changeset 0:6b81ee6c18d3

Imported from capsule None
author devteam
date Tue, 01 Apr 2014 09:13:22 -0400
parents
children 8039a43a0663
files coverage.xml gops_coverage.py operation_filter.py test-data/1.bed test-data/2.bed test-data/2_mod.bed test-data/gops_bigint.interval test-data/gops_bigint2.interval test-data/gops_coverage_out.interval test-data/gops_coverage_out2.interval test-data/gops_coverage_out_diffCols.interval tool_dependencies.xml
diffstat 12 files changed, 625 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coverage.xml	Tue Apr 01 09:13:22 2014 -0400
@@ -0,0 +1,95 @@
+<tool id="gops_coverage_1" name="Coverage" version="0.0.1">
+  <description>of a set of intervals on second set of intervals</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_coverage.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}</command>
+  <inputs>
+    <param format="interval" name="input1" type="data" help="First dataset">
+      <label>What portion of</label>
+    </param>
+    <param format="interval" name="input2" type="data" help="Second dataset">
+      <label>is covered by</label>
+    </param>
+   </inputs>
+  <outputs>
+    <data format="interval" name="output" metadata_source="input1" />
+  </outputs>
+  <code file="operation_filter.py"/>
+  <tests>
+    <test>
+      <param name="input1" value="1.bed" />
+      <param name="input2" value="2.bed" />
+      <output name="output" file="gops_coverage_out.interval" />
+    </test>
+    <test>
+      <param name="input1" value="1.bed" />
+      <param name="input2" value="2_mod.bed" ftype="interval"/>
+      <output name="output" file="gops_coverage_out_diffCols.interval" />
+    </test>
+    <test>
+      <param name="input1" value="gops_bigint.interval" />
+      <param name="input2" value="gops_bigint2.interval" />
+      <output name="output" file="gops_coverage_out2.interval" />
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**TIP:** If your dataset does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
+
+Find the coverage of intervals in the first dataset on intervals in the second dataset.  The coverage is added as two columns, the first being bases covered, and the second being the fraction of bases covered by that 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
+
+-----
+
+**Example**
+
+
+    if **First dataset** are genes ::
+
+      chr11 5203271 5204877 NM_000518 0 -
+      chr11 5210634 5212434 NM_000519 0 -
+      chr11 5226077 5227663 NM_000559 0 -
+      chr11 5226079 5232587 BC020719  0 -
+      chr11 5230996 5232587 NM_000184 0 -
+
+    and **Second dataset** are repeats::
+
+       chr11      5203895 5203991 L1MA6     500 +
+       chr11      5204163 5204239 A-rich    219 +
+       chr11      5211034 5211167 (CATATA)n 245 +
+       chr11      5211642 5211673 AT_rich    24 +
+       chr11      5226551 5226606 (CA)n     303 +
+       chr11      5228782 5228825 (TTTTTG)n 208 +
+       chr11      5229045 5229121 L1PA11    440 +
+       chr11      5229133 5229319 MER41A   1106 +
+       chr11      5229374 5229485 L2        244 -
+       chr11      5229751 5230083 MLT1A     913 -
+       chr11      5231469 5231526 (CA)n     330 +
+
+    the Result is the coverage density of repeats in the genes::
+
+       chr11 5203271 5204877 NM_000518 0 - 172   0.107098
+       chr11 5210634 5212434 NM_000519 0 - 164   0.091111
+       chr11 5226077 5227663 NM_000559 0 -  55   0.034678
+       chr11 5226079 5232587 BC020719  0 - 860   0.132145
+       chr11 5230996 5232587 NM_000184 0 -  57   0.035827
+
+    For example, the following line of output::
+
+      chr11 5203271 5204877 NM_000518 0 - 172   0.107098
+
+   implies that 172 nucleotides accounting for 10.7% of the this interval (chr11:5203271-5204877) overlap with repetitive elements.
+
+</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gops_coverage.py	Tue Apr 01 09:13:22 2014 -0400
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+"""
+Calculate coverage of one query on another, and append the coverage to
+the last two columns as bases covered and percent coverage.
