--- /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 @@
+<tool id="gops_complement_1" name="Complement" version="0.0.1">
+  <description>intervals of a dataset</description>
+  <requirements>
+    <requirement type="package" version="0.7.1">bx-python</requirement>
+    <requirement type="package" version="1.0.0">galaxy-ops</requirement>
+  </requirements>
+  <command interpreter="python">gops_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${chromInfo} $allchroms</command>
+  <inputs>
+    <param format="interval" name="input1" type="data">
+      <label>Complement regions of</label>
+    </param>
+    <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement">
+    </param>
+   </inputs>
+  <outputs>
+    <data format="input" name="output" metadata_source="input1" />
+  </outputs>
+  <code file="operation_filter.py"/>
+  <tests>
+    <test>
+      <param name="input1" value="1.bed" dbkey="hg17" />
+      <param name="allchroms" value="true" />
+      <output name="output" file="gops_complement_out.bed" />
+    </test>
+    <test>
+      <param name="input1" value="2_mod.bed" ftype="interval" dbkey="hg17" />
+      <param name="allchroms" value="true" />
+      <output name="output" file="gops_complement_out_diffCols.dat" />
+    </test>
+    <test>
+      <param name="input1" value="gops_bigint.interval" dbkey="hg17" />
+      <param name="allchroms" value="true" />
+      <output name="output" file="gops_complement_out2.bed" />
+    </test>
+  </tests>
+  <help>
+
+.. 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
+
+</help>
+</tool>

--- /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()

--- /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, '<p><font color="yellow">Both Queries must be from the same genome build</font></p>'
+
+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

--- /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	-

--- /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

--- /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

--- /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

--- /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

--- /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	.	.	+	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	131311206
+chr5	.	.	+	131311254	131424298
+chr5	.	.	+	131424460	131556601
+chr5	.	.	+	131556672	131621326
+chr5	.	.	+	131621419	536870912
+chrX	.	.	+	0	122745047
+chrX	.	.	+	122745924	152648964
+chrX	.	.	+	152649196	152691446
+chrX	.	.	+	152691471	152694029
+chrX	.	.	+	152694263	536870912
+chr2	.	.	+	0	118288583
+chr2	.	.	+	118288668	118390395
+chr2	.	.	+	118390500	220108689
+chr2	.	.	+	220109267	220229609
+chr2	.	.	+	220230869	536870912
+chr1	.	.	+	0	147962192
+chr1	.	.	+	147962580	147984545
+chr1	.	.	+	147984630	148078400
+chr1	.	.	+	148078582	148185136
+chr1	.	.	+	148185276	536870912
+chr21	.	.	+	0	32687402
+chr21	.	.	+	32687588	32869641
+chr21	.	.	+	32870022	33321040
+chr21	.	.	+	33322012	33728358
+chr21	.	.	+	33728724	536870912
+chr9	.	.	+	0	128764156
+chr9	.	.	+	128764189	128787519
+chr9	.	.	+	128789136	128789552
+chr9	.	.	+	128789584	128850516
+chr9	.	.	+	128850624	536870912
+chr8	.	.	+	0	118881131
+chr8	.	.	+	118881317	536870912
+chr13	.	.	+	0	29680676
+chr13	.	.	+	29680875	112381694
+chr13	.	.	+	112381953	536870912
+chr12	.	.	+	0	38440094
+chr12	.	.	+	38440321	38905200
+chr12	.	.	+	38905351	536870912
+chr11	.	.	+	0	116124407
+chr11	.	.	+	116124501	116206508
+chr11	.	.	+	116206563	116211733
+chr11	.	.	+	116212337	130745911
+chr11	.	.	+	130745993	536870912
+chr10	.	.	+	0	55251623
+chr10	.	.	+	55253124	536870912
+chr22	.	.	+	0	30120223
+chr22	.	.	+	30120265	30160419
+chr22	.	.	+	30160661	30228824
+chr22	.	.	+	30228916	30340151
+chr22	.	.	+	30340376	536870912
+chr16	.	.	+	0	142908
+chr16	.	.	+	143003	179197
+chr16	.	.	+	179339	244413
+chr16	.	.	+	244681	259268
+chr16	.	.	+	259383	536870912
+chr15	.	.	+	0	41486872
+chr15	.	.	+	41487060	41673708
+chr15	.	.	+	41673857	41679161
+chr15	.	.	+	41679250	41773540
+chr15	.	.	+	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

--- /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 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="bx-python" version="0.7.1">
+      <repository changeset_revision="41eb9d9f667d" name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="galaxy-ops" version="1.0.0">
+      <repository changeset_revision="4e39032e4ec6" name="package_galaxy_ops_1_0_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>