Mercurial > repos > yutaka-saito > commet

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ComMet_wrapper.pl	Sun Apr 19 20:55:17 2015 +0900
@@ -0,0 +1,56 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+use FindBin;
+
+print STDOUT "The tool script is called with:\n", join(" ", ($0, @ARGV)), "\n\n";
+
+my ($in, $outdmc, $outdmr) = ("", "", "");
+my $default_option = "";
+#my $default_option = "--nobeta --nodual";
+
+my $tooldir = shift(@ARGV);
+$tooldir = $FindBin::Bin;
+my $intype_mapper = shift(@ARGV);
+
+if ($intype_mapper eq "bsf-call") {
+    my $in1 = shift(@ARGV);
+    my $in2 = shift(@ARGV);
+    my $tmp = "ComMet.tmp.$$";
+    ($outdmc, $outdmr) = @ARGV;
+    &invoke_command("$tooldir/bin/Bsf2ComMetIn.pl $in1 $in2 > $tmp");
+    &invoke_command("$tooldir/bin/ComMet $default_option $tmp $outdmc $outdmr");
+}
+elsif ($intype_mapper eq "commet") {
+    ($in, $outdmc, $outdmr) = @ARGV;
+    &invoke_command("$tooldir/bin/ComMet $default_option $in $outdmc $outdmr");
+}
+else {
+    die "never reach here\n";
+}
+
+sub invoke_command {
+    my ($command) = @_;
+    print "invoking: $command\n";
+    system($command);
+}
+
+=pod
+<!--
+    <conditional name="advancedset">
+      <param name="advancedset_use" type="select" label="use advanced setting">
+        <option value="No" selected="true">No</option>
+        <option value="Yes">Yes</option>
+      </param>
+      <when value="No">
+      </when>
+      <when value="Yes">
+        <param name="beta" type="boolean" falsevalue="--nobeta" label="use beta mixture distributions"/>
+        <param name="dual" type="boolean" falsevalue="--nodual" label="use dual HMM architectures"/>
+        <param name="cpg" type="boolean" falsevalue="--noncpg" label="input files contain cytosine sites only in CpG context"/>
+      </when>
+    </conditional>
+-->
+=cut
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ComMet_wrapper.xml	Sun Apr 19 20:55:17 2015 +0900
@@ -0,0 +1,176 @@
+<tool id="ComMet" name="ComMet" version="1.0.0">
+  <description>Detection of differentially methylated regions from bisulfite-seq mapping data</description>
+<!--
+  <version_command></version_command>
+-->
+
+  <requirements>
+    <requirement type="set_environment">TOOLDIR</requirement>
+  </requirements>
+
+  <command interpreter="perl">
+    ComMet_wrapper.pl TOOLDIR $intype.mapper
+
+    #if $intype.mapper=="bsf-call"
+      $in1 $in2
+    #else if $intype.mapper=="commet"
+      $in
+    #else
+
+    #end if
+
+    $outdmc $outdmr
+  </command>
+
+  <inputs>
+    <conditional name="intype">
+      <param name="mapper" type="select" label="input type">
+        <option value="bsf-call">bsf-call</option>
+        <option value="commet">commet</option>
+      </param>
+      <when value="bsf-call">
+        <param name="in1" type="data" format="tabular" label="bsf-call file for sample 1"/>
+        <param name="in2" type="data" format="tabular" label="bsf-call file for sample 2"/>
+      </when>
+      <when value="commet">
+        <param name="in" type="data" format="tabular" label="commet input file"/>
+      </when>
+    </conditional>
+
+  </inputs>
+
+  <outputs>
+    <data name="outdmc" format="tabular" label="${tool.name} on ${on_string}: differential methylation at individual cytosine sites"/>
+    <data name="outdmr" format="tabular" label="${tool.name} on ${on_string}: differentially methylated regions"/>
+  </outputs>
+
+  <help>
+**ComMet**
+
+Detection of differentially methylated regions from bisulfite-seq mapping data
+
+------
+
+**Input format**
+
+Let us consider that we detect differentially methylated regions by comparing sample1 and sample2.
+Inputs are a pair of two files, each of which contain bisulfite-seq mapping data obtained from sample1 or sample2.
+Each file should be in the format supported by the bsf-call tool::
+
+  Col.| Description
+  ----+--------------------------------------
+  1   | chromosome label (e.g. chr1)
+  2   | genomic position (0-based)
+  3   | strand (+,-)
+  4   | mC context (CG, CHG, CHH)
+  5   | mC rate (float)
+  6   | read coverage
+
+Alternatively, you can use one input file, which contains bisulfite-seq mapping data for both samples (commet format)::
+
+  Col.| Description
+  ----+--------------------------------------
+  1   | chromosome name
+  2   | 0-based genomic position
+  3   | number of reads supporting mC in sample1
+  4   | number of reads not supporting mC in sample1
+  5   | number of reads supporting mC in sample2
+  6   | number of reads not supporting mC in sample2
+
+  reads supporting mC = C-C matches
+  reads not supporting mC = otherwise
+
+Make sure chromosome names and genomic positions are sorted by "sort -k1,1 -k2,2n".
+
+Note that input files do not contain strand information.
+Normally, you should integrate both strands by summing the read counts at two neighbor CpGs,
+i.e. the 5'-CpG-3' in the plus strand, and the neighboring 3'-GpC-5' in the minus strand.
+Alternatively, if you are interested in strand-specific DMRs, you can prepare two input files
+for plus and minus strands, and apply them to ComMet separately.
+
+
+------
+
+**Output format**
+
+Output1 contains information of differential methylation at individual cytosine sites::
+
+  Col.| Description
+  ----+--------------------------------------
+  1   | chromosome name
+  2   | 0-based genomic position
+  3   | mC ratio in sample1
+  4   | mC ratio in sample2
+  5   | prob. for hypermethylation (UP) in sample1 against sample2
+  6   | prob. for hypomethylation (DOWN) in sample1 against sample2
+  7   | prob. for no methylation change (NoCh) between sample1 and sample2
+
+Output2 contains information of detected DMRs::
+
+  Col.| Description
+  ----+--------------------------------------
+  1   | chromosome name
+  2   | 0-based genomic start position
+  3   | 0-based genomic stop position
+  4   | direction of differential methylation (UP/DOWN) comparing sample1 to sample2
+  5   | log-likelihood ratio score
+  6   | log-likelihood ratio score divided by DMR length
+
+Make sure output1 and output2 are used properly considering the purpose of your study.
+You should use output1 if you are interested only in differential methylation at
+individual cytosine sites (Note that it is the purpose of most existing packages for
+bisulfite sequencing data analysis developed by other groups).
+ComMet is mainly designed for DMR detection, i.e. determining precise boundaries of
+regional differential methylation, even if DMRs include some cytosine sites whose
+observed methylation changes are relatively weak due to limited sequencing depth.
+Such an analysis is useful for identifying biologically important DMRs such as
+cis regulatory elements; output2 is suitable for this purpose.
+
+------
+
+**FAQ**
+
+\Q. What is the meaning of the error "distance between neighbor CpGs must not be less than 2"?
+::
+
+  A.
+  Your input file contains invalid genomic positions.
+  By definition of CpG, the base next to C must be G, and therefore two neighbor CpGs should be
+  separated by at least two bases. Your input file may violate this rule for several reasons.
+  First, the input file may contain two neighbor CpGs from different strands,
+  i.e. the 5'-CpG-3' in the plus strand, and the neighboring 3'-GpC-5' in the minus strand.
+  See the "Input format" section above for this issue.
+  Second, the input file may contain cytosines in non-CpG context; just remove them.
+
+
+\Q. The read counts in the example input file are decimals rather than integers. Why?
+::
+
+  A.
+  Either decimals or integers can be used for read counts in input files.