+
+usage: %prog bed_file_1 bed_file_2 out_file
+    -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
+    -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
+"""
+import sys, traceback, fileinput
+from warnings import warn
+from bx.intervals import *
+from bx.intervals.io import *
+from bx.intervals.operations.coverage import *
+from bx.cookbook import doc_optparse
+from galaxy.tools.util.galaxyops import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def main():
+    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 )
+        chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )      
+        in_fname, in2_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 )
+    g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ),
+                            chrom_col=chr_col_2,
+                            start_col=start_col_2,
+                            end_col=end_col_2,
+                            strand_col=strand_col_2,
+                            fix_strand=True )
+
+    out_file = open( out_fname, "w" )
+
+    try:
+        for line in coverage( [g1,g2] ):
+            if type( line ) is GenomicInterval:
+                out_file.write( "%s\n" % "\t".join( line.fields ) )
+            else:
+                out_file.write( "%s\n" % line )
+    except ParseError, exc:
+        out_file.close()
+        fail( "Invalid file format: %s" % str( exc ) )
+
+    out_file.close()
+
+    if g1.skipped > 0:
+        print skipped( g1, filedesc=" of 1st dataset" )
+    if g2.skipped > 0:
+        print skipped( g2, filedesc=" of 2nd dataset" )
+
+if __name__ == "__main__":
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/operation_filter.py	Tue Apr 01 09:13:22 2014 -0400
@@ -0,0 +1,99 @@
+# runs after the job (and after the default post-filter)
+import os
+from galaxy import eggs
+from galaxy import jobs
+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 09:13:22 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.bed	Tue Apr 01 09:13:22 2014 -0400
@@ -0,0 +1,68 @@
+chr1	147962192	147962580	NM_005997_cds_0_0_chr1_147962193_r	0	-
+chr1	147984545	147984630	BC007833_cds_0_0_chr1_147984546_f	0	+
+chr1	148078400	148078582	AJ011123_cds_0_0_chr1_148078401_r	0	-
+chr1	148185136	148185276	NM_002796_cds_0_0_chr1_148185137_f	0	+
+chr10	55251623	55253124	AY029205_cds_0_0_chr10_55251624_r	0	-
+chr11	116124407	116124501	AK057832_cds_0_0_chr11_116124408_r	0	-
+chr11	116206508	116206563	NM_000040_cds_1_0_chr11_116206509_f	0	+
+chr11	116211733	116212337	BC005380_cds_0_0_chr11_116211734_r	0	-
+chr11	130745911	130745993	AY358331_cds_0_0_chr11_130745912_f	0	+
+chr12	38440094	38440321	NM_052885_cds_0_0_chr12_38440095_r	0	-
+chr12	38905200	38905351	AY792511_cds_0_0_chr12_38905201_f	0	+
+chr13	112381694	112381953	NM_207440_cds_1_0_chr13_112381695_f	0	+
+chr13	29680676	29680875	NM_032116_cds_0_0_chr13_29680677_r	0	-
+chr14	98521864	98521922	U88895_cds_0_0_chr14_98521865_f	0	+
+chr14	98710240	98712285	NM_022898_cds_0_0_chr14_98710241_r	0	-
+chr15	41486872	41487060	BX537418_cds_0_0_chr15_41486873_r	0	-
+chr15	41673708	41673857	AK223365_cds_0_0_chr15_41673709_f	0	+
+chr15	41679161	41679250	NM_153700_cds_0_0_chr15_41679162_r	0	-
+chr15	41773540	41773689	AK223365_cds_0_0_chr15_41773541_f	0	+
+chr16	142908	143003	NM_005332_cds_0_0_chr16_142909_f	0	+
+chr16	179197	179339	BC065198_cds_0_0_chr16_179198_r	0	-
+chr16	244413	244681	AK057165_cds_2_0_chr16_244414_f	0	+
