changeset 0:a0c8dc671a23 draft

Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:27:03 -0500
parents
children 201d8e7dfc43
files ccat_wrapper.py ccat_wrapper.xml test-data/1.interval test-data/1.txt test-data/2.interval test-data/2.txt test-data/a.tab test-data/chipseq_enriched.bed.gz test-data/chipseq_input.bed.gz test-data/peakcalling_ccat/3.0/ccat_test_log_out_1.txt test-data/peakcalling_ccat/3.0/ccat_test_log_out_2.txt test-data/peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match test-data/peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match test-data/peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match test-data/peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match test-data/peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match test-data/peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match tool-data/ccat_configurations.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 20 files changed, 2990 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ccat_wrapper.py	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,41 @@
+import sys, subprocess, tempfile, shutil, os.path
+
+CCAT_BINARY = "CCAT"
+
+def get_top_count( filename ):
+    for line in open( filename ):
+        if line.startswith( 'outputNum' ):
+            return int( line.split()[-1].strip() ) 
+
+def stop_err( tmp_dir, exception ):
+    print >> sys.stderr, "Error running CCAT."
+    shutil.rmtree( tmp_dir ) #some error has occurred, provide info and remove possibly non-empty temp directory
+    raise exception
+
+def main():
+    input_tag_file = sys.argv[1]
+    input_control_file = sys.argv[2]
+    chrom_info_file = sys.argv[3]
+    input_config_file = sys.argv[4]
+    project_name = sys.argv[5]
+    output_peak_file = sys.argv[6]
+    output_region_file = sys.argv[7]
+    output_top_file = sys.argv[8]
+    output_log_file = sys.argv[9]
+    
+    tmp_dir = tempfile.mkdtemp()
+    try:
+        assert os.path.exists( chrom_info_file ), "The required chromosome length file does not exist."
+        proc = subprocess.Popen( args="%s %s > %s" % ( CCAT_BINARY, " ".join( map( lambda x: "'%s'" % x, [ input_tag_file, input_control_file, chrom_info_file, input_config_file, project_name ] ) ), output_log_file ), shell=True, cwd=tmp_dir )
+        proc.wait()
+        if proc.returncode:
+            raise Exception( "Error code: %i" % proc.returncode )
+        output_num = get_top_count( input_config_file )
+        shutil.move( os.path.join( tmp_dir, "%s.significant.peak" % project_name ), output_peak_file )
+        shutil.move( os.path.join( tmp_dir, "%s.significant.region" % project_name ), output_region_file )
+        shutil.move( os.path.join( tmp_dir, "%s.top%i.peak" % ( project_name, output_num ) ), output_top_file )
+    except Exception, e:
+        return stop_err( tmp_dir, e )
+    os.rmdir( tmp_dir ) #clean up empty temp working directory
+
+if __name__ == "__main__": main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ccat_wrapper.xml	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,148 @@
+<tool id="peakcalling_ccat" name="CCAT" version="0.0.1">
+  <description>Control-based ChIP-seq Analysis Tool</description>
+  <requirements>
+    <requirement type="package" version="3.0">CCAT</requirement>
+  </requirements>
+  <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' 
+  #if str( $options_type[ 'options_type_selector' ] ) == 'advanced':
+  '$input_advanced_config_file' 
+  #else:
+  '${ options_type.input_config_file.fields.path }'
+  #end if
+  'CCAT in Galaxy' 
+  '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command>
+  <inputs>
+    <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" >
+      <validator type="unspecified_build" />
+    </param>
+    <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" >
+      <validator type="unspecified_build" />
+    </param>
+    <conditional name="options_type">
+      <param name="options_type_selector" type="select" label="Advanced Options">
+        <option value="basic" selected="True">Hide Advanced Options</option>
+        <option value="advanced">Show Advanced Options</option>
+      </param>
+      <when value="basic">
+        <param name="input_config_file" type="select" label="Select a pre-defined configuration file">
+          <options from_data_table="ccat_configurations">
+            <validator type="no_options" message="No configurations are available"/>
+          </options>
+        </param>
+      </when>
+      <when value="advanced">
+        <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/>
+        <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/>
+        <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/>
+        <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" >
+          <option value="1">Transition from sense strand to anti-sense strand</option>
+          <option value="0" selected="True">Local maximum of read-enrichment profile</option>
+        </param>
+        <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/>
+        <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/>
+        <param name="random_seed" type="integer" label="Random Seed" value="123456"/>
+        <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/>
+        <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)">
+      <actions>
+        <action type="metadata" name="chromCol" default="1"/>
+        <action type="metadata" name="startCol" default="3"/>
+        <action type="metadata" name="endCol" default="4"/>
+      </actions>
+    </data>
+    <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)">
+      <actions>
+        <action type="metadata" name="chromCol" default="1"/>
+        <action type="metadata" name="startCol" default="3"/>
+        <action type="metadata" name="endCol" default="4"/>
+      </actions>
+    </data>
+    <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)">
+      <actions>
+        <action type="metadata" name="chromCol" default="1"/>
+        <action type="metadata" name="startCol" default="3"/>
+        <action type="metadata" name="endCol" default="4"/>
+      </actions>
+    </data>
+    <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
+  </outputs>
+  <configfiles>
+    <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced':
+fragmentSize	${options_type[ 'fragment_size' ]}
+slidingWinSize	${options_type[ 'sliding_window_size' ]}
+movingStep	${options_type[ 'moving_step' ]}
+isStrandSensitiveMode	${options_type[ 'is_strand_sensitive_mode' ]}
+minCount	${options_type[ 'min_count' ]}
+outputNum	${options_type[ 'output_num' ]}
+randomSeed	${options_type[ 'random_seed' ]}
+minScore	${options_type[ 'min_score' ]}	
+bootstrapPass	${options_type[ 'bootstrap_pass' ]}
+#end if</configfile>
+  </configfiles>
+  <tests>
+    <test>
+      <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
+      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
+      <param name="options_type_selector" value="advanced" />
+      <param name="fragment_size" value="200" />
+      <param name="sliding_window_size" value="500" />
+      <param name="moving_step" value="50" />
+      <param name="is_strand_sensitive_mode" value="0" />
+      <param name="min_count" value="4" />
+      <param name="output_num" value="100000" />
+      <param name="random_seed" value="123456" />
+      <param name="min_score" value="5.0" />
+      <param name="bootstrap_pass" value="50" />
+      <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
+      <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
+      <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="True" />
+      <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
+    </test>
+    <test>
+      <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
+      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
+      <param name="options_type_selector" value="basic" />
+      <param name="input_config_file" value="ccat_3.0_histone_config" />
+      <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
+      <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
+      <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" />
+      <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
+    </test>
+    <!-- Test below gives different answers on different architectures, 
+    e.g.: x86_64 GNU/Linux gave an extra line (additional peak called) when compared to the version running on 10.6.0 Darwin i386 
+    slidingWinSize was fixed to be 1000, default as per readme.txt
+    -->
+    <!--
+    <test>
+      <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
+      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
+      <param name="options_type_selector" value="basic" />
+      <param name="input_config_file" value="ccat_3.0_histone_config_readme" />
+      <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match" compare="re_match" />
+      <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match" compare="re_match" />
+      <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match" compare="re_match" sort="true" />
+      <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_2.txt" />
+    </test>
+  -->
+  </tests>
+  <help>
+**What it does**
+
+This tool allows ChIP-seq peak/region calling using CCAT.