+  The reason that the example input file contains decimals is that some alignment tools produce
+  probability-weighted read counts. Of course, you can use your favorite aligners for preparing
+  input files that may contain integers only.
+
+
+\Q. Can ComMet compute statistical significance (p-values) rather than likelihood ratio scores?
+::
+
+  A.
+  No. But we are planning to address this issue in the next version of ComMet.
+
+------
+
+**Contact**
+
+Yutaka Saito
+
+yutaka.saito AT aist.go.jp
+  </help>
+
+  <citations>
+    <citation type="doi">10.1093/nar/gkt1373</citation>
+  </citations>
+
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/Bsf2ComMetIn.pl	Sun Apr 19 20:55:17 2015 +0900
@@ -0,0 +1,196 @@
+#!/usr/bin/perl
+
+# Bisulfighter http://epigenome.cbrc.jp/bisulfighter
+# by National Institute of Advanced Industrial Science and Technology (AIST)
+# is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
+# http://creativecommons.org/licenses/by-nc-sa/3.0/
+
+use strict;
+use warnings;
+
+# format Bisulfighter's input to ComMet's input
+# (data from both strands are integrated)
+#
+# usage:
+# ./this_program sample1.tsv sample2.tsv > ComMetInput
+
+# input format
+=pod
+# sample1
+chr1  123      +  CG   0.8    10
+chr1  128      +  CHG  0.7    8
+chr1  1000000  +  CG   0.234  9
+chr2  987      +  CG   0.654  12
+chr2  1000     +  CHG  0.788  10
+chr2  1057     +  CG   0.826  50
+=cut
+
+=pod
+# sample2
+chr1  123      +  CG   0.3    30
+chr1  128      +  CHG  0.24   20
+chr1  1000000  +  CG   0.36   8
+chr2  987      +  CG   0.64   12
+chr2  1000     +  CHG  0.820  9
+chr2  1057     +  CG   0.0    32
+=cut
+
+# output format
+=pod
+chr1  123      10*(0.8)    10*(1-0.8)    30*(0.3)   30*(1-0.3)
+chr1  1000000  9*(0.234)   9*(1-0.234)   8*(0.36)   8*(1-0.36)
+chr2  987      12*(0.654)  12*(1-0.654)  12*(0.64)  12*(1-0.64)
+chr2  1057     50*(0.826)  50*(1-0.826)  32*(0.0)   32*(1-0.0)
+=cut
+
+my $command = "";
+my $tmpout1 = "Bsf2ComMetIn.pl.tmp.$$.1";
+my $tmpout2 = "Bsf2ComMetIn.pl.tmp.$$.2";
+
+&uniq_add($ARGV[0], $tmpout1);
+&uniq_add($ARGV[1], $tmpout2);
+
+my ($nm1, $pos1, $m1, $u1) = ("", -1, -1, -1);
+my ($nm2, $pos2, $m2, $u2) = ("", -1, -1, -1);
+open(IN1, $tmpout1) or die "couldn't open input file $tmpout1\n";
+open(IN2, $tmpout2) or die "couldn't open input file $tmpout2\n";
+while (1) {
+    my ($line1, $line2);
+
+    if (&chreq($nm1,$pos1,$nm2,$pos2)) {
+	(defined($line1=<IN1>) and defined($line2=<IN2>)) or last;
+	chomp $line1;
+	($nm1,$pos1,$m1,$u1) = split(/\s+/, $line1);
+	chomp $line2;
+	($nm2,$pos2,$m2,$u2) = split(/\s+/, $line2);
+    }
+    elsif (&chrlt($nm1,$pos1,$nm2,$pos2)) {
+	defined($line1=<IN1>) or last;
+	chomp $line1;
+	($nm1,$pos1,$m1,$u1) = split(/\s+/, $line1);
+    }
+    elsif (&chrgt($nm1,$pos1,$nm2,$pos2)) {
+	defined($line2=<IN2>) or last;
+	chomp $line2;
+	($nm2,$pos2,$m2,$u2) = split(/\s+/, $line2);
+    }
+    else {
+	die "wrong position\n";
+    }
+
+    if (&chreq($nm1,$pos1,$nm2,$pos2)) {
+	print STDOUT join("\t", ($nm1, $pos1, $m1, $u1, $m2, $u2)), "\n";
+    }
+}
+close(IN1);
+close(IN2);
+
+&invoke_command("\\rm -f $tmpout1");
+&invoke_command("\\rm -f $tmpout2");
+
+sub invoke_command {
+    my ($command) = @_;
+#    print STDERR $command, "\n";
+    system $command;
+}
+
+sub chrgt {
+    my ($nm1, $pos1, $nm2, $pos2) = @_;
+
+    if ($nm1 gt $nm2 || ($nm1 eq $nm2 && $pos1 > $pos2)) {
+	return 1;
+    }
+    else {
+	return 0;
+    }
+}
+sub chrlt {
+    my ($nm1, $pos1, $nm2, $pos2) = @_;
+
+    if ($nm1 lt $nm2 || ($nm1 eq $nm2 && $pos1 < $pos2)) {
+	return 1;
+    }
+    else {
+	return 0;
+    }
+}
+sub chreq {
+    my ($nm1, $pos1, $nm2, $pos2) = @_;
+
+    if ($nm1 eq $nm2 && $pos1 == $pos2) {
+	return 1;
+    }
+    else {
+	return 0;
+    }
+}
+
+sub uniq_add {
+    my ($infile, $outfile) = @_;
+    my ($nm, $str, $pos, $m, $u) = ("", "", -1, -1, -1);
+    my ($pre_nm, $pre_str, $pre_pos, $pre_m, $pre_u) = ("", "", -1, -1, -1);
+    my $mind = 2; # minimum distance between two CpGs
+    my $thsh = 0;
+
+    open(IN, $infile) or die "couldn't open input file $infile\n";
+    open(OUT, "> $outfile") or die "couldn't open output file $outfile\n";
+    while (my $line=<IN>) {
+	chomp $line;
+	$line =~ /^\#/ and next;
+	$line =~ /CG/ or next;
+	my @cells = split(/\s+/, $line);
+	$nm = $cells[0];
+	$str = $cells[2];
+	$pos = $cells[1];
+	$m = $cells[5] * $cells[4];
+	$u = $cells[5] * (1.0-$cells[4]);
+
+	if ($str eq "+") {
+	}
+	elsif ($str eq "-") {
+	    $str = "+";
+	    $pos -= $mind - 1;
+	}
+	else {
+	    print STDERR "warning: abnormal strand $str was removed\n";
