# HG changeset patch
# User iuc
# Date 1538123325 14400
# Node ID bc0cc7bfbfe9f08f057a14097d906b6c6a5c5977

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb

diff -r 000000000000 -r bc0cc7bfbfe9 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,172 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">1.9</token>
+    <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
+    <token name="@PREPARE_IDX@"><![CDATA[
+        ##prepare input and indices 
+        ln -s '$input' infile &&
+        #if $input.is_of_type('bam'):
+            #if str( $input.metadata.bam_index ) != "None":
+                ln -s '${input.metadata.bam_index}' infile.bai &&
+            #else:
+                samtools index infile infile.bai &&
+            #end if
+        #elif $input.is_of_type('cram'):
+            #if str( $input.metadata.cram_index ) != "None":
+                ln -s '${input.metadata.cram_index}' infile.crai &&
+            #else:
+                samtools index infile infile.crai &&
+            #end if
+        #end if
+    ]]></token>
+    <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
+        ##prepare input and indices 
+        #for $i, $bam in enumerate( $input_bams ):
+            ln -s '$bam' '${i}' &&
+            #if $bam.is_of_type('bam'):
+                #if str( $bam.metadata.bam_index ) != "None":
+                    ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
+                #else:
+                    samtools index '${i}' '${i}.bai' &&
+                #end if
+            #elif $bam.is_of_type('cram'):
+                #if str( $bam.metadata.cram_index ) != "None":
+                    ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
+                #else:
+                    samtools index '${i}' '${i}.crai' &&
+                #end if
+            #end if
+        #end for
+    ]]></token>
+    <token name="@PREPARE_FASTA_IDX@"><![CDATA[
+        ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")
+        ##and sets the -t/-T parameters accordingly:
+        ##- in case of history a symbolic link is used because samtools (view) will generate
+        ##  the index which might not be possible in the directory containing the fasta file
+        ##- in case of cached the absolute path is used which allows to read the cram file
+        ##  without specifying the reference
+        #if $addref_cond.addref_select == "history":
+            ln -s '${addref_cond.ref}' reference.fa &&
+            samtools faidx reference.fa &&
+            #set reffa="reference.fa"
+            #set reffai="reference.fa.fai"
+        #elif $addref_cond.addref_select == "cached":
+            #set reffa=str($addref_cond.ref.fields.path)
+            #set reffai=str($addref_cond.ref.fields.path)+".fai"
+        #else
+            #set reffa=None
+            #set reffai=None
+        #end if
+    ]]></token>
+    <token name="@ADDTHREADS@"><![CDATA[
+        ##compute the number of ADDITIONAL threads to be used by samtools (-@)
+        addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
+    ]]></token>
+    <token name="@ADDMEMORY@"><![CDATA[
+        ##compute the number of memory available to samtools sort (-m)
+        ##use only 75% of available: https://github.com/samtools/samtools/issues/831
+        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && 
+        ((addmemory=addmemory*75/100)) &&
+    ]]></token>
+    <xml name="seed_input">
+       <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> 
+    </xml>
+    <xml name="flag_options">
+        <option value="1">read is paired</option>
+        <option value="2">read is mapped in a proper pair</option>
+        <option value="4">read is unmapped</option>
+        <option value="8">mate is unmapped</option>
+        <option value="16">read reverse strand</option>
+        <option value="32">mate reverse strand</option>
+        <option value="64">read is the first in a pair</option>
+        <option value="128">read is the second in a pair</option>
+        <option value="256">alignment or read is not primary</option>
+        <option value="512">read fails platform/vendor quality checks</option>
+        <option value="1024">read is a PCR or optical duplicate</option>
+        <option value="2048">supplementary alignment</option>
+    </xml>
+
+    <!-- region specification macros and tokens for tools that allow the specification 
+         of region by bed file / space separated list of regions -->
+    <token name="@REGIONS_FILE@"><![CDATA[
+        #if $cond_region.select_region == 'tab':
+            -t '$cond_region.targetregions'
+        #end if
+    ]]></token>
+    <token name="@REGIONS_MANUAL@"><![CDATA[
+        #if $cond_region.select_region == 'text':
+            #for $i, $x in enumerate($cond_region.regions_repeat):
+               '${x.region}'
+            #end for
+        #end if
+    ]]></token>
+    <xml name="regions_macro">
+        <conditional name="cond_region">
+            <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
+                <option value="no" selected="True">No</option>
+                <option value="text">Manualy specify regions</option>
+                <option value="tab">Regions from tabular file</option>
+            </param>
+            <when value="no"/>
+            <when value="text">
+                <repeat name="regions_repeat" min="1" default="1" title="Regions">
+                    <param name="region" type="text" label="region" help="format chr:from-to">