+
+View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm.
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20371496&gt;`_
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.interval	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,5 @@
+chr1	4348187	4348589	3.70	4.90	2.55	0.24	0.46
+chr1	4488177	4488442	4.03	5.77	1.92	-0.67	0.81
+chr1	4774091	4774440	8.07	8.33	7.82	0.85	-0.40
+chr1	4800122	4800409	6.40	7.35	5.44	1.19	-0.42
+chr1	4878925	4879277	2.18	0.28	4.93	-0.96	1.24
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.txt	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,10 @@
+chr1    4225    19670
+chr10   6       8
+chr1    24417   24420
+chr6_hla_hap2   0       150
+chr2    1       5
+chr10   2       10
+chr1    30      55
+chrY    1       20
+chr1    1225979 42287290
+chr10   7       8
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.interval	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,14 @@
+chrX	151117436	151117437	+	0.14351
+chrX	151117437	151117438	+	0.139843
+chrX	151117438	151117439	+	0.132509
+chrX	151117439	151117440	+	0.139843
+chrX	151117440	151117441	+	0.169179
+chrX	151117441	151117442	+	0.257185
+chrX	151117442	151117443	+	0.319523
+chrX	151117443	151117444	+	0.367193
+chrX	151117444	151117445	+	0.400195
+chrX	151117445	151117446	+	0.425864
+chrX	151117446	151117447	+	0.444198
+chrX	151117447	151117448	+	0.455199
+chrX	151117448	151117449	+	0.462533
+chrX	151117449	151117450	+	0.4662
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.txt	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,8 @@
+chr1    4225    19670
+chr10   6       8
+chr1    24417   24420
+chr6_hla_hap2   0       150
+chr2    1       5
+chr1    30      55
+chrY    1       20
+chr1    1225979 42287290
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/a.tab	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,15 @@
+CHR	SNP	BP	A1	TEST	NMISS	BETA	STAT	P
+1	rs1181876	3671541	T	DOMDEV	958	-1.415	-3.326	0.0009161
+1	rs10492923	5092886	C	ADD	1007	5.105	4.368	1.382e-05
+1	rs10492923	5092886	C	DOMDEV	1007	-5.612	-4.249	2.35e-05
+1	rs10492923	5092886	C	GENO_2DF	1007	NA	19.9	4.775e-05
+1	rs1801133	11778965	T	ADD	1022	1.23	3.97	7.682e-05
+1	rs1801133	11778965	T	GENO_2DF	1022	NA	16.07	0.0003233
+1	rs1361912	12663121	A	ADD	1021	12.69	4.093	4.596e-05
+1	rs1361912	12663121	A	DOMDEV	1021	-12.37	-3.945	8.533e-05
+1	rs1361912	12663121	A	GENO_2DF	1021	NA	17.05	0.0001982
+1	rs1009806	19373138	G	ADD	1021	-1.334	-3.756	0.0001826
+1	rs1009806	19373138	G	GENO_2DF	1021	NA	19.36	6.244e-05
+1	rs873654	29550948	A	DOMDEV	1012	1.526	3.6	0.0003339
+1	rs10489527	36800027	C	ADD	1016	12.67	4.114	4.211e-05
+1	rs10489527	36800027	C	DOMDEV	1016	-13.05	-4.02	6.249e-05
Binary file test-data/chipseq_enriched.bed.gz has changed
Binary file test-data/chipseq_input.bed.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_ccat/3.0/ccat_test_log_out_1.txt	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,131 @@
+chromosome length information read. chromNum = 49!
+config file read.
+fragmentSize = 200
+isStrandSensitiveMode = 0
+slidingWinSize = 500
+movingStep = 50
+outputNum = 100000
+minCount = 4
+minScore = 5.000000
+bootstrapPass = 50
+randSeed = 123456
+reading tag files......
+10000 tags in L1, 10000 tags in L2.
+tag file read.
+pre-processing......
+pre-processing finished.
+estimating noise rate......
+not enough reads for noise rate estimation.
+noise rate estimation failed. noise rate set to be 1.0
+noise rate = 1.000000
+peak-finding......
+chr1......884 candidate peaks.
+chr1_random......0 candidate peaks.
+chr10......0 candidate peaks.
+chr10_random......0 candidate peaks.
+chr11......0 candidate peaks.
+chr11_random......0 candidate peaks.
+chr12......0 candidate peaks.
+chr13......0 candidate peaks.
+chr13_random......0 candidate peaks.
+chr14......0 candidate peaks.
+chr15......0 candidate peaks.
+chr15_random......0 candidate peaks.
+chr16......0 candidate peaks.
+chr16_random......0 candidate peaks.
+chr17......0 candidate peaks.
+chr17_random......0 candidate peaks.
+chr18......0 candidate peaks.
+chr18_random......0 candidate peaks.
+chr19......0 candidate peaks.
+chr19_random......0 candidate peaks.
+chr2......0 candidate peaks.
+chr2_random......0 candidate peaks.
+chr20......0 candidate peaks.
+chr21......0 candidate peaks.
+chr21_random......0 candidate peaks.
+chr22......0 candidate peaks.
+chr22_random......0 candidate peaks.
+chr22_h2_hap1......0 candidate peaks.
+chr3......0 candidate peaks.
+chr3_random......0 candidate peaks.
+chr4......0 candidate peaks.
+chr4_random......0 candidate peaks.
+chr5......0 candidate peaks.
+chr5_random......0 candidate peaks.
+chr5_h2_hap1......0 candidate peaks.
+chr6......0 candidate peaks.
+chr6_random......0 candidate peaks.
+chr6_cox_hap1......0 candidate peaks.
+chr6_qbl_hap2......0 candidate peaks.
+chr7......0 candidate peaks.
+chr7_random......0 candidate peaks.
+chr8......0 candidate peaks.
+chr8_random......0 candidate peaks.
+chr9......0 candidate peaks.
+chr9_random......0 candidate peaks.
+chrM......0 candidate peaks.
+chrX......0 candidate peaks.
+chrX_random......0 candidate peaks.
+chrY......0 candidate peaks.
+peak-finding finished.
+Significance Analysis......
+estimating paramters......
+smoothing factor = 0.356298
+estimating local FDR.....
+FDR at the threshold 5.000000 is 0.999000. You may want to adjust the threshold by inspecting the output files.
+post-processing......
+chr1......finished.
+chr1_random......finished.
+chr10......finished.
+chr10_random......finished.
+chr11......finished.
+chr11_random......finished.
+chr12......finished.
+chr13......finished.
+chr13_random......finished.
+chr14......finished.
+chr15......finished.
+chr15_random......finished.
+chr16......finished.
+chr16_random......finished.
+chr17......finished.
+chr17_random......finished.
+chr18......finished.
+chr18_random......finished.
+chr19......finished.
+chr19_random......finished.
+chr2......finished.
+chr2_random......finished.
+chr20......finished.
+chr21......finished.
+chr21_random......finished.
+chr22......finished.
+chr22_random......finished.
