| Next changeset 1:4a14714649b4 (2015-07-21) |
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Commit message:
Imported from capsule None |
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added:
sicer_wrapper.py sicer_wrapper.xml test-data/chipseq_enriched.bed.gz test-data/chipseq_input.bed.gz test-data/peakcalling_sicer/test_1/output_log_file.contains test-data/peakcalling_sicer/test_1/test-1-removed.bed test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01.scoreisland test-data/peakcalling_sicer/test_1/test-W200-normalized.wig test-data/peakcalling_sicer/test_1/test-W200.graph test-data/peakcalling_sicer/test_2/control-1-removed.bed test-data/peakcalling_sicer/test_2/output_log_file.contains test-data/peakcalling_sicer/test_2/test-1-removed.bed test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-island.bed test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01 test-data/peakcalling_sicer/test_2/test-W200-G600.scoreisland test-data/peakcalling_sicer/test_2/test-W200-normalized.wig test-data/peakcalling_sicer/test_2/test-W200.graph test-data/peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01 test-data/peakcalling_sicer/test_3/test-W200-G600.scoreisland test-data/peakcalling_sicer/test_3/test-W200.graph test-data/peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland test-data/peakcalling_sicer/test_4/test-W200.graph tool_dependencies.xml |
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| diff -r 000000000000 -r 82a8234e03f2 sicer_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sicer_wrapper.py Mon Jan 27 09:28:33 2014 -0500 |
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| b'@@ -0,0 +1,157 @@\n+#!/usr/bin/env python\n+#Dan Blankenberg\n+\n+"""\n+A wrapper script for running SICER (spatial clustering approach for the identification of ChIP-enriched regions) region caller.\n+"""\n+\n+import sys, optparse, os, tempfile, subprocess, shutil\n+\n+CHUNK_SIZE = 2**20 #1mb\n+\n+#HACK! FIXME: allow using all specified builds, would currently require hacking SICER\'s "GenomeData.py" on the fly.\n+VALID_BUILDS = [ \'mm8\', \'mm9\', \'hg18\', \'hg19\', \'dm2\', \'dm3\', \'sacCer1\', \'pombe\', \'rn4\', \'tair8\' ] \n+\n+def cleanup_before_exit( tmp_dir ):\n+ if tmp_dir and os.path.exists( tmp_dir ):\n+ shutil.rmtree( tmp_dir )\n+\n+\n+def open_file_from_option( filename, mode = \'rb\' ):\n+ if filename:\n+ return open( filename, mode = mode )\n+ return None\n+\n+def add_one_to_file_column( filename, column, split_char = "\\t", startswith_skip = None ):\n+ tmp_out = tempfile.TemporaryFile( mode=\'w+b\' )\n+ tmp_in = open( filename )\n+ for line in tmp_in:\n+ if startswith_skip and line.startswith( startswith_skip ):\n+ tmp_out.write( line )\n+ else:\n+ fields = line.rstrip( \'\\n\\r\' ).split( split_char )\n+ if len( fields ) <= column:\n+ tmp_out.write( line )\n+ else:\n+ fields[ column ] = str( int( fields[ column ] ) + 1 )\n+ tmp_out.write( "%s\\n" % ( split_char.join( fields ) ) )\n+ tmp_in.close()\n+ tmp_out.seek( 0 )\n+ tmp_in = open( filename, \'wb\' )\n+ while True:\n+ chunk = tmp_out.read( CHUNK_SIZE )\n+ if chunk:\n+ tmp_in.write( chunk )\n+ else:\n+ break\n+ tmp_in.close()\n+ tmp_out.close()\n+\n+def __main__():\n+ #Parse Command Line\n+ parser = optparse.OptionParser()\n+ #stdout/err\n+ parser.add_option( \'\', \'--stdout\', dest=\'stdout\', action=\'store\', type="string", default=None, help=\'If specified, the output of stdout will be written to this file.\' )\n+ parser.add_option( \'\', \'--stderr\', dest=\'stderr\', action=\'store\', type="string", default=None, help=\'If specified, the output of stderr will be written to this file.\' )\n+ parser.add_option( \'\', \'--fix_off_by_one_errors\', dest=\'fix_off_by_one_errors\', action=\'store_true\', default=False, help=\'If specified, fix off-by-one errors in output files\' )\n+ #inputs\n+ parser.add_option( \'-b\', \'--bed_file\', dest=\'bed_file\', action=\'store\', type="string", default=None, help=\'Input ChIP BED file.\' )\n+ parser.add_option( \'-c\', \'--control_file\', dest=\'control_file\', action=\'store\', type="string", default=None, help=\'Input control BED file.\' )\n+ parser.add_option( \'-d\', \'--dbkey\', dest=\'dbkey\', action=\'store\', type="string", default=None, help=\'Input dbkey.\' )\n+ parser.add_option( \'-r\', \'--redundancy_threshold\', dest=\'redundancy_threshold\', action=\'store\', type="int", default=1, help=\'Redundancy Threshold: The number of copies of identical reads allowed in a library.\' )\n+ parser.add_option( \'-w\', \'--window_size\', dest=\'window_size\', action=\'store\', type="int", default=200, help=\'Window size: resolution of SICER algorithm. For histone modifications, one can use 200 bp\' )\n+ parser.add_option( \'-f\', \'--fragment_size\', dest=\'fragment_size\', action=\'store\', type="int", default=150, help=\'Fragment size: is for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75.\' )\n+ parser.add_option( \'-e\', \'--effective_genome_fraction\', dest=\'effective_genome_fraction\', action=\'store\', type="float", default=0.74, help=\'Effective genome fraction: Effective Genome as fraction of the genome size. It depends on read length.\' )\n+ parser.add_option( \'-g\', \'--gap_size\', dest=\'gap_size\', action=\'store\', type="int", default=600, help=\'Gap size: needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ... .\' )\n+ parser.add_option( \'-o\', \'--error_cut_off\', dest=\'error_cut_off'..b'( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )\n+ return_code = proc.wait()\n+ \n+ if return_code:\n+ stderr_target = sys.stderr\n+ else:\n+ stderr_target = stdout #sys.stdout\n+ stderr_target.write( "\\nAdditionally, these warnings were reported:\\n" )\n+ stderr.flush()\n+ stderr.seek(0)\n+ while True:\n+ chunk = stderr.read( CHUNK_SIZE )\n+ if chunk:\n+ stderr_target.write( chunk )\n+ else:\n+ break\n+ stderr.close()\n+ \n+ try:\n+ #move files to where they belong\n+ shutil.move( os.path.join( tmp_dir,\'%s-%i-removed.bed\' % ( bed_base_filename, options.redundancy_threshold ) ), options.redundancy_removed_test_bed_output_file )\n+ shutil.move( os.path.join( tmp_dir,\'%s-W%i.graph\' % ( bed_base_filename, options.window_size ) ), options.summary_graph_output_file )\n+ if options.fix_off_by_one_errors: add_one_to_file_column( options.summary_graph_output_file, 2 )\n+ shutil.move( os.path.join( tmp_dir,\'%s-W%i-normalized.wig\' % ( bed_base_filename, options.window_size ) ), options.test_normalized_wig_output_file )\n+ if options.control_file is not None:\n+ shutil.move( os.path.join( tmp_dir,\'%s-%i-removed.bed\' % ( control_base_filename, options.redundancy_threshold ) ), options.redundancy_removed_control_bed_output_file )\n+ shutil.move( os.path.join( tmp_dir,\'%s-W%i-G%i.scoreisland\' % ( bed_base_filename, options.window_size, options.gap_size ) ), options.score_island_output_file )\n+ if options.fix_off_by_one_errors: add_one_to_file_column( options.score_island_output_file, 2 )\n+ shutil.move( os.path.join( tmp_dir,\'%s-W%i-G%i-islands-summary\' % ( bed_base_filename, options.window_size, options.gap_size ) ), options.islands_summary_output_file )\n+ if options.fix_off_by_one_errors: add_one_to_file_column( options.islands_summary_output_file, 2 )\n+ shutil.move( os.path.join( tmp_dir,\'%s-W%i-G%i-islands-summary-FDR%s\' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.significant_islands_summary_output_file )\n+ if options.fix_off_by_one_errors: add_one_to_file_column( options.significant_islands_summary_output_file, 2 )\n+ shutil.move( os.path.join( tmp_dir,\'%s-W%i-G%i-FDR%s-island.bed\' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.significant_islands_output_file )\n+ if options.fix_off_by_one_errors: add_one_to_file_column( options.significant_islands_output_file, 2 )\n+ shutil.move( os.path.join( tmp_dir,\'%s-W%i-G%i-FDR%s-islandfiltered.bed\' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.island_filtered_output_file )\n+ shutil.move( os.path.join( tmp_dir,\'%s-W%i-G%i-FDR%s-islandfiltered-normalized.wig\' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.island_filtered_normalized_wig_output_file )\n+ else:\n+ shutil.move( os.path.join( tmp_dir,\'%s-W%i-G%i-E%s.scoreisland\' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.score_island_output_file )\n+ if options.fix_off_by_one_errors: add_one_to_file_column( options.score_island_output_file, 2 )\n+ shutil.move( os.path.join( tmp_dir,\'%s-W%i-G%i-E%s-islandfiltered.bed\' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.island_filtered_output_file )\n+ shutil.move( os.path.join( tmp_dir,\'%s-W%i-G%i-E%s-islandfiltered-normalized.wig\' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.island_filtered_normalized_wig_output_file )\n+ except Exception, e:\n+ raise e\n+ finally:\n+ cleanup_before_exit( tmp_dir )\n+\n+if __name__=="__main__": __main__()\n' |
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| diff -r 000000000000 -r 82a8234e03f2 sicer_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sicer_wrapper.xml Mon Jan 27 09:28:33 2014 -0500 |
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| b'@@ -0,0 +1,178 @@\n+<tool id="peakcalling_sicer" name="SICER" version="0.0.1">\n+ <description>Statistical approach for the Identification of ChIP-Enriched Regions</description>\n+ <command interpreter="python">sicer_wrapper.py \n+ --bed_file \'${input_bed_file}\' \n+ #if str( $input_control_file ) != \'None\':\n+ --control_file \'${input_control_file}\'\n+ --significant_islands_output_file "${significant_islands_output_file}"\n+ --islands_summary_output_file "${islands_summary_output_file}"\n+ --significant_islands_summary_output_file "${significant_islands_summary_output_file}"\n+ #end if\n+ ${fix_off_by_one_errors}\n+ --dbkey \'${input_bed_file.dbkey}\'\n+ --redundancy_threshold \'${redundancy_threshold}\'\n+ --window_size \'${window_size}\'\n+ --fragment_size \'${fragment_size}\'\n+ --effective_genome_fraction \'${effective_genome_fraction}\'\n+ --gap_size \'${gap_size}\'\n+ --error_cut_off \'${error_cut_off}\'\n+ ##output files\n+ --stdout "${output_log_file}"\n+ --redundancy_removed_test_bed_output_file "${redundancy_removed_test_bed_output_file}"\n+ --redundancy_removed_control_bed_output_file "${redundancy_removed_control_bed_output_file}"\n+ --score_island_output_file "${score_island_output_file}"\n+ --summary_graph_output_file "${summary_graph_output_file}"\n+ --test_normalized_wig_output_file "${test_normalized_wig_output_file}"\n+ --island_filtered_output_file "${island_filtered_output_file}"\n+ --island_filtered_normalized_wig_output_file "${island_filtered_normalized_wig_output_file}"\n+ </command>\n+ <requirements>\n+ <requirement type="package" version="1.1">SICER</requirement>\n+ </requirements>\n+ <inputs>\n+ <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" >\n+ <validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in [ \'mm8\', \'mm9\', \'hg18\', \'hg19\', \'dm2\', \'dm3\', \'sacCer1\', \'pombe\', \'rn4\', \'tair8\' ]</validator>\n+ </param>\n+ <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="True"> <!