changeset 0:ac6218e2b686 draft default tip

Imported from capsule None
author devteam
date Tue, 01 Apr 2014 10:51:34 -0400
parents
children
files featureCounter.py featureCounter.xml test-data/1.bed test-data/2.bed test-data/6_feature_coverage.bed test-data/chrY1.bed test-data/chrY2.bed test-data/chrY_Coverage.bed tool_dependencies.xml
diffstat 9 files changed, 1341 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/featureCounter.py	Tue Apr 01 10:51:34 2014 -0400
@@ -0,0 +1,146 @@
+#!/usr/bin/env python
+#Guruprasad Ananda
+"""
+Calculate count and coverage of one query on another, and append the Coverage and counts to
+the last four columns as bases covered, percent coverage, number of completely present features, number of partially present/overlapping features.
+
+usage: %prog bed_file_1 bed_file_2 out_file
+    -1, --cols1=N,N,N,N: Columns for chr, start, end, strand in first file
+    -2, --cols2=N,N,N,N: Columns for chr, start, end, strand in second file
+"""
+import sys, fileinput
+from bx.intervals.io import *
+from bx.cookbook import doc_optparse
+from bx.intervals.operations import quicksect
+from galaxy.tools.util.galaxyops import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+def counter(node, start, end):
+    global full, partial
+    if node.start <= start and node.maxend > start:
+        if node.end >= end or (node.start == start and end > node.end > start):
+            full += 1
+        elif end > node.end > start:
+            partial += 1
+        if node.left and node.left.maxend > start:
+            counter(node.left, start, end)
+        if node.right:
+            counter(node.right, start, end)
+    elif start < node.start < end:
+        if node.end <= end:
+            full += 1
+        else:
+            partial += 1
+        if node.left and node.left.maxend > start:
+            counter(node.left, start, end)
+        if node.right:
+            counter(node.right, start, end)
+    else:
+        if node.left:
+            counter(node.left, start, end)
+
+def count_coverage( readers, comments=True ):
+    primary = readers[0]
+    secondary = readers[1]
+    secondary_copy = readers[2]
+    
+    rightTree = quicksect.IntervalTree()
+    for item in secondary:
+        if type( item ) is GenomicInterval:
+            rightTree.insert( item, secondary.linenum, item.fields )
+    
+    bitsets = secondary_copy.binned_bitsets()
+    
+    global full, partial
+    
+    for interval in primary:
+        if type( interval ) is Header:
+            yield interval
+        if type( interval ) is Comment and comments:
+            yield interval
+        elif type( interval ) == GenomicInterval:
+            chrom = interval.chrom
+            start = int(interval.start)
+            end = int(interval.end)
+            full = 0
+            partial = 0
+            if chrom not in bitsets:
+                bases_covered = 0
+                percent = 0.0
+                full = 0
+                partial = 0
+            else:
+                bases_covered = bitsets[ chrom ].count_range( start, end-start )
+                if (end - start) == 0:
+                    percent = 0
+                else:
+                    percent = float(bases_covered) / float(end - start)
+                if bases_covered:
+                    root = rightTree.chroms[chrom]    #root node for the chrom tree
+                    counter(root, start, end)
+            interval.fields.append(str(bases_covered))
+            interval.fields.append(str(percent))
+            interval.fields.append(str(full))
+            interval.fields.append(str(partial))
+            yield interval
+
+
+def main():
+    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 )
+        in1_fname, in2_fname, out_fname = args
+    except:
+        stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )
+    
+    g1 = NiceReaderWrapper( fileinput.FileInput( in1_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 )
+    g2_copy = 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 count_coverage([g1, g2, g2_copy]):
+            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( 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" )
+    elif g2_copy.skipped > 0:
+        print skipped( g2_copy, filedesc=" of 2nd dataset" )
+
+
+if __name__ == "__main__":
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/featureCounter.xml	Tue Apr 01 10:51:34 2014 -0400
@@ -0,0 +1,79 @@
+<tool id="featureCoverage1" name="Feature coverage" version="2.0.0">
+  <description></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">featureCounter.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>
+  
+  <tests>
+    <test>
+      <param name="input1" value="1.bed" />
+      <param name="input2" value="2.bed" />
+      <output name="output" file="6_feature_coverage.bed" />
+    </test>
+    <test>
+      <param name="input1" value="chrY1.bed" />
+      <param name="input2" value="chrY2.bed" />
+      <output name="output" file="chrY_Coverage.bed" />
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool finds the coverage of intervals in the first dataset on intervals in the second dataset. The coverage and count are appended as 4 new columns in the resulting dataset.
+
+-----
+
+**Example**
+
+- If **First dataset** consists of the following windows::
+
+    chrX 1     10001 seg 0 -
+    chrX 10001 20001 seg 0 -
+    chrX 20001 30001 seg 0 -
+    chrX 30001 40001 seg 0 -
+      
+- and **Second dataset** consists of the following exons::
+
+    chrX 5000  6000  seg2 0 -
+    chrX 5500  7000  seg2 0 -
+    chrX 9000  22000 seg2 0 -
+    chrX 24000 34000 seg2 0 -
+    chrX 36000 38000 seg2 0 -
+      
+- the **Result** is the coverage of exons of the second dataset in each of the windows contained in first dataset::
+
+    chrX 1     10001 seg 0 - 3001  0.3001 2 1
+    chrX 10001 20001 seg 0 - 10000 1.0    1 0
+    chrX 20001 30001 seg 0 - 8000  0.8    0 2
+    chrX 30001 40001 seg 0 - 5999  0.5999 1 1
+	  
+- To clarify, the following line of output ( added columns are indexed by a, b and c )::
+
+                         a    b      c d
+    chrX 1 10001 seg 0 - 3001 0.3001 2 1
+                                  
+  implies that 2 exons (c) fall fully in this window (chrX:1-10001), 1 exon (d) partially overlaps this window, and these 3 exons cover 30.01% (c) of the window size, spanning 3001 nucleotides (a).
+
+  * a: number of nucleotides in this window covered by the features in (c) and (d) - features overlapping with each other will be merged to calculate (a)
+  * b: fraction of window size covered by features in (c) and (d) - features overlapping with each other will be merged to calculate (b)
+  * c: number of features in the 2nd dataset that fall **completely** within this window
+  * d: number of features in the 2nd dataset that **partially** overlap this window
+  	 
+</help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.bed	Tue Apr 01 10:51:34 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 10:51:34 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/6_feature_coverage.bed	Tue Apr 01 10:51:34 2014 -0400
@@ -0,0 +1,65 @@
+chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-	388	1.0	1	0
+chr1	147984545	147984630	CCDS990.1_cds_0_0_chr1_147984546_f	0	+	85	1.0	1	0
+chr1	148078400	148078582	CCDS993.1_cds_0_0_chr1_148078401_r	0	-	182	1.0	1	0
+chr1	148185136	148185276	CCDS996.1_cds_0_0_chr1_148185137_f	0	+	140	1.0	1	0
+chr10	55251623	55253124	CCDS7248.1_cds_0_0_chr10_55251624_r	0	-	1501	1.0	1	0
+chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-	94	1.0	1	0
+chr11	116206508	116206563	CCDS8377.1_cds_0_0_chr11_116206509_f	0	+	55	1.0	1	0
+chr11	116211733	116212337	CCDS8378.1_cds_0_0_chr11_116211734_r	0	-	604	1.0	1	0
+chr11	1812377	1812407	CCDS7726.1_cds_0_0_chr11_1812378_f	0	+	0	0.0	0	0
+chr12	38440094	38440321	CCDS8736.1_cds_0_0_chr12_38440095_r	0	-	227	1.0	1	0
+chr13	112381694	112381953	CCDS9526.1_cds_0_0_chr13_112381695_f	0	+	259	1.0	1	0
+chr14	98710240	98712285	CCDS9949.1_cds_0_0_chr14_98710241_r	0	-	2045	1.0	1	0
+chr15	41486872	41487060	CCDS10096.1_cds_0_0_chr15_41486873_r	0	-	188	1.0	1	0
+chr15	41673708	41673857	CCDS10097.1_cds_0_0_chr15_41673709_f	0	+	149	1.0	1	0