+chr22_h2_hap1......finished.
+chr3......finished.
+chr3_random......finished.
+chr4......finished.
+chr4_random......finished.
+chr5......finished.
+chr5_random......finished.
+chr5_h2_hap1......finished.
+chr6......finished.
+chr6_random......finished.
+chr6_cox_hap1......finished.
+chr6_qbl_hap2......finished.
+chr7......finished.
+chr7_random......finished.
+chr8......finished.
+chr8_random......finished.
+chr9......finished.
+chr9_random......finished.
+chrM......finished.
+chrX......finished.
+chrX_random......finished.
+chrY......finished.
+post-processing finished.
+Significance analysis finished.
+saving results.......
+results saved.
+CCAT process completed!
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_ccat/3.0/ccat_test_log_out_2.txt	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,131 @@
+chromosome length information read. chromNum = 49!
+config file read.
+fragmentSize = 200
+isStrandSensitiveMode = 0
+slidingWinSize = 1000
+movingStep = 50
+outputNum = 100000
+minCount = 4
+minScore = 5.000000
+bootstrapPass = 50
+randSeed = 123456
+reading tag files......
+10000 tags in L1, 10000 tags in L2.
+tag file read.
+pre-processing......
+pre-processing finished.
+estimating noise rate......
+not enough reads for noise rate estimation.
+noise rate estimation failed. noise rate set to be 1.0
+noise rate = 1.000000
+peak-finding......
+chr1......673 candidate peaks.
+chr1_random......0 candidate peaks.
+chr10......0 candidate peaks.
+chr10_random......0 candidate peaks.
+chr11......0 candidate peaks.
+chr11_random......0 candidate peaks.
+chr12......0 candidate peaks.
+chr13......0 candidate peaks.
+chr13_random......0 candidate peaks.
+chr14......0 candidate peaks.
+chr15......0 candidate peaks.
+chr15_random......0 candidate peaks.
+chr16......0 candidate peaks.
+chr16_random......0 candidate peaks.
+chr17......0 candidate peaks.
+chr17_random......0 candidate peaks.
+chr18......0 candidate peaks.
+chr18_random......0 candidate peaks.
+chr19......0 candidate peaks.
+chr19_random......0 candidate peaks.
+chr2......0 candidate peaks.
+chr2_random......0 candidate peaks.
+chr20......0 candidate peaks.
+chr21......0 candidate peaks.
+chr21_random......0 candidate peaks.
+chr22......0 candidate peaks.
+chr22_random......0 candidate peaks.
+chr22_h2_hap1......0 candidate peaks.
+chr3......0 candidate peaks.
+chr3_random......0 candidate peaks.
+chr4......0 candidate peaks.
+chr4_random......0 candidate peaks.
+chr5......0 candidate peaks.
+chr5_random......0 candidate peaks.
+chr5_h2_hap1......0 candidate peaks.
+chr6......0 candidate peaks.
+chr6_random......0 candidate peaks.
+chr6_cox_hap1......0 candidate peaks.
+chr6_qbl_hap2......0 candidate peaks.
+chr7......0 candidate peaks.
+chr7_random......0 candidate peaks.
+chr8......0 candidate peaks.
+chr8_random......0 candidate peaks.
+chr9......0 candidate peaks.
+chr9_random......0 candidate peaks.
+chrM......0 candidate peaks.
+chrX......0 candidate peaks.
+chrX_random......0 candidate peaks.
+chrY......0 candidate peaks.
+peak-finding finished.
+Significance Analysis......
+estimating paramters......
+smoothing factor = 0.287387
+estimating local FDR.....
+FDR at the threshold 5.000000 is 0.999000. You may want to adjust the threshold by inspecting the output files.
+post-processing......
+chr1......finished.
+chr1_random......finished.
+chr10......finished.
+chr10_random......finished.
+chr11......finished.
+chr11_random......finished.
+chr12......finished.
+chr13......finished.
+chr13_random......finished.
+chr14......finished.
+chr15......finished.
+chr15_random......finished.
+chr16......finished.
+chr16_random......finished.
+chr17......finished.
+chr17_random......finished.
+chr18......finished.
+chr18_random......finished.
+chr19......finished.
+chr19_random......finished.
+chr2......finished.
+chr2_random......finished.
+chr20......finished.
+chr21......finished.
+chr21_random......finished.
+chr22......finished.
+chr22_random......finished.
+chr22_h2_hap1......finished.
+chr3......finished.
+chr3_random......finished.
+chr4......finished.
+chr4_random......finished.
+chr5......finished.
+chr5_random......finished.
+chr5_h2_hap1......finished.
+chr6......finished.
+chr6_random......finished.
+chr6_cox_hap1......finished.
+chr6_qbl_hap2......finished.
+chr7......finished.
+chr7_random......finished.
+chr8......finished.
+chr8_random......finished.
+chr9......finished.
+chr9_random......finished.
+chrM......finished.
+chrX......finished.
+chrX_random......finished.
+chrY......finished.
+post-processing finished.
+Significance analysis finished.
+saving results.......
+results saved.
+CCAT process completed!
