# HG changeset patch # User devteam # Date 1396363908 14400 # Node ID d958d5a0d1e8d9e9c4ec15fde59fa8cc891dcaca Imported from capsule None diff -r 000000000000 -r d958d5a0d1e8 complement.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/complement.xml Tue Apr 01 10:51:48 2014 -0400 @@ -0,0 +1,65 @@ + + intervals of a dataset + + bx-python + galaxy-ops + + gops_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${chromInfo} $allchroms + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. + +This operation complements the regions of a set of intervals. Regions are returned that represent the empty space in the input interval. + +----- + +**Screencasts!** + +See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). + +.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations + +----- + +**Syntax** + +- **Genome-wide complement** will complement all chromosomes of the genome. Leaving this option unchecked will only complement chromosomes present in the dataset. + +----- + +**Example** + +.. image:: ${static_path}/operation_icons/gops_complement.gif + + + diff -r 000000000000 -r d958d5a0d1e8 gops_complement.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gops_complement.py Tue Apr 01 10:51:48 2014 -0400 @@ -0,0 +1,96 @@ +#!/usr/bin/env python +""" +Complement regions. + +usage: %prog in_file out_file + -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file + -l, --lengths=N: Filename of .len file for species (chromosome lengths) + -a, --all: Complement all chromosomes (Genome-wide complement) +""" + +import sys, traceback, fileinput +from warnings import warn +from bx.intervals import * +from bx.intervals.io import * +from bx.intervals.operations.complement import complement +from bx.intervals.operations.subtract import subtract +from bx.cookbook import doc_optparse +from galaxy.tools.util.galaxyops import * + +assert sys.version_info[:2] >= ( 2, 4 ) + +def main(): + allchroms = False + upstream_pad = 0 + downstream_pad = 0 + + options, args = doc_optparse.parse( __doc__ ) + try: + chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) + lengths = options.lengths + if options.all: allchroms = True + in_fname, out_fname = args + except: + doc_optparse.exception() + + g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), + chrom_col=chr_col_1, + start_col=start_col_1, + end_col=end_col_1, + strand_col=strand_col_1, + fix_strand=True ) + + lens = dict() + chroms = list() + # dbfile is used to determine the length of each chromosome. The lengths + # are added to the lens dict and passed copmlement operation code in bx. + dbfile = fileinput.FileInput( lengths ) + + if dbfile: + if not allchroms: + try: + for line in dbfile: + fields = line.split("\t") + lens[fields[0]] = int(fields[1]) + except: + # assume LEN doesn't exist or is corrupt somehow + pass + elif allchroms: + try: + for line in dbfile: + fields = line.split("\t") + end = int(fields[1]) + chroms.append("\t".join([fields[0],"0",str(end)])) + except: + pass + + # Safety...if the dbfile didn't exist and we're on allchroms, then + # default to generic complement + if allchroms and len(chroms) == 0: + allchroms = False + + if allchroms: + chromReader = GenomicIntervalReader(chroms) + generator = subtract([chromReader, g1]) + else: + generator = complement(g1, lens) + + out_file = open( out_fname, "w" ) + + try: + for interval in generator: + if type( interval ) is GenomicInterval: + out_file.write( "%s\n" % "\t".join( interval ) ) + else: + out_file.write( "%s\n" % interval ) + except ParseError, exc: + out_file.close() + fail( "Invalid file format: %s" % str( exc ) ) + + out_file.close() + + if g1.skipped > 0: + print skipped( g1, filedesc="" ) + +if __name__ == "__main__": + main() diff -r 000000000000 -r d958d5a0d1e8 operation_filter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/operation_filter.py Tue Apr 01 10:51:48 2014 -0400 @@ -0,0 +1,97 @@ +# runs after the job (and after the default post-filter) +import os +from galaxy.tools.parameters import DataToolParameter + +from galaxy.jobs.handler import JOB_ERROR + +# Older py compatibility +try: + set() +except: + from sets import Set as set + +#def exec_before_process(app, inp_data, out_data, param_dict, tool=None): +# """Sets the name of the data""" +# dbkeys = sets.Set( [data.dbkey for data in inp_data.values() ] ) +# if len(dbkeys) != 1: +# raise Exception, '

Both Queries must be from the same genome build

' + +def validate_input( trans, error_map, param_values, page_param_map ): + dbkeys = set() + data_param_names = set() + data_params = 0 + for name, param in page_param_map.iteritems(): + if isinstance( param, DataToolParameter ): + # for each dataset parameter + if param_values.get(name, None) != None: + dbkeys.add( param_values[name].dbkey ) + data_params += 1 + # check meta data + try: + param = param_values[name] + if isinstance( param.datatype, trans.app.datatypes_registry.get_datatype_by_extension( 'gff' ).__class__ ): + # TODO: currently cannot validate GFF inputs b/c they are not derived from interval. + pass + else: # Validate interval datatype. + startCol = int( param.metadata.startCol ) + endCol = int( param.metadata.endCol ) + chromCol = int( param.metadata.chromCol ) + if param.metadata.strandCol is not None: + strandCol = int ( param.metadata.strandCol ) + else: + strandCol = 0 + except: + error_msg = "The attributes of this dataset are not properly set. " + \ + "Click the pencil icon in the history item to set the chrom, start, end and strand columns." + error_map[name] = error_msg + data_param_names.add( name ) + if len( dbkeys ) > 1: + for name in data_param_names: + error_map[name] = "All datasets must belong to same genomic build, " \ + "this dataset is linked to build '%s'" % param_values[name].dbkey + if data_params != len(data_param_names): + for name in data_param_names: + error_map[name] = "A dataset of the appropriate type is required" + +# Commented out by INS, 5/30/2007. What is the PURPOSE of this? +def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): + """Verify the output data after each run""" + items = out_data.items() + + for name, data in items: + try: + if stderr and len( stderr ) > 0: + raise Exception( stderr ) + + except Exception, exc: + data.blurb = JOB_ERROR + data.state = JOB_ERROR + +## def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): +## pass + + +def