# HG changeset patch
# User iuc
# Date 1601279141 0
# Node ID 629a0066003d1ecd8e379194930c1ba0ecc16ed2

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"

diff -r 000000000000 -r 629a0066003d lr.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lr.xml	Mon Sep 28 07:45:41 2020 +0000
@@ -0,0 +1,305 @@
+<?xml version="1.0"?>
+<tool id="delly_lr" name="Delly long-read (lr)" version="@TOOL_VERSION@+galaxy0" profile="18.01">
+    <description>optimized calling and genotyping of structural variants</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+## initialize
+#for $i, $current in enumerate($samples)
+    ln -s '${current}' 'sample_${i}.bam' &&
+    ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' &&
+#end for
+        
+## run
+delly lr
+## generic options
+--svtype $generic.svtype
+--technology $generic.technology
+--genome '$generic.genome'
+#if $generic.exclude
+    --exclude '$generic.exclude'
+#end if
+--outfile 'result.bcf'
+## discovery options
+--mapqual $discovery.mapqual
+--minclip $discovery.minclip
+--minrefsep $discovery.minrefsep
+--maxreadsep $discovery.maxreadsep
+## genotyping options
+#if $genotyping.vcffile
+    --vcffile '$genotyping.vcffile'
+#end if
+--geno-qual $genotyping.genoqual
+#if 'dump' in $oo.out
+    --dump 'dump.tsv.gz'
+#end if
+## samples
+#for $i, $current in enumerate($samples)
+    'sample_${i}.bam'
+#end for
+
+## postprocessing
+#if 'log' in $oo.out
+    |& tee 'log.txt'
+#end if
+#if 'vcf' in $oo.out
+    && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
+#end if
+#if 'dump' in $oo.out
+    && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
+#end if
+    ]]></command>
+    <inputs>
+        <expand macro="samples"/>
+        <section name="generic" title="Generic options" expanded="true">
+            <expand macro="genome"/>
+            <expand macro="svtype"/>
+            <expand macro="exclude"/>
+            <param argument="--technology" type="select" label="Select sequencing technology">
+                <option value="ont" selected="true">Oxford Nanopore (ont)</option>
+                <option value="pb">Pacbio (pb)</option>
+            </param>
+        </section>
+        <section name="discovery" title="Discovery options" expanded="true">
+            <param argument="--mapqual" type="integer" value="1" label="Set minimum mapping quality"/>
+            <expand macro="minclip"/>
+            <expand macro="minrefsep"/>
+            <expand macro="maxreadsep"/>
+        </section>
+        <section name="genotyping" title="Genotyping options" expanded="true">
+            <expand macro="vcffile"/>
+            <expand macro="genoqual"/>
+        </section>
+        <section name="oo" title="Output options">
+            <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
+                <option value="bcf" selected="true">BCF</option>
+                <option value="vcf">VCF</option>
+                <option value="dump">SV-reads</option>
+                <option value="log">Log</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <expand macro="vcf"/>
+        <expand macro="bcf"/>
+        <expand macro="dump"/>
+        <expand macro="log"/>
+    </outputs>
+    <tests>
+        <!-- no test implemented for parameter vcffile -->
+
+        <!-- #1 default, single -->
+        <test expect_num_outputs="2">
+            <param name="samples" value="normal.bam"/>
+            <section name="generic">
+                <param name="genome" value="genome.fasta"/>
+            </section>
+            <section name="oo">
+                <param name="out" value="vcf,bcf"/>
+            </section>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_size value="3661" delta="10"/>
+                    <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
+                </assert_contents>
+            </output>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="1184" delta="10"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #2 default, multi; test data to small, results are empty -->
+        <test expect_num_outputs="3">
+            <param name="samples" value="normal.bam,tumor.bam"/>
+            <section name="generic">
+                <param name="genome" value="genome.fasta"/>
+            </section>
+            <section name="oo">
+                <param name="out" value="vcf,bcf,log"/>
+            </section>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_size value="3667" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="1189" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done.+"/>
+                </assert_contents>
+            </output>
+        </test>
+       <!-- #3 -->
+        <test expect_num_outputs="4">
+            <param name="samples" value="normal.bam"/>
+            <section name="generic">
+                <param name="genome" value="genome.fasta"/>
+                <param name="exclude" value="exclude.tsv"/>
+            </section>
+            <section name="oo">
+                <param name="out" value="vcf,bcf,dump,log"/>
+            </section>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_size value="3661" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="1186" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="out_dump">
+                <assert_contents>
+                    <has_n_lines n="0"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done.+"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #4 -->
+        <test expect_num_outputs="4">
+            <param name="samples" value="normal.bam"/>
+            <section name="generic">
+                <param name="genome" value="genome.fasta"/>
+                <param name="svtype" value="DEL"/>
+                <param name="technology" value="pb"/>
+            </section>
+            <section name="discovery">
+                <param name="mapqual" value="2"/>
+                <param name="qualtra" value="19"/>
+                <param name="madcutoff" value="8"/>
+                <param name="minclip" value="24"/>
+                <param name="minrefsep" value="24"/>
+                <param name="maxreadsep" value="39"/>
+            </section>
+            <section name="genotyping">
+                <param name="genoqual" value="4"/>
+            </section>
+            <section name="oo">
+                <param name="out" value="vcf,bcf,dump,log"/>
+            </section>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="1182" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_size value="3661" delta="10"/>
+                    <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
+                </assert_contents>
+            </output>
+            <output name="out_dump">
+                <assert_contents>
+                    <has_size value="0"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #5 -->
+        <test expect_num_outputs="1">
+            <param name="samples" value="normal.bam"/>
+            <section name="generic">
+                <param name="genome" value="genome.fasta"/>
+                <param name="svtype" value="INS"/>
+            </section>
+            <section name="oo">
+                <param name="out" value="vcf"/>
+            </section>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_size value="3661" delta="10"/>
+                    <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #6 -->
+        <test expect_num_outputs="1">
+            <param name="samples" value="normal.bam"/>
+            <section name="generic">
+                <param name="genome" value="genome.fasta"/>
+                <param name="svtype" value="DUP"/>
+            </section>
+            <section name="oo">
+                <param name="out" value="bcf"/>
+            </section>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="1182" delta="10"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #7 -->
+        <test expect_num_outputs="1">
+            <param name="samples" value="normal.bam"/>
+            <section name="generic">
+                <param name="genome" value="genome.fasta"/>
+                <param name="svtype" value="INV"/>
+            </section>
+            <section name="oo">
+                <param name="out" value="dump"/>
+            </section>
+            <output name="out_dump">
+                <assert_contents>
+                    <has_size value="0"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #8 -->
+        <test expect_num_outputs="1">
+            <param name="samples" value="normal.bam"/>
+            <section name="generic">
+                <param name="genome" value="genome.fasta"/>
+                <param name="svtype" value="BND"/>
+            </section>
+            <section name="oo">
+                <param name="out" value="log"/>
+            </section>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+Delly *lr* uses the long-read SV discovery mode.
+
+**Input**
+
+Delly *lr* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a VCF/BCF file for genotyping can be applied.