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,382 @@
+chr1	4760025	4756750	4762650	128	0	399\.\d+	0\.133000
+chr1	4761475	4756750	4762650	74	0	230\.\d+	0\.133000
+chr1	4771725	4768050	4778800	37	0	115\.\d+	0\.133000
+chr1	5061925	5060800	5063500	15	0	46\.\d+	0\.133000
+chr1	5174925	5172300	5175650	15	0	46\.\d+	0\.133000
+chr1	5198225	5193500	5203550	13	0	40\.\d+	0\.133000
+chr1	5094525	5090900	5098600	12	0	37\.\d+	0\.133000
+chr1	5649775	5646050	5655200	12	0	37\.\d+	0\.133000
+chr1	4764325	4763100	4767650	11	0	34\.\d+	0\.189000
+chr1	5250175	5247500	5252250	11	0	34\.\d+	0\.189000
+chr1	4861125	4856150	4863100	11	0	34\.\d+	0\.189000
+chr1	5202075	5193500	5203550	11	0	34\.\d+	0\.189000
+chr1	4961625	4952100	4964300	11	0	34\.\d+	0\.189000
+chr1	4830175	4828350	4831300	11	0	34\.\d+	0\.189000
+chr1	5177075	5175750	5180950	11	0	34\.\d+	0\.189000
+chr1	4849575	4842300	4852000	10	0	31\.\d+	0\.189000
+chr1	4792275	4789000	4793650	10	0	31\.\d+	0\.189000
+chr1	4996125	4991700	4999350	10	0	31\.\d+	0\.189000
+chr1	5132325	5128000	5136550	10	0	31\.\d+	0\.189000
+chr1	5270525	5269800	5276000	10	0	31\.\d+	0\.189000
+chr1	4716525	4708050	4718500	10	0	31\.\d+	0\.189000
+chr1	4766575	4763100	4767650	10	0	31\.\d+	0\.189000
+chr1	4740375	4733200	4746750	10	0	31\.\d+	0\.189000
+chr1	5594075	5591050	5602000	10	0	31\.\d+	0\.189000
+chr1	4908575	4907850	4911250	10	0	31\.\d+	0\.189000
+chr1	4806875	4800850	4808250	9	0	28\.\d+	0\.189000
+chr1	5078275	5075400	5080200	9	0	28\.\d+	0\.189000
+chr1	5221425	5215900	5227150	9	0	28\.\d+	0\.189000
+chr1	5616925	5614250	5618100	9	0	28\.\d+	0\.189000
+chr1	4811775	4809250	4818000	9	0	28\.\d+	0\.189000
+chr1	5224375	5215900	5227150	9	0	28\.\d+	0\.189000
+chr1	4712925	4708050	4718500	9	0	28\.\d+	0\.189000
+chr1	4820775	4819250	4824400	9	0	28\.\d+	0\.189000
+chr1	5510975	5510050	5511700	9	0	28\.\d+	0\.189000
+chr1	4757975	4756750	4762650	9	0	28\.\d+	0\.189000
+chr1	4902125	4896550	4904200	9	0	28\.\d+	0\.189000
+chr1	4754525	4746800	4756450	9	0	28\.\d+	0\.189000
+chr1	4752925	4746800	4756450	9	0	28\.\d+	0\.189000
+chr1	4663075	4662250	4664800	9	0	28\.\d+	0\.189000
+chr1	4747475	4746800	4756450	9	0	28\.\d+	0\.189000
+chr1	5726225	5725050	5728250	9	0	28\.\d+	0\.189000
+chr1	4666125	4665400	4667400	9	0	28\.\d+	0\.189000
+chr1	5311275	5309550	5312000	9	0	28\.\d+	0\.189000
+chr1	5653625	5646050	5655200	9	0	28\.\d+	0\.189000
+chr1	5267625	5265900	5268400	9	0	28\.\d+	0\.189000
+chr1	5648725	5646050	5655200	9	0	28\.\d+	0\.189000
+chr1	4732075	4728950	4732850	9	0	28\.\d+	0\.189000
+chr1	4955725	4952100	4964300	9	0	28\.\d+	0\.189000
+chr1	4892675	4889250	4896100	9	0	28\.\d+	0\.189000
+chr1	4891925	4889250	4896100	9	0	28\.\d+	0\.189000
+chr1	5306625	5303150	5309300	9	0	28\.\d+	0\.189000
+chr1	4337575	4337150	4338250	54	2	25\.\d+	0\.193000
+chr1	5208725	5206650	5210650	8	0	24\.\d+	0\.193000
+chr1	5217175	5215900	5227150	8	0	24\.\d+	0\.193000
+chr1	5305275	5303150	5309300	8	0	24\.\d+	0\.193000
+chr1	5429675	5427700	5430400	8	0	24\.\d+	0\.193000
+chr1	4714325	4708050	4718500	8	0	24\.\d+	0\.193000
+chr1	4743875	4733200	4746750	8	0	24\.\d+	0\.193000
+chr1	5412375	5411500	5413450	8	0	24\.\d+	0\.193000
+chr1	4882725	4879050	4885000	8	0	24\.\d+	0\.193000
+chr1	4927275	4924450	4935350	8	0	24\.\d+	0\.193000
+chr1	4844075	4842300	4852000	8	0	24\.\d+	0\.193000
+chr1	4915625	4913050	4924250	8	0	24\.\d+	0\.193000
+chr1	4918175	4913050	4924250	8	0	24\.\d+	0\.193000
+chr1	4691975	4687200	4694150	8	0	24\.\d+	0\.193000
+chr1	4967025	4965550	4970250	8	0	24\.\d+	0\.193000
+chr1	4960075	4952100	4964300	8	0	24\.\d+	0\.193000
+chr1	4957475	4952100	4964300	8	0	24\.\d+	0\.193000
+chr1	4928675	4924450	4935350	8	0	24\.\d+	0\.193000
+chr1	4934125	4924450	4935350	8	0	24\.\d+	0\.193000
+chr1	4936125	4935500	4937950	8	0	24\.\d+	0\.193000
+chr1	5122725	5122100	5123350	8	0	24\.\d+	0\.193000
+chr1	5129925	5128000	5136550	8	0	24\.\d+	0\.193000
+chr1	4833925	4831400	4840050	8	0	24\.\d+	0\.193000
+chr1	5114275	5113600	5116850	8	0	24\.\d+	0\.193000
+chr1	5045775	5044700	5048150	8	0	24\.\d+	0\.193000
+chr1	4809925	4809250	4818000	8	0	24\.\d+	0\.193000
+chr1	5055525	5053900	5058050	8	0	24\.\d+	0\.193000
+chr1	4944975	4944400	4947700	7	0	21\.\d+	0\.193000
+chr1	4893575	4889250	4896100	7	0	21\.\d+	0\.193000
+chr1	5314975	5312250	5316300	7	0	21\.\d+	0\.193000
+chr1	4899675	4896550	4904200	7	0	21\.\d+	0\.193000
+chr1	4905925	4905100	4907750	7	0	21\.\d+	0\.193000
+chr1	4917125	4913050	4924250	7	0	21\.\d+	0\.193000
+chr1	5365125	5363650	5365850	7	0	21\.\d+	0\.193000
+chr1	4890875	4889250	4896100	7	0	21\.\d+	0\.193000
+chr1	4765275	4763100	4767650	7	0	21\.\d+	0\.193000
+chr1	4880925	4879050	4885000	7	0	21\.\d+	0\.193000
+chr1	4874225	4871650	4875600	7	0	21\.\d+	0\.193000
+chr1	5212225	5210850	5215150	7	0	21\.\d+	0\.193000
+chr1	4801975	4800850	4808250	7	0	21\.\d+	0\.193000
+chr1	5017525	5015500	5020500	7	0	21\.\d+	0\.193000
+chr1	5018825	5015500	5020500	7	0	21\.\d+	0\.193000
+chr1	5178875	5175750	5180950	7	0	21\.\d+	0\.193000
+chr1	4804975	4800850	4808250	7	0	21\.\d+	0\.193000
