# HG changeset patch
# User iuc
# Date 1559265298 14400
# Node ID e6ef29001647809082b4ec32b8606a3a29163171

planemo upload commit b89c8017aeef91f940543a1cc7dadb4a85290865

diff -r 000000000000 -r e6ef29001647 basil.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/basil.xml	Thu May 30 21:14:58 2019 -0400
@@ -0,0 +1,61 @@
+<tool id="basil" name="basil" version="1.2.0">
+    <description>Breakpoint detection, including large insertions</description>
+    <requirements>
+        <requirement type="package" version="1.2.0">anise_basil</requirement>
+    </requirements>
+    <version_command>basil --version 2>&amp;1 | grep 'basil version' | cut -f 3 -d ' '</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        ln -s '$ref' 'ref.fa' &&
+        ln -s '$bam' 'in.bam' &&
+        ln -s '$vcf' 'out.vcf' &&
+        basil
+        --input-reference 'ref.fa'
+        --input-mapping 'in.bam'
+        --out-vcf 'out.vcf'
+        --oea-min-support-each-side '$min_oea_each_side'
+    ]]></command>
+    <inputs>
+        <param name="ref" argument="--input-reference" type="data" format="Fasta" label="Reference Sequence File" help="FASTA file with the reference."/>
+        <param name="bam" argument="--input-mapping" type="data" format="sam,bam" label="Alignment File" help="SAM/BAM file to use as the input."/>
+        <param name="min_oea_each_side" argument="--oea-min-support-each-side" type="integer" value="2" label="Minimum supporting reads, each side" help="Smallest number of OEA (one-end-anchor) reads on each side to support an insertion.  In range [1..inf].  This is the minimum number of supporting reads (without mapped partners) on each side of an insertion breakpoint required to not be filtered." />
+    </inputs>
+    <outputs>
+        <data name="vcf" format="vcf" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="ref" value="ref.fa"/>
+            <param name="bam" value="simulated.bam"/>
+            <param name="min_oea_each_side"  value="2"/>
+            <output name="vcf" file="basil.vcf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        BASIL is a method to detect breakpoints for structural variants (including insertion breakpoints) from aligned paired HTS reads in BAM format.  Use BASIL to analyze BAM files for tentative insertion sites.
+
+        Note that BASIL will in general detect all kinds of breakpoints, e.g. for inversions on real-world data.
+
+        BASIL VCF fields
+
+        A typical line in BASIL might look as follows.
+
+        1 5001 site_0 T <INS>   . PASS IMPRECISE;SVTYPE=INS GSCORE:CLEFT:CRIGHT:OEALEFT:OEARIGHT    46.4256:10:12:35:32
+
+        The first seven columns are as usually in VCF files (ref name, 1-based position, reference base, abbreviation for long insertion, no assigned quality, passing all filters, imprecise insertion SV).
+
+        The eighth column contains the names of the score values given in the ninth column:
+
+        GSCORE Geometric mean of the sum of "1 + $score" for all of the following scores.
+        CLEFT Number of clipping signatures supporting the site from the left side.
+        CRIGHT Number of clipping signatures supporting the site from the right side.
+        OEALEFT Number of OEA alignments supporting the site from the left.
+        OEARIGHT Number of OEA alignmetns supproting the site from the right.
+
+        Generally, one should filter for a minimum support of OEA records on each side, e.g. a value of 10 makes sense for a 30x coverage and showed good results on simulated data.