+                        <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
+                    </param>
+                </repeat>
+            </when>
+            <when value="tab">
+                <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" />
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{SAM_def,
+                title={Definition of SAM/BAM format},
+                url = {https://samtools.github.io/hts-specs/},}
+            </citation>
+            <citation type="doi">10.1093/bioinformatics/btp352</citation>
+            <citation type="doi">10.1093/bioinformatics/btr076</citation>
+            <citation type="doi">10.1093/bioinformatics/btr509</citation>
+            <citation type="bibtex">
+                @misc{Danecek_et_al,
+                Author={Danecek, P., Schiffels, S., Durbin, R.},
+                title={Multiallelic calling model in bcftools (-m)},
+                url = {http://samtools.github.io/bcftools/call-m.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{Durbin_VCQC,
+                Author={Durbin, R.},
+                title={Segregation based metric for variant call QC},
+                url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{Li_SamMath,
+                Author={Li, H.},
+                title={Mathematical Notes on SAMtools Algorithms},
+                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{SamTools_github,
+                title={SAMTools GitHub page},
+                url = {https://github.com/samtools/samtools},}
+            </citation>
+        </citations>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="Error" />
+        </stdio>
+    </xml>
+</macros>
diff -r 000000000000 -r bc0cc7bfbfe9 samtools_fixmate.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_fixmate.xml	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,86 @@
+<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@">
+    <description>fill mate coordinates, ISIZE and mate related flags</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @ADDTHREADS@
+        ## name sort input 
+        #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'):
+            samtools sort
+            -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
+            -n 
+            -O BAM
+            -o namesorted.bam
+            '$bamfile' &&
+        #else:
+            ln -s '$bamfile' namesorted.bam &&
+        #end if
+
+        samtools fixmate
+            -@ \$addthreads
+            $remsec
+            $noprop
+            $tempcigar
+            $addms
+            -O BAM
+            namesorted.bam
+            '$output'
+    ]]></command>
+    <inputs>
+        <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Select alignment" help="Set of aligned reads." />
+        <param name="remsec" type="boolean" argument="-r" truevalue="-r" falsevalue="" checked="false" label="Remove secondary and unmapped reads" />
+        <param name="noprop" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Disable FR proper pair check" />
+        <param name="tempcigar" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Add template cigar ct tag" />
+        <param name="addms" type="boolean" argument="-m" truevalue="-m" falsevalue="" checked="false" label="Add ms (mate score) tags" help="These are used by markdup to select the best reads to keep." />
+    </inputs>
+    <outputs>
+	<!--<data name="output" format="sam" />-->
+	<data name="output" format="qname_sorted.bam"/>
+    </outputs>
+    <tests>
+<!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493-->
+<!--    test_cmd($opts,out=>'fixmate/1_coord_sort.sam.expected', err=>'fixmate/1_coord_sort.sam.expected.err', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/1_coord_sort.sam -", expect_fail=>1);-->
+<test>
+    <param name="bamfile" value="2_isize_overflow.sam" />
+    <output name="output" file="2_isize_overflow.bam.expected" />
+</test>
+<!--    test_cmd($opts,out=>'fixmate/2_isize_overflow.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/2_isize_overflow.sam -");-->
+<test>
+    <param name="bamfile" value="3_reverse_read_pp_lt.sam" />
+    <output name="output" file="3_reverse_read_pp_lt.bam.expected" />
+</test>
+<!--    test_cmd($opts,out=>'fixmate/3_reverse_read_pp_lt.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/3_reverse_read_pp_lt.sam -");-->
+<test>
+    <param name="bamfile" value="4_reverse_read_pp_equal.sam" />
+    <output name="output" file="4_reverse_read_pp_equal.bam.expected" />
+</test>
+<!--    test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");-->
+<test>
+    <param name="bamfile" value="5_ct.sam" />
+    <param name="tempcigar" value="-c" />
+    <output name="output" file="5_ct.bam.expected" />
+</test>
+<!--    test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");-->
+<test>
+    <param name="bamfile" value="6_ct_replace.sam" />
+    <param name="tempcigar" value="-c" />
+    <output name="output" file="6_ct_replace.bam.expected" />
+</test>
+<!--    test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");-->
+<test>
+    <param name="bamfile" value="7_two_read_mapped.sam" />
+    <output name="output" file="7_two_read_mapped.bam.expected" />
+</test>
+<!--test_cmd($opts,out=>'fixmate/7_two_read_mapped.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/7_two_read_mapped.sam -");-->
+    </tests>
+    <help>
+**What it does**
+
+Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment.