+chr15	41679161	41679250	CCDS10098.1_cds_0_0_chr15_41679162_r	0	-	89	1.0	1	0
+chr15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+	0	0.0	0	0
+chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+	95	1.0	1	0
+chr16	179963	180135	CCDS10401.1_cds_0_0_chr16_179964_r	0	-	0	0.0	0	0
+chr16	244413	244681	CCDS10402.1_cds_0_0_chr16_244414_f	0	+	268	1.0	1	0
+chr16	259268	259383	CCDS10403.1_cds_0_0_chr16_259269_r	0	-	115	1.0	1	0
+chr18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-	207	1.0	1	0
+chr18	59406881	59407046	CCDS11985.1_cds_0_0_chr18_59406882_f	0	+	165	1.0	1	0
+chr18	59455932	59456337	CCDS11986.1_cds_0_0_chr18_59455933_r	0	-	405	1.0	1	0
+chr18	59600586	59600754	CCDS11988.1_cds_0_0_chr18_59600587_f	0	+	0	0.0	0	0
+chr19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+	969	1.0	1	0
+chr19	59236026	59236146	CCDS12872.1_cds_0_0_chr19_59236027_r	0	-	120	1.0	1	0
+chr19	59297998	59298008	CCDS12877.1_cds_0_0_chr19_59297999_f	0	+	10	1.0	1	0
+chr19	59302168	59302288	CCDS12878.1_cds_0_0_chr19_59302169_r	0	-	0	0.0	0	0
+chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+	85	1.0	1	0
+chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_r	0	-	0	0.0	0	0
+chr2	220190202	220190242	CCDS2441.1_cds_0_0_chr2_220190203_f	0	+	0	0.0	0	0
+chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-	1260	1.0	1	0
+chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-	10	1.0	1	0
+chr20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+	186	1.0	1	0
+chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-	0	0.0	0	0
+chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+	0	0.0	0	0
+chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+	0	0.0	0	0
+chr21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-	381	1.0	1	0
+chr21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+	972	1.0	1	0
+chr21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-	0	0.0	0	0
+chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+	42	1.0	1	0
+chr22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-	242	1.0	1	0
+chr22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+	0	0.0	0	0
+chr22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_r	0	-	0	0.0	0	0
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+	162	1.0	1	0
+chr5	131556601	131556672	CCDS4151.1_cds_0_0_chr5_131556602_r	0	-	71	1.0	1	0
+chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+	93	1.0	1	0
+chr5	131847541	131847666	CCDS4155.1_cds_0_0_chr5_131847542_r	0	-	0	0.0	0	0
+chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-	144	1.0	1	0
+chr6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+	25	1.0	1	0
+chr6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-	106	1.0	1	0
+chr6	108722976	108723115	CCDS5067.1_cds_0_0_chr6_108722977_f	0	+	139	1.0	1	0
+chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+	168	1.0	1	0
+chr7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-	230	1.0	1	0
+chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+	53	1.0	1	0
+chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	0	-	246	1.0	1	0
+chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-	186	1.0	1	0
+chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+	33	1.0	1	0
+chr9	128787519	128789136	CCDS6915.1_cds_0_0_chr9_128787520_r	0	-	1617	1.0	1	0
+chr9	128882427	128882523	CCDS6917.1_cds_0_0_chr9_128882428_f	0	+	0	0.0	0	0
+chr9	128937229	128937445	CCDS6919.1_cds_0_0_chr9_128937230_r	0	-	0	0.0	0	0
+chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_f	0	+	877	1.0	1	0
+chrX	152648964	152649196	CCDS14733.1_cds_0_0_chrX_152648965_r	0	-	232	1.0	1	0
+chrX	152691446	152691471	CCDS14735.1_cds_0_0_chrX_152691447_f	0	+	25	1.0	1	0
+chrX	152694029	152694263	CCDS14736.1_cds_0_0_chrX_152694030_r	0	-	234	1.0	1	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrY1.bed	Tue Apr 01 10:51:34 2014 -0400
@@ -0,0 +1,237 @@
+chrY	132990	160020	uc004fon.1	0	+	140854	156002	0	9	71,203,148,137,129,156,184,296,761,	0,5158,7843,12409,14324,15175,16711,22773,26269,
+chrY	138078	156125	uc004foo.1	0	+	140854	156002	0	7	273,148,137,129,156,184,362,	0,2755,7321,9236,10087,11623,17685,
+chrY	157538	160020	uc004fop.1	0	+	157538	157538	0	1	2482,	0,
+chrY	161425	168795	uc004foq.1	0	-	161740	168184	0	4	439,153,149,710,	0,2601,2973,6660,
+chrY	161425	170887	uc004for.1	0	-	161740	170886	0	6	439,153,149,209,159,71,	0,2601,2973,6660,8007,9391,
+chrY	214969	222590	uc004fos.1	0	-	215101	221653	0	5	283,107,119,176,549,	0,4369,4543,6530,7072,
+chrY	214969	267627	uc004fot.1	0	-	215101	267426	0	13	283,107,119,176,90,49,157,87,75,103,104,186,525,	0,4369,4543,6530,7072,7648,11281,11939,12466,12999,13355,27170,52133,
+chrY	505078	527558	uc004fou.1	0	+	511632	525371	0	6	259,709,209,58,89,2433,	0,6122,10274,16477,16655,20047,
+chrY	505078	540146	uc004fov.1	0	+	511632	539564	0	6	259,709,209,58,89,627,	0,6122,10274,16477,16655,34441,
+chrY	720013	720042	uc004fow.1	0	+	720013	720013	0	1	29,	0,
+chrY	1274886	1291530	uc004fox.1	0	-	1274889	1291527	0	6	128,163,134,167,103,82,	0,2532,6385,10439,12812,16562,
+chrY	1274886	1291530	uc004foy.1	0	-	1274889	1285338	0	5	128,163,134,167,82,	0,2532,6385,10439,16562,
+chrY	1274886	1291530	uc004foz.1	0	-	1274886	1274886	0	6	128,345,134,167,100,82,	0,2777,6385,10439,12812,16562,
+chrY	1347700	1388827	uc004fpa.1	0	+	1361596	1388372	0	13	72,88,102,143,124,130,173,134,30,136,97,82,533,	0,5947,13870,16970,19711,19951,21529,25520,26619,31683,35115,36638,40594,
+chrY	1347700	1388827	uc004fpb.1	0	+	1361596	1388372	0	13	72,64,102,143,124,130,173,134,30,136,97,82,533,	0,5947,13870,16970,19711,19951,21529,25520,26619,31683,35115,36638,40594,
+chrY	1347700	1388827	uc004fpc.1	0	+	1361596	1388482	0	11	72,88,102,143,124,130,173,134,30,136,533,	0,5947,13870,16970,19711,19951,21529,25520,26619,31683,40594,
+chrY	1347700	1388827	uc004fpd.1	0	+	1361596	1384394	0	9	72,88,102,143,124,130,173,82,533,	0,5947,13870,16970,19711,19951,21529,36638,40594,
+chrY	1361570	1388827	uc004fpe.1	0	+	1361596	1384394	0	10	102,143,124,130,173,134,30,136,82,533,	0,3100,5841,6081,7659,11650,12749,17813,22768,26724,
+chrY	1415508	1461582	uc004fpf.1	0	+	1420658	1461358	0	12	311,102,119,115,133,185,116,27,115,106,82,299,	0,5112,8700,11815,15484,15706,19605,22245,28522,42043,44407,45775,
+chrY	1465044	1470994	uc004fpg.1	0	-	1465494	1470902	0	4	608,141,487,203,	0,1127,3089,5747,
+chrY	1465044	1470994	uc004fph.1	0	-	1465044	1465044	0	5	608,141,487,211,203,	0,1127,3089,3931,5747,
+chrY	1480908	1492007	uc004fpi.1	0	+	1480988	1491908	0	3	210,125,372,	0,1445,10727,
+chrY	1480908	1494107	uc004fpj.1	0	+	1480908	1480908	0	5	210,125,146,549,472,	0,1445,10727,11746,12727,
+chrY	1482031	1531844	uc004fpk.1	0	-	1482161	1531733	0	13	351,123,144,133,185,163,388,109,62,65,48,132,204,	0,9593,14834,15843,18519,22386,24595,29130,31883,32555,35958,39047,49609,
+chrY	1482031	1531844	uc004fpl.1	0	-	1482161	1531733	0	12	351,123,144,133,185,163,388,109,62,65,132,204,	0,9593,14834,15843,18519,22386,24595,29130,31883,32555,39047,49609,
+chrY	1541465	1616000	uc004fpm.1	0	-	1544371	1545451	0	2	4010,187,	0,74348,
+chrY	1670485	1681411	uc004fpn.1	0	+	1672355	1680487	0	5	177,781,149,241,1860,	0,1851,3791,7599,9066,
+chrY	1670485	1681411	uc004fpo.1	0	+	1670485	1670485	0	6	177,781,149,241,70,1860,	0,1851,3791,7599,8545,9066,
+chrY	1674276	1721974	uc004fpp.1	0	+	1694092	1721907	0	10	149,172,175,130,69,119,84,141,123,279,	0,19713,27755,28885,32319,34437,37320,37766,41054,47419,
+chrY	1674276	1721974	uc004fpq.1	0	+	1694092	1721907	0	10	149,136,175,130,69,119,84,141,123,279,	0,19749,27755,28885,32319,34437,37320,37766,41054,47419,
+chrY	1694025	1721974	uc004fpr.1	0	+	1694092	1721907	0	7	136,175,130,69,119,123,279,	0,8006,9136,12570,14688,21305,27670,
+chrY	2147552	2429008	uc004fps.1	0	-	2149081	2428966	0	7	1718,208,208,102,69,108,151,	0,23511,47228,71990,189233,205685,281305,
+chrY	2414454	2429008	uc004fpt.1	0	-	2416675	2418760	0	2	4356,151,	0,14403,
+chrY	2414467	2428580	uc004fpu.1	0	-	2416675	2418760	0	2	4346,229,	0,13884,
+chrY	2537432	2566735	uc004fpv.1	0	+	2537432	2537432	0	10	90,43,69,154,45,69,45,69,46,721,	0,1604,2758,6424,9348,10037,13298,13993,17205,28582,
+chrY	2537432	2585270	uc004fpw.1	0	+	2537432	2537432	0	9	90,43,69,154,45,69,69,46,2203,	0,1604,2758,6424,9348,10037,13993,17205,45635,
