Mercurial > repos > greg > cwpair2
changeset 0:507521bf124a draft
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cwpair2.py Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,74 @@ +""" +cwpair2.py + +Takes a list of called peaks on both strands and produces a list of matched pairs and a list +of unmatched orphans using a specified method for finding matched pairs. Methods for finding +matched pairs are mode, closest, largest or all, where the analysis is run for each method + +Input: list of one or more gff format files + +Output: files produced for each input/mode combination: +S (simple), D (detailed), O (orphans), P (frequency preview plot), F (final frequency plot), +C (statistics graph), statistics.tabular +""" + +import argparse +import csv +import cwpair2_util + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('--input', dest='inputs', action='append', nargs=2, help="Input datasets") + parser.add_argument('--method', dest='method', default='mode', help='Method of finding match.') + parser.add_argument('--up_distance', dest='up_distance', type=int, default=50, help='Distance upstream from a pair.') + parser.add_argument('--down_distance', dest='down_distance', type=int, default=100, help='Distance downstream of a pair.') + parser.add_argument('--binsize', dest='binsize', type=int, default=1, help='Width of bins for plots and mode.') + parser.add_argument('--threshold_format', dest='threshold_format', help='Percentage to filter the 95th percentile.') + parser.add_argument('--relative_threshold', dest='relative_threshold', type=float, default=0.0, help='Percentage to filter the 95th percentile.') + parser.add_argument('--absolute_threshold', dest='absolute_threshold', type=float, default=0.0, help='Absolute value to filter.') + parser.add_argument('--output_files', dest='output_files', default='simple', help='Restrict output dataset collections.') + parser.add_argument('--plot_format', dest='plot_format', default=None, help='Format of output graph.') + parser.add_argument('--sort_chromosome', dest='sort_chromosome', default='asc', help='Sort output by chromosome.') + parser.add_argument('--sort_score', dest='sort_score', default='no', help='Sort output by score.') + parser.add_argument('--statistics_output', dest='statistics_output', help='Statistics output file.') + args = parser.parse_args() + + cwpair2_util.create_directories(args.method) + + statistics = [] + if args.absolute_threshold > 0: + threshold = args.absolute_threshold + elif args.relative_threshold > 0: + threshold = args.relative_threshold / 100.0 + else: + threshold = 0 + for (dataset_path, hid) in args.inputs: + stats = cwpair2_util.process_file(dataset_path, + hid, + args.method, + threshold, + args.up_distance, + args.down_distance, + args.binsize, + args.output_files, + args.plot_format, + args.sort_chromosome, + args.sort_score) + statistics.extend(stats) + # Accumulate statistics. + by_file = {} + for stats in statistics: + # Skip "None" statistics from failed files + if not stats: + continue + path = stats['stats_path'] + if path not in by_file: + by_file[path] = [] + by_file[path].append(stats) + # Write tabular statistics file. + keys = ['fname', 'final_mode', 'preview_mode', 'perc95', 'paired', 'orphans'] + statistics_out = csv.writer(open(args.statistics_output, 'wt'), delimiter='\t') + statistics_out.writerow(keys) + for file_path, statistics in by_file.items(): + for stats in statistics: + statistics_out.writerow([stats[key] for key in keys])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cwpair2.xml Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,342 @@ +<?xml version="1.0"?> +<tool id="cwpair2" name="CWPair2" version="@WRAPPER_VERSION@.0"> + <description>find matched pairs and unmatched orphans</description> + <macros> + <import>cwpair2_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> + <![CDATA[ + python $__tool_directory__/cwpair2.py + #for $i in $input: + --input "${i}" "${i.hid}" + #end for + --method $method + --up_distance $up_distance + --down_distance $down_distance + --binsize $binsize + --threshold_format $threshold_format_cond.threshold_format + #if str($threshold_format_cond.threshold_format) == "absolute_threshold": + --absolute_threshold $threshold_format_cond.absolute_threshold + #elif str($threshold_format_cond.threshold_format) == "relative_threshold": + --relative_threshold $threshold_format_cond.relative_threshold + #end if + --output_files $output_files_cond.output_files + #if str($output_files_cond.output_files) == "all" + --plot_format $output_files_cond.plot_format + #end if + --sort_chromosome $sort_chromosome + --sort_score $sort_score + --statistics_output "$statistics_output" + ]]> + </command> + <inputs> + <param name="input" type="data" format="gff" multiple="True" label="Find matched pairs on" /> + <param name="method" type="select" label="Method of finding a match"> + <option value="mode" selected="True">Mode</option> + <option value="closest">Closest</option> + <option value="largest">Largest</option> + <option value="all">All</option> + </param> + <param name="up_distance" type="integer" value="50" min="0" label="Distance upstream from a peak to allow a pair" /> + <param name="down_distance" type="integer" value="100" min="0" label="Distance downstream from a peak to allow a pair" /> + <param name="binsize" type="integer" value="1" min="0" label="Width of bins for frequency plots and mode calculation" help="Value 1 implies no bins" /> + <conditional name="threshold_format_cond"> + <param name="threshold_format" type="select" label="Filter using"> + <option value="relative_threshold" selected="True">Relative threshold</option> + <option value="absolute_threshold">Absolute threshold</option> + </param> + <when value="relative_threshold"> + <param name="relative_threshold" type="float" value="0.0" min="0.0" label="Percentage of the 95 percentile value to filter below" help="Value 0 results in no filtering" /> + </when> + <when value="absolute_threshold"> + <param name="absolute_threshold" type="float" value="0.0" min="0.0" label="Absolute value to filter below" /> + </when> + </conditional> + <conditional name="output_files_cond"> + <param name="output_files" type="select" label="Restrict output to" help="Statistics will always be generated." > + <option value="simple" selected="True">matched pairs only (S)</option> + <option value="simple_orphan">matched pairs and orphans only (O,S)</option> + <option value="simple_orphan_detail">matched pairs, orphans and details only (D,O,S)</option> + <option value="all">no restrictions (output everything: C,D,F,O,P,S)</option> + </param> + <when value="simple" /> + <when value="simple_orphan" /> + <when value="simple_orphan_detail" /> + <when value="all"> + <param name="plot_format" type="select" label="Output format for graph"> + <option value="pdf" selected="True">Pdf</option> + <option value="png">Png</option> + <option value="svg">Svg</option> + </param> + </when> + </conditional> + <param name="sort_chromosome" type="select" label="Sort output by chromosomes in" help="Chromosome strings that are not numeric will not be sorted" > + <option value="asc" selected="True">ascending order</option> + <option value="desc">descending order</option> + </param> + <param name="sort_score" type="select" label="Sort output by score?"> + <option value="no" selected="True">No</option> + <option value="asc">Yes, in ascending order</option> + <option value="desc">Yes, in descending order</option> + </param> + </inputs> + <outputs> + <collection name="closest_C_pdf" type="list" label="closest C: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="closest_C" ext="pdf" visible="false" /> + </collection> + <collection name="closest_C_png" type="list" label="closest C: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "closest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="closest_C" ext="png" visible="false" /> + </collection> + <collection name="closest_C_svg" type="list" label="closest C: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "closest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="closest_C" ext="svg" visible="false" /> + </collection> + <collection name="largest_C_pdf" type="list" label="largest C: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "largest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="largest_C" ext="pdf" visible="false" /> + </collection> + <collection name="largest_C_png" type="list" label="largest C: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "largest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="largest_C" ext="png" visible="false" /> + </collection> + <collection name="largest_C_svg" type="list" label="largest C: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "largest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="largest_C" ext="svg" visible="false" /> + </collection> + <collection name="mode_C_pdf" type="list" label="mode C: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "mode"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="mode_C" ext="pdf" visible="false" /> + </collection> + <collection name="mode_C_png" type="list" label="mode C: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "mode"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="mode_C" ext="png" visible="false" /> + </collection> + <collection name="mode_C_svg" type="list" label="mode C: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "mode"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="mode_C" ext="svg" visible="false" /> + </collection> + <collection name="closest_D" type="list" label="closest D: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] in ["all", "simple_orphan_detail"] and method in ["all", "closest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="closest_D" ext="tabular" visible="false" /> + </collection> + <collection name="largest_D" type="list" label="largest D: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] in ["all", "simple_orphan_detail"] and method in ["all", "largest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="largest_D" ext="tabular" visible="false" /> + </collection> + <collection name="mode_D" type="list" label="mode D: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] in ["all", "simple_orphan_detail"] and method in ["all", "mode"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="mode_D" ext="tabular" visible="false" /> + </collection> + <collection name="closest_F_pdf" type="list" label="closest F: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="closest_F" ext="pdf" visible="false" /> + </collection> + <collection name="closest_F_png" type="list" label="closest F: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "closest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="closest_F" ext="png" visible="false" /> + </collection> + <collection name="closest_F_svg" type="list" label="closest F: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "closest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="closest_F" ext="svg" visible="false" /> + </collection> + <collection name="largest_F_pdf" type="list" label="largest F: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "largest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="largest_F" ext="pdf" visible="false" /> + </collection> + <collection name="largest_F_png" type="list" label="largest F: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "largest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="largest_F" ext="png" visible="false" /> + </collection> + <collection name="largest_F_svg" type="list" label="largest F: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "largest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="largest_F" ext="svg" visible="false" /> + </collection> + <collection name="mode_F_pdf" type="list" label="mode F: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "mode"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="mode_F" ext="pdf" visible="false" /> + </collection> + <collection name="mode_F_png" type="list" label="mode