+
+        For a ranking, GSCORE is a suitable measure but we did not develop any statistical model for BASIL matches and it is a mean of pseudocounts only. It carries no statistically precise meaning.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btv051</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r e6ef29001647 test-data/basil.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/basil.vcf	Thu May 30 21:14:58 2019 -0400
@@ -0,0 +1,15 @@
+##fileformat=VCFv4.1
+##source=BASIL
+##reference=ref.fa
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=OEA_ONLY,Number=0,Type=Flag,Description="Breakpoint support by OEA signature only">
+##ALT=<ID=INS,Description="Insertion of novel sequence">
+##FORMAT=<ID=GSCORE,Number=1,Type=String,Description="Sum of Geometric score means (see BASIL documentation)">
+##FORMAT=<ID=CLEFT,Number=1,Type=String,Description="Clipped alignments supporting call from left side.">
+##FORMAT=<ID=CRIGHT,Number=1,Type=String,Description="Clipped alignments supporting call from right side.">
+##FORMAT=<ID=OEALEFT,Number=1,Type=String,Description="One-end anchored alignments supporting call from left side.">
+##FORMAT=<ID=OEARIGHT,Number=1,Type=String,Description="One-end anchored alignments supporting call from right side.">
+##contig=<ID=1,length=10000>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	individual
+1	5001	site_0	T	<INS>	.	PASS	IMPRECISE;SVTYPE=INS	GSCORE:CLEFT:CRIGHT:OEALEFT:OEARIGHT	46.4256:10:12:35:32
diff -r 000000000000 -r e6ef29001647 test-data/ref.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref.fa	Thu May 30 21:14:58 2019 -0400
@@ -0,0 +1,144 @@
+>1
+CTGTAACTAAACACCGCTGTCCGGACTAAGGTCCGCATATTGTTCAGGTTTTATACAATGAGCGTCGAGC
+CAGTTCAATGTGGCCCTAAACCTACTCAAGAAGTATCCCGAGGGATGCGAAGCTGCCGATGAGAGTTAGT
+TGACATTCCGAGTCCGTGGATGGGTCCTCCTTCTTAGCGAATTACCGTCCATTTGCATGACGGATGCCTT
+GCACTTGGTAACAGTAGCAATGTATAGGAAACAAAGAATCGAGTTCAACAGGTCGCATTCAGTGCCTTGC
+GCACAAATATATAGGAGGAAACTCGCAACAGAATGCTATGACCAGTTTATAGAACTGTGCCGTAGACGGA