+chr1	5059325	5058600	5060000	7	0	21\.\d+	0\.193000
+chr1	4835275	4831400	4840050	7	0	21\.\d+	0\.193000
+chr1	5223575	5215900	5227150	7	0	21\.\d+	0\.193000
+chr1	4998775	4991700	4999350	7	0	21\.\d+	0\.193000
+chr1	4775325	4768050	4778800	7	0	21\.\d+	0\.193000
+chr1	4872275	4871650	4875600	7	0	21\.\d+	0\.193000
+chr1	4963075	4952100	4964300	7	0	21\.\d+	0\.193000
+chr1	5004175	5001700	5010700	7	0	21\.\d+	0\.193000
+chr1	4794975	4794200	4797900	7	0	21\.\d+	0\.193000
+chr1	4789675	4789000	4793650	7	0	21\.\d+	0\.193000
+chr1	5229975	5229250	5231850	7	0	21\.\d+	0\.193000
+chr1	4734375	4733200	4746750	7	0	21\.\d+	0\.193000
+chr1	5448175	5447500	5449550	7	0	21\.\d+	0\.193000
+chr1	4736675	4733200	4746750	7	0	21\.\d+	0\.193000
+chr1	4696225	4694250	4697100	7	0	21\.\d+	0\.193000
+chr1	5679225	5678650	5681350	7	0	21\.\d+	0\.193000
+chr1	4688525	4687200	4694150	7	0	21\.\d+	0\.193000
+chr1	5570575	5569100	5573050	7	0	21\.\d+	0\.193000
+chr1	5651925	5646050	5655200	7	0	21\.\d+	0\.193000
+chr1	5568475	5567950	5569000	7	0	21\.\d+	0\.193000
+chr1	5400875	5399200	5403500	7	0	21\.\d+	0\.193000
+chr1	4744975	4733200	4746750	7	0	21\.\d+	0\.193000
+chr1	5386625	5385650	5387700	7	0	21\.\d+	0\.193000
+chr1	4749875	4746800	4756450	7	0	21\.\d+	0\.193000
+chr1	5384325	5383800	5385000	7	0	21\.\d+	0\.193000
+chr1	4508175	4507350	4508650	41	2	19\.\d+	0\.193000
+chr1	5612875	5610500	5613650	6	0	18\.\d+	0\.193000
+chr1	5006175	5001700	5010700	6	0	18\.\d+	0\.193000
+chr1	4718025	4708050	4718500	6	0	18\.\d+	0\.193000
+chr1	4678925	4678250	4679650	6	0	18\.\d+	0\.193000
+chr1	5203125	5193500	5203550	6	0	18\.\d+	0\.193000
+chr1	5533875	5531900	5534450	6	0	18\.\d+	0\.193000
+chr1	5532625	5531900	5534450	6	0	18\.\d+	0\.193000
+chr1	4670175	4668300	4670850	6	0	18\.\d+	0\.193000
+chr1	4954225	4952100	4964300	6	0	18\.\d+	0\.193000
+chr1	5220175	5215900	5227150	6	0	18\.\d+	0\.193000
+chr1	5106325	5105550	5109300	6	0	18\.\d+	0\.193000
+chr1	5512575	5511900	5513200	6	0	18\.\d+	0\.193000
+chr1	5011925	5010800	5015150	6	0	18\.\d+	0\.193000
+chr1	4845975	4842300	4852000	6	0	18\.\d+	0\.193000
+chr1	4799975	4799000	4800750	6	0	18\.\d+	0\.193000
+chr1	5581475	5575800	5590800	6	0	18\.\d+	0\.193000
+chr1	5014425	5010800	5015150	6	0	18\.\d+	0\.193000
+chr1	5614875	5614250	5618100	6	0	18\.\d+	0\.193000
+chr1	4858375	4856150	4863100	6	0	18\.\d+	0\.193000
+chr1	5134825	5128000	5136550	6	0	18\.\d+	0\.193000
+chr1	5577775	5575800	5590800	6	0	18\.\d+	0\.193000
+chr1	4968175	4965550	4970250	6	0	18\.\d+	0\.193000
+chr1	5151525	5150800	5156200	6	0	18\.\d+	0\.193000
+chr1	5751675	5751000	5752900	6	0	18\.\d+	0\.193000
+chr1	5571625	5569100	5573050	6	0	18\.\d+	0\.193000
+chr1	4981675	4979400	4983450	6	0	18\.\d+	0\.193000
+chr1	4813825	4809250	4818000	6	0	18\.\d+	0\.193000
+chr1	5125975	5124950	5127600	6	0	18\.\d+	0\.193000
+chr1	5549025	5548350	5551750	6	0	18\.\d+	0\.193000
+chr1	4865525	4864400	4866300	6	0	18\.\d+	0\.193000
+chr1	5196775	5193500	5203550	6	0	18\.\d+	0\.193000
+chr1	5646825	5646050	5655200	6	0	18\.\d+	0\.193000
+chr1	5167125	5165800	5169800	6	0	18\.\d+	0\.193000
+chr1	5024625	5020800	5026100	6	0	18\.\d+	0\.193000
+chr1	4751325	4746800	4756450	6	0	18\.\d+	0\.193000
+chr1	5168375	5165800	5169800	6	0	18\.\d+	0\.193000
+chr1	5225975	5215900	5227150	6	0	18\.\d+	0\.193000
+chr1	5295475	5294850	5299450	6	0	18\.\d+	0\.193000
+chr1	4910325	4907850	4911250	6	0	18\.\d+	0\.193000
+chr1	5718675	5716950	5719450	6	0	18\.\d+	0\.193000
+chr1	5065525	5063900	5068050	6	0	18\.\d+	0\.193000
+chr1	5745875	5743300	5747400	6	0	18\.\d+	0\.193000
+chr1	5279825	5279200	5281050	6	0	18\.\d+	0\.193000
+chr1	5277575	5276150	5279150	6	0	18\.\d+	0\.193000
+chr1	5590125	5575800	5590800	6	0	18\.\d+	0\.193000
+chr1	5285775	5285150	5287400	6	0	18\.\d+	0\.193000
+chr1	5409525	5407000	5411350	6	0	18\.\d+	0\.193000
+chr1	5057325	5053900	5058050	6	0	18\.\d+	0\.193000
+chr1	5324825	5323050	5329500	6	0	18\.\d+	0\.193000
+chr1	4738225	4733200	4746750	6	0	18\.\d+	0\.193000
+chr1	4769325	4768050	4778800	6	0	18\.\d+	0\.193000
+chr1	5596625	5591050	5602000	6	0	18\.\d+	0\.193000
+chr1	5442275	5441650	5444200	6	0	18\.\d+	0\.193000
+chr1	3218225	3217950	3218650	6	0	18\.\d+	0\.193000
+chr1	5348875	5348250	5349450	6	0	18\.\d+	0\.193000
+chr1	5075925	5075400	5080200	6	0	18\.\d+	0\.193000
+chr1	4776975	4768050	4778800	6	0	18\.\d+	0\.193000
+chr1	5240125	5239500	5241650	6	0	18\.\d+	0\.193000
+chr1	4693475	4687200	4694150	6	0	18\.\d+	0\.193000
+chr1	5088175	5082600	5090800	6	0	18\.\d+	0\.193000
+chr1	4697725	4697150	4699850	6	0	18\.\d+	0\.193000
+chr1	4790975	4789000	4793650	6	0	18\.\d+	0\.193000
+chr1	4689325	4687200	4694150	6	0	18\.\d+	0\.193000
+chr1	4787025	4786400	4787800	6	0	18\.\d+	0\.193000
+chr1	5586075	5575800	5590800	6	0	18\.\d+	0\.193000
+chr1	5706275	5704550	5709600	6	0	18\.\d+	0\.193000
+chr1	5265025	5264250	5265800	6	0	18\.\d+	0\.193000
+chr1	5077225	5075400	5080200	6	0	18\.\d+	0\.193000
+chr1	5453725	5451600	5457500	6	0	18\.\d+	0\.193000
+chr1	5697075	5696100	5697750	6	0	18\.\d+	0\.193000
