# HG changeset patch
# User iuc
# Date 1510656632 18000
# Node ID 44027547ce8f999c849efe41e62f3295ea53b77c

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48

diff -r 000000000000 -r 44027547ce8f extract_aln_ends.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_aln_ends.xml	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,49 @@
+<tool id="bctools_extract_alignment_ends" name="Extract alignment ends" version="@VERSION@">
+    <description>from SAM or BAM</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        extract_aln_ends.py
+        '$alignments'
+        > '$alignment_ends'
+    ]]></command>
+    <inputs>
+        <param name="alignments" type="data" format="sam,bam" label="Alignments in SAM or BAM format"/>
+    </inputs>
+    <outputs>
+        <data name="alignment_ends" format="bed"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="alignments" value="twomates.sam"/>
+            <output name="alignment_ends" file="tworeads_aln_ends.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+bctools - Extract alignment ends from from SAM or BAM alignments
+================================================================
+
+The resulting BED file contains the outer coordinates of the alignments. The BED
+name field is set to the read id and the score field is set to the edit distance
+of the alignment. The crosslinked nucleotide is one nt upstream of the 5'-end of
+the BED entries.
+
+This tool only reports results for alignments that are properly aligned in FR
+("forward-reverse") direction.
+
+Input:
+------
+
+* BAM file containing alignments (paired-end sequencing)
+
+Output:
+-------
+
+* BED file containing outer coordinates (sorted by read id)
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r 44027547ce8f macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,13 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">bctools</requirement>
+        </requirements>
+    </xml>
+    <token name="@VERSION@">0.2.1</token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1016/j.molcel.2013.07.001</citation>
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r 44027547ce8f test-data/converted_bcs.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/converted_bcs.fastq	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,400 @@
+@UID0
+NYYRRY
++
+#0<FFF
+@UID1
+RRYRYR
++
+BBBFFF
+@UID2
+RYYRRY
++
+B<BF<B
+@UID3
+YRYRYR
++
+BBBFFF
+@UID4
+NRRRRY
++
+#0<FFF
+@UID5
+RRRRRY
++
+BBBFFF
+@UID6
+YRRRYR
++
+BBBFFF
+@UID7
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++
+#0<FFF
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++
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++
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++
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++
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++
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++
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++
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++
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+NYYRRY
++
+#00FFF
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++
+BBBFFF
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++
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++
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++
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++
+#0<BFF
+@UID74
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++
+BBBFFF
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++
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++
+BBBFFF
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+NRYRYR
++
+#0<FFF
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++
+#0<FFF
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++
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++
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+@UID81
+NYYRYR
++
+#0<FFF
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++
+#0<FFF
+@UID83
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+#0<FFF
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+#0<FFF
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+#0<FFF
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++
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++
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++
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++
+BBBFFF