+GTGCCAATCAGAAATAACCATAATGGGTTGCCAGGGTGTATGACAGGTTCTTGATAGTCCCAGAGCTTTC
+CGTAACAAAGGAACTTTCACAACGATTGCCTCGTTATATTCCGCTGCACTGCATGACATTCATTGGAATG
+GAAACAGCTGATTTCCTAGATAGCGCCGGGTATATTGTTACCGCCCCACACGCAGGCATCGGACCACATA
+TTTTGGCACCTGGTTAGAGAGCTAGACTCGATCGAATAACTTTAGGGAAGCTCCATGTCATGTCCAACAC
+CCGAAGAGTACAGGACATGTCAAAGGGAGGATTAAAGTTGACCCTATCGATGTATGTCAAGGGTGCTGAG
+TTGCCCCAGGCTTGCGTATCCTACTGGCTTGATTGGGTACCTAGAGGTACCGTTGCGCATCGGCTCACAA
+CGTTCAATGCAGTCCCAAGATACGGTGTGATGTCAGGACCTAAGCGACCCATGATCGCTGCTTCCTTGGA
+AGAGAGAGCGACATTTCCGTCTCGCGCATTCTTTAGTAAGGGAGGAACTTTTTGTGAAAGATGGTGTTGG
+GCTTCGAGACATTTATCGTGCCTTCTGGCTTACTCAGATTACGCTGAAGCCTTTGGGCCTGCCCATGACT
+GTTGCAATCATTTGTCTGAAACACCAATGACTTAACGAATGCCCACAAGACTGAAGGTTATCGATCTTGG
+AGAAAACTCCTGATTCTATAGGGACCATCTCAGGCCCGACAATCCTTAACCGGATCCTAACAGGGTTCAC
+ATGTTCATGGGTCGTAGTAACCTGTGGCGTGACCGTGGCATAAAGACGTCCGTCCAATTCCTGAGAAAAG
+ACACCGAAATGGTGAAAGAGTGGGGACCTCCGTAGACAACTTACATCGCCACGCAAGCTTATGTGTGCGT
+CAGCTACTTCATTGACCACAAATTCGGCCGAAAGATGGCGCTATTGATTTATGGATTAAGGGGCACGCAG
+TTGTACTTATTCGGCGTAGGTTCCAATCTAGTGGGATTCCTATGGGCCGAAGTCTGAGAAACCTTAGACA
+AACGGTCACCCATGCGCCGCACCTCCGGTGCCTCCAGTAACATAGTTTGTCCTCAGGTTTGAAATGCTGG
+GTTTGGTAAGTGAACCTTAATATCCGCTTGCGATTGTCCATGCGGACCGGATTTCAAGAAAGGAGATAGA
+TTGATCCAGGAACCATCTATCGTACATCGGCCTCGCCCTGCACGCAGACCTGCAGTCATCTTATGATGCG
+TCCCGTGCAAACCCTCCGTTATCTAGGAGCGGCAGCAGCGCACGAAGAGCGGGAAGATGATTATCTCCCG
+AGCTCTTGTGCCGAAGGGCATTGTGGAACATTTGGAACGGGGCTCGGATCTCGCTCACTAAAATCTAAGG
+ATCGAGGAGACAAAGTCATTCGGCAAGACAAACTCACGTCCGTGGTTGCAACTGATTAGACTTTATGGAT
+GAACGCTATGCTGCTACCGAACCGACGACCCGTGGTCACCAGCTATCCGCTCAAGACATTATATCATTAA
+TCCGAGACCCCTGCAGACACACGTCTCGGCTATTGTTGAGAGCCCTTCCTGCTCCATACCCCCGGCACGT
+ATAATAAACCGAGTACTATGTCCCGGCGGATTCCGTCTTACCTATCTACGAGATCCAGGTGCCGTAGCAT
+AAAGCTATGCGGGACGTTCTACTCGTTCTAACAGAACCTCAGCCATTGTAACCCACTTTTGTTGCATCCT
+ATTGGCAGTGGGGCGACCGCTGAGATTGGGGTAGCTTCCTAGTAACTGTGCAGCGAGGTACGTCGCAGAG
+GGATACACTTGTTACGGCGGGGACTTTGGCAGTGACCCTAGGTTGATGTCCTAAGACGATGTAAATTGAG
+CTATTCGACGTAGTCGGTCCCTCTAAGTGAACTTTCTATCACCGCGGCCCGAGGGGGAATTATGTGATAG