+chrY	2544659	2566735	uc004fpx.1	0	+	2544659	2544659	0	5	2166,69,69,46,721,	0,2810,6766,9978,21355,
+chrY	2592344	2594082	uc004fpy.1	0	+	2592344	2592344	0	1	1738,	0,
+chrY	2619227	2669350	uc004fpz.1	0	+	2619401	2668845	0	10	241,33,48,45,69,48,51,114,57,531,	0,23235,26418,28474,29169,31440,32127,35073,47013,49592,
+chrY	2619227	2669350	uc004fqa.1	0	+	2619227	2619227	0	11	241,33,48,45,69,48,51,114,18,54,531,	0,23235,26418,28474,29169,31440,32127,35073,42170,47016,49592,
+chrY	2619227	2669350	uc004fqb.1	0	+	2619401	2668845	0	10	241,33,48,45,69,48,51,114,54,531,	0,23235,26418,28474,29169,31440,32127,35073,47016,49592,
+chrY	2680336	2715675	uc004fqc.1	0	+	2680336	2680336	0	5	40,42,24,59,155,	0,18254,22420,34699,35184,
+chrY	2680336	2718962	uc004fqd.1	0	+	2680336	2680336	0	4	40,42,24,1173,	0,18254,22420,37453,
+chrY	2680336	2773784	uc004fqe.1	0	+	2769665	2773784	0	8	40,42,24,56,142,78,181,98,	0,18254,22420,88732,89190,89869,91781,93350,
+chrY	2680336	2782812	uc004fqf.1	0	+	2680363	2782811	0	5	40,42,24,98,172,	0,18254,22420,93350,102304,
+chrY	2714895	2715792	uc004fqg.1	0	-	2715029	2715644	0	1	897,	0,
+chrY	2717789	2718962	uc004fqh.1	0	+	2717789	2717789	0	1	1173,	0,
+chrY	2769526	2794997	uc004fqi.1	0	+	2769665	2794935	0	7	142,78,181,98,172,158,164,	0,679,2591,4160,13114,23602,25307,
+chrY	2863545	2909891	uc004fqj.1	0	+	2881977	2908034	0	8	265,89,573,150,144,153,141,3041,	0,18404,25569,39590,40006,41165,42435,43305,
+chrY	3507125	3508082	uc004fqk.1	0	+	3507285	3507843	0	2	43,818,	0,139,
+chrY	4928266	5033485	uc004fql.1	0	+	4960737	5032402	0	6	380,106,59,571,2493,1101,	0,31680,32444,56663,97989,104118,
+chrY	4928266	5033485	uc004fqm.1	0	+	4960737	5032402	0	7	380,169,106,59,571,2493,1101,	0,30673,31680,32444,56663,97989,104118,
+chrY	4984130	5033485	uc004fqn.1	0	+	4984864	5032402	0	3	1370,2493,1101,	0,42125,48254,
+chrY	4984130	5670264	uc004fqo.1	0	+	4984864	5665983	0	5	1370,2493,199,24,4952,	0,42125,444967,525685,681182,
+chrY	5026255	5029478	uc004fqp.1	0	+	5026306	5028781	0	1	3223,	0,
+chrY	6170486	6171651	uc004fqq.1	0	-	6170486	6170486	0	3	309,146,57,	0,849,1108,
+chrY	6174263	6177053	uc004fqr.1	0	+	6174309	6176866	0	6	532,78,112,146,82,210,	0,1133,1339,1552,1804,2580,
+chrY	6174263	6177053	uc004fqs.1	0	+	6174309	6176119	0	6	532,78,112,146,93,210,	0,1133,1339,1552,1793,2580,
+chrY	6318471	6339605	uc004fqt.1	0	+	6318471	6318471	0	5	245,160,109,138,258,	0,3669,10692,13157,20876,
+chrY	6334284	6352186	uc004fqu.1	0	-	6334284	6334284	0	7	680,198,79,157,149,87,1818,	0,1903,2221,5130,5979,13521,16084,
+chrY	6371474	6375118	uc004fqv.1	0	+	6371474	6371474	0	2	202,105,	0,3539,
+chrY	6377508	6385947	uc004fqw.1	0	+	6377508	6377508	0	7	37,162,75,477,114,256,246,	0,978,3447,4210,6604,7691,8193,
+chrY	6377508	6385947	uc004fqx.1	0	+	6377508	6377508	0	6	37,162,75,477,114,246,	0,978,3447,4210,6604,8193,
+chrY	6399071	6401671	uc004fqy.1	0	-	6399071	6399071	0	3	190,205,136,	0,1782,2464,
+chrY	6793958	6802068	uc004fqz.1	0	-	6794113	6800649	0	6	161,426,45,48,66,56,	0,2119,2814,4088,6637,8054,
+chrY	6796077	6800661	uc004fra.1	0	-	6796077	6800649	0	5	426,45,42,48,66,	0,695,831,1969,4518,
+chrY	6838726	7019724	uc004frb.1	0	+	6953125	7019533	0	19	297,85,31,95,89,108,146,253,133,142,64,98,61,122,75,128,166,102,212,	0,1402,67527,85118,110763,114349,132294,153211,159510,160034,160874,161047,163874,170046,175212,175604,176581,179403,180786,
+chrY	6838726	7019724	uc004frc.1	0	+	6953125	7019533	0	18	297,85,95,89,108,146,253,133,142,64,98,61,122,75,128,166,102,212,	0,1402,85118,110763,114349,132294,153211,159510,160034,160874,161047,163874,170046,175212,175604,176581,179403,180786,
+chrY	6838726	7019724	uc004frd.1	0	+	6953125	7019533	0	18	297,85,31,89,108,146,253,133,142,64,98,61,122,75,128,166,102,212,	0,1402,67527,110763,114349,132294,153211,159510,160034,160874,161047,163874,170046,175212,175604,176581,179403,180786,
+chrY	7202013	7309588	uc004fre.1	0	+	7202353	7295415	0	8	506,169,264,120,96,78,147,5836,	0,29964,51933,67142,82162,93383,97770,101739,
+chrY	7627397	7629288	uc004frf.1	0	-	7627397	7627397	0	2	131,61,	0,1830,
+chrY	7670635	7737302	uc004frg.1	0	-	7670635	7670635	0	5	433,187,195,110,108,	0,33926,34239,62900,66559,
+chrY	7732964	7738723	uc004frh.1	0	+	7732964	7732964	0	2	156,822,	0,4937,
+chrY	8611410	8611919	uc004fri.1	0	-	8611410	8611410	0	2	63,158,	0,351,
+chrY	8632512	8633324	uc004frj.1	0	+	8632512	8632512	0	2	88,181,	0,631,
+chrY	8711360	8745423	uc004frk.1	0	-	8711360	8711360	0	5	87,316,303,84,37,	0,568,5680,11541,34026,
+chrY	9214669	9220483	uc004frl.1	0	-	9214669	9214669	0	4	31,178,104,114,	0,1931,5124,5700,
+chrY	9227488	9232441	uc004frm.1	0	-	9227488	9227488	0	2	177,82,	0,4871,
+chrY	9235072	9237886	uc004frn.1	0	+	9235118	9236952	0	7	265,267,78,112,146,93,210,	0,283,1157,1363,1576,1817,2604,
+chrY	9235072	9237886	uc004fro.1	0	+	9235118	9237699	0	7	265,267,78,112,146,82,210,	0,283,1157,1363,1576,1828,2604,
+chrY	9247188	9273071	uc004frp.1	0	-	9247188	9247188	0	8	60,159,146,102,60,159,146,102,	0,3610,5269,5501,20277,23886,25549,25781,
+chrY	9255405	9258201	uc004frq.1	0	+	9255451	9257267	0	6	532,78,112,146,93,210,	0,1139,1345,1558,1799,2586,
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+chrY	9275684	9278479	uc004frs.1	0	+	9275684	9275684	0	6	531,78,112,146,93,210,	0,1138,1344,1557,1798,2585,
+chrY	9275684	9298825	uc004frt.1	0	+	9296075	9298638	0	12	531,78,112,146,82,210,532,78,112,146,82,210,	0,1138,1344,1557,1809,2585,20345,21484,21690,21903,22155,22931,
+chrY	9296029	9298825	uc004fru.1	0	+	9296075	9297891	0	6	532,78,112,146,93,210,	0,1139,1345,1558,1799,2586,
+chrY	9906351	9911962	uc004frv.1	0	-	9906351	9906351	0	4	60,159,146,110,	0,3615,5269,5501,
+chrY	9914563	9917357	uc004frw.1	0	+	9914609	9917170	0	6	532,78,112,146,82,210,	0,1139,1345,1558,1810,2584,
+chrY	9914563	9917357	uc004frx.1	0	+	9914609	9916425	0	6	532,78,112,146,93,210,	0,1139,1345,1558,1799,2584,
+chrY	9926661	9932263	uc004fry.1	0	-	9926661	9926661	0	4	60,159,146,102,	0,3611,5268,5500,
+chrY	9934894	9937527	uc004frz.1	0	+	9934921	9937502	0	7	246,267,78,112,146,82,48,	0,264,1138,1344,1557,1809,2585,
+chrY	9934894	9937527	uc004fsa.1	0	+	9934921	9936755	0	7	246,267,78,112,146,93,48,	0,264,1138,1344,1557,1798,2585,
+chrY	9955177	9957971	uc004fsb.1	0	+	9955527	9957037	0	7	246,266,78,112,146,93,210,	0,264,1137,1343,1556,1797,2584,
+chrY	9955177	9957971	uc004fsc.1	0	+	9955527	9957784	0	7	246,266,78,112,146,82,210,	0,264,1137,1343,1556,1808,2584,
+chrY	9967274	9972885	uc004fsd.1	0	-	9967274	9967274	0	4	60,159,146,110,	0,3610,5269,5501,
+chrY	9975488	9978284	uc004fse.1	0	+	9975534	9978097	0	6	532,78,112,146,82,210,	0,1139,1345,1558,1810,2586,
+chrY	9975488	9978284	uc004fsf.1	0	+	9975534	9977350	0	6	532,78,112,146,93,210,	0,1139,1345,1558,1799,2586,
+chrY	10058329	10062762	uc004fsg.1	0	-	10058329	10058329	0	3	151,102,64,	0,4061,4369,
+chrY	10138708	10141308	uc004fsh.1	0	+	10138708	10138708	0	3	136,205,190,	0,613,2410,
+chrY	10154432	10162871	uc004fsi.1	0	-	10154432	10154432	0	7	246,256,114,477,75,162,37,	0,492,1721,3752,4917,7299,8402,
+chrY	10154432	10162871	uc004fsj.1	0	-	10154432	10154432	0	6	246,114,477,75,162,37,	0,1721,3752,4917,7299,8402,
+chrY	10165261	10168905	uc004fsk.1	0	-	10165261	10165261	0	2	105,202,	0,3442,
+chrY	10188192	10206085	uc004fsl.1	0	+	10188192	10188192	0	7	1818,87,149,157,79,198,680,	0,4294,11765,12606,15593,15792,17213,
+chrY	10200764	10221898	uc004fsm.1	0	-	10200764	10200764	0	5	258,138,109,160,245,	0,7839,10333,17305,20889,
+chrY	10248761	10260854	uc004fsn.1	0	+	10248761	10248761	0	5	155,112,75,39,46,	0,3621,8158,8918,12047,
+chrY	10358406	10359571	uc004fso.1	0	+	10358406	10358406	0	3	57,146,309,	0,170,856,
+chrY	10540971	10542306	uc004fsp.1	0	+	10540971	10540971	0	2	285,158,	0,1177,
+chrY	11792095	11792124	uc004fsq.1	0	+	11792095	11792095	0	1	29,	0,
+chrY	11794588	11794618	uc004fsr.1	0	-	11794588	11794588	0	1	30,	0,
+chrY	13283691	13313547	uc004fss.1	0	+	13283691	13283691	0	4	340,47,94,4761,	0,2273,24144,25095,
+chrY	13322553	13482162	uc004fst.1	0	+	13330774	13480735	0	46	825,60,156,149,80,113,219,116,252,139,153,105,207,137,134,88,343,96,212,241,150,121,131,279,126,126,170,109,147,147,223,221,191,174,142,751,124,226,130,186,221,89,157,213,96,1565,	0,7407,8161,19362,20881,23886,25348,34386,34772,35185,36931,38299,55962,57276,59254,69842,72357,74245,75423,76793,77380,78300,84977,85295,89180,90272,91805,108954,109447,110410,111605,114899,117195,132454,136677,138630,139776,141006,141829,145098,145698,146004,155105,155398,156331,158044,