diff -r 000000000000 -r 44027547ce8f test-data/extracted_bcs.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extracted_bcs.fastq	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,400 @@
+@UID0
+NCTAAT
++
+#0<FFF
+@UID1
+GGTACG
++
+BBBFFF
+@UID2
+GCTAAT
++
+B<BF<B
+@UID3
+CATACG
++
+BBBFFF
+@UID4
+NAAAAT
++
+#0<FFF
+@UID5
+AAGAAT
++
+BBBFFF
+@UID6
+CAAACG
++
+BBBFFF
+@UID7
+NCCGGT
++
+#0<FFF
+@UID8
+ACAAAT
++
+BBBFFF
+@UID9
+AAGAAT
++
+BBBFFF
+@UID10
+NAAAAT
++
+#0<FFF
+@UID11
+NCAACG
++
+#0<FFF
+@UID12
+NGCAAT
++
+#0<FFF
+@UID13
+NAGAAT
++
+#0<FFF
+@UID14
+TCAACG
++
+BBBFFF
+@UID15
+TCGAAT
++
+BBBFFF
+@UID16
+CCCGCG
++
+BBBFFF
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+CAAGCG
++
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++
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+ACTCTT
++
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++
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++
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++
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++
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++
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+GATTGA
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++
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++
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+CACAAT
++
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++
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+GCCAAT
++
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++
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++
+#0<FFF
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+CTAGCG
++
+BBBFFF
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+GAGAAT
++
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++
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+CCAAAT
++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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diff -r 000000000000 -r 44027547ce8f test-data/merged_pcr_dupes.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/merged_pcr_dupes.bed	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,3 @@
+chr1	10	20	readid_11	10	+
+chr1	10	20	readid_0	5	-
+chrX	20	30	readid_10	7	+
diff -r 000000000000 -r 44027547ce8f test-data/merged_pcr_dupes_clnts.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/merged_pcr_dupes_clnts.bed	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,3 @@
+chr1	9	10	readid_11	10	+
+chr1	20	21	readid_0	5	-
+chrX	19	20	readid_10	7	+
diff -r 000000000000 -r 44027547ce8f test-data/merged_pcr_dupes_spurious.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/merged_pcr_dupes_spurious.bed	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,12 @@
+chr1	10	20	AAAAA	1	+
+chr1	10	20	AAAAA	2	+
+chr1	10	20	AAAAA	3	+
+chr1	10	20	AAAAA	4	+
+chr1	10	20	AAAAA	5	+
+chr1	10	20	AAAAA	10	+
+chr1	10	20	AAAAA	100	+
+chr1	10	20	AAAAA	3	-
+chr1	10	20	AAAAA	5	-
+chr1	10	20	AAAAA	4	-
+chr1	10	20	AAAAA	5	-
+chrX	20	30	TTTTT	7	+
diff -r 000000000000 -r 44027547ce8f test-data/merged_pcr_dupes_spurious_filtered_thresh05.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/merged_pcr_dupes_spurious_filtered_thresh05.bed	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,6 @@
+chr1	10	20	AAAAA	5	-
+chr1	10	20	AAAAA	5	-
+chr1	10	20	AAAAA	4	-
+chr1	10	20	AAAAA	3	-
+chr1	10	20	AAAAA	100	+
+chrX	20	30	TTTTT	7	+
diff -r 000000000000 -r 44027547ce8f test-data/pcr_dupes_randomdict.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pcr_dupes_randomdict.fastq	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,88 @@
+@readid_0
+AAAAA
++
+BBBBB
+@readid_1
+AAAAA
++
+BBBBB
+@readid_2
+AAAAA
++
+BBBBB
+@readid_3
+TTTTT
++
+BBBBB
+@readid_4
+AAAAA
++
+BBBBB
+@readid_5
+AAAAA
++
+BBBBB
+@readid_6
+AAAAA
++
+BBBBB
+@readid_7
+TTTTT
++
+BBBBB
+@readid_8
+AAAAA
++
+BBBBB
+@readid_9
+AAAAA
++
+BBBBB
+@readid_10
+TTTTT
++
+BBBBB
+@readid_11
+AAAAA
++
+BBBBB
+@readid_12
+TTTTT
++
+BBBBB
+@readid_13
+TTTTT
++
+BBBBB
+@readid_14
+TTTTT
++
+BBBBB
+@readid_15
+AAAAA
++
+BBBBB
+@readid_16
+AAAAA
++
+BBBBB
+@readid_17
+AAAAA
++
+BBBBB
+@readid_18
+AAAAA
++
+BBBBB
+@readid_19
+AAAAA
++
+BBBBB
+@readid_20
+TTTTT
++
+BBBBB
+@readid_21
+AAAAA
++
+BBBBB
diff -r 000000000000 -r 44027547ce8f test-data/pcr_dupes_sorted_2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pcr_dupes_sorted_2.bed	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,22 @@
+chr1	10	20	readid_0	0	-
+chr1	10	20	readid_1	0	-
+chr1	10	20	readid_2	0	+