+	    next;
+	}
+
+
+	if ($nm eq $pre_nm && $str eq $pre_str && $pos==$pre_pos) {
+	    $pre_m += $m;
+	    $pre_u += $u;
+	}
+	else {
+	    if ($nm eq $pre_nm && $pos-$pre_pos < $mind) {
+		print STDERR "warning: abnormal position difference $pre_pos $pos, ";
+		if ($m + $u > $pre_m + $pre_u) {
+		    print STDERR "$pre_pos was removed.\n";
+		    $pre_nm = $nm;
+		    $pre_str = $str;
+		    $pre_pos = $pos;
+		    $pre_m = $m;
+		    $pre_u = $u;
+		}
+		else {
+		    print STDERR "$pos was removed.\n"
+		    }
+		next;
+	    }
+	    if ($pre_m + $pre_u > $thsh) {
+		print OUT join("\t", ($pre_nm, $pre_pos, $pre_m, $pre_u)), "\n";
+	    }
+	    $pre_nm = $nm;
+	    $pre_str = $str;
+	    $pre_pos = $pos;
+	    $pre_m = $m;
+	    $pre_u = $u;
+	}
+    }
+    if ($pre_m + $pre_u > $thsh) {
+	print OUT join("\t", ($pre_nm, $pre_pos, $pre_m, $pre_u)), "\n";
+    }
+    close(IN);
+    close(OUT);
+}
+
Binary file bin/ComMet has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example-data/example.bsf-call.in1	Sun Apr 19 20:55:17 2015 +0900
@@ -0,0 +1,2130 @@
+chrX	2998	-	CHH	0.0844952	5
+chrX	5034	+	CHH	0.204611	5
+chrX	5821	+	CHH	1	7
+chrX	5834	+	CHH	0.166656	7
+chrX	5865	+	CHH	0.255032	6
+chrX	10271	+	CHH	0.0845069	5
+chrX	12491	-	CHH	1	5
+chrX	12492	-	CHH	0.200329	5
+chrX	12497	-	CG	0.200186	5
+chrX	12684	-	CG	1	5
+chrX	15333	+	CHH	0.201029	5
+chrX	17796	+	CHH	0.20002	5
+chrX	19122	-	CHH	0.199971	5
+chrX	19141	+	CHG	0.200042	5
+chrX	19282	+	CHG	0.200246	5
+chrX	21083	-	CHH	0.200256	5
+chrX	21930	+	CG	1	5
+chrX	21976	+	CHG	0.109576	5
+chrX	21980	+	CHG	0.10972	5
+chrX	21985	+	CHH	0.666214	5
+chrX	21993	+	CG	1	5
+chrX	23146	-	CHG	0.135249	5
+chrX	23149	-	CHH	0.0990318	5
+chrX	23172	-	CHH	0.200102	5
+chrX	24757	-	CHG	0.109659	5
+chrX	24764	-	CHH	0.0847126	5
+chrX	25393	+	CG	1	5
+chrX	26370	-	CHG	0.313416	5
+chrX	26383	-	CHG	0.600885	5
+chrX	26594	+	CG	1	5
+chrX	26604	+	CHH	0.200042	5
+chrX	26635	+	CHH	0.197938	5
+chrX	28680	+	CHH	0.400571	5
+chrX	28728	+	CHH	0.200106	5
+chrX	30833	-	CHH	0.147271	6
+chrX	32877	-	CHG	0.0845411	5
+chrX	32879	-	CHH	0.199991	5
+chrX	32884	-	CHH	1	5
+chrX	34215	+	CHH	0.166655	6
+chrX	34424	+	CG	1	5
+chrX	36461	-	CHH	0.200088	5
+chrX	37182	+	CHH	1	5
+chrX	37192	+	CG	1	5
+chrX	38917	+	CHG	0.200241	5
+chrX	38924	+	CHH	0.541307	5
+chrX	39162	+	CHH	0.254971	6
+chrX	39332	-	CHH	0.0845057	5
+chrX	39483	-	CHH	0.400018	5
+chrX	39494	-	CHH	0.399969	5
+chrX	39513	-	CG	0.200061	5
+chrX	43472	+	CHG	0.600105	5
+chrX	43479	+	CG	0.599988	5
+chrX	43482	+	CHG	0.199997	5
+chrX	43630	-	CG	1	5
+chrX	45072	-	CHH	1	6
+chrX	45089	-	CHH	0.571646	7
+chrX	45091	-	CHH	1	7
+chrX	46630	+	CG	1	6
+chrX	47689	-	CG	1	5
+chrX	52301	-	CHH	0.0696125	6
+chrX	52321	-	CG	1	5
+chrX	52329	-	CHH	0.200046	5
+chrX	52891	+	CG	1	5
+chrX	53467	-	CHH	0.196883	5
+chrX	54243	-	CG	1	5
+chrX	55290	-	CHH	0.313363	5
+chrX	55390	+	CHH	1	5
+chrX	57150	-	CHG	0.200028	5
+chrX	57172	-	CHG	0.133077	7
+chrX	57959	-	CHH	0.0687657	6
+chrX	57965	-	CHG	0.186264	6
+chrX	58153	-	CHH	0.0695654	6
+chrX	58182	-	CHH	0.207143	7
+chrX	58206	-	CHH	0.166656	6
+chrX	58381	-	CG	1	5
+chrX	60062	-	CHG	0.0845234	5
+chrX	61257	-	CHG	0.200559	5
+chrX	63019	-	CHH	1	5
+chrX	63077	-	CHH	0.142847	7
+chrX	64009	-	CHH	0.0871136	5
+chrX	64010	-	CHH	0.0847634	5
+chrX	66202	+	CHH	0.399924	5
+chrX	66777	-	CG	1	5
+chrX	67313	+	CHG	0.399929	5
+chrX	67353	+	CHH	1	5
+chrX	67361	+	CHH	0.0846822	5
+chrX	67362	+	CHG	0.0854955	5
+chrX	68818	+	CHH	0.203085	5
+chrX	68821	+	CG	1	5
+chrX	74024	-	CHH	0.238628	7
+chrX	74030	-	CHH	0.0779078	6
+chrX	74489	+	CHH	0.79998	5
+chrX	74534	+	CHG	0.109637	5
+chrX	74822	-	CHH	0.200003	5
+chrX	74825	-	CHH	0.200041	5
+chrX	74827	-	CHH	0.199931	5
+chrX	75814	+	CHH	0.0688603	6
+chrX	85167	+	CG	0.40006	5
+chrX	87464	+	CG	1	5
+chrX	88247	+	CHH	0.0845903	5
+chrX	89221	+	CHG	1	5
+chrX	91191	+	CHH	0.202007	5
+chrX	93914	+	CHG	0.0501003	8
+chrX	95638	+	CHH	0.166588	6
+chrX	96470	+	CHG	0.890401	5
+chrX	100044	-	CHH	0.200139	5
+chrX	100045	-	CHH	0.1998	5
+chrX	100048	-	CHG	0.199995	5
+chrX	100053	-	CG	0.600182	6
+chrX	105375	+	CHG	1	5
+chrX	105403	+	CHH	0.125032	8
+chrX	105405	+	CG	1	8
+chrX	108177	+	CHH	0.142869	7
+chrX	108192	+	CHH	0.16666	6
+chrX	108573	+	CG	1	6
+chrX	109277	-	CHH	0.494728	6
+chrX	111099	-	CHH	1	5
+chrX	111103	-	CHH	0.206534	5
+chrX	111876	+	CHH	0.1429	7
+chrX	113075	+	CHG	0.228891	5
+chrX	113809	+	CG	1	5
+chrX	115760	+	CHH	0.179427	5
+chrX	118445	-	CHG	0.157404	7
+chrX	118467	-	CHH	0.0501558	8
+chrX	118476	-	CHH	0.0500962	8
+chrX	118477	-	CHH	0.050102	8
+chrX	118494	-	CHG	0.249957	8
+chrX	118528	-	CHG	0.2052	5
+chrX	121429	-	CHG	1	5