exec_after_merge(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): + exec_after_process( + app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr) + + # strip strand column if clusters were merged + items = out_data.items() + for name, data in items: + if param_dict['returntype'] == True: + data.metadata.chromCol = 1 + data.metadata.startCol = 2 + data.metadata.endCol = 3 + # merge always clobbers strand + data.metadata.strandCol = None + + +def exec_after_cluster(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): + exec_after_process( + app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr) + + # strip strand column if clusters were merged + if param_dict["returntype"] == '1': + items = out_data.items() + for name, data in items: + data.metadata.strandCol = None diff -r 000000000000 -r d958d5a0d1e8 test-data/1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.bed Tue Apr 01 10:51:48 2014 -0400 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - diff -r 000000000000 -r d958d5a0d1e8 test-data/2_mod.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_mod.bed Tue Apr 01 10:51:48 2014 -0400 @@ -0,0 +1,69 @@ +#chr name score strand start end +chr1 NM_005997_cds_0_0_chr1_147962193_r 0 - 147962192 147962580 +chr1 BC007833_cds_0_0_chr1_147984546_f 0 + 147984545 147984630 +chr1 AJ011123_cds_0_0_chr1_148078401_r 0 - 148078400 148078582 +chr1 NM_002796_cds_0_0_chr1_148185137_f 0 + 148185136 148185276 +chr10 AY029205_cds_0_0_chr10_55251624_r 0 - 55251623 55253124 +chr11 AK057832_cds_0_0_chr11_116124408_r 0 - 116124407 116124501 +chr11 NM_000040_cds_1_0_chr11_116206509_f 0 + 116206508 116206563 +chr11 BC005380_cds_0_0_chr11_116211734_r 0 - 116211733 116212337 +chr11 AY358331_cds_0_0_chr11_130745912_f 0 + 130745911 130745993 +chr12 NM_052885_cds_0_0_chr12_38440095_r 0 - 38440094 38440321 +chr12 AY792511_cds_0_0_chr12_38905201_f 0 + 38905200 38905351 +chr13 NM_207440_cds_1_0_chr13_112381695_f 0 + 112381694 112381953 +chr13 NM_032116_cds_0_0_chr13_29680677_r 0 - 29680676 29680875 +chr14 U88895_cds_0_0_chr14_98521865_f 0 + 98521864 98521922 +chr14 NM_022898_cds_0_0_chr14_98710241_r 0 - 98710240 98712285 +chr15 BX537418_cds_0_0_chr15_41486873_r 0 - 41486872 41487060 +chr15 AK223365_cds_0_0_chr15_41673709_f 0 + 41673708 41673857 +chr15 NM_153700_cds_0_0_chr15_41679162_r 0 - 41679161 41679250 +chr15 AK223365_cds_0_0_chr15_41773541_f 0 + 41773540 41773689 +chr16 NM_005332_cds_0_0_chr16_142909_f 0 + 142908 143003 +chr16 BC065198_cds_0_0_chr16_179198_r 0 - 179197 179339 +chr16 AK057165_cds_2_0_chr16_244414_f 0 + 244413 244681 +chr16 AB016929_cds_0_0_chr16_259269_r 0 - 259268 259383 +chr18 NM_001792_cds_0_0_chr18_23786115_r 0 - 23786114 23786321 +chr18 NM_012397_cds_1_0_chr18_59406882_f 0 + 59406881 59407046 +chr18 AB046400_cds_0_0_chr18_59455933_r 0 - 59455932 59456337 +chr18 AY792326_cds_0_0_chr18_59528408_f 0 + 59528407 59528575 +chr19 BC013995_cds_1_0_chr19_59068596_f 0 + 59068595 59069564 +chr19 NM_198481_cds_0_0_chr19_59236027_r 0 - 59236026 59236146 +chr19 NM_004542_cds_0_0_chr19_59297999_f 0 + 59297998 59298008 +chr19 AK128544_cds_3_0_chr19_59318206_r 0 - 59318205 59318718 +chr2 NM_006773_cds_0_0_chr2_118288584_f 0 + 118288583 118288668 +chr2 BC005078_cds_0_0_chr2_118390396_r 0 - 118390395 118390500 +chr2 AY125465_cds_0_0_chr2_220108690_f 