+chr1	5588975	5575800	5590800	6	0	18\.\d+	0\.193000
+chr1	4926425	4924450	4935350	6	0	18\.\d+	0\.193000
+chr1	5256375	5255600	5256950	6	0	18\.\d+	0\.193000
+chr1	4921425	4913050	4924250	6	0	18\.\d+	0\.193000
+chr1	4408225	4407650	4408750	81	5	16\.\d+	0\.193000
+chr1	5714575	5714000	5716900	5	0	15\.\d+	0\.193000
+chr1	4925175	4924450	4935350	5	0	15\.\d+	0\.193000
+chr1	5716125	5714000	5716900	5	0	15\.\d+	0\.193000
+chr1	4885925	4885150	4886550	5	0	15\.\d+	0\.193000
+chr1	4931325	4924450	4935350	5	0	15\.\d+	0\.193000
+chr1	3832625	3831950	3833100	5	0	15\.\d+	0\.193000
+chr1	5680325	5678650	5681350	5	0	15\.\d+	0\.193000
+chr1	5606575	5604350	5609750	5	0	15\.\d+	0\.193000
+chr1	4668925	4668300	4670850	5	0	15\.\d+	0\.193000
+chr1	4894525	4889250	4896100	5	0	15\.\d+	0\.193000
+chr1	5022225	5020800	5026100	5	0	15\.\d+	0\.193000
+chr1	4843075	4842300	4852000	5	0	15\.\d+	0\.193000
+chr1	5746675	5743300	5747400	5	0	15\.\d+	0\.193000
+chr1	5023175	5020800	5026100	5	0	15\.\d+	0\.193000
+chr1	5727525	5725050	5728250	5	0	15\.\d+	0\.193000
+chr1	3054875	3054500	3055300	5	0	15\.\d+	0\.193000
+chr1	5019775	5015500	5020500	5	0	15\.\d+	0\.193000
+chr1	4897525	4896550	4904200	5	0	15\.\d+	0\.193000
+chr1	5742225	5741500	5743250	5	0	15\.\d+	0\.193000
+chr1	4932625	4924450	4935350	5	0	15\.\d+	0\.193000
+chr1	4687675	4687200	4694150	5	0	15\.\d+	0\.193000
+chr1	4997775	4991700	4999350	5	0	15\.\d+	0\.193000
+chr1	4855025	4854250	4856100	5	0	15\.\d+	0\.193000
+chr1	5633525	5631850	5636000	5	0	15\.\d+	0\.193000
+chr1	5621725	5621000	5622450	5	0	15\.\d+	0\.193000
+chr1	4857375	4856150	4863100	5	0	15\.\d+	0\.193000
+chr1	4993025	4991700	4999350	5	0	15\.\d+	0\.193000
+chr1	4994875	4991700	4999350	5	0	15\.\d+	0\.193000
+chr1	4979975	4979400	4983450	5	0	15\.\d+	0\.193000
+chr1	4681775	4679750	4684100	5	0	15\.\d+	0\.193000
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+chr1	5013425	5010800	5015150	5	0	15\.\d+	0\.193000
+chr1	5666675	5666250	5667300	5	0	15\.\d+	0\.193000
+chr1	4092425	4091800	4092950	5	0	15\.\d+	0\.193000
+chr1	4879825	4879050	4885000	5	0	15\.\d+	0\.193000
+chr1	5655975	5655300	5656700	5	0	15\.\d+	0\.193000
+chr1	3139075	3138350	3139350	5	0	15\.\d+	0\.193000
+chr1	4947075	4944400	4947700	5	0	15\.\d+	0\.193000
+chr1	4952725	4952100	4964300	5	0	15\.\d+	0\.193000
+chr1	5497825	5495700	5499250	5	0	15\.\d+	0\.193000
+chr1	4730925	4728950	4732850	5	0	15\.\d+	0\.193000
+chr1	4727375	4725950	4728150	5	0	15\.\d+	0\.193000
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+chr1	4895575	4889250	4896100	4	0	12\.\d+	0\.193000
+chr1	4323875	4323250	4324550	47	4	11\.\d+	1\.000000
+chr1	4629425	4629150	4629700	9	1	7\.\d+	1\.000000
+chr1	3462625	3462250	3463300	8	1	6\.\d+	1\.000000
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+chr1	3677375	3677100	3677700	7	1	5\.\d+	1\.000000
+chr1	4247375	4247100	4247650	11	2	5\.\d+	1\.000000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,272 @@
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+chr1	4324025	4322650	4324900	48	7	6\.\d+	1\.000000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,183 @@
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+chr1	5512575	5511900	5513200	6	0	18\.\d+	0\.193000
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+chr1	4681775	4679750	4684100	5	0	15\.\d+	0\.193000
+chr1	3832625	3831950	3833100	5	0	15\.\d+	0\.193000
+chr1	5655975	5655300	5656700	5	0	15\.\d+	0\.193000
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+chr1	5666675	5666250	5667300	5	0	15\.\d+	0\.193000
+chr1	5606575	5604350	5609750	5	0	15\.\d+	0\.193000
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+chr1	5288675	5288100	5291550	5	0	15\.\d+	0\.193000
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+chr1	4975375	4974700	4976400	4	0	12\.\d+	0\.193000
+chr1	4887025	4886600	4887750	4	0	12\.\d+	0\.193000
+chr1	3196025	3195750	3196350	4	0	12\.\d+	0\.193000
+chr1	5257475	5257000	5258200	4	0	12\.\d+	0\.193000
+chr1	4852675	4852100	4853850	4	0	12\.\d+	0\.193000
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+chr1	5234475	5233800	5237550	4	0	12\.\d+	0\.193000
+chr1	3062525	3062250	3062900	4	0	12\.\d+	0\.193000
+chr1	5440025	5439250	5440800	4	0	12\.\d+	0\.193000
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+chr1	5529975	5529250	5531450	4	0	12\.\d+	0\.193000
+chr1	5434275	5433650	5434750	4	0	12\.\d+	0\.193000
+chr1	5074275	5073700	5074850	4	0	12\.\d+	0\.193000
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+chr1	4323875	4323250	4324550	47	4	11\.\d+	1\.000000
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+chr1	4247375	4247100	4247650	11	2	5\.\d+	1\.000000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,74 @@
+chr1	4760225	4725450	4779800	139	0	507\.\d+	0\.025000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,884 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,673 @@
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+chr1	4975525	4974200	4976900	6	0	21\.\d+	0\.135000
+chr1	4981425	4978900	4987150	10	0	36\.\d+	0\.034000
+chr1	4984925	4978900	4987150	4	0	14\.\d+	1\.000000