+chrY	13525412	13541784	uc004fsu.1	0	+	13526241	13539428	0	18	307,47,58,48,130,156,100,136,86,99,161,145,145,182,118,154,140,2436,	0,827,3429,5252,7732,8620,8856,9611,10457,10777,10960,11523,11776,12154,12410,12800,13296,13936,
+chrY	13526170	13541784	uc004fsv.1	0	+	13526241	13539428	0	17	116,58,48,130,156,100,136,86,99,161,145,145,182,118,154,140,2436,	0,2671,4494,6974,7862,8098,8853,9699,10019,10202,10765,11018,11396,11652,12042,12538,13178,
+chrY	13855854	13980437	uc004fsw.1	0	-	13855855	13980379	0	18	247,171,127,142,188,115,149,75,65,206,106,130,773,396,96,93,156,76,	0,16436,25697,63126,64376,68296,70818,71457,71605,88974,90020,91640,100982,120422,121342,123296,123883,124507,
+chrY	13869656	14101944	uc004fsx.1	0	-	13871129	14100939	0	28	1500,171,127,142,188,115,149,75,65,206,106,130,773,396,96,93,220,99,127,94,35,55,121,59,50,109,64,1157,	0,2634,11895,49324,50574,54494,57016,57655,57803,75172,76218,77838,87180,106620,107540,109494,111384,112047,117884,120873,145476,148535,162610,166352,200634,221738,230871,231131,
+chrY	13918782	14101944	uc004fsy.1	0	-	13918976	14100939	0	25	340,188,115,149,75,65,206,106,130,773,396,96,93,220,99,127,94,35,55,121,59,50,109,64,1157,	0,1448,5368,7890,8529,8677,26046,27092,28712,38054,57494,58414,60368,62258,62921,68758,71747,96350,99409,113484,117226,151508,172612,181745,182005,
+chrY	13944307	14101944	uc004fsz.1	0	-	13944387	14100939	0	20	335,206,106,130,773,396,96,93,220,99,127,94,35,55,121,59,50,109,64,1157,	0,521,1567,3187,12529,31969,32889,34843,36733,37396,43233,46222,70825,73884,87959,91701,125983,147087,156220,156480,
+chrY	14017575	14101944	uc004fta.1	0	-	14018177	14100939	0	7	671,121,59,50,109,64,1157,	0,14691,18433,52715,73819,82952,83212,
+chrY	14324840	14327296	uc004ftb.1	0	+	14325609	14326533	0	2	869,798,	0,1658,
+chrY	14607045	14607786	uc004ftc.1	0	-	14607144	14607714	0	2	375,174,	0,567,
+chrY	14677491	14678232	uc004ftd.1	0	+	14677563	14678133	0	2	174,375,	0,366,
+chrY	15144025	15464921	uc004fte.1	0	+	15344422	15462536	0	6	190,60,153,186,790,3235,	0,196707,200365,301436,306978,317661,
+chrY	15145019	15464921	uc004ftf.1	0	+	15451113	15462536	0	9	153,571,60,153,111,122,186,790,3235,	0,98275,195713,199371,224873,227935,300442,305984,316667,
+chrY	15145019	15464921	uc004ftg.1	0	+	15243393	15462536	0	6	153,571,153,186,790,3235,	0,98275,199371,300442,305984,316667,
+chrY	15145847	15464921	uc004fth.1	0	+	15243393	15462536	0	6	363,583,153,186,790,3235,	0,97435,198543,299614,305156,315839,
+chrY	15243294	15354818	uc004fti.1	0	+	15243393	15354811	0	4	571,60,153,93,	0,97438,101096,111431,
+chrY	18196434	18200747	uc004ftj.1	0	-	18196434	18196434	0	3	207,118,158,	0,1542,4155,
+chrY	18390253	18391834	uc004ftk.1	0	-	18390817	18391171	0	1	1581,	0,
+chrY	18499533	18501494	uc004ftl.1	0	-	18499540	18501166	0	1	1961,	0,
+chrY	18647060	18649021	uc004ftm.1	0	+	18647388	18649014	0	1	1961,	0,
+chrY	18756722	18758303	uc004ftn.1	0	+	18757385	18757739	0	1	1581,	0,
+chrY	18947806	18952124	uc004fto.1	0	+	18947806	18947806	0	3	158,118,207,	0,2658,4111,
+chrY	19167944	19169866	uc004ftp.1	0	+	19168061	19169745	0	2	630,814,	0,1108,
+chrY	19167944	19210237	uc004ftq.1	0	+	19168061	19172078	0	6	630,110,87,155,86,428,	0,3443,4112,5246,36002,41865,
+chrY	19167944	19210237	uc004ftr.1	0	+	19168061	19209908	0	2	630,428,	0,41865,
+chrY	19202479	19211795	uc004fts.1	0	-	19202479	19202479	0	5	1143,137,114,101,142,	0,6206,6925,7400,9174,
+chrY	19351155	19360471	uc004ftt.1	0	+	19351155	19351155	0	5	142,101,114,137,1143,	0,1815,2277,2973,8173,
+chrY	19352713	19395009	uc004ftu.1	0	-	19390871	19394892	0	6	428,86,155,87,110,630,	0,6205,36891,38093,38743,41666,
+chrY	19352713	19395009	uc004ftv.1	0	-	19353042	19394892	0	2	428,630,	0,41666,
+chrY	19393087	19395009	uc004ftw.1	0	-	19393208	19394892	0	2	814,630,	0,1292,
+chrY	19493774	19499502	uc004ftx.1	0	-	19493774	19493774	0	2	334,1161,	0,4567,
+chrY	19553972	19698690	uc004fty.1	0	-	19553972	19553972	0	2	143,372,	0,144346,
+chrY	19611913	19614093	uc004ftz.1	0	-	19613740	19613983	0	1	2180,	0,
+chrY	20076704	20124427	uc004fua.1	0	-	20076704	20076704	0	9	1434,156,78,122,919,240,264,126,122,	0,3493,3858,9675,11025,18474,19209,24738,47601,
+chrY	20076704	20124427	uc004fub.1	0	-	20076704	20076704	0	11	1434,61,156,78,146,122,919,240,264,126,122,	0,1626,3493,3858,4528,9675,11025,18474,19209,24738,47601,
+chrY	20188623	20211564	uc004fuc.1	0	+	20208498	20209756	0	4	221,298,1243,208,	0,19860,21020,22733,
+chrY	20188655	20211564	uc004fud.1	0	+	20208498	20211377	0	4	101,298,92,208,	0,19828,22139,22701,
+chrY	20213723	20225769	uc004fue.1	0	+	20218906	20225394	0	5	365,4267,93,96,699,	0,949,7289,9766,11347,
+chrY	20326688	20337013	uc004fuf.1	0	-	20327268	20336982	0	11	931,200,70,600,138,180,139,128,97,148,125,	0,1026,1379,1732,2519,2829,3460,4036,4961,9937,10200,
+chrY	20326688	20366212	uc004fug.1	0	-	20327268	20365808	0	27	931,200,70,600,138,180,139,359,97,148,125,182,195,120,163,182,159,120,159,146,130,135,171,123,78,169,268,	0,1026,1379,1732,2519,2829,3460,4036,4961,9937,10200,10408,10864,11181,15457,15715,26357,26631,27169,29937,30206,34113,35903,36320,37747,38970,39256,
+chrY	20342403	20366212	uc004fuh.1	0	-	20342405	20365808	0	11	182,159,120,159,146,130,171,123,78,169,268,	0,10642,10916,11454,14222,14491,20188,20605,22032,23255,23541,
+chrY	21021299	21023423	uc004fui.1	0	-	21021299	21021299	0	1	2124,	0,
+chrY	21036941	21090502	uc004fuj.1	0	-	21036941	21036941	0	6	155,240,60,110,105,958,	0,760,2521,4204,41684,52603,
+chrY	21146998	21164428	uc004fuk.1	0	+	21147145	21163620	0	7	163,84,104,51,82,92,814,	0,3883,6865,8749,12299,13759,16616,
+chrY	21146998	21164428	uc004ful.1	0	+	21147145	21163620	0	6	163,84,104,82,92,814,	0,3883,6865,12299,13759,16616,
+chrY	21327341	21352306	uc004fum.1	0	+	21327437	21352306	0	7	99,78,181,98,172,158,102,	0,710,3800,5216,12737,23441,24863,
+chrY	21966421	21972836	uc004fun.1	0	-	21966473	21972204	0	5	144,89,111,104,86,	0,552,723,5775,6329,
+chrY	22082636	22097060	uc004fuo.1	0	+	22084624	22096782	0	12	123,113,104,178,153,115,111,111,111,111,89,577,	0,1984,2571,5694,7787,9950,11020,11572,12117,13149,13347,13847,
+chrY	22082636	22097060	uc004fup.1	0	+	22090452	22096782	0	11	123,113,104,153,115,111,111,111,111,89,577,	0,1984,2571,7787,9950,11020,11572,12117,13149,13347,13847,
+chrY	22106177	22120600	uc004fuq.1	0	+	22108165	22120322	0	12	123,113,104,178,153,115,111,111,111,111,89,577,	0,1984,2571,5694,7787,9950,11020,11572,12117,13149,13346,13846,
+chrY	22106177	22120600	uc004fur.1	0	+	22113993	22120322	0	11	123,113,104,153,115,111,111,111,111,89,577,	0,1984,2571,7787,9950,11020,11572,12117,13149,13346,13846,
+chrY	22154873	22165940	uc004fus.1	0	-	22154873	22154873	0	6	63,92,162,99,162,81,	0,1183,3901,5672,6366,10986,
+chrY	22381088	22702366	uc004fut.1	0	+	22381088	22381088	0	4	25,114,138,239,	0,319412,319744,321039,
+chrY	22435610	22450036	uc004fuu.1	0	-	22435888	22448048	0	12	577,89,111,111,111,111,115,153,178,104,113,123,	0,988,1164,2196,2741,3293,4359,6484,8552,11749,12329,14303,
+chrY	22435610	22450036	uc004fuv.1	0	-	22435888	22442218	0	11	577,89,111,111,111,111,115,153,104,113,123,	0,988,1164,2196,2741,3293,4359,6484,11749,12329,14303,
+chrY	22459152	22473577	uc004fuw.1	0	-	22459430	22471589	0	12	577,89,111,111,111,111,115,153,178,104,113,123,	0,988,1163,2195,2740,3292,4358,6483,8551,11748,12328,14302,
+chrY	22459152	22473577	uc004fux.1	0	-	22459430	22465759	0	11	577,89,111,111,111,111,115,153,104,113,123,	0,988,1163,2195,2740,3292,4358,6483,11748,12328,14302,
+chrY	22627290	22651542	uc004fuy.1	0	-	22627857	22640374	0	5	826,116,121,87,88,	0,10324,13015,23976,24164,
+chrY	22700521	22702366	uc004fuz.1	0	-	22700521	22700521	0	3	93,138,239,	0,311,1606,
+chrY	22724076	22738477	uc004fva.1	0	-	22724354	22736504	0	12	577,89,111,111,111,111,115,153,178,104,113,108,	0,988,1163,2197,2742,3293,4359,6484,8552,11749,12319,14293,
+chrY	22852332	22854411	uc004fvb.1	0	-	22852332	22852332	0	2	991,571,	0,1508,
+chrY	22864393	22871740	uc004fvc.1	0	+	22866398	22870300	0	4	112,113,104,1713,	0,2001,2536,5634,