+chrX	121462	-	CHG	0.228919	5
+chrX	122702	-	CHH	1	5
+chrX	123035	-	CHG	0.200132	5
+chrX	123039	-	CG	1	5
+chrX	124417	+	CHH	0.499923	6
+chrX	127831	+	CHH	1	5
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+chrX	2036905	+	CHH	0.599987	5
+chrX	2040736	-	CHH	0.200026	5
+chrX	2044270	-	CHG	0.166667	6
+chrX	2044715	-	CHH	0.068756	6
+chrX	2044722	-	CHH	0.441246	6
+chrX	2045764	+	CHH	0.254119	5
+chrX	2045766	+	CHH	0.0846104	5
+chrX	2046106	-	CG	1	5
+chrX	2046128	-	CHH	0.794984	5
+chrX	2046972	+	CHH	1	5
+chrX	2048992	+	CHH	0.202546	5
+chrX	2056065	+	CHH	0.25043	5
+chrX	2064703	+	CHH	0.0845059	5
+chrX	2064705	+	CHG	0.0845156	5
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+chrX	2065727	+	CHH	0.199988	5
+chrX	2068387	-	CHH	0.16947	6
+chrX	2068400	-	CG	1	6
+chrX	2068421	-	CHH	0.313478	5
+chrX	2071819	+	CHH	0.0847216	5
+chrX	2072551	+	CHH	0.200142	5
+chrX	2073265	+	CHG	0.200126	5
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+chrX	2073340	+	CHH	0.0845365	5
+chrX	2074096	+	CHG	0.166746	6
+chrX	2074097	+	CG	0.326287	6
+chrX	2076839	+	CHH	0.200088	5
+chrX	2076849	+	CHG	0.399452	5
+chrX	2076881	+	CG	0.333405	6
+chrX	2079655	-	CHH	0.200036	5
+chrX	2079656	-	CHH	1	5
+chrX	2080411	-	CG	1	6
+chrX	2080437	-	CG	1	6
+chrX	2080444	-	CHH	1	6
+chrX	2084659	+	CG	1	5
+chrX	2084699	+	CG	1	5
+chrX	2084714	+	CHH	0.166693	6
+chrX	2084812	-	CHH	0.165405	6
+chrX	2087347	+	CHG	0.228613	5
+chrX	2087505	-	CHH	0.0987418	5
+chrX	2087509	-	CG	1	5
+chrX	2087511	-	CHH	0.365787	5
+chrX	2087512	-	CHH	0.109556	5
+chrX	2087525	-	CHG	1	5
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+chrX	2101268	+	CHG	0.200022	5
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+chrX	2105043	-	CHH	0.187498	5
+chrX	2105055	-	CHH	0.599989	5
+chrX	2111323	-	CG	0.458794	5
+chrX	2113599	+	CHH	0.0779063	6
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+chrX	2135379	-	CHG	0.0845262	5
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+chrX	2136257	-	CHH	0.06876	6
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+chrX	2143824	-	CHH	0.400088	5
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+chrX	2149514	+	CHG	0.20055	5
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+chrX	2154855	-	CG	0.942028	7
+chrX	2154873	+	CG	0.799969	5
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+chrX	2154877	+	CHH	0.200189	5
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+chrX	2156424	+	CG	0.400121	5
+chrX	2157120	+	CHH	0.200383	5
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+chrX	2164338	+	CHH	0.200045	5
+chrX	2164347	+	CHH	0.200042	5
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+chrX	2165853	+	CHH	0.800131	5
+chrX	2165854	+	CHH	0.399926	5
+chrX	2166724	+	CHH	0.799547	5
+chrX	2166740	+	CHG	0.200014	5
+chrX	2167196	+	CHG	1	5
+chrX	2167770	+	CHG	0.166665	6
+chrX	2173106	-	CHH	0.189813	5
+chrX	2175645	-	CHH	1	5
+chrX	2176503	-	CG	0.915492	5
+chrX	2176504	-	CHG	0.0844868	5
+chrX	2176518	-	CHH	1	5
+chrX	2177047	+	CHG	0.200856	5
+chrX	2177580	-	CHH	0.66643	6
+chrX	2177592	-	CHG	0.600012	5
+chrX	2178466	+	CHH	0.0845011	5
+chrX	2183785	+	CHG	0.0693975	6
+chrX	2183928	+	CHH	0.199995	5
+chrX	2184031	-	CG	1	5
+chrX	2184076	-	CHH	0.166828	6
+chrX	2184695	-	CHH	0.17396	6
+chrX	2184720	-	CHH	0.142965	7
+chrX	2184759	-	CG	1	5
+chrX	2184767	-	CHH	0.203361	5
+chrX	2185093	-	CHG	0.0844902	5
+chrX	2186642	+	CHH	0.143275	7
+chrX	2186658	+	CHG	0.125254	8
+chrX	2186702	+	CHG	0.0708885	7
+chrX	2187269	+	CHH	0.166682	6
+chrX	2187274	+	CHH	0.166574	6
+chrX	2188149	+	CHG	0.79999	5
+chrX	2188603	-	CHH	0.200073	5
+chrX	2188622	-	CHH	0.0844843	5
+chrX	2188625	-	CHH	1	5
+chrX	2188900	+	CHH	0.201532	5
+chrX	2191161	-	CG	0.399955	5
+chrX	2191167	-	CHH	0.20005	5
+chrX	2191216	-	CHH	0.203671	5
+chrX	2193637	-	CHH	0.499938	6
+chrX	2195438	-	CHH	0.200012	5
+chrX	2198635	+	CHG	0.200058	5
+chrX	2198968	+	CHG	0.199965	5
+chrX	2199882	+	CG	1	5
+chrX	2201733	+	CHH	1	5
+chrX	2203106	+	CHH	0.166669	6
+chrX	2203121	+	CHH	0.109577	5
+chrX	2208362	+	CHH	0.0845295	5
+chrX	2209080	+	CHH	0.200065	5
+chrX	2213204	+	CHH	0.202615	5
+chrX	2213267	-	CHH	0.200063	5
+chrX	2218050	+	CHH	0.200007	5
+chrX	2218074	+	CHH	0.20006	5
+chrX	2218081	+	CHH	0.199602	5
+chrX	2222581	+	CG	1	6
+chrX	2223550	+	CHH	0.199806	5
+chrX	2223565	+	CHG	0.333537	6
+chrX	2223574	+	CHH	0.0579717	7
+chrX	2224896	-	CHH	0.228952	5
+chrX	2225384	+	CG	0.500147	6
+chrX	2231915	-	CHG	0.0845091	5
+chrX	2231925	-	CHH	0.0844997	5
+chrX	2231927	-	CHH	0.0844979	5
+chrX	2232707	+	CHH	1	5
+chrX	2232919	-	CHG	0.084724	5
+chrX	2235122	+	CG	0.200125	5
+chrX	2235155	+	CHG	0.0849841	5
+chrX	2236287	+	CHH	0.135142	7
+chrX	2239321	-	CHH	0.200056	5
