrM	852	G	3	.,,	III
+chrM	853	G	3	.,,	III
+chrM	854	A	3	.,,	EII
+chrM	855	G	3	.,,	DII
+chrM	856	A	3	.,,	III
+chrM	857	C	3	.,,	III
+chrM	858	T	4	.,,^:,	IIIA
+chrM	859	A	4	.,,,	@III
+chrM	860	A	4	.,,,	IIII
+chrM	861	A	4	.$,,,	EIII
+chrM	862	G	3	,,,	III
+chrM	863	G	3	,,,	III
+chrM	864	A	3	,$,,	III
+chrM	865	G	2	,,	II
+chrM	866	G	2	,,	II
+chrM	867	A	2	,,	II
+chrM	868	T	2	,,	II
+chrM	869	T	2	,,	II
+chrM	870	T	2	,,	II
+chrM	871	A	2	,,	II
+chrM	872	G	2	,,	II
+chrM	873	C	2	,,	II
+chrM	874	A	2	,$,	II
+chrM	875	G	1	,	I
+chrM	876	T	1	,	I
+chrM	877	A	1	,	I
+chrM	878	A	1	,	I
+chrM	879	A	1	,	I
+chrM	880	T	1	,	I
+chrM	881	T	1	,	I
+chrM	882	A	1	,	I
+chrM	883	A	1	,	I
+chrM	884	G	1	,	I
+chrM	885	A	1	,	I
+chrM	886	A	1	,	I
+chrM	887	T	1	,	(
+chrM	888	A	1	,	I
+chrM	889	G	1	,	I
+chrM	890	A	1	,	I
+chrM	891	G	1	,	I
+chrM	892	A	1	,	I
+chrM	893	G	1	,$	I
+chrM	898	A	1	^:,	I
+chrM	899	T	2	,^:.	/I
+chrM	900	T	2	,.	7I
+chrM	901	G	2	,.	CI
+chrM	902	A	2	,.	II
+chrM	903	A	2	,.	II
+chrM	904	T	2	,.	II
+chrM	905	C	3	,.^:,	III
+chrM	906	A	3	,.,	III
+chrM	907	G	3	,.,	III
+chrM	908	G	3	,.,	III
+chrM	909	C	3	,.,	III
+chrM	910	C	3	,.,	III
+chrM	911	A	4	,.,^:,	IIII
+chrM	912	T	4	,.,,	IIEG
+chrM	913	G	4	,.,,	III:
+chrM	914	A	4	,.,,	IIII
+chrM	915	A	4	,.,,	IIII
+chrM	916	G	4	,.,,	III5
+chrM	917	C	4	,.,,	III5
+chrM	918	G	4	,.,,	IIII
+chrM	919	C	4	,.,,	III<
+chrM	920	G	4	,.,,	IIII
+chrM	921	C	4	,.,,	IIII
+chrM	922	A	4	,.,,	IIII
+chrM	923	C	4	,.,,	III8
+chrM	924	A	4	,.,,	IFII
+chrM	925	C	4	,.,,	IIII
+chrM	926	A	4	,.,,	IIII
+chrM	927	C	4	,.,,	IIII
+chrM	928	C	5	,.,,^:,	IIII:
+chrM	929	G	5	,.,,,	IIIE:
+chrM	930	C	5	,.,,,	IIIII
+chrM	931	C	5	,.,,,	IIIIF
+chrM	932	C	5	,.,,,	IIIIC
+chrM	933	G	5	,$.,,,	I?II:
+chrM	934	T	4	.$,,,	4II>
+chrM	935	C	3	,,,	III
+chrM	936	A	3	,,,	III
+chrM	937	C	3	,,,	II1
+chrM	938	C	3	,,,	III
+chrM	939	C	3	,,,	III
+chrM	940	T	3	,$,,	III
+chrM	941	C	2	,,	II
+chrM	942	C	2	,,	I'
+chrM	943	T	2	,,	II
+chrM	944	T	2	,,	II
+chrM	945	A	2	,,	II
+chrM	946	A	2	,$,	II
+chrM	947	A	1	,	I
+chrM	948	T	1	,	I
+chrM	949	A	1	,	I
+chrM	950	T	1	,	I
+chrM	951	C	1	,	I
+chrM	952	A	1	,	I
+chrM	953	C	1	,	I
+chrM	954	A	1	,	I
+chrM	955	A	2	,^:.	II
+chrM	956	A	2	,.	II
+chrM	957	T	2	,.	II
+chrM	958	C	3	,.^:.	III
+chrM	959	A	3	,..	III
+chrM	960	T	3	,..	III
+chrM	961	A	3	,..	III
+chrM	962	A	3	,..	III
+chrM	963	C	4	,$..^:.	IIII
+chrM	964	A	3	...	I(;
+chrM	965	T	3	...	III
+chrM	966	A	4	...^:.	IIII
+chrM	967	A	4	....	IIII
+chrM	968	C	4	....	IEII
+chrM	969	A	4	....	IIII
+chrM	970	T	4	....	IIII
+chrM	971	A	4	....	IIII
+chrM	972	A	4	....	IIII
+chrM	973	A	4	....	II0I
+chrM	974	A	5	....^:.	IIIII
+chrM	975	C	5	.....	IIIII