+chrY	22864393	22973416	uc004fvd.1	0	+	22960982	22973138	0	12	112,113,104,178,153,115,111,111,111,111,89,577,	0,96585,97166,100293,102386,104549,105619,106170,106715,107749,107946,108446,
+chrY	22959010	22973416	uc004fve.1	0	+	22960982	22973138	0	12	107,113,104,178,153,115,111,111,111,111,89,577,	0,1968,2549,5676,7769,9932,11002,11553,12098,13132,13329,13829,
+chrY	22995127	22996972	uc004fvf.1	0	+	22995127	22995127	0	3	239,138,93,	0,1396,1752,
+chrY	22995127	22996994	uc004fvg.1	0	-	22995127	22995127	0	4	239,99,138,115,	0,1187,1396,1752,
+chrY	23045931	23070172	uc004fvh.1	0	+	23057099	23069605	0	5	88,87,121,116,826,	0,189,11116,13812,23415,
+chrY	23407118	23408250	uc004fvi.1	0	+	23407118	23407118	0	2	60,106,	0,1026,
+chrY	23539797	23560998	uc004fvj.1	0	+	23547878	23553803	0	9	31,123,137,119,118,106,125,125,320,	0,306,3494,8040,10218,13189,13987,20662,20881,
+chrY	23684894	23696347	uc004fvk.1	0	-	23690744	23696301	0	5	1852,99,72,35,187,	0,5815,8850,10487,11266,
+chrY	23684894	23735812	uc004fvl.1	0	-	23690744	23725624	0	20	1852,99,35,72,72,72,72,72,72,72,72,72,140,64,52,92,147,140,64,52,	0,5815,10487,11266,13651,23437,25814,28210,30593,32989,35380,37825,39297,39526,40026,40638,41004,50137,50366,50866,
+chrY	23684894	23754545	uc004fvm.1	0	-	23690744	23754335	0	23	1852,99,35,72,72,72,72,72,72,72,72,72,140,64,52,92,147,140,64,52,92,147,213,	0,5815,10487,11266,13651,23437,25814,28210,30593,32989,35380,37825,39297,39526,40026,40638,41004,60985,61214,61714,62326,62692,69438,
+chrY	23684894	23754545	uc004fvn.1	0	-	23690744	23754335	0	17	1852,99,35,72,72,72,72,72,72,72,72,140,64,52,92,147,213,	0,5815,10487,11266,23437,25814,28210,30593,32989,35380,37825,39297,39526,40026,40638,41004,69438,
+chrY	23684894	23754545	uc004fvo.1	0	-	23690744	23754335	0	16	1852,99,35,72,72,72,72,72,72,72,140,64,52,92,147,213,	0,5815,10487,11266,13651,23437,28210,32989,35380,37825,39297,39526,40026,40638,41004,69438,
+chrY	23715487	23754545	uc004fvp.1	0	-	23715487	23754335	0	20	72,72,72,72,140,64,52,92,147,140,64,52,92,147,140,64,52,92,147,213,	0,2396,4787,7232,8704,8933,9433,10045,10411,19544,19773,20273,20885,21251,30392,30621,31121,31733,32099,38845,
+chrY	23775009	23846886	uc004fvq.1	0	+	23775275	23841036	0	24	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,14957,22131,24515,26911,29288,31670,46232,48616,51001,53385,55769,58153,60538,61354,65963,70025,
+chrY	23775009	23846886	uc004fvr.1	0	+	23775275	23841036	0	23	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,14957,22131,24515,26911,29288,46232,48616,51001,53385,55769,58153,60538,61354,65963,70025,
+chrY	23775009	23846886	uc004fvs.1	0	+	23775275	23841036	0	19	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,14957,17353,22131,26911,29288,34066,36443,60538,61354,65963,70025,
+chrY	23775009	23846886	uc004fvt.1	0	+	23775275	23841036	0	17	269,147,92,52,64,140,72,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,14957,22131,24515,26911,29288,60538,61354,65963,70025,
+chrY	23775009	23846886	uc004fvu.1	0	+	23775275	23841036	0	16	269,147,92,52,64,140,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,19735,51001,55769,58153,60538,61354,65963,70025,
+chrY	23775009	23846886	uc004fvv.1	0	+	23775275	23841036	0	25	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,14957,17353,19735,22131,24515,26911,29288,34066,36443,48616,53385,55769,58153,60538,61354,65963,70025,
+chrY	23775009	23846886	uc004fvw.1	0	+	23775275	23841036	0	21	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,14957,17353,19735,22131,24515,26911,29288,34066,36443,60538,61354,65963,70025,
+chrY	24237509	24250098	uc004fvx.1	0	-	24237541	24250062	0	3	291,116,105,	0,9782,12484,
+chrY	24492261	24497157	uc004fvy.1	0	-	24492261	24492261	0	3	105,135,104,	0,2459,4792,
+chrY	24600763	24603549	uc004fvz.1	0	-	24601138	24603223	0	2	448,1918,	0,868,
+chrY	24601327	24603549	uc004fwa.1	0	-	24601600	24603223	0	1	2222,	0,
+chrY	24735846	24735884	uc004fwb.1	0	-	24735846	24735846	0	1	38,	0,
+chrY	24738968	24742766	uc004fwc.1	0	-	24742065	24742758	0	2	72,723,	0,3075,
+chrY	24765501	24770366	uc004fwd.1	0	-	24765501	24765501	0	9	84,93,189,89,75,58,352,79,43,	0,166,348,792,1301,2732,3086,4557,4822,
+chrY	24766145	24766176	uc004fwe.1	0	+	24766145	24766145	0	1	31,	0,
+chrY	24832038	24832067	uc004fwf.1	0	+	24832038	24832038	0	1	29,	0,
+chrY	25040866	25041998	uc004fwg.1	0	+	25040866	25040866	0	2	60,106,	0,1026,
+chrY	25125736	25162560	uc004fwh.1	0	+	25125736	25125736	0	4	161,76,108,1001,	0,27167,29047,35823,
+chrY	25173538	25194740	uc004fwi.1	0	+	25181619	25187545	0	9	31,123,137,119,118,106,125,125,320,	0,306,3494,8040,10218,13190,13988,20663,20882,
+chrY	25318609	25330071	uc004fwj.1	0	-	25324468	25330025	0	5	1851,99,72,35,187,	0,5824,8858,10495,11275,
+chrY	25318609	25368905	uc004fwk.1	0	-	25324468	25368720	0	19	1851,99,35,72,72,72,72,72,72,72,72,72,72,140,64,52,92,147,188,	0,5824,10495,11275,21062,23439,25819,28196,30575,32952,35348,37738,40181,41653,41882,42382,42994,43360,50108,
+chrY	25318609	25368905	uc004fwl.1	0	-	25324468	25368720	0	17	1851,99,35,72,72,72,72,72,72,72,72,140,64,52,92,147,188,	0,5824,10495,11275,21062,23439,25819,32952,35348,37738,40181,41653,41882,42382,42994,43360,50108,
+chrY	25389395	25462570	uc004fwm.1	0	+	25389661	25456710	0	23	269,147,92,52,64,140,147,92,52,64,140,72,72,72,72,72,72,72,72,72,35,99,1852,	0,6870,7291,7943,8431,8584,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,37738,40115,59442,61827,62644,67251,71323,
+chrY	25389395	25462570	uc004fwn.1	0	+	25389661	25456710	0	23	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,32981,35358,40115,49903,52288,54673,57057,59442,61827,62644,67251,71323,
+chrY	25389395	25462570	uc004fwo.1	0	+	25389661	25456710	0	19	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,32981,35358,37738,40115,61827,62644,67251,71323,
+chrY	25389395	25462570	uc004fwp.1	0	+	25389661	25456710	0	17	269,147,92,52,64,140,72,72,72,72,72,72,72,72,35,99,1852,	0,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,37738,40115,61827,62644,67251,71323,
+chrY	25389395	25462570	uc004fwq.1	0	+	25389661	25456710	0	16	269,147,92,52,64,140,72,72,72,72,72,72,72,35,99,1852,	0,17718,18139,18791,19279,19432,20972,23415,30585,54673,57057,59442,61827,62644,67251,71323,
+chrY	25389395	25462570	uc004fwr.1	0	+	25389661	25456710	0	24	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,32981,35358,37738,40115,49903,52288,54673,57057,59442,61827,62644,67251,71323,
+chrY	25586437	25607639	uc004fws.1	0	-	25593632	25599558	0	9	320,125,125,106,118,119,137,123,31,	0,414,7089,7906,10866,13043,17571,20773,21171,
+chrY	25739177	25740308	uc004fwt.1	0	-	25739177	25739177	0	2	106,60,	0,1071,
+chrY	25949150	25949179	uc004fwu.1	0	-	25949150	25949150	0	1	29,	0,
+chrY	26010845	26015710	uc004fwv.1	0	+	26010845	26010845	0	9	43,79,350,58,75,89,189,93,84,	0,229,1427,2075,3489,3984,4328,4606,4781,
+chrY	26012853	26012887	uc004fww.1	0	-	26012853	26012853	0	1	34,	0,
+chrY	26015032	26015066	uc004fwx.1	0	-	26015032	26015032	0	1	34,	0,
+chrY	26015781	26015809	uc004fwy.1	0	-	26015781	26015781	0	1	28,	0,
+chrY	26016791	26016820	uc004fwz.1	0	-	26016791	26016791	0	1	29,	0,
+chrY	26033830	26033856	uc004fxa.1	0	+	26033830	26033830	0	1	26,	0,
+chrY	26033938	26033965	uc004fxb.1	0	+	26033938	26033938	0	1	27,	0,
+chrY	26038442	26042240	uc004fxc.1	0	+	26038450	26039143	0	2	723,72,	0,3726,
+chrY	26045324	26045355	uc004fxd.1	0	+	26045324	26045324	0	1	31,	0,
+chrY	26177651	26179873	uc004fxe.1	0	+	26177977	26179600	0	1	2222,	0,
+chrY	26177651	26180436	uc004fxf.1	0	+	26177977	26180062	0	2	1918,447,	0,2338,
+chrY	26284024	26288923	uc004fxg.1	0	+	26284024	26284024	0	3	104,135,105,	0,2302,4794,
+chrY	26531047	26543636	uc004fxh.1	0	+	26531083	26543604	0	3	105,116,291,	0,2691,12298,
+chrY	57509844	57524511	uc004fxi.1	0	+	57515927	57516794	0	2	348,8690,	0,5977,
+chrY	57623412	57685814	uc004fxj.1	0	+	57631523	57684009	0	8	93,155,58,138,91,68,93,1874,	0,8102,14267,16757,19142,38458,58346,60528,
+chrY	57623412	57685814	uc004fxk.1	0	+	57631523	57684197	0	7	93,155,58,138,91,93,1874,	0,8102,14267,16757,19142,58346,60528,
+chrY	57623412	57685814	uc004fxl.1	0	+	57631523	57684009	0	7	93,90,138,91,68,93,1874,	0,8102,16757,19142,38458,58346,60528,