+chrX	2242280	+	CG	1	6
+chrX	2242303	+	CHH	0.168481	6
+chrX	2246920	-	CHH	0.799781	5
+chrX	2246933	-	CHG	0.402806	5
+chrX	2246990	-	CG	1	6
+chrX	2249040	-	CHH	1	5
+chrX	2252514	-	CHH	0.201416	5
+chrX	2252549	-	CHH	0.50008	5
+chrX	2252558	-	CHH	0.542314	5
+chrX	2252572	-	CG	1	6
+chrX	2253218	-	CHH	0.186276	6
+chrX	2253535	-	CG	1	6
+chrX	2253541	-	CHH	0.166694	6
+chrX	2254091	+	CG	1	5
+chrX	2258514	-	CHG	0.0845109	5
+chrX	2263829	-	CHG	0.166036	6
+chrX	2263836	-	CHH	0.607659	5
+chrX	2269358	-	CHG	0.183804	5
+chrX	2269779	-	CG	1	5
+chrX	2269782	-	CHG	0.199975	5
+chrX	2270161	-	CHH	0.625037	8
+chrX	2270198	-	CHH	0.799974	5
+chrX	2276123	-	CG	0.686655	5
+chrX	2278705	-	CG	0.10956	5
+chrX	2278718	-	CHH	0.40091	5
+chrX	2279020	-	CHG	0.202202	5
+chrX	2279035	-	CHH	0.200027	5
+chrX	2279062	-	CHH	0.166747	6
+chrX	2279083	-	CHG	0.200042	5
+chrX	2279086	-	CHG	0.0579905	7
+chrX	2279118	-	CHH	0.202539	5
+chrX	2279131	-	CHH	0.200119	5
+chrX	2280738	+	CHG	0.200132	5
+chrX	2280754	+	CHH	0.0844896	5
+chrX	2282210	-	CHH	0.109657	5
+chrX	2282222	-	CHH	1	5
+chrX	2285134	-	CHH	0.499629	5
+chrX	2287248	-	CHH	0.0845427	5
+chrX	2289652	-	CG	1	6
+chrX	2290753	-	CG	1	5
+chrX	2291488	-	CHH	1	5
+chrX	2292014	+	CG	1	5
+chrX	2292054	+	CHH	0.0896725	5
+chrX	2292581	-	CHG	0.142796	7
+chrX	2293497	-	CG	1	5
+chrX	2293514	-	CHG	0.0845132	5
+chrX	2293993	+	CHH	1	5
+chrX	2298848	-	CHH	0.200034	5
+chrX	2299239	-	CG	1	5
+chrX	2304265	+	CHH	0.199987	5
+chrX	2304269	+	CG	0.200039	5
+chrX	2304283	+	CG	1	6
+chrX	2308927	+	CHH	0.200032	5
+chrX	2312709	+	CHG	0.174079	5
+chrX	2312718	+	CHG	0.168869	6
+chrX	2312737	+	CHG	0.285575	7
+chrX	2312775	+	CHH	0.0501157	8
+chrX	2313326	-	CHH	0.594825	5
+chrX	2313669	+	CHG	0.186267	6
+chrX	2314897	+	CHH	0.200041	5
+chrX	2314911	+	CHH	0.179435	5
+chrX	2316409	+	CHG	0.20007	5
+chrX	2316910	-	CHH	0.14288	7
+chrX	2316918	-	CHH	0.166656	6
+chrX	2316925	-	CHH	0.166718	6
+chrX	2316941	-	CG	1	6
+chrX	2316946	-	CG	1	5
+chrX	2317600	-	CHH	1	5
+chrX	2320231	+	CHG	0.0844907	5
+chrX	2320237	+	CHG	0.084483	5
+chrX	2323646	+	CHH	0.200266	5
+chrX	2324859	-	CHH	0.600096	5
+chrX	2324970	+	CHG	0.0689754	6
+chrX	2324986	+	CHH	0.599926	5
+chrX	2324990	+	CHH	0.200041	5
+chrX	2334787	+	CG	1	5
+chrX	2335256	+	CHG	0.0844817	5
+chrX	2335261	+	CHG	0.0844925	5
+chrX	2335281	+	CHH	0.20004	5
+chrX	2340268	-	CG	1	5
+chrX	2340303	-	CHG	0.200302	5
+chrX	2340863	+	CG	1	5
+chrX	2340872	+	CHH	0.200044	5
+chrX	2340906	+	CHH	0.166643	6
+chrX	2340921	+	CHH	0.166686	6
+chrX	2340937	+	CHH	0.0690123	6
+chrX	2345942	+	CHH	0.599902	5
+chrX	2345944	+	CG	0.200117	5
+chrX	2346168	+	CG	0.810133	5
+chrX	2346179	+	CG	1	5
+chrX	2347748	+	CHH	1	5
+chrX	2347760	+	CHG	0.146222	5
+chrX	2347767	+	CHH	0.200053	5
+chrX	2348321	+	CHH	0.199709	5
+chrX	2348334	+	CHH	0.232086	5
+chrX	2349225	-	CHG	0.199962	5
+chrX	2353907	-	CHH	0.142959	7
+chrX	2353968	-	CHH	0.0687618	6
+chrX	2354016	-	CHH	0.166719	6
+chrX	2354216	-	CHH	0.199987	5
+chrX	2355145	+	CHH	0.0844925	5
+chrX	2355155	+	CHH	0.200064	5
+chrX	2355209	-	CG	0.200012	5
+chrX	2355224	-	CHH	0.200019	5
+chrX	2357202	+	CHH	0.166711	6
+chrX	2357638	+	CHH	0.200286	5
+chrX	2357640	+	CHH	0.200153	5
+chrX	2357654	+	CHH	0.0687705	6
+chrX	2358240	-	CHH	0.19994	5
+chrX	2358862	+	CHH	0.200378	5
+chrX	2359263	+	CG	1	5
+chrX	2360449	-	CHH	1	6
+chrX	2360610	+	CHH	0.0688157	6
+chrX	2360614	+	CHH	0.0688073	6
+chrX	2360621	+	CHH	0.0847254	5
+chrX	2361396	+	CHG	0.200001	5
+chrX	2364693	+	CHH	0.166656	6
+chrX	2364714	+	CHH	0.166709	6
+chrX	2364753	+	CG	1	6
+chrX	2365493	-	CG	1	6
+chrX	2365499	-	CHH	0.666623	6
+chrX	2365506	-	CHH	0.057962	7
+chrX	2365538	-	CG	1	5
+chrX	2366131	-	CG	1	5
+chrX	2368482	+	CHG	0.0845054	5
+chrX	2368880	+	CHH	0.200026	5
+chrX	2370888	-	CHH	1	5
+chrX	2370940	-	CG	1	6
+chrX	2370952	-	CHH	0.200064	5
+chrX	2371073	-	CG	0.931243	6
+chrX	2373485	-	CHH	0.184079	5
+chrX	2373797	-	CHH	0.199051	5
+chrX	2376670	-	CHH	0.0845275	5
+chrX	2376727	-	CHH	0.200035	5
+chrX	2377755	+	CHH	0.166669	6
+chrX	2377766	+	CHH	1	6
+chrX	2382502	-	CHH	0.25	5
+chrX	2382869	+	CG	1	5
+chrX	2391071	-	CHH	0.200056	5
+chrX	2391089	-	CHG	0.166703	6
+chrX	2391133	-	CG	1	6
+chrX	2391177	-	CHH	0.0579741	7
+chrX	2397535	+	CHH	0.200078	5
+chrX	2397579	+	CHG	1	5
+chrX	2397749	-	CHH	0.199942	5
+chrX	2398235	+	CG	1	6
+chrX	2402668	+	CG	1	5
+chrX	2403668	+	CG	1	5
+chrX	2404664	-	CHH	0.165692	6
+chrX	2405917	-	CHH	0.179376	5
+chrX	2406135	+	CG	1	6
+chrX	2406149	+	CHG	0.166675	6
+chrX	2406589	+	CHH	0.199904	5
+chrX	2406593	+	CG	1	5
+chrX	2406603	+	CHH	0.200069	5
+chrX	2406647	+	CHG	0.192125	5
+chrX	2409570	+	CHH	0.0844874	5
+chrX	2410519	+	CG	0.202531	5
+chrX	2410535	+	CHH	0.0846264	5