+chr1	4993575	4990250	5026600	7	0	25\.\d+	0\.135000
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+chr1	5014125	4990250	5026600	9	0	32\.\d+	0\.034000
+chr1	5017375	4990250	5026600	9	0	32\.\d+	0\.034000
+chr1	5019075	4990250	5026600	10	0	36\.\d+	0\.034000
+chr1	5022575	4990250	5026600	8	0	29\.\d+	0\.034000
+chr1	5024225	4990250	5026600	9	0	32\.\d+	0\.034000
+chr1	5033175	5032000	5036100	4	0	14\.\d+	1\.000000
+chr1	5039275	5037850	5040800	5	0	18\.\d+	0\.199000
+chr1	5045675	5044200	5048700	11	0	40\.\d+	0\.034000
+chr1	5055275	5053400	5068550	9	0	32\.\d+	0\.034000
+chr1	5057075	5053400	5068550	10	0	36\.\d+	0\.034000
+chr1	5059225	5053400	5068550	8	0	29\.\d+	0\.034000
+chr1	5061725	5053400	5068550	19	0	69\.\d+	0\.025000
+chr1	5064875	5053400	5068550	9	0	32\.\d+	0\.034000
+chr1	5078525	5073200	5080700	13	0	47\.\d+	0\.025000
+chr1	5083325	5080750	5101500	6	0	21\.\d+	0\.135000
+chr1	5086225	5080750	5101500	7	0	25\.\d+	0\.135000
+chr1	5088225	5080750	5101500	8	0	29\.\d+	0\.034000
+chr1	5092375	5080750	5101500	6	0	21\.\d+	0\.135000
+chr1	5094825	5080750	5101500	19	0	69\.\d+	0\.025000
+chr1	5097675	5080750	5101500	6	0	21\.\d+	0\.135000
+chr1	5106525	5105050	5117450	11	0	40\.\d+	0\.034000
+chr1	5110775	5105050	5117450	7	0	25\.\d+	0\.135000
+chr1	5112225	5105050	5117450	7	0	25\.\d+	0\.135000
+chr1	5114025	5105050	5117450	9	0	32\.\d+	0\.034000
+chr1	5116025	5105050	5117450	5	0	18\.\d+	0\.199000
+chr1	5119225	5117850	5121550	6	0	21\.\d+	0\.135000
+chr1	5122775	5121600	5140300	9	0	32\.\d+	0\.034000
+chr1	5125725	5121600	5140300	8	0	29\.\d+	0\.034000
+chr1	5130175	5121600	5140300	13	0	47\.\d+	0\.025000
+chr1	5132075	5121600	5140300	14	0	51\.\d+	0\.025000
+chr1	5134725	5121600	5140300	8	0	29\.\d+	0\.034000
+chr1	5137425	5121600	5140300	5	0	18\.\d+	0\.199000
+chr1	5138925	5121600	5140300	6	0	21\.\d+	0\.135000
+chr1	5143275	5140350	5157200	7	0	25\.\d+	0\.135000
+chr1	5148975	5140350	5157200	9	0	32\.\d+	0\.034000
+chr1	5151825	5140350	5157200	10	0	36\.\d+	0\.034000
+chr1	5153825	5140350	5157200	8	0	29\.\d+	0\.034000
+chr1	5161725	5159000	5163250	5	0	18\.\d+	0\.199000
+chr1	5164425	5163300	5181450	6	0	21\.\d+	0\.135000
+chr1	5167425	5163300	5181450	10	0	36\.\d+	0\.034000
+chr1	5174775	5163300	5181450	19	0	69\.\d+	0\.025000
+chr1	5177325	5163300	5181450	17	0	62\.\d+	0\.025000
+chr1	5179175	5163300	5181450	11	0	40\.\d+	0\.034000
+chr1	5195375	5193000	5227900	9	0	32\.\d+	0\.034000
+chr1	5198075	5193000	5227900	17	0	62\.\d+	0\.025000
+chr1	5201925	5193000	5227900	15	0	54\.\d+	0\.025000
+chr1	5205575	5193000	5227900	5	0	18\.\d+	0\.199000
+chr1	5208475	5193000	5227900	13	0	47\.\d+	0\.025000
+chr1	5211875	5193000	5227900	10	0	36\.\d+	0\.034000
+chr1	5213875	5193000	5227900	9	0	32\.\d+	0\.034000
+chr1	5216925	5193000	5227900	10	0	36\.\d+	0\.034000
+chr1	5220875	5193000	5227900	13	0	47\.\d+	0\.025000
+chr1	5224025	5193000	5227900	13	0	47\.\d+	0\.025000
+chr1	5229925	5228750	5242150	8	0	29\.\d+	0\.034000
+chr1	5232775	5228750	5242150	5	0	18\.\d+	0\.199000
+chr1	5234575	5228750	5242150	6	0	21\.\d+	0\.135000
+chr1	5236125	5228750	5242150	6	0	21\.\d+	0\.135000
+chr1	5237875	5228750	5242150	4	0	14\.\d+	1\.000000
+chr1	5240425	5228750	5242150	7	0	25\.\d+	0\.135000
+chr1	5249925	5247000	5258700	13	0	47\.\d+	0\.025000
+chr1	5253675	5247000	5258700	8	0	29\.\d+	0\.034000
+chr1	5256175	5247000	5258700	7	0	25\.\d+	0\.135000
+chr1	5264925	5263750	5268900	8	0	29\.\d+	0\.034000
+chr1	5267725	5263750	5268900	10	0	36\.\d+	0\.034000
+chr1	5270275	5269300	5281550	11	0	40\.\d+	0\.034000
+chr1	5273425	5269300	5281550	6	0	21\.\d+	0\.135000
+chr1	5277575	5269300	5281550	9	0	32\.\d+	0\.034000
+chr1	5280075	5269300	5281550	7	0	25\.\d+	0\.135000
+chr1	5283375	5282250	5299950	5	0	18\.\d+	0\.199000
+chr1	5286125	5282250	5299950	11	0	40\.\d+	0\.034000
+chr1	5289075	5282250	5299950	9	0	32\.\d+	0\.034000
+chr1	5292575	5282250	5299950	9	0	32\.\d+	0\.034000
+chr1	5295575	5282250	5299950	8	0	29\.\d+	0\.034000
+chr1	5297125	5282250	5299950	7	0	25\.\d+	0\.135000
+chr1	5302025	5300700	5319250	4	0	14\.\d+	1\.000000
+chr1	5305425	5300700	5319250	10	0	36\.\d+	0\.034000
+chr1	5306825	5300700	5319250	12	0	43\.\d+	0\.025000
+chr1	5311175	5300700	5319250	10	0	36\.\d+	0\.034000
+chr1	5313325	5300700	5319250	8	0	29\.\d+	0\.034000
+chr1	5315275	5300700	5319250	8	0	29\.\d+	0\.034000
+chr1	5317425	5300700	5319250	7	0	25\.\d+	0\.135000
+chr1	5324575	5322550	5334750	8	0	29\.\d+	0\.034000
+chr1	5327875	5322550	5334750	7	0	25\.\d+	0\.135000
+chr1	5331125	5322550	5334750	6	0	21\.\d+	0\.135000
+chr1	5348875	5347750	5349950	6	0	21\.\d+	0\.135000
+chr1	5354175	5352900	5357500	6	0	21\.\d+	0\.135000
+chr1	5355975	5352900	5357500	7	0	25\.\d+	0\.135000
+chr1	5361225	5357550	5366350	6	0	21\.\d+	0\.135000
+chr1	5364775	5357550	5366350	8	0	29\.\d+	0\.034000
+chr1	5370375	5368500	5389350	8	0	29\.\d+	0\.034000
+chr1	5372525	5368500	5389350	6	0	21\.\d+	0\.135000
+chr1	5374275	5368500	5389350	6	0	21\.\d+	0\.135000
+chr1	5377125	5368500	5389350	4	0	14\.\d+	1\.000000
+chr1	5381625	5368500	5389350	4	0	14\.\d+	1\.000000