+chrY	57739639	57752876	uc004fxm.1	0	+	57739832	57751911	0	9	207,101,138,112,172,117,202,106,1002,	0,3827,5301,5868,6103,6868,7697,8502,12235,
+chrY	57739639	57752876	uc004fxn.1	0	+	57739818	57752468	0	9	207,114,112,179,146,202,106,85,1002,	0,5325,5868,6096,6839,7697,8502,9942,12235,
+chrY	57762360	57765519	uc004fxo.1	0	+	57763019	57765518	0	7	847,112,147,137,136,202,159,	0,1379,1697,2021,2397,2710,3000,
+chrY	57763739	57767724	uc004fxp.1	0	+	57764815	57767433	0	9	112,147,137,136,202,159,153,69,425,	0,318,642,1018,1331,1621,2439,3351,3560,
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrY2.bed	Tue Apr 01 10:51:34 2014 -0400
@@ -0,0 +1,435 @@
+chrY	132990	133061	uc004fon.1_utr5_0_0_chrY_132991_f	0	+
+chrY	138148	138351	uc004fon.1_utr5_1_0_chrY_138149_f	0	+
+chrY	140833	140854	uc004fon.1_utr5_2_0_chrY_140834_f	0	+
+chrY	138078	138351	uc004foo.1_utr5_0_0_chrY_138079_f	0	+
+chrY	140833	140854	uc004foo.1_utr5_1_0_chrY_140834_f	0	+
+chrY	168184	168795	uc004foq.1_utr5_3_0_chrY_168185_r	0	-
+chrY	170886	170887	uc004for.1_utr5_5_0_chrY_170887_r	0	-
+chrY	221653	221675	uc004fos.1_utr5_3_0_chrY_221654_r	0	-
+chrY	222041	222590	uc004fos.1_utr5_4_0_chrY_222042_r	0	-
+chrY	267426	267627	uc004fot.1_utr5_12_0_chrY_267427_r	0	-
+chrY	505078	505337	uc004fou.1_utr5_0_0_chrY_505079_f	0	+
+chrY	511200	511632	uc004fou.1_utr5_1_0_chrY_511201_f	0	+
+chrY	505078	505337	uc004fov.1_utr5_0_0_chrY_505079_f	0	+
+chrY	511200	511632	uc004fov.1_utr5_1_0_chrY_511201_f	0	+
+chrY	1291527	1291530	uc004fox.1_utr5_5_0_chrY_1291528_r	0	-
+chrY	1285338	1285492	uc004foy.1_utr5_3_0_chrY_1285339_r	0	-
+chrY	1291448	1291530	uc004foy.1_utr5_4_0_chrY_1291449_r	0	-
+chrY	1274886	1275014	uc004foz.1_utr5_0_0_chrY_1274887_r	0	-
+chrY	1277663	1278008	uc004foz.1_utr5_1_0_chrY_1277664_r	0	-
+chrY	1281271	1281405	uc004foz.1_utr5_2_0_chrY_1281272_r	0	-
+chrY	1285325	1285492	uc004foz.1_utr5_3_0_chrY_1285326_r	0	-
+chrY	1287698	1287798	uc004foz.1_utr5_4_0_chrY_1287699_r	0	-
+chrY	1291448	1291530	uc004foz.1_utr5_5_0_chrY_1291449_r	0	-
+chrY	1347700	1347772	uc004fpa.1_utr5_0_0_chrY_1347701_f	0	+
+chrY	1353647	1353735	uc004fpa.1_utr5_1_0_chrY_1353648_f	0	+
+chrY	1361570	1361596	uc004fpa.1_utr5_2_0_chrY_1361571_f	0	+
+chrY	1347700	1347772	uc004fpb.1_utr5_0_0_chrY_1347701_f	0	+
+chrY	1353647	1353711	uc004fpb.1_utr5_1_0_chrY_1353648_f	0	+
+chrY	1361570	1361596	uc004fpb.1_utr5_2_0_chrY_1361571_f	0	+
+chrY	1347700	1347772	uc004fpc.1_utr5_0_0_chrY_1347701_f	0	+
+chrY	1353647	1353735	uc004fpc.1_utr5_1_0_chrY_1353648_f	0	+
+chrY	1361570	1361596	uc004fpc.1_utr5_2_0_chrY_1361571_f	0	+
+chrY	1347700	1347772	uc004fpd.1_utr5_0_0_chrY_1347701_f	0	+
+chrY	1353647	1353735	uc004fpd.1_utr5_1_0_chrY_1353648_f	0	+
+chrY	1361570	1361596	uc004fpd.1_utr5_2_0_chrY_1361571_f	0	+
+chrY	1361570	1361596	uc004fpe.1_utr5_0_0_chrY_1361571_f	0	+
+chrY	1415508	1415819	uc004fpf.1_utr5_0_0_chrY_1415509_f	0	+
+chrY	1420620	1420658	uc004fpf.1_utr5_1_0_chrY_1420621_f	0	+
+chrY	1470902	1470994	uc004fpg.1_utr5_3_0_chrY_1470903_r	0	-
+chrY	1465044	1465652	uc004fph.1_utr5_0_0_chrY_1465045_r	0	-
+chrY	1466171	1466312	uc004fph.1_utr5_1_0_chrY_1466172_r	0	-
+chrY	1468133	1468620	uc004fph.1_utr5_2_0_chrY_1468134_r	0	-
+chrY	1468975	1469186	uc004fph.1_utr5_3_0_chrY_1468976_r	0	-
+chrY	1470791	1470994	uc004fph.1_utr5_4_0_chrY_1470792_r	0	-
+chrY	1480908	1480988	uc004fpi.1_utr5_0_0_chrY_1480909_f	0	+
+chrY	1531733	1531844	uc004fpk.1_utr5_12_0_chrY_1531734_r	0	-
+chrY	1531733	1531844	uc004fpl.1_utr5_11_0_chrY_1531734_r	0	-
+chrY	1545451	1545475	uc004fpm.1_utr5_0_0_chrY_1545452_r	0	-
+chrY	1615813	1616000	uc004fpm.1_utr5_1_0_chrY_1615814_r	0	-
+chrY	1670485	1670662	uc004fpn.1_utr5_0_0_chrY_1670486_f	0	+
+chrY	1672336	1672355	uc004fpn.1_utr5_1_0_chrY_1672337_f	0	+
+chrY	1674276	1674425	uc004fpp.1_utr5_0_0_chrY_1674277_f	0	+
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+chrY	19208685	19208822	uc004fts.1_utr5_1_0_chrY_19208686_r	0	-
+chrY	19209404	19209518	uc004fts.1_utr5_2_0_chrY_19209405_r	0	-
+chrY	19209879	19209980	uc004fts.1_utr5_3_0_chrY_19209880_r	0	-
+chrY	19211653	19211795	uc004fts.1_utr5_4_0_chrY_19211654_r	0	-
+chrY	19394892	19395009	uc004ftu.1_utr5_5_0_chrY_19394893_r	0	-
+chrY	19394892	19395009	uc004ftv.1_utr5_1_0_chrY_19394893_r	0	-
+chrY	19394892	19395009	uc004ftw.1_utr5_1_0_chrY_19394893_r	0	-
+chrY	19493774	19494108	uc004ftx.1_utr5_0_0_chrY_19493775_r	0	-
+chrY	19498341	19499502	uc004ftx.1_utr5_1_0_chrY_19498342_r	0	-
+chrY	19553972	19554115	uc004fty.1_utr5_0_0_chrY_19553973_r	0	-
+chrY	19698318	19698690	uc004fty.1_utr5_1_0_chrY_19698319_r	0	-
+chrY	19613983	19614093	uc004ftz.1_utr5_0_0_chrY_19613984_r	0	-
+chrY	20076704	20078138	uc004fua.1_utr5_0_0_chrY_20076705_r	0	-
+chrY	20080197	20080353	uc004fua.1_utr5_1_0_chrY_20080198_r	0	-
+chrY	20080562	20080640	uc004fua.1_utr5_2_0_chrY_20080563_r	0	-
+chrY	20086379	20086501	uc004fua.1_utr5_3_0_chrY_20086380_r	0	-
+chrY	20087729	20088648	uc004fua.1_utr5_4_0_chrY_20087730_r	0	-
+chrY	20095178	20095418	uc004fua.1_utr5_5_0_chrY_20095179_r	0	-
+chrY	20095913	20096177	uc004fua.1_utr5_6_0_chrY_20095914_r	0	-
+chrY	20101442	20101568	uc004fua.1_utr5_7_0_chrY_20101443_r	0	-
+chrY	20124305	20124427	uc004fua.1_utr5_8_0_chrY_20124306_r	0	-
+chrY	20076704	20078138	uc004fub.1_utr5_0_0_chrY_20076705_r	0	-
+chrY	20078330	20078391	uc004fub.1_utr5_1_0_chrY_20078331_r	0	-
+chrY	20080197	20080353	uc004fub.1_utr5_2_0_chrY_20080198_r	0	-
+chrY	20080562	20080640	uc004fub.1_utr5_3_0_chrY_20080563_r	0	-
+chrY	20081232	20081378	uc004fub.1_utr5_4_0_chrY_20081233_r	0	-
+chrY	20086379	20086501	uc004fub.1_utr5_5_0_chrY_20086380_r	0	-
+chrY	20087729	20088648	uc004fub.1_utr5_6_0_chrY_20087730_r	0	-
+chrY	20095178	20095418	uc004fub.1_utr5_7_0_chrY_20095179_r	0	-
+chrY	20095913	20096177	uc004fub.1_utr5_8_0_chrY_20095914_r	0	-
+chrY	20101442	20101568	uc004fub.1_utr5_9_0_chrY_20101443_r	0	-
+chrY	20124305	20124427	uc004fub.1_utr5_10_0_chrY_20124306_r	0	-
+chrY	20188623	20188844	uc004fuc.1_utr5_0_0_chrY_20188624_f	0	+
+chrY	20208483	20208498	uc004fuc.1_utr5_1_0_chrY_20208484_f	0	+
+chrY	20188655	20188756	uc004fud.1_utr5_0_0_chrY_20188656_f	0	+
+chrY	20208483	20208498	uc004fud.1_utr5_1_0_chrY_20208484_f	0	+
+chrY	20213723	20214088	uc004fue.1_utr5_0_0_chrY_20213724_f	0	+
+chrY	20214672	20218906	uc004fue.1_utr5_1_0_chrY_20214673_f	0	+
+chrY	20336982	20337013	uc004fuf.1_utr5_10_0_chrY_20336983_r	0	-
+chrY	20365808	20365827	uc004fug.1_utr5_25_0_chrY_20365809_r	0	-
+chrY	20365944	20366212	uc004fug.1_utr5_26_0_chrY_20365945_r	0	-
+chrY	20365808	20365827	uc004fuh.1_utr5_9_0_chrY_20365809_r	0	-
+chrY	20365944	20366212	uc004fuh.1_utr5_10_0_chrY_20365945_r	0	-
+chrY	21021299	21023423	uc004fui.1_utr5_0_0_chrY_21021300_r	0	-
+chrY	21036941	21037096	uc004fuj.1_utr5_0_0_chrY_21036942_r	0	-
+chrY	21037701	21037941	uc004fuj.1_utr5_1_0_chrY_21037702_r	0	-
+chrY	21039462	21039522	uc004fuj.1_utr5_2_0_chrY_21039463_r	0	-
+chrY	21041145	21041255	uc004fuj.1_utr5_3_0_chrY_21041146_r	0	-
+chrY	21078625	21078730	uc004fuj.1_utr5_4_0_chrY_21078626_r	0	-
+chrY	21089544	21090502	uc004fuj.1_utr5_5_0_chrY_21089545_r	0	-
+chrY	21146998	21147145	uc004fuk.1_utr5_0_0_chrY_21146999_f	0	+
+chrY	21146998	21147145	uc004ful.1_utr5_0_0_chrY_21146999_f	0	+
+chrY	21327341	21327437	uc004fum.1_utr5_0_0_chrY_21327342_f	0	+
+chrY	21972204	21972300	uc004fun.1_utr5_3_0_chrY_21972205_r	0	-
+chrY	21972750	21972836	uc004fun.1_utr5_4_0_chrY_21972751_r	0	-
+chrY	22082636	22082759	uc004fuo.1_utr5_0_0_chrY_22082637_f	0	+
+chrY	22084620	22084624	uc004fuo.1_utr5_1_0_chrY_22084621_f	0	+
+chrY	22082636	22082759	uc004fup.1_utr5_0_0_chrY_22082637_f	0	+
+chrY	22084620	22084733	uc004fup.1_utr5_1_0_chrY_22084621_f	0	+
+chrY	22085207	22085311	uc004fup.1_utr5_2_0_chrY_22085208_f	0	+
+chrY	22090423	22090452	uc004fup.1_utr5_3_0_chrY_22090424_f	0	+
+chrY	22106177	22106300	uc004fuq.1_utr5_0_0_chrY_22106178_f	0	+
+chrY	22108161	22108165	uc004fuq.1_utr5_1_0_chrY_22108162_f	0	+
+chrY	22106177	22106300	uc004fur.1_utr5_0_0_chrY_22106178_f	0	+
+chrY	22108161	22108274	uc004fur.1_utr5_1_0_chrY_22108162_f	0	+
+chrY	22108748	22108852	uc004fur.1_utr5_2_0_chrY_22108749_f	0	+
+chrY	22113964	22113993	uc004fur.1_utr5_3_0_chrY_22113965_f	0	+
+chrY	22154873	22154936	uc004fus.1_utr5_0_0_chrY_22154874_r	0	-
+chrY	22156056	22156148	uc004fus.1_utr5_1_0_chrY_22156057_r	0	-