F: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "mode"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="mode_F" ext="png" visible="false" /> + </collection> + <collection name="mode_F_svg" type="list" label="mode F: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "mode"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="mode_F" ext="svg" visible="false" /> + </collection> + <collection name="closest_O" type="list" label="closest O: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "closest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="closest_O" ext="tabular" visible="false" /> + </collection> + <collection name="largest_O" type="list" label="largest O: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "largest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="largest_O" ext="tabular" visible="false" /> + </collection> + <collection name="mode_O" type="list" label="mode O: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "mode"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="mode_O" ext="tabular" visible="false" /> + </collection> + <collection name="closest_P_pdf" type="list" label="closest P: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="closest_P" ext="pdf" visible="false" /> + </collection> + <collection name="closest_P_png" type="list" label="closest P: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "closest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="closest_P" ext="png" visible="false" /> + </collection> + <collection name="closest_P_svg" type="list" label="closest P: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "closest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="closest_P" ext="svg" visible="false" /> + </collection> + <collection name="largest_P_pdf" type="list" label="largest P: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "largest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="largest_P" ext="pdf" visible="false" /> + </collection> + <collection name="largest_P_png" type="list" label="largest P: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "largest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="largest_P" ext="png" visible="false" /> + </collection> + <collection name="largest_P_svg" type="list" label="largest P: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "largest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="largest_P" ext="svg" visible="false" /> + </collection> + <collection name="mode_P_pdf" type="list" label="mode P: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "mode"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="mode_P" ext="pdf" visible="false" /> + </collection> + <collection name="mode_P_png" type="list" label="mode P: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "mode"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="mode_P" ext="png" visible="false" /> + </collection> + <collection name="mode_P_svg" type="list" label="mode P: ${tool.name} on ${on_string}"> + <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "mode"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="mode_P" ext="svg" visible="false" /> + </collection> + <collection name="closest_S" type="list" label="closest S: ${tool.name} on ${on_string}"> + <filter>method in ["all", "closest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="closest_S" ext="gff" visible="false" /> + </collection> + <collection name="largest_S" type="list" label="largest S: ${tool.name} on ${on_string}"> + <filter>method in ["all", "largest"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="largest_S" ext="gff" visible="false" /> + </collection> + <collection name="mode_S" type="list" label="mode S: ${tool.name} on ${on_string}"> + <filter>method in ["all", "mode"]</filter> + <discover_datasets pattern="(?P<designation>.*)" directory="mode_S" ext="gff" visible="false" /> + </collection> + <data name="statistics_output" format="tabular" label="Statistics: ${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="input" value="cwpair2_input1.gff" /> + <param name="method" value="all" /> + <param name="up_distance" value="25" /> + <param name="down_distance" value="100" /> + <param name="binsize" value="1" /> + <param name="threshold_format" value="relative_threshold" /> + <param name="relative_threshold" value="0.0" /> + <param name="output_files" value="simple" /> + <param name="sort_chromosome" value="asc" /> + <param name="sort_score" value="asc" /> + <output_collection name="closest_S" type="list"> + <element name="closest_S_data_1_f0u25d100b1" file="closest_s_output1.gff" ftype="gff" /> + </output_collection> + <output_collection name="largest_S" type="list"> + <element name="largest_S_data_1_f0u25d100b1" file="largest_s_output1.gff" ftype="gff" /> + </output_collection> + <output_collection name="mode_S" type="list"> + <element name="mode_S_data_1_f0u25d100b1" file="mode_s_output1.gff" ftype="gff" /> + </output_collection> + <output name="statistics_output" file="statistics1.tabular" ftype="tabular" /> + </test> + <test> + <param name="input" value="cwpair2_input1.gff" /> + <param name="method" value="all" /> + <param name="up_distance" value="50" /> + <param name="down_distance" value="100" /> + <param name="binsize" value="1" /> + <param name="threshold_format" value="relative_threshold" /> + <param name="relative_threshold" value="0.0" /> + <param name="output_files" value="all" /> + <param name="plot_format" value="pdf" /> + <param name="sort_chromosome" value="asc" /> + <param name="sort_score" value="no" /> + <output_collection name="closest_D" type="list"> + <element name="closest_D_data_1_f0u50d100b1" file="closest_d_output2.tabular" ftype="tabular" /> + </output_collection> + <output_collection name="closest_F" type="list"> + <element name="closest_F_data_1_f0u50d100b1" file="closest_f_output2.pdf" ftype="pdf" compare="sim_size" /> + </output_collection> + <output_collection name="closest_O" type="list"> + <element name="closest_O_data_1_f0u50d100b1" file="closest_o_output2.tabular" ftype="tabular" /> + </output_collection> + <output_collection name="closest_S" type="list"> + <element name="closest_S_data_1_f0u50d100b1" file="closest_s_output2.gff" ftype="gff" /> + </output_collection> + <output_collection name="largest_D" type="list"> + <element name="largest_D_data_1_f0u50d100b1" file="largest_d_output2.tabular" ftype="tabular" /> + </output_collection> + <output_collection name="largest_F" type="list"> + <element name="largest_F_data_1_f0u50d100b1" file="largest_f_output2.pdf" ftype="pdf" compare="sim_size" /> + </output_collection> + <output_collection name="largest_O" type="list"> + <element name="largest_O_data_1_f0u50d100b1" file="largest_o_output2.tabular" ftype="tabular" /> + </output_collection> + <output_collection name="largest_S" type="list"> + <element name="largest_S_data_1_f0u50d100b1" file="largest_s_output2.gff" ftype="gff" /> + </output_collection> + <output_collection name="mode_C" type="list"> + <element name="mode_C_data_1_f0u50d100b1" file="mode_c_output2.pdf" ftype="pdf" compare="sim_size" /> + </output_collection> + <output_collection name="mode_D" type="list"> + <element name="mode_D_data_1_f0u50d100b1" file="mode_d_output2.tabular" ftype="tabular" /> + </output_collection> + <output_collection name="mode_F" type="list"> + <element name="mode_F_data_1_f0u50d100b1" file="mode_f_output2.pdf" ftype="pdf" compare="sim_size" /> + </output_collection> + <output_collection name="mode_O" type="list"> + <element name="mode_O_data_1_f0u50d100b1" file="mode_o_output2.tabular" ftype="tabular" /> + </output_collection> + <output_collection name="mode_P" type="list"> + <element name="mode_P_data_1_f0u50d100b1" file="mode_p_output2.pdf" ftype="pdf" compare="sim_size" /> + </output_collection> + <output_collection name="mode_S" type="list"> + <element name="mode_S_data_1_f0u50d100b1" file="mode_s_output2.gff" ftype="gff" /> + </output_collection> + <output name="statistics_output" file="statistics2.tabular" ftype="tabular" /> + </test> + </tests> + <help> +**What it does** + +Takes a list of called peaks on both strands and produces a list of matched pairs and a list of unmatched orphans +using a specified method for finding matched pairs. Methods for finding matched pairs are mode, closest, largest +or all (where the analysis is run for each method). A statistics dataset is generated and a collection of datasets +is produced for each method as follows. + +* **closest/largest/mode C** - the stastics graph in a specified format: pdf, png or svg +* **closest/largest/mode D** - the details in tabular format +* **closest/largest/mode F** - the final plots graph in a specified format: pdf, png or svg +* **closest/largest/mode O** - the orphans in tabular format +* **closest/largest/mode P** - the preview plots graph in a specified format: pdf, png or svg +* **closest/largest/mode S** - the matched pairs in gff format + + +**Options** + +* **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types. +* **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method). +* **Distance upstream from a peak to allow a pair** - Distance upstream from a Watson peak to allow a Crick pair. +* **Distance downstream from a peak to allow a pair** - Distance downstream from a Watson peak to allow a Crick pair. +* **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold. +* **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold. +* **Output format for graph** - Output format for graph. +* **Sort output by chromosomes in** - Output will be sorted by chromsome in the specified order. +* **Sort output by score?** - If yes, output will be sorted by score in the specified order. +* **Summary output format** - Format for summary output. + + </help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cwpair2_macros.xml Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,29 @@ +<?xml version='1.0' encoding='UTF-8'?> +<macros> + <token name="@WRAPPER_VERSION@">1.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.3.0">anaconda</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <regex match="Error:"/> + <regex match="Exception:"/> + </stdio> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @unpublished{None, + author = {None}, + title = {None}, + year = {None}, + eprint = {None}, + url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} + }</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cwpair2_util.py Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,410 @@ +import bisect +import csv +import os +import sys +import traceback + +from matplotlib import pyplot + +DETAILS = 'D' +FINAL_PLOTS = 'F' +ORPHANS = 'O' +PREVIEW_PLOTS = 'P' +SIMPLES = 'S' +STATS_GRAPH = 'C' +GFF_EXT = 'gff' +TABULAR_EXT = 'tabular' + +# Graph settings. +COLORS = 'krg' +Y_LABEL = 'Peak-pair counts' +X_LABEL = 'Peak-pair distance (bp)' +TICK_WIDTH = 3 +ADJUST = [0.140, 0.9, 0.9, 0.1] +pyplot.rc('xtick.major', size=10.00) +pyplot.rc('ytick.major', size=10.00) +pyplot.rc('lines', linewidth=4.00) +pyplot.rc('axes', linewidth=3.00) +pyplot.rc('font', family='Arial', size=32.0) + + +class FrequencyDistribution(object): + + def __init__(self, start, end, binsize=10, d=None): + self.start = start + self.end = end + self.dist = d or {} + self.binsize = binsize + + def get_bin(self, x): + """ + Returns the bin in which a data point falls + """ + return self.start + (x-self.start) // self.binsize * self.binsize + self.binsize/2.0 + + def add(self, x): + x = self.get_bin(x) + self.dist[x] = self.dist.get(x, 0) + 1 + + def graph_series(self): + x = [] + y = [] + for i in range(self.start, self.end, self.binsize): + center = self.get_bin(i) + x.append(center) + y.append(self.dist.get(center, 0)) + return x, y + + def mode(self): + return max(self.dist.items(), key=lambda data: data[1])[0] + + def size(self): + return sum(self.dist.values()) + + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit(1) + + +def distance(peak1, peak2): + return (peak2[1]+peak2[2])/2 - (peak1[1]+peak1[2])/2 + + +def gff_row(cname, start, end, score, source, type='.', strand='.', phase='.', attrs={}): + return (cname, source, type, start, end, score, strand, phase, gff_attrs(attrs)) + + +def gff_attrs(d): + if not d: + return '.' + return ';'.join('%s=%s' % item for item in d.items()) + + +def parse_chromosomes(reader): + # This version of cwpair2 accepts only gff format as input. + chromosomes = {} + reader.next() + for line in reader: + cname, junk, junk, start, end, value, strand, junk, junk = line + start = int(start) + end = int(end) + value = float(value) + if cname not in chromosomes: + chromosomes[cname] = [] + peaks = chromosomes[cname] + peaks.append((strand, start, end, value)) + return chromosomes + + +def perc95(chromosomes): + """ + Returns the 95th percentile value of the given chromosomes. + """ + values = [] + for peaks in chromosomes.values(): + for peak in peaks: + values.append(peak[3]) + values.sort() + # Get 95% value + return values[int(len(values)*0.95)] + + +def filter(chromosomes, threshold=0.05): + """ + Filters the peaks to those above a threshold. Threshold < 1.0 is interpreted + as a proportion of the maximum, >=1.0 as an absolute value. + """ + if threshold < 1: + p95 = perc95(chromosomes) + threshold = p95 * threshold + # Make the threshold a proportion of the + for cname, peaks in chromosomes.items(): + chromosomes[cname] = [peak for peak in peaks if peak[3] > threshold] + + +def split_strands(chromosome): + watson = [peak for peak in chromosome if peak[0] == '+'] + crick = [peak for peak in chromosome if peak[0] == '-'] + return watson, crick + + +def all_pair_distribution(chromosomes, up_distance, down_distance, binsize): + dist = FrequencyDistribution(-up_distance, down_distance, binsize=binsize) + for cname, data in chromosomes.items(): + watson, crick = split_strands(data) + crick.sort(key=lambda data: float(data[1])) + keys = make_keys(crick) + for peak in watson: + for cpeak in get_window(crick, peak, up_distance, down_distance, keys): + dist.add(distance(peak, cpeak)) + return dist + + +def make_keys(crick): + return [(data[1] + data[2])//2 for data in crick] + + +def get_window(crick, peak, up_distance, down_distance, keys=None): + """ + Returns a window of all crick peaks within a distance of a watson peak. + crick strand MUST be sorted by distance + """ + strand, start, end, value = peak + midpoint = (start + end) // 2 + lower = midpoint - up_distance + upper = midpoint + down_distance + keys = keys or make_keys(crick) + start_index = bisect.bisect_left(keys, lower) + end_index = bisect.bisect_right(keys, upper) + return [cpeak for cpeak in crick[start_index:end_index]] + + +def match_largest(window, peak): + if not window: + return None + return max(window, key=lambda cpeak: cpeak[3]) + + +def match_closest(window, peak): + if not window: + return None + + def key(cpeak): + d = distance(peak, cpeak) + # Search negative distances last + if d < 0: + # And then prefer less negative distances + d = 10000 - d + return d + return min(window, key=key) + + +def match_mode(window, peak, mode): + if not window: + return None + return min(window, key=lambda cpeak: abs(distance(peak, cpeak)-mode)) + +METHODS = {'mode': match_mode, 'closest': match_closest, 'largest': match_largest} + + +def frequency_plot(freqs, fname, labels=[], title=''): + pyplot.clf() + pyplot.figure(figsize=(10, 10)) + for i, freq in enumerate(freqs): + x, y = freq.graph_series() + pyplot.plot(x, y, '%s-' % COLORS[i]) + if len(freqs) > 1: + pyplot.legend(labels) + pyplot.xlim(freq.start, freq.end) + pyplot.ylim(ymin=0) + pyplot.ylabel(Y_LABEL) + pyplot.xlabel(X_LABEL) + pyplot.subplots_adjust(left=ADJUST[0], right=ADJUST[1], top=ADJUST[2], bottom=ADJUST[3]) + # Get the current axes + ax = pyplot.gca() + for l in ax.get_xticklines() + ax.get_yticklines(): + l.set_markeredgewidth(TICK_WIDTH) + pyplot.savefig(fname) + + +def create_directories(method): + if method == 'all': + match_methods = METHODS.keys() + else: + match_methods = [method] + for match_method in match_methods: + os.mkdir('%s_%s' % (match_method, DETAILS)) + os.mkdir('%s_%s' % (match_method, FINAL_PLOTS)) + os.mkdir('%s_%s' % (match_method, ORPHANS)) + os.mkdir('%s_%s' % (match_method, PREVIEW_PLOTS)) + os.mkdir('%s_%s' % (match_method, SIMPLES)) + os.mkdir('%s_%s' % (match_method, STATS_GRAPH)) + + +def process_file(dataset_path, galaxy_hid, method, threshold, up_distance, down_distance, + binsize, output_files, plot_format, sort_chromosome, sort_score): + if method == 'all': + match_methods = METHODS.keys() + else: + match_methods = [method] + statistics = [] + for match_method in match_methods: + stats = perform_process(dataset_path, + galaxy_hid, + match_method, + threshold, + up_distance, + down_distance, + binsize, + output_files, + plot_format, + sort_chromosome, + sort_score) + statistics.append(stats) + if output_files == 'all' and method == 'all': + frequency_plot([s['dist'] for s in statistics], + statistics[0]['graph_path'], + labels=METHODS.keys()) + return statistics + + +def perform_process(dataset_path, galaxy_hid, method, threshold, up_distance, + down_distance, binsize, output_files, plot_format, sort_chromosome, sort_score): + output_details = output_files in ["all", "simple_orphan_detail"] + output_plots = output_files in ["all"] + output_orphans = output_files in ["all", "simple_orphan", "simple_orphan_detail"] + # Keep track of statistics for the output file + statistics = {} + input = csv.reader(open(dataset_path, 'rt'), delimiter='\t') + fpath, fname = os.path.split(dataset_path) + statistics['fname'] = '%s: data %s' % (method, str(galaxy_hid)) + statistics['dir'] = fpath + if threshold >= 1: + filter_string = 'fa%d' % threshold + else: + filter_string = 'f%d' % (threshold * 100) + fname = 'data_%s_%su%dd%db%d' % (galaxy_hid, filter_string, up_distance, down_distance, binsize) + + def make_path(output_type, extension=TABULAR_EXT): + # Returns the full path for a certain output. + return os.path.join(output_type, '%s_%s.%s' % (output_type, fname, extension)) + + def td_writer(output_type, extension=TABULAR_EXT): + # Returns a tab-delimited writer for a specified output. + output_file_path = make_path(output_type, extension) + return csv.writer(open(output_file_path, 'wt'), delimiter='\t') + + try: + chromosomes = parse_chromosomes(input) + except Exception: + stop_err('Unable to parse file "%s".\n%s' % (dataset_path, traceback.format_exc())) + if output_details: + # Details + detailed_output = td_writer('%s_%s' % (method, DETAILS), extension=TABULAR_EXT) + detailed_output.writerow(('chrom', 'start', 'end', 'value', 'strand') * 2 + ('midpoint', 'c-w reads sum', 'c-w distance (bp)')) + if output_plots: + # Final Plot + final_plot_path = make_path('%s_%s' % (method, FINAL_PLOTS), plot_format) + if output_orphans: + # Orphans + orphan_output = td_writer('%s_%s' % (method, ORPHANS), extension=TABULAR_EXT) + orphan_output.writerow(('chrom', 'strand', 'start', 'end', 'value')) + if output_plots: + # Preview Plot + preview_plot_path = make_path('%s_%s' % (method, PREVIEW_PLOTS), plot_format) + # Simple + simple_output = td_writer('%s_%s' % (method, SIMPLES), extension=GFF_EXT) + statistics['stats_path'] = 'statistics.%s' % TABULAR_EXT + if output_plots: + statistics['graph_path'] = make_path('%s_%s' % (method, STATS_GRAPH), plot_format) + statistics['perc95'] = perc95(chromosomes) + if threshold > 0: + # Apply filter + filter(chromosomes, threshold) + if method == 'mode': + freq = all_pair_distribution(chromosomes, up_distance, down_distance, binsize) + mode = freq.mode() + statistics['preview_mode'] = mode + if output_plots: + frequency_plot([freq], preview_plot_path, title='Preview frequency plot') + else: + statistics['preview_mode'] = 'NA' + dist = FrequencyDistribution(-up_distance, down_distance, binsize=binsize) + orphans = 0 + # x will be used to archive the summary dataset + x = [] + for cname, chromosome in chromosomes.items(): + # Each peak is (strand, start, end, value) + watson, crick = split_strands(chromosome) + # Sort by value of each peak + watson.sort(key=lambda data: -float(data[3])) + # Sort by position to facilitate binary search + crick.sort(key=lambda data: float(data[1])) + keys = make_keys(crick) + for peak in watson: + window = get_window(crick, peak, up_distance, down_distance, keys) + if method == 'mode': + match = match_mode(window, peak, mode) + else: + match = METHODS[method](window, peak) + if match: + midpoint = (match[1] + match[2] + peak[1] + peak[2]) // 4 + d = distance(peak, match) + dist.add(d) + # Simple output in gff format. + x.append(gff_row(cname, + source='cwpair', + start=midpoint, + end=midpoint + 1, + score=peak[3] + match[3], + attrs={'cw_distance': d})) + if output_details: + detailed_output.writerow((cname, + peak[1], + peak[2], + peak[3], + '+', + cname, + match[1], + match[2], + match[3], '-', + midpoint, + peak[3]+match[3], + d)) + i = bisect.bisect_left(keys, (match[1]+match[2])/2) + del crick[i] + del keys[i] + else: + if output_orphans: + orphan_output.writerow((cname, peak[0], peak[1], peak[2], peak[3])) + # Keep track of orphans for statistics. + orphans += 1 + # Remaining crick peaks are orphans + if output_orphans: + for cpeak in crick: + orphan_output.writerow((cname, cpeak[0], cpeak[1], cpeak[2], cpeak[3])) + # Keep track of orphans for statistics. + orphans += len(crick) + # Sort output by chromosome if specified. + if sort_chromosome == "asc": + try: + x.sort(key=lambda data: int(data[3])) + x.sort(key=lambda data: int(data[0])) + except: + # Cannot sort because chromosome number is not a numeric. + pass + elif sort_chromosome == "desc": + try: + x.sort(key=lambda data: int(data[0]), reverse=True) + x.sort(key=lambda data: int(data[3]), reverse=True) + except: + # Cannot sort because chromosome number is not a numeric. + pass + # Sort output by score if specified. + if sort_score == "desc": + x.sort(key=lambda data: float(data[5]), reverse=True) + elif sort_score == "asc": + x.sort(key=lambda data: float(data[5])) + # Writing a summary to txt or gff format file + for row in x: + row_tmp = list(row) + # Dataset in tuple cannot be modified in Python, so row will + # be converted to list format to add 'chr'. + if row_tmp[0] == "999": + row_tmp[0] = 'chrM' + elif row_tmp[0] == "998": + row_tmp[0] = 'chrY' + elif row_tmp[0] == "997": + row_tmp[0] = 'chrX' + else: + row_tmp[0] = row_tmp[0] + # Print row_tmp. + simple_output.writerow(row_tmp) + statistics['paired'] = dist.size() * 2 + statistics['orphans'] = orphans + statistics['final_mode'] = dist.mode() + if output_plots: + frequency_plot([dist], final_plot_path, title='Frequency distribution') + statistics['dist'] = dist + return statistics