-- fix me, add filter to match dbkeys -->\n+ <options>\n+ <filter type="data_meta" ref="input_bed_file" key="dbkey" />\n+ </options>\n+ </param>\n+ <param name="fix_off_by_one_errors" type="boolean" truevalue="--fix_off_by_one_errors" falsevalue="" checked="True" label="Fix off-by-one errors in output files" help="SICER creates non-standard output files, this option will fix these coordinates"/> \n+ <param name="redundancy_threshold" type="integer" label="Redundancy Threshold" value="1" help="The number of copies of identical reads allowed in a library" />\n+ <param name="window_size" type="integer" label="Window size" value="200" help="Resolution of SICER algorithm. For histone modifications, one can use 200 bp" />\n+ <param name="fragment_size" type="integer" label="Fragment size" value="150" help="for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75." />\n+ <param name="effective_genome_fraction" type="float" label="Effective genome fraction" value="0.74" help="Effective Genome as fraction of the genome size. It depends on read length." />\n+ <param name="gap_size" type="integer" label="Gap size" value="600" help="Needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ..." />\n+ <param name="error_cut_off" type="float" label="Statistic threshold value" value="0.01" help="FDR (with control) or E-value (without control)" />\n+ </inputs>\n+ <outputs>\n+ <data name="redundancy_removed_test_bed_output_file" format="bed" label="${tool.name} on ${on_string} (test-${redundancy_threshold}-removed.bed)"/>\n+ <data name="redundancy_removed_control_bed_output_file" format="bed" label="${tool.name} on ${on_string} (control-${redundancy_threshold}-removed.bed)">\n+ <filter>input_control_fil'..b'="600" />\n+ <param name="error_cut_off" value="0.01" />\n+ <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_2/test-1-removed.bed" />\n+ <output name="redundancy_removed_control_bed_output_file" file="peakcalling_sicer/test_2/control-1-removed.bed" />\n+ <output name="summary_graph_output_file" file="peakcalling_sicer/test_3/test-W200.graph" />\n+ <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-normalized.wig" />\n+ <output name="significant_islands_output_file" file="peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed" />\n+ <output name="island_filtered_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed" />\n+ <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />\n+ <output name="score_island_output_file" file="peakcalling_sicer/test_3/test-W200-G600.scoreisland" />\n+ <output name="islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary" />\n+ <output name="significant_islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01" />\n+ <output name="output_log_file" file="peakcalling_sicer/test_2/output_log_file.contains" compare="contains"/>\n+ </test>\n+ <test>\n+ <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />\n+ <param name="input_control_file" />\n+ <param name="fix_off_by_one_errors" value="True" />\n+ <param name="redundancy_threshold" value="1" />\n+ <param name="window_size" value="200" />\n+ <param name="fragment_size" value="150" />\n+ <param name="effective_genome_fraction" value="0.74" />\n+ <param name="gap_size" value="600" />\n+ <param name="error_cut_off" value="0.01" />\n+ <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_1/test-1-removed.bed" />\n+ <output name="summary_graph_output_file" file="peakcalling_sicer/test_4/test-W200.graph" />\n+ <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-normalized.wig" />\n+ <output name="island_filtered_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed" />\n+ <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig" />\n+ <output name="score_island_output_file" file="peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland" />\n+ <output name="output_log_file" file="peakcalling_sicer/test_1/output_log_file.contains" compare="contains"/>\n+ </test>\n+ </tests>\n+ <help>\n+**What it does**\n+\n+SICER first and foremost is a filtering tool. Its main functions are::\n+ \n+ 1. Delineation of the significantly ChIP-enriched regions, which can be used to associate with other genomic landmarks. \n+ 2. Identification of reads on the ChIP-enriched regions, which can be used for profiling and other quantitative analysis.\n+\n+View the original SICER documentation: http://home.gwu.edu/~wpeng/Software.htm.\n+\n+------\n+\n+.. class:: warningmark\n+\n+ By default, SICER creates files that do not conform to standards (e.g. BED files are closed, not half-open). This could have implications for downstream analysis.\n+ To force the output of SICER to be formatted properly to standard file formats, check the **"Fix off-by-one errors in output files"** option.\n+\n+------\n+\n+**Citation**\n+\n+For the underlying tool, please cite `Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics. 2009 Aug 1;25(15):1952-8. <http://www.ncbi.nlm.nih.gov/pubmed/19505939>`_\n+\n+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*\n+\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r 82a8234e03f2 test-data/chipseq_enriched.bed.gz |
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| Binary file test-data/chipseq_enriched.bed.gz has changed |
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| diff -r 000000000000 -r 82a8234e03f2 test-data/chipseq_input.bed.gz |
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| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_1/output_log_file.contains --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_1/output_log_file.contains Mon Jan 27 09:28:33 2014 -0500 |
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| b'@@ -0,0 +1,190 @@\n+#############################################\n+###### SICER v1.1 ######\n+#############################################\n+Input library directory:\n+ChIP library:\n+Output directory:\n+Species: mm8\n+Threshold for redundancy allowed for reads: 1\n+Window size: 200 bps\n+Fragment size: 150 bps. The shift for reads is half of 150\n+Effective genome size as a fraction of the reference genome of mm8: 0.740000\n+Gap size: 600 bps\n+Evalue for identification of significant islands: 0.01\n+Preprocess the raw input_bed_file file to remove redundancy with threshold 1...\n+chr1 \tPlus reads: 4989 \tRetained plus reads: 4935 ;\tMinus reads: 5011 \tRetained minus reads: 4963\n+chr2 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr3 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr4 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr5 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr6 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr7 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr8 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr9 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr10 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr11 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr12 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr13 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr14 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr15 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr16 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr17 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr18 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr19 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chrX \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chrY \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chrM \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+Partion the genome in windows ...\n+Generate summary files for input_bed_file...\n+total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0\n+total tag count in chr2.bed is: 0.0 = 0.0+0.0\n+total tag count in chr3.bed is: 0.0 = 0.0+0.0\n+total tag count in chr4.bed is: 0.0 = 0.0+0.0\n+total tag count in chr5.bed is: 0.0 = 0.0+0.0\n+total tag count in chr6.bed is: 0.0 = 0.0+0.0\n+total tag count in chr7.bed is: 0.0 = 0.0+0.0\n+total tag count in chr8.bed is: 0.0 = 0.0+0.0\n+total tag count in chr9.bed is: 0.0 = 0.0+0.0\n+total tag count in chr10.bed is: 0.0 = 0.0+0.0\n+total tag count in chr11.bed is: 0.0 = 0.0+0.0\n+total tag count in chr12.bed is: 0.0 = 0.0+0.0\n+total tag count in chr13.bed is: 0.0 = 0.0+0.0\n+total tag count in chr14.bed is: 0.0 = 0.0+0.0\n+total tag count in chr15.bed is: 0.0 = 0.0+0.0\n+total tag count in chr16.bed is: 0.0 = 0.0+0.0\n+total tag count in chr17.bed is: 0.0 = 0.0+0.0\n+total tag count in chr18.bed is: 0.0 = 0.0+0.0\n+total tag count in chr19.bed is: 0.0 = 0.0+0.0\n+total tag count in chrX.bed is: 0.0 = 0.0+0.0\n+total tag count in chrY.bed is: 0.0 = 0.0+0.0\n+total tag count in chrM.bed is: 0.0 = 0.0+0.0\n+Normalize summary graph by total redundancy-removed reads per million for input_bed_file ...\n+Convert the normalized summary graph into wig vstep format...\n+Find significant islands with E-value 0.01 for input_bed_file...\n+Species: mm8\n+Window_size: 200\n+Gap size: 600\n+E value is: 0.01\n+Total read count: 9898.0\n+Genome Length: '..b'ed is: 0.0 = 0.0+0.0\n+total tag count in chr12.bed is: 0.0 = 0.0+0.0\n+total tag count in chr13.bed is: 0.0 = 0.0+0.0\n+total tag count in chr14.bed is: 0.0 = 0.0+0.0\n+total tag count in chr15.bed is: 0.0 = 0.0+0.0\n+total tag count in chr16.bed is: 0.0 = 0.0+0.0\n+total tag count in chr17.bed is: 0.0 = 0.0+0.0\n+total tag count in chr18.bed is: 0.0 = 0.0+0.0\n+total tag count in chr19.bed is: 0.0 = 0.0+0.0\n+total tag count in chrX.bed is: 0.0 = 0.0+0.0\n+total tag count in chrY.bed is: 0.0 = 0.0+0.0\n+total tag count in chrM.bed is: 0.0 = 0.0+0.0\n+Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million...\n+Convert the summary graph made with the filtered reads into wig vstep format and normalize by total island-filtered read count per million...\n+Done!\n+Additionally, these warnings were reported:\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n' |
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_1/test-1-removed.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_1/test-1-removed.bed Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,9898 @@\n+chr1\t3002286\t3002322\tregion_1\t0\t+\n+chr1\t3002729\t3002765\tregion_3\t0\t+\n+chr1\t3002805\t3002841\tregion_4\t0\t+\n+chr1\t3003028\t3003064\tregion_6\t0\t+\n+chr1\t3003396\t3003432\tregion_8\t0\t+\n+chr1\t3003492\t3003528\tregion_9\t0\t+\n+chr1\t3004029\t3004065\tregion_10\t0\t+\n+chr1\t3004174\t3004210\tregion_11\t0\t+\n+chr1\t3004969\t3005005\tregion_12\t0\t+\n+chr1\t3005783\t3005819\tregion_13\t0\t+\n+chr1\t3017794\t3017830\tregion_15\t0\t+\n+chr1\t3018455\t3018491\tregion_16\t0\t+\n+chr1\t3018653\t3018689\tregion_18\t0\t+\n+chr1\t3018889\t3018925\tregion_19\t0\t+\n+chr1\t3019304\t3019340\tregion_21\t0\t+\n+chr1\t3019346\t3019382\tregion_22\t0\t+\n+chr1\t3019560\t3019596\tregion_23\t0\t+\n+chr1\t3019905\t3019941\tregion_25\t0\t+\n+chr1\t3020128\t3020164\tregion_26\t0\t+\n+chr1\t3020299\t3020335\tregion_27\t0\t+\n+chr1\t3020303\t3020339\tregion_28\t0\t+\n+chr1\t3020996\t3021032\tregion_29\t0\t+\n+chr1\t3021378\t3021414\tregion_33\t0\t+\n+chr1\t3022271\t3022307\tregion_40\t0\t+\n+chr1\t3023138\t3023174\tregion_41\t0\t+\n+chr1\t3023773\t3023809\tregion_43\t0\t+\n+chr1\t3025015\t3025051\tregion_45\t0\t+\n+chr1\t3027918\t3027954\tregion_50\t0\t+\n+chr1\t3028566\t3028602\tregion_51\t0\t+\n+chr1\t3028982\t3029018\tregion_54\t0\t+\n+chr1\t3035363\t3035399\tregion_55\t0\t+\n+chr1\t3035560\t3035596\tregion_56\t0\t+\n+chr1\t3035715\t3035751\tregion_57\t0\t+\n+chr1\t3035966\t3036002\tregion_59\t0\t+\n+chr1\t3037066\t3037102\tregion_61\t0\t+\n+chr1\t3037157\t3037193\tregion_62\t0\t+\n+chr1\t3037308\t3037344\tregion_63\t0\t+\n+chr1\t3038417\t3038453\tregion_65\t0\t+\n+chr1\t3038604\t3038640\tregion_66\t0\t+\n+chr1\t3038835\t3038871\tregion_69\t0\t+\n+chr1\t3038963\t3038999\tregion_71\t0\t+\n+chr1\t3039636\t3039672\tregion_73\t0\t+\n+chr1\t3039701\t3039737\tregion_74\t0\t+\n+chr1\t3040850\t3040886\tregion_75\t0\t+\n+chr1\t3041041\t3041077\tregion_76\t0\t+\n+chr1\t3041114\t3041150\tregion_78\t0\t+\n+chr1\t3051857\t3051893\tregion_83\t0\t+\n+chr1\t3052457\t3052493\tregion_85\t0\t+\n+chr1\t3052861\t3052897\tregion_87\t0\t+\n+chr1\t3053796\t3053832\tregion_89\t0\t+\n+chr1\t3054897\t3054933\tregion_91\t0\t+\n+chr1\t3054909\t3054945\tregion_92\t0\t+\n+chr1\t3062375\t3062411\tregion_97\t0\t+\n+chr1\t3062534\t3062570\tregion_99\t0\t+\n+chr1\t3063396\t3063432\tregion_103\t0\t+\n+chr1\t3063897\t3063933\tregion_106\t0\t+\n+chr1\t3065126\t3065162\tregion_108\t0\t+\n+chr1\t3066173\t3066209\tregion_111\t0\t+\n+chr1\t3066814\t3066850\tregion_113\t0\t+\n+chr1\t3071120\t3071156\tregion_117\t0\t+\n+chr1\t3071179\t3071215\tregion_118\t0\t+\n+chr1\t3073396\t3073432\tregion_122\t0\t+\n+chr1\t3073909\t3073945\tregion_124\t0\t+\n+chr1\t3086155\t3086191\tregion_130\t0\t+\n+chr1\t3086250\t3086286\tregion_132\t0\t+\n+chr1\t3086270\t3086306\tregion_133\t0\t+\n+chr1\t3086415\t3086451\tregion_135\t0\t+\n+chr1\t3086574\t3086610\tregion_139\t0\t+\n+chr1\t3087024\t3087060\tregion_143\t0\t+\n+chr1\t3088412\t3088448\tregion_145\t0\t+\n+chr1\t3088472\t3088508\tregion_146\t0\t+\n+chr1\t3089407\t3089443\tregion_148\t0\t+\n+chr1\t3089585\t3089621\tregion_151\t0\t+\n+chr1\t3089753\t3089789\tregion_152\t0\t+\n+chr1\t3091619\t3091655\tregion_153\t0\t+\n+chr1\t3092970\t3093006\tregion_155\t0\t+\n+chr1\t3093527\t3093563\tregion_157\t0\t+\n+chr1\t3093611\t3093647\tregion_158\t0\t+\n+chr1\t3094840\t3094876\tregion_159\t0\t+\n+chr1\t3094882\t3094918\tregion_160\t0\t+\n+chr1\t3095157\t3095193\tregion_161\t0\t+\n+chr1\t3095265\t3095301\tregion_162\t0\t+\n+chr1\t3095496\t3095532\tregion_165\t0\t+\n+chr1\t3095568\t3095604\tregion_166\t0\t+\n+chr1\t3096928\t3096964\tregion_168\t0\t+\n+chr1\t3104823\t3104859\tregion_170\t0\t+\n+chr1\t3104903\t3104939\tregion_171\t0\t+\n+chr1\t3104938\t3104974\tregion_172\t0\t+\n+chr1\t3107164\t3107200\tregion_181\t0\t+\n+chr1\t3107336\t3107372\tregion_183\t0\t+\n+chr1\t3107467\t3107503\tregion_184\t0\t+\n+chr1\t3107538\t3107574\tregion_185\t0\t+\n+chr1\t3108402\t3108438\tregion_188\t0\t+\n+chr1\t3108670\t3108706\tregion_190\t0\t+\n+chr1\t3109213\t3109249\tregion_191\t0\t+\n+chr1\t3109452\t3109488\tregion_193\t0\t+\n+chr1\t3110185\t3110221\tregion_194\t0\t+\n+chr1\t3110273\t3110309\tregion_195\t0\t+\n+chr1\t3110328\t3110364\tregion_196\t0\t+\n+chr1\t3110471\t3110507\tregion_198\t0\t+\n+chr1\t3110478\t3110514\tregion_199\t0\t+\n+chr1\t3110792\t3110828\tregion_204\t0\t+\n+chr1\t3110908\t3110944\tregion_205\t0\t+\n+chr1\t3111399\t3111435\tregion_208\t0\t+\n+chr1\t3111641\t3111677\tregion_209\t0\t+\n+chr1\t3112106\t3112142\tregion_212\t0\t+\n+chr1\t3112414\t3112450\tregion_214\t0\t+\n+chr1\t3112532\t3112568\tregion_215\t0\t+\n+chr1\t3112820\t3112856\tregion_217\t0\t+\n+chr1\t3'..b'9788\t0\t-\n+chr1\t5662580\t5662616\tregion_9791\t0\t-\n+chr1\t5662598\t5662634\tregion_9792\t0\t-\n+chr1\t5662661\t5662697\tregion_9793\t0\t-\n+chr1\t5663767\t5663803\tregion_9795\t0\t-\n+chr1\t5664658\t5664694\tregion_9798\t0\t-\n+chr1\t5665152\t5665188\tregion_9799\t0\t-\n+chr1\t5665971\t5666007\tregion_9800\t0\t-\n+chr1\t5666823\t5666859\tregion_9804\t0\t-\n+chr1\t5666894\t5666930\tregion_9805\t0\t-\n+chr1\t5667898\t5667934\tregion_9807\t0\t-\n+chr1\t5674133\t5674169\tregion_9808\t0\t-\n+chr1\t5675139\t5675175\tregion_9809\t0\t-\n+chr1\t5676675\t5676711\tregion_9811\t0\t-\n+chr1\t5677304\t5677340\tregion_9812\t0\t-\n+chr1\t5679098\t5679134\tregion_9814\t0\t-\n+chr1\t5679255\t5679291\tregion_9815\t0\t-\n+chr1\t5679303\t5679339\tregion_9817\t0\t-\n+chr1\t5679429\t5679465\tregion_9820\t0\t-\n+chr1\t5680276\t5680312\tregion_9824\t0\t-\n+chr1\t5680603\t5680639\tregion_9826\t0\t-\n+chr1\t5688108\t5688144\tregion_9830\t0\t-\n+chr1\t5688411\t5688447\tregion_9831\t0\t-\n+chr1\t5688571\t5688607\tregion_9834\t0\t-\n+chr1\t5689163\t5689199\tregion_9836\t0\t-\n+chr1\t5689312\t5689348\tregion_9837\t0\t-\n+chr1\t5689551\t5689587\tregion_9838\t0\t-\n+chr1\t5689847\t5689883\tregion_9839\t0\t-\n+chr1\t5694818\t5694854\tregion_9843\t0\t-\n+chr1\t5694996\t5695032\tregion_9844\t0\t-\n+chr1\t5695025\t5695061\tregion_9845\t0\t-\n+chr1\t5695144\t5695180\tregion_9846\t0\t-\n+chr1\t5695639\t5695675\tregion_9849\t0\t-\n+chr1\t5696688\t5696724\tregion_9851\t0\t-\n+chr1\t5696950\t5696986\tregion_9854\t0\t-\n+chr1\t5697092\t5697128\tregion_9855\t0\t-\n+chr1\t5698985\t5699021\tregion_9862\t0\t-\n+chr1\t5699555\t5699591\tregion_9863\t0\t-\n+chr1\t5700463\t5700499\tregion_9865\t0\t-\n+chr1\t5700467\t5700503\tregion_9866\t0\t-\n+chr1\t5703812\t5703848\tregion_9867\t0\t-\n+chr1\t5705804\t5705840\tregion_9872\t0\t-\n+chr1\t5706289\t5706325\tregion_9874\t0\t-\n+chr1\t5706307\t5706343\tregion_9875\t0\t-\n+chr1\t5706339\t5706375\tregion_9876\t0\t-\n+chr1\t5706399\t5706435\tregion_9877\t0\t-\n+chr1\t5706446\t5706482\tregion_9878\t0\t-\n+chr1\t5706955\t5706991\tregion_9879\t0\t-\n+chr1\t5707287\t5707323\tregion_9880\t0\t-\n+chr1\t5707378\t5707414\tregion_9881\t0\t-\n+chr1\t5709132\t5709168\tregion_9887\t0\t-\n+chr1\t5710251\t5710287\tregion_9889\t0\t-\n+chr1\t5711567\t5711603\tregion_9890\t0\t-\n+chr1\t5712819\t5712855\tregion_9894\t0\t-\n+chr1\t5714565\t5714601\tregion_9897\t0\t-\n+chr1\t5714689\t5714725\tregion_9898\t0\t-\n+chr1\t5715757\t5715793\tregion_9902\t0\t-\n+chr1\t5715995\t5716031\tregion_9903\t0\t-\n+chr1\t5716291\t5716327\tregion_9907\t0\t-\n+chr1\t5717567\t5717603\tregion_9911\t0\t-\n+chr1\t5717738\t5717774\tregion_9912\t0\t-\n+chr1\t5718495\t5718531\tregion_9915\t0\t-\n+chr1\t5718830\t5718866\tregion_9917\t0\t-\n+chr1\t5718966\t5719002\tregion_9919\t0\t-\n+chr1\t5719703\t5719739\tregion_9920\t0\t-\n+chr1\t5721599\t5721635\tregion_9922\t0\t-\n+chr1\t5721807\t5721843\tregion_9923\t0\t-\n+chr1\t5722297\t5722333\tregion_9925\t0\t-\n+chr1\t5722815\t5722851\tregion_9926\t0\t-\n+chr1\t5724418\t5724454\tregion_9930\t0\t-\n+chr1\t5725529\t5725565\tregion_9933\t0\t-\n+chr1\t5726039\t5726075\tregion_9935\t0\t-\n+chr1\t5726278\t5726314\tregion_9937\t0\t-\n+chr1\t5726381\t5726417\tregion_9939\t0\t-\n+chr1\t5726530\t5726566\tregion_9940\t0\t-\n+chr1\t5726534\t5726570\tregion_9941\t0\t-\n+chr1\t5726557\t5726593\tregion_9942\t0\t-\n+chr1\t5726561\t5726597\tregion_9943\t0\t-\n+chr1\t5726611\t5726647\tregion_9944\t0\t-\n+chr1\t5727379\t5727415\tregion_9946\t0\t-\n+chr1\t5727617\t5727653\tregion_9950\t0\t-\n+chr1\t5728091\t5728127\tregion_9951\t0\t-\n+chr1\t5728737\t5728773\tregion_9952\t0\t-\n+chr1\t5728886\t5728922\tregion_9953\t0\t-\n+chr1\t5729667\t5729703\tregion_9954\t0\t-\n+chr1\t5730047\t5730083\tregion_9956\t0\t-\n+chr1\t5738241\t5738277\tregion_9958\t0\t-\n+chr1\t5742298\t5742334\tregion_9962\t0\t-\n+chr1\t5742856\t5742892\tregion_9965\t0\t-\n+chr1\t5743555\t5743591\tregion_9966\t0\t-\n+chr1\t5743878\t5743914\tregion_9968\t0\t-\n+chr1\t5744403\t5744439\tregion_9969\t0\t-\n+chr1\t5744937\t5744973\tregion_9972\t0\t-\n+chr1\t5744965\t5745001\tregion_9973\t0\t-\n+chr1\t5745800\t5745836\tregion_9975\t0\t-\n+chr1\t5745885\t5745921\tregion_9976\t0\t-\n+chr1\t5745951\t5745987\tregion_9977\t0\t-\n+chr1\t5746138\t5746174\tregion_9979\t0\t-\n+chr1\t5746558\t5746594\tregion_9981\t0\t-\n+chr1\t5746574\t5746610\tregion_9982\t0\t-\n+chr1\t5746733\t5746769\tregion_9983\t0\t-\n+chr1\t5746922\t5746958\tregion_9984\t0\t-\n+chr1\t5751506\t5751542\tregion_9991\t0\t-\n+chr1\t5751966\t5752002\tregion_9995\t0\t-\n+chr1\t5752456\t5752492\tregion_9996\t0\t-\n+chr1\t5752543\t5752579\tregion_9997\t0\t-\n' |
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,5454 @@\n+track type=wiggle_0 name=input_bed_file-islandfiltered\n+variableStep chrom=chr1 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|
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,9654 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|
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01.scoreisland --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01.scoreisland Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,352 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|
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_1/test-W200-normalized.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_1/test-W200-normalized.wig Mon Jan 27 09:28:33 2014 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_1/test-W200.graph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_1/test-W200.graph Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,5667 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\t2\n+chr1\t5652800\t5652999\t3\n+chr1\t5653400\t5653599\t6\n+chr1\t5653600\t5653799\t2\n+chr1\t5653800\t5653999\t1\n+chr1\t5654200\t5654399\t1\n+chr1\t5654600\t5654799\t1\n+chr1\t5654800\t5654999\t1\n+chr1\t5655800\t5655999\t4\n+chr1\t5656000\t5656199\t1\n+chr1\t5656200\t5656399\t1\n+chr1\t5657200\t5657399\t1\n+chr1\t5657600\t5657799\t3\n+chr1\t5657800\t5657999\t1\n+chr1\t5658400\t5658599\t1\n+chr1\t5659200\t5659399\t2\n+chr1\t5660400\t5660599\t3\n+chr1\t5660800\t5660999\t1\n+chr1\t5661400\t5661599\t1\n+chr1\t5662400\t5662599\t2\n+chr1\t5662600\t5662799\t1\n+chr1\t5663600\t5663799\t2\n+chr1\t5663800\t5663999\t1\n+chr1\t5664600\t5664799\t2\n+chr1\t5665000\t5665199\t1\n+chr1\t5665800\t5665999\t1\n+chr1\t5666400\t5666599\t1\n+chr1\t5666600\t5666799\t3\n+chr1\t5666800\t5666999\t1\n+chr1\t5667800\t5667999\t2\n+chr1\t5674000\t5674199\t1\n+chr1\t5675000\t5675199\t1\n+chr1\t5676200\t5676399\t1\n+chr1\t5676600\t5676799\t1\n+chr1\t5677200\t5677399\t1\n+chr1\t5677800\t5677999\t1\n+chr1\t5679000\t5679199\t1\n+chr1\t5679200\t5679399\t4\n+chr1\t5679400\t5679599\t2\n+chr1\t5679600\t5679799\t1\n+chr1\t5680000\t5680199\t1\n+chr1\t5680200\t5680399\t2\n+chr1\t5680400\t5680599\t2\n+chr1\t5680800\t5680999\t2\n+chr1\t5682800\t5682999\t1\n+chr1\t5688000\t5688199\t1\n+chr1\t5688200\t5688399\t1\n+chr1\t5688400\t5688599\t1\n+chr1\t5688600\t5688799\t1\n+chr1\t5688800\t5688999\t1\n+chr1\t5689000\t5689199\t1\n+chr1\t5689200\t5689399\t1\n+chr1\t5689400\t5689599\t1\n+chr1\t5689800\t5689999\t1\n+chr1\t5690200\t5690399\t1\n+chr1\t5690800\t5690999\t2\n+chr1\t5694600\t5694799\t1\n+chr1\t5694800\t5694999\t2\n+chr1\t5695000\t5695199\t1\n+chr1\t5695400\t5695599\t3\n+chr1\t5696000\t5696199\t1\n+chr1\t5696600\t5696799\t1\n+chr1\t5696800\t5696999\t3\n+chr1\t5697000\t5697199\t1\n+chr1\t5697200\t5697399\t2\n+chr1\t5698000\t5698199\t1\n+chr1\t5698200\t5698399\t2\n+chr1\t5698800\t5698999\t2\n+chr1\t5699400\t5699599\t1\n+chr1\t5700000\t5700199\t1\n+chr1\t5700400\t5700599\t2\n+chr1\t5703600\t5703799\t1\n+chr1\t5704600\t5704799\t1\n+chr1\t5705000\t5705199\t3\n+chr1\t5705600\t5705799\t1\n+chr1\t5706200\t5706399\t5\n+chr1\t5706400\t5706599\t1\n+chr1\t5706800\t5706999\t1\n+chr1\t5707200\t5707399\t2\n+chr1\t5707800\t5707999\t2\n+chr1\t5708400\t5708599\t1\n+chr1\t5708600\t5708799\t1\n+chr1\t5709000\t5709199\t2\n+chr1\t5709600\t5709799\t1\n+chr1\t5710200\t5710399\t1\n+chr1\t5711400\t5711599\t1\n+chr1\t5712400\t5712599\t1\n+chr1\t5712600\t5712799\t2\n+chr1\t5712800\t5712999\t1\n+chr1\t5713600\t5713799\t1\n+chr1\t5714200\t5714399\t1\n+chr1\t5714400\t5714599\t1\n+chr1\t5714600\t5714799\t3\n+chr1\t5715600\t5715799\t2\n+chr1\t5715800\t5715999\t1\n+chr1\t5716200\t5716399\t4\n+chr1\t5717000\t5717199\t1\n+chr1\t5717400\t5717599\t2\n+chr1\t5717600\t5717799\t1\n+chr1\t5718200\t5718399\t1\n+chr1\t5718400\t5718599\t2\n+chr1\t5718600\t5718799\t1\n+chr1\t5718800\t5718999\t3\n+chr1\t5719600\t5719799\t1\n+chr1\t5720600\t5720799\t1\n+chr1\t5721400\t5721599\t1\n+chr1\t5721600\t5721799\t1\n+chr1\t5722200\t5722399\t2\n+chr1\t5722600\t5722799\t1\n+chr1\t5723200\t5723399\t3\n+chr1\t5724200\t5724399\t1\n+chr1\t5724400\t5724599\t1\n+chr1\t5725400\t5725599\t2\n+chr1\t5725800\t5725999\t1\n+chr1\t5726000\t5726199\t1\n+chr1\t5726200\t5726399\t3\n+chr1\t5726400\t5726599\t5\n+chr1\t5726800\t5726999\t1\n+chr1\t5727200\t5727399\t1\n+chr1\t5727400\t5727599\t1\n+chr1\t5727600\t5727799\t3\n+chr1\t5728000\t5728199\t1\n+chr1\t5728600\t5728799\t1\n+chr1\t5728800\t5728999\t1\n+chr1\t5729600\t5729799\t1\n+chr1\t5730000\t5730199\t2\n+chr1\t5735000\t5735199\t1\n+chr1\t5738200\t5738399\t1\n+chr1\t5741800\t5741999\t2\n+chr1\t5742200\t5742399\t2\n+chr1\t5742400\t5742599\t1\n+chr1\t5742600\t5742799\t1\n+chr1\t5742800\t5742999\t1\n+chr1\t5743400\t5743599\t1\n+chr1\t5743800\t5743999\t2\n+chr1\t5744200\t5744399\t1\n+chr1\t5744600\t5744799\t2\n+chr1\t5744800\t5744999\t2\n+chr1\t5745600\t5745799\t2\n+chr1\t5745800\t5745999\t2\n+chr1\t5746000\t5746199\t2\n+chr1\t5746400\t5746599\t2\n+chr1\t5746600\t5746799\t2\n+chr1\t5746800\t5746999\t1\n+chr1\t5747000\t5747199\t1\n+chr1\t5747800\t5747999\t1\n+chr1\t5749400\t5749599\t1\n+chr1\t5750000\t5750199\t1\n+chr1\t5750400\t5750599\t1\n+chr1\t5751400\t5751599\t2\n+chr1\t5751600\t5751799\t2\n+chr1\t5751800\t5751999\t2\n+chr1\t5752400\t5752599\t2\n+chr1\t5753000\t5753199\t1\n+chr1\t5754400\t5754599\t1\n' |