+chrM	976	C	5	.....	IIIII
+chrM	977	G	5	.....	IIIII
+chrM	978	T	5	.....	IIIII
+chrM	979	G	5	.....	I0III
+chrM	980	A	5	.....	IIII4
+chrM	981	C	5	.....	IIIII
+chrM	982	C	5	.....	IIIII
+chrM	983	C	5	.....	IIIII
+chrM	984	A	5	.....	-IGII
+chrM	985	A	5	.....	4GIII
+chrM	986	A	5	.....	BDGII
+chrM	987	C	5	.....	IDIII
+chrM	988	A	5	.....	@<III
+chrM	989	T	5	.....	IIIII
+chrM	990	A	5	.$....	I@III
+chrM	991	T	4	....	IICI
+chrM	992	G	4	T...	)III
+chrM	993	A	4	.$...	?ICI
+chrM	994	A	3	...	III
+chrM	995	A	3	...	III
+chrM	996	G	3	...	III
+chrM	997	G	3	...	III
+chrM	998	A	3	.$..	4II
+chrM	999	G	3	..^:.	III
+chrM	1000	A	3	...	III
+chrM	1001	C	3	.$..	III
+chrM	1002	A	2	..	II
+chrM	1003	A	2	..	II
+chrM	1004	G	2	..	II
+chrM	1005	T	2	..	II
+chrM	1006	C	2	..	II
+chrM	1007	G	2	..	CI
+chrM	1008	T	2	..	II
+chrM	1009	A	2	.$.	II
+chrM	1010	A	1	.	I
+chrM	1011	C	1	.	I
+chrM	1012	A	1	.	I
+chrM	1013	A	1	.	I
+chrM	1014	G	1	.	I
+chrM	1015	G	1	.	I
+chrM	1016	T	1	.	I
+chrM	1017	A	1	.	I
+chrM	1018	A	1	.	I
+chrM	1019	G	1	.	I
+chrM	1020	T	1	.	I
+chrM	1021	A	1	.	I
+chrM	1022	T	1	.	I
+chrM	1023	A	1	.	I
+chrM	1024	C	1	.	I
+chrM	1025	C	1	.	I
+chrM	1026	G	1	.	I
+chrM	1027	G	1	.	I
+chrM	1028	A	1	.	I
+chrM	1029	A	1	.	I
+chrM	1030	G	1	.	I
+chrM	1031	G	2	.^:.	II
+chrM	1032	T	2	..	EI
+chrM	1033	G	2	..	II
+chrM	1034	T	2	.$.	II
+chrM	1035	A	2	.^:.	II
+chrM	1036	C	2	..	II
+chrM	1037	T	2	..	II
+chrM	1038	T	2	..	II
+chrM	1039	G	2	..	II
+chrM	1040	G	2	..	II
+chrM	1041	A	2	..	II
+chrM	1042	T	2	..	II
+chrM	1043	A	3	..^:,	III
+chrM	1044	A	3	..,	III
+chrM	1045	C	3	..,	II7
+chrM	1046	C	3	..,	II-
+chrM	1047	A	3	..,	III
+chrM	1048	A	3	..,	III
+chrM	1049	A	3	..,	III
+chrM	1050	G	3	..,	III
+chrM	1051	T	3	..,	III
+chrM	1052	G	3	..,	III
+chrM	1053	T	3	..,	GII
+chrM	1054	A	3	..,	III
+chrM	1055	G	3	..,	:II
+chrM	1056	C	3	..a	HI%
+chrM	1057	T	3	..,	III
+chrM	1058	T	3	..,	III
+chrM	1059	A	3	..,	BII
+chrM	1060	A	3	..,	GII
+chrM	1061	A	3	..,	HII
+chrM	1062	C	3	..,	III
+chrM	1063	A	3	..,	DII
+chrM	1064	A	3	..,	BII
+chrM	1065	A	3	..,	1II
+chrM	1066	G	3	.$.,	&II
+chrM	1067	C	2	.,	II
+chrM	1068	A	2	.,	II
+chrM	1069	T	2	.,	II
+chrM	1070	C	2	.$,	II
+chrM	1071	C	1	,	I
+chrM	1072	A	1	,	I
+chrM	1073	G	1	,	I
+chrM	1074	C	1	,	I
+chrM	1075	T	1	,	I
+chrM	1076	T	1	,	I
+chrM	1077	A	1	,	I
+chrM	1078	C	1	,$	I
+chrM	1090	T	1	^:,	I
+chrM	1091	T	1	,	I
+chrM	1092	C	1	n	"
+chrM	1093	A	1	,	I
+chrM	1094	C	1	,	I
+chrM	1095	T	1	,	7
+chrM	1096	C	1	a	B
+chrM	1097	A	1	,	I
+chrM	1098	A	1	,	I
+chrM	1099	A	1	,	I
+chrM	1100	A	1	,	I
+chrM	1101	T	1	,	I
+chrM	1102	G	2	,^:,	(I
+chrM	1103	A	2	,,	II
+chrM	1104	A	2	,,	I+
+chrM	1105	C	2	,,	.I
+chrM	1106	A	2	,,	8I