+chr16	259268	259383	AB016929_cds_0_0_chr16_259269_r	0	-
+chr18	23786114	23786321	NM_001792_cds_0_0_chr18_23786115_r	0	-
+chr18	59406881	59407046	NM_012397_cds_1_0_chr18_59406882_f	0	+
+chr18	59455932	59456337	AB046400_cds_0_0_chr18_59455933_r	0	-
+chr18	59528407	59528575	AY792326_cds_0_0_chr18_59528408_f	0	+
+chr19	59068595	59069564	BC013995_cds_1_0_chr19_59068596_f	0	+
+chr19	59236026	59236146	NM_198481_cds_0_0_chr19_59236027_r	0	-
+chr19	59297998	59298008	NM_004542_cds_0_0_chr19_59297999_f	0	+
+chr19	59318205	59318718	AK128544_cds_3_0_chr19_59318206_r	0	-
+chr2	118288583	118288668	NM_006773_cds_0_0_chr2_118288584_f	0	+
+chr2	118390395	118390500	BC005078_cds_0_0_chr2_118390396_r	0	-
+chr2	220108689	220109267	AY125465_cds_0_0_chr2_220108690_f	0	+
+chr2	220229609	220230869	NM_024536_cds_0_0_chr2_220229610_r	0	-
+chr20	33330413	33330423	NM_181466_cds_0_0_chr20_33330414_r	0	-
+chr20	33485370	33486123	BC085019_cds_1_0_chr20_33485371_f	0	+
+chr20	33488491	33489122	NM_000557_cds_1_0_chr20_33488492_r	0	-
+chr20	33513606	33513792	AF022655_cds_1_0_chr20_33513607_f	0	+
+chr21	32687402	32687588	NM_032910_cds_0_0_chr21_32687403_f	0	+
+chr21	32869641	32870022	NM_018277_cds_3_0_chr21_32869642_r	0	-
+chr21	33321040	33322012	NM_005806_cds_1_0_chr21_33321041_f	0	+
+chr21	33728358	33728724	AK129657_cds_0_0_chr21_33728359_r	0	-
+chr22	30120223	30120265	NM_004147_cds_0_0_chr22_30120224_f	0	+
+chr22	30160419	30160661	BC032941_cds_0_0_chr22_30160420_r	0	-
+chr22	30228824	30228916	NM_001007467_cds_1_0_chr22_30228825_f	0	+
+chr22	30340151	30340376	CR456540_cds_0_0_chr22_30340152_r	0	-
+chr5	131311206	131311254	AF099740_cds_11_0_chr5_131311207_r	0	-
+chr5	131424298	131424460	NM_000588_cds_0_0_chr5_131424299_f	0	+
+chr5	131556601	131556672	BC035813_cds_0_0_chr5_131556602_r	0	-
+chr5	131621326	131621419	BC003096_cds_0_0_chr5_131621327_f	0	+
+chr6	108299600	108299744	NM_007214_cds_0_0_chr6_108299601_r	0	-
+chr6	108594662	108594687	NM_003269_cds_0_0_chr6_108594663_f	0	+
+chr6	108640045	108640151	NM_003795_cds_0_0_chr6_108640046_r	0	-
+chr6	108722976	108723115	NM_145315_cds_0_0_chr6_108722977_f	0	+
+chr7	113660517	113660685	AF467257_cds_1_0_chr7_113660518_f	0	+
+chr7	116512159	116512389	NM_003391_cds_0_0_chr7_116512160_r	0	-
+chr7	116714099	116714152	NM_000492_cds_0_0_chr7_116714100_f	0	+
+chr7	116945541	116945787	AF377960_cds_0_0_chr7_116945542_r	0	-
+chr8	118881131	118881317	NM_000127_cds_0_0_chr8_118881132_r	0	-
+chr9	128764156	128764189	BC051300_cds_0_0_chr9_128764157_f	0	+
+chr9	128787519	128789136	NM_014908_cds_0_0_chr9_128787520_r	0	-
+chr9	128789552	128789584	NM_015354_cds_0_0_chr9_128789553_f	0	+
+chr9	128850516	128850624	AB058751_cds_0_0_chr9_128850517_r	0	-
+chrX	122745047	122745924	NM_001167_cds_1_0_chrX_122745048_f	0	+
+chrX	152648964	152649196	NM_000425_cds_0_0_chrX_152648965_r	0	-
+chrX	152691446	152691471	AF101728_cds_0_0_chrX_152691447_f	0	+
+chrX	152694029	152694263	BC052303_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 09:13:22 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 09:13:22 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_bigint2.interval	Tue Apr 01 09:13:22 2014 -0400
@@ -0,0 +1,8 @@
+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	+
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gops_coverage_out.interval	Tue Apr 01 09:13:22 2014 -0400
@@ -0,0 +1,65 @@
+chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-	388	1.0