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/control-1-removed.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/control-1-removed.bed Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,9896 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\t0\t-\n+chr1\t4636587\t4636623\tregion_9819\t0\t-\n+chr1\t4636746\t4636782\tregion_9820\t0\t-\n+chr1\t4636838\t4636874\tregion_9822\t0\t-\n+chr1\t4636902\t4636938\tregion_9825\t0\t-\n+chr1\t4637144\t4637180\tregion_9826\t0\t-\n+chr1\t4637146\t4637182\tregion_9827\t0\t-\n+chr1\t4637147\t4637183\tregion_9828\t0\t-\n+chr1\t4637203\t4637239\tregion_9829\t0\t-\n+chr1\t4637427\t4637463\tregion_9832\t0\t-\n+chr1\t4637457\t4637493\tregion_9834\t0\t-\n+chr1\t4638156\t4638192\tregion_9839\t0\t-\n+chr1\t4638493\t4638529\tregion_9840\t0\t-\n+chr1\t4638579\t4638615\tregion_9842\t0\t-\n+chr1\t4638640\t4638676\tregion_9843\t0\t-\n+chr1\t4638803\t4638839\tregion_9845\t0\t-\n+chr1\t4638946\t4638982\tregion_9846\t0\t-\n+chr1\t4638984\t4639020\tregion_9847\t0\t-\n+chr1\t4639170\t4639206\tregion_9848\t0\t-\n+chr1\t4639244\t4639280\tregion_9849\t0\t-\n+chr1\t4641241\t4641277\tregion_9852\t0\t-\n+chr1\t4641335\t4641371\tregion_9853\t0\t-\n+chr1\t4641663\t4641699\tregion_9855\t0\t-\n+chr1\t4641708\t4641744\tregion_9857\t0\t-\n+chr1\t4641729\t4641765\tregion_9858\t0\t-\n+chr1\t4641824\t4641860\tregion_9861\t0\t-\n+chr1\t4643866\t4643902\tregion_9863\t0\t-\n+chr1\t4644097\t4644133\tregion_9866\t0\t-\n+chr1\t4644105\t4644141\tregion_9867\t0\t-\n+chr1\t4644703\t4644739\tregion_9868\t0\t-\n+chr1\t4645149\t4645185\tregion_9872\t0\t-\n+chr1\t4645237\t4645273\tregion_9873\t0\t-\n+chr1\t4645497\t4645533\tregion_9875\t0\t-\n+chr1\t4645690\t4645726\tregion_9876\t0\t-\n+chr1\t4645789\t4645825\tregion_9877\t0\t-\n+chr1\t4645969\t4646005\tregion_9880\t0\t-\n+chr1\t4646298\t4646334\tregion_9884\t0\t-\n+chr1\t4646461\t4646497\tregion_9885\t0\t-\n+chr1\t4646550\t4646586\tregion_9887\t0\t-\n+chr1\t4646719\t4646755\tregion_9889\t0\t-\n+chr1\t4646807\t4646843\tregion_9891\t0\t-\n+chr1\t4646879\t4646915\tregion_9893\t0\t-\n+chr1\t4646916\t4646952\tregion_9894\t0\t-\n+chr1\t4646987\t4647023\tregion_9896\t0\t-\n+chr1\t4647088\t4647124\tregion_9898\t0\t-\n+chr1\t4647559\t4647595\tregion_9901\t0\t-\n+chr1\t4647582\t4647618\tregion_9902\t0\t-\n+chr1\t4647696\t4647732\tregion_9905\t0\t-\n+chr1\t4648124\t4648160\tregion_9908\t0\t-\n+chr1\t4648129\t4648165\tregion_9909\t0\t-\n+chr1\t4648179\t4648215\tregion_9910\t0\t-\n+chr1\t4648523\t4648559\tregion_9912\t0\t-\n+chr1\t4648554\t4648590\tregion_9914\t0\t-\n+chr1\t4650119\t4650155\tregion_9916\t0\t-\n+chr1\t4650645\t4650681\tregion_9917\t0\t-\n+chr1\t4652025\t4652061\tregion_9918\t0\t-\n+chr1\t4652368\t4652404\tregion_9921\t0\t-\n+chr1\t4652487\t4652523\tregion_9922\t0\t-\n+chr1\t4652701\t4652737\tregion_9924\t0\t-\n+chr1\t4653073\t4653109\tregion_9925\t0\t-\n+chr1\t4653175\t4653211\tregion_9926\t0\t-\n+chr1\t4653199\t4653235\tregion_9928\t0\t-\n+chr1\t4653387\t4653423\tregion_9931\t0\t-\n+chr1\t4653471\t4653507\tregion_9932\t0\t-\n+chr1\t4653503\t4653539\tregion_9933\t0\t-\n+chr1\t4653574\t4653610\tregion_9934\t0\t-\n+chr1\t4656708\t4656744\tregion_9938\t0\t-\n+chr1\t4656721\t4656757\tregion_9939\t0\t-\n+chr1\t4656810\t4656846\tregion_9941\t0\t-\n+chr1\t4657008\t4657044\tregion_9942\t0\t-\n+chr1\t4657224\t4657260\tregion_9943\t0\t-\n+chr1\t4657590\t4657626\tregion_9949\t0\t-\n+chr1\t4657717\t4657753\tregion_9950\t0\t-\n+chr1\t4657724\t4657760\tregion_9951\t0\t-\n+chr1\t4657836\t4657872\tregion_9953\t0\t-\n+chr1\t4657909\t4657945\tregion_9954\t0\t-\n+chr1\t4657928\t4657964\tregion_9956\t0\t-\n+chr1\t4658311\t4658347\tregion_9958\t0\t-\n+chr1\t4658664\t4658700\tregion_9963\t0\t-\n+chr1\t4658713\t4658749\tregion_9964\t0\t-\n+chr1\t4658824\t4658860\tregion_9965\t0\t-\n+chr1\t4658866\t4658902\tregion_9966\t0\t-\n+chr1\t4658971\t4659007\tregion_9969\t0\t-\n+chr1\t4659035\t4659071\tregion_9970\t0\t-\n+chr1\t4659244\t4659280\tregion_9971\t0\t-\n+chr1\t4659465\t4659501\tregion_9973\t0\t-\n+chr1\t4659470\t4659506\tregion_9974\t0\t-\n+chr1\t4659504\t4659540\tregion_9975\t0\t-\n+chr1\t4659511\t4659547\tregion_9977\t0\t-\n+chr1\t4659530\t4659566\tregion_9979\t0\t-\n+chr1\t4659563\t4659599\tregion_9980\t0\t-\n+chr1\t4659578\t4659614\tregion_9981\t0\t-\n+chr1\t4659880\t4659916\tregion_9986\t0\t-\n+chr1\t4660125\t4660161\tregion_9987\t0\t-\n+chr1\t4660431\t4660467\tregion_9991\t0\t-\n+chr1\t4661557\t4661593\tregion_9996\t0\t-\n+chr1\t4661619\t4661655\tregion_9997\t0\t-\n+chr1\t4662104\t4662140\tregion_9998\t0\t-\n' |
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/output_log_file.contains --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/output_log_file.contains Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,287 @@\n+#############################################\n+###### SICER v1.1 ######\n+#############################################\n+Input library directory:\n+ChIP library: input_bed_file.bed\n+Control library: input_control_file.bed\n+Output directory:\n+Species: mm8\n+Threshold for redundancy allowed for chip reads: 1\n+Threshold for redundancy allowed for control reads: 1\n+Window size: 200 bps\n+Fragment size: 150 bps. The shift for reads is half of 150\n+Effective genome size as a fraction of the reference genome of mm8: 0.740000\n+Gap size: 600 bps\n+Evalue for identification of candidate islands that exhibit clustering: 1000\n+False discovery rate controlling significance: 0.01\n+Preprocess the raw input_bed_file file to remove redundancy with threshold 1...\n+chr1 \tPlus reads: 4989 \tRetained plus reads: 4935 ;\tMinus reads: 5011 \tRetained minus reads: 4963\n+chr2 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr3 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr4 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr5 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr6 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr7 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr8 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr9 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr10 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr11 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr12 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr13 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr14 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr15 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr16 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr17 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr18 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr19 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chrX \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chrY \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chrM \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+Preprocess the raw input_control_file file to remove redundancy with threshold 1...\n+chr1 \tPlus reads: 4980 \tRetained plus reads: 4937 ;\tMinus reads: 5020 \tRetained minus reads: 4959\n+chr2 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr3 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr4 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr5 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr6 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr7 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr8 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr9 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr10 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr11 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr12 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr13 \tPlus reads: 0 \tRetained plus reads: 0 ;\tMinus reads: 0 \tRetained minus reads: 0\n+chr14 \tPlus reads: 0 \tRetained plus rea'..b'chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n+Warning: chr2 reads do not exist in\n+Warning: chr3 reads do not exist in\n+Warning: chr4 reads do not exist in\n+Warning: chr5 reads do not exist in\n+Warning: chr6 reads do not exist in\n+Warning: chr7 reads do not exist in\n+Warning: chr8 reads do not exist in\n+Warning: chr9 reads do not exist in\n+Warning: chr10 reads do not exist in\n+Warning: chr11 reads do not exist in\n+Warning: chr12 reads do not exist in\n+Warning: chr13 reads do not exist in\n+Warning: chr14 reads do not exist in\n+Warning: chr15 reads do not exist in\n+Warning: chr16 reads do not exist in\n+Warning: chr17 reads do not exist in\n+Warning: chr18 reads do not exist in\n+Warning: chr19 reads do not exist in\n+Warning: chrX reads do not exist in\n+Warning: chrY reads do not exist in\n+Warning: chrM reads do not exist in\n' |