+chrX	2410542	+	CHH	0.229094	5
+chrX	2411271	-	CHH	0.0844945	5
+chrX	2411283	-	CHG	0.068881	6
+chrX	2414010	-	CHH	0.134804	5
+chrX	2414050	-	CHH	0.200011	5
+chrX	2419038	-	CHH	1	6
+chrX	2419814	+	CHH	0.19992	5
+chrX	2420935	+	CHG	0.250102	5
+chrX	2421427	-	CG	1	5
+chrX	2421719	-	CHG	0.200981	5
+chrX	2426401	+	CHH	1	5
+chrX	2436077	-	CHH	0.16672	6
+chrX	2436100	-	CG	0.500085	6
+chrX	2436761	+	CHH	0.0845694	5
+chrX	2436888	+	CHH	0.199727	5
+chrX	2437227	-	CHH	0.0987765	5
+chrX	2437233	-	CHH	0.228878	5
+chrX	2437235	+	CHH	0.200033	5
+chrX	2437456	+	CG	1	5
+chrX	2439245	-	CHH	0.199841	5
+chrX	2441710	+	CHH	0.599516	5
+chrX	2442147	+	CG	1	5
+chrX	2442160	+	CG	1	5
+chrX	2442166	+	CHH	0.0845324	5
+chrX	2444428	-	CG	0.400041	5
+chrX	2447132	-	CG	0.915496	5
+chrX	2452534	+	CHH	0.200048	5
+chrX	2453852	-	CHG	0.0896671	5
+chrX	2458385	-	CG	1	5
+chrX	2458413	-	CHH	0.2	5
+chrX	2459107	-	CHH	0.068762	6
+chrX	2459116	-	CHH	0.199986	5
+chrX	2460671	+	CHG	0.0849812	5
+chrX	2460862	-	CHH	0.3982	5
+chrX	2460902	-	CHH	0.333078	6
+chrX	2460942	-	CG	0.200203	5
+chrX	2462646	-	CHH	0.205318	5
+chrX	2463293	+	CHG	0.0845327	5
+chrX	2463296	+	CHG	0.109596	5
+chrX	2463521	+	CHG	0.199646	5
+chrX	2471171	+	CHG	0.199973	5
+chrX	2471197	+	CHH	0.166686	6
+chrX	2471209	+	CHH	0.196674	5
+chrX	2471211	+	CHH	0.157744	5
+chrX	2476444	-	CHH	0.0845094	5
+chrX	2478674	+	CG	1	5
+chrX	2478863	-	CHG	0.200033	5
+chrX	2479099	-	CHG	0.0688182	6
+chrX	2479623	-	CHH	0.399975	5
+chrX	2480847	-	CG	1	5
+chrX	2482118	-	CHH	0.542377	5
+chrX	2482124	-	CG	1	7
+chrX	2482167	-	CHH	0.166667	6
+chrX	2482627	+	CHH	0.799739	5
+chrX	2483793	-	CHH	1	5
+chrX	2483809	-	CHG	0.250233	5
+chrX	2483810	-	CHH	0.0844968	5
+chrX	2484096	-	CHH	0.166674	6
+chrX	2484129	-	CHH	0.199977	5
+chrX	2486908	-	CHH	0.799936	5
+chrX	2486911	-	CHG	0.200279	5
+chrX	2486947	-	CG	1	5
+chrX	2496317	-	CHH	0.206507	5
+chrX	2496924	+	CHG	0.199997	5
+chrX	2496933	+	CHH	0.200118	5
+chrX	2497559	-	CG	1	5
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example-data/example.bsf-call.in2	Sun Apr 19 20:55:17 2015 +0900
@@ -0,0 +1,2058 @@
+chrX	2993	-	CHH	0.0844937	5
+chrX	2998	-	CHH	0.0844952	5
+chrX	5042	+	CHH	0.200036	5
+chrX	5821	+	CHH	1	7
+chrX	5865	+	CHH	0.0687671	6
+chrX	6894	-	CHH	0.201062	5
+chrX	6905	-	CHH	0.203164	5
+chrX	10271	+	CHH	0.0845069	5
+chrX	12491	-	CHH	1	5
+chrX	12497	-	CG	0.399917	5
+chrX	12684	-	CG	1	5
+chrX	19122	-	CHH	0.400029	5
+chrX	19149	+	CHH	0.200237	5
+chrX	21670	+	CHH	0.204098	5
+chrX	21683	+	CHH	0.142448	7
+chrX	21698	+	CHH	0.167228	6
+chrX	21930	+	CG	1	5
+chrX	21976	+	CHG	0.109576	5
+chrX	21980	+	CHG	0.10972	5
+chrX	21985	+	CHH	0.297159	5
+chrX	21993	+	CG	1	5
+chrX	23146	-	CHG	0.135249	5
+chrX	23149	-	CHH	0.0990318	5
+chrX	23169	-	CHG	0.199919	5
+chrX	24757	-	CHG	0.109659	5
+chrX	24764	-	CHH	0.0847126	5
+chrX	25393	+	CG	1	5
+chrX	26370	-	CHG	0.0845241	5
+chrX	26383	-	CHG	0.801223	5
+chrX	26392	-	CHG	0.199981	5
+chrX	26594	+	CG	1	5
+chrX	30833	-	CHH	0.147271	6
+chrX	32877	-	CHG	0.0845411	5
+chrX	32884	-	CHH	1	5
+chrX	34215	+	CHH	0.499929	6
+chrX	34226	+	CHH	0.166645	6
+chrX	34424	+	CG	1	5
+chrX	36455	-	CHG	0.200055	5
+chrX	37182	+	CHH	1	5
+chrX	37192	+	CG	1	5
+chrX	38924	+	CHH	0.685828	5
+chrX	39162	+	CHH	0.0687508	6
+chrX	39332	-	CHH	0.0845057	5
+chrX	39483	-	CHH	0.399955	5
+chrX	39494	-	CHH	0.799927	5
+chrX	43216	+	CHH	0.250007	5
+chrX	43472	+	CHG	0.600105	5
+chrX	43479	+	CG	0.199997	5
+chrX	43630	-	CG	1	5
+chrX	45072	-	CHH	0.666791	6
+chrX	45089	-	CHH	0.714881	7
+chrX	45091	-	CHH	1	7
+chrX	45100	-	CHH	0.167211	6
+chrX	45109	-	CHH	0.166705	6
+chrX	46622	+	CHH	0.16669	6
+chrX	46630	+	CG	1	6
+chrX	47689	-	CG	1	5
+chrX	52301	-	CHH	0.0696125	6
+chrX	52321	-	CG	1	5
+chrX	52329	-	CHH	0.399793	5
+chrX	52891	+	CG	1	5
+chrX	54243	-	CG	1	5
+chrX	55290	-	CHH	0.771123	5
+chrX	55390	+	CHH	1	5
+chrX	55405	+	CHH	0.0844866	5
+chrX	57150	-	CHG	0.200028	5
+chrX	57158	-	CHH	0.200038	5
+chrX	57172	-	CHG	0.133077	7
+chrX	57959	-	CHH	0.0687657	6
+chrX	58153	-	CHH	0.0695654	6
+chrX	58182	-	CHH	0.207143	7
+chrX	58381	-	CG	1	5
+chrX	60062	-	CHG	0.0845234	5
+chrX	63019	-	CHH	1	5
+chrX	63028	-	CHH	0.392596	5
+chrX	64009	-	CHH	0.0871136	5
+chrX	64010	-	CHH	0.0847634	5
+chrX	66202	+	CHH	0.200025	5
+chrX	66777	-	CG	1	5
+chrX	67307	+	CHH	0.200013	5
+chrX	67313	+	CHG	0.199964	5
+chrX	67353	+	CHH	1	5
+chrX	67359	+	CHH	0.229064	5
+chrX	67361	+	CHH	0.0846822	5
+chrX	67362	+	CHG	0.0854955	5
+chrX	68821	+	CG	1	5
+chrX	74024	-	CHH	0.0643487	7
+chrX	74030	-	CHH	0.288962	6
+chrX	74489	+	CHH	0.599972	5
+chrX	74534	+	CHG	0.109637	5
+chrX	75814	+	CHH	0.255405	6
+chrX	76626	+	CHH	0.199235	5
+chrX	85167	+	CG	0.60009	5
+chrX	87464	+	CG	1	5