+chr1	147984545	147984630	CCDS990.1_cds_0_0_chr1_147984546_f	0	+	85	1.0
+chr1	148078400	148078582	CCDS993.1_cds_0_0_chr1_148078401_r	0	-	182	1.0
+chr1	148185136	148185276	CCDS996.1_cds_0_0_chr1_148185137_f	0	+	140	1.0
+chr10	55251623	55253124	CCDS7248.1_cds_0_0_chr10_55251624_r	0	-	1501	1.0
+chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-	94	1.0
+chr11	116206508	116206563	CCDS8377.1_cds_0_0_chr11_116206509_f	0	+	55	1.0
+chr11	116211733	116212337	CCDS8378.1_cds_0_0_chr11_116211734_r	0	-	604	1.0
+chr11	1812377	1812407	CCDS7726.1_cds_0_0_chr11_1812378_f	0	+	0	0.0
+chr12	38440094	38440321	CCDS8736.1_cds_0_0_chr12_38440095_r	0	-	227	1.0
+chr13	112381694	112381953	CCDS9526.1_cds_0_0_chr13_112381695_f	0	+	259	1.0
+chr14	98710240	98712285	CCDS9949.1_cds_0_0_chr14_98710241_r	0	-	2045	1.0
+chr15	41486872	41487060	CCDS10096.1_cds_0_0_chr15_41486873_r	0	-	188	1.0
+chr15	41673708	41673857	CCDS10097.1_cds_0_0_chr15_41673709_f	0	+	149	1.0
+chr15	41679161	41679250	CCDS10098.1_cds_0_0_chr15_41679162_r	0	-	89	1.0
+chr15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+	0	0.0
+chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+	95	1.0
+chr16	179963	180135	CCDS10401.1_cds_0_0_chr16_179964_r	0	-	0	0.0
+chr16	244413	244681	CCDS10402.1_cds_0_0_chr16_244414_f	0	+	268	1.0
+chr16	259268	259383	CCDS10403.1_cds_0_0_chr16_259269_r	0	-	115	1.0
+chr18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-	207	1.0
+chr18	59406881	59407046	CCDS11985.1_cds_0_0_chr18_59406882_f	0	+	165	1.0
+chr18	59455932	59456337	CCDS11986.1_cds_0_0_chr18_59455933_r	0	-	405	1.0
+chr18	59600586	59600754	CCDS11988.1_cds_0_0_chr18_59600587_f	0	+	0	0.0
+chr19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+	969	1.0
+chr19	59236026	59236146	CCDS12872.1_cds_0_0_chr19_59236027_r	0	-	120	1.0
+chr19	59297998	59298008	CCDS12877.1_cds_0_0_chr19_59297999_f	0	+	10	1.0
+chr19	59302168	59302288	CCDS12878.1_cds_0_0_chr19_59302169_r	0	-	0	0.0
+chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+	85	1.0
+chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_r	0	-	0	0.0
+chr2	220190202	220190242	CCDS2441.1_cds_0_0_chr2_220190203_f	0	+	0	0.0
+chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-	1260	1.0
+chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-	10	1.0
+chr20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+	186	1.0
+chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-	0	0.0
+chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+	0	0.0
+chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+	0	0.0
+chr21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-	381	1.0
+chr21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+	972	1.0
+chr21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-	0	0.0
+chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+	42	1.0
+chr22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-	242	1.0
+chr22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+	0	0.0
+chr22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_r	0	-	0	0.0
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+	162	1.0
+chr5	131556601	131556672	CCDS4151.1_cds_0_0_chr5_131556602_r	0	-	71	1.0
+chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+	93	1.0
+chr5	131847541	131847666	CCDS4155.1_cds_0_0_chr5_131847542_r	0	-	0	0.0
+chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-	144	1.0