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_d_output2.tabular Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,67 @@ +chrom start end value strand chrom start end value strand midpoint c-w reads sum c-w distance (bp) +chr1 87147 87167 3492.0 + chr1 87158 87178 2039.0 - 87162 5531.0 11 +chr1 87 107 3211.0 + chr1 139 159 993.0 - 123 4204.0 52 +chr1 48 68 2842.0 + chr1 50 70 39.0 - 59 2881.0 2 +chr1 255 275 2810.0 + chr1 261 281 1278.0 - 268 4088.0 6 +chr1 117 137 2163.0 + chr1 176 196 14.0 - 156 2177.0 59 +chr1 86954 86974 1948.0 + chr1 86991 87011 65.0 - 86982 2013.0 37 +chr1 169107 169127 1811.0 + chr1 169064 169084 76.0 - 169095 1887.0 -43 +chr1 87171 87191 1436.0 + chr1 87198 87218 2207.0 - 87194 3643.0 27 +chr1 201 221 1411.0 + chr1 215 235 2611.0 - 218 4022.0 14 +chr1 229741 229761 1380.0 + chr1 229757 229777 3151.0 - 229759 4531.0 16 +chr1 185076 185096 1309.0 + chr1 185122 185142 62.0 - 185109 1371.0 46 +chr1 39081 39101 1268.0 + chr1 39052 39072 82.0 - 39076 1350.0 -29 +chr1 92411 92431 1252.0 + chr1 92411 92431 136.0 - 92421 1388.0 0 +chr1 203872 203892 1234.0 + chr1 203835 203855 242.0 - 203863 1476.0 -37 +chr1 70776 70796 1148.0 + chr1 70788 70808 998.0 - 70792 2146.0 12 +chr1 231 251 1146.0 + chr1 279 299 1328.0 - 265 2474.0 48 +chr1 87098 87118 1125.0 + chr1 87101 87121 1134.0 - 87109 2259.0 3 +chr1 6163 6183 1049.0 + chr1 6254 6274 1076.0 - 6218 2125.0 91 +chr1 25246 25266 995.0 + chr1 25345 25365 188.0 - 25305 1183.0 99 +chr1 101411 101431 973.0 + chr1 101367 101387 1388.0 - 101399 2361.0 -44 +chr1 139213 139233 965.0 + chr1 139228 139248 214.0 - 139230 1179.0 15 +chr1 87019 87039 769.0 + chr1 87049 87069 422.0 - 87044 1191.0 30 +chr1 124318 124338 749.0 + chr1 124275 124295 12.0 - 124306 761.0 -43 +chr1 348 368 699.0 + chr1 373 393 200.0 - 370 899.0 25 +chr1 92543 92563 699.0 + chr1 92571 92591 90.0 - 92567 789.0 28 +chr1 138868 138888 698.0 + chr1 138864 138884 13.0 - 138876 711.0 -4 +chr1 307 327 685.0 + chr1 323 343 486.0 - 325 1171.0 16 +chr1 6413 6433 682.0 + chr1 6476 6496 567.0 - 6454 1249.0 63 +chr1 72781 72801 657.0 + chr1 72810 72830 212.0 - 72805 869.0 29 +chr1 22571 22591 609.0 + chr1 22569 22589 254.0 - 22580 863.0 -2 +chr1 65152 65172 575.0 + chr1 65148 65168 43.0 - 65160 618.0 -4 +chr1 106034 106054 558.0 + chr1 106041 106061 14.0 - 106047 572.0 7 +chr1 155028 155048 522.0 + chr1 155111 155131 1051.0 - 155079 1573.0 83 +chr1 32449 32469 476.0 + chr1 32497 32517 2.0 - 32483 478.0 48 +chr1 6706 6726 431.0 + chr1 6702 6722 2.0 - 6714 433.0 -4 +chr1 113782 113802 420.0 + chr1 113762 113782 296.0 - 113782 716.0 -20 +chr1 228633 228653 371.0 + chr1 228691 228711 255.0 - 228672 626.0 58 +chr1 438 458 334.0 + chr1 446 466 170.0 - 452 504.0 8 +chr1 72671 72691 304.0 + chr1 72771 72791 406.0 - 72731 710.0 100 +chr1 170119 170139 284.0 + chr1 170129 170149 373.0 - 170134 657.0 10 +chr1 92631 92651 260.0 + chr1 92639 92659 2137.0 - 92645 2397.0 8 +chr1 136366 136386 248.0 + chr1 136352 136372 117.0 - 136369 365.0 -14 +chr1 108624 108644 206.0 + chr1 108579 108599 367.0 - 108611 573.0 -45 +chr1 45678 45698 198.0 + chr1 45643 45663 295.0 - 45670 493.0 -35 +chr1 368 388 192.0 + chr1 388 408 167.0 - 388 359.0 20 +chr1 682 702 168.0 + chr1 634 654 151.0 - 668 319.0 -48 +chr1 59190 59210 168.0 + chr1 59246 59266 397.0 - 59228 565.0 56 +chr1 134170 134190 151.0 + chr1 134270 134290 508.0 - 134230 659.0 100 +chr1 55495 55515 125.0 + chr1 55581 55601 831.0 - 55548 956.0 86 +chr1 512 532 101.0 + chr1 468 488 468.0 - 500 569.0 -44 +chr1 39197 39217 101.0 + chr1 39258 39278 261.0 - 39237 362.0 61 +chr1 229721 229741 84.0 + chr1 229784 229804 615.0 - 229762 699.0 63 +chr1 116660 116680 74.0 + chr1 116619 116639 699.0 - 116649 773.0 -41 +chr1 19216 19236 42.0 + chr1 19191 19211 736.0 - 19213 778.0 -25 +chr1 230110 230130 42.0 + chr1 230120 230140 2.0 - 230125 44.0 10 +chr1 31627 31647 40.0 + chr1 31693 31713 450.0 - 31670 490.0 66 +chr1 180280 180300 38.0 + chr1 180362 180382 59.0 - 180331 97.0 82 +chr1 98528 98548 34.0 + chr1 98555 98575 88.0 - 98551 122.0 27 +chr1 230163 230183 23.0 + chr1 230173 230193 33.0 - 230178 56.0 10 +chr1 173262 173282 11.0 + chr1 173270 173290 535.0 - 173276 546.0 8 +chr1 230145 230165 8.0 + chr1 230150 230170 7.0 - 230157 15.0 5 +chr1 95920 95940 5.0 + chr1 95971 95991 684.0 - 95955 689.0 51 +chr1 199418 199438 5.0 + chr1 199388 199408 805.0 - 199413 810.0 -30 +chr1 197489 197509 3.0 + chr1 197562 197582 2.0 - 197535 5.0 73 +chr1 96908 96928 2.0 + chr1 96911 96931 10.0 - 96919 12.0 3 +chr1 151369 151389 2.0 + chr1 151341 151361 593.0 - 151365 595.0 -28
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_o_output2.tabular Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,367 @@ +chrom strand start end value +chr1 + 100364 100384 2695.0 +chr1 + 30 50 2140.0 +chr1 + 5379 5399 1572.0 +chr1 + 52440 52460 1562.0 +chr1 + 73234 73254 1492.0 +chr1 + 31096 31116 1481.0 +chr1 + 145253 145273 1394.0 +chr1 + 10641 10661 1359.0 +chr1 + 200580 200600 1298.0 +chr1 + 64772 64792 1292.0 +chr1 + 86886 86906 1253.0 +chr1 + 103207 103227 1229.0 +chr1 + 43835 43855 1173.0 +chr1 + 29570 29590 1130.0 +chr1 + 83774 83794 1125.0 +chr1 + 165827 165847 1109.0 +chr1 + 92775 92795 1105.0 +chr1 + 4748 4768 1077.0 +chr1 + 126733 126753 952.0 +chr1 + 71041 71061 881.0 +chr1 + 35773 35793 866.0 +chr1 + 53097 53117 835.0 +chr1 + 71556 71576 835.0 +chr1 + 30964 30984 829.0 +chr1 + 31019 31039 810.0 +chr1 + 55349 55369 794.0 +chr1 + 203193 203213 789.0 +chr1 + 39794 39814 780.0 +chr1 + 153928 153948 768.0 +chr1 + 179472 179492 696.0 +chr1 + 178117 178137 686.0 +chr1 + 1298 1318 684.0 +chr1 + 87085 87105 676.0 +chr1 + 192754 192774 668.0 +chr1 + 89611 89631 640.0 +chr1 + 20205 20225 634.0 +chr1 + 118428 118448 633.0 +chr1 + 110736 110756 621.0 +chr1 + 48642 48662 610.0 +chr1 + 159372 159392 605.0 +chr1 + 6453 6473 601.0 +chr1 + 112137 112157 601.0 +chr1 + 142905 142925 599.0 +chr1 + 167443 167463 597.0 +chr1 + 126073 126093 590.0 +chr1 + 6233 6253 589.0 +chr1 + 43657 43677 586.0 +chr1 + 134021 134041 572.0 +chr1 + 29864 29884 570.0 +chr1 + 70953 70973 555.0 +chr1 + 87002 87022 550.0 +chr1 + 129555 129575 536.0 +chr1 + 119754 119774 515.0 +chr1 + 43523 43543 505.0 +chr1 + 97898 97918 501.0 +chr1 + 40830 40850 491.0 +chr1 + 153095 153115 490.0 +chr1 + 7303 7323 484.0 +chr1 + 115866 115886 480.0 +chr1 + 129680 129700 464.0 +chr1 + 187155 187175 455.0 +chr1 + 192271 192291 453.0 +chr1 + 160 180 451.0 +chr1 + 150449 150469 436.0 +chr1 + 9367 9387 425.0 +chr1 + 93793 93813 415.0 +chr1 + 87572 87592 407.0 +chr1 + 124845 124865 383.0 +chr1 + 4053 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130869 130889 718.0 +chr1 - 133644 133664 122.0 +chr1 - 135051 135071 63.0 +chr1 - 137428 137448 1200.0 +chr1 - 137816 137836 695.0 +chr1 - 139627 139647 531.0 +chr1 - 140133 140153 441.0 +chr1 - 140770 140790 556.0 +chr1 - 141182 141202 14.0 +chr1 - 143551 143571 3.0 +chr1 - 144669 144689 1192.0 +chr1 - 145383 145403 326.0 +chr1 - 147573 147593 255.0 +chr1 - 148690 148710 2.0 +chr1 - 149704 149724 74.0 +chr1 - 150358 150378 153.0 +chr1 - 152984 153004 106.0 +chr1 - 153812 153832 168.0 +chr1 - 154862 154882 14.0 +chr1 - 155456 155476 23.0 +chr1 - 155897 155917 10.0 +chr1 - 157559 157579 337.0 +chr1 - 166467 166487 582.0 +chr1 - 166631 166651 173.0 +chr1 - 169500 169520 814.0 +chr1 - 170282 170302 63.0 +chr1 - 171063 171083 212.0 +chr1 - 175188 175208 117.0 +chr1 - 175474 175494 1119.0 +chr1 - 176004 176024 1473.0 +chr1 - 177140 177160 93.0 +chr1 - 177386 177406 289.0 +chr1 - 178846 178866 601.0 +chr1 - 178971 178991 723.0 +chr1 - 179116 179136 71.0 +chr1 - 180272 180292 25.0 +chr1 - 180995 181015 299.0 +chr1 - 182588 182608 465.0 +chr1 - 182790 182810 355.0 +chr1 - 185673 185693 190.0 +chr1 - 187422 187442 20.0 +chr1 - 187976 187996 728.0 +chr1 - 196499 196519 224.0 +chr1 - 197060 197080 224.0 +chr1 - 197151 197171 1464.0 +chr1 - 197342 197362 204.0 +chr1 - 198423 198443 598.0 +chr1 - 198953 198973 3.0 +chr1 - 199935 199955 31.0 +chr1 - 201308 201328 1287.0 +chr1 - 201651 201671 892.0 +chr1 - 202977 202997 163.0 +chr1 - 203452 203472 76.0 +chr1 - 206245 206265 22.0 +chr1 - 207675 207695 313.0 +chr1 - 208559 208579 121.0 +chr1 - 209205 209225 176.0 +chr1 - 220863 220883 2.0 +chr1 - 223035 223055 62.0 +chr1 - 225156 225176 2.0 +chr1 - 226777 226797 444.0 +chr1 - 227608 227628 1311.0 +chr1 - 228405 228425 1447.0 +chr1 - 229031 229051 6.0 +chr1 - 229583 229603 62.0 +chr1 - 229665 229685 131.0 +chr1 - 229965 229985 13.0 +chr1 - 230132 230152 2.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_s_output1.gff Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,56 @@ +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59 +chr1 cwpair . 218 219 4022.0 . . cw_distance=14 +chr1 cwpair . 265 266 2474.0 . . cw_distance=48 +chr1 cwpair . 268 269 4088.0 . . cw_distance=6 +chr1 cwpair . 325 326 1171.0 . . cw_distance=16 +chr1 cwpair . 370 371 899.0 . . cw_distance=25 +chr1 cwpair . 388 389 359.0 . . cw_distance=20 +chr1 cwpair . 452 453 504.0 . . cw_distance=8 +chr1 cwpair . 477 478 566.0 . . cw_distance=1 +chr1 cwpair . 627 628 247.0 . . cw_distance=33 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 +chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 +chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11 +chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 92567 92568 789.0 . . cw_distance=28 +chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 +chr1 cwpair . 230125 230126 44.0 . . cw_distance=10 +chr1 cwpair . 230157 230158 15.0 . . cw_distance=5 +chr1 cwpair . 230178 230179 56.0 . . cw_distance=10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_s_output2.gff Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,66 @@ +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59 +chr1 cwpair . 218 219 4022.0 . . cw_distance=14 +chr1 cwpair . 265 266 2474.0 . . cw_distance=48 +chr1 cwpair . 268 269 4088.0 . . cw_distance=6 +chr1 cwpair . 325 326 1171.0 . . cw_distance=16 +chr1 cwpair . 370 371 899.0 . . cw_distance=25 +chr1 cwpair . 388 389 359.0 . . cw_distance=20 +chr1 cwpair . 452 453 504.0 . . cw_distance=8 +chr1 cwpair . 500 501 569.0 . . cw_distance=-44 +chr1 cwpair . 668 669 319.0 . . cw_distance=-48 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 +chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 +chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11 +chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 92567 92568 789.0 . . cw_distance=28 +chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 +chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 +chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 +chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 +chr1 cwpair . 230125 230126 44.0 . . cw_distance=10 +chr1 cwpair . 230157 230158 15.0 . . cw_distance=5 +chr1 cwpair . 230178 230179 56.0 . . cw_distance=10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cwpair2_input1.gff Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,499 @@ +chr1 genetrack . 11 31 414 + . stddev=2.26073020752 +chr1 genetrack . 30 50 2140 + . stddev=4.43077587195 +chr1 genetrack . 48 68 2842 + . stddev=4.88263527016 +chr1 genetrack . 87 107 3211 + . stddev=5.51553909779 +chr1 genetrack . 117 137 2163 + . stddev=4.21572697137 +chr1 genetrack . 160 180 451 + . stddev=0.724882503432 +chr1 genetrack . 201 221 1411 + . stddev=5.79752503059 +chr1 genetrack . 231 251 1146 + . stddev=1.48216146131 +chr1 genetrack . 255 275 2810 + . stddev=1.35163759113 +chr1 genetrack . 307 327 685 + . stddev=0.0 +chr1 genetrack . 348 368 699 + . stddev=2.60206286017 +chr1 genetrack . 368 388 192 + . stddev=0.0 +chr1 genetrack . 438 458 334 + . stddev=0.109271183179 +chr1 genetrack . 467 487 98 + . stddev=0.0 +chr1 genetrack . 512 532 101 + . stddev=0.792079207921 +chr1 genetrack . 601 621 96 + . stddev=0.0 +chr1 genetrack . 682 702 168 + . stddev=0.0 +chr1 genetrack . 1298 1318 684 + . stddev=0.0 +chr1 genetrack . 2293 2313 12 + . stddev=0.0 +chr1 genetrack . 2613 2633 202 + . stddev=0.0 +chr1 genetrack . 2976 2996 356 + . stddev=0.0 +chr1 genetrack . 4053 4073 381 + . stddev=0.0 +chr1 genetrack . 4445 4465 94 + . stddev=0.0 +chr1 genetrack . 4748 4768 1077 + . stddev=0.0 +chr1 genetrack . 5379 5399 1572 + . stddev=0.0 +chr1 genetrack . 5750 5770 25 + . stddev=0.0 +chr1 genetrack . 5794 5814 148 + . stddev=0.0 +chr1 genetrack . 6163 6183 1049 + . stddev=0.645595472695 +chr1 genetrack . 6233 6253 589 + . stddev=2.54134583729 +chr1 genetrack . 6255 6275 26 + . stddev=0.0 +chr1 genetrack . 6413 6433 682 + . stddev=0.0 +chr1 genetrack . 6453 6473 601 + . stddev=0.0 +chr1 genetrack . 6706 6726 431 + . stddev=0.0 +chr1 genetrack . 7303 7323 484 + . stddev=0.0 +chr1 genetrack . 7753 7773 14 + . stddev=0.0 +chr1 genetrack . 9367 9387 425 + . stddev=0.0 +chr1 genetrack . 10641 10661 1359 + . stddev=0.0 +chr1 genetrack . 12305 12325 13 + . stddev=0.0 +chr1 genetrack . 16173 16193 12 + . stddev=0.0 +chr1 genetrack . 16501 16521 15 + . stddev=0.0 +chr1 genetrack . 19216 19236 42 + . stddev=0.0 +chr1 genetrack . 20117 20137 8 + . stddev=0.0 +chr1 genetrack . 20205 20225 634 + . stddev=0.0 +chr1 genetrack . 20391 20411 173 + . stddev=0.0 +chr1 genetrack . 20626 20646 171 + . stddev=0.0 +chr1 genetrack . 21406 21426 177 + . stddev=0.0 +chr1 genetrack . 22268 22288 15 + . stddev=0.0 +chr1 genetrack . 22571 22591 609 + . stddev=0.0 +chr1 genetrack . 24765 24785 4 + . stddev=0.0 +chr1 genetrack . 25246 25266 995 + . stddev=0.0 +chr1 genetrack . 27978 27998 354 + . stddev=0.0 +chr1 genetrack . 29570 29590 1130 + . stddev=0.0 +chr1 genetrack . 29864 29884 570 + . stddev=0.0 +chr1 genetrack . 30964 30984 829 + . stddev=0.0 +chr1 genetrack . 31019 31039 810 + . stddev=0.0 +chr1 genetrack . 31096 31116 1481 + . stddev=0.0 +chr1 genetrack . 