+    </help>
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/2_isize_overflow.bam.expected
Binary file test-data/2_isize_overflow.bam.expected has changed
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/2_isize_overflow.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_isize_overflow.sam	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,20 @@
+@HD	VN:1.4	SO:queryname
+@SQ	SN:ref1	LN:45
+@SQ	SN:ref2	LN:40
+of1	99	ref1	10	30	23M	=	8	2	AAGTCGGCAGCGTCAGATGTGTA	???????????????????????
+of1	147	ref1	8	30	23M	=	10	-2	CTGTCTCTTATACACATCTCCTT	???????????????????????
+r001	83	ref1	37	30	9M	=	7	-39	CAGCGCCAT	*
+r001	163	ref1	7	30	8M4I4M1D3M	=	37	39	TTAGATAAAGAGGATACTG	*	XX:B:S,12561,2,20,112	YY:i:100
+r002	0	ref1	9	30	1S2I6M1P1I1P1I4M2I	*	0	0	AAAAGATAAGGGATAAA	*	XA:Z:abc	XB:i:-10
+r003	0	ref1	9	30	5H6M	*	0	0	AGCTAA	*
+r003	16	ref1	29	30	6H5M	*	0	0	TAGGC	*
+r004	0	ref1	16	30	6M14N1I5M	*	0	0	ATAGCTCTCAGC	*
+r007	8	ref1	9	30	5H6M	*	0	0	AGCTAA	*
+r007	4	ref1	9	30	*	*	0	0	GGGGGG	*
+u1	4	*	0	30	*	*	0	0	TAATTGGGTCTTCAGAGCACCTA	???????????????????????
+x1	0	ref2	1	30	20M	*	0	0	AGGTTTTATAAAACAAATAA	*
+x2	0	ref2	2	30	21M	*	0	0	GGTTTTATAAAACAAATAATT	?????????????????????
+x3	0	ref2	6	30	9M4I13M	*	0	0	TTATAAAACAAATAATTAAGTCTACA	??????????????????????????
+x4	0	ref2	10	30	25M	*	0	0	CAAATAATTAAGTCTACAGAGCAAC	?????????????????????????
+x5	0	ref2	12	30	24M	*	0	0	AATAATTAAGTCTACAGAGCAACT	????????????????????????
+x6	0	ref2	14	30	23M	*	0	0	TAATTAAGTCTACAGAGCAACTA	???????????????????????
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/2_isize_overflow.sam.expected
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_isize_overflow.sam.expected	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,20 @@
+@HD	VN:1.4	SO:queryname
+@SQ	SN:ref1	LN:45
+@SQ	SN:ref2	LN:40
+of1	99	ref1	10	30	23M	=	8	21	AAGTCGGCAGCGTCAGATGTGTA	???????????????????????	MQ:i:30	MC:Z:23M
+of1	147	ref1	8	30	23M	=	10	-21	CTGTCTCTTATACACATCTCCTT	???????????????????????	MQ:i:30	MC:Z:23M
+r001	83	ref1	37	30	9M	=	7	-39	CAGCGCCAT	*	MQ:i:30	MC:Z:8M4I4M1D3M
+r001	163	ref1	7	30	8M4I4M1D3M	=	37	39	TTAGATAAAGAGGATACTG	*	XX:B:S,12561,2,20,112	YY:i:100	MQ:i:30	MC:Z:9M
+r002	0	ref1	9	30	1S2I6M1P1I1P1I4M2I	*	0	0	AAAAGATAAGGGATAAA	*	XA:Z:abc	XB:i:-10
+r003	33	ref1	9	30	5H6M	=	29	25	AGCTAA	*	MQ:i:30	MC:Z:6H5M
+r003	17	ref1	29	30	6H5M	=	9	-25	TAGGC	*	MQ:i:30	MC:Z:5H6M
+r004	0	ref1	16	30	6M14N1I5M	*	0	0	ATAGCTCTCAGC	*
+r007	9	ref1	9	30	5H6M	=	9	0	AGCTAA	*	MC:Z:*
+r007	5	ref1	9	30	*	=	9	0	GGGGGG	*	MQ:i:30	MC:Z:5H6M
+u1	4	*	0	30	*	*	0	0	TAATTGGGTCTTCAGAGCACCTA	???????????????????????