+CGCGTGGCTCCAACATCTATTCGGGGCAAAACCGACACGTGTCGTACGTTGCGTACGTTACCTTTTCTGG
+TTACTTATTCGACCAAGTTATTGCTTGTATCACTTTCGTTGTAAACCTATGCCCTTTTAACACAGCTACG
+CCCATGAGTGACGTCATGACATTAGACAAAACACAGTATTGCCATTCCCACCTTCTCACATGCCCAGCAA
+AATGGGGAACGTGTCGACTTCCTGCTGTCACAACAGAACGGAGCGTATGTGAAGAAACTGTATCCCTCGG
+TGCCGTTCAAGACCGGTACACTTTGACGGCCAACCGCAAGTGGCGCGGGGGCTGTTAGCTAATCAGGCAT
+ATGCATCGGCCAGCGGCGGGGCGAGACGGGTGGGTGCGGAAATAGAATCCGATGAGGTTCGTTAATCGTC
+TTGCTTTGTGTTACATACAATAAATCGTCCCCCCCATGGTAACACGAGTTTCCATTCACATTTGGCTCTT
+GCCCGGCAGGTGTGCGATAAGTCTTATGACTTTTTTAGACATCCACCACTTGCACGGCGTACTCTTTATT
+CTCCATAATGCCTGTGTGATTCGCAGCTACCAATAAAGGTGCTTACGCAAGGTATTACCCAAATATCAAC
+CCGGCCCCGCCCGCCGGACCCCAATATGTTATTCTGCCCTGTAGCGACTCCGTGGTCGTCAAGAGTCTAT
+CACATACTCTATGGTAACTAAGATAGTGTCCGTGTCCTCTGGATAACGAAGCGACCTAACATCAAGACTC
+AGGTAAATGGTCTTCTACTATCTTGATGTCCTGTGAGCGAGATGGATACCATTCGCCTGATCAAACGCAG
+TAGCGTATAGGGCTAGCGGGAATTTCTTGACGGCCGCAGAGTTTCTTGTGATCGGATGACTGCTTGATAC
+TTGGCGACGAAGCCCTGTGGTATGGGGGCCTGACTTCCGCGGACATGGTCGTAATGCCTAGGATAGTTGC
+TACGGTGGGAACCTATTTTTATGCCCGCCAGACTCGTGTGGGACTCTATCAGTTAAGCGCGACTTCTCGC
+AGAGAAAGATTAAGATTATGGCTTAATTCTTCTGTACATTCCTTGGTGAGGCGGCTCTCTAGAGTTGCAT
+TTGGGTGGCATCACTCTTCCAGGTAGTTCACCTCTTGTTGCCTGCCCCAATGCGGGGCGAACTTTCGCTG
+CTGACCGCCGTTACACAGAACCTGAAGGGACAACACACGAGACCGGAATGTAGTCTCTCTTGTCCAGTTC
+TGGGGGCATATAGATTTATGATGTTATTCGTGCCCTTATGTTACCCATCCGTGTCGCCGTGAGCGACATC
+CGGCTAATGTATGGGCAATGGGAATCAGGTATGACTGCGCGAGCTATCGACGCGTAGAAGGCTCACTCTG
+CAAAAATCACCAGCACTAACGCGTAACACATTGGCTGTCAGCGCACTCGTTGATCTTTGTGTCGGGTGAT
+TCTAAAATAGTTAGTCCGTGACCTTTGGCGGCGGCGAGAGATATGGTCCTAACCGCCGTATTTGGACAGA
+AATTAGTCTATGCGATCTTCCCTCCAGATGGTAACGCTGCCAAGGGGCTGACTCTGGCATCCCAGGCGCG
+TATGTCTAGGTGGCGGCTGTAGATATGAAACGATATTAGTAGGTTTTTCACATGAGCAACTACTGGGTTA
+CGACTCAGTCGGTGGCCGCGGATTATGTCATTTGCGAAATAGCAGATCACTTGCGTTTCCGAGAGCCCAC
+CATCGGTCGTAGGACAAATACCCAGTTAACAGCTATCGTTTCGAATATGGATGGGTAAATAGAATGACAT
+ATGTAACGAGCCCCCCCCAGTAAACCCGCAGCGGAACGCTGCACTTGAGGCGAACGTGACCGTCGTCCCT
+CGGGGTTTGAACTATTCTCGTGAAGTCTTACTGTAACGTTCTAGGCTACTCGTATCGCGTTATAATCCGA