+
+**Output**
+
+The output is available in BCF and VCF format. Additionally a output file for SV-reads is provided.
+
+.. class:: infomark
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 629a0066003d macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Sep 28 07:45:41 2020 +0000
@@ -0,0 +1,94 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">0.8.3</token>
+    <token name="@DESCRIPTION@"></token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">delly</requirement>
+            <requirement type="package" version="1.10.2">bcftools</requirement>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[delly -v 2>&1 | grep 'Delly version' | cut -f 3 -d ' ']]></version_command>
+    </xml>
+	<xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/bts378</citation>
+        </citations>
+    </xml>
+	
+    <!--
+        input 
+    -->
+
+    <xml name="exclude">
+        <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
+    </xml>
+    <xml name="genome">
+        <param argument="--genome" type="data" format="fasta" label="Select genome"/>
+    </xml>
+    <xml name="genoqual">
+        <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
+    </xml>
+    <xml name="minclip">
+        <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
+    </xml>
+    <xml name="maxreadsep">
+        <param argument="--maxreadsep" type="integer" value="40" label="Set maximum read separation"/>
+    </xml>
+    <xml name="minrefsep">
+        <param argument="--minrefsep" type="integer" value="25" label="Set minimum reference separation"/>
+    </xml>
+    <xml name="samples" token_format="bam" token_multiple="true" token_label="Select sample file(s)">
+        <param name="samples" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
+    </xml>
+    <xml name="svtype">
+        <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
+            <option value="ALL" selected="true">All types (ALL)</option>
+            <option value="DEL">Deletion (DEL)</option>
+            <option value="INS">Insertion (INS)</option>
+            <option value="DUP">Duplication (DUP)</option>
+            <option value="INV">Inversion (INV)</option>
+            <option value="BND">Translocation (BND)</option>
+        </param>
+    </xml>
+    <xml name="vcffile">
+        <param argument="--vcffile" type="data" format="vcf,bcf" optional="true" label="Select genotyping file"/>
+    </xml>
+
+    <!--
+        output 
+    -->
+
+    <xml name="vcf">
+        <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
+            <filter>'vcf' in oo['out']</filter>
+        </data>
+    </xml>
+     <xml name="bcf">
+        <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
+            <filter>'bcf' in oo['out']</filter>
+        </data>
+    </xml>
+    <xml name="dump">
+        <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
+            <filter>'dump' in oo['out']</filter>
+        </data>
+    </xml>
+    <xml name="log">
+        <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
+            <filter>'log' in oo['out']</filter>
+        </data>
+    </xml>
+
+    <!--
+        Help
+    -->
+
+    <token name="@WID@"><![CDATA[
+Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.
+    ]]></token>
+    <token name="@REFERENCES@"><![CDATA[
+More information are available on `github <https://github.com/dellytools/delly>`_.
+    ]]></token>
+</macros>
\ No newline at end of file
diff -r 000000000000 -r 629a0066003d test-data/call_1.bcf.gz
Binary file test-data/call_1.bcf.gz has changed
diff -r 000000000000 -r 629a0066003d test-data/call_1.vcf.gz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/call_1.vcf.gz	Mon Sep 28 07:45:41 2020 +0000
@@ -0,0 +1,146 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20200728
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INV,Description="Inversion">
+##ALT=<ID=BND,Description="Translocation">
+##ALT=<ID=INS,Description="Insertion">
+##FILTER=<ID=LowQual,Description="Poor quality and insufficient number of PEs and SRs.">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="PE confidence interval around END">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="PE confidence interval around POS">
+##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for POS2 coordinate in case of an inter-chromosomal translocation">
+##INFO=<ID=POS2,Number=1,Type=Integer,Description="Genomic position for CHR2 in case of an inter-chromosomal translocation">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
+##INFO=<ID=PE,Number=1,Type=Integer,Description="Paired-end support of the structural variant">
+##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">
+##INFO=<ID=SRMAPQ,Number=1,Type=Integer,Description="Median mapping quality of split-reads">
+##INFO=<ID=SR,Number=1,Type=Integer,Description="Split-read support">
+##INFO=<ID=SRQ,Number=1,Type=Float,Description="Split-read consensus alignment quality">
+##INFO=<ID=CONSENSUS,Number=1,Type=String,Description="Split-read consensus sequence">
+##INFO=<ID=CE,Number=1,Type=Float,Description="Consensus sequence entropy">
+##INFO=<ID=CT,Number=1,Type=String,Description="Paired-end signature induced connection type">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Insertion length for SVTYPE=INS.">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
+##INFO=<ID=INSLEN,Number=1,Type=Integer,Description="Predicted length of the insertion">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Predicted microhomology length using a max. edit distance of 2">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Log10-scaled genotype likelihoods for RR,RA,AA genotypes">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample genotype filter">
+##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the SV">
+##FORMAT=<ID=RCL,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the left control region">
+##FORMAT=<ID=RCR,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the right control region">
+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Read-depth based copy-number estimate for autosomal sites">
+##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference pairs">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant pairs">
+##FORMAT=<ID=RR,Number=1,Type=Integer,Description="# high-quality reference junction reads">
+##FORMAT=<ID=RV,Number=1,Type=Integer,Description="# high-quality variant junction reads">
+##reference=../data/v1/genome.fasta
+##contig=<ID=chr10,length=135534747>
+##contig=<ID=chr11,length=135006516>
+##contig=<ID=chr11_gl000202_random,length=40103>
+##contig=<ID=chr12,length=133851895>
+##contig=<ID=chr13,length=115169878>
+##contig=<ID=chr14,length=107349540>
+##contig=<ID=chr15,length=102531392>
+##contig=<ID=chr16,length=90354753>
+##contig=<ID=chr17_ctg5_hap1,length=1680828>
+##contig=<ID=chr17,length=81195210>
+##contig=<ID=chr17_gl000203_random,length=37498>
+##contig=<ID=chr17_gl000204_random,length=81310>
+##contig=<ID=chr17_gl000205_random,length=174588>
+##contig=<ID=chr17_gl000206_random,length=41001>
+##contig=<ID=chr18,length=78077248>
+##contig=<ID=chr18_gl000207_random,length=4262>
+##contig=<ID=chr19,length=59128983>
+##contig=<ID=chr19_gl000208_random,length=92689>
+##contig=<ID=chr19_gl000209_random,length=159169>
+##contig=<ID=chr1,length=249250621>
+##contig=<ID=chr1_gl000191_random,length=106433>
+##contig=<ID=chr1_gl000192_random,length=547496>
+##contig=<ID=chr20,length=63025520>
+##contig=<ID=chr21,length=48129895>
+##contig=<ID=chr21_gl000210_random,length=27682>
+##contig=<ID=chr22,length=51304566>
+##contig=<ID=chr2,length=243199373>
+##contig=<ID=chr3,length=198022430>
+##contig=<ID=chr4_ctg9_hap1,length=590426>
+##contig=<ID=chr4,length=191154276>
+##contig=<ID=chr4_gl000193_random,length=189789>
+##contig=<ID=chr4_gl000194_random,length=191469>
+##contig=<ID=chr5,length=180915260>
+##contig=<ID=chr6_apd_hap1,length=4622290>
+##contig=<ID=chr6_cox_hap2,length=4795371>
+##contig=<ID=chr6_dbb_hap3,length=4610396>
+##contig=<ID=chr6,length=171115067>
+##contig=<ID=chr6_mann_hap4,length=4683263>
+##contig=<ID=chr6_mcf_hap5,length=4833398>
+##contig=<ID=chr6_qbl_hap6,length=4611984>
+##contig=<ID=chr6_ssto_hap7,length=4928567>
+##contig=<ID=chr7,length=159138663>
+##contig=<ID=chr7_gl000195_random,length=182896>
+##contig=<ID=chr8,length=146364022>
+##contig=<ID=chr8_gl000196_random,length=38914>