+x1	0	ref2	1	30	20M	*	0	0	AGGTTTTATAAAACAAATAA	*
+x2	0	ref2	2	30	21M	*	0	0	GGTTTTATAAAACAAATAATT	?????????????????????
+x3	0	ref2	6	30	9M4I13M	*	0	0	TTATAAAACAAATAATTAAGTCTACA	??????????????????????????
+x4	0	ref2	10	30	25M	*	0	0	CAAATAATTAAGTCTACAGAGCAAC	?????????????????????????
+x5	0	ref2	12	30	24M	*	0	0	AATAATTAAGTCTACAGAGCAACT	????????????????????????
+x6	0	ref2	14	30	23M	*	0	0	TAATTAAGTCTACAGAGCAACTA	???????????????????????
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/3_reverse_read_pp_lt.bam.expected
Binary file test-data/3_reverse_read_pp_lt.bam.expected has changed
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/3_reverse_read_pp_lt.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3_reverse_read_pp_lt.sam	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,5 @@
+@HD	VN:1.4	SO:queryname
+@SQ	SN:1	LN:4569345
+@RG	ID:1#6	LB:1	SM:a
+MS0_12500:1:2114:20577:3664#6	99	1	40346	23	75M	=	40340	75	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD	X0:i:1	X1:i:1	XA:Z:X,+8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	MQ:i:23	XT:A:U
+MS0_12500:1:2114:20577:3664#6	147	1	40340	23	75M	=	40346	-75	CAAAATCTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGT	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC	X0:i:1	X1:i:1	XA:Z:X,-8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	MQ:i:23	XT:A:U
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/3_reverse_read_pp_lt.sam.expected
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3_reverse_read_pp_lt.sam.expected	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,5 @@
+@HD	VN:1.4	SO:queryname
+@SQ	SN:1	LN:4569345
+@RG	ID:1#6	LB:1	SM:a
+MS0_12500:1:2114:20577:3664#6	99	1	40346	23	75M	=	40340	69	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD	X0:i:1	X1:i:1	XA:Z:X,+8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	XT:A:U	MQ:i:23	MC:Z:75M
+MS0_12500:1:2114:20577:3664#6	147	1	40340	23	75M	=	40346	-69	CAAAATCTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGT	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC	X0:i:1	X1:i:1	XA:Z:X,-8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	XT:A:U	MQ:i:23	MC:Z:75M
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/4_reverse_read_pp_equal.bam.expected
Binary file test-data/4_reverse_read_pp_equal.bam.expected has changed
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/4_reverse_read_pp_equal.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/4_reverse_read_pp_equal.sam	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,5 @@
+@HD	VN:1.4	SO:queryname
+@SQ	SN:1	LN:4569345
+@RG	ID:1#6	LB:1	SM:a
+MS0_12500:1:2114:20577:3664#6	99	1	40346	23	75M	=	40346	75	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD	X0:i:1	X1:i:1	XA:Z:X,+8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	MQ:i:23	XT:A:U
+MS0_12500:1:2114:20577:3664#6	147	1	40346	23	75M	=	40346	-75	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC	X0:i:1	X1:i:1	XA:Z:X,-8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	MQ:i:23	XT:A:U
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/4_reverse_read_pp_equal.sam.expected
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/4_reverse_read_pp_equal.sam.expected	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,5 @@
+@HD	VN:1.4	SO:queryname
+@SQ	SN:1	LN:4569345
+@RG	ID:1#6	LB:1	SM:a
+MS0_12500:1:2114:20577:3664#6	99	1	40346	23	75M	=	40346	75	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD	X0:i:1	X1:i:1	XA:Z:X,+8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	XT:A:U	MQ:i:23	MC:Z:75M
+MS0_12500:1:2114:20577:3664#6	147	1	40346	23	75M	=	40346	-75	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC	X0:i:1	X1:i:1	XA:Z:X,-8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	XT:A:U	MQ:i:23	MC:Z:75M