31627 31647 40 + . stddev=0.0 +chr1 genetrack . 32145 32165 66 + . stddev=0.0 +chr1 genetrack . 32449 32469 476 + . stddev=0.0 +chr1 genetrack . 33426 33446 2 + . stddev=0.0 +chr1 genetrack . 33829 33849 48 + . stddev=0.0 +chr1 genetrack . 35773 35793 866 + . stddev=0.0 +chr1 genetrack . 39081 39101 1268 + . stddev=0.0 +chr1 genetrack . 39197 39217 101 + . stddev=0.0 +chr1 genetrack . 39591 39611 10 + . stddev=0.0 +chr1 genetrack . 39794 39814 780 + . stddev=0.0 +chr1 genetrack . 39942 39962 375 + . stddev=0.0 +chr1 genetrack . 40264 40284 199 + . stddev=0.0 +chr1 genetrack . 40830 40850 491 + . stddev=0.0 +chr1 genetrack . 41008 41028 132 + . stddev=0.0 +chr1 genetrack . 42843 42863 218 + . stddev=0.0 +chr1 genetrack . 42925 42945 77 + . stddev=0.0 +chr1 genetrack . 43147 43167 9 + . stddev=0.0 +chr1 genetrack . 43523 43543 505 + . stddev=0.0 +chr1 genetrack . 43657 43677 586 + . stddev=0.0 +chr1 genetrack . 43835 43855 1173 + . stddev=0.0 +chr1 genetrack . 44687 44707 100 + . stddev=0.0 +chr1 genetrack . 45248 45268 305 + . stddev=0.139642881568 +chr1 genetrack . 45409 45429 307 + . stddev=0.0 +chr1 genetrack . 45678 45698 198 + . stddev=0.0 +chr1 genetrack . 47015 47035 133 + . stddev=0.0 +chr1 genetrack . 48319 48339 290 + . stddev=0.0 +chr1 genetrack . 48431 48451 57 + . stddev=0.0 +chr1 genetrack . 48642 48662 610 + . stddev=0.0 +chr1 genetrack . 48772 48792 284 + . stddev=0.0 +chr1 genetrack . 49283 49303 2 + . stddev=0.0 +chr1 genetrack . 52440 52460 1562 + . stddev=0.0 +chr1 genetrack . 53097 53117 835 + . stddev=0.0 +chr1 genetrack . 55349 55369 794 + . stddev=0.0 +chr1 genetrack . 55495 55515 125 + . stddev=0.0 +chr1 genetrack . 55692 55712 228 + . stddev=0.0 +chr1 genetrack . 59190 59210 168 + . stddev=0.0 +chr1 genetrack . 59248 59268 80 + . stddev=0.0 +chr1 genetrack . 59583 59603 204 + . stddev=0.0 +chr1 genetrack . 61977 61997 368 + . stddev=0.0 +chr1 genetrack . 64772 64792 1292 + . stddev=0.0 +chr1 genetrack . 65152 65172 575 + . stddev=0.0 +chr1 genetrack . 68018 68038 62 + . stddev=0.0 +chr1 genetrack . 68564 68584 303 + . stddev=0.0 +chr1 genetrack . 70776 70796 1148 + . stddev=0.0 +chr1 genetrack . 70953 70973 555 + . stddev=0.0 +chr1 genetrack . 71041 71061 881 + . stddev=0.0 +chr1 genetrack . 71556 71576 835 + . stddev=0.0345856983909 +chr1 genetrack . 72671 72691 304 + . stddev=0.0572595236366 +chr1 genetrack . 72781 72801 657 + . stddev=0.0 +chr1 genetrack . 73234 73254 1492 + . stddev=0.0 +chr1 genetrack . 76365 76385 47 + . stddev=0.0 +chr1 genetrack . 76501 76521 33 + . stddev=0.0 +chr1 genetrack . 77731 77751 113 + . stddev=0.0 +chr1 genetrack . 81481 81501 5 + . stddev=0.0 +chr1 genetrack . 83774 83794 1125 + . stddev=0.0 +chr1 genetrack . 86865 86885 81 + . stddev=0.0 +chr1 genetrack . 86886 86906 1253 + . stddev=0.0 +chr1 genetrack . 86954 86974 1948 + . stddev=5.39208071191 +chr1 genetrack . 87002 87022 550 + . stddev=0.0 +chr1 genetrack . 87019 87039 769 + . stddev=0.0 +chr1 genetrack . 87085 87105 676 + . stddev=0.0 +chr1 genetrack . 87098 87118 1125 + . stddev=1.98839815175 +chr1 genetrack . 87147 87167 3492 + . stddev=2.59487167975 +chr1 genetrack . 87171 87191 1436 + . stddev=1.75985539692 +chr1 genetrack . 87572 87592 407 + . stddev=0.0 +chr1 genetrack . 89611 89631 640 + . stddev=0.0 +chr1 genetrack . 89663 89683 2 + . stddev=0.0 +chr1 genetrack . 90040 90060 82 + . stddev=0.0 +chr1 genetrack . 90412 90432 86 + . stddev=0.0 +chr1 genetrack . 91215 91235 11 + . stddev=0.0 +chr1 genetrack . 91379 91399 120 + . stddev=0.0 +chr1 genetrack . 92411 92431 1252 + . stddev=0.169502292497 +chr1 genetrack . 92543 92563 699 + . stddev=0.0 +chr1 genetrack . 92631 92651 260 + . stddev=0.0 +chr1 genetrack . 92775 92795 1105 + . stddev=0.923076923077 +chr1 genetrack . 92982 93002 44 + . stddev=0.0 +chr1 genetrack . 93793 93813 415 + . stddev=0.0 +chr1 genetrack . 95920 95940 5 + . stddev=0.0 +chr1 genetrack . 96908 96928 2 + . stddev=0.0 +chr1 genetrack . 97898 97918 501 + . stddev=0.0 +chr1 genetrack . 97967 97987 50 + . stddev=0.0 +chr1 genetrack . 98528 98548 34 + . stddev=0.0 +chr1 genetrack . 100364 100384 2695 + . stddev=4.98845945981 +chr1 genetrack . 101411 101431 973 + . stddev=0.0 +chr1 genetrack . 102337 102357 36 + . stddev=0.0 +chr1 genetrack . 103108 103128 90 + . stddev=0.0 +chr1 genetrack . 103207 103227 1229 + . stddev=0.0 +chr1 genetrack . 105499 105519 46 + . stddev=0.145830520272 +chr1 genetrack . 105942 105962 25 + . stddev=0.0 +chr1 genetrack . 106034 106054 558 + . stddev=0.0 +chr1 genetrack . 108624 108644 206 + . stddev=0.0 +chr1 genetrack . 110130 110150 42 + . stddev=0.0 +chr1 genetrack . 110540 110560 91 + . stddev=0.0 +chr1 genetrack . 110602 110622 8 + . stddev=0.0 +chr1 genetrack . 110736 110756 621 + . stddev=0.0400962950016 +chr1 genetrack . 111317 111337 17 + . stddev=0.0 +chr1 genetrack . 112137 112157 601 + . stddev=0.0 +chr1 genetrack . 112900 112920 125 + . stddev=0.0 +chr1 genetrack . 113226 113246 28 + . stddev=0.0 +chr1 genetrack . 113782 113802 420 + . stddev=0.0 +chr1 genetrack . 115866 115886 480 + . stddev=0.0 +chr1 genetrack . 116432 116452 267 + . stddev=0.0 +chr1 genetrack . 116660 116680 74 + . stddev=0.0 +chr1 genetrack . 117198 117218 228 + . stddev=0.0 +chr1 genetrack . 118428 118448 633 + . stddev=0.039715023981 +chr1 genetrack . 119155 119175 9 + . stddev=0.0 +chr1 genetrack . 119736 119756 135 + . stddev=0.0 +chr1 genetrack . 119754 119774 515 + . stddev=0.0 +chr1 genetrack . 119953 119973 295 + . stddev=0.0 +chr1 genetrack . 121016 121036 155 + . stddev=0.0 +chr1 genetrack . 121289 121309 89 + . stddev=0.0 +chr1 genetrack . 124318 124338 749 + . stddev=0.0 +chr1 genetrack . 124669 124689 203 + . stddev=0.0 +chr1 genetrack . 124845 124865 383 + . stddev=0.0 +chr1 genetrack . 125727 125747 3 + . stddev=0.0 +chr1 genetrack . 126073 126093 590 + . stddev=0.329075555241 +chr1 genetrack . 126369 126389 284 + . stddev=0.0592345205678 +chr1 genetrack . 126733 126753 952 + . stddev=0.484392920736 +chr1 genetrack . 129555 129575 536 + . stddev=0.0431531100978 +chr1 genetrack . 129680 129700 464 + . stddev=0.0 +chr1 genetrack . 130514 130534 243 + . stddev=0.0 +chr1 genetrack . 133139 133159 84 + . stddev=0.0 +chr1 genetrack . 134021 134041 572 + . stddev=0.0 +chr1 genetrack . 134170 134190 151 + . stddev=0.0 +chr1 genetrack . 134559 134579 87 + . stddev=0.0 +chr1 genetrack . 134868 134888 36 + . stddev=0.0 +chr1 genetrack . 136072 136092 380 + . stddev=0.0 +chr1 genetrack . 136366 136386 248 + . stddev=0.0 +chr1 genetrack . 138030 138050 2 + . stddev=0.0 +chr1 genetrack . 138051 138071 5 + . stddev=0.0 +chr1 genetrack . 138868 138888 698 + . stddev=0.0 +chr1 genetrack . 139213 139233 965 + . stddev=0.0 +chr1 genetrack . 140857 140877 23 + . stddev=0.0 +chr1 genetrack . 142139 142159 43 + . stddev=0.0 +chr1 genetrack . 142905 142925 599 + . stddev=0.0 +chr1 genetrack . 142950 142970 12 + . stddev=0.0 +chr1 genetrack . 143657 143677 328 + . stddev=0.0 +chr1 genetrack . 145253 145273 1394 + . stddev=0.0 +chr1 genetrack . 146517 146537 69 + . stddev=0.0 +chr1 genetrack . 147211 147231 130 + . stddev=0.0 +chr1 genetrack . 147227 147247 101 + . stddev=0.0 +chr1 genetrack . 147322 147342 15 + . stddev=0.0 +chr1 genetrack . 149343 149363 159 + . stddev=0.0 +chr1 genetrack . 150449 150469 436 + . stddev=0.0 +chr1 genetrack . 151369 151389 2 + . stddev=0.0 +chr1 genetrack . 151431 151451 38 + . stddev=0.0 +chr1 genetrack . 152678 152698 135 + . stddev=0.0 +chr1 genetrack . 153095 153115 490 + . stddev=0.0 +chr1 genetrack . 153928 153948 768 + . stddev=0.0 +chr1 genetrack . 155028 155048 522 + . stddev=0.0 +chr1 genetrack . 156097 156117 2 + . stddev=0.0 +chr1 genetrack . 156252 156272 133 + . stddev=0.0 +chr1 genetrack . 158038 158058 2 + . stddev=0.0 +chr1 genetrack . 159372 159392 605 + . stddev=0.0 +chr1 genetrack . 165827 165847 1109 + . stddev=0.0 +chr1 genetrack . 166238 166258 21 + . stddev=0.0 +chr1 genetrack . 167443 167463 597 + . stddev=0.0 +chr1 genetrack . 167652 167672 5 + . stddev=0.0 +chr1 genetrack . 169107 169127 1811 + . stddev=0.0 +chr1 genetrack . 169159 169179 91 + . stddev=0.0 +chr1 genetrack . 169338 169358 2 + . stddev=0.0 +chr1 genetrack . 170119 170139 284 + . stddev=0.0 +chr1 genetrack . 172223 172243 338 + . stddev=0.0 +chr1 genetrack . 173262 173282 11 + . stddev=0.0 +chr1 genetrack . 175899 175919 2 + . stddev=0.0 +chr1 genetrack . 176858 176878 46 + . stddev=0.0 +chr1 genetrack . 177627 177647 51 + . stddev=0.0 +chr1 genetrack . 178117 178137 686 + . stddev=0.0 +chr1 genetrack . 179472 179492 696 + . stddev=0.0 +chr1 genetrack . 179554 179574 31 + . stddev=0.176684695969 +chr1 genetrack . 180280 180300 38 + . stddev=0.0 +chr1 genetrack . 180652 180672 154 + . stddev=0.0 +chr1 genetrack . 183610 183630 4 + . stddev=0.433012701892 +chr1 genetrack . 185076 185096 1309 + . stddev=0.0 +chr1 genetrack . 187009 187029 139 + . stddev=0.0 +chr1 genetrack . 187155 187175 455 + . stddev=0.0 +chr1 genetrack . 188920 188940 7 + . stddev=1.97948663722 +chr1 genetrack . 189494 189514 70 + . stddev=0.0 +chr1 genetrack . 191408 191428 50 + . stddev=0.0 +chr1 genetrack . 192271 192291 453 + . stddev=0.0 +chr1 genetrack . 192754 192774 668 + . stddev=0.0 +chr1 genetrack . 195756 195776 348 + . stddev=0.0 +chr1 genetrack . 197489 197509 3 + . stddev=0.0 +chr1 genetrack . 198594 198614 170 + . stddev=0.0 +chr1 genetrack . 199141 199161 2 + . stddev=0.0 +chr1 genetrack . 199418 199438 5 + . stddev=0.0 +chr1 genetrack . 199649 199669 264 + . stddev=0.0 +chr1 genetrack . 200580 200600 1298 + . stddev=0.0 +chr1 genetrack . 201841 201861 15 + . stddev=0.0 +chr1 genetrack . 203193 203213 789 + . stddev=0.0 +chr1 genetrack . 203872 203892 1234 + . stddev=0.0 +chr1 genetrack . 204126 204146 261 + . stddev=0.0 +chr1 genetrack . 204214 204234 36 + . stddev=0.0 +chr1 genetrack . 206684 206704 8 + . stddev=0.0 +chr1 genetrack . 210175 210195 62 + . stddev=0.0 +chr1 genetrack . 219301 219321 37 + . stddev=0.0 +chr1 genetrack . 227346 227366 114 + . stddev=0.0 +chr1 genetrack . 228150 228170 5 + . stddev=0.0 +chr1 genetrack . 228633 228653 371 + . stddev=0.0 +chr1 genetrack . 229721 229741 84 + . stddev=0.0 +chr1 genetrack . 229741 229761 1380 + . stddev=0.0 +chr1 genetrack . 229862 229882 110 + . stddev=0.0 +chr1 genetrack . 230110 230130 42 + . stddev=3.55113280767 +chr1 genetrack . 230145 230165 8 + . stddev=3.08220700148 +chr1 genetrack . 230163 230183 23 + . stddev=1.62796915016 +chr1 genetrack . 50 70 39 - . stddev=1.95948442816 +chr1 genetrack . 139 159 993 - . stddev=4.91699987402 +chr1 genetrack . 176 196 14 - . stddev=0.0 +chr1 genetrack . 215 235 2611 - . stddev=5.10619852562 +chr1 genetrack . 261 281 1278 - . stddev=3.36870454509 +chr1 genetrack . 279 299 1328 - . stddev=2.15740829792 +chr1 genetrack . 323 343 486 - . stddev=0.0453142295176 +chr1 genetrack . 373 393 200 - . stddev=0.551339278485 +chr1 genetrack . 388 408 167 - . stddev=0.0 +chr1 genetrack . 410 430 8 - . stddev=0.0 +chr1 genetrack . 446 466 170 - . stddev=0.748724405435 +chr1 genetrack . 468 488 468 - . stddev=0.0 +chr1 genetrack . 634 654 151 - . stddev=0.0 +chr1 genetrack . 1457 1477 111 - . stddev=0.0 +chr1 genetrack . 1970 1990 629 - . stddev=0.0 +chr1 genetrack . 3148 3168 1420 - . stddev=0.0265278988758 +chr1 genetrack . 4892 4912 272 - . stddev=0.0 +chr1 genetrack . 5546 5566 27 - . stddev=0.0 +chr1 genetrack . 6254 6274 1076 - . stddev=1.26363262979 +chr1 genetrack . 6476 6496 567 - . stddev=0.0 +chr1 genetrack . 6702 6722 2 - . stddev=0.0 +chr1 genetrack . 7659 7679 243 - . stddev=0.0 +chr1 genetrack . 8596 8616 114 - . stddev=0.0 +chr1 genetrack . 8904 8924 80 - . stddev=0.0 +chr1 genetrack . 9119 9139 22 - . stddev=0.0 +chr1 genetrack . 10107 10127 1622 - . stddev=0.0 +chr1 genetrack . 12157 12177 40 - . stddev=0.0 +chr1 genetrack . 13415 13435 634 - . stddev=0.0 +chr1 genetrack . 16739 16759 3 - . stddev=0.0 +chr1 genetrack . 19145 19165 618 - . stddev=0.0 +chr1 genetrack . 19191 19211 736 - . stddev=0.0 +chr1 genetrack . 20550 20570 865 - . stddev=0.0 +chr1 genetrack . 22383 22403 141 - . stddev=0.0 +chr1 genetrack . 22569 22589 254 - . stddev=0.0 +chr1 genetrack . 