+##contig=<ID=chr8_gl000197_random,length=37175>
+##contig=<ID=chr9,length=141213431>
+##contig=<ID=chr9_gl000198_random,length=90085>
+##contig=<ID=chr9_gl000199_random,length=169874>
+##contig=<ID=chr9_gl000200_random,length=187035>
+##contig=<ID=chr9_gl000201_random,length=36148>
+##contig=<ID=chrM,length=16571>
+##contig=<ID=chrUn_gl000211,length=166566>
+##contig=<ID=chrUn_gl000212,length=186858>
+##contig=<ID=chrUn_gl000213,length=164239>
+##contig=<ID=chrUn_gl000214,length=137718>
+##contig=<ID=chrUn_gl000215,length=172545>
+##contig=<ID=chrUn_gl000216,length=172294>
+##contig=<ID=chrUn_gl000217,length=172149>
+##contig=<ID=chrUn_gl000218,length=161147>
+##contig=<ID=chrUn_gl000219,length=179198>
+##contig=<ID=chrUn_gl000220,length=161802>
+##contig=<ID=chrUn_gl000221,length=155397>
+##contig=<ID=chrUn_gl000222,length=186861>
+##contig=<ID=chrUn_gl000223,length=180455>
+##contig=<ID=chrUn_gl000224,length=179693>
+##contig=<ID=chrUn_gl000225,length=211173>
+##contig=<ID=chrUn_gl000226,length=15008>
+##contig=<ID=chrUn_gl000227,length=128374>
+##contig=<ID=chrUn_gl000228,length=129120>
+##contig=<ID=chrUn_gl000229,length=19913>
+##contig=<ID=chrUn_gl000230,length=43691>
+##contig=<ID=chrUn_gl000231,length=27386>
+##contig=<ID=chrUn_gl000232,length=40652>
+##contig=<ID=chrUn_gl000233,length=45941>
+##contig=<ID=chrUn_gl000234,length=40531>
+##contig=<ID=chrUn_gl000235,length=34474>
+##contig=<ID=chrUn_gl000236,length=41934>
+##contig=<ID=chrUn_gl000237,length=45867>
+##contig=<ID=chrUn_gl000238,length=39939>
+##contig=<ID=chrUn_gl000239,length=33824>
+##contig=<ID=chrUn_gl000240,length=41933>
+##contig=<ID=chrUn_gl000241,length=42152>
+##contig=<ID=chrUn_gl000242,length=43523>
+##contig=<ID=chrUn_gl000243,length=43341>
+##contig=<ID=chrUn_gl000244,length=39929>
+##contig=<ID=chrUn_gl000245,length=36651>
+##contig=<ID=chrUn_gl000246,length=38154>
+##contig=<ID=chrUn_gl000247,length=36422>
+##contig=<ID=chrUn_gl000248,length=39786>
+##contig=<ID=chrUn_gl000249,length=38502>
+##contig=<ID=chrX,length=155270560>
+##contig=<ID=chrY,length=59373566>
+##bcftools_viewVersion=1.10.2+htslib-1.10.2
+##bcftools_viewCommand=view -Ov call_1.bcf.gz; Date=Sun Sep 27 02:27:42 2020
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
+chr12	132969151	DEL00000000	G	<DEL>	107	PASS	PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=132969179;PE=0;MAPQ=0;CT=3to5;CIPOS=-20,20;CIEND=-20,20;SRMAPQ=41;INSLEN=0;HOMLEN=19;SR=3;SRQ=1;CONSENSUS=CCCCACTCTCCCCCCGGACCCTCCGGCCACCCTGCTCTCCCCCGGGACCCTCCGACCACGTTGCTCTTCCCAGGGTTCTGGCAC;CE=1.70498	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	1/1:-10.3982,-0.901271,0:10:LowQual:28:44:28:2:0:0:0:3	0/1:-11.9941,0,-5.30498:53:PASS:92:160:127:1:0:0:2:4
+chr17	40726730	DEL00000001	C	<DEL>	133	PASS	PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=40726765;PE=0;MAPQ=0;CT=3to5;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=50;INSLEN=0;HOMLEN=9;SR=3;SRQ=1;CONSENSUS=CTCTCTCCCTCCTTCCTTCCTTCCTTTTTCCTCCCTCCCTCCCTCTTTCTCCCTCCCTTCCCTCTTTTCCTCTCTTTCTTTCTCTGT;CE=1.07866	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	1/1:-7.79989,-0.601951,0:7:LowQual:31:1:20:0:0:0:0:2	1/1:-6.29935,-0.601408,0:7:LowQual:66:5:34:0:0:0:0:2
+chr17	74283142	DEL00000002	C	<DEL>	145	PASS	PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=74283171;PE=0;MAPQ=0;CT=3to5;CIPOS=-18,18;CIEND=-18,18;SRMAPQ=50;INSLEN=0;HOMLEN=18;SR=3;SRQ=1;CONSENSUS=CCCACCCCCTGCCCACACACCACATAACACACACACACACACACGATGGGAGGGACCTAGTTTTTGATGAGAGGTGGGAGGGCAGGGCCAAGCCAG;CE=1.91042	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	1/1:-6.99973,-0.601785,0:7:LowQual:28:89:217:1:0:0:0:2	1/1:-13.3977,-1.20187,0:12:LowQual:28:10:70:0:0:0:0:4
+chr17	79612049	DEL00000003	A	<DEL>	840	PASS	PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=79612086;PE=0;MAPQ=0;CT=3to5;CIPOS=-5,5;CIEND=-5,5;SRMAPQ=50;INSLEN=0;HOMLEN=8;SR=17;SRQ=1;CONSENSUS=TTCCTCTTCCCTCTGCAGGAAACTGCAGGCCAGAAGCCCCTCTCTGTGCACAGGGAGGACCAGGCGGAGGCCTGGGGCTGCAGCTGCTGTCCCCCGGAGACCAAGCAC;CE=1.9233	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	0/1:-34.0593,0,-106.559:10000:PASS:844:1944:1927:1:0:0:30:12	0/1:-235.677,0,-181.078:10000:PASS:1973:3537:4588:1:0:0:54:68
+chr5	13830007	DEL00000004	T	<DEL>	135	PASS	PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=13830038;PE=0;MAPQ=0;CT=3to5;CIPOS=-6,6;CIEND=-6,6;SRMAPQ=45;INSLEN=0;HOMLEN=5;SR=3;SRQ=0.987179;CONSENSUS=CTATTCATATGATCTTTGCTTAACACCAAAAGGTTTTCCATTCAAGAAAACAGATGACATATGACCAGGGAGATGCAT;CE=1.93383	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	0/1:-14.6949,0,-2.59501:26:PASS:67:26:69:0:0:0:1:4	0/1:-3.39797,0,-3.49798:31:PASS:30:37:47:1:0:0:1:1
+chr5	74363006	DEL00000005	C	<DEL>	350	PASS	PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=74363047;PE=0;MAPQ=0;CT=3to5;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=50;INSLEN=0;HOMLEN=5;SR=7;SRQ=1;CONSENSUS=AAAGTGGTTTCTTGAGACAAAATCTACTCCTGGTGTGGTGATGTGAACACTTAGATGATAAAGCAGCAGCAGGGTGTAAGAGGATTGACTCCGATTTTCAA;CE=1.95354	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	0/1:-11.1851,0,-39.1848:112:PASS:382:637:460:2:0:0:11:4	0/1:-12.7889,0,-25.2888:128:PASS:279:415:490:1:0:0:7:4
+chr5	75911568	DEL00000006	T	<DEL>	745	PASS	PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=75911598;PE=0;MAPQ=0;CT=3to5;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=50;INSLEN=0;HOMLEN=1;SR=15;SRQ=1;CONSENSUS=TGTCTAATCACTAATGTCTTCCTTCCTGTCTAATCACTGAGTTAAGGGAAAAATAGTCATTTACTAATTCCATTTCCCCATTAAAAGCTATGTCTAAGAAAAAAAATAGTGGAGGCATTATTTAAAAC;CE=1.88992	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	0/1:-61.5633,0,-65.3615:10000:PASS:779:810:615:1:0:0:20:18	0/1:-39.5838,0,-14.884:149:PASS:357:220:320:1:0:0:5:11
+chr5	79865393	DEL00000007	G	<DEL>	150	PASS	PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=79865420;PE=0;MAPQ=0;CT=3to5;CIPOS=-29,29;CIEND=-29,29;SRMAPQ=50;INSLEN=0;HOMLEN=31;SR=3;SRQ=1;CONSENSUS=CTCCTGCTGCCCAGCTGCCGAGGCACCTGCGGAGACGCGCCCAAGTCAGCCCCTCCGACCCGCGCGCTCTTGCGGCCCAGCGCGCGCCGCT;CE=1.74972	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:12:0:0:0:0:0:0:0	0/1:-13.9933,0,-8.89295:89:PASS:117:172:133:1:0:0:3:4
diff -r 000000000000 -r 629a0066003d test-data/call_2.bcf.gz
Binary file test-data/call_2.bcf.gz has changed
diff -r 000000000000 -r 629a0066003d test-data/call_2.vcf.gz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/call_2.vcf.gz	Mon Sep 28 07:45:41 2020 +0000
@@ -0,0 +1,120 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20200728
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INV,Description="Inversion">
+##ALT=<ID=BND,Description="Translocation">
+##ALT=<ID=INS,Description="Insertion">
+##FILTER=<ID=LowQual,Description="Poor quality and insufficient number of PEs and SRs.">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="PE confidence interval around END">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="PE confidence interval around POS">
+##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for POS2 coordinate in case of an inter-chromosomal translocation">
+##INFO=<ID=POS2,Number=1,Type=Integer,Description="Genomic position for CHR2 in case of an inter-chromosomal translocation">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
+##INFO=<ID=PE,Number=1,Type=Integer,Description="Paired-end support of the structural variant">
+##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">
+##INFO=<ID=SRMAPQ,Number=1,Type=Integer,Description="Median mapping quality of split-reads">
+##INFO=<ID=SR,Number=1,Type=Integer,Description="Split-read support">
+##INFO=<ID=SRQ,Number=1,Type=Float,Description="Split-read consensus alignment quality">
+##INFO=<ID=CONSENSUS,Number=1,Type=String,Description="Split-read consensus sequence">
+##INFO=<ID=CE,Number=1,Type=Float,Description="Consensus sequence entropy">
+##INFO=<ID=CT,Number=1,Type=String,Description="Paired-end signature induced connection type">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Insertion length for SVTYPE=INS.">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
+##INFO=<ID=INSLEN,Number=1,Type=Integer,Description="Predicted length of the insertion">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Predicted microhomology length using a max. edit distance of 2">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Log10-scaled genotype likelihoods for RR,RA,AA genotypes">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample genotype filter">