+chrX	88247	+	CHH	0.0845903	5
+chrX	89221	+	CHG	1	5
+chrX	91145	+	CHH	0.200016	5
+chrX	93899	+	CHH	0.125121	8
+chrX	93901	+	CHH	0.124999	8
+chrX	93914	+	CHG	0.0501003	8
+chrX	95642	+	CHG	0.166843	6
+chrX	96470	+	CHG	0.890401	5
+chrX	100031	-	CHH	0.200067	5
+chrX	100045	-	CHH	0.199991	5
+chrX	100053	-	CG	0.372587	6
+chrX	105375	+	CHG	1	5
+chrX	105400	+	CHH	0.143893	7
+chrX	105405	+	CG	1	8
+chrX	108177	+	CHH	0.142877	7
+chrX	108184	+	CHH	0.166956	6
+chrX	108573	+	CG	1	6
+chrX	109277	-	CHH	0.168442	6
+chrX	109961	+	CHH	0.166688	6
+chrX	111099	-	CHH	1	5
+chrX	113809	+	CG	1	5
+chrX	115760	+	CHH	0.384491	5
+chrX	118445	-	CHG	0.157404	7
+chrX	118467	-	CHH	0.0501558	8
+chrX	118471	-	CHG	0.135672	8
+chrX	118476	-	CHH	0.0500962	8
+chrX	118477	-	CHH	0.050102	8
+chrX	118494	-	CHG	0.374914	8
+chrX	118504	-	CHH	0.123971	8
+chrX	119468	+	CHH	0.199916	5
+chrX	121429	-	CHG	1	5
+chrX	122702	-	CHH	1	5
+chrX	123035	-	CHG	0.200124	5
+chrX	123039	-	CG	1	5
+chrX	123045	-	CHH	0.199906	5
+chrX	124406	+	CHG	0.200149	5
+chrX	124416	+	CHH	0.166692	6
+chrX	124417	+	CHH	0.166717	6
+chrX	127824	+	CHG	0.200042	5
+chrX	127831	+	CHH	1	5
+chrX	134280	+	CG	1	5
+chrX	134324	+	CHH	0.166673	6
+chrX	134336	+	CHG	0.0687663	6
+chrX	134339	+	CHH	0.600041	6
+chrX	142221	-	CHH	1	5
+chrX	143129	-	CHG	0.0845003	5
+chrX	143247	-	CHH	0.0844986	5
+chrX	144105	-	CG	1	6
+chrX	149264	-	CG	1	5
+chrX	149790	+	CG	0.912331	5
+chrX	152872	+	CHH	0.200096	5
+chrX	153344	-	CG	0.200228	5
+chrX	157869	-	CHG	0.0844872	5
+chrX	157874	-	CG	0.600694	5
+chrX	158404	+	CHH	0.19994	5
+chrX	159040	+	CHG	0.0987412	5
+chrX	160926	+	CHH	0.199844	5
+chrX	161429	-	CHH	0.101455	5
+chrX	161441	-	CHH	0.0583508	7
+chrX	161454	-	CHG	0.0580589	7
+chrX	161462	-	CG	1	6
+chrX	161465	-	CHH	0.16665	6
+chrX	162374	+	CHG	0.08449	5
+chrX	162375	+	CG	1	5
+chrX	162384	+	CHH	0.086048	5
+chrX	163894	-	CHH	0.199969	5
+chrX	165277	-	CHH	0.400022	5
+chrX	165318	-	CHH	0.0896461	5
+chrX	165326	-	CHH	0.599993	5
+chrX	168447	-	CHH	0.915503	5
+chrX	168456	-	CHH	0.0844872	5
+chrX	169720	+	CHG	0.183756	5
+chrX	170046	-	CHH	0.200062	5
+chrX	170081	-	CHH	0.200035	5
+chrX	172590	+	CHG	0.199999	5
+chrX	174809	+	CHH	0.201674	5
+chrX	174831	+	CHH	0.166651	6
+chrX	174840	+	CG	0.802483	5
+chrX	176321	+	CHH	0.217727	5
+chrX	176322	+	CHH	0.22644	5
+chrX	176323	+	CHH	0.250711	5
+chrX	176453	-	CHH	0.799911	5
+chrX	176795	+	CG	1	5
+chrX	176819	+	CHH	0.109573	5
+chrX	182336	-	CHH	0.400053	5
+chrX	183271	+	CHH	0.205075	5
+chrX	183405	-	CG	1	6
+chrX	183412	-	CHG	0.199977	5
+chrX	184541	+	CHG	0.333917	6
+chrX	188894	+	CHH	0.199971	5
+chrX	193312	-	CHH	0.199992	5
+chrX	193426	-	CHG	0.0846365	5
+chrX	193607	-	CHH	0.166678	6
+chrX	202217	+	CHH	1	5
+chrX	202234	+	CG	1	5
+chrX	206884	+	CHH	1	5
+chrX	206896	+	CHH	0.200046	5
+chrX	209032	+	CHH	0.250018	5
+chrX	209609	+	CHH	0.200154	5
+chrX	212230	+	CHH	0.0844937	5
+chrX	213112	+	CHG	0.084496	5
+chrX	213113	+	CG	0.915503	5
+chrX	215171	+	CHH	1	5
+chrX	218426	-	CHH	1	5
+chrX	218429	-	CG	1	5
+chrX	218879	-	CHH	0.0845158	5
+chrX	218902	-	CHH	0.125098	8
+chrX	218922	-	CHH	1	6
+chrX	221233	+	CHH	0.19996	5
+chrX	223039	-	CHG	0.200038	5
+chrX	225745	+	CHG	0.0846515	5
+chrX	225768	+	CHH	0.0994051	5
+chrX	226069	-	CG	1	5
+chrX	226092	-	CHG	0.19999	5
+chrX	227229	-	CHH	1	5
+chrX	227259	-	CHH	0.200044	5
+chrX	228472	+	CHH	0.200008	5
+chrX	228474	+	CG	0.600292	5
+chrX	228490	+	CHH	0.19876	5
+chrX	228496	+	CHH	0.200004	5
+chrX	230349	-	CG	1	5
+chrX	230351	-	CHH	0.0845427	5
+chrX	231931	+	CHH	0.569001	7
+chrX	231980	+	CHH	0.0687554	7
+chrX	233581	-	CHH	0.200031	5
+chrX	233586	-	CHH	0.200559	5
+chrX	237896	-	CHH	0.19996	5
+chrX	237961	-	CHH	0.0844838	5
+chrX	237966	-	CG	0.0844864	5
+chrX	242617	+	CHH	0.200418	5
+chrX	243594	+	CHH	0.200039	5
+chrX	244955	+	CHH	0.200082	5
+chrX	244977	+	CG	0.600028	5
+chrX	248755	+	CHG	0.168461	6
+chrX	248781	+	CHG	0.200683	5
+chrX	248782	+	CG	1	5
+chrX	248893	+	CG	1	6
+chrX	249124	-	CHG	0.250321	5
+chrX	249159	-	CG	1	6
+chrX	259420	-	CHH	0.200156	5
+chrX	260814	+	CHH	0.197518	5
+chrX	260830	+	CHH	0.19023	5
+chrX	260833	+	CG	1	5
+chrX	262377	+	CHH	1	5
+chrX	263381	+	CG	1	6
+chrX	263393	+	CHH	0.084497	5
+chrX	263438	-	CHH	0.199883	5
+chrX	264237	+	CHH	0.600215	5
+chrX	266024	+	CG	1	5
+chrX	266785	+	CHH	0.199793	5
+chrX	266790	+	CHG	0.600083	5
+chrX	267326	-	CG	0.399904	5
+chrX	268711	-	CHG	0.0845166	5
+chrX	268720	-	CHH	0.200614	5
+chrX	268734	-	CHH	0.200114	5
+chrX	273661	+	CHH	0.0846825	5
+chrX	274129	+	CHG	0.599879	5
+chrX	275091	-	CHH	0.199998	5
+chrX	275952	-	CHG	0.166368	6
+chrX	275969	-	CHG	1	7
+chrX	275997	-	CHH	0.166701	6
+chrX	277975	-	CHH	0.109621	5
+chrX	278167	-	CHH	0.229978	5