+GTACCACCCACGGGCAGAGTCCACAACGAAGAGCGACGGGAGATGTCAGGATAGCCGCAGATCCGTTCAA
+GCCAGTACGGATAACGAGGCGATACCTTGTCAGGGGCCCGATCGACCGCTGAAGGGCAGAGTCGGAACTT
+ACTAACCATGGGGTCCTCTTCGGGAACACTTTACGTGTGCAAATCCAAGCTGGTGCGACCCCGTTCAACG
+GCCCAGAGAACCGCTCTACCTGCGCACACGATCAACTAGCTCGTCTTGGGCTGTGGCGAGCCTGTCGTAT
+TCGCTATATAGTTAGTGGTATATCCTACTGGGGTTAAGTGATGGGAGTCTCCGCTAGAGGCGTGGGCGGC
+GTTACTACAACTTCCTGCGACCAGGACCCTCGGGAGGTATTTGACTATGGTGCTTACATGGTGTTCCTTA
+GTTAGATAGGATGACTTCAGCTAACTGGGCTTCGCCTAGGGTCTCGGGAGAAATCTAGGGACCCCAATCT
+ATTAGACGAACACGTCCAGGGCATGGTCAGGTATACACCTTCCGACTAGACGTGTTCGAAGATTCGGGAA
+AATTACCTGAAGAGCCCCCGTAAGCCGTAGTAGAAGAGGACACTTCATTTAAACAATACCGAAAAAGTGT
+CTTGGCAGACCGTATCTTCACAGGGCCGAAGCACTTTTGGCAGGCTTATAAACGCCCAGAATGAAGCACT
+CGCCATAGGTGGAAACCTTTAAGCGACGCGTTGGGTCCGCGCAGCGCCAACGATTTCAACCGGGAGACGT
+TCGTTCATGATGAGAAGACGGCATATGATCTGTGACATACGCTAGGTGAATCATAGCTGCTTAACAAACT
+CTGGCGTGTCTGAGGCATTCAGACCCCGCGACAACCTTATGTCTACAAAACGTTGCCCCCTGTACGAAAA
+GTCCCTAATTGAGACTGCAACCCCCTAGGCTTTCCAGTCAACAGGCGTAGCGGTAATAGTGGGTTCGATG
+CAGCTCGGCGGGCTCGGGATCATACCATCGTGTATAAACGTCAGCGTTACGACCATTTAAGTGCGCGGAA
+CGGTCGGGTTAGTGCATTGCTTGCGACTAACTATATCTAGTGATACGCTGCAACTAGCCACAGTCCTAGT
+TACTTTCGGAGATCCTCGTGGGTCTGAGAGGAGGGCTACCCGCACAGCGAATCCTTCGACTAGTAATTCA
+TACTAGAACCTGACCGTAGTAAACGTTCTGTGGTTCACCCGCTTGGACTATGAAAGCCGGTGGTATCGAG
+TTTTGGCTACCCAGTCGAATAGCCCACTCGGAACCAGTTGTAAGATAATAATTGCTATGTGTATCGTGAC
+ACGTTGAGGCGCATACTTAACTGACAAGGTCCAATCATGGTCTTATACACTGTTGCAAATGACACCACAT
+CCGAGCTAAATCTAGGCATCTCAATCAGGCGGTTCGAGGGATCATGTAAATGTTTAACCTTTGCGGGCAC
+AAGCCCCCGTGTACTCCGGATGGCCAGGGACAGCTTCCACGAAAACTTCTTACACTCCATGTTGAGATGA
+GTGGCCAACTAAATGCTTCGCTGATGTGGACAGCATCATATTAGCAATCAAGGTGCATACTTCCGGTCTT
+CAAAGGCCAGTACTGGTATAGACGATAACCGTGGACATCTGCTAGACCGCCAGATTGTGGCATCTTTTGA
+AACTCACCCGGAAGATAACGCGCATCTCCCTCAGGTCGTTTTAGCGACGCTAATATTATCGTGGCATCGT
+GAAATCTGGGGTAAGGAAGGAGTCCGATGGCCTTACTCTCCGTTTTCACTCTTGCTTTCATCTTAGGAGC
+CTATCTTTATATGAGGCCCGGCTCCCTTCGGTGACTTCGCGACTGTCATCATAAGCGCCCTTTTCATGCG
+GTATACTCTGCCGTCGAACCCGATCATATAGCCAAATCGGACAATAACACAGTGGACATCGTCCATTACA