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-1-removed.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/test-1-removed.bed Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,9898 @@\n+chr1\t3002286\t3002322\tregion_1\t0\t+\n+chr1\t3002729\t3002765\tregion_3\t0\t+\n+chr1\t3002805\t3002841\tregion_4\t0\t+\n+chr1\t3003028\t3003064\tregion_6\t0\t+\n+chr1\t3003396\t3003432\tregion_8\t0\t+\n+chr1\t3003492\t3003528\tregion_9\t0\t+\n+chr1\t3004029\t3004065\tregion_10\t0\t+\n+chr1\t3004174\t3004210\tregion_11\t0\t+\n+chr1\t3004969\t3005005\tregion_12\t0\t+\n+chr1\t3005783\t3005819\tregion_13\t0\t+\n+chr1\t3017794\t3017830\tregion_15\t0\t+\n+chr1\t3018455\t3018491\tregion_16\t0\t+\n+chr1\t3018653\t3018689\tregion_18\t0\t+\n+chr1\t3018889\t3018925\tregion_19\t0\t+\n+chr1\t3019304\t3019340\tregion_21\t0\t+\n+chr1\t3019346\t3019382\tregion_22\t0\t+\n+chr1\t3019560\t3019596\tregion_23\t0\t+\n+chr1\t3019905\t3019941\tregion_25\t0\t+\n+chr1\t3020128\t3020164\tregion_26\t0\t+\n+chr1\t3020299\t3020335\tregion_27\t0\t+\n+chr1\t3020303\t3020339\tregion_28\t0\t+\n+chr1\t3020996\t3021032\tregion_29\t0\t+\n+chr1\t3021378\t3021414\tregion_33\t0\t+\n+chr1\t3022271\t3022307\tregion_40\t0\t+\n+chr1\t3023138\t3023174\tregion_41\t0\t+\n+chr1\t3023773\t3023809\tregion_43\t0\t+\n+chr1\t3025015\t3025051\tregion_45\t0\t+\n+chr1\t3027918\t3027954\tregion_50\t0\t+\n+chr1\t3028566\t3028602\tregion_51\t0\t+\n+chr1\t3028982\t3029018\tregion_54\t0\t+\n+chr1\t3035363\t3035399\tregion_55\t0\t+\n+chr1\t3035560\t3035596\tregion_56\t0\t+\n+chr1\t3035715\t3035751\tregion_57\t0\t+\n+chr1\t3035966\t3036002\tregion_59\t0\t+\n+chr1\t3037066\t3037102\tregion_61\t0\t+\n+chr1\t3037157\t3037193\tregion_62\t0\t+\n+chr1\t3037308\t3037344\tregion_63\t0\t+\n+chr1\t3038417\t3038453\tregion_65\t0\t+\n+chr1\t3038604\t3038640\tregion_66\t0\t+\n+chr1\t3038835\t3038871\tregion_69\t0\t+\n+chr1\t3038963\t3038999\tregion_71\t0\t+\n+chr1\t3039636\t3039672\tregion_73\t0\t+\n+chr1\t3039701\t3039737\tregion_74\t0\t+\n+chr1\t3040850\t3040886\tregion_75\t0\t+\n+chr1\t3041041\t3041077\tregion_76\t0\t+\n+chr1\t3041114\t3041150\tregion_78\t0\t+\n+chr1\t3051857\t3051893\tregion_83\t0\t+\n+chr1\t3052457\t3052493\tregion_85\t0\t+\n+chr1\t3052861\t3052897\tregion_87\t0\t+\n+chr1\t3053796\t3053832\tregion_89\t0\t+\n+chr1\t3054897\t3054933\tregion_91\t0\t+\n+chr1\t3054909\t3054945\tregion_92\t0\t+\n+chr1\t3062375\t3062411\tregion_97\t0\t+\n+chr1\t3062534\t3062570\tregion_99\t0\t+\n+chr1\t3063396\t3063432\tregion_103\t0\t+\n+chr1\t3063897\t3063933\tregion_106\t0\t+\n+chr1\t3065126\t3065162\tregion_108\t0\t+\n+chr1\t3066173\t3066209\tregion_111\t0\t+\n+chr1\t3066814\t3066850\tregion_113\t0\t+\n+chr1\t3071120\t3071156\tregion_117\t0\t+\n+chr1\t3071179\t3071215\tregion_118\t0\t+\n+chr1\t3073396\t3073432\tregion_122\t0\t+\n+chr1\t3073909\t3073945\tregion_124\t0\t+\n+chr1\t3086155\t3086191\tregion_130\t0\t+\n+chr1\t3086250\t3086286\tregion_132\t0\t+\n+chr1\t3086270\t3086306\tregion_133\t0\t+\n+chr1\t3086415\t3086451\tregion_135\t0\t+\n+chr1\t3086574\t3086610\tregion_139\t0\t+\n+chr1\t3087024\t3087060\tregion_143\t0\t+\n+chr1\t3088412\t3088448\tregion_145\t0\t+\n+chr1\t3088472\t3088508\tregion_146\t0\t+\n+chr1\t3089407\t3089443\tregion_148\t0\t+\n+chr1\t3089585\t3089621\tregion_151\t0\t+\n+chr1\t3089753\t3089789\tregion_152\t0\t+\n+chr1\t3091619\t3091655\tregion_153\t0\t+\n+chr1\t3092970\t3093006\tregion_155\t0\t+\n+chr1\t3093527\t3093563\tregion_157\t0\t+\n+chr1\t3093611\t3093647\tregion_158\t0\t+\n+chr1\t3094840\t3094876\tregion_159\t0\t+\n+chr1\t3094882\t3094918\tregion_160\t0\t+\n+chr1\t3095157\t3095193\tregion_161\t0\t+\n+chr1\t3095265\t3095301\tregion_162\t0\t+\n+chr1\t3095496\t3095532\tregion_165\t0\t+\n+chr1\t3095568\t3095604\tregion_166\t0\t+\n+chr1\t3096928\t3096964\tregion_168\t0\t+\n+chr1\t3104823\t3104859\tregion_170\t0\t+\n+chr1\t3104903\t3104939\tregion_171\t0\t+\n+chr1\t3104938\t3104974\tregion_172\t0\t+\n+chr1\t3107164\t3107200\tregion_181\t0\t+\n+chr1\t3107336\t3107372\tregion_183\t0\t+\n+chr1\t3107467\t3107503\tregion_184\t0\t+\n+chr1\t3107538\t3107574\tregion_185\t0\t+\n+chr1\t3108402\t3108438\tregion_188\t0\t+\n+chr1\t3108670\t3108706\tregion_190\t0\t+\n+chr1\t3109213\t3109249\tregion_191\t0\t+\n+chr1\t3109452\t3109488\tregion_193\t0\t+\n+chr1\t3110185\t3110221\tregion_194\t0\t+\n+chr1\t3110273\t3110309\tregion_195\t0\t+\n+chr1\t3110328\t3110364\tregion_196\t0\t+\n+chr1\t3110471\t3110507\tregion_198\t0\t+\n+chr1\t3110478\t3110514\tregion_199\t0\t+\n+chr1\t3110792\t3110828\tregion_204\t0\t+\n+chr1\t3110908\t3110944\tregion_205\t0\t+\n+chr1\t3111399\t3111435\tregion_208\t0\t+\n+chr1\t3111641\t3111677\tregion_209\t0\t+\n+chr1\t3112106\t3112142\tregion_212\t0\t+\n+chr1\t3112414\t3112450\tregion_214\t0\t+\n+chr1\t3112532\t3112568\tregion_215\t0\t+\n+chr1\t3112820\t3112856\tregion_217\t0\t+\n+chr1\t3'..b'9788\t0\t-\n+chr1\t5662580\t5662616\tregion_9791\t0\t-\n+chr1\t5662598\t5662634\tregion_9792\t0\t-\n+chr1\t5662661\t5662697\tregion_9793\t0\t-\n+chr1\t5663767\t5663803\tregion_9795\t0\t-\n+chr1\t5664658\t5664694\tregion_9798\t0\t-\n+chr1\t5665152\t5665188\tregion_9799\t0\t-\n+chr1\t5665971\t5666007\tregion_9800\t0\t-\n+chr1\t5666823\t5666859\tregion_9804\t0\t-\n+chr1\t5666894\t5666930\tregion_9805\t0\t-\n+chr1\t5667898\t5667934\tregion_9807\t0\t-\n+chr1\t5674133\t5674169\tregion_9808\t0\t-\n+chr1\t5675139\t5675175\tregion_9809\t0\t-\n+chr1\t5676675\t5676711\tregion_9811\t0\t-\n+chr1\t5677304\t5677340\tregion_9812\t0\t-\n+chr1\t5679098\t5679134\tregion_9814\t0\t-\n+chr1\t5679255\t5679291\tregion_9815\t0\t-\n+chr1\t5679303\t5679339\tregion_9817\t0\t-\n+chr1\t5679429\t5679465\tregion_9820\t0\t-\n+chr1\t5680276\t5680312\tregion_9824\t0\t-\n+chr1\t5680603\t5680639\tregion_9826\t0\t-\n+chr1\t5688108\t5688144\tregion_9830\t0\t-\n+chr1\t5688411\t5688447\tregion_9831\t0\t-\n+chr1\t5688571\t5688607\tregion_9834\t0\t-\n+chr1\t5689163\t5689199\tregion_9836\t0\t-\n+chr1\t5689312\t5689348\tregion_9837\t0\t-\n+chr1\t5689551\t5689587\tregion_9838\t0\t-\n+chr1\t5689847\t5689883\tregion_9839\t0\t-\n+chr1\t5694818\t5694854\tregion_9843\t0\t-\n+chr1\t5694996\t5695032\tregion_9844\t0\t-\n+chr1\t5695025\t5695061\tregion_9845\t0\t-\n+chr1\t5695144\t5695180\tregion_9846\t0\t-\n+chr1\t5695639\t5695675\tregion_9849\t0\t-\n+chr1\t5696688\t5696724\tregion_9851\t0\t-\n+chr1\t5696950\t5696986\tregion_9854\t0\t-\n+chr1\t5697092\t5697128\tregion_9855\t0\t-\n+chr1\t5698985\t5699021\tregion_9862\t0\t-\n+chr1\t5699555\t5699591\tregion_9863\t0\t-\n+chr1\t5700463\t5700499\tregion_9865\t0\t-\n+chr1\t5700467\t5700503\tregion_9866\t0\t-\n+chr1\t5703812\t5703848\tregion_9867\t0\t-\n+chr1\t5705804\t5705840\tregion_9872\t0\t-\n+chr1\t5706289\t5706325\tregion_9874\t0\t-\n+chr1\t5706307\t5706343\tregion_9875\t0\t-\n+chr1\t5706339\t5706375\tregion_9876\t0\t-\n+chr1\t5706399\t5706435\tregion_9877\t0\t-\n+chr1\t5706446\t5706482\tregion_9878\t0\t-\n+chr1\t5706955\t5706991\tregion_9879\t0\t-\n+chr1\t5707287\t5707323\tregion_9880\t0\t-\n+chr1\t5707378\t5707414\tregion_9881\t0\t-\n+chr1\t5709132\t5709168\tregion_9887\t0\t-\n+chr1\t5710251\t5710287\tregion_9889\t0\t-\n+chr1\t5711567\t5711603\tregion_9890\t0\t-\n+chr1\t5712819\t5712855\tregion_9894\t0\t-\n+chr1\t5714565\t5714601\tregion_9897\t0\t-\n+chr1\t5714689\t5714725\tregion_9898\t0\t-\n+chr1\t5715757\t5715793\tregion_9902\t0\t-\n+chr1\t5715995\t5716031\tregion_9903\t0\t-\n+chr1\t5716291\t5716327\tregion_9907\t0\t-\n+chr1\t5717567\t5717603\tregion_9911\t0\t-\n+chr1\t5717738\t5717774\tregion_9912\t0\t-\n+chr1\t5718495\t5718531\tregion_9915\t0\t-\n+chr1\t5718830\t5718866\tregion_9917\t0\t-\n+chr1\t5718966\t5719002\tregion_9919\t0\t-\n+chr1\t5719703\t5719739\tregion_9920\t0\t-\n+chr1\t5721599\t5721635\tregion_9922\t0\t-\n+chr1\t5721807\t5721843\tregion_9923\t0\t-\n+chr1\t5722297\t5722333\tregion_9925\t0\t-\n+chr1\t5722815\t5722851\tregion_9926\t0\t-\n+chr1\t5724418\t5724454\tregion_9930\t0\t-\n+chr1\t5725529\t5725565\tregion_9933\t0\t-\n+chr1\t5726039\t5726075\tregion_9935\t0\t-\n+chr1\t5726278\t5726314\tregion_9937\t0\t-\n+chr1\t5726381\t5726417\tregion_9939\t0\t-\n+chr1\t5726530\t5726566\tregion_9940\t0\t-\n+chr1\t5726534\t5726570\tregion_9941\t0\t-\n+chr1\t5726557\t5726593\tregion_9942\t0\t-\n+chr1\t5726561\t5726597\tregion_9943\t0\t-\n+chr1\t5726611\t5726647\tregion_9944\t0\t-\n+chr1\t5727379\t5727415\tregion_9946\t0\t-\n+chr1\t5727617\t5727653\tregion_9950\t0\t-\n+chr1\t5728091\t5728127\tregion_9951\t0\t-\n+chr1\t5728737\t5728773\tregion_9952\t0\t-\n+chr1\t5728886\t5728922\tregion_9953\t0\t-\n+chr1\t5729667\t5729703\tregion_9954\t0\t-\n+chr1\t5730047\t5730083\tregion_9956\t0\t-\n+chr1\t5738241\t5738277\tregion_9958\t0\t-\n+chr1\t5742298\t5742334\tregion_9962\t0\t-\n+chr1\t5742856\t5742892\tregion_9965\t0\t-\n+chr1\t5743555\t5743591\tregion_9966\t0\t-\n+chr1\t5743878\t5743914\tregion_9968\t0\t-\n+chr1\t5744403\t5744439\tregion_9969\t0\t-\n+chr1\t5744937\t5744973\tregion_9972\t0\t-\n+chr1\t5744965\t5745001\tregion_9973\t0\t-\n+chr1\t5745800\t5745836\tregion_9975\t0\t-\n+chr1\t5745885\t5745921\tregion_9976\t0\t-\n+chr1\t5745951\t5745987\tregion_9977\t0\t-\n+chr1\t5746138\t5746174\tregion_9979\t0\t-\n+chr1\t5746558\t5746594\tregion_9981\t0\t-\n+chr1\t5746574\t5746610\tregion_9982\t0\t-\n+chr1\t5746733\t5746769\tregion_9983\t0\t-\n+chr1\t5746922\t5746958\tregion_9984\t0\t-\n+chr1\t5751506\t5751542\tregion_9991\t0\t-\n+chr1\t5751966\t5752002\tregion_9995\t0\t-\n+chr1\t5752456\t5752492\tregion_9996\t0\t-\n+chr1\t5752543\t5752579\tregion_9997\t0\t-\n' |
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-island.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-island.bed Mon Jan 27 09:28:33 2014 -0500 |
| b |
| @@ -0,0 +1,184 @@ +chr1 3023200 3023999 4 +chr1 3088400 3088599 3 +chr1 3138800 3139399 5 +chr1 3165800 3165999 2 +chr1 3273000 3273399 2 +chr1 3294800 3295199 2 +chr1 3672800 3672999 4 +chr1 3810800 3811199 2 +chr1 3872600 3873599 2 +chr1 3976600 3976799 2 +chr1 4122200 4122399 2 +chr1 4232600 4232799 2 +chr1 4278600 4279199 6 +chr1 4323600 4327199 59 +chr1 4334200 4339399 83 +chr1 4392400 4392599 3 +chr1 4456400 4456799 2 +chr1 4625200 4625599 3 +chr1 4627200 4627399 2 +chr1 4668600 4670399 15 +chr1 4673800 4675199 7 +chr1 4676200 4700999 114 +chr1 4708400 4718199 71 +chr1 4719000 4722399 8 +chr1 4726200 4727999 12 +chr1 4729000 4746399 127 +chr1 4747200 4755999 66 +chr1 4756800 4762199 264 +chr1 4763200 4779399 145 +chr1 4780800 4781799 5 +chr1 4784200 4785599 6 +chr1 4786800 4787799 7 +chr1 4789400 4793399 31 +chr1 4794400 4797999 18 +chr1 4799000 4808199 50 +chr1 4809600 4818399 58 +chr1 4819600 4825999 35 +chr1 4827000 4827799 3 +chr1 4828600 4839599 64 +chr1 4840400 4853599 67 +chr1 4854400 4863599 49 +chr1 4864800 4866599 10 +chr1 4867600 4867799 2 +chr1 4868600 4869799 4 +chr1 4872000 4875199 25 +chr1 4876600 4887799 51 +chr1 4889400 4895799 50 +chr1 4896600 4907399 66 +chr1 4908200 4910999 22 +chr1 4912200 4912399 2 +chr1 4913400 4923799 64 +chr1 4924800 4931599 50 +chr1 4932400 4934999 22 +chr1 4935800 4937999 15 +chr1 4944800 4948799 22 +chr1 4952400 4963999 86 +chr1 4965800 4970599 31 +chr1 4975200 4975999 6 +chr1 4979800 4981999 16 +chr1 4982800 4982999 2 +chr1 4984400 4986199 6 +chr1 4991200 5000799 56 +chr1 5002000 5025799 121 +chr1 5032600 5035199 7 +chr1 5038800 5040199 6 +chr1 5044400 5048399 21 +chr1 5054200 5057799 24 +chr1 5058800 5063399 34 +chr1 5064200 5067599 19 +chr1 5074000 5079799 35 +chr1 5081600 5098199 89 +chr1 5099000 5100799 4 +chr1 5106000 5112799 37 +chr1 5113600 5117199 17 +chr1 5118800 5120799 10 +chr1 5122400 5123199 9 +chr1 5124200 5127599 14 +chr1 5128400 5136199 56 +chr1 5137200 5139599 11 +chr1 5140400 5144599 14 +chr1 5145400 5145599 3 +chr1 5146800 5147399 2 +chr1 5148400 5156199 45 +chr1 5160000 5162599 9 +chr1 5164200 5164799 6 +chr1 5166000 5169399 22 +chr1 5170200 5171599 4 +chr1 5172600 5175199 24 +chr1 5176200 5180599 41 +chr1 5187000 5187599 3 +chr1 5193800 5205999 83 +chr1 5206800 5219199 78 +chr1 5220000 5227799 55 +chr1 5229400 5231599 13 +chr1 5232400 5233199 5 +chr1 5234200 5238399 17 +chr1 5239800 5241199 10 +chr1 5247800 5251999 28 +chr1 5253200 5258199 25 +chr1 5264400 5265399 8 +chr1 5266200 5266399 2 +chr1 5267200 5268199 10 +chr1 5269800 5278799 43 +chr1 5279600 5280999 8 +chr1 5282800 5284599 7 +chr1 5285600 5287199 14 +chr1 5288200 5299399 47 +chr1 5301600 5302599 4 +chr1 5303400 5308999 36 +chr1 5310000 5311599 15 +chr1 5312400 5318599 29 +chr1 5323400 5333999 41 +chr1 5336200 5336799 3 +chr1 5338400 5338999 3 +chr1 5348600 5349199 6 +chr1 5353800 5356999 16 +chr1 5358400 5362799 15 +chr1 5363800 5365599 12 +chr1 5369400 5375799 29 +chr1 5376600 5378999 6 +chr1 5379800 5383199 11 +chr1 5384000 5384999 8 +chr1 5385800 5388799 15 +chr1 5391800 5398399 20 +chr1 5399600 5399799 2 +chr1 5400600 5404399 16 +chr1 5405200 5405799 2 +chr1 5407400 5413799 32 +chr1 5420800 5421199 3 +chr1 5428000 5433199 24 +chr1 5434000 5434599 4 +chr1 5439600 5440599 6 +chr1 5442000 5444999 15 +chr1 5446200 5446999 3 +chr1 5447800 5449199 11 +chr1 5451000 5458199 27 +chr1 5470600 5470999 3 +chr1 5475400 5475799 5 +chr1 5476600 5476799 2 +chr1 5478200 5478999 3 +chr1 5480800 5482199 3 +chr1 5483400 5483799 3 +chr1 5484800 5488999 13 +chr1 5492600 5493999 5 +chr1 5496000 5498999 15 +chr1 5501800 5512799 52 +chr1 5514400 5516599 11 +chr1 5522400 5524599 8 +chr1 5525800 5531199 18 +chr1 5532200 5535999 21 +chr1 5539400 5541799 11 +chr1 5548200 5551399 17 +chr1 5560800 5561599 3 +chr1 5563400 5565399 6 +chr1 5568400 5573599 33 +chr1 5576200 5590399 71 +chr1 5591200 5592399 5 +chr1 5593200 5613599 89 +chr1 5614400 5617799 22 +chr1 5619800 5620599 3 +chr1 5621400 5621999 6 +chr1 5624600 5625399 2 +chr1 5632000 5637799 20 +chr1 5643200 5643399 2 +chr1 5646400 5654999 60 +chr1 5655800 5656399 6 +chr1 5657200 5659399 8 +chr1 5660400 5661599 5 +chr1 5662400 5662799 3 +chr1 5663600 5666999 12 +chr1 5667800 5667999 2 +chr1 5676200 5677999 4 +chr1 5679000 5680999 15 +chr1 5688000 5690999 12 +chr1 5694600 5700599 24 +chr1 5704600 5710399 22 +chr1 5712400 5714799 10 +chr1 5715600 5719799 19 +chr1 5720600 5723399 9 +chr1 5724200 5724599 2 +chr1 5725400 5730199 24 +chr1 5741800 5747999 28 +chr1 5749400 5750599 3 +chr1 5751400 5753199 9 |