+chr6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+	25	1.0
+chr6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-	106	1.0
+chr6	108722976	108723115	CCDS5067.1_cds_0_0_chr6_108722977_f	0	+	139	1.0
+chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+	168	1.0
+chr7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-	230	1.0
+chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+	53	1.0
+chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	0	-	246	1.0
+chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-	186	1.0
+chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+	33	1.0
+chr9	128787519	128789136	CCDS6915.1_cds_0_0_chr9_128787520_r	0	-	1617	1.0
+chr9	128882427	128882523	CCDS6917.1_cds_0_0_chr9_128882428_f	0	+	0	0.0
+chr9	128937229	128937445	CCDS6919.1_cds_0_0_chr9_128937230_r	0	-	0	0.0
+chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_f	0	+	877	1.0
+chrX	152648964	152649196	CCDS14733.1_cds_0_0_chrX_152648965_r	0	-	232	1.0
+chrX	152691446	152691471	CCDS14735.1_cds_0_0_chrX_152691447_f	0	+	25	1.0
+chrX	152694029	152694263	CCDS14736.1_cds_0_0_chrX_152694030_r	0	-	234	1.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gops_coverage_out2.interval	Tue Apr 01 09:13:22 2014 -0400
@@ -0,0 +1,8 @@
+chrM	69	852	uc009vev.1_exon_0_0_chrM_70_f	0	+	783	1.0
+chrM	1148	3703	uc009vew.1_exon_0_0_chrM_1149_f	0	+	2555	1.0
+chrM	3848	4933	uc009vex.1_exon_0_0_chrM_3849_f	0	+	1085	1.0
+chrM	5326	6938	uc009vey.1_exon_0_0_chrM_5327_f	0	+	1612	1.0
+chrM	7009	7699	uc009vez.1_exon_0_0_chrM_7010_f	0	+	690	1.0
+chrM	7765	8607	uc009vfa.1_exon_0_0_chrM_7766_f	0	+	842	1.0
+chrM	9875	11542	uc009vfb.1_exon_0_0_chrM_9876_f	0	+	1667	1.0
+chrM	12405	15288	uc009vfc.1_exon_0_0_chrM_12406_f	0	+	2883	1.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gops_coverage_out_diffCols.interval	Tue Apr 01 09:13:22 2014 -0400
@@ -0,0 +1,65 @@
+chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-	388	1.0
+chr1	147984545	147984630	CCDS990.1_cds_0_0_chr1_147984546_f	0	+	85	1.0
+chr1	148078400	148078582	CCDS993.1_cds_0_0_chr1_148078401_r	0	-	182	1.0
+chr1	148185136	148185276	CCDS996.1_cds_0_0_chr1_148185137_f	0	+	140	1.0
+chr10	55251623	55253124	CCDS7248.1_cds_0_0_chr10_55251624_r	0	-	1501	1.0
+chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-	94	1.0
+chr11	116206508	116206563	CCDS8377.1_cds_0_0_chr11_116206509_f	0	+	55	1.0
+chr11	116211733	116212337	CCDS8378.1_cds_0_0_chr11_116211734_r	0	-	604	1.0
+chr11	1812377	1812407	CCDS7726.1_cds_0_0_chr11_1812378_f	0	+	0	0.0
+chr12	38440094	38440321	CCDS8736.1_cds_0_0_chr12_38440095_r	0	-	227	1.0
+chr13	112381694	112381953	CCDS9526.1_cds_0_0_chr13_112381695_f	0	+	259	1.0
+chr14	98710240	98712285	CCDS9949.1_cds_0_0_chr14_98710241_r	0	-	2045	1.0
+chr15	41486872	41487060	CCDS10096.1_cds_0_0_chr15_41486873_r	0	-	188	1.0
+chr15	41673708	41673857	CCDS10097.1_cds_0_0_chr15_41673709_f	0	+	149	1.0
+chr15	41679161	41679250	CCDS10098.1_cds_0_0_chr15_41679162_r	0	-	89	1.0
+chr15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+	0	0.0
+chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+	95	1.0
+chr16	179963	180135	CCDS10401.1_cds_0_0_chr16_179964_r	0	-	0	0.0
+chr16	244413	244681	CCDS10402.1_cds_0_0_chr16_244414_f	0	+	268	1.0
+chr16	259268	259383	CCDS10403.1_cds_0_0_chr16_259269_r	0	-	115	1.0
+chr18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-	207	1.0
+chr18	59406881	59407046	CCDS11985.1_cds_0_0_chr18_59406882_f	0	+	165	1.0