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/5_ct.bam.expected
Binary file test-data/5_ct.bam.expected has changed
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/5_ct.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/5_ct.sam	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,5 @@
+@HD	VN:1.4	SO:queryname
+@SQ	SN:1	LN:4569345
+@RG	ID:1#6	LB:1	SM:a
+MS0_12500:1:2114:20577:3664#6	99	1	40346	23	75M	=	40346	75	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD	X0:i:1	X1:i:1	XA:Z:X,+8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	MQ:i:23	XT:A:U
+MS0_12500:1:2114:20577:3664#6	147	1	40346	23	75M	=	40346	-75	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC	X0:i:1	X1:i:1	XA:Z:X,-8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	MQ:i:23	XT:A:U
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/5_ct.sam.expected
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/5_ct.sam.expected	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,5 @@
+@HD	VN:1.4	SO:queryname
+@SQ	SN:1	LN:4569345
+@RG	ID:1#6	LB:1	SM:a
+MS0_12500:1:2114:20577:3664#6	99	1	40346	23	75M	=	40346	75	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD	X0:i:1	X1:i:1	XA:Z:X,+8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	XT:A:U	MQ:i:23	MC:Z:75M	ct:Z:1F75M-75T2R75M
+MS0_12500:1:2114:20577:3664#6	147	1	40346	23	75M	=	40346	-75	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC	X0:i:1	X1:i:1	XA:Z:X,-8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	XT:A:U	MQ:i:23	MC:Z:75M
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/6_ct_replace.bam.expected
Binary file test-data/6_ct_replace.bam.expected has changed
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/6_ct_replace.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/6_ct_replace.sam	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,5 @@
+@HD	VN:1.4	SO:queryname
+@SQ	SN:1	LN:4569345
+@RG	ID:1#6	LB:1	SM:a
+MS0_12500:1:2114:20577:3664#6	99	1	40346	23	75M	=	40346	75	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD	X0:i:1	X1:i:1	XA:Z:X,+8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	XT:A:U	MQ:i:23
+MS0_12500:1:2114:20577:3664#6	147	1	40346	23	75M	=	40346	-75	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC	X0:i:1	X1:i:1	XA:Z:X,-8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	XT:A:U	MQ:i:23	ct:Z:1F70M-75T2R70M
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/6_ct_replace.sam.expected
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/6_ct_replace.sam.expected	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,5 @@
+@HD	VN:1.4	SO:queryname
+@SQ	SN:1	LN:4569345
+@RG	ID:1#6	LB:1	SM:a
+MS0_12500:1:2114:20577:3664#6	99	1	40346	23	75M	=	40346	75	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD	X0:i:1	X1:i:1	XA:Z:X,+8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	XT:A:U	MQ:i:23	MC:Z:75M	ct:Z:1F75M-75T2R75M
+MS0_12500:1:2114:20577:3664#6	147	1	40346	23	75M	=	40346	-75	CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC	X0:i:1	X1:i:1	XA:Z:X,-8796,75M,2;	MD:Z:22C52	RG:Z:1#6	XG:i:0	AM:i:23	NM:i:1	SM:i:23	XM:i:1	XO:i:0	XT:A:U	MQ:i:23	MC:Z:75M
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/7_two_read_mapped.bam.expected
Binary file test-data/7_two_read_mapped.bam.expected has changed
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/7_two_read_mapped.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/7_two_read_mapped.sam	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,22 @@
+@HD	VN:1.4	SO:queryname
+@SQ	SN:ref1	LN:45
+@SQ	SN:ref2	LN:40
+of1	99	ref1	10	30	23M	=	8	2	AAGTCGGCAGCGTCAGATGTGTA	???????????????????????
+of1	147	ref1	8	30	23M	=	10	-2	CTGTCTCTTATACACATCTCCTT	???????????????????????