+chrX	285031	-	CHH	0.0844993	5
+chrX	285033	-	CHH	0.0845411	5
+chrX	286309	-	CHH	1	5
+chrX	286310	-	CHH	0.400768	5
+chrX	287913	+	CHH	0.399938	5
+chrX	287914	+	CHH	0.200021	5
+chrX	289901	+	CHH	0.199568	5
+chrX	291367	-	CHG	0.200781	5
+chrX	292963	+	CHH	0.200012	5
+chrX	293042	-	CG	1	5
+chrX	293240	+	CHH	0.20006	5
+chrX	297192	-	CHH	0.0579714	7
+chrX	297243	-	CHH	0.166674	6
+chrX	300936	-	CHH	1	5
+chrX	304412	+	CHH	0.189855	5
+chrX	304477	+	CHH	0.0846381	5
+chrX	304479	+	CHH	0.200371	5
+chrX	306768	+	CG	1	5
+chrX	307043	+	CHH	0.137912	7
+chrX	307046	+	CHH	0.143431	7
+chrX	307074	+	CHH	0.0688002	6
+chrX	308833	+	CHH	0.200006	5
+chrX	314220	-	CHH	0.166709	6
+chrX	315949	-	CHH	0.146052	5
+chrX	317827	-	CHH	0.333327	6
+chrX	317884	-	CHG	0.199957	5
+chrX	319903	+	CHG	0.200095	5
+chrX	319942	+	CHH	0.166986	6
+chrX	324865	+	CG	0.833291	6
+chrX	328990	-	CHH	0.0845443	5
+chrX	329820	+	CHH	0.0845246	5
+chrX	329872	+	CG	0.200203	5
+chrX	329874	+	CG	1	5
+chrX	331167	-	CHG	0.084587	5
+chrX	331204	-	CHH	0.200115	5
+chrX	332821	-	CHH	0.200013	5
+chrX	335417	+	CG	1	5
+chrX	335532	-	CHH	0.199785	5
+chrX	336866	+	CHH	0.200068	5
+chrX	336879	+	CHH	0.0687588	6
+chrX	336902	+	CG	1	5
+chrX	337692	-	CHG	0.200994	5
+chrX	337787	+	CHH	0.197475	5
+chrX	338823	+	CHH	0.200092	5
+chrX	342024	+	CHH	0.0687631	6
+chrX	342047	+	CG	1	5
+chrX	343817	-	CHH	0.796724	5
+chrX	344235	-	CHG	0.191975	5
+chrX	345794	+	CHH	1	5
+chrX	347230	-	CHH	0.402464	5
+chrX	351136	-	CHH	0.541447	5
+chrX	351187	-	CG	0.200011	5
+chrX	355578	-	CHH	0.202548	5
+chrX	355582	-	CG	1	6
+chrX	358321	+	CHH	0.0688325	6
+chrX	361250	-	CHG	0.399985	5
+chrX	361255	-	CHH	0.200022	5
+chrX	362322	+	CHH	0.197592	5
+chrX	362686	+	CHH	0.200057	5
+chrX	362687	+	CHH	1	5
+chrX	362694	+	CHH	0.200152	5
+chrX	365706	-	CHH	0.198742	5
+chrX	365765	-	CHH	0.199889	5
+chrX	366952	-	CHH	0.599983	5
+chrX	366966	-	CG	1	5
+chrX	368822	+	CHG	0.194974	5
+chrX	368823	+	CG	1	5
+chrX	369701	-	CG	0.200425	5
+chrX	369767	-	CG	1	5
+chrX	372624	+	CHH	0.200202	5
+chrX	372658	+	CHH	1	8
+chrX	372698	+	CHH	0.200188	5
+chrX	372970	+	CG	1	5
+chrX	372974	+	CHH	0.197474	5
+chrX	373157	+	CHH	0.200008	5
+chrX	374806	+	CHH	0.199563	5
+chrX	376740	+	CHH	1	7
+chrX	376757	-	CHH	0.084587	5
+chrX	376758	-	CHH	0.0845387	5
+chrX	377554	+	CG	0.156844	7
+chrX	377557	+	CHH	0.0579669	7
+chrX	379747	+	CHH	0.200048	5
+chrX	379759	+	CG	1	5
+chrX	381654	+	CHH	0.0688681	6
+chrX	383154	+	CHH	0.249836	5
+chrX	385496	-	CHG	0.0860717	5
+chrX	385531	-	CG	0.199894	5
+chrX	386894	+	CG	1	5
+chrX	386916	+	CHH	0.199856	5
+chrX	391650	+	CHH	0.200114	5
+chrX	391676	+	CHH	0.20835	5
+chrX	391685	+	CHH	0.200375	5
+chrX	391687	+	CG	1	5
+chrX	400422	-	CG	0.812869	5
+chrX	400766	+	CHH	0.199931	5
+chrX	400782	+	CHH	0.165671	6
+chrX	400793	+	CHH	0.200101	5
+chrX	400807	+	CHH	0.196026	5
+chrX	411499	-	CG	1	6
+chrX	413271	+	CHG	0.0845035	5
+chrX	413277	+	CHG	0.0846253	5
+chrX	413280	+	CHG	1	5
+chrX	413484	+	CHH	0.400589	5
+chrX	413492	+	CG	1	6
+chrX	413495	+	CHH	0.311099	6
+chrX	414225	-	CHG	0.205211	5
+chrX	414234	-	CG	1	5
+chrX	414272	-	CHH	0.199832	5
+chrX	418234	+	CHH	1	5
+chrX	420043	+	CHH	1	5
+chrX	423302	+	CHG	0.199872	5
+chrX	423331	+	CG	1	5
+chrX	424834	-	CG	1	5
+chrX	424874	-	CHH	0.199995	5
+chrX	427781	-	CHH	0.0844866	5
+chrX	429020	+	CG	0.16677	6
+chrX	429028	+	CHH	1	6
+chrX	435598	-	CHH	0.199974	5
+chrX	440238	+	CHH	0.199971	5
+chrX	440344	-	CHG	0.594932	5
+chrX	440348	-	CHG	0.399986	5
+chrX	443087	+	CG	1	5
+chrX	450439	+	CHH	0.200394	5
+chrX	452528	+	CG	1	5
+chrX	452765	-	CHH	0.599973	5
+chrX	455507	-	CHH	0.20003	5
+chrX	455737	-	CHH	0.0846746	5
+chrX	458885	-	CHH	0.400993	5
+chrX	459829	-	CG	1	5
+chrX	459858	-	CG	1	7
+chrX	459872	-	CHH	0.142923	7
+chrX	459905	-	CHG	0.200014	5
+chrX	465133	-	CHH	0.0845335	5
+chrX	465611	-	CG	1	5
+chrX	465901	-	CG	0.802467	5
+chrX	465913	-	CHH	0.166693	6
+chrX	470145	+	CHH	0.399975	5
+chrX	470148	+	CHH	0.199974	5
+chrX	471153	+	CHH	0.0848962	5
+chrX	473221	+	CHH	0.799992	5
+chrX	473910	-	CHH	0.0844957	5
+chrX	475565	+	CHH	0.084504	5
+chrX	476125	+	CHH	0.199885	5
+chrX	476196	+	CHH	0.0845111	5
+chrX	476198	+	CHG	0.0845143	5
+chrX	478452	-	CHH	0.0845683	5
+chrX	479044	-	CHH	0.401257	5
+chrX	479099	+	CHH	0.0847013	5
+chrX	479109	+	CHH	0.214841	5
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example-data/example.commet.in	Sun Apr 19 20:55:17 2015 +0900
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sun Apr 19 20:55:17 2015 +0900
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <set_environment>
+    <environment_variable name="TOOLDIR" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+  </set_environment>
+</tool_dependency>