+chr1	10	20	readid_4	0	+
+chr1	10	20	readid_5	0	+
+chr1	10	20	readid_6	0	-
+chr1	10	20	readid_8	0	+
+chr1	10	20	readid_9	0	-
+chr1	10	20	readid_11	0	+
+chr1	10	20	readid_15	0	+
+chr1	10	20	readid_16	0	+
+chr1	10	20	readid_17	0	-
+chr1	10	20	readid_18	0	+
+chr1	10	20	readid_19	0	+
+chr1	10	20	readid_21	0	+
+chrX	20	30	readid_3	0	+
+chrX	20	30	readid_7	0	+
+chrX	20	30	readid_10	0	+
+chrX	20	30	readid_12	0	+
+chrX	20	30	readid_13	0	+
+chrX	20	30	readid_14	0	+
+chrX	20	30	readid_20	0	+
diff -r 000000000000 -r 44027547ce8f test-data/reads.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.fastq	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,400 @@
+@UID0
+NCTAGAATGAAAAATGTATGCTTGTGACCAATAAATATAAAAGGTTAAGATCGGAAGAGCACACGTCTG
++
+#0<FFFFFFFFFFFFIFIIIIIIIIIIIIIIFIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@UID1
+GGTTAACGCCAGTTGGTCCGAGTGTTGTGGGTTATTGTTAACTAAGATCGGAAGAGCACACGTCTGAAC
++
+BBBFFFFFFFFFFIIIIIIIFFFFFIIIIIIFIFIIIIIIIIIFFIFIIIIFFIIFFFFFFFFFFFBFB
+@UID2
+GCTAGAATCCTTTTCCTTTGCCCTGATCTTGTCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT
++
+B<B<BF<BFBFBFIFFFBFFFFFFFBBB0BBFFFBB<FB707'BFF0FFB'<B<BF#############
+@UID3
+CATTCACGTGGTTGGCGTTTGGTGTGTGGCTGTTTCTGCTCATTGATAGATCGGAAGAGCACACGTCTG
++
+BBBFFFFFFFFFFIIFFFFIIIFFFFFFIFIIFIIFFIFIIIFIIFFIIIIFIIFFFFFFFFFFFFBFF
+@UID4
+NAAAGAATACTGCTTTAATTCTAAATAAAAATTTATTGCCAAGATCGGAAGAGCACACGTCTGAACTCC
++
+#0<BFFFFFFFFFIIIFFFIIIIIIFIIFIFFIFIIIIFFIIIIIIIIIIIBFFFIIIIIIIIFIIIFF
+@UID5
+AAGAGAATGAATTGCCCCCCCCCACAACCGCGCTTGACTAGCGTAGCAGATCGGAAGAGCACACGTCTG
++
+BBBFFFFFFFFFFI0<FFFFIIIIIIIIIIIFBFFBFFFFBBFBFFFBBFFFFFFFFBBBFBFFFBBBB
+@UID6
+CAATCACGAAGTGTCCTCAGCAAAAGCTGGGTGGTTACCAAGATCGGAAGAGCACACGTCTGAACTCCA
++
+BBBFFFFFFFFFFFFFFIIIIIIFIFFIIIIBFFIIBBF<BFBFFFFIII7FFBFFFFBBBBBBFF<<B
+@UID7
+NCCGAGGTCAATCCGAGTCACGGCACCATGTTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC
++
+#0<FFFFFFFFFFIIIIFIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFB
+@UID8
+ACAAGAATAATCTTCTTAGAGTTGGTTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCATTCA
++
+BBBFFFFFFFFFFIFFIFI<FBFFFFFFIFFFFFFIBFBBFBFFFFFFFFFBBFFBB<7BFFF<<BB<B
+@UID9
+AAGAGAATAAATTACTAAATGTGAAAAACATAATGTGAAAAGTATATGTTAAGATCGGAAGAGCACACG
++
+BBBFFFFFFFFFFIIIIFFIIFIFIFIIFIFFFFF<BFFFIFFFIIIIIIIFFFIFF<FIIIIIIFIFI
+@UID10
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diff -r 000000000000 -r 44027547ce8f test-data/readswithtail.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/readswithtail.fastq	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,8 @@
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diff -r 000000000000 -r 44027547ce8f test-data/readswithtailremoved.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/readswithtailremoved.fastq	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,8 @@
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++
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diff -r 000000000000 -r 44027547ce8f test-data/result_original_head.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result_original_head.fastq	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,400 @@
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diff -r 000000000000 -r 44027547ce8f test-data/twomates.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/twomates.sam	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,5 @@
+@HD	VN:1.0	SO:unsorted
+@SQ	SN:chr1	LN:249250621
+@PG	ID:bowtie2	PN:bowtie2	VN:2.2.0	CL:"/usr/local/user/bowtie2/bowtie2-2.2.0/bowtie2-align-s --wrapper basic-0 --very-sensitive --end-to-end --no-mixed --no-discordant --fr --omit-sec-seq --minins=0 --maxins=200 --threads 24 --time -x ../genome/hg19/hg19 --passthrough -1 /tmp/10410.inpipe1 -2 /tmp/10410.inpipe2"
+39V34V1:167:HAWHUADXX:1:1101:19513:10724	99	chr1	45244081	40	41M	=	45244081	-41	GTCCAGTTCTGCTACCGACAGTAAGTGAAGATAAAGTGTGT	FFFIIIFIIIIIIFIIIIIIIFIIIBFFIIIIIIIIFFFFF	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T25	YS:i:-6	YT:Z:CP
+39V34V1:167:HAWHUADXX:1:1101:19513:10724	147	chr1	45244081	40	41M	=	45244081	-41	GTCCAGTTCTGCTACCGACAGTAAGTGAAGATAAAGTGTGT	IFIIFIIIFIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFF	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T25	YS:i:-6	YT:Z:CP
diff -r 000000000000 -r 44027547ce8f test-data/tworeads_aln_ends.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tworeads_aln_ends.bed	Tue Nov 14 05:50:32 2017 -0500
@@ -0,0 +1,1 @@
+chr1	45244080	45244121	39V34V1:167:HAWHUADXX:1:1101:19513:10724	2	+