+##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the SV">
+##FORMAT=<ID=RCL,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the left control region">
+##FORMAT=<ID=RCR,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the right control region">
+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Read-depth based copy-number estimate for autosomal sites">
+##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference pairs">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant pairs">
+##FORMAT=<ID=RR,Number=1,Type=Integer,Description="# high-quality reference junction reads">
+##FORMAT=<ID=RV,Number=1,Type=Integer,Description="# high-quality variant junction reads">
+##reference=../data/v4/genome.fasta
+##contig=<ID=chr16,length=10000000>
+##bcftools_viewVersion=1.10.2+htslib-1.10.2
+##bcftools_viewCommand=view -Ov call_2.bcf.gz; Date=Sun Sep 27 02:27:49 2020
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal
+chr16	825909	DEL00000000	T	<DEL>	173	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=827789;PE=5;MAPQ=37;CT=3to5;CIPOS=-125,125;CIEND=-125,125	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	850905	DEL00000001	G	<DEL>	247	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=855131;PE=7;MAPQ=37;CT=3to5;CIPOS=-119,119;CIEND=-119,119	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	1177241	DEL00000002	T	<DEL>	111	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=1178921;PE=3;MAPQ=37;CT=3to5;CIPOS=-177,177;CIEND=-177,177	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	1477778	DEL00000003	C	<DEL>	74	LowQual	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=1482173;PE=2;MAPQ=37;CT=3to5;CIPOS=-189,189;CIEND=-189,189	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	1515871	DEL00000004	A	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=1520228;PE=4;MAPQ=37;CT=3to5;CIPOS=-122,122;CIEND=-122,122	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	1541592	DEL00000005	T	<DEL>	259	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=1542580;PE=7;MAPQ=37;CT=3to5;CIPOS=-71,71;CIEND=-71,71	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	2403786	DEL00000006	T	<DEL>	185	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=2408122;PE=5;MAPQ=37;CT=3to5;CIPOS=-97,97;CIEND=-97,97	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	2434561	DEL00000007	A	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=2439435;PE=4;MAPQ=37;CT=3to5;CIPOS=-112,112;CIEND=-112,112	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	2582432	DEL00000008	A	<DEL>	284	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=2586962;PE=8;MAPQ=37;CT=3to5;CIPOS=-70,70;CIEND=-70,70	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	2844663	DEL00000009	C	<DEL>	296	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=2846416;PE=8;MAPQ=37;CT=3to5;CIPOS=-100,100;CIEND=-100,100	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	2979587	DEL00000010	G	<DEL>	185	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=2980899;PE=5;MAPQ=37;CT=3to5;CIPOS=-99,99;CIEND=-99,99	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	3014404	DEL00000011	A	<DEL>	222	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=3017741;PE=6;MAPQ=37;CT=3to5;CIPOS=-82,82;CIEND=-82,82	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	3039934	DEL00000012	C	<DEL>	185	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=3041007;PE=5;MAPQ=37;CT=3to5;CIPOS=-171,171;CIEND=-171,171	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	3049108	DEL00000013	C	<DEL>	259	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=3049850;PE=7;MAPQ=37;CT=3to5;CIPOS=-111,111;CIEND=-111,111	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	3278470	DEL00000014	T	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=3280840;PE=4;MAPQ=37;CT=3to5;CIPOS=-110,110;CIEND=-110,110	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	3297293	DEL00000015	A	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=3301472;PE=4;MAPQ=37;CT=3to5;CIPOS=-67,67;CIEND=-67,67	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	3447681	DEL00000016	A	<DEL>	46	LowQual	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=3451639;PE=2;MAPQ=23;CT=3to5;CIPOS=-237,237;CIEND=-237,237	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	4038286	DEL00000017	A	<DEL>	46	LowQual	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=4039676;PE=2;MAPQ=23;CT=3to5;CIPOS=-210,210;CIEND=-210,210	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	4097148	DEL00000018	A	<DEL>	62	LowQual	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=4101557;PE=2;MAPQ=37;CT=3to5;CIPOS=-141,141;CIEND=-141,141	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	4139307	DEL00000019	T	<DEL>	74	LowQual	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=4141836;PE=2;MAPQ=37;CT=3to5;CIPOS=-133,133;CIEND=-133,133	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	4174965	DEL00000020	T	<DEL>	171	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=4179470;PE=5;MAPQ=37;CT=3to5;CIPOS=-120,120;CIEND=-120,120	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	4434261	DEL00000021	A	<DEL>	210	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=4438571;PE=6;MAPQ=37;CT=3to5;CIPOS=-85,85;CIEND=-85,85	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	4576771	DEL00000022	T	<DEL>	185	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=4578602;PE=5;MAPQ=37;CT=3to5;CIPOS=-81,81;CIEND=-81,81	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	4587255	DEL00000023	A	<DEL>	370	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=4590513;PE=10;MAPQ=37;CT=3to5;CIPOS=-50,50;CIEND=-50,50	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	4594048	DEL00000024	T	<DEL>	111	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=4599030;PE=3;MAPQ=37;CT=3to5;CIPOS=-129,129;CIEND=-129,129	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	4745978	DEL00000025	T	<DEL>	111	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=4749430;PE=3;MAPQ=37;CT=3to5;CIPOS=-186,186;CIEND=-186,186	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	4771579	DEL00000026	A	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=4774817;PE=4;MAPQ=37;CT=3to5;CIPOS=-166,166;CIEND=-166,166	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	4986942	DEL00000027	T	<DEL>	185	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=4988061;PE=5;MAPQ=37;CT=3to5;CIPOS=-173,173;CIEND=-173,173	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	5038084	DEL00000028	A	<DEL>	111	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=5041782;PE=3;MAPQ=37;CT=3to5;CIPOS=-165,165;CIEND=-165,165	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	5255973	DEL00000029	A	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=5259495;PE=4;MAPQ=37;CT=3to5;CIPOS=-120,120;CIEND=-120,120	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	5270064	DEL00000030	G	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=5274277;PE=4;MAPQ=37;CT=3to5;CIPOS=-175,175;CIEND=-175,175	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	5300777	DEL00000031	T	<DEL>	222	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=5304511;PE=6;MAPQ=37;CT=3to5;CIPOS=-97,97;CIEND=-97,97	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	5683371	DEL00000032	T	<DEL>	185	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=5684564;PE=5;MAPQ=37;CT=3to5;CIPOS=-150,150;CIEND=-150,150	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	5749292	DEL00000033	G	<DEL>	69	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=5754058;PE=3;MAPQ=23;CT=3to5;CIPOS=-189,189;CIEND=-189,189	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	5853119	DEL00000034	T	<DEL>	69	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=5854135;PE=3;MAPQ=23;CT=3to5;CIPOS=-160,160;CIEND=-160,160	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	5993608	DEL00000035	C	<DEL>	247	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=5997715;PE=7;MAPQ=37;CT=3to5;CIPOS=-50,50;CIEND=-50,50	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	6233812	DEL00000036	G	<DEL>	222	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=6234827;PE=6;MAPQ=37;CT=3to5;CIPOS=-137,137;CIEND=-137,137	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	6268528	DEL00000037	T	<DEL>	333	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=6269313;PE=9;MAPQ=37;CT=3to5;CIPOS=-84,84;CIEND=-84,84	