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,2296 @@\n+track type=wiggle_0 name=input_bed_file-islandfiltered\n+variableStep chrom=chr1 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|
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,4303 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663803\tregion_9795\t0\t-\n+chr1\t5664658\t5664694\tregion_9798\t0\t-\n+chr1\t5665152\t5665188\tregion_9799\t0\t-\n+chr1\t5665971\t5666007\tregion_9800\t0\t-\n+chr1\t5666823\t5666859\tregion_9804\t0\t-\n+chr1\t5666894\t5666930\tregion_9805\t0\t-\n+chr1\t5667898\t5667934\tregion_9807\t0\t-\n+chr1\t5676675\t5676711\tregion_9811\t0\t-\n+chr1\t5677304\t5677340\tregion_9812\t0\t-\n+chr1\t5679098\t5679134\tregion_9814\t0\t-\n+chr1\t5679255\t5679291\tregion_9815\t0\t-\n+chr1\t5679303\t5679339\tregion_9817\t0\t-\n+chr1\t5679429\t5679465\tregion_9820\t0\t-\n+chr1\t5680276\t5680312\tregion_9824\t0\t-\n+chr1\t5680603\t5680639\tregion_9826\t0\t-\n+chr1\t5688108\t5688144\tregion_9830\t0\t-\n+chr1\t5688411\t5688447\tregion_9831\t0\t-\n+chr1\t5688571\t5688607\tregion_9834\t0\t-\n+chr1\t5689163\t5689199\tregion_9836\t0\t-\n+chr1\t5689312\t5689348\tregion_9837\t0\t-\n+chr1\t5689551\t5689587\tregion_9838\t0\t-\n+chr1\t5689847\t5689883\tregion_9839\t0\t-\n+chr1\t5694818\t5694854\tregion_9843\t0\t-\n+chr1\t5694996\t5695032\tregion_9844\t0\t-\n+chr1\t5695025\t5695061\tregion_9845\t0\t-\n+chr1\t5695144\t5695180\tregion_9846\t0\t-\n+chr1\t5695639\t5695675\tregion_9849\t0\t-\n+chr1\t5696688\t5696724\tregion_9851\t0\t-\n+chr1\t5696950\t5696986\tregion_9854\t0\t-\n+chr1\t5697092\t5697128\tregion_9855\t0\t-\n+chr1\t5698985\t5699021\tregion_9862\t0\t-\n+chr1\t5699555\t5699591\tregion_9863\t0\t-\n+chr1\t5700463\t5700499\tregion_9865\t0\t-\n+chr1\t5700467\t5700503\tregion_9866\t0\t-\n+chr1\t5705804\t5705840\tregion_9872\t0\t-\n+chr1\t5706289\t5706325\tregion_9874\t0\t-\n+chr1\t5706307\t5706343\tregion_9875\t0\t-\n+chr1\t5706339\t5706375\tregion_9876\t0\t-\n+chr1\t5706399\t5706435\tregion_9877\t0\t-\n+chr1\t5706446\t5706482\tregion_9878\t0\t-\n+chr1\t5706955\t5706991\tregion_9879\t0\t-\n+chr1\t5707287\t5707323\tregion_9880\t0\t-\n+chr1\t5707378\t5707414\tregion_9881\t0\t-\n+chr1\t5709132\t5709168\tregion_9887\t0\t-\n+chr1\t5710251\t5710287\tregion_9889\t0\t-\n+chr1\t5712819\t5712855\tregion_9894\t0\t-\n+chr1\t5714565\t5714601\tregion_9897\t0\t-\n+chr1\t5714689\t5714725\tregion_9898\t0\t-\n+chr1\t5715757\t5715793\tregion_9902\t0\t-\n+chr1\t5715995\t5716031\tregion_9903\t0\t-\n+chr1\t5716291\t5716327\tregion_9907\t0\t-\n+chr1\t5717567\t5717603\tregion_9911\t0\t-\n+chr1\t5717738\t5717774\tregion_9912\t0\t-\n+chr1\t5718495\t5718531\tregion_9915\t0\t-\n+chr1\t5718830\t5718866\tregion_9917\t0\t-\n+chr1\t5718966\t5719002\tregion_9919\t0\t-\n+chr1\t5719703\t5719739\tregion_9920\t0\t-\n+chr1\t5721599\t5721635\tregion_9922\t0\t-\n+chr1\t5721807\t5721843\tregion_9923\t0\t-\n+chr1\t5722297\t5722333\tregion_9925\t0\t-\n+chr1\t5722815\t5722851\tregion_9926\t0\t-\n+chr1\t5724418\t5724454\tregion_9930\t0\t-\n+chr1\t5725529\t5725565\tregion_9933\t0\t-\n+chr1\t5726039\t5726075\tregion_9935\t0\t-\n+chr1\t5726278\t5726314\tregion_9937\t0\t-\n+chr1\t5726381\t5726417\tregion_9939\t0\t-\n+chr1\t5726530\t5726566\tregion_9940\t0\t-\n+chr1\t5726534\t5726570\tregion_9941\t0\t-\n+chr1\t5726557\t5726593\tregion_9942\t0\t-\n+chr1\t5726561\t5726597\tregion_9943\t0\t-\n+chr1\t5726611\t5726647\tregion_9944\t0\t-\n+chr1\t5727379\t5727415\tregion_9946\t0\t-\n+chr1\t5727617\t5727653\tregion_9950\t0\t-\n+chr1\t5728091\t5728127\tregion_9951\t0\t-\n+chr1\t5728737\t5728773\tregion_9952\t0\t-\n+chr1\t5728886\t5728922\tregion_9953\t0\t-\n+chr1\t5729667\t5729703\tregion_9954\t0\t-\n+chr1\t5730047\t5730083\tregion_9956\t0\t-\n+chr1\t5742298\t5742334\tregion_9962\t0\t-\n+chr1\t5742856\t5742892\tregion_9965\t0\t-\n+chr1\t5743555\t5743591\tregion_9966\t0\t-\n+chr1\t5743878\t5743914\tregion_9968\t0\t-\n+chr1\t5744403\t5744439\tregion_9969\t0\t-\n+chr1\t5744937\t5744973\tregion_9972\t0\t-\n+chr1\t5744965\t5745001\tregion_9973\t0\t-\n+chr1\t5745800\t5745836\tregion_9975\t0\t-\n+chr1\t5745885\t5745921\tregion_9976\t0\t-\n+chr1\t5745951\t5745987\tregion_9977\t0\t-\n+chr1\t5746138\t5746174\tregion_9979\t0\t-\n+chr1\t5746558\t5746594\tregion_9981\t0\t-\n+chr1\t5746574\t5746610\tregion_9982\t0\t-\n+chr1\t5746733\t5746769\tregion_9983\t0\t-\n+chr1\t5746922\t5746958\tregion_9984\t0\t-\n+chr1\t5751506\t5751542\tregion_9991\t0\t-\n+chr1\t5751966\t5752002\tregion_9995\t0\t-\n+chr1\t5752456\t5752492\tregion_9996\t0\t-\n+chr1\t5752543\t5752579\tregion_9997\t0\t-\n' |
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,417 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\t3\t0\t6.9739861846e-13\t1482.59462855\t2.00562223378e-12\n+chr1\t5475400\t5475799\t5\t0\t9.51715771411e-20\t2470.99104759\t3.25299571048e-19\n+chr1\t5476600\t5476799\t2\t0\t1.72474829123e-10\t1976.79283807\t4.38548803318e-10\n+chr1\t5478200\t5478999\t3\t0\t1.11403313324e-11\t741.297314276\t3.03628638276e-11\n+chr1\t5480800\t5482199\t3\t0\t1.04230772109e-10\t423.5984653\t2.76842241844e-10\n+chr1\t5483400\t5483799\t3\t0\t6.9739861846e-13\t1482.59462855\t2.00562223378e-12\n+chr1\t5484800\t5488999\t13\t0\t4.29550042819e-35\t611.864449878\t1.99024853173e-34\n+chr1\t5492600\t5493999\t5\t0\t1.74193751606e-16\t705.997442167\t5.5029389712e-16\n+chr1\t5496000\t5498999\t15\t0\t3.73025822818e-43\t988.396419034\t1.92039219895e-42\n+chr1\t5501800\t5512799\t52\t0\t7.13226981e-137\t934.483887087\t1.18966260431e-135\n+chr1\t5514400\t5516599\t11\t0\t7.46001852337e-33\t988.396419034\t3.30939119601e-32\n+chr1\t5522400\t5524599\t8\t0\t7.14563606489e-24\t718.833759298\t2.72121483019e-23\n+chr1\t5525800\t5531199\t18\t0\t1.56983761643e-47\t658.930946023\t9.2200321979e-47\n+chr1\t5532200\t5535999\t21\t0\t1.53229253222e-59\t1092.43814735\t1.0649433099e-58\n+chr1\t5539400\t5541799\t11\t0\t2.11737152809e-32\t906.030050781\t9.24548614881e-32\n+chr1\t5548200\t5551399\t17\t0\t8.96184848873e-49\t1050.17119522\t5.49572179382e-48\n+chr1\t5560800\t5561599\t3\t0\t1.11403313324e-11\t741.297314276\t3.03628638276e-11\n+chr1\t5563400\t5565399\t6\t0\t2.13406135789e-18\t593.03785142\t7.06272687492e-18\n+chr1\t5568400\t5573599\t33\t0\t6.31207251012e-93\t1254.50314724\t6.74906214543e-92\n+chr1\t5576200\t5590399\t71\t0\t6.88322753807e-187\t988.396419034\t2.39192156948e-185\n+chr1\t5591200\t5592399\t5\t0\t6.91398468476e-17\t823.663682528\t2.20929625559e-16\n+chr1\t5593200\t5613599\t89\t0\t1.03264171646e-227\t862.424326412\t4.78457328624e-226\n+chr1\t5614400\t5617799\t22\t0\t9.93700860484e-64\t1279.10124816\t7.20649145777e-63\n+chr1\t5619800\t5620599\t3\t0\t1.11403313324e-11\t741.297314276\t3.03628638276e-11\n+chr1\t5621400\t5621999\t6\t0\t4.6962014822e-22\t1976.79283807\t1.69551170396e-21\n+chr1\t5624600\t5625399\t2\t0\t1.10132928648e-08\t494.198209517\t2.58008040709e-08\n+chr1\t5632000\t5637799\t20\t0\t1.24823619241e-52\t681.652702782\t8.13303894114e-52\n+chr1\t5643200\t5643399\t2\t0\t1.72474829123e-10\t1976.79283807\t4.38548803318e-10\n+chr1\t5646400\t5654999\t60\t0\t1.68531501493e-167\t1379.157794\t3.90431311793e-166\n+chr1\t5655800\t5656399\t6\t0\t4.6962014822e-22\t1976.79283807\t1.69551170396e-21\n+chr1\t5657200\t5659399\t8\t0\t7.14563606489e-24\t718.833759298\t2.72121483019e-23\n+chr1\t5660400\t5661599\t5\t0\t6.91398468476e-17\t823.663682528\t2.20929625559e-16\n+chr1\t5662400\t5662799\t3\t0\t6.9739861846e-13\t1482.59462855\t2.00562223378e-12\n+chr1\t5663600\t5666999\t12\t0\t1.82185869849e-33\t697.691589906\t8.16897932548e-33\n+chr1\t5667800\t5667999\t2\t0\t1.72474829123e-10\t1976.79283807\t4.38548803318e-10\n+chr1\t5676200\t5677999\t4\t0\t5.17702657752e-13\t439.287297349\t1.52566790306e-12\n+chr1\t5679000\t5680999\t15\t0\t5.70619223493e-46\t1482.59462855\t3.17264288262e-45\n+chr1\t5688000\t5690999\t12\t0\t3.58658421651e-34\t790.717135227\t1.64352265746e-33\n+chr1\t5694600\t5700599\t24\t0\t7.1028408348e-64\t790.717135227\t5.28907969305e-63\n+chr1\t5704600\t5710399\t22\t0\t2.12339896992e-58\t749.81797306\t1.42815704912e-57\n+chr1\t5712400\t5714799\t10\t0\t2.09296544133e-29\t823.663682528\t8.5565351866e-29\n+chr1\t5715600\t5719799\t19\t0\t1.4153060204e-52\t894.263426745\t9.07973246931e-52\n+chr1\t5720600\t5723399\t9\t0\t8.84328693377e-26\t635.397697951\t3.44640247793e-25\n+chr1\t5724200\t5724599\t2\t0\t1.37875211161e-09\t988.396419034\t3.32335046556e-09\n+chr1\t5725400\t5730199\t24\t0\t2.6990853539e-66\t988.396419034\t2.12361998599e-65\n+chr1\t5741800\t5747999\t28\t0\t2.73388123455e-75\t892.745152676\t2.47832277132e-74\n+chr1\t5749400\t5750599\t3\t0\t5.63067205566e-11\t494.198209517\t1.50512195334e-10\n+chr1\t5751400\t5753199\t9\t0\t1.07091627571e-27\t988.396419034\t4.3356513298e-27\n' |
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01 Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,184 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|
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-G600.scoreisland --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/test-W200-G600.scoreisland Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,417 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|