+chrY	22158774	22158936	uc004fus.1_utr5_2_0_chrY_22158775_r	0	-
+chrY	22160545	22160644	uc004fus.1_utr5_3_0_chrY_22160546_r	0	-
+chrY	22161239	22161401	uc004fus.1_utr5_4_0_chrY_22161240_r	0	-
+chrY	22165859	22165940	uc004fus.1_utr5_5_0_chrY_22165860_r	0	-
+chrY	22448048	22448052	uc004fuu.1_utr5_10_0_chrY_22448049_r	0	-
+chrY	22449913	22450036	uc004fuu.1_utr5_11_0_chrY_22449914_r	0	-
+chrY	22442218	22442247	uc004fuv.1_utr5_7_0_chrY_22442219_r	0	-
+chrY	22447359	22447463	uc004fuv.1_utr5_8_0_chrY_22447360_r	0	-
+chrY	22447939	22448052	uc004fuv.1_utr5_9_0_chrY_22447940_r	0	-
+chrY	22449913	22450036	uc004fuv.1_utr5_10_0_chrY_22449914_r	0	-
+chrY	22471589	22471593	uc004fuw.1_utr5_10_0_chrY_22471590_r	0	-
+chrY	22473454	22473577	uc004fuw.1_utr5_11_0_chrY_22473455_r	0	-
+chrY	22465759	22465788	uc004fux.1_utr5_7_0_chrY_22465760_r	0	-
+chrY	22470900	22471004	uc004fux.1_utr5_8_0_chrY_22470901_r	0	-
+chrY	22471480	22471593	uc004fux.1_utr5_9_0_chrY_22471481_r	0	-
+chrY	22473454	22473577	uc004fux.1_utr5_10_0_chrY_22473455_r	0	-
+chrY	22640374	22640426	uc004fuy.1_utr5_2_0_chrY_22640375_r	0	-
+chrY	22651266	22651353	uc004fuy.1_utr5_3_0_chrY_22651267_r	0	-
+chrY	22651454	22651542	uc004fuy.1_utr5_4_0_chrY_22651455_r	0	-
+chrY	22700521	22700614	uc004fuz.1_utr5_0_0_chrY_22700522_r	0	-
+chrY	22700832	22700970	uc004fuz.1_utr5_1_0_chrY_22700833_r	0	-
+chrY	22702127	22702366	uc004fuz.1_utr5_2_0_chrY_22702128_r	0	-
+chrY	22736504	22736508	uc004fva.1_utr5_10_0_chrY_22736505_r	0	-
+chrY	22738369	22738477	uc004fva.1_utr5_11_0_chrY_22738370_r	0	-
+chrY	22852332	22853323	uc004fvb.1_utr5_0_0_chrY_22852333_r	0	-
+chrY	22853840	22854411	uc004fvb.1_utr5_1_0_chrY_22853841_r	0	-
+chrY	22864393	22864505	uc004fvc.1_utr5_0_0_chrY_22864394_f	0	+
+chrY	22866394	22866398	uc004fvc.1_utr5_1_0_chrY_22866395_f	0	+
+chrY	22864393	22864505	uc004fvd.1_utr5_0_0_chrY_22864394_f	0	+
+chrY	22960978	22960982	uc004fvd.1_utr5_1_0_chrY_22960979_f	0	+
+chrY	22959010	22959117	uc004fve.1_utr5_0_0_chrY_22959011_f	0	+
+chrY	22960978	22960982	uc004fve.1_utr5_1_0_chrY_22960979_f	0	+
+chrY	22995127	22995366	uc004fvg.1_utr5_0_0_chrY_22995128_r	0	-
+chrY	22996314	22996413	uc004fvg.1_utr5_1_0_chrY_22996315_r	0	-
+chrY	22996523	22996661	uc004fvg.1_utr5_2_0_chrY_22996524_r	0	-
+chrY	22996879	22996994	uc004fvg.1_utr5_3_0_chrY_22996880_r	0	-
+chrY	23045931	23046019	uc004fvh.1_utr5_0_0_chrY_23045932_f	0	+
+chrY	23046120	23046207	uc004fvh.1_utr5_1_0_chrY_23046121_f	0	+
+chrY	23057047	23057099	uc004fvh.1_utr5_2_0_chrY_23057048_f	0	+
+chrY	23539797	23539828	uc004fvj.1_utr5_0_0_chrY_23539798_f	0	+
+chrY	23540103	23540226	uc004fvj.1_utr5_1_0_chrY_23540104_f	0	+
+chrY	23543291	23543428	uc004fvj.1_utr5_2_0_chrY_23543292_f	0	+
+chrY	23547837	23547878	uc004fvj.1_utr5_3_0_chrY_23547838_f	0	+
+chrY	23696301	23696347	uc004fvk.1_utr5_4_0_chrY_23696302_r	0	-
+chrY	23725898	23726045	uc004fvl.1_utr5_16_0_chrY_23725899_r	0	-
+chrY	23735031	23735171	uc004fvl.1_utr5_17_0_chrY_23735032_r	0	-
+chrY	23735260	23735324	uc004fvl.1_utr5_18_0_chrY_23735261_r	0	-
+chrY	23735760	23735812	uc004fvl.1_utr5_19_0_chrY_23735761_r	0	-
+chrY	23754335	23754545	uc004fvm.1_utr5_22_0_chrY_23754336_r	0	-
+chrY	23754335	23754545	uc004fvn.1_utr5_16_0_chrY_23754336_r	0	-
+chrY	23754335	23754545	uc004fvo.1_utr5_15_0_chrY_23754336_r	0	-
+chrY	23754335	23754545	uc004fvp.1_utr5_19_0_chrY_23754336_r	0	-
+chrY	23775009	23775275	uc004fvq.1_utr5_0_0_chrY_23775010_f	0	+
+chrY	23775009	23775275	uc004fvr.1_utr5_0_0_chrY_23775010_f	0	+
+chrY	23775009	23775275	uc004fvs.1_utr5_0_0_chrY_23775010_f	0	+
+chrY	23775009	23775275	uc004fvt.1_utr5_0_0_chrY_23775010_f	0	+
+chrY	23775009	23775275	uc004fvu.1_utr5_0_0_chrY_23775010_f	0	+
+chrY	23775009	23775275	uc004fvv.1_utr5_0_0_chrY_23775010_f	0	+
+chrY	23775009	23775275	uc004fvw.1_utr5_0_0_chrY_23775010_f	0	+
+chrY	24250062	24250098	uc004fvx.1_utr5_2_0_chrY_24250063_r	0	-
+chrY	24492261	24492366	uc004fvy.1_utr5_0_0_chrY_24492262_r	0	-
+chrY	24494720	24494855	uc004fvy.1_utr5_1_0_chrY_24494721_r	0	-
+chrY	24497053	24497157	uc004fvy.1_utr5_2_0_chrY_24497054_r	0	-
+chrY	24603223	24603549	uc004fvz.1_utr5_1_0_chrY_24603224_r	0	-
+chrY	24603223	24603549	uc004fwa.1_utr5_0_0_chrY_24603224_r	0	-
+chrY	24735846	24735884	uc004fwb.1_utr5_0_0_chrY_24735847_r	0	-
+chrY	24742758	24742766	uc004fwc.1_utr5_1_0_chrY_24742759_r	0	-
+chrY	24765501	24765585	uc004fwd.1_utr5_0_0_chrY_24765502_r	0	-
+chrY	24765667	24765760	uc004fwd.1_utr5_1_0_chrY_24765668_r	0	-
+chrY	24765849	24766038	uc004fwd.1_utr5_2_0_chrY_24765850_r	0	-
+chrY	24766293	24766382	uc004fwd.1_utr5_3_0_chrY_24766294_r	0	-
+chrY	24766802	24766877	uc004fwd.1_utr5_4_0_chrY_24766803_r	0	-
+chrY	24768233	24768291	uc004fwd.1_utr5_5_0_chrY_24768234_r	0	-
+chrY	24768587	24768939	uc004fwd.1_utr5_6_0_chrY_24768588_r	0	-
+chrY	24770058	24770137	uc004fwd.1_utr5_7_0_chrY_24770059_r	0	-
+chrY	24770323	24770366	uc004fwd.1_utr5_8_0_chrY_24770324_r	0	-
+chrY	25173538	25173569	uc004fwi.1_utr5_0_0_chrY_25173539_f	0	+
+chrY	25173844	25173967	uc004fwi.1_utr5_1_0_chrY_25173845_f	0	+
+chrY	25177032	25177169	uc004fwi.1_utr5_2_0_chrY_25177033_f	0	+
+chrY	25181578	25181619	uc004fwi.1_utr5_3_0_chrY_25181579_f	0	+
+chrY	25330025	25330071	uc004fwj.1_utr5_4_0_chrY_25330026_r	0	-
+chrY	25368720	25368905	uc004fwk.1_utr5_18_0_chrY_25368721_r	0	-
+chrY	25368720	25368905	uc004fwl.1_utr5_16_0_chrY_25368721_r	0	-
+chrY	25389395	25389661	uc004fwm.1_utr5_0_0_chrY_25389396_f	0	+
+chrY	25389395	25389661	uc004fwn.1_utr5_0_0_chrY_25389396_f	0	+
+chrY	25389395	25389661	uc004fwo.1_utr5_0_0_chrY_25389396_f	0	+
+chrY	25389395	25389661	uc004fwp.1_utr5_0_0_chrY_25389396_f	0	+
+chrY	25389395	25389661	uc004fwq.1_utr5_0_0_chrY_25389396_f	0	+
+chrY	25389395	25389661	uc004fwr.1_utr5_0_0_chrY_25389396_f	0	+
+chrY	25599558	25599599	uc004fws.1_utr5_5_0_chrY_25599559_r	0	-
+chrY	25604008	25604145	uc004fws.1_utr5_6_0_chrY_25604009_r	0	-
+chrY	25607210	25607333	uc004fws.1_utr5_7_0_chrY_25607211_r	0	-
+chrY	25607608	25607639	uc004fws.1_utr5_8_0_chrY_25607609_r	0	-
+chrY	25739177	25739283	uc004fwt.1_utr5_0_0_chrY_25739178_r	0	-
+chrY	25740248	25740308	uc004fwt.1_utr5_1_0_chrY_25740249_r	0	-
+chrY	25949150	25949179	uc004fwu.1_utr5_0_0_chrY_25949151_r	0	-
+chrY	26012853	26012887	uc004fww.1_utr5_0_0_chrY_26012854_r	0	-
+chrY	26015032	26015066	uc004fwx.1_utr5_0_0_chrY_26015033_r	0	-
+chrY	26015781	26015809	uc004fwy.1_utr5_0_0_chrY_26015782_r	0	-
+chrY	26016791	26016820	uc004fwz.1_utr5_0_0_chrY_26016792_r	0	-
+chrY	26038442	26038450	uc004fxc.1_utr5_0_0_chrY_26038443_f	0	+
+chrY	26177651	26177977	uc004fxe.1_utr5_0_0_chrY_26177652_f	0	+
+chrY	26177651	26177977	uc004fxf.1_utr5_0_0_chrY_26177652_f	0	+
+chrY	26531047	26531083	uc004fxh.1_utr5_0_0_chrY_26531048_f	0	+
+chrY	57509844	57510192	uc004fxi.1_utr5_0_0_chrY_57509845_f	0	+
+chrY	57515821	57515927	uc004fxi.1_utr5_1_0_chrY_57515822_f	0	+
+chrY	57623412	57623505	uc004fxj.1_utr5_0_0_chrY_57623413_f	0	+
+chrY	57631514	57631523	uc004fxj.1_utr5_1_0_chrY_57631515_f	0	+
+chrY	57623412	57623505	uc004fxk.1_utr5_0_0_chrY_57623413_f	0	+
+chrY	57631514	57631523	uc004fxk.1_utr5_1_0_chrY_57631515_f	0	+
+chrY	57623412	57623505	uc004fxl.1_utr5_0_0_chrY_57623413_f	0	+
+chrY	57631514	57631523	uc004fxl.1_utr5_1_0_chrY_57631515_f	0	+
+chrY	57739639	57739832	uc004fxm.1_utr5_0_0_chrY_57739640_f	0	+
+chrY	57739639	57739818	uc004fxn.1_utr5_0_0_chrY_57739640_f	0	+
+chrY	57762360	57763019	uc004fxo.1_utr5_0_0_chrY_57762361_f	0	+
+chrY	57763739	57763851	uc004fxp.1_utr5_0_0_chrY_57763740_f	0	+
+chrY	57764057	57764204	uc004fxp.1_utr5_1_0_chrY_57764058_f	0	+
+chrY	57764381	57764518	uc004fxp.1_utr5_2_0_chrY_57764382_f	0	+
+chrY	57764757	57764815	uc004fxp.1_utr5_3_0_chrY_57764758_f	0	+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrY_Coverage.bed	Tue Apr 01 10:51:34 2014 -0400
@@ -0,0 +1,237 @@
+chrY	132990	160020	uc004fon.1	0	+	140854	156002	0	9	71,203,148,137,129,156,184,296,761,	0,5158,7843,12409,14324,15175,16711,22773,26269,	365	0.0135035146134	5	0
+chrY	138078	156125	uc004foo.1	0	+	140854	156002	0	7	273,148,137,129,156,184,362,	0,2755,7321,9236,10087,11623,17685,	294	0.0162907962542	4	0
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+chrY	23684894	23754545	uc004fvo.1	0	-	23690744	23754335	0	16	1852,99,35,72,72,72,72,72,72,72,140,64,52,92,147,213,	0,5815,10487,11266,13651,23437,28210,32989,35380,37825,39297,39526,40026,40638,41004,69438,	659	0.0094614578398	9	0