+GATTAGTCGTACTGTGGGGGACTCCAATTATCGTAGATGACATCTTTCGGTTCTATTACGCCGCGACACC
+AGGAATTTGGATTCTGATAACCCGGTGCTCACGTCGTGTCGCGAACAAATCTACGAGGAGCCAGGAGCGC
+TGAAGCCTATCAATTGGGATTACCTTCTTGAACGCTATCCGACCTGCCCTCTGTACAGTCCCGTAGACAT
+TCATGGATCCTGGATGGGAGCCACCACTGCAAGACAGCACATTCCAGAGCTTTCCCAAGCGGGATCTTGG
+GTACGTTCTTTCGTCTCCTTGTTTGCGTCCGCAATAGTAGTCATACCGTAAGATTTTCTTCCCGCGGAGA
+TGGCGGCTCTCCCAGCTAGAACATTATTATAATGGCAAGGGTGGCACACCAAAGGTGCGCACCCAAGGTT
+CACATGTCCCTTTCACGCTACCCATGAGCGGTAGTTTATCGAAGTTTAGGTGTTTAGTGCTTGAATGAGT
+CAATACGTTGTCAGAATTCACAATAAAGATCTTCTGTGCGGACTATACACTAGCCGGAGGAACCTAAATT
+TTTCACGGGGTAAATCCCGAGGTTCGGACATATACCTGGCTTACCCAGCGCGGGCTGACTAGCCCACTTG
+CGCGAGCGCTGACTCAGGTAAGACAAGAACGAAGTGCAGTATCTCCGGGCTTACTCGAGCGTACACCAGG
+ACCCCGTAAATTTGCTTACATACAGAAGGTATGCCTTGCATGCCCTTGCTCAGCTAGACGACGATGAACG
+TAGAGTAAGTGGACTTAGGGCCAACACTCGACGTTTTCGTCTAGACCAAAGGTTTAAAAGCTTTCCGAGT
+GTCGACTCAAAACATGGGCTAATCTGATTCGTCAGTATCCAGGCCACACTTCAGCGGGTGGAGCACCTAC
+GATAAACTAAGAAGGTAGTTAGCAAGTGCGTTAGCTTCTGGAAGTTAATATCGGCCTTAGATCGGAGACG
+CGACTGCCCATAGTCTATCACTTCCCAAACAGAACACTTATAAGTTAAGCGTAATATGTACGAATTTCAA
+CGTGGGATTGCCAGAGTAGAATGTGTGTAGATTCGCAACAGATAAAAGCTTTCGAAAGCAAAGCGACAGC
+GCGAACGTGGGTCGGAATCCACATCCGTCCAGGGTTGTAATCACCTTGCGAATATCCCAGAATCGGTGCC
+ACCGAGGCGACTCGACCACGGATCCGATTCTTCTCATACGGATCAGCAAATTGTAATAGCGGTTTCTTAC
+AGAGAGGTGGGCACCCTAGCCAGGCTAGGGCGCATAGCGAACCCCTGCCACCTTAGAAAAGTGATGCCTG
+GAGTTCGACAACGCGCGGCAGAAAGGATTGAGCGTATTTTCGTCTGGGTATTCACCCTATCGCCTATGTA
+CCGAGAAGTGAGGGAGAGGCGGCGTTCGTCTGTACGCGGCTGGATGTACTGCGAGGTCGTTTGGCCGTTT
+GCGAGACCACCCATTCGCCGAATGGGTAAAACAAGAACTGCCGTAGGTATATTATAAATCTCGGGATAGA
+CGGGGGTAAGTTTATGTCTCCGGTTCTTTGTAGTCGTAACTCAGGGGCCCTCGACCCTAGCGAGGCGTTT
+GTAGTGGGACACCAGGTATCTCCCGGAATAATTCTAGCATCATGAGAGGTGGAGTCGGGATTTGATCAAC
+CTACATCATTTTTCAGGCAGATACATGGGACCGATCACACCTCACCTCCGTGTTGTCAAACTTAAGGACA
+ACTTAAGGTTGGCTACGCGGCCGCGGATTGCGCTTGCGCGGGAGGGGCGGGGGATATCAGCCAAACGGAG
+AGTGCTCCGTTGATGAGATTAAGCAGATGTATAAATCATTTGAATGTATGCAATTTGTCTAGATCACCCC