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-normalized.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/test-W200-normalized.wig Mon Jan 27 09:28:33 2014 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200.graph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/test-W200.graph Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,5667 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\t2\n+chr1\t5652800\t5652999\t3\n+chr1\t5653400\t5653599\t6\n+chr1\t5653600\t5653799\t2\n+chr1\t5653800\t5653999\t1\n+chr1\t5654200\t5654399\t1\n+chr1\t5654600\t5654799\t1\n+chr1\t5654800\t5654999\t1\n+chr1\t5655800\t5655999\t4\n+chr1\t5656000\t5656199\t1\n+chr1\t5656200\t5656399\t1\n+chr1\t5657200\t5657399\t1\n+chr1\t5657600\t5657799\t3\n+chr1\t5657800\t5657999\t1\n+chr1\t5658400\t5658599\t1\n+chr1\t5659200\t5659399\t2\n+chr1\t5660400\t5660599\t3\n+chr1\t5660800\t5660999\t1\n+chr1\t5661400\t5661599\t1\n+chr1\t5662400\t5662599\t2\n+chr1\t5662600\t5662799\t1\n+chr1\t5663600\t5663799\t2\n+chr1\t5663800\t5663999\t1\n+chr1\t5664600\t5664799\t2\n+chr1\t5665000\t5665199\t1\n+chr1\t5665800\t5665999\t1\n+chr1\t5666400\t5666599\t1\n+chr1\t5666600\t5666799\t3\n+chr1\t5666800\t5666999\t1\n+chr1\t5667800\t5667999\t2\n+chr1\t5674000\t5674199\t1\n+chr1\t5675000\t5675199\t1\n+chr1\t5676200\t5676399\t1\n+chr1\t5676600\t5676799\t1\n+chr1\t5677200\t5677399\t1\n+chr1\t5677800\t5677999\t1\n+chr1\t5679000\t5679199\t1\n+chr1\t5679200\t5679399\t4\n+chr1\t5679400\t5679599\t2\n+chr1\t5679600\t5679799\t1\n+chr1\t5680000\t5680199\t1\n+chr1\t5680200\t5680399\t2\n+chr1\t5680400\t5680599\t2\n+chr1\t5680800\t5680999\t2\n+chr1\t5682800\t5682999\t1\n+chr1\t5688000\t5688199\t1\n+chr1\t5688200\t5688399\t1\n+chr1\t5688400\t5688599\t1\n+chr1\t5688600\t5688799\t1\n+chr1\t5688800\t5688999\t1\n+chr1\t5689000\t5689199\t1\n+chr1\t5689200\t5689399\t1\n+chr1\t5689400\t5689599\t1\n+chr1\t5689800\t5689999\t1\n+chr1\t5690200\t5690399\t1\n+chr1\t5690800\t5690999\t2\n+chr1\t5694600\t5694799\t1\n+chr1\t5694800\t5694999\t2\n+chr1\t5695000\t5695199\t1\n+chr1\t5695400\t5695599\t3\n+chr1\t5696000\t5696199\t1\n+chr1\t5696600\t5696799\t1\n+chr1\t5696800\t5696999\t3\n+chr1\t5697000\t5697199\t1\n+chr1\t5697200\t5697399\t2\n+chr1\t5698000\t5698199\t1\n+chr1\t5698200\t5698399\t2\n+chr1\t5698800\t5698999\t2\n+chr1\t5699400\t5699599\t1\n+chr1\t5700000\t5700199\t1\n+chr1\t5700400\t5700599\t2\n+chr1\t5703600\t5703799\t1\n+chr1\t5704600\t5704799\t1\n+chr1\t5705000\t5705199\t3\n+chr1\t5705600\t5705799\t1\n+chr1\t5706200\t5706399\t5\n+chr1\t5706400\t5706599\t1\n+chr1\t5706800\t5706999\t1\n+chr1\t5707200\t5707399\t2\n+chr1\t5707800\t5707999\t2\n+chr1\t5708400\t5708599\t1\n+chr1\t5708600\t5708799\t1\n+chr1\t5709000\t5709199\t2\n+chr1\t5709600\t5709799\t1\n+chr1\t5710200\t5710399\t1\n+chr1\t5711400\t5711599\t1\n+chr1\t5712400\t5712599\t1\n+chr1\t5712600\t5712799\t2\n+chr1\t5712800\t5712999\t1\n+chr1\t5713600\t5713799\t1\n+chr1\t5714200\t5714399\t1\n+chr1\t5714400\t5714599\t1\n+chr1\t5714600\t5714799\t3\n+chr1\t5715600\t5715799\t2\n+chr1\t5715800\t5715999\t1\n+chr1\t5716200\t5716399\t4\n+chr1\t5717000\t5717199\t1\n+chr1\t5717400\t5717599\t2\n+chr1\t5717600\t5717799\t1\n+chr1\t5718200\t5718399\t1\n+chr1\t5718400\t5718599\t2\n+chr1\t5718600\t5718799\t1\n+chr1\t5718800\t5718999\t3\n+chr1\t5719600\t5719799\t1\n+chr1\t5720600\t5720799\t1\n+chr1\t5721400\t5721599\t1\n+chr1\t5721600\t5721799\t1\n+chr1\t5722200\t5722399\t2\n+chr1\t5722600\t5722799\t1\n+chr1\t5723200\t5723399\t3\n+chr1\t5724200\t5724399\t1\n+chr1\t5724400\t5724599\t1\n+chr1\t5725400\t5725599\t2\n+chr1\t5725800\t5725999\t1\n+chr1\t5726000\t5726199\t1\n+chr1\t5726200\t5726399\t3\n+chr1\t5726400\t5726599\t5\n+chr1\t5726800\t5726999\t1\n+chr1\t5727200\t5727399\t1\n+chr1\t5727400\t5727599\t1\n+chr1\t5727600\t5727799\t3\n+chr1\t5728000\t5728199\t1\n+chr1\t5728600\t5728799\t1\n+chr1\t5728800\t5728999\t1\n+chr1\t5729600\t5729799\t1\n+chr1\t5730000\t5730199\t2\n+chr1\t5735000\t5735199\t1\n+chr1\t5738200\t5738399\t1\n+chr1\t5741800\t5741999\t2\n+chr1\t5742200\t5742399\t2\n+chr1\t5742400\t5742599\t1\n+chr1\t5742600\t5742799\t1\n+chr1\t5742800\t5742999\t1\n+chr1\t5743400\t5743599\t1\n+chr1\t5743800\t5743999\t2\n+chr1\t5744200\t5744399\t1\n+chr1\t5744600\t5744799\t2\n+chr1\t5744800\t5744999\t2\n+chr1\t5745600\t5745799\t2\n+chr1\t5745800\t5745999\t2\n+chr1\t5746000\t5746199\t2\n+chr1\t5746400\t5746599\t2\n+chr1\t5746600\t5746799\t2\n+chr1\t5746800\t5746999\t1\n+chr1\t5747000\t5747199\t1\n+chr1\t5747800\t5747999\t1\n+chr1\t5749400\t5749599\t1\n+chr1\t5750000\t5750199\t1\n+chr1\t5750400\t5750599\t1\n+chr1\t5751400\t5751599\t2\n+chr1\t5751600\t5751799\t2\n+chr1\t5751800\t5751999\t2\n+chr1\t5752400\t5752599\t2\n+chr1\t5753000\t5753199\t1\n+chr1\t5754400\t5754599\t1\n' |
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed Mon Jan 27 09:28:33 2014 -0500 |
| b |
| @@ -0,0 +1,184 @@ +chr1 3023200 3024000 4 +chr1 3088400 3088600 3 +chr1 3138800 3139400 5 +chr1 3165800 3166000 2 +chr1 3273000 3273400 2 +chr1 3294800 3295200 2 +chr1 3672800 3673000 4 +chr1 3810800 3811200 2 +chr1 3872600 3873600 2 +chr1 3976600 3976800 2 +chr1 4122200 4122400 2 +chr1 4232600 4232800 2 +chr1 4278600 4279200 6 +chr1 4323600 4327200 59 +chr1 4334200 4339400 83 +chr1 4392400 4392600 3 +chr1 4456400 4456800 2 +chr1 4625200 4625600 3 +chr1 4627200 4627400 2 +chr1 4668600 4670400 15 +chr1 4673800 4675200 7 +chr1 4676200 4701000 114 +chr1 4708400 4718200 71 +chr1 4719000 4722400 8 +chr1 4726200 4728000 12 +chr1 4729000 4746400 127 +chr1 4747200 4756000 66 +chr1 4756800 4762200 264 +chr1 4763200 4779400 145 +chr1 4780800 4781800 5 +chr1 4784200 4785600 6 +chr1 4786800 4787800 7 +chr1 4789400 4793400 31 +chr1 4794400 4798000 18 +chr1 4799000 4808200 50 +chr1 4809600 4818400 58 +chr1 4819600 4826000 35 +chr1 4827000 4827800 3 +chr1 4828600 4839600 64 +chr1 4840400 4853600 67 +chr1 4854400 4863600 49 +chr1 4864800 4866600 10 +chr1 4867600 4867800 2 +chr1 4868600 4869800 4 +chr1 4872000 4875200 25 +chr1 4876600 4887800 51 +chr1 4889400 4895800 50 +chr1 4896600 4907400 66 +chr1 4908200 4911000 22 +chr1 4912200 4912400 2 +chr1 4913400 4923800 64 +chr1 4924800 4931600 50 +chr1 4932400 4935000 22 +chr1 4935800 4938000 15 +chr1 4944800 4948800 22 +chr1 4952400 4964000 86 +chr1 4965800 4970600 31 +chr1 4975200 4976000 6 +chr1 4979800 4982000 16 +chr1 4982800 4983000 2 +chr1 4984400 4986200 6 +chr1 4991200 5000800 56 +chr1 5002000 5025800 121 +chr1 5032600 5035200 7 +chr1 5038800 5040200 6 +chr1 5044400 5048400 21 +chr1 5054200 5057800 24 +chr1 5058800 5063400 34 +chr1 5064200 5067600 19 +chr1 5074000 5079800 35 +chr1 5081600 5098200 89 +chr1 5099000 5100800 4 +chr1 5106000 5112800 37 +chr1 5113600 5117200 17 +chr1 5118800 5120800 10 +chr1 5122400 5123200 9 +chr1 5124200 5127600 14 +chr1 5128400 5136200 56 +chr1 5137200 5139600 11 +chr1 5140400 5144600 14 +chr1 5145400 5145600 3 +chr1 5146800 5147400 2 +chr1 5148400 5156200 45 +chr1 5160000 5162600 9 +chr1 5164200 5164800 6 +chr1 5166000 5169400 22 +chr1 5170200 5171600 4 +chr1 5172600 5175200 24 +chr1 5176200 5180600 41 +chr1 5187000 5187600 3 +chr1 5193800 5206000 83 +chr1 5206800 5219200 78 +chr1 5220000 5227800 55 +chr1 5229400 5231600 13 +chr1 5232400 5233200 5 +chr1 5234200 5238400 17 +chr1 5239800 5241200 10 +chr1 5247800 5252000 28 +chr1 5253200 5258200 25 +chr1 5264400 5265400 8 +chr1 5266200 5266400 2 +chr1 5267200 5268200 10 +chr1 5269800 5278800 43 +chr1 5279600 5281000 8 +chr1 5282800 5284600 7 +chr1 5285600 5287200 14 +chr1 5288200 5299400 47 +chr1 5301600 5302600 4 +chr1 5303400 5309000 36 +chr1 5310000 5311600 15 +chr1 5312400 5318600 29 +chr1 5323400 5334000 41 +chr1 5336200 5336800 3 +chr1 5338400 5339000 3 +chr1 5348600 5349200 6 +chr1 5353800 5357000 16 +chr1 5358400 5362800 15 +chr1 5363800 5365600 12 +chr1 5369400 5375800 29 +chr1 5376600 5379000 6 +chr1 5379800 5383200 11 +chr1 5384000 5385000 8 +chr1 5385800 5388800 15 +chr1 5391800 5398400 20 +chr1 5399600 5399800 2 +chr1 5400600 5404400 16 +chr1 5405200 5405800 2 +chr1 5407400 5413800 32 +chr1 5420800 5421200 3 +chr1 5428000 5433200 24 +chr1 5434000 5434600 4 +chr1 5439600 5440600 6 +chr1 5442000 5445000 15 +chr1 5446200 5447000 3 +chr1 5447800 5449200 11 +chr1 5451000 5458200 27 +chr1 5470600 5471000 3 +chr1 5475400 5475800 5 +chr1 5476600 5476800 2 +chr1 5478200 5479000 3 +chr1 5480800 5482200 3 +chr1 5483400 5483800 3 +chr1 5484800 5489000 13 +chr1 5492600 5494000 5 +chr1 5496000 5499000 15 +chr1 5501800 5512800 52 +chr1 5514400 5516600 11 +chr1 5522400 5524600 8 +chr1 5525800 5531200 18 +chr1 5532200 5536000 21 +chr1 5539400 5541800 11 +chr1 5548200 5551400 17 +chr1 5560800 5561600 3 +chr1 5563400 5565400 6 +chr1 5568400 5573600 33 +chr1 5576200 5590400 71 +chr1 5591200 5592400 5 +chr1 5593200 5613600 89 +chr1 5614400 5617800 22 +chr1 5619800 5620600 3 +chr1 5621400 5622000 6 +chr1 5624600 5625400 2 +chr1 5632000 5637800 20 +chr1 5643200 5643400 2 +chr1 5646400 5655000 60 +chr1 5655800 5656400 6 +chr1 5657200 5659400 8 +chr1 5660400 5661600 5 +chr1 5662400 5662800 3 +chr1 5663600 5667000 12 +chr1 5667800 5668000 2 +chr1 5676200 5678000 4 +chr1 5679000 5681000 15 +chr1 5688000 5691000 12 +chr1 5694600 5700600 24 +chr1 5704600 5710400 22 +chr1 5712400 5714800 10 +chr1 5715600 5719800 19 +chr1 5720600 5723400 9 +chr1 5724200 5724600 2 +chr1 5725400 5730200 24 +chr1 5741800 5748000 28 +chr1 5749400 5750600 3 +chr1 5751400 5753200 9 |
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,417 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\t3\t0\t6.9739861846e-13\t1482.59462855\t2.00562223378e-12\n+chr1\t5475400\t5475800\t5\t0\t9.51715771411e-20\t2470.99104759\t3.25299571048e-19\n+chr1\t5476600\t5476800\t2\t0\t1.72474829123e-10\t1976.79283807\t4.38548803318e-10\n+chr1\t5478200\t5479000\t3\t0\t1.11403313324e-11\t741.297314276\t3.03628638276e-11\n+chr1\t5480800\t5482200\t3\t0\t1.04230772109e-10\t423.5984653\t2.76842241844e-10\n+chr1\t5483400\t5483800\t3\t0\t6.9739861846e-13\t1482.59462855\t2.00562223378e-12\n+chr1\t5484800\t5489000\t13\t0\t4.29550042819e-35\t611.864449878\t1.99024853173e-34\n+chr1\t5492600\t5494000\t5\t0\t1.74193751606e-16\t705.997442167\t5.5029389712e-16\n+chr1\t5496000\t5499000\t15\t0\t3.73025822818e-43\t988.396419034\t1.92039219895e-42\n+chr1\t5501800\t5512800\t52\t0\t7.13226981e-137\t934.483887087\t1.18966260431e-135\n+chr1\t5514400\t5516600\t11\t0\t7.46001852337e-33\t988.396419034\t3.30939119601e-32\n+chr1\t5522400\t5524600\t8\t0\t7.14563606489e-24\t718.833759298\t2.72121483019e-23\n+chr1\t5525800\t5531200\t18\t0\t1.56983761643e-47\t658.930946023\t9.2200321979e-47\n+chr1\t5532200\t5536000\t21\t0\t1.53229253222e-59\t1092.43814735\t1.0649433099e-58\n+chr1\t5539400\t5541800\t11\t0\t2.11737152809e-32\t906.030050781\t9.24548614881e-32\n+chr1\t5548200\t5551400\t17\t0\t8.96184848873e-49\t1050.17119522\t5.49572179382e-48\n+chr1\t5560800\t5561600\t3\t0\t1.11403313324e-11\t741.297314276\t3.03628638276e-11\n+chr1\t5563400\t5565400\t6\t0\t2.13406135789e-18\t593.03785142\t7.06272687492e-18\n+chr1\t5568400\t5573600\t33\t0\t6.31207251012e-93\t1254.50314724\t6.74906214543e-92\n+chr1\t5576200\t5590400\t71\t0\t6.88322753807e-187\t988.396419034\t2.39192156948e-185\n+chr1\t5591200\t5592400\t5\t0\t6.91398468476e-17\t823.663682528\t2.20929625559e-16\n+chr1\t5593200\t5613600\t89\t0\t1.03264171646e-227\t862.424326412\t4.78457328624e-226\n+chr1\t5614400\t5617800\t22\t0\t9.93700860484e-64\t1279.10124816\t7.20649145777e-63\n+chr1\t5619800\t5620600\t3\t0\t1.11403313324e-11\t741.297314276\t3.03628638276e-11\n+chr1\t5621400\t5622000\t6\t0\t4.6962014822e-22\t1976.79283807\t1.69551170396e-21\n+chr1\t5624600\t5625400\t2\t0\t1.10132928648e-08\t494.198209517\t2.58008040709e-08\n+chr1\t5632000\t5637800\t20\t0\t1.24823619241e-52\t681.652702782\t8.13303894114e-52\n+chr1\t5643200\t5643400\t2\t0\t1.72474829123e-10\t1976.79283807\t4.38548803318e-10\n+chr1\t5646400\t5655000\t60\t0\t1.68531501493e-167\t1379.157794\t3.90431311793e-166\n+chr1\t5655800\t5656400\t6\t0\t4.6962014822e-22\t1976.79283807\t1.69551170396e-21\n+chr1\t5657200\t5659400\t8\t0\t7.14563606489e-24\t718.833759298\t2.72121483019e-23\n+chr1\t5660400\t5661600\t5\t0\t6.91398468476e-17\t823.663682528\t2.20929625559e-16\n+chr1\t5662400\t5662800\t3\t0\t6.9739861846e-13\t1482.59462855\t2.00562223378e-12\n+chr1\t5663600\t5667000\t12\t0\t1.82185869849e-33\t697.691589906\t8.16897932548e-33\n+chr1\t5667800\t5668000\t2\t0\t1.72474829123e-10\t1976.79283807\t4.38548803318e-10\n+chr1\t5676200\t5678000\t4\t0\t5.17702657752e-13\t439.287297349\t1.52566790306e-12\n+chr1\t5679000\t5681000\t15\t0\t5.70619223493e-46\t1482.59462855\t3.17264288262e-45\n+chr1\t5688000\t5691000\t12\t0\t3.58658421651e-34\t790.717135227\t1.64352265746e-33\n+chr1\t5694600\t5700600\t24\t0\t7.1028408348e-64\t790.717135227\t5.28907969305e-63\n+chr1\t5704600\t5710400\t22\t0\t2.12339896992e-58\t749.81797306\t1.42815704912e-57\n+chr1\t5712400\t5714800\t10\t0\t2.09296544133e-29\t823.663682528\t8.5565351866e-29\n+chr1\t5715600\t5719800\t19\t0\t1.4153060204e-52\t894.263426745\t9.07973246931e-52\n+chr1\t5720600\t5723400\t9\t0\t8.84328693377e-26\t635.397697951\t3.44640247793e-25\n+chr1\t5724200\t5724600\t2\t0\t1.37875211161e-09\t988.396419034\t3.32335046556e-09\n+chr1\t5725400\t5730200\t24\t0\t2.6990853539e-66\t988.396419034\t2.12361998599e-65\n+chr1\t5741800\t5748000\t28\t0\t2.73388123455e-75\t892.745152676\t2.47832277132e-74\n+chr1\t5749400\t5750600\t3\t0\t5.63067205566e-11\t494.198209517\t1.50512195334e-10\n+chr1\t5751400\t5753200\t9\t0\t1.07091627571e-27\t988.396419034\t4.3356513298e-27\n' |
