Mercurial > repos > iuc > flair
changeset 0:5d17cf201540 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
| author | iuc |
|---|---|
| date | Fri, 27 Nov 2020 18:45:47 +0000 |
| parents | |
| children | |
| files | flair_collapse.xml flair_correct.xml flair_macros.xml test-data/UCSC_Main_on_Human_knownGene_region_chrM.gtf test-data/chrM.bed12 test-data/chrM.fa test-data/chrM.fa.fai test-data/chrM.fastq.gz test-data/fasta_indexes.loc test-data/flair.collapse.isoforms.bed test-data/flair.collapse.isoforms.fa test-data/flair.collapse.isoforms.gtf test-data/flair_all_corrected.bed test-data/flair_all_inconsistent.bed tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 17 files changed, 3604 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flair_collapse.xml Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,188 @@ +<tool id="flair_collapse" name="FLAIR collapse" version="@TOOL_VERSION@" profile="20.01"> + <description>defines high-confidence isoforms from flair-corrected reads</description> + + <macros> + <import>flair_macros.xml</import> + </macros> + + <expand macro="requirements" /> + <expand macro="version_command" /> + + <command detect_errors="exit_code"><![CDATA[ + +@PREPARE_REF@ + +ln -s '$input_query' query.bed && + +flair.py collapse + +########### +## Input ## +########### + +-q query.bed +-r '$input_reads' +-g reference.fa +-f '$input_gtf' + +#if $input_promotors: + -p '$input_promotors' +#end if + +######################## +## Additional Options ## +######################## + +-w $additional_options.window +-s $additional_options.support +$additional_options.stringent + +#if str($additional_options.select_uniqueness): + -n str($additional_options.select_uniqueness) +#end if + +$additional_options.isoform +--max_ends $additional_options.maxends +$additional_options.trustends + +#if str($additional_options.select_filter): + -e str($additional_options.select_filter) +#end if + +######### +## END ## +######### + + ]]></command> + <inputs> + <param name="input_query" argument="-q" type="data" format="bed" label="Corrected Reads as BED file"/> + <param name="input_reads" argument="-r" type="data" format="fasta,fastq" label="FASTA/FASTQ file of raw reads"/> + <expand macro="reference_interface" /> + <param name="input_gtf" argument="-f" type="data" format="gtf" label="GTF annotation file"/> + <param name="input_promotors" optional="true" argument="-p" type="data" format="bed" label="Promotor BED file to identify full-length reads" /> + + <!-- Additional Options --> + <section name="additional_options" title="Additional Options"> + <param name="window" argument="-w" type="integer" min="1" value="100" label="Window Size" help="Window size for comparing TSS/TES (Default=100)" /> + <param name="support" argument="-s" type="integer" min="1" value="3" label="Supporting Reads" help="Minimum number of supporting reads for an isoform (Default=3)" /> + <param name="stringent" argument="--stringent" type="boolean" checked="false" truevalue="--stringent" falsevalue="" label="Use Stringent Mode" help="Specify if all supporting reads need to be full-length (80% coverage and spanning 25 bp of the first and last exons) (Default=false)"/> + <param name="select_uniqueness" argument="-n" type="select" label="Choose the TSS/TES for each unique set of splice junction." > + <option value="" selected="true">No Selection</option> + <option value="none">Best TSSs/TESs</option> + <option value="longest">Single TSS/TES chosen to maximize length</option> + <option value="best_only">Single most supported TSS/TES used in conjunction chosen</option> + </param> + <param name="isoform" argument="-i" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Use Isoform Mode" help="TSS/TES for each isoform will be determined from supporting reads for individual isoforms (Default=false)"/> + <param name="maxends" argument="--max_ends" type="integer" min="0" value="2" label="Maximum Number of TSS/TES picked per isoform" help="(Default=2)" /> + <param name="trustends" argument="--trust_ends" type="boolean" checked="false" truevalue="--trust_ends" falsevalue="" label="Reads are generated from a long read method with minimal fragmentation?" /> + <param name="select_filter" argument="-e" type="select" label="Filter for isoforms." > + <option value="" selected="true">No Filter</option> + <option value="nosubset">Any isoforms that are a proper set of another isoform are removed</option> + <option value="default">Subset isoforms are removed based on support</option> + <option value="comprehensive">Default set + all subset isoforms</option> + <option value="ginormous">Comprehensive set + single exon subset isoforms</option> + </param> + <param name="mapq" argument="--quality" type="integer" min="0