23046 23066 213 - . stddev=0.0 +chr1 genetrack . 25345 25365 188 - . stddev=0.0 +chr1 genetrack . 27517 27537 1459 - . stddev=0.0 +chr1 genetrack . 29325 29345 1074 - . stddev=0.0 +chr1 genetrack . 30046 30066 17 - . stddev=0.0 +chr1 genetrack . 31693 31713 450 - . stddev=0.0 +chr1 genetrack . 31876 31896 1344 - . stddev=0.0 +chr1 genetrack . 32497 32517 2 - . stddev=0.0 +chr1 genetrack . 37166 37186 1000 - . stddev=0.0 +chr1 genetrack . 38768 38788 1064 - . stddev=0.0 +chr1 genetrack . 38799 38819 9 - . stddev=0.0 +chr1 genetrack . 39000 39020 3 - . stddev=0.0 +chr1 genetrack . 39052 39072 82 - . stddev=0.0 +chr1 genetrack . 39258 39278 261 - . stddev=0.0 +chr1 genetrack . 39293 39313 2 - . stddev=0.0 +chr1 genetrack . 41867 41887 7 - . stddev=0.0 +chr1 genetrack . 45565 45585 246 - . stddev=1.46097357384 +chr1 genetrack . 45579 45599 78 - . stddev=0.0 +chr1 genetrack . 45643 45663 295 - . stddev=1.27157056343 +chr1 genetrack . 46616 46636 741 - . stddev=0.0 +chr1 genetrack . 49660 49680 6 - . stddev=0.0 +chr1 genetrack . 50091 50111 156 - . stddev=0.0 +chr1 genetrack . 51978 51998 633 - . stddev=0.0 +chr1 genetrack . 52308 52328 549 - . stddev=0.0 +chr1 genetrack . 53045 53065 31 - . stddev=0.0 +chr1 genetrack . 55581 55601 831 - . stddev=0.124372757427 +chr1 genetrack . 55616 55636 984 - . stddev=0.0 +chr1 genetrack . 56542 56562 606 - . stddev=0.0 +chr1 genetrack . 56664 56684 67 - . stddev=0.0 +chr1 genetrack . 56995 57015 1393 - . stddev=0.0 +chr1 genetrack . 57121 57141 4 - . stddev=0.0 +chr1 genetrack . 57212 57232 667 - . stddev=0.0 +chr1 genetrack . 57543 57563 2 - . stddev=0.0 +chr1 genetrack . 59157 59177 168 - . stddev=0.0 +chr1 genetrack . 59246 59266 397 - . stddev=0.0 +chr1 genetrack . 61877 61897 607 - . stddev=0.0 +chr1 genetrack . 65148 65168 43 - . stddev=0.0 +chr1 genetrack . 65687 65707 596 - . stddev=0.0 +chr1 genetrack . 66306 66326 2 - . stddev=0.0 +chr1 genetrack . 68423 68443 139 - . stddev=0.0 +chr1 genetrack . 70336 70356 652 - . stddev=0.0 +chr1 genetrack . 70788 70808 998 - . stddev=0.0 +chr1 genetrack . 72771 72791 406 - . stddev=0.0 +chr1 genetrack . 72810 72830 212 - . stddev=0.0 +chr1 genetrack . 74763 74783 430 - . stddev=0.0 +chr1 genetrack . 75897 75917 10 - . stddev=0.0 +chr1 genetrack . 77515 77535 797 - . stddev=0.0 +chr1 genetrack . 77530 77550 513 - . stddev=0.0 +chr1 genetrack . 78813 78833 113 - . stddev=0.0 +chr1 genetrack . 80958 80978 137 - . stddev=0.0 +chr1 genetrack . 81037 81057 4 - . stddev=0.0 +chr1 genetrack . 81972 81992 49 - . stddev=0.0 +chr1 genetrack . 85759 85779 77 - . stddev=0.0 +chr1 genetrack . 86166 86186 969 - . stddev=0.0 +chr1 genetrack . 86280 86300 14 - . stddev=0.0 +chr1 genetrack . 86991 87011 65 - . stddev=0.0 +chr1 genetrack . 87049 87069 422 - . stddev=2.00428551887 +chr1 genetrack . 87101 87121 1134 - . stddev=0.0296825973187 +chr1 genetrack . 87158 87178 2039 - . stddev=2.64919364477 +chr1 genetrack . 87198 87218 2207 - . stddev=4.88766842837 +chr1 genetrack . 87234 87254 637 - . stddev=0.0 +chr1 genetrack . 87262 87282 505 - . stddev=0.0 +chr1 genetrack . 87289 87309 1270 - . stddev=0.0 +chr1 genetrack . 87327 87347 729 - . stddev=0.517094014402 +chr1 genetrack . 87468 87488 304 - . stddev=0.0 +chr1 genetrack . 88213 88233 301 - . stddev=0.0 +chr1 genetrack . 88376 88396 56 - . stddev=0.0 +chr1 genetrack . 89175 89195 23 - . stddev=0.0 +chr1 genetrack . 91926 91946 10 - . stddev=0.0 +chr1 genetrack . 92411 92431 136 - . stddev=0.0 +chr1 genetrack . 92541 92561 602 - . stddev=0.0 +chr1 genetrack . 92571 92591 90 - . stddev=0.0 +chr1 genetrack . 92639 92659 2137 - . stddev=3.28540359906 +chr1 genetrack . 92664 92684 187 - . stddev=0.390044546071 +chr1 genetrack . 94913 94933 1437 - . stddev=0.0 +chr1 genetrack . 95971 95991 684 - . stddev=0.0 +chr1 genetrack . 96278 96298 166 - . stddev=0.0 +chr1 genetrack . 96315 96335 2 - . stddev=0.0 +chr1 genetrack . 96566 96586 6 - . stddev=0.0 +chr1 genetrack . 96911 96931 10 - . stddev=0.0 +chr1 genetrack . 98555 98575 88 - . stddev=0.0 +chr1 genetrack . 101301 101321 48 - . stddev=0.0 +chr1 genetrack . 101367 101387 1388 - . stddev=0.0268317355181 +chr1 genetrack . 102072 102092 14 - . stddev=0.0 +chr1 genetrack . 102903 102923 846 - . stddev=0.0 +chr1 genetrack . 104110 104130 117 - . stddev=0.0 +chr1 genetrack . 105663 105683 417 - . stddev=0.0 +chr1 genetrack . 105814 105834 529 - . stddev=0.0 +chr1 genetrack . 105846 105866 177 - . stddev=0.0 +chr1 genetrack . 105889 105909 84 - . stddev=0.0 +chr1 genetrack . 106041 106061 14 - . stddev=0.0 +chr1 genetrack . 106340 106360 421 - . stddev=0.0 +chr1 genetrack . 108072 108092 72 - . stddev=0.0 +chr1 genetrack . 108263 108283 145 - . stddev=0.0 +chr1 genetrack . 108579 108599 367 - . stddev=0.0 +chr1 genetrack . 111947 111967 585 - . stddev=1.43661357803 +chr1 genetrack . 113762 113782 296 - . stddev=0.0 +chr1 genetrack . 114306 114326 2 - . stddev=0.0 +chr1 genetrack . 116148 116168 248 - . stddev=0.0 +chr1 genetrack . 116619 116639 699 - . stddev=0.0 +chr1 genetrack . 117522 117542 1573 - . stddev=0.0 +chr1 genetrack . 117845 117865 16 - . stddev=0.0 +chr1 genetrack . 118841 118861 7 - . stddev=0.0 +chr1 genetrack . 119430 119450 1093 - . stddev=0.0 +chr1 genetrack . 119596 119616 842 - . stddev=0.0 +chr1 genetrack . 119657 119677 499 - . stddev=0.0 +chr1 genetrack . 119669 119689 665 - . stddev=0.0 +chr1 genetrack . 119866 119886 846 - . stddev=0.0 +chr1 genetrack . 119880 119900 1136 - . stddev=0.0 +chr1 genetrack . 120788 120808 105 - . stddev=0.0 +chr1 genetrack . 122624 122644 201 - . stddev=0.0 +chr1 genetrack . 122777 122797 20 - . stddev=0.0 +chr1 genetrack . 123718 123738 751 - . stddev=0.0 +chr1 genetrack . 124275 124295 12 - . stddev=0.0 +chr1 genetrack . 125840 125860 273 - . stddev=0.0 +chr1 genetrack . 127027 127047 590 - . stddev=0.0 +chr1 genetrack . 130869 130889 718 - . stddev=0.0 +chr1 genetrack . 133644 133664 122 - . stddev=0.0 +chr1 genetrack . 134270 134290 508 - . stddev=0.0 +chr1 genetrack . 135051 135071 63 - . stddev=0.0 +chr1 genetrack . 136352 136372 117 - . stddev=0.0 +chr1 genetrack . 137428 137448 1200 - . stddev=0.028855482822 +chr1 genetrack . 137816 137836 695 - . stddev=0.0 +chr1 genetrack . 138864 138884 13 - . stddev=0.0 +chr1 genetrack . 139228 139248 214 - . stddev=0.0 +chr1 genetrack . 139627 139647 531 - . stddev=0.0 +chr1 genetrack . 140133 140153 441 - . stddev=0.0 +chr1 genetrack . 140770 140790 556 - . stddev=0.0 +chr1 genetrack . 141182 141202 14 - . stddev=0.0 +chr1 genetrack . 143551 143571 3 - . stddev=0.0 +chr1 genetrack . 144669 144689 1192 - . stddev=0.0959718343646 +chr1 genetrack . 145383 145403 326 - . stddev=0.0 +chr1 genetrack . 147573 147593 255 - . stddev=0.0 +chr1 genetrack . 148690 148710 2 - . stddev=0.0 +chr1 genetrack . 149704 149724 74 - . stddev=0.0 +chr1 genetrack . 150358 150378 153 - . stddev=0.0 +chr1 genetrack . 151341 151361 593 - . stddev=0.0 +chr1 genetrack . 152984 153004 106 - . stddev=0.0 +chr1 genetrack . 153812 153832 168 - . stddev=0.0 +chr1 genetrack . 154862 154882 14 - . stddev=0.0 +chr1 genetrack . 155111 155131 1051 - . stddev=0.0 +chr1 genetrack . 155456 155476 23 - . stddev=0.0 +chr1 genetrack . 155897 155917 10 - . stddev=0.0 +chr1 genetrack . 157559 157579 337 - . stddev=0.0 +chr1 genetrack . 166467 166487 582 - . stddev=0.0 +chr1 genetrack . 166631 166651 173 - . stddev=0.0 +chr1 genetrack . 169064 169084 76 - . stddev=0.0 +chr1 genetrack . 169500 169520 814 - . stddev=0.0 +chr1 genetrack . 170129 170149 373 - . stddev=0.0 +chr1 genetrack . 170282 170302 63 - . stddev=0.0 +chr1 genetrack . 171063 171083 212 - . stddev=0.0 +chr1 genetrack . 173270 173290 535 - . stddev=0.0863866916508 +chr1 genetrack . 175188 175208 117 - . stddev=0.0 +chr1 genetrack . 175474 175494 1119 - . stddev=0.0 +chr1 genetrack . 176004 176024 1473 - . stddev=0.0 +chr1 genetrack . 177140 177160 93 - . stddev=0.0 +chr1 genetrack . 177386 177406 289 - . stddev=0.0 +chr1 genetrack . 178846 178866 601 - . stddev=0.0 +chr1 genetrack . 178971 178991 723 - . stddev=0.0 +chr1 genetrack . 179116 179136 71 - . stddev=0.0 +chr1 genetrack . 180272 180292 25 - . stddev=0.0 +chr1 genetrack . 180362 180382 59 - . stddev=0.0 +chr1 genetrack . 180995 181015 299 - . stddev=0.0 +chr1 genetrack . 182588 182608 465 - . stddev=0.0 +chr1 genetrack . 182790 182810 355 - . stddev=0.0 +chr1 genetrack . 185122 185142 62 - . stddev=0.0 +chr1 genetrack . 185673 185693 190 - . stddev=0.0 +chr1 genetrack . 187422 187442 20 - . stddev=0.0 +chr1 genetrack . 187976 187996 728 - . stddev=0.0 +chr1 genetrack . 196499 196519 224 - . stddev=0.0 +chr1 genetrack . 197060 197080 224 - . stddev=0.0 +chr1 genetrack . 197151 197171 1464 - . stddev=0.0 +chr1 genetrack . 197342 197362 204 - . stddev=0.0 +chr1 genetrack . 197562 197582 2 - . stddev=0.0 +chr1 genetrack . 198423 198443 598 - . stddev=0.0 +chr1 genetrack . 198953 198973 3 - . stddev=0.0 +chr1 genetrack . 199388 199408 805 - . stddev=0.0 +chr1 genetrack . 199935 199955 31 - . stddev=0.0 +chr1 genetrack . 201308 201328 1287 - . stddev=0.0 +chr1 genetrack . 201651 201671 892 - . stddev=0.0 +chr1 genetrack . 202977 202997 163 - . stddev=0.0 +chr1 genetrack . 203452 203472 76 - . stddev=0.0 +chr1 genetrack . 203835 203855 242 - . stddev=0.0 +chr1 genetrack . 206245 206265 22 - . stddev=0.0 +chr1 genetrack . 207675 207695 313 - . stddev=0.0 +chr1 genetrack . 208559 208579 121 - . stddev=0.89393833276 +chr1 genetrack . 209205 209225 176 - . stddev=0.0 +chr1 genetrack . 220863 220883 2 - . stddev=0.0 +chr1 genetrack . 223035 223055 62 - . stddev=0.0 +chr1 genetrack . 225156 225176 2 - . stddev=0.0 +chr1 genetrack . 226777 226797 444 - . stddev=0.0 +chr1 genetrack . 227608 227628 1311 - . stddev=0.0 +chr1 genetrack . 228405 228425 1447 - . stddev=2.78971080368 +chr1 genetrack . 228691 228711 255 - . stddev=0.0 +chr1 genetrack . 229031 229051 6 - . stddev=0.0 +chr1 genetrack . 229583 229603 62 - . stddev=0.0 +chr1 genetrack . 229665 229685 131 - . stddev=0.0 +chr1 genetrack . 229757 229777 3151 - . stddev=2.79078905805 +chr1 genetrack . 229784 229804 615 - . stddev=0.0 +chr1 genetrack . 229965 229985 13 - . stddev=0.0 +chr1 genetrack . 230120 230140 2 - . stddev=0.0 +chr1 genetrack . 230132 230152 2 - . stddev=0.0 +chr1 genetrack . 230150 230170 7 - . stddev=0.699854212224 +chr1 genetrack . 230173 230193 33 - . stddev=0.477212598425