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	6285559	DEL00000038	A	<DEL>	111	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=6288501;PE=3;MAPQ=37;CT=3to5;CIPOS=-198,198;CIEND=-198,198	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	6309245	DEL00000039	T	<DEL>	333	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=6313800;PE=9;MAPQ=37;CT=3to5;CIPOS=-98,98;CIEND=-98,98	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	6410877	DEL00000040	G	<DEL>	370	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=6413829;PE=10;MAPQ=37;CT=3to5;CIPOS=-50,50;CIEND=-50,50	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	6820642	DEL00000041	T	<DEL>	111	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=6825570;PE=3;MAPQ=37;CT=3to5;CIPOS=-157,157;CIEND=-157,157	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	6905368	DEL00000042	A	<DEL>	222	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=6909093;PE=6;MAPQ=37;CT=3to5;CIPOS=-110,110;CIEND=-110,110	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	7234607	DEL00000043	C	<DEL>	222	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=7235889;PE=6;MAPQ=37;CT=3to5;CIPOS=-97,97;CIEND=-97,97	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	7394046	DEL00000044	A	<DEL>	185	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=7397480;PE=5;MAPQ=37;CT=3to5;CIPOS=-137,137;CIEND=-137,137	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	7519284	DEL00000045	G	<DEL>	222	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=7522345;PE=6;MAPQ=37;CT=3to5;CIPOS=-95,95;CIEND=-95,95	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	7527833	DEL00000046	C	<DEL>	259	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=7532827;PE=7;MAPQ=37;CT=3to5;CIPOS=-61,61;CIEND=-61,61	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	7906163	DEL00000047	C	<DEL>	115	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=7906861;PE=5;MAPQ=23;CT=3to5;CIPOS=-132,132;CIEND=-132,132	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	7998010	DEL00000048	A	<DEL>	223	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8001533;PE=7;MAPQ=37;CT=3to5;CIPOS=-50,50;CIEND=-50,50	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	8004170	DEL00000049	T	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8008183;PE=4;MAPQ=37;CT=3to5;CIPOS=-112,112;CIEND=-112,112	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	8063189	DEL00000050	C	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8064849;PE=4;MAPQ=37;CT=3to5;CIPOS=-187,187;CIEND=-187,187	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	8264688	DEL00000051	C	<DEL>	222	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8266131;PE=6;MAPQ=37;CT=3to5;CIPOS=-86,86;CIEND=-86,86	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	8282480	DEL00000052	A	<DEL>	185	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8285481;PE=5;MAPQ=37;CT=3to5;CIPOS=-106,106;CIEND=-106,106	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	8347101	DEL00000053	C	<DEL>	259	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8351327;PE=7;MAPQ=37;CT=3to5;CIPOS=-63,63;CIEND=-63,63	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	8387696	DEL00000054	A	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8392116;PE=4;MAPQ=37;CT=3to5;CIPOS=-99,99;CIEND=-99,99	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	8405853	DEL00000055	C	<DEL>	111	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8410818;PE=3;MAPQ=37;CT=3to5;CIPOS=-76,76;CIEND=-76,76	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	8507352	DEL00000056	A	<DEL>	185	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8508193;PE=5;MAPQ=37;CT=3to5;CIPOS=-121,121;CIEND=-121,121	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	8540750	DEL00000057	T	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8544830;PE=4;MAPQ=37;CT=3to5;CIPOS=-181,181;CIEND=-181,181	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	8607361	DEL00000058	A	<DEL>	222	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8608882;PE=6;MAPQ=37;CT=3to5;CIPOS=-68,68;CIEND=-68,68	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	8681669	DEL00000059	C	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8685132;PE=4;MAPQ=37;CT=3to5;CIPOS=-74,74;CIEND=-74,74	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	8824490	DEL00000060	G	<DEL>	111	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8826563;PE=3;MAPQ=37;CT=3to5;CIPOS=-60,60;CIEND=-60,60	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	8923597	DEL00000061	C	<DEL>	134	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8926010;PE=4;MAPQ=37;CT=3to5;CIPOS=-156,156;CIEND=-156,156	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	9090265	DEL00000062	C	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9093228;PE=4;MAPQ=37;CT=3to5;CIPOS=-128,128;CIEND=-128,128	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	9119366	DEL00000063	T	<DEL>	74	LowQual	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9123335;PE=2;MAPQ=37;CT=3to5;CIPOS=-140,140;CIEND=-140,140	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	9178997	DEL00000064	T	<DEL>	185	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9182500;PE=5;MAPQ=37;CT=3to5;CIPOS=-66,66;CIEND=-66,66	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	9226404	DEL00000065	T	<DEL>	111	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9227636;PE=3;MAPQ=37;CT=3to5;CIPOS=-127,127;CIEND=-127,127	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	9319688	DEL00000066	C	<DEL>	111	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9320353;PE=3;MAPQ=37;CT=3to5;CIPOS=-133,133;CIEND=-133,133	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	9359380	DEL00000067	A	<DEL>	333	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9361199;PE=9;MAPQ=37;CT=3to5;CIPOS=-80,80;CIEND=-80,80	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	9501567	DEL00000068	G	<DEL>	247	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9504493;PE=7;MAPQ=37;CT=3to5;CIPOS=-62,62;CIEND=-62,62	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	9596261	DEL00000069	A	<DEL>	370	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9599737;PE=10;MAPQ=37;CT=3to5;CIPOS=-64,64;CIEND=-64,64	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	9670189	DEL00000070	A	<DEL>	185	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9673420;PE=5;MAPQ=37;CT=3to5;CIPOS=-145,145;CIEND=-145,145	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	9721367	DEL00000071	T	<DEL>	370	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9723693;PE=10;MAPQ=37;CT=3to5;CIPOS=-62,62;CIEND=-62,62	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	9754516	DEL00000072	T	<DEL>	284	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9757726;PE=8;MAPQ=37;CT=3to5;CIPOS=-50,50;CIEND=-50,50	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
+chr16	9894428	DEL00000073	T	<DEL>	148	PASS	IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9898668;PE=4;MAPQ=37;CT=3to5;CIPOS=-91,91;CIEND=-91,91	GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV	./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0
diff -r 000000000000 -r 629a0066003d test-data/exclude.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclude.tsv	Mon Sep 28 07:45:41 2020 +0000
@@ -0,0 +1,267 @@
+chr1	0	10000	telomere
+chr1	121535434	124535434	centromere
+chr1	249240621	249250621	telomere
+chr10	0	10000	telomere
+chr10	39254935	42254935	centromere
+chr10	135524747	135534747	telomere
+chr11	0	10000	telomere
+chr11	51644205	54644205	centromere
+chr11	134996516	135006516	telomere
+chr12	0	10000	telomere
+chr12	34856694	37856694	centromere
+chr12	133841895	133851895	telomere
+chr13	0	10000	telomere
+chr13	16000000	19000000	centromere
+chr13	115159878	115169878	telomere
+chr14	0	10000	telomere
+chr14	16000000	19000000	centromere
+chr14	107339540	107349540	telomere
+chr15	0	10000	telomere
+chr15	17000000	20000000	centromere
+chr15	102521392	102531392	telomere
+chr16	0	10000	telomere
+chr16	35335801	38335801	centromere
+chr16	46380000	46450000	lowcomplexity
+chr16	90344753	90354753	telomere
+chr17	22263006	25263006	centromere
+chr18	0	10000	telomere
+chr18	15460898	18460898	centromere
+chr18	78067248	78077248	telomere
+chr19	0	10000	telomere
+chr19	24681782	27681782	centromere
+chr19	59118983	59128983	telomere
+chr2	0	10000	telomere
+chr2	33141000	33142000	lowcomplexity
+chr2	92326171	95326171	centromere
+chr2	243189373	243199373	telomere
+chr20	0	10000	telomere
+chr20	26369569	29369569	centromere
+chr20	63015520	63025520	telomere
+chr21	0	10000	telomere
+chr21	11288129	14288129	centromere
+chr21	48119895	48129895	telomere
+chr22	0	10000	telomere
+chr22	13000000	16000000	centromere
+chr22	51294566	51304566	telomere
+chr3	0	10000	telomere
+chr3	90504854	93504854	centromere
+chr3	198012430	198022430	telomere
+chr4	0	10000	telomere
+chr4	49660117	52660117	centromere
+chr4	191144276	191154276	telomere
+chr5	0	10000	telomere
+chr5	46405641	49405641	centromere
+chr5	180905260	180915260	telomere
+chr6	0	10000	telomere
+chr6	58830166	61830166	centromere
+chr6	171105067	171115067	telomere
+chr7	0	10000	telomere
+chr7	58054331	61054331	centromere
+chr7	159128663	159138663	telomere
+chr8	0	10000	telomere
+chr8	43793000	46857000	centromere
+chr8	146354022	146364022	telomere
+chr9	0	10000	telomere
+chr9	47367679	50367679	centromere
+chr9	141203431	141213431	telomere
+chrX	0	10000	telomere
+chrX	58632012	61632012	centromere
+chrX	155260560	155270560	telomere
+chrY	0	10000	telomere
+chrY	10104553	13104553	centromere
+chrY	59363566	59373566	telomere
+1	0	10000	telomere
+1	121535434	124535434	centromere
+1	249240621	249250621	telomere
+10	0	10000	telomere
+10	39254935	42254935	centromere
+10	135524747	135534747	telomere
+11	0	10000	telomere
+11	51644205	54644205	centromere
+11	134996516	135006516	telomere
+12	0	10000	telomere
+12	34856694	37856694	centromere
+12	133841895	133851895	telomere
+13	0	10000	telomere
+13	16000000	19000000	centromere
+13	115159878	115169878	telomere
+14	0	10000	telomere
+14	16000000	19000000	centromere
+14	107339540	107349540	telomere
+15	0	10000	telomere
+15	17000000	20000000	centromere
+15	102521392	102531392	telomere
+16	0	10000	telomere
+16	35335801	38335801	centromere
+16	46380000	46450000	lowcomplexity
+16	90344753	90354753	telomere
+17	22263006	25263006	centromere
+18	0	10000	telomere
+18	15460898	18460898	centromere
+18	78067248	78077248	telomere
+19	0	10000	telomere
+19	24681782	27681782	centromere
+19	59118983	59128983	telomere
+2	0	10000	telomere
+2	33141000	33142000	lowcomplexity
+2	92326171	95326171	centromere
+2	243189373	243199373	telomere
+20	0	10000	telomere
+20	26369569	29369569	centromere
+20	63015520	63025520	telomere
+21	0	10000	telomere
+21	11288129	14288129	centromere
+21	48119895	48129895	telomere
+22	0	10000	telomere
+22	13000000	16000000	centromere
+22	51294566	51304566	telomere
+3	0	10000	telomere
+3	90504854	93504854	centromere
+3	198012430	198022430	telomere
+4	0	10000	telomere
+4	49660117	52660117	centromere
+4	191144276	191154276	telomere
+5	0	10000	telomere
+5	46405641	49405641	centromere
+5	180905260	180915260	telomere
+6	0	10000	telomere
+6	58830166	61830166	centromere
+6	171105067	171115067	telomere
+7	0	10000	telomere
+7	58054331	61054331	centromere
+7	159128663	159138663	telomere
+8	0	10000	telomere
+8	43793000	46857000	centromere
+8	146354022	146364022	telomere
+9	0	10000	telomere
+9	47367679	50367679	centromere
+9	141203431	141213431	telomere
+X	0	10000	telomere
+X	58632012	61632012	centromere
+X	155260560	155270560	telomere
+Y	0	10000	telomere
+Y	10104553	13104553	centromere
+Y	59363566	59373566	telomere
+chrM
+chrMT
+MT
+GL000207.1
+GL000226.1
+GL000229.1
+GL000231.1
+GL000210.1
+GL000239.1
+GL000235.1
+GL000201.1
+GL000247.1
+GL000245.1
+GL000197.1
+GL000203.1
+GL000246.1
+GL000249.1
+GL000196.1
+GL000248.1
+GL000244.1
+GL000238.1
+GL000202.1
+GL000234.1
+GL000232.1
+GL000206.1
+GL000240.1
+GL000236.1
+GL000241.1
+GL000243.1
+GL000242.1
+GL000230.1
+GL000237.1
+GL000233.1
+GL000204.1
+GL000198.1
+GL000208.1
+GL000191.1
+GL000227.1
+GL000228.1
+GL000214.1
+GL000221.1
+GL000209.1
+GL000218.1
+GL000220.1
+GL000213.1
+GL000211.1
+GL000199.1
+GL000217.1
+GL000216.1
+GL000215.1
+GL000205.1
+GL000219.1
+GL000224.1
+GL000223.1
+GL000195.1
+GL000212.1
+GL000222.1
+GL000200.1
+GL000193.1
+GL000194.1
+GL000225.1
+GL000192.1
+NC_007605
+hs37d5
+chr11_gl000202_random
+chr17_gl000203_random
+chr17_gl000204_random
+chr17_gl000205_random
+chr17_gl000206_random
+chr18_gl000207_random
+chr19_gl000208_random
+chr19_gl000209_random
+chr1_gl000191_random
+chr1_gl000192_random
+chr21_gl000210_random
+chr4_gl000193_random
+chr4_gl000194_random
+chr7_gl000195_random
+chr8_gl000196_random
+chr8_gl000197_random
+chr9_gl000198_random
+chr9_gl000199_random
+chr9_gl000200_random
+chr9_gl000201_random
+chrUn_gl000211
+chrUn_gl000212
+chrUn_gl000213
+chrUn_gl000214
+chrUn_gl000215
+chrUn_gl000216
+chrUn_gl000217
+chrUn_gl000218
+chrUn_gl000219
+chrUn_gl000220
+chrUn_gl000221
+chrUn_gl000222
+chrUn_gl000223
+chrUn_gl000224
+chrUn_gl000225
+chrUn_gl000226
+chrUn_gl000227
+chrUn_gl000228
+chrUn_gl000229
+chrUn_gl000230
+chrUn_gl000231
+chrUn_gl000232
+chrUn_gl000233
+chrUn_gl000234
+chrUn_gl000235
+chrUn_gl000236
+chrUn_gl000237
+chrUn_gl000238
+chrUn_gl000239
+chrUn_gl000240
+chrUn_gl000241
+chrUn_gl000242
+chrUn_gl000243
+chrUn_gl000244
+chrUn_gl000245
+chrUn_gl000246
+chrUn_gl000247
+chrUn_gl000248
+chrUn_gl000249
diff -r 000000000000 -r 629a0066003d test-data/genome.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fasta	Mon Sep 28 07:45:41 2020 +0000
@@ -0,0 +1,333 @@
+>chrM
+NNNCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT
+TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG
+GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT
+CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA
+AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT
+GTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA
+AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGC
+CAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAAT
+TTTATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACA
+TTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCC
+GCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAAC
+CAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA
+AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAA
+ATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGC
+AAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAG
+GGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCC
+ACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGT
+TTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC
+GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTT
+TAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAA
+CTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAAC
+ACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGC
+CCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGA
+GCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA
+GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGC
+TCAGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGT
+AAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGG
+TGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTT
+ATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTGAGAGTAGAGT
+GCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC
+TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATA
+GAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACG
+AACCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTT
+CAACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCAC
+CTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGG
+CGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA
+TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTT
+CTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAA
+GACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCC
+GTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCT
+ACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTT
+TAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG
+TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGA
+GTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGA
+AAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACT
+GAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAA
+TGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCA
+GATCAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA
+ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAG
+GAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAACCTTACCCCGCCTGTT
+TACCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCC
+CAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagca
+taatcacttgttccttaaatagggacctgtatgaatggctccacgagggt
+tcagctgtctcttacttttaaccagtgaaattgacctgcccgtgaagagg
+cgggcatgacacagcaagacgagaagaccctatggagctttaatttaTTA
+ATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCA
+TTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCA
+GTACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGAT
+CCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATC
+CTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT
+CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGA
+TTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTT
+CTATCTACTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCC
+TACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTAT
+TATACCCACACCCACCCAAGAACAGGGTTTgttaagatggcagagcccgg
+taatcgcataaaacttaaaactttacagtcagaggttcaattcctcttct
+taacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAA
+TCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATA
+CAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACC
+CTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCA
+CATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATC
+GCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCT
+CAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACT
+CAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGC
+GCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCAT
+CATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCC
+TTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTG
+GCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTT
+CGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAAT
+ACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATT
+ATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGA
+CGCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTAC
+TTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGC
+TACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCT
+AGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTC
+CCCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGT
+AAATAATAGGAGCTTAAACCCCCTTATTTctaggactatgagaatcgaac
+ccatccctgagaatccaaaattctccgtgccacctatcacaccccatcct
+aAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTG
+GTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTAC
+TCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATT
+TTTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTC
+TAACCAAAAAAATAAACCCTCGTTCCACAGAAGCTGCCATCAAGTATTTC
+CTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTTCAA
+CAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACT
+CATCATTAATAATCATAATGGCTATAGCAATAAAACTAGGAATAGCCCCC
+TTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGG
+CCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACC
+AAATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTA
+TCCATCATAGCAGGCAGTTGAGGTGGATTAAACCAAACCCAGCTACGCAA
+AATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTC
+TACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATC
+CTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGAC
+CCTACTACTATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAA
+TTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTT
+TTGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCAT
+CATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACC
+TACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAAC
+GTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCC
+CACACTCATCGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATAC
+TAATAATCTTATAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAG
+CCCTCAGTAAGTTGCAATACTTAATTTCTGCAACAGCTAAGGACTGCAAA
+ACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAA
+GCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGC
+TAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAA
+AAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCA
+ATTCAATATGAAAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTG
+TCTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACCTCACCCCC
+ACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTG
+GAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCT
+CTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGG
+TAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAA
+TCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTA
+GTTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAA
+CATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTG
+CTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTA
+GCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTC
+CTTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCA
+CAACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCC
+CTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCT
+CCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCA
+ACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAA
+CACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACC
+AGGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAG
+AACCATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTC
+CTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGT
+AGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCA
+CCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATG
+AAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCAC
+CGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCG
+TACTACACGACACGTACTACGTTGTAGCTCACTTCCACTATGTCCTATCA
+ATAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCT
+ATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTA
+TCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGC
+CTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCAC
+ATGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAA
+TATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTC
+CTAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCC
+CCCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTAGACAaa
+aaaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggc
+ctccatgactttttcAAAAAGGTATTAGAAAAACCATTTCATAACTTTGT
+CAAAGTTAAATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGC
+GCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCA
+CCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTC
+CTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACAT
+CTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCA
+TCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGAC
+GAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTA
+CTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACA
+TACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTT
+GACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTAC
+ATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAA
+CAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGA
+CCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAG
+TTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAG
+GGCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTG
+TAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAAC
+ACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCA
+TAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATA
+TTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAA
+AAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTC
+ATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTC
+TATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGA
+CTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGAT
+AGCCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCT
+TAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCA
+TTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTT
+ATGAGCGGGCGCAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCC
+TAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTA
+GTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGT
+ACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTG
+GAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATC
+ATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTT
+AATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACA
+ACACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCC
+CATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTA
+GCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACT
+AACCAACACACTAACCATATACCAATGGTGGCGCGATGTAACACGAGAAA
+GCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATAC
+GGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTT
+CTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAACTAGGAGGGC
+ACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTC
+CTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCA
+CCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTA
+TTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTAC
+TTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTT
+TGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCC
+TCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACAT
+CACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGT
+TTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTA
+GTATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAA
+AAAAGAGTAATAAACTTCGCCTTAATTTTAATAATCAACACCCTCCTAGC
+CTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACA
+TAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCC
+CGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATT
+ATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAA
+CAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATC
+CTAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAGC
+CGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATT
+ATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTA
+GCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCAT
+ATCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAG
+CTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCT
+ATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCT
+ACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAA
+ACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCAC
+TGACATGACTTTCCAAAAAGCACATAATTTGAATCAACACAACCACCCAC
+AGCCTAATTATTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAA
+CAACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCC
+CCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGC
+CAACGCCACTTATCCAGCGAACCACTATCACGAAAAAAACTCTACCTCTC
+TATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAG
+AACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTG
+GCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCAC
+ATACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCAC
+TAATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACT
+CTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACT
+AGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACT
+TATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTA
+CTTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCAC
+ACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTAC
+TATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACA
+GACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGT
+AGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCA
+TTCTCATAATCGCCCACGGACTCACATCCTCATTACTATTCTGCCTAGCA
+AACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGG
+ACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCC
+TCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCT
+GTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGG
+ACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAA
+CACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTC
+ACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCT
+ATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTT
+TAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCCTT
+ATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAA
+CAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTA
+GGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACA
+CTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACC
+ACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATC
+CATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCA
+TGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACC
+CAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAAT
+ATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCAC
+TGTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTA
+CTCATTTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATT
+CCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCA
+TCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCA
+GTCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATG
+ATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAA
+ACGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCA
+GGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGA
+AGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAG
+CAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCA
+CTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGC
+AGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCT
+CCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAA
+CCACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCAT
+ACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAG
+ATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACC
+TCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGG
+TTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAA
+ACGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCC
+TATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCC
+CACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTA
+AACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAAC
+ATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACT
+CACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCA
+ACTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTAT
+TTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCC
+CTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACC
+TAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATC
+TCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTT
+CCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAAC
+CTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGT
+TCAACCAGTAACCACTACTAATCAACGCCCATAATCATACAAAGCCCCCG
+CACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATT
+ATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATA
+CTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAA
+CACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCA
+ATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATA
+AATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAA
+TAACACACCCGACCACACCGCTAACAATCAGTACTAAACCCCCATAAATA
+GGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACT
+CAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGA
+CCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATG
+ACCCCAATACGCAAAATTAACCCCCTAATAAAATTAATTAACCACTCATT
+CATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCT
+CACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTA
+GCCATACACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCA
+CATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCA
+ATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGC
+CTATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTAT
+CCTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGT
+GAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCC
+GCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTA
+CTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCT
+TACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCAC
+GAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAAT
+CACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCT
+TCCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGC
+GACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACAT
+CAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCC
+CTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTA
+GCAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCG
+CCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTC
+TAACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGA
+CAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAAC
+TATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTA
+TAAACTAATACACCAGTCTTGTAAACCGGAGACGAAAACCTTTTTCCAAG
+GACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAA
+GATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCA
+CCTGTAGTACATAAAAACCCAACCCACATCAAACCCCCCCCCCCCATGCT
+TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAAC
+TCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTT
+AACAGTACATAGTACATAAAGTCATTTACCGTACATAGCACATTACAGTC
+AAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTG
+ACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCT
+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC
+ATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCC
+CTTAAATAAGACATCACGATG
diff -r 000000000000 -r 629a0066003d test-data/normal.bam
Binary file test-data/normal.bam has changed
diff -r 000000000000 -r 629a0066003d test-data/samples.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples.tsv	Mon Sep 28 07:45:41 2020 +0000
@@ -0,0 +1,2 @@
+NORMAL	control
+TUMOR	tumor
diff -r 000000000000 -r 629a0066003d test-data/tumor.bam
Binary file test-data/tumor.bam has changed