0 + 220108689 220109267 +chr2 NM_024536_cds_0_0_chr2_220229610_r 0 - 220229609 220230869 +chr20 NM_181466_cds_0_0_chr20_33330414_r 0 - 33330413 33330423 +chr20 BC085019_cds_1_0_chr20_33485371_f 0 + 33485370 33486123 +chr20 NM_000557_cds_1_0_chr20_33488492_r 0 - 33488491 33489122 +chr20 AF022655_cds_1_0_chr20_33513607_f 0 + 33513606 33513792 +chr21 NM_032910_cds_0_0_chr21_32687403_f 0 + 32687402 32687588 +chr21 NM_018277_cds_3_0_chr21_32869642_r 0 - 32869641 32870022 +chr21 NM_005806_cds_1_0_chr21_33321041_f 0 + 33321040 33322012 +chr21 AK129657_cds_0_0_chr21_33728359_r 0 - 33728358 33728724 +chr22 NM_004147_cds_0_0_chr22_30120224_f 0 + 30120223 30120265 +chr22 BC032941_cds_0_0_chr22_30160420_r 0 - 30160419 30160661 +chr22 NM_001007467_cds_1_0_chr22_30228825_f 0 + 30228824 30228916 +chr22 CR456540_cds_0_0_chr22_30340152_r 0 - 30340151 30340376 +chr5 AF099740_cds_11_0_chr5_131311207_r 0 - 131311206 131311254 +chr5 NM_000588_cds_0_0_chr5_131424299_f 0 + 131424298 131424460 +chr5 BC035813_cds_0_0_chr5_131556602_r 0 - 131556601 131556672 +chr5 BC003096_cds_0_0_chr5_131621327_f 0 + 131621326 131621419 +chr6 NM_007214_cds_0_0_chr6_108299601_r 0 - 108299600 108299744 +chr6 NM_003269_cds_0_0_chr6_108594663_f 0 + 108594662 108594687 +chr6 NM_003795_cds_0_0_chr6_108640046_r 0 - 108640045 108640151 +chr6 NM_145315_cds_0_0_chr6_108722977_f 0 + 108722976 108723115 +chr7 AF467257_cds_1_0_chr7_113660518_f 0 + 113660517 113660685 +chr7 NM_003391_cds_0_0_chr7_116512160_r 0 - 116512159 116512389 +chr7 NM_000492_cds_0_0_chr7_116714100_f 0 + 116714099 116714152 +chr7 AF377960_cds_0_0_chr7_116945542_r 0 - 116945541 116945787 +chr8 NM_000127_cds_0_0_chr8_118881132_r 0 - 118881131 118881317 +chr9 BC051300_cds_0_0_chr9_128764157_f 0 + 128764156 128764189 +chr9 NM_014908_cds_0_0_chr9_128787520_r 0 - 128787519 128789136 +chr9 NM_015354_cds_0_0_chr9_128789553_f 0 + 128789552 128789584 +chr9 AB058751_cds_0_0_chr9_128850517_r 0 - 128850516 128850624 +chrX NM_001167_cds_1_0_chrX_122745048_f 0 + 122745047 122745924 +chrX NM_000425_cds_0_0_chrX_152648965_r 0 - 152648964 152649196 +chrX AF101728_cds_0_0_chrX_152691447_f 0 + 152691446 152691471 +chrX BC052303_cds_0_0_chrX_152694030_r 0 - 152694029 152694263 diff -r 000000000000 -r d958d5a0d1e8 test-data/gops_bigint.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_bigint.interval Tue Apr 01 10:51:48 2014 -0400 @@ -0,0 +1,9 @@ +chrM 69 852 uc009vev.1_exon_0_0_chrM_70_f 0 + +chrM 1148 3703 uc009vew.1_exon_0_0_chrM_1149_f 0 + +chrM 3848 4933 uc009vex.1_exon_0_0_chrM_3849_f 0 + +chrM 5326 6938 uc009vey.1_exon_0_0_chrM_5327_f 0 + +chrM 7009 7699 uc009vez.1_exon_0_0_chrM_7010_f 0 + +chrM 7765 8607 uc009vfa.1_exon_0_0_chrM_7766_f 0 + +chrM 9875 11542 uc009vfb.1_exon_0_0_chrM_9876_f 0 + +chrM 12405 15288 uc009vfc.1_exon_0_0_chrM_12406_f 0 + +chrM 4294967295 4294967322 EAS38_1_45_638_677 2 + \ No newline at end of file diff -r 000000000000 -r d958d5a0d1e8 test-data/gops_complement_out.