+chr1	5384575	5368500	5389350	8	0	29\.\d+	0\.034000
+chr1	5386675	5368500	5389350	11	0	40\.\d+	0\.034000
+chr1	5395375	5390850	5406350	5	0	18\.\d+	0\.199000
+chr1	5396875	5390850	5406350	5	0	18\.\d+	0\.199000
+chr1	5401025	5390850	5406350	8	0	29\.\d+	0\.034000
+chr1	5409325	5406500	5414000	9	0	32\.\d+	0\.034000
+chr1	5412475	5406500	5414000	11	0	40\.\d+	0\.034000
+chr1	5429475	5427200	5435250	11	0	40\.\d+	0\.034000
+chr1	5431425	5427200	5435250	6	0	21\.\d+	0\.135000
+chr1	5434275	5427200	5435250	4	0	14\.\d+	1\.000000
+chr1	5440025	5438750	5445150	6	0	21\.\d+	0\.135000
+chr1	5442625	5438750	5445150	10	0	36\.\d+	0\.034000
+chr1	5448375	5445350	5450050	9	0	32\.\d+	0\.034000
+chr1	5453625	5450900	5458700	7	0	25\.\d+	0\.135000
+chr1	5456475	5450900	5458700	6	0	21\.\d+	0\.135000
+chr1	5475625	5474600	5479600	5	0	18\.\d+	0\.199000
+chr1	5485175	5482700	5489150	4	0	14\.\d+	1\.000000
+chr1	5487825	5482700	5489150	6	0	21\.\d+	0\.135000
+chr1	5496625	5495200	5499750	7	0	25\.\d+	0\.135000
+chr1	5502325	5501200	5517200	5	0	18\.\d+	0\.199000
+chr1	5505875	5501200	5517200	6	0	21\.\d+	0\.135000
+chr1	5507675	5501200	5517200	6	0	21\.\d+	0\.135000
+chr1	5510825	5501200	5517200	12	0	43\.\d+	0\.025000
+chr1	5515275	5501200	5517200	7	0	25\.\d+	0\.135000
+chr1	5524125	5521900	5536850	5	0	18\.\d+	0\.199000
+chr1	5530525	5521900	5536850	8	0	29\.\d+	0\.034000
+chr1	5532875	5521900	5536850	11	0	40\.\d+	0\.034000
+chr1	5539925	5538950	5542250	6	0	21\.\d+	0\.135000
+chr1	5548775	5547250	5552250	7	0	25\.\d+	0\.135000
+chr1	5550725	5547250	5552250	7	0	25\.\d+	0\.135000
+chr1	5564125	5562650	5566050	4	0	14\.\d+	1\.000000
+chr1	5568875	5567450	5573850	8	0	29\.\d+	0\.034000
+chr1	5570325	5567450	5573850	11	0	40\.\d+	0\.034000
+chr1	5571725	5567450	5573850	9	0	32\.\d+	0\.034000
+chr1	5577575	5575300	5618600	9	0	32\.\d+	0\.034000
+chr1	5579625	5575300	5618600	8	0	29\.\d+	0\.034000
+chr1	5581825	5575300	5618600	9	0	32\.\d+	0\.034000
+chr1	5584125	5575300	5618600	4	0	14\.\d+	1\.000000
+chr1	5585925	5575300	5618600	9	0	32\.\d+	0\.034000
+chr1	5588325	5575300	5618600	7	0	25\.\d+	0\.135000
+chr1	5591875	5575300	5618600	5	0	18\.\d+	0\.199000
+chr1	5593825	5575300	5618600	17	0	62\.\d+	0\.025000
+chr1	5596475	5575300	5618600	7	0	25\.\d+	0\.135000
+chr1	5598575	5575300	5618600	5	0	18\.\d+	0\.199000
+chr1	5603475	5575300	5618600	5	0	18\.\d+	0\.199000
+chr1	5606225	5575300	5618600	6	0	21\.\d+	0\.135000
+chr1	5612475	5575300	5618600	8	0	29\.\d+	0\.034000
+chr1	5614975	5575300	5618600	8	0	29\.\d+	0\.034000
+chr1	5616675	5575300	5618600	11	0	40\.\d+	0\.034000
+chr1	5621625	5618950	5622950	6	0	21\.\d+	0\.135000
+chr1	5632975	5631350	5638100	6	0	21\.\d+	0\.135000
+chr1	5635025	5631350	5638100	5	0	18\.\d+	0\.199000
+chr1	5637125	5631350	5638100	4	0	14\.\d+	1\.000000
+chr1	5647075	5645550	5668850	8	0	29\.\d+	0\.034000
+chr1	5649475	5645550	5668850	13	0	47\.\d+	0\.025000
+chr1	5651825	5645550	5668850	9	0	32\.\d+	0\.034000
+chr1	5653275	5645550	5668850	11	0	40\.\d+	0\.034000
+chr1	5656025	5645550	5668850	6	0	21\.\d+	0\.135000
+chr1	5660675	5645550	5668850	4	0	14\.\d+	1\.000000
+chr1	5664225	5645550	5668850	5	0	18\.\d+	0\.199000
+chr1	5666375	5645550	5668850	6	0	21\.\d+	0\.135000
+chr1	5679325	5675600	5681850	8	0	29\.\d+	0\.034000
+chr1	5688775	5687300	5691900	6	0	21\.\d+	0\.135000
+chr1	5695175	5693900	5701400	7	0	25\.\d+	0\.135000
+chr1	5696975	5693900	5701400	7	0	25\.\d+	0\.135000
+chr1	5699925	5693900	5701400	4	0	14\.\d+	1\.000000
+chr1	5706725	5703650	5710750	8	0	29\.\d+	0\.034000
+chr1	5712725	5711700	5719950	4	0	14\.\d+	1\.000000
+chr1	5716025	5711700	5719950	7	0	25\.\d+	0\.135000
+chr1	5718625	5711700	5719950	7	0	25\.\d+	0\.135000
+chr1	5722875	5720500	5731000	5	0	18\.\d+	0\.199000
+chr1	5726025	5720500	5731000	11	0	40\.\d+	0\.034000
+chr1	5742375	5741000	5748200	7	0	25\.\d+	0\.135000
+chr1	5744425	5741000	5748200	6	0	21\.\d+	0\.135000
+chr1	5746175	5741000	5748200	9	0	32\.\d+	0\.034000
+chr1	5751925	5749150	5753500	7	0	25\.\d+	0\.135000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ccat_configurations.loc.sample	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,5 @@
+#Provide Pre-compiled CCAT peak/region caller configuration files
+#UID	Description	path_to_config_file
+#ccat_3.0_tf_config	CCAT 3.0 provided Transcription Factor Binding	/path_to/ccat/configs/3.0/config_TF.txt
+#ccat_3.0_histone_config	CCAT 3.0 provided Histone Modification	/path_to/ccat/configs/3.0/config_histone.txt
+#ccat_3.0_histone_config_fixed	CCAT 3.0 Histone Factor Binding (readme.txt defaults: slidingWinSize=1000)	/path_to/ccat/configs/3.0/config_histone_readme.txt
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of configurations in the CCAT peak/region caller format -->
+    <table name="ccat_configurations" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/ccat_configurations.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="CCAT" version="3.0">
+      <repository changeset_revision="b65b1bab9226" name="package_ccat_3_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>