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/largest_d_output2.tabular Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,65 @@ +chrom start end value strand chrom start end value strand midpoint c-w reads sum c-w distance (bp) +chr1 87147 87167 3492.0 + chr1 87198 87218 2207.0 - 87182 5699.0 51 +chr1 87 107 3211.0 + chr1 139 159 993.0 - 123 4204.0 52 +chr1 48 68 2842.0 + chr1 50 70 39.0 - 59 2881.0 2 +chr1 255 275 2810.0 + chr1 215 235 2611.0 - 245 5421.0 -40 +chr1 117 137 2163.0 + chr1 176 196 14.0 - 156 2177.0 59 +chr1 86954 86974 1948.0 + chr1 87049 87069 422.0 - 87011 2370.0 95 +chr1 169107 169127 1811.0 + chr1 169064 169084 76.0 - 169095 1887.0 -43 +chr1 87171 87191 1436.0 + chr1 87158 87178 2039.0 - 87174 3475.0 -13 +chr1 201 221 1411.0 + chr1 279 299 1328.0 - 250 2739.0 78 +chr1 229741 229761 1380.0 + chr1 229757 229777 3151.0 - 229759 4531.0 16 +chr1 185076 185096 1309.0 + chr1 185122 185142 62.0 - 185109 1371.0 46 +chr1 39081 39101 1268.0 + chr1 39052 39072 82.0 - 39076 1350.0 -29 +chr1 92411 92431 1252.0 + chr1 92411 92431 136.0 - 92421 1388.0 0 +chr1 203872 203892 1234.0 + chr1 203835 203855 242.0 - 203863 1476.0 -37 +chr1 70776 70796 1148.0 + chr1 70788 70808 998.0 - 70792 2146.0 12 +chr1 231 251 1146.0 + chr1 261 281 1278.0 - 256 2424.0 30 +chr1 87098 87118 1125.0 + chr1 87101 87121 1134.0 - 87109 2259.0 3 +chr1 6163 6183 1049.0 + chr1 6254 6274 1076.0 - 6218 2125.0 91 +chr1 25246 25266 995.0 + chr1 25345 25365 188.0 - 25305 1183.0 99 +chr1 101411 101431 973.0 + chr1 101367 101387 1388.0 - 101399 2361.0 -44 +chr1 139213 139233 965.0 + chr1 139228 139248 214.0 - 139230 1179.0 15 +chr1 87019 87039 769.0 + chr1 86991 87011 65.0 - 87015 834.0 -28 +chr1 124318 124338 749.0 + chr1 124275 124295 12.0 - 124306 761.0 -43 +chr1 348 368 699.0 + chr1 323 343 486.0 - 345 1185.0 -25 +chr1 92543 92563 699.0 + chr1 92639 92659 2137.0 - 92601 2836.0 96 +chr1 138868 138888 698.0 + chr1 138864 138884 13.0 - 138876 711.0 -4 +chr1 307 327 685.0 + chr1 373 393 200.0 - 350 885.0 66 +chr1 6413 6433 682.0 + chr1 6476 6496 567.0 - 6454 1249.0 63 +chr1 72781 72801 657.0 + chr1 72771 72791 406.0 - 72786 1063.0 -10 +chr1 22571 22591 609.0 + chr1 22569 22589 254.0 - 22580 863.0 -2 +chr1 65152 65172 575.0 + chr1 65148 65168 43.0 - 65160 618.0 -4 +chr1 106034 106054 558.0 + chr1 106041 106061 14.0 - 106047 572.0 7 +chr1 155028 155048 522.0 + chr1 155111 155131 1051.0 - 155079 1573.0 83 +chr1 32449 32469 476.0 + chr1 32497 32517 2.0 - 32483 478.0 48 +chr1 6706 6726 431.0 + chr1 6702 6722 2.0 - 6714 433.0 -4 +chr1 113782 113802 420.0 + chr1 113762 113782 296.0 - 113782 716.0 -20 +chr1 228633 228653 371.0 + chr1 228691 228711 255.0 - 228672 626.0 58 +chr1 438 458 334.0 + chr1 468 488 468.0 - 463 802.0 30 +chr1 170119 170139 284.0 + chr1 170129 170149 373.0 - 170134 657.0 10 +chr1 92631 92651 260.0 + chr1 92664 92684 187.0 - 92657 447.0 33 +chr1 136366 136386 248.0 + chr1 136352 136372 117.0 - 136369 365.0 -14 +chr1 108624 108644 206.0 + chr1 108579 108599 367.0 - 108611 573.0 -45 +chr1 45678 45698 198.0 + chr1 45643 45663 295.0 - 45670 493.0 -35 +chr1 368 388 192.0 + chr1 446 466 170.0 - 417 362.0 78 +chr1 682 702 168.0 + chr1 634 654 151.0 - 668 319.0 -48 +chr1 59190 59210 168.0 + chr1 59246 59266 397.0 - 59228 565.0 56 +chr1 134170 134190 151.0 + chr1 134270 134290 508.0 - 134230 659.0 100 +chr1 55495 55515 125.0 + chr1 55581 55601 831.0 - 55548 956.0 86 +chr1 39197 39217 101.0 + chr1 39258 39278 261.0 - 39237 362.0 61 +chr1 229721 229741 84.0 + chr1 229784 229804 615.0 - 229762 699.0 63 +chr1 116660 116680 74.0 + chr1 116619 116639 699.0 - 116649 773.0 -41 +chr1 19216 19236 42.0 + chr1 19191 19211 736.0 - 19213 778.0 -25 +chr1 230110 230130 42.0 + chr1 230173 230193 33.0 - 230151 75.0 63 +chr1 31627 31647 40.0 + chr1 31693 31713 450.0 - 31670 490.0 66 +chr1 180280 180300 38.0 + chr1 180362 180382 59.0 - 180331 97.0 82 +chr1 98528 98548 34.0 + chr1 98555 98575 88.0 - 98551 122.0 27 +chr1 230163 230183 23.0 + chr1 230150 230170 7.0 - 230166 30.0 -13 +chr1 173262 173282 11.0 + chr1 173270 173290 535.0 - 173276 546.0 8 +chr1 230145 230165 8.0 + chr1 230120 230140 2.0 - 230142 10.0 -25 +chr1 95920 95940 5.0 + chr1 95971 95991 684.0 - 95955 689.0 51 +chr1 199418 199438 5.0 + chr1 199388 199408 805.0 - 199413 810.0 -30 +chr1 197489 197509 3.0 + chr1 197562 197582 2.0 - 197535 5.0 73 +chr1 96908 96928 2.0 + chr1 96911 96931 10.0 - 96919 12.0 3 +chr1 151369 151389 2.0 + chr1 151341 151361 593.0 - 151365 595.0 -28
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/largest_o_output2.tabular Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,371 @@ +chrom strand start end value +chr1 + 100364 100384 2695.0 +chr1 + 30 50 2140.0 +chr1 + 5379 5399 1572.0 +chr1 + 52440 52460 1562.0 +chr1 + 73234 73254 1492.0 +chr1 + 31096 31116 1481.0 +chr1 + 145253 145273 1394.0 +chr1 + 10641 10661 1359.0 +chr1 + 200580 200600 1298.0 +chr1 + 64772 64792 1292.0 +chr1 + 86886 86906 1253.0 +chr1 + 103207 103227 1229.0 +chr1 + 43835 43855 1173.0 +chr1 + 29570 29590 1130.0 +chr1 + 83774 83794 1125.0 +chr1 + 165827 165847 1109.0 +chr1 + 92775 92795 1105.0 +chr1 + 4748 4768 1077.0 +chr1 + 126733 126753 952.0 +chr1 + 71041 71061 881.0 +chr1 + 35773 35793 866.0 +chr1 + 53097 53117 835.0 +chr1 + 71556 71576 835.0 +chr1 + 30964 30984 829.0 +chr1 + 31019 31039 810.0 +chr1 + 55349 55369 794.0 +chr1 + 203193 203213 789.0 +chr1 + 39794 39814 780.0 +chr1 + 153928 153948 768.0 +chr1 + 179472 179492 696.0 +chr1 + 178117 178137 686.0 +chr1 + 1298 1318 684.0 +chr1 + 87085 87105 676.0 +chr1 + 192754 192774 668.0 +chr1 + 89611 89631 640.0 +chr1 + 20205 20225 634.0 +chr1 + 118428 118448 633.0 +chr1 + 110736 110756 621.0 +chr1 + 48642 48662 610.0 +chr1 + 159372 159392 605.0 +chr1 + 6453 6473 601.0 +chr1 + 112137 112157 601.0 +chr1 + 142905 142925 599.0 +chr1 + 167443 167463 597.0 +chr1 + 126073 126093 590.0 +chr1 + 6233 6253 589.0 +chr1 + 43657 43677 586.0 +chr1 + 134021 134041 572.0 +chr1 + 29864 29884 570.0 +chr1 + 70953 70973 555.0 +chr1 + 87002 87022 550.0 +chr1 + 129555 129575 536.0 +chr1 + 119754 119774 515.0 +chr1 + 43523 43543 505.0 +chr1 + 97898 97918 501.0 +chr1 + 40830 40850 491.0 +chr1 + 153095 153115 490.0 +chr1 + 7303 7323 484.0 +chr1 + 115866 115886 480.0 +chr1 + 129680 129700 464.0 +chr1 + 187155 187175 455.0 +chr1 + 192271 192291 453.0 +chr1 + 160 180 451.0 +chr1 + 150449 150469 436.0 +chr1 + 9367 9387 425.0 +chr1 + 93793 93813 415.0 +chr1 + 87572 87592 407.0 +chr1 + 124845 124865 383.0 +chr1 + 4053 4073 381.0 +chr1 + 136072 136092 380.0 +chr1 + 39942 39962 375.0 +chr1 + 61977 61997 368.0 +chr1 + 2976 2996 356.0 +chr1 + 27978 27998 354.0 +chr1 + 195756 195776 348.0 +chr1 + 172223 172243 338.0 +chr1 + 143657 143677 328.0 +chr1 + 45409 45429 307.0 +chr1 + 45248 45268 305.0 +chr1 + 72671 72691 304.0 +chr1 + 68564 68584 303.0 +chr1 + 119953 119973 295.0 +chr1 + 48319 48339 290.0 +chr1 + 48772 48792 284.0 +chr1 + 126369 126389 284.0 +chr1 + 116432 116452 267.0 +chr1 + 199649 199669 264.0 +chr1 + 204126 204146 261.0 +chr1 + 130514 130534 243.0 +chr1 + 55692 55712 228.0 +chr1 + 117198 117218 228.0 +chr1 + 42843 42863 218.0 +chr1 + 59583 59603 204.0 +chr1 + 124669 124689 203.0 +chr1 + 2613 2633 202.0 +chr1 + 40264 40284 199.0 +chr1 + 21406 21426 177.0 +chr1 + 20391 20411 173.0 +chr1 + 20626 20646 171.0 +chr1 + 198594 198614 170.0 +chr1 + 149343 149363 159.0 +chr1 + 121016 121036 155.0 +chr1 + 180652 180672 154.0 +chr1 + 5794 5814 148.0 +chr1 + 187009 187029 139.0 +chr1 + 119736 119756 135.0 +chr1 + 152678 152698 135.0 +chr1 + 47015 47035 133.0 +chr1 + 156252 156272 133.0 +chr1 + 41008 41028 132.0 +chr1 + 147211 147231 130.0 +chr1 + 112900 112920 125.0 +chr1 + 91379 91399 120.0 +chr1 + 227346 227366 114.0 +chr1 + 77731 77751 113.0 +chr1 + 229862 229882 110.0 +chr1 + 512 532 101.0 +chr1 + 147227 147247 101.0 +chr1 + 44687 44707 100.0 +chr1 + 467 487 98.0 +chr1 + 601 621 96.0 +chr1 + 4445 4465 94.0 +chr1 + 110540 110560 91.0 +chr1 + 169159 169179 91.0 +chr1 + 103108 103128 90.0 +chr1 + 121289 121309 89.0 +chr1 + 134559 134579 87.0 +chr1 + 90412 90432 86.0 +chr1 + 133139 133159 84.0 +chr1 + 90040 90060 82.0 +chr1 + 86865 86885 81.0 +chr1 + 59248 59268 80.0 +chr1 + 42925 42945 77.0 +chr1 + 189494 189514 70.0 +chr1 + 146517 146537 69.0 +chr1 + 32145 32165 66.0 +chr1 + 68018 68038 62.0 +chr1 + 210175 210195 62.0 +chr1 + 48431 48451 57.0 +chr1 + 177627 177647 51.0 +chr1 + 97967 97987 50.0 +chr1 + 191408 191428 50.0 +chr1 + 33829 33849 48.0 +chr1 + 76365 76385 47.0 +chr1 + 105499 105519 46.0 +chr1 + 176858 176878 46.0 +chr1 + 92982 93002 44.0 +chr1 + 142139 142159 43.0 +chr1 + 110130 110150 42.0 +chr1 + 151431 151451 38.0 +chr1 + 219301 219321 37.0 +chr1 + 102337 102357 36.0 +chr1 + 134868 134888 36.0 +chr1 + 204214 204234 36.0 +chr1 + 76501 76521 33.0 +chr1 + 179554 179574 31.0 +chr1 + 113226 113246 28.0 +chr1 + 6255 6275 26.0 +chr1 + 5750 5770 25.0 +chr1 + 105942 105962 25.0 +chr1 + 140857 140877 23.0 +chr1 + 166238 166258 21.0 +chr1 + 111317 111337 17.0 +chr1 + 16501 16521 15.0 +chr1 + 22268 22288 15.0 +chr1 + 147322 147342 15.0 +chr1 + 201841 201861 15.0 +chr1 + 7753 7773 14.0 +chr1 + 12305 12325 13.0 +chr1 + 2293 2313 12.0 +chr1 + 16173 16193 12.0 +chr1 + 142950 142970 12.0 +chr1 + 91215 91235 11.0 +chr1 + 39591 39611 10.0 +chr1 + 43147 43167 9.0 +chr1 + 119155 119175 9.0 +chr1 + 20117 20137 8.0 +chr1 + 110602 110622 8.0 +chr1 + 206684 206704 8.0 +chr1 + 188920 188940 7.0 +chr1 + 81481 81501 5.0 +chr1 + 138051 138071 5.0 +chr1 + 167652 167672 5.0 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- 87468 87488 304.0 +chr1 - 88213 88233 301.0 +chr1 - 88376 88396 56.0 +chr1 - 89175 89195 23.0 +chr1 - 91926 91946 10.0 +chr1 - 92541 92561 602.0 +chr1 - 92571 92591 90.0 +chr1 - 94913 94933 1437.0 +chr1 - 96278 96298 166.0 +chr1 - 96315 96335 2.0 +chr1 - 96566 96586 6.0 +chr1 - 101301 101321 48.0 +chr1 - 102072 102092 14.0 +chr1 - 102903 102923 846.0 +chr1 - 104110 104130 117.0 +chr1 - 105663 105683 417.0 +chr1 - 105814 105834 529.0 +chr1 - 105846 105866 177.0 +chr1 - 105889 105909 84.0 +chr1 - 106340 106360 421.0 +chr1 - 108072 108092 72.0 +chr1 - 108263 108283 145.0 +chr1 - 111947 111967 585.0 +chr1 - 114306 114326 2.0 +chr1 - 116148 116168 248.0 +chr1 - 117522 117542 1573.0 +chr1 - 117845 117865 16.0 +chr1 - 118841 118861 7.0 +chr1 - 119430 119450 1093.0 +chr1 - 119596 119616 842.0 +chr1 - 119657 119677 499.0 +chr1 - 119669 119689 665.0 +chr1 - 119866 119886 846.0 +chr1 - 119880 119900 1136.0 +chr1 - 120788 120808 105.0 +chr1 - 122624 122644 201.0 +chr1 - 122777 122797 20.0 +chr1 - 123718 123738 751.0 +chr1 - 125840 125860 273.0 +chr1 - 127027 127047 590.0 +chr1 - 130869 130889 718.0 +chr1 - 133644 133664 122.0 +chr1 - 135051 135071 63.0 +chr1 - 137428 137448 1200.0 +chr1 - 137816 137836 695.0 +chr1 - 139627 139647 531.0 +chr1 - 140133 140153 441.0 +chr1 - 140770 140790 556.0 +chr1 - 141182 141202 14.0 +chr1 - 143551 143571 3.0 +chr1 - 144669 144689 1192.0 +chr1 - 145383 145403 326.0 +chr1 - 147573 147593 255.0 +chr1 - 148690 148710 2.0 +chr1 - 149704 149724 74.0 +chr1 - 150358 150378 153.0 +chr1 - 152984 153004 106.0 +chr1 - 153812 153832 168.0 +chr1 - 154862 154882 14.0 +chr1 - 155456 155476 23.0 +chr1 - 155897 155917 10.0 +chr1 - 157559 157579 337.0 +chr1 - 166467 166487 582.0 +chr1 - 166631 166651 173.0 +chr1 - 169500 169520 814.0 +chr1 - 170282 170302 63.0 +chr1 - 171063 171083 212.0 +chr1 - 175188 175208 117.0 +chr1 - 175474 175494 1119.0 +chr1 - 176004 176024 1473.0 +chr1 - 177140 177160 93.0 +chr1 - 177386 177406 289.0 +chr1 - 178846 178866 601.0 +chr1 - 178971 178991 723.0 +chr1 - 179116 179136 71.0 +chr1 - 180272 180292 25.0 +chr1 - 180995 181015 299.0 +chr1 - 182588 182608 465.0 +chr1 - 182790 182810 355.0 +chr1 - 185673 185693 190.0 +chr1 - 187422 187442 20.0 +chr1 - 187976 187996 728.0 +chr1 - 196499 196519 224.0 +chr1 - 197060 197080 224.0 +chr1 - 197151 197171 1464.0 +chr1 - 197342 197362 204.0 +chr1 - 198423 198443 598.0 +chr1 - 198953 198973 3.0 +chr1 - 199935 199955 31.0 +chr1 - 201308 201328 1287.0 +chr1 - 201651 201671 892.0 +chr1 - 202977 202997 163.0 +chr1 - 203452 203472 76.0 +chr1 - 206245 206265 22.0 +chr1 - 207675 207695 313.0 +chr1 - 208559 208579 121.0 +chr1 - 209205 209225 176.0 +chr1 - 220863 220883 2.0 +chr1 - 223035 223055 62.0 +chr1 - 225156 225176 2.0 +chr1 - 226777 226797 444.0 +chr1 - 227608 227628 1311.0 +chr1 - 228405 228425 1447.0 +chr1 - 229031 229051 6.0 +chr1 - 229583 229603 62.0 +chr1 - 229665 229685 131.0 +chr1 - 229965 229985 13.0 +chr1 - 230132 230152 2.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/largest_s_output1.gff Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,55 @@ +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 176 177 4774.0 . . cw_distance=98 +chr1 cwpair . 178 179 465.0 . . cw_distance=16 +chr1 cwpair . 241 242 2689.0 . . cw_distance=60 +chr1 cwpair . 277 278 4138.0 . . cw_distance=24 +chr1 cwpair . 287 288 1632.0 . . cw_distance=92 +chr1 cwpair . 357 358 852.0 . . cw_distance=81 +chr1 cwpair . 370 371 899.0 . . cw_distance=25 +chr1 cwpair . 417 418 362.0 . . cw_distance=78 +chr1 cwpair . 463 464 802.0 . . cw_distance=30 +chr1 cwpair . 627 628 247.0 . . cw_distance=33 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 72786 72787 1063.0 . . cw_distance=-10 +chr1 cwpair . 87006 87007 615.0 . . cw_distance=-11 +chr1 cwpair . 87011 87012 2370.0 . . cw_distance=95 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 +chr1 cwpair . 87174 87175 3475.0 . . cw_distance=-13 +chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 +chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 +chr1 cwpair . 230142 230143 10.0 . . cw_distance=-25 +chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 +chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/largest_s_output2.gff Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,64 @@ +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59 +chr1 cwpair . 245 246 5421.0 . . cw_distance=-40 +chr1 cwpair . 