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_complement_out.bed Tue Apr 01 10:51:48 2014 -0400 @@ -0,0 +1,85 @@ +chr7 0 113660517 +chr7 113660685 116512159 +chr7 116512389 116714099 +chr7 116714152 116945541 +chr7 116945787 536870912 +chr6 0 108299600 +chr6 108299744 108594662 +chr6 108594687 108640045 +chr6 108640151 108722976 +chr6 108723115 536870912 +chr5 0 131424298 +chr5 131424460 131556601 +chr5 131556672 131621326 +chr5 131621419 131847541 +chr5 131847666 536870912 +chrX 0 122745047 +chrX 122745924 152648964 +chrX 152649196 152691446 +chrX 152691471 152694029 +chrX 152694263 536870912 +chr2 0 118288583 +chr2 118288668 118394148 +chr2 118394202 220190202 +chr2 220190242 220229609 +chr2 220230869 536870912 +chr1 0 147962192 +chr1 147962580 147984545 +chr1 147984630 148078400 +chr1 148078582 148185136 +chr1 148185276 536870912 +chr21 0 32707032 +chr21 32707192 32869641 +chr21 32870022 33321040 +chr21 33322012 33744994 +chr21 33745040 536870912 +chr9 0 128764156 +chr9 128764189 128787519 +chr9 128789136 128882427 +chr9 128882523 128937229 +chr9 128937445 536870912 +chr8 0 118881131 +chr8 118881317 536870912 +chr13 0 112381694 +chr13 112381953 536870912 +chr12 0 38440094 +chr12 38440321 536870912 +chr11 0 1812377 +chr11 1812407 116124407 +chr11 116124501 116206508 +chr11 116206563 116211733 +chr11 116212337 536870912 +chr10 0 55251623 +chr10 55253124 536870912 +chr22 0 30120223 +chr22 30120265 30160419 +chr22 30160661 30665273 +chr22 30665360 30939054 +chr22 30939266 536870912 +chr16 0 142908 +chr16 143003 179963 +chr16 180135 244413 +chr16 244681 259268 +chr16 259383 536870912 +chr15 0 41486872 +chr15 41487060 41673708 +chr15 41673857 41679161 +chr15 41679250 41826029 +chr15 41826196 536870912 +chr14 0 98710240 +chr14 98712285 536870912 +chr20 0 33330413 +chr20 33330423 33513606 +chr20 33513792 33579500 +chr20 33579527 33593260 +chr20 33593348 536870912 +chr19 0 59068595 +chr19 59069564 59236026 +chr19 59236146 59297998 +chr19 59298008 59302168 +chr19 59302288 536870912 +chr18 0 23786114 +chr18 23786321 59406881 +chr18 59407046 59455932 +chr18 59456337 59600586 +chr18 59600754 536870912 diff -r 000000000000 -r d958d5a0d1e8 test-data/gops_complement_out2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_complement_out2.bed Tue Apr 01 10:51:48 2014 -0400 @@ -0,0 +1,9 @@ +chrM 0 69 +chrM 852 1148 +chrM 3703 3848 +chrM 4933 5326 +chrM 6938 7009 +chrM 7699 7765 +chrM 8607 9875 +chrM 11542 12405 +chrM 15288 536870912 diff -r 000000000000 -r d958d5a0d1e8 test-data/gops_complement_out_diffCols.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_complement_out_diffCols.dat Tue Apr 01 10:51:48 2014 -0400 @@ -0,0 +1,88 @@ +chr7 . . + 0 113660517 +chr7 . . + 113660685 116512159 +chr7 . . + 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41773689 536870912 +chr14 . . + 0 98521864 +chr14 . . + 98521922 98710240 +chr14 . . + 98712285 536870912 +chr20 . . + 0 33330413 +chr20 . . + 33330423 33485370 +chr20 . . + 33486123 33488491 +chr20 . . + 33489122 33513606 +chr20 . . + 33513792 536870912 +chr19 . . + 0 59068595 +chr19 . . + 59069564 59236026 +chr19 . . + 59236146 59297998 +chr19 . . + 59298008 59318205 +chr19 . . + 59318718 536870912 +chr18 . . + 0 23786114 +chr18 . . + 23786321 59406881 +chr18 . . + 59407046 59455932 +chr18 . . + 59456337 59528407 +chr18 . . + 59528575 536870912 diff -r 000000000000 -r d958d5a0d1e8 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Apr 01 10:51:48 2014 -0400 @@ -0,0 +1,9 @@ + + + + + + + + +