+chr18	59455932	59456337	CCDS11986.1_cds_0_0_chr18_59455933_r	0	-	405	1.0
+chr18	59600586	59600754	CCDS11988.1_cds_0_0_chr18_59600587_f	0	+	0	0.0
+chr19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+	969	1.0
+chr19	59236026	59236146	CCDS12872.1_cds_0_0_chr19_59236027_r	0	-	120	1.0
+chr19	59297998	59298008	CCDS12877.1_cds_0_0_chr19_59297999_f	0	+	10	1.0
+chr19	59302168	59302288	CCDS12878.1_cds_0_0_chr19_59302169_r	0	-	0	0.0
+chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+	85	1.0
+chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_r	0	-	0	0.0
+chr2	220190202	220190242	CCDS2441.1_cds_0_0_chr2_220190203_f	0	+	0	0.0
+chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-	1260	1.0
+chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-	10	1.0
+chr20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+	186	1.0
+chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-	0	0.0
+chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+	0	0.0
+chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+	0	0.0
+chr21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-	381	1.0
+chr21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+	972	1.0
+chr21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-	0	0.0
+chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+	42	1.0
+chr22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-	242	1.0
+chr22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+	0	0.0
+chr22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_r	0	-	0	0.0
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+	162	1.0
+chr5	131556601	131556672	CCDS4151.1_cds_0_0_chr5_131556602_r	0	-	71	1.0
+chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+	93	1.0
+chr5	131847541	131847666	CCDS4155.1_cds_0_0_chr5_131847542_r	0	-	0	0.0
+chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-	144	1.0
+chr6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+	25	1.0
+chr6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-	106	1.0
+chr6	108722976	108723115	CCDS5067.1_cds_0_0_chr6_108722977_f	0	+	139	1.0
+chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+	168	1.0
+chr7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-	230	1.0
+chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+	53	1.0
+chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	0	-	246	1.0
+chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-	186	1.0
+chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+	33	1.0
+chr9	128787519	128789136	CCDS6915.1_cds_0_0_chr9_128787520_r	0	-	1617	1.0
+chr9	128882427	128882523	CCDS6917.1_cds_0_0_chr9_128882428_f	0	+	0	0.0
+chr9	128937229	128937445	CCDS6919.1_cds_0_0_chr9_128937230_r	0	-	0	0.0
+chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_f	0	+	877	1.0
+chrX	152648964	152649196	CCDS14733.1_cds_0_0_chrX_152648965_r	0	-	232	1.0
+chrX	152691446	152691471	CCDS14735.1_cds_0_0_chrX_152691447_f	0	+	25	1.0
+chrX	152694029	152694263	CCDS14736.1_cds_0_0_chrX_152694030_r	0	-	234	1.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Apr 01 09:13:22 2014 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="bx-python" version="0.7.1">
+      <repository changeset_revision="cdb5991f9790" name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="galaxy-ops" version="1.0.0">
+      <repository changeset_revision="3287c55c02b8" name="package_galaxy_ops_1_0_0" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>