+TACACATCCTTCTTGAGTAAGTCACAAATACGCCGCAGGTTTGGCGGTTTTTGTCCCCGGCACCTCACTA
+GATTTTCATCCAACATACGTAGTGACGTTCCGGTGGCTCCGGAAATCGATCCACACTGCCGAGACTGACT
+TGAGGTCGCGCAGTAGCCCCAACAACTGGGGAGATGGCGGACCCGAGATCAAGGCGCTTTCGCGCCACCT
+GGGCTTGAGCGTACTAACCCCGGAGACGTGTGTACGGCCCCAGAACATGTATCGTGTGATGAATACCAGT
+GTATTCCTTCAAAGGTCTAGAGACATACGGCCTGACTCGTTCAAACTAGAGAAGGATTTACCCGCCACAC
+CTGGGGTCATGGTTGACAACAACAGGAGCCCATGTGTTTATCACTGAATTCTCGGGAATTCCTCGCGAGT
+CGGAGCACTATCTCGTTCAAACCCGCTAGCCATGCCGTAGAGCGCGCGTGCCAAGGTGCGCGTAGGAGTG
+CGCTGGCCCCGCATCCGCTAAATATATATCACTCAGCCCTCGCCGCAGCAGAATATCTAATCCCCGCTCG
+ACTAGCCGAAACCGACACCGTTCAGGGCTGACGACCTGCCTTTTGCACAAAATAACTGAGCCCAGCGATC
+GTATATTGGAGTCGGACTCAGACGATTCTACGGGTGCTTAAGGCTGACAGGGCGGCAACCATAGGCACGA
+CTTCGTTGGCGCCGCCCAATAGCTACGTCGCGATGATTAAATCAGCCCTATTCGCCAGGGAGAGAGACAA
+AATTGGCAATATTTCTACAGGTCTAGCTAACCGACCTAAAGGAGAACCAGGTCGTTGTAGGTCTGTGTAC
+CACTGGCAGTCCGTCATCGCTGAGAAGGATGTCACGATAGGCTCCGCCTAGTAACTTTTCCCTGCTAGCT
+ACACCGTTGCGGATATATAGTTTGAGCTCGGGGTCAATGGATTAGAACGTACAACATTGTGTCTGCTTAC
+GATTGCATAGGTAATAGTCAGCCAGTATATGATCGTACAACACATCTGAAAACTAGTCAAGATACGTGCG
+TTTGTCCATCTGTATTTACTCAATTCCTTAAACAGCTCGTCCAACGCGGGTCAAAACTGTGGCTTGGTAC
+AAGTCGTACTTAAACCTCAACCACTACTTGTCAACTCGTTTACGTTTTCTACGTGGAAGTCCGAAAGTGT
+CATGCGCCCTGCTTCGTATGCAAGCTCACTGATGATCACACCGATGCTTTACGTGCTCTATTGATTGTAA
+AGTCGGCAATGCGTGTGCCTTAGCTGGTGAGATAATCGTTATAACCACGCTCCATAAGGAGGTTGGTTCC
+TCTTCCCGATCTATCCCTGGCAGTTGTCGACACTAGCGCTAGTGGCTTCGCAGACTGATGGCAGTGTCTA
+CCGCGGATTACAGTTAGCTAGCACGCCCCGTTTTTAAGGCTAGAAATGTTGCGATATTTCCGTGAAGCCG
+AAAGTGAGGTAGGAAACCCCGGTCCTGTAGATCATTAATACTACGTAAGCGATTGTCAACGGAATGGGAA
+GGCAGTTTATGAACGGCTGGACTGCTTAACCGTTTTCTTGGCACCTATGCCTAGTATGCACAATACGAGA
+TGGGTTGCGGAGGGACGGAGAATGAGCCTAAGCGAGTTACCTCAGACCACCGGTTACGCTGACCCCTCGG
+TTAAAGGCGATTCTCGATGCTTTCAGAACTACGGGTCTGTAATCAAAATCTCTATACGTTAGACGTCAGG
+CGCCGTTCATTAGGAGTCCGCCATAGGATAAACAAGTCGAGTGTTGTGGTCGCTACTAGTTGCATATTTG
+AACAATTTGCCGCGGCGTTATGTCCTTCAGTATATTGGCAAATGTGGCTACTGCCATACC
diff -r 000000000000 -r e6ef29001647 test-data/simulated.bam
Binary file test-data/simulated.bam has changed