250 251 2739.0 . . cw_distance=78 +chr1 cwpair . 256 257 2424.0 . . cw_distance=30 +chr1 cwpair . 345 346 1185.0 . . cw_distance=-25 +chr1 cwpair . 350 351 885.0 . . cw_distance=66 +chr1 cwpair . 417 418 362.0 . . cw_distance=78 +chr1 cwpair . 463 464 802.0 . . cw_distance=30 +chr1 cwpair . 668 669 319.0 . . cw_distance=-48 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 72786 72787 1063.0 . . cw_distance=-10 +chr1 cwpair . 87011 87012 2370.0 . . cw_distance=95 +chr1 cwpair . 87015 87016 834.0 . . cw_distance=-28 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 +chr1 cwpair . 87174 87175 3475.0 . . cw_distance=-13 +chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 +chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 +chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 +chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 +chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 +chr1 cwpair . 230142 230143 10.0 . . cw_distance=-25 +chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 +chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mode_d_output2.tabular Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,68 @@ +chrom start end value strand chrom start end value strand midpoint c-w reads sum c-w distance (bp) +chr1 87147 87167 3492.0 + chr1 87198 87218 2207.0 - 87182 5699.0 51 +chr1 87 107 3211.0 + chr1 139 159 993.0 - 123 4204.0 52 +chr1 48 68 2842.0 + chr1 50 70 39.0 - 59 2881.0 2 +chr1 255 275 2810.0 + chr1 323 343 486.0 - 299 3296.0 68 +chr1 117 137 2163.0 + chr1 176 196 14.0 - 156 2177.0 59 +chr1 86954 86974 1948.0 + chr1 86991 87011 65.0 - 86982 2013.0 37 +chr1 169107 169127 1811.0 + chr1 169064 169084 76.0 - 169095 1887.0 -43 +chr1 87171 87191 1436.0 + chr1 87234 87254 637.0 - 87212 2073.0 63 +chr1 201 221 1411.0 + chr1 261 281 1278.0 - 241 2689.0 60 +chr1 229741 229761 1380.0 + chr1 229784 229804 615.0 - 229772 1995.0 43 +chr1 185076 185096 1309.0 + chr1 185122 185142 62.0 - 185109 1371.0 46 +chr1 39081 39101 1268.0 + chr1 39052 39072 82.0 - 39076 1350.0 -29 +chr1 92411 92431 1252.0 + chr1 92411 92431 136.0 - 92421 1388.0 0 +chr1 203872 203892 1234.0 + chr1 203835 203855 242.0 - 203863 1476.0 -37 +chr1 70776 70796 1148.0 + chr1 70788 70808 998.0 - 70792 2146.0 12 +chr1 231 251 1146.0 + chr1 279 299 1328.0 - 265 2474.0 48 +chr1 87098 87118 1125.0 + chr1 87158 87178 2039.0 - 87138 3164.0 60 +chr1 6163 6183 1049.0 + chr1 6254 6274 1076.0 - 6218 2125.0 91 +chr1 25246 25266 995.0 + chr1 25345 25365 188.0 - 25305 1183.0 99 +chr1 101411 101431 973.0 + chr1 101367 101387 1388.0 - 101399 2361.0 -44 +chr1 139213 139233 965.0 + chr1 139228 139248 214.0 - 139230 1179.0 15 +chr1 87019 87039 769.0 + chr1 87101 87121 1134.0 - 87070 1903.0 82 +chr1 124318 124338 749.0 + chr1 124275 124295 12.0 - 124306 761.0 -43 +chr1 348 368 699.0 + chr1 410 430 8.0 - 389 707.0 62 +chr1 92543 92563 699.0 + chr1 92639 92659 2137.0 - 92601 2836.0 96 +chr1 138868 138888 698.0 + chr1 138864 138884 13.0 - 138876 711.0 -4 +chr1 307 327 685.0 + chr1 373 393 200.0 - 350 885.0 66 +chr1 6413 6433 682.0 + chr1 6476 6496 567.0 - 6454 1249.0 63 +chr1 87085 87105 676.0 + chr1 87049 87069 422.0 - 87077 1098.0 -36 +chr1 72781 72801 657.0 + chr1 72810 72830 212.0 - 72805 869.0 29 +chr1 22571 22591 609.0 + chr1 22569 22589 254.0 - 22580 863.0 -2 +chr1 65152 65172 575.0 + chr1 65148 65168 43.0 - 65160 618.0 -4 +chr1 106034 106054 558.0 + chr1 106041 106061 14.0 - 106047 572.0 7 +chr1 155028 155048 522.0 + chr1 155111 155131 1051.0 - 155079 1573.0 83 +chr1 32449 32469 476.0 + chr1 32497 32517 2.0 - 32483 478.0 48 +chr1 160 180 451.0 + chr1 215 235 2611.0 - 197 3062.0 55 +chr1 6706 6726 431.0 + chr1 6702 6722 2.0 - 6714 433.0 -4 +chr1 113782 113802 420.0 + chr1 113762 113782 296.0 - 113782 716.0 -20 +chr1 228633 228653 371.0 + chr1 228691 228711 255.0 - 228672 626.0 58 +chr1 438 458 334.0 + chr1 468 488 468.0 - 463 802.0 30 +chr1 72671 72691 304.0 + chr1 72771 72791 406.0 - 72731 710.0 100 +chr1 170119 170139 284.0 + chr1 170129 170149 373.0 - 170134 657.0 10 +chr1 92631 92651 260.0 + chr1 92664 92684 187.0 - 92657 447.0 33 +chr1 136366 136386 248.0 + chr1 136352 136372 117.0 - 136369 365.0 -14 +chr1 108624 108644 206.0 + chr1 108579 108599 367.0 - 108611 573.0 -45 +chr1 45678 45698 198.0 + chr1 45643 45663 295.0 - 45670 493.0 -35 +chr1 368 388 192.0 + chr1 446 466 170.0 - 417 362.0 78 +chr1 682 702 168.0 + chr1 634 654 151.0 - 668 319.0 -48 +chr1 59190 59210 168.0 + chr1 59246 59266 397.0 - 59228 565.0 56 +chr1 134170 134190 151.0 + chr1 134270 134290 508.0 - 134230 659.0 100 +chr1 55495 55515 125.0 + chr1 55581 55601 831.0 - 55548 956.0 86 +chr1 39197 39217 101.0 + chr1 39258 39278 261.0 - 39237 362.0 61 +chr1 229721 229741 84.0 + chr1 229757 229777 3151.0 - 229749 3235.0 36 +chr1 116660 116680 74.0 + chr1 116619 116639 699.0 - 116649 773.0 -41 +chr1 19216 19236 42.0 + chr1 19191 19211 736.0 - 19213 778.0 -25 +chr1 230110 230130 42.0 + chr1 230173 230193 33.0 - 230151 75.0 63 +chr1 31627 31647 40.0 + chr1 31693 31713 450.0 - 31670 490.0 66 +chr1 180280 180300 38.0 + chr1 180362 180382 59.0 - 180331 97.0 82 +chr1 98528 98548 34.0 + chr1 98555 98575 88.0 - 98551 122.0 27 +chr1 230163 230183 23.0 + chr1 230150 230170 7.0 - 230166 30.0 -13 +chr1 173262 173282 11.0 + chr1 173270 173290 535.0 - 173276 546.0 8 +chr1 230145 230165 8.0 + chr1 230132 230152 2.0 - 230148 10.0 -13 +chr1 95920 95940 5.0 + chr1 95971 95991 684.0 - 95955 689.0 51 +chr1 199418 199438 5.0 + chr1 199388 199408 805.0 - 199413 810.0 -30 +chr1 197489 197509 3.0 + chr1 197562 197582 2.0 - 197535 5.0 73 +chr1 96908 96928 2.0 + chr1 96911 96931 10.0 - 96919 12.0 3 +chr1 151369 151389 2.0 + chr1 151341 151361 593.0 - 151365 595.0 -28
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mode_o_output2.tabular Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,365 @@ +chrom strand start end value +chr1 + 100364 100384 2695.0 +chr1 + 30 50 2140.0 +chr1 + 5379 5399 1572.0 +chr1 + 52440 52460 1562.0 +chr1 + 73234 73254 1492.0 +chr1 + 31096 31116 1481.0 +chr1 + 145253 145273 1394.0 +chr1 + 10641 10661 1359.0 +chr1 + 200580 200600 1298.0 +chr1 + 64772 64792 1292.0 +chr1 + 86886 86906 1253.0 +chr1 + 103207 103227 1229.0 +chr1 + 43835 43855 1173.0 +chr1 + 29570 29590 1130.0 +chr1 + 83774 83794 1125.0 +chr1 + 165827 165847 1109.0 +chr1 + 92775 92795 1105.0 +chr1 + 4748 4768 1077.0 +chr1 + 126733 126753 952.0 +chr1 + 71041 71061 881.0 +chr1 + 35773 35793 866.0 +chr1 + 53097 53117 835.0 +chr1 + 71556 71576 835.0 +chr1 + 30964 30984 829.0 +chr1 + 31019 31039 810.0 +chr1 + 55349 55369 794.0 +chr1 + 203193 203213 789.0 +chr1 + 39794 39814 780.0 +chr1 + 153928 153948 768.0 +chr1 + 179472 179492 696.0 +chr1 + 178117 178137 686.0 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135051 135071 63.0 +chr1 - 137428 137448 1200.0 +chr1 - 137816 137836 695.0 +chr1 - 139627 139647 531.0 +chr1 - 140133 140153 441.0 +chr1 - 140770 140790 556.0 +chr1 - 141182 141202 14.0 +chr1 - 143551 143571 3.0 +chr1 - 144669 144689 1192.0 +chr1 - 145383 145403 326.0 +chr1 - 147573 147593 255.0 +chr1 - 148690 148710 2.0 +chr1 - 149704 149724 74.0 +chr1 - 150358 150378 153.0 +chr1 - 152984 153004 106.0 +chr1 - 153812 153832 168.0 +chr1 - 154862 154882 14.0 +chr1 - 155456 155476 23.0 +chr1 - 155897 155917 10.0 +chr1 - 157559 157579 337.0 +chr1 - 166467 166487 582.0 +chr1 - 166631 166651 173.0 +chr1 - 169500 169520 814.0 +chr1 - 170282 170302 63.0 +chr1 - 171063 171083 212.0 +chr1 - 175188 175208 117.0 +chr1 - 175474 175494 1119.0 +chr1 - 176004 176024 1473.0 +chr1 - 177140 177160 93.0 +chr1 - 177386 177406 289.0 +chr1 - 178846 178866 601.0 +chr1 - 178971 178991 723.0 +chr1 - 179116 179136 71.0 +chr1 - 180272 180292 25.0 +chr1 - 180995 181015 299.0 +chr1 - 182588 182608 465.0 +chr1 - 182790 182810 355.0 +chr1 - 185673 185693 190.0 +chr1 - 187422 187442 20.0 +chr1 - 187976 187996 728.0 +chr1 - 196499 196519 224.0 +chr1 - 197060 197080 224.0 +chr1 - 197151 197171 1464.0 +chr1 - 197342 197362 204.0 +chr1 - 198423 198443 598.0 +chr1 - 198953 198973 3.0 +chr1 - 199935 199955 31.0 +chr1 - 201308 201328 1287.0 +chr1 - 201651 201671 892.0 +chr1 - 202977 202997 163.0 +chr1 - 203452 203472 76.0 +chr1 - 206245 206265 22.0 +chr1 - 207675 207695 313.0 +chr1 - 208559 208579 121.0 +chr1 - 209205 209225 176.0 +chr1 - 220863 220883 2.0 +chr1 - 223035 223055 62.0 +chr1 - 225156 225176 2.0 +chr1 - 226777 226797 444.0 +chr1 - 227608 227628 1311.0 +chr1 - 228405 228425 1447.0 +chr1 - 229031 229051 6.0 +chr1 - 229583 229603 62.0 +chr1 - 229665 229685 131.0 +chr1 - 229965 229985 13.0 +chr1 - 230120 230140 2.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mode_s_output1.gff Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,57 @@ +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59 +chr1 cwpair . 197 198 3062.0 . . cw_distance=55 +chr1 cwpair . 241 242 2689.0 . . cw_distance=60 +chr1 cwpair . 265 266 2474.0 . . cw_distance=48 +chr1 cwpair . 299 300 3296.0 . . cw_distance=68 +chr1 cwpair . 350 351 885.0 . . cw_distance=66 +chr1 cwpair . 389 390 707.0 . . cw_distance=62 +chr1 cwpair . 417 418 362.0 . . cw_distance=78 +chr1 cwpair . 463 464 802.0 . . cw_distance=30 +chr1 cwpair . 627 628 247.0 . . cw_distance=33 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 +chr1 cwpair . 87035 87036 972.0 . . cw_distance=47 +chr1 cwpair . 87070 87071 1903.0 . . cw_distance=82 +chr1 cwpair . 87138 87139 3164.0 . . cw_distance=60 +chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 +chr1 cwpair . 87212 87213 2073.0 . . cw_distance=63 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 +chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 229749 229750 3235.0 . . cw_distance=36 +chr1 cwpair . 229772 229773 1995.0 . . cw_distance=43 +chr1 cwpair . 230148 230149 10.0 . . cw_distance=-13 +chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 +chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mode_s_output2.gff Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,67 @@ +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59 +chr1 cwpair . 197 198 3062.0 . . cw_distance=55 +chr1 cwpair . 241 242 2689.0 . . cw_distance=60 +chr1 cwpair . 265 266 2474.0 . . cw_distance=48 +chr1 cwpair . 299 300 3296.0 . . cw_distance=68 +chr1 cwpair . 350 351 885.0 . . cw_distance=66 +chr1 cwpair . 389 390 707.0 . . cw_distance=62 +chr1 cwpair . 417 418 362.0 . . cw_distance=78 +chr1 cwpair . 463 464 802.0 . . cw_distance=30 +chr1 cwpair . 668 669 319.0 . . cw_distance=-48 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 +chr1 cwpair . 87070 87071 1903.0 . . cw_distance=82 +chr1 cwpair . 87077 87078 1098.0 . . cw_distance=-36 +chr1 cwpair . 87138 87139 3164.0 . . cw_distance=60 +chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 +chr1 cwpair . 87212 87213 2073.0 . . cw_distance=63 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 +chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 +chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 +chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 +chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 229749 229750 3235.0 . . cw_distance=36 +chr1 cwpair . 229772 229773 1995.0 . . cw_distance=43 +chr1 cwpair . 230148 230149 10.0 . . cw_distance=-13 +chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 +chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/statistics1.tabular Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,4 @@ +fname final_mode preview_mode perc95 paired orphans +closest: data 1 10.5 NA 1437.0 112 386 +largest: data 1 -3.5 NA 1437.0 110 388 +mode: data 1 63.5 63.5 1437.0 114 384
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/statistics2.tabular Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,4 @@ +fname final_mode preview_mode perc95 paired orphans +closest: data 1 8.5 NA 1437.0 132 366 +largest: data 1 -24.5 NA 1437.0 128 370 +mode: data 1 63.5 63.5 1437.0 134 364
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Nov 17 14:06:28 2015 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="anaconda" version="2.3.0"> + <repository changeset_revision="1da77309352e" name="package_anaconda_2_3_0" owner="greg" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>