+r001	83	ref1	37	30	9M	=	7	-39	CAGCGCCAT	*
+r001	163	ref1	7	30	8M4I4M1D3M	=	37	39	TTAGATAAAGAGGATACTG	*	XX:B:S,12561,2,20,112	YY:i:100
+r002	0	ref1	9	30	1S2I6M1P1I1P1I4M2I	*	0	0	AAAAGATAAGGGATAAA	*	XA:Z:abc	XB:i:-10
+r003	0	ref1	9	30	5H6M	*	0	0	AGCTAA	*
+r003	16	ref1	29	30	6H5M	*	0	0	TAGGC	*
+r004	0	ref1	16	30	6M14N1I5M	*	0	0	ATAGCTCTCAGC	*
+r007	8	ref1	9	30	5H6M	*	0	0	AGCTAA	*
+r007	4	ref1	9	30	*	*	0	0	GGGGGG	*
+r008	12	ref1	9	30	5H6M	*	0	0	AGCTAA	*
+r008	4	ref1	9	30	*	*	0	0	GGGGGG	*
+uu1	4	*	0	30	*	*	0	0	TAATTGGGTCTTCAGAGCACCTA	???????????????????????
+x1	0	ref2	1	30	20M	*	0	0	AGGTTTTATAAAACAAATAA	*
+x2	0	ref2	2	30	21M	*	0	0	GGTTTTATAAAACAAATAATT	?????????????????????
+x3	0	ref2	6	30	9M4I13M	*	0	0	TTATAAAACAAATAATTAAGTCTACA	??????????????????????????
+x4	0	ref2	10	30	25M	*	0	0	CAAATAATTAAGTCTACAGAGCAAC	?????????????????????????
+x5	0	ref2	12	30	24M	*	0	0	AATAATTAAGTCTACAGAGCAACT	????????????????????????
+x6	0	ref2	14	30	23M	*	0	0	TAATTAAGTCTACAGAGCAACTA	???????????????????????
diff -r 000000000000 -r bc0cc7bfbfe9 test-data/7_two_read_mapped.sam.expected
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/7_two_read_mapped.sam.expected	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,22 @@
+@HD	VN:1.4	SO:queryname
+@SQ	SN:ref1	LN:45
+@SQ	SN:ref2	LN:40
+of1	99	ref1	10	30	23M	=	8	21	AAGTCGGCAGCGTCAGATGTGTA	???????????????????????	MQ:i:30	MC:Z:23M
+of1	147	ref1	8	30	23M	=	10	-21	CTGTCTCTTATACACATCTCCTT	???????????????????????	MQ:i:30	MC:Z:23M
+r001	83	ref1	37	30	9M	=	7	-39	CAGCGCCAT	*	MQ:i:30	MC:Z:8M4I4M1D3M
+r001	163	ref1	7	30	8M4I4M1D3M	=	37	39	TTAGATAAAGAGGATACTG	*	XX:B:S,12561,2,20,112	YY:i:100	MQ:i:30	MC:Z:9M
+r002	0	ref1	9	30	1S2I6M1P1I1P1I4M2I	*	0	0	AAAAGATAAGGGATAAA	*	XA:Z:abc	XB:i:-10
+r003	33	ref1	9	30	5H6M	=	29	25	AGCTAA	*	MQ:i:30	MC:Z:6H5M
+r003	17	ref1	29	30	6H5M	=	9	-25	TAGGC	*	MQ:i:30	MC:Z:5H6M
+r004	0	ref1	16	30	6M14N1I5M	*	0	0	ATAGCTCTCAGC	*
+r007	9	ref1	9	30	5H6M	=	9	0	AGCTAA	*	MC:Z:*
+r007	5	ref1	9	30	*	=	9	0	GGGGGG	*	MQ:i:30	MC:Z:5H6M
+r008	13	ref1	9	30	5H6M	=	9	0	AGCTAA	*
+r008	13	ref1	9	30	*	=	9	0	GGGGGG	*
+uu1	4	*	0	30	*	*	0	0	TAATTGGGTCTTCAGAGCACCTA	???????????????????????
+x1	0	ref2	1	30	20M	*	0	0	AGGTTTTATAAAACAAATAA	*
+x2	0	ref2	2	30	21M	*	0	0	GGTTTTATAAAACAAATAATT	?????????????????????
+x3	0	ref2	6	30	9M4I13M	*	0	0	TTATAAAACAAATAATTAAGTCTACA	??????????????????????????
+x4	0	ref2	10	30	25M	*	0	0	CAAATAATTAAGTCTACAGAGCAAC	?????????????????????????
+x5	0	ref2	12	30	24M	*	0	0	AATAATTAAGTCTACAGAGCAACT	????????????????????????
+x6	0	ref2	14	30	23M	*	0	0	TAATTAAGTCTACAGAGCAACTA	???????????????????????