+chrY	23715487	23754545	uc004fvp.1	0	-	23715487	23754335	0	20	72,72,72,72,140,64,52,92,147,140,64,52,92,147,140,64,52,92,147,213,	0,2396,4787,7232,8704,8933,9433,10045,10411,19544,19773,20273,20885,21251,30392,30621,31121,31733,32099,38845,	613	0.0156946080188	8	0
+chrY	23775009	23846886	uc004fvq.1	0	+	23775275	23841036	0	24	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,14957,22131,24515,26911,29288,31670,46232,48616,51001,53385,55769,58153,60538,61354,65963,70025,	266	0.00370076658736	7	0
+chrY	23775009	23846886	uc004fvr.1	0	+	23775275	23841036	0	23	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,14957,22131,24515,26911,29288,46232,48616,51001,53385,55769,58153,60538,61354,65963,70025,	266	0.00370076658736	7	0
+chrY	23775009	23846886	uc004fvs.1	0	+	23775275	23841036	0	19	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,14957,17353,22131,26911,29288,34066,36443,60538,61354,65963,70025,	266	0.00370076658736	7	0
+chrY	23775009	23846886	uc004fvt.1	0	+	23775275	23841036	0	17	269,147,92,52,64,140,72,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,14957,22131,24515,26911,29288,60538,61354,65963,70025,	266	0.00370076658736	7	0
+chrY	23775009	23846886	uc004fvu.1	0	+	23775275	23841036	0	16	269,147,92,52,64,140,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,19735,51001,55769,58153,60538,61354,65963,70025,	266	0.00370076658736	7	0
+chrY	23775009	23846886	uc004fvv.1	0	+	23775275	23841036	0	25	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,14957,17353,19735,22131,24515,26911,29288,34066,36443,48616,53385,55769,58153,60538,61354,65963,70025,	266	0.00370076658736	7	0
+chrY	23775009	23846886	uc004fvw.1	0	+	23775275	23841036	0	21	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,6869,7290,7942,8430,8583,10123,12566,14957,17353,19735,22131,24515,26911,29288,34066,36443,60538,61354,65963,70025,	266	0.00370076658736	7	0
+chrY	24237509	24250098	uc004fvx.1	0	-	24237541	24250062	0	3	291,116,105,	0,9782,12484,	36	0.0028596393677	1	0
+chrY	24492261	24497157	uc004fvy.1	0	-	24492261	24492261	0	3	105,135,104,	0,2459,4792,	344	0.0702614379085	3	0
+chrY	24600763	24603549	uc004fvz.1	0	-	24601138	24603223	0	2	448,1918,	0,868,	326	0.117013639627	2	0
+chrY	24601327	24603549	uc004fwa.1	0	-	24601600	24603223	0	1	2222,	0,	326	0.146714671467	2	0
+chrY	24735846	24735884	uc004fwb.1	0	-	24735846	24735846	0	1	38,	0,	38	1.0	1	0
+chrY	24738968	24742766	uc004fwc.1	0	-	24742065	24742758	0	2	72,723,	0,3075,	8	0.00210637177462	1	0
+chrY	24765501	24770366	uc004fwd.1	0	-	24765501	24765501	0	9	84,93,189,89,75,58,352,79,43,	0,166,348,792,1301,2732,3086,4557,4822,	1062	0.21829393628	9	0
+chrY	24766145	24766176	uc004fwe.1	0	+	24766145	24766145	0	1	31,	0,	0	0.0	0	0
+chrY	24832038	24832067	uc004fwf.1	0	+	24832038	24832038	0	1	29,	0,	0	0.0	0	0
+chrY	25040866	25041998	uc004fwg.1	0	+	25040866	25040866	0	2	60,106,	0,1026,	0	0.0	0	0
+chrY	25125736	25162560	uc004fwh.1	0	+	25125736	25125736	0	4	161,76,108,1001,	0,27167,29047,35823,	0	0.0	0	0
+chrY	25173538	25194740	uc004fwi.1	0	+	25181619	25187545	0	9	31,123,137,119,118,106,125,125,320,	0,306,3494,8040,10218,13190,13988,20663,20882,	332	0.0156589001038	4	0
+chrY	25318609	25330071	uc004fwj.1	0	-	25324468	25330025	0	5	1851,99,72,35,187,	0,5824,8858,10495,11275,	46	0.00401326121096	1	0
+chrY	25318609	25368905	uc004fwk.1	0	-	25324468	25368720	0	19	1851,99,35,72,72,72,72,72,72,72,72,72,72,140,64,52,92,147,188,	0,5824,10495,11275,21062,23439,25819,28196,30575,32952,35348,37738,40181,41653,41882,42382,42994,43360,50108,	231	0.00459281056148	3	0
+chrY	25318609	25368905	uc004fwl.1	0	-	25324468	25368720	0	17	1851,99,35,72,72,72,72,72,72,72,72,140,64,52,92,147,188,	0,5824,10495,11275,21062,23439,25819,32952,35348,37738,40181,41653,41882,42382,42994,43360,50108,	231	0.00459281056148	3	0
+chrY	25389395	25462570	uc004fwm.1	0	+	25389661	25456710	0	23	269,147,92,52,64,140,147,92,52,64,140,72,72,72,72,72,72,72,72,72,35,99,1852,	0,6870,7291,7943,8431,8584,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,37738,40115,59442,61827,62644,67251,71323,	266	0.00363512128459	6	0
+chrY	25389395	25462570	uc004fwn.1	0	+	25389661	25456710	0	23	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,32981,35358,40115,49903,52288,54673,57057,59442,61827,62644,67251,71323,	266	0.00363512128459	6	0
+chrY	25389395	25462570	uc004fwo.1	0	+	25389661	25456710	0	19	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,32981,35358,37738,40115,61827,62644,67251,71323,	266	0.00363512128459	6	0
+chrY	25389395	25462570	uc004fwp.1	0	+	25389661	25456710	0	17	269,147,92,52,64,140,72,72,72,72,72,72,72,72,35,99,1852,	0,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,37738,40115,61827,62644,67251,71323,	266	0.00363512128459	6	0
+chrY	25389395	25462570	uc004fwq.1	0	+	25389661	25456710	0	16	269,147,92,52,64,140,72,72,72,72,72,72,72,35,99,1852,	0,17718,18139,18791,19279,19432,20972,23415,30585,54673,57057,59442,61827,62644,67251,71323,	266	0.00363512128459	6	0
+chrY	25389395	25462570	uc004fwr.1	0	+	25389661	25456710	0	24	269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852,	0,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,32981,35358,37738,40115,49903,52288,54673,57057,59442,61827,62644,67251,71323,	266	0.00363512128459	6	0
+chrY	25586437	25607639	uc004fws.1	0	-	25593632	25599558	0	9	320,125,125,106,118,119,137,123,31,	0,414,7089,7906,10866,13043,17571,20773,21171,	332	0.0156589001038	4	0
+chrY	25739177	25740308	uc004fwt.1	0	-	25739177	25739177	0	2	106,60,	0,1071,	166	0.146772767462	2	0
+chrY	25949150	25949179	uc004fwu.1	0	-	25949150	25949150	0	1	29,	0,	29	1.0	1	0
+chrY	26010845	26015710	uc004fwv.1	0	+	26010845	26010845	0	9	43,79,350,58,75,89,189,93,84,	0,229,1427,2075,3489,3984,4328,4606,4781,	68	0.013977389517	2	0
+chrY	26012853	26012887	uc004fww.1	0	-	26012853	26012853	0	1	34,	0,	34	1.0	1	0
+chrY	26015032	26015066	uc004fwx.1	0	-	26015032	26015032	0	1	34,	0,	34	1.0	1	0
+chrY	26015781	26015809	uc004fwy.1	0	-	26015781	26015781	0	1	28,	0,	28	1.0	1	0
+chrY	26016791	26016820	uc004fwz.1	0	-	26016791	26016791	0	1	29,	0,	29	1.0	1	0
+chrY	26033830	26033856	uc004fxa.1	0	+	26033830	26033830	0	1	26,	0,	0	0.0	0	0
+chrY	26033938	26033965	uc004fxb.1	0	+	26033938	26033938	0	1	27,	0,	0	0.0	0	0
+chrY	26038442	26042240	uc004fxc.1	0	+	26038450	26039143	0	2	723,72,	0,3726,	8	0.00210637177462	1	0
+chrY	26045324	26045355	uc004fxd.1	0	+	26045324	26045324	0	1	31,	0,	0	0.0	0	0
+chrY	26177651	26179873	uc004fxe.1	0	+	26177977	26179600	0	1	2222,	0,	326	0.146714671467	2	0
+chrY	26177651	26180436	uc004fxf.1	0	+	26177977	26180062	0	2	1918,447,	0,2338,	326	0.117055655296	2	0
+chrY	26284024	26288923	uc004fxg.1	0	+	26284024	26284024	0	3	104,135,105,	0,2302,4794,	0	0.0	0	0
+chrY	26531047	26543636	uc004fxh.1	0	+	26531083	26543604	0	3	105,116,291,	0,2691,12298,	36	0.0028596393677	1	0
+chrY	57509844	57524511	uc004fxi.1	0	+	57515927	57516794	0	2	348,8690,	0,5977,	454	0.0309538419581	2	0
+chrY	57623412	57685814	uc004fxj.1	0	+	57631523	57684009	0	8	93,155,58,138,91,68,93,1874,	0,8102,14267,16757,19142,38458,58346,60528,	102	0.00163456299478	6	0
+chrY	57623412	57685814	uc004fxk.1	0	+	57631523	57684197	0	7	93,155,58,138,91,93,1874,	0,8102,14267,16757,19142,58346,60528,	102	0.00163456299478	6	0
+chrY	57623412	57685814	uc004fxl.1	0	+	57631523	57684009	0	7	93,90,138,91,68,93,1874,	0,8102,16757,19142,38458,58346,60528,	102	0.00163456299478	6	0
+chrY	57739639	57752876	uc004fxm.1	0	+	57739832	57751911	0	9	207,101,138,112,172,117,202,106,1002,	0,3827,5301,5868,6103,6868,7697,8502,12235,	193	0.014580342978	2	0
+chrY	57739639	57752876	uc004fxn.1	0	+	57739818	57752468	0	9	207,114,112,179,146,202,106,85,1002,	0,5325,5868,6096,6839,7697,8502,9942,12235,	193	0.014580342978	2	0
+chrY	57762360	57765519	uc004fxo.1	0	+	57763019	57765518	0	7	847,112,147,137,136,202,159,	0,1379,1697,2021,2397,2710,3000,	1113	0.35232668566	5	0
+chrY	57763739	57767724	uc004fxp.1	0	+	57764815	57767433	0	9	112,147,137,136,202,159,153,69,425,	0,318,642,1018,1331,1621,2439,3351,3560,	454	0.113927227102	4	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Apr 01 10:51:34 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>