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01 Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,184 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|
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_3/test-W200-G600.scoreisland --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_3/test-W200-G600.scoreisland Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,417 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|
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_3/test-W200.graph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_3/test-W200.graph Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,5667 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\t2\n+chr1\t5652800\t5653000\t3\n+chr1\t5653400\t5653600\t6\n+chr1\t5653600\t5653800\t2\n+chr1\t5653800\t5654000\t1\n+chr1\t5654200\t5654400\t1\n+chr1\t5654600\t5654800\t1\n+chr1\t5654800\t5655000\t1\n+chr1\t5655800\t5656000\t4\n+chr1\t5656000\t5656200\t1\n+chr1\t5656200\t5656400\t1\n+chr1\t5657200\t5657400\t1\n+chr1\t5657600\t5657800\t3\n+chr1\t5657800\t5658000\t1\n+chr1\t5658400\t5658600\t1\n+chr1\t5659200\t5659400\t2\n+chr1\t5660400\t5660600\t3\n+chr1\t5660800\t5661000\t1\n+chr1\t5661400\t5661600\t1\n+chr1\t5662400\t5662600\t2\n+chr1\t5662600\t5662800\t1\n+chr1\t5663600\t5663800\t2\n+chr1\t5663800\t5664000\t1\n+chr1\t5664600\t5664800\t2\n+chr1\t5665000\t5665200\t1\n+chr1\t5665800\t5666000\t1\n+chr1\t5666400\t5666600\t1\n+chr1\t5666600\t5666800\t3\n+chr1\t5666800\t5667000\t1\n+chr1\t5667800\t5668000\t2\n+chr1\t5674000\t5674200\t1\n+chr1\t5675000\t5675200\t1\n+chr1\t5676200\t5676400\t1\n+chr1\t5676600\t5676800\t1\n+chr1\t5677200\t5677400\t1\n+chr1\t5677800\t5678000\t1\n+chr1\t5679000\t5679200\t1\n+chr1\t5679200\t5679400\t4\n+chr1\t5679400\t5679600\t2\n+chr1\t5679600\t5679800\t1\n+chr1\t5680000\t5680200\t1\n+chr1\t5680200\t5680400\t2\n+chr1\t5680400\t5680600\t2\n+chr1\t5680800\t5681000\t2\n+chr1\t5682800\t5683000\t1\n+chr1\t5688000\t5688200\t1\n+chr1\t5688200\t5688400\t1\n+chr1\t5688400\t5688600\t1\n+chr1\t5688600\t5688800\t1\n+chr1\t5688800\t5689000\t1\n+chr1\t5689000\t5689200\t1\n+chr1\t5689200\t5689400\t1\n+chr1\t5689400\t5689600\t1\n+chr1\t5689800\t5690000\t1\n+chr1\t5690200\t5690400\t1\n+chr1\t5690800\t5691000\t2\n+chr1\t5694600\t5694800\t1\n+chr1\t5694800\t5695000\t2\n+chr1\t5695000\t5695200\t1\n+chr1\t5695400\t5695600\t3\n+chr1\t5696000\t5696200\t1\n+chr1\t5696600\t5696800\t1\n+chr1\t5696800\t5697000\t3\n+chr1\t5697000\t5697200\t1\n+chr1\t5697200\t5697400\t2\n+chr1\t5698000\t5698200\t1\n+chr1\t5698200\t5698400\t2\n+chr1\t5698800\t5699000\t2\n+chr1\t5699400\t5699600\t1\n+chr1\t5700000\t5700200\t1\n+chr1\t5700400\t5700600\t2\n+chr1\t5703600\t5703800\t1\n+chr1\t5704600\t5704800\t1\n+chr1\t5705000\t5705200\t3\n+chr1\t5705600\t5705800\t1\n+chr1\t5706200\t5706400\t5\n+chr1\t5706400\t5706600\t1\n+chr1\t5706800\t5707000\t1\n+chr1\t5707200\t5707400\t2\n+chr1\t5707800\t5708000\t2\n+chr1\t5708400\t5708600\t1\n+chr1\t5708600\t5708800\t1\n+chr1\t5709000\t5709200\t2\n+chr1\t5709600\t5709800\t1\n+chr1\t5710200\t5710400\t1\n+chr1\t5711400\t5711600\t1\n+chr1\t5712400\t5712600\t1\n+chr1\t5712600\t5712800\t2\n+chr1\t5712800\t5713000\t1\n+chr1\t5713600\t5713800\t1\n+chr1\t5714200\t5714400\t1\n+chr1\t5714400\t5714600\t1\n+chr1\t5714600\t5714800\t3\n+chr1\t5715600\t5715800\t2\n+chr1\t5715800\t5716000\t1\n+chr1\t5716200\t5716400\t4\n+chr1\t5717000\t5717200\t1\n+chr1\t5717400\t5717600\t2\n+chr1\t5717600\t5717800\t1\n+chr1\t5718200\t5718400\t1\n+chr1\t5718400\t5718600\t2\n+chr1\t5718600\t5718800\t1\n+chr1\t5718800\t5719000\t3\n+chr1\t5719600\t5719800\t1\n+chr1\t5720600\t5720800\t1\n+chr1\t5721400\t5721600\t1\n+chr1\t5721600\t5721800\t1\n+chr1\t5722200\t5722400\t2\n+chr1\t5722600\t5722800\t1\n+chr1\t5723200\t5723400\t3\n+chr1\t5724200\t5724400\t1\n+chr1\t5724400\t5724600\t1\n+chr1\t5725400\t5725600\t2\n+chr1\t5725800\t5726000\t1\n+chr1\t5726000\t5726200\t1\n+chr1\t5726200\t5726400\t3\n+chr1\t5726400\t5726600\t5\n+chr1\t5726800\t5727000\t1\n+chr1\t5727200\t5727400\t1\n+chr1\t5727400\t5727600\t1\n+chr1\t5727600\t5727800\t3\n+chr1\t5728000\t5728200\t1\n+chr1\t5728600\t5728800\t1\n+chr1\t5728800\t5729000\t1\n+chr1\t5729600\t5729800\t1\n+chr1\t5730000\t5730200\t2\n+chr1\t5735000\t5735200\t1\n+chr1\t5738200\t5738400\t1\n+chr1\t5741800\t5742000\t2\n+chr1\t5742200\t5742400\t2\n+chr1\t5742400\t5742600\t1\n+chr1\t5742600\t5742800\t1\n+chr1\t5742800\t5743000\t1\n+chr1\t5743400\t5743600\t1\n+chr1\t5743800\t5744000\t2\n+chr1\t5744200\t5744400\t1\n+chr1\t5744600\t5744800\t2\n+chr1\t5744800\t5745000\t2\n+chr1\t5745600\t5745800\t2\n+chr1\t5745800\t5746000\t2\n+chr1\t5746000\t5746200\t2\n+chr1\t5746400\t5746600\t2\n+chr1\t5746600\t5746800\t2\n+chr1\t5746800\t5747000\t1\n+chr1\t5747000\t5747200\t1\n+chr1\t5747800\t5748000\t1\n+chr1\t5749400\t5749600\t1\n+chr1\t5750000\t5750200\t1\n+chr1\t5750400\t5750600\t1\n+chr1\t5751400\t5751600\t2\n+chr1\t5751600\t5751800\t2\n+chr1\t5751800\t5752000\t2\n+chr1\t5752400\t5752600\t2\n+chr1\t5753000\t5753200\t1\n+chr1\t5754400\t5754600\t1\n' |
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,352 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|
| b |
| diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_4/test-W200.graph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_4/test-W200.graph Mon Jan 27 09:28:33 2014 -0500 |
| b |
| b'@@ -0,0 +1,5667 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\t2\n+chr1\t5652800\t5653000\t3\n+chr1\t5653400\t5653600\t6\n+chr1\t5653600\t5653800\t2\n+chr1\t5653800\t5654000\t1\n+chr1\t5654200\t5654400\t1\n+chr1\t5654600\t5654800\t1\n+chr1\t5654800\t5655000\t1\n+chr1\t5655800\t5656000\t4\n+chr1\t5656000\t5656200\t1\n+chr1\t5656200\t5656400\t1\n+chr1\t5657200\t5657400\t1\n+chr1\t5657600\t5657800\t3\n+chr1\t5657800\t5658000\t1\n+chr1\t5658400\t5658600\t1\n+chr1\t5659200\t5659400\t2\n+chr1\t5660400\t5660600\t3\n+chr1\t5660800\t5661000\t1\n+chr1\t5661400\t5661600\t1\n+chr1\t5662400\t5662600\t2\n+chr1\t5662600\t5662800\t1\n+chr1\t5663600\t5663800\t2\n+chr1\t5663800\t5664000\t1\n+chr1\t5664600\t5664800\t2\n+chr1\t5665000\t5665200\t1\n+chr1\t5665800\t5666000\t1\n+chr1\t5666400\t5666600\t1\n+chr1\t5666600\t5666800\t3\n+chr1\t5666800\t5667000\t1\n+chr1\t5667800\t5668000\t2\n+chr1\t5674000\t5674200\t1\n+chr1\t5675000\t5675200\t1\n+chr1\t5676200\t5676400\t1\n+chr1\t5676600\t5676800\t1\n+chr1\t5677200\t5677400\t1\n+chr1\t5677800\t5678000\t1\n+chr1\t5679000\t5679200\t1\n+chr1\t5679200\t5679400\t4\n+chr1\t5679400\t5679600\t2\n+chr1\t5679600\t5679800\t1\n+chr1\t5680000\t5680200\t1\n+chr1\t5680200\t5680400\t2\n+chr1\t5680400\t5680600\t2\n+chr1\t5680800\t5681000\t2\n+chr1\t5682800\t5683000\t1\n+chr1\t5688000\t5688200\t1\n+chr1\t5688200\t5688400\t1\n+chr1\t5688400\t5688600\t1\n+chr1\t5688600\t5688800\t1\n+chr1\t5688800\t5689000\t1\n+chr1\t5689000\t5689200\t1\n+chr1\t5689200\t5689400\t1\n+chr1\t5689400\t5689600\t1\n+chr1\t5689800\t5690000\t1\n+chr1\t5690200\t5690400\t1\n+chr1\t5690800\t5691000\t2\n+chr1\t5694600\t5694800\t1\n+chr1\t5694800\t5695000\t2\n+chr1\t5695000\t5695200\t1\n+chr1\t5695400\t5695600\t3\n+chr1\t5696000\t5696200\t1\n+chr1\t5696600\t5696800\t1\n+chr1\t5696800\t5697000\t3\n+chr1\t5697000\t5697200\t1\n+chr1\t5697200\t5697400\t2\n+chr1\t5698000\t5698200\t1\n+chr1\t5698200\t5698400\t2\n+chr1\t5698800\t5699000\t2\n+chr1\t5699400\t5699600\t1\n+chr1\t5700000\t5700200\t1\n+chr1\t5700400\t5700600\t2\n+chr1\t5703600\t5703800\t1\n+chr1\t5704600\t5704800\t1\n+chr1\t5705000\t5705200\t3\n+chr1\t5705600\t5705800\t1\n+chr1\t5706200\t5706400\t5\n+chr1\t5706400\t5706600\t1\n+chr1\t5706800\t5707000\t1\n+chr1\t5707200\t5707400\t2\n+chr1\t5707800\t5708000\t2\n+chr1\t5708400\t5708600\t1\n+chr1\t5708600\t5708800\t1\n+chr1\t5709000\t5709200\t2\n+chr1\t5709600\t5709800\t1\n+chr1\t5710200\t5710400\t1\n+chr1\t5711400\t5711600\t1\n+chr1\t5712400\t5712600\t1\n+chr1\t5712600\t5712800\t2\n+chr1\t5712800\t5713000\t1\n+chr1\t5713600\t5713800\t1\n+chr1\t5714200\t5714400\t1\n+chr1\t5714400\t5714600\t1\n+chr1\t5714600\t5714800\t3\n+chr1\t5715600\t5715800\t2\n+chr1\t5715800\t5716000\t1\n+chr1\t5716200\t5716400\t4\n+chr1\t5717000\t5717200\t1\n+chr1\t5717400\t5717600\t2\n+chr1\t5717600\t5717800\t1\n+chr1\t5718200\t5718400\t1\n+chr1\t5718400\t5718600\t2\n+chr1\t5718600\t5718800\t1\n+chr1\t5718800\t5719000\t3\n+chr1\t5719600\t5719800\t1\n+chr1\t5720600\t5720800\t1\n+chr1\t5721400\t5721600\t1\n+chr1\t5721600\t5721800\t1\n+chr1\t5722200\t5722400\t2\n+chr1\t5722600\t5722800\t1\n+chr1\t5723200\t5723400\t3\n+chr1\t5724200\t5724400\t1\n+chr1\t5724400\t5724600\t1\n+chr1\t5725400\t5725600\t2\n+chr1\t5725800\t5726000\t1\n+chr1\t5726000\t5726200\t1\n+chr1\t5726200\t5726400\t3\n+chr1\t5726400\t5726600\t5\n+chr1\t5726800\t5727000\t1\n+chr1\t5727200\t5727400\t1\n+chr1\t5727400\t5727600\t1\n+chr1\t5727600\t5727800\t3\n+chr1\t5728000\t5728200\t1\n+chr1\t5728600\t5728800\t1\n+chr1\t5728800\t5729000\t1\n+chr1\t5729600\t5729800\t1\n+chr1\t5730000\t5730200\t2\n+chr1\t5735000\t5735200\t1\n+chr1\t5738200\t5738400\t1\n+chr1\t5741800\t5742000\t2\n+chr1\t5742200\t5742400\t2\n+chr1\t5742400\t5742600\t1\n+chr1\t5742600\t5742800\t1\n+chr1\t5742800\t5743000\t1\n+chr1\t5743400\t5743600\t1\n+chr1\t5743800\t5744000\t2\n+chr1\t5744200\t5744400\t1\n+chr1\t5744600\t5744800\t2\n+chr1\t5744800\t5745000\t2\n+chr1\t5745600\t5745800\t2\n+chr1\t5745800\t5746000\t2\n+chr1\t5746000\t5746200\t2\n+chr1\t5746400\t5746600\t2\n+chr1\t5746600\t5746800\t2\n+chr1\t5746800\t5747000\t1\n+chr1\t5747000\t5747200\t1\n+chr1\t5747800\t5748000\t1\n+chr1\t5749400\t5749600\t1\n+chr1\t5750000\t5750200\t1\n+chr1\t5750400\t5750600\t1\n+chr1\t5751400\t5751600\t2\n+chr1\t5751600\t5751800\t2\n+chr1\t5751800\t5752000\t2\n+chr1\t5752400\t5752600\t2\n+chr1\t5753000\t5753200\t1\n+chr1\t5754400\t5754600\t1\n' |
| b |
| diff -r 000000000000 -r 82a8234e03f2 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 27 09:28:33 2014 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="SICER" version="1.1"> + <repository changeset_revision="48c84c1cab2b" name="package_sicer_1_1" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |