Mercurial > repos > iuc > delly_filter
changeset 0:a75e05f20a66 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
| author | iuc |
|---|---|
| date | Mon, 28 Sep 2020 07:44:40 +0000 |
| parents | |
| children | 9919057a466c |
| files | filter.xml macros.xml test-data/call_1.bcf.gz test-data/call_1.vcf.gz test-data/call_2.bcf.gz test-data/call_2.vcf.gz test-data/exclude.tsv test-data/genome.fasta test-data/normal.bam test-data/samples.tsv test-data/tumor.bam |
| diffstat | 11 files changed, 1234 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter.xml Mon Sep 28 07:44:40 2020 +0000 @@ -0,0 +1,272 @@ +<?xml version="1.0"?> +<tool id="delly_filter" name="Delly filter" version="@TOOL_VERSION@+galaxy0" profile="18.01"> + <description>somatic or germline structural variants</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"><![CDATA[ +## initialize +#if $samples.is_of_type('vcf') + bcftools view -Ob '$samples' > 'sample.bcf.gz' && + bcftools index 'sample.bcf.gz' && +#else + ln -s '${samples}' 'sample.bcf.gz' && + ln -s '${samples.metadata.bcf_index}' 'sample.bcf.gz.csi' && +#end if + +## run +delly filter +## generic options +--filter $sv.mode_cond.mode_sel +--outfile 'result.bcf' +--altaf $generic.altaf +--minsize $generic.minsize +--maxsize $generic.maxsize +--ratiogeno $generic.ratiogeno +$generic.pass +## somatic options +#if $sv.mode_cond.mode_sel == 'somatic' + --samples '$sv.mode_cond.samples' + --coverage $sv.mode_cond.coverage + --controlcontamination $sv.mode_cond.controlcontamination +#end if +## germline options +#if $sv.mode_cond.mode_sel == 'germline' + --gq $sv.mode_cond.gq + --rddel $sv.mode_cond.rddel + --rddup $sv.mode_cond.rddup +#end if +## samples +'sample.bcf.gz' ## input + +## 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 + ]]></command> + <inputs> + <expand macro="samples" format="bcf,vcf" multiple="false" label="Select file"/> + <section name="generic" title="Generic options" expanded="true"> + <param argument="--altaf" type="float" value="0.2" min="0.0" max="1.0" label="Set minimum fractional ALT support"/> + <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/> + <param argument="--maxsize" type="integer" value="500000000" label="Set maximum SV size"/> + <param argument="--ratiogeno" type="float" value="0.75" min="0.0" max="1.0" label="Set minimum fraction of genotyped samples"/> + <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/> + </section> + <section name="sv" title="SV calling options" expanded="true"> + <conditional name="mode_cond"> + <param argument="mode_sel" type="select" label="Select filter mode"> + <option value="somatic" selected="true">Somatic</option> + <option value="germline">Germline</option> + </param> + <when value="somatic"> + <param argument="--samples" type="data" format="tabular" label="Select sample file" help="Two-column sample file listing sample name and tumor or control."/> + <param argument="--coverage" type="integer" value="10" label="Set minimum coverage in tumor."/> + <param argument="--controlcontamination" type="float" value="0.0" min="0.0" max="1.0" label="Set maximum fractional ALT support in control"/> + </when> + <when value="germline"> + <param argument="--gq" type="integer" value="15" label="Set minimum median GQ for carriers and non-carriers"/> + <param argument="--rddel" type="float" value="0.8" label="Set maximum read-depth ratio of carrier vs. non-carrier for a deletion"/> + <param argument="--rddup" type="float" value="1.2" label="Set minimum read-depth ratio of carrier vs. non-carrier for a duplication"/> + </when> + </conditional> + </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="log">Log</option> + </param> + </section> + </inputs> + <outputs> + <expand macro="vcf"/> + <expand macro="bcf"/> + <expand macro="log"/> + </outputs> + <tests> + <!-- #1 default, somatic, bcf --> + <test expect_num_outputs="2"> + <param name="samples" value="call_1.bcf.gz"/> + <section name="sv"> + <conditional name="mode_cond"> + <param name="mode_sel" value="somatic"/> + <param name="samples" value="samples.tsv"/> + </conditional> + </section> + <section name="oo"> + <param name="out" value="vcf,bcf"/> + </section> + <output name="out_bcf"> + <assert_contents> + <has_size value="2281" delta="10"/> + </assert_contents> + </output> + <output name="out_vcf"> + <assert_contents> + <has_n_lines n="140"/> + <has_line line="##fileformat=VCFv4.2"/> + <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> + </assert_contents> + </output> + </test> + <!-- #2 somatic, bcf --> + <test expect_num_outputs="3"> + <param name="samples" value="call_1.bcf.gz"/> + <section name="generic"> + <param name="altaf" value="0.3"/> + <param name="minsize" value="1"/> + <param name="maxsize" value="500000001"/> + <param name="ratiogeno" value="0.76"/> + <param name="pass" value="true"/> + </section> + <section name="sv"> + <conditional name="mode_cond"> + <param name="mode_sel" value="somatic"/> + <param name="samples" value="samples.tsv"/> + <param name="coverage" value="11"/> + <param name="controlcontamination" value="0.1"/> + </conditional> + </section> + <section name="oo"> + <param name="out" value="vcf,bcf,log"/> + </section> + <output name="out_bcf"> + <assert_contents> + <has_size value="2281" delta="10"/> + </assert_contents> + </output> + <output name="out_vcf"> + <assert_contents> + <has_n_lines n="140"/> + <has_line line="##fileformat=VCFv4.2"/> + <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> + </assert_contents> + </output> + <output name="out_log"> + <assert_contents> + <has_text_matching expression=".+Done\."/> + </assert_contents> + </output> + </test> + <!-- #3 default, germline, bcf --> + <test expect_num_outputs="2"> + <param name="samples" value="call_1.bcf.gz"/> + <section name="sv"> + <conditional name="mode_cond"> + <param name="mode_sel" value="germline"/> + </conditional> + </section> + <section name="oo"> + <param name="out" value="vcf,bcf"/> + </section> + <output name="out_bcf"> + <assert_contents> + <has_size value="2264" delta="10"/> + </assert_contents> + </output> + <output name="out_vcf"> + <assert_contents> + <has_n_lines n="139"/> + <has_line line="##fileformat=VCFv4.2"/> + <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> + </assert_contents> + </output> + </test> + <!-- #4 germline, bcf --> + <test expect_num_outputs="3"> + <param name="samples" value="call_1.bcf.gz"/> + <section name="generic"> + <param name="altaf" value="0.1"/> + <param name="minsize" value="1"/> + <param name="maxsize" value="500000001"/> + <param name="ratiogeno" value="0.76"/> + <param name="pass" value="true"/> + </section> + <section name="sv"> + <conditional name="mode_cond"> + <param name="mode_sel" value="germline"/> + <param name="gq" value="14"/> + <param name="rddel" value="0.7"/> + <param name="rddup" value="1.3"/> + </conditional> + </section> + <section name="oo"> + <param name="out" value="vcf,bcf,log"/> + </section> + <output name="out_bcf"> + <assert_contents> + <has_size value="2264" delta="10"/> + </assert_contents> + </output> + <output name="out_vcf"> + <assert_contents> + <has_n_lines n="139"/> + <has_line line="##fileformat=VCFv4.2"/> + <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> + </assert_contents> + </output> + <output name="out_log"> + <assert_contents> + <has_text_matching expression=".+Done\."/> + </assert_contents> + </output> + </test> + <!-- #5 default, somatic, vcf --> + <test expect_num_outputs="2"> + <param name="samples" value="call_1.vcf.gz"/> + <section name="sv"> + <conditional name="mode_cond"> + <param name="mode_sel" value="somatic"/> + <param name="samples" value="samples.tsv"/> + </conditional> + </section> + <section name="oo"> + <param name="out" value="vcf,bcf"/> + </section> + <output name="out_bcf"> + <assert_contents> + <has_size value="2440" delta="10"/> + </assert_contents> + </output> + <output name="out_vcf"> + <assert_contents> + <has_n_lines n="142"/> + <has_line line="##fileformat=VCFv4.2"/> + <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +@WID@ + +Delly *filter* contains workflows for germline and somatic SV calling. + +**Input** + +*Somatic* filtering requires a called SV input with at least one tumor sample and a matched control sample. In addition, a tab-delimited sample description needs to be provided, in which the first column holds the sample ids (as found in the VCF/BCF input) and the second column specifies either tumor or control. + +*Germline* SV calling is done by sample for high-coverage genomes or in small batches for low-coverage genomes. + +**Output** + +The output is available in BCF and VCF format. + +.. class:: infomark + +**References** + +@REFERENCES@ + ]]></help> + <expand macro="citations"/> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Sep 28 07:44:40 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/call_1.vcf.gz Mon Sep 28 07:44:40 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/call_2.vcf.gz Mon Sep 28 07:44:40 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclude.tsv Mon Sep 28 07:44:40 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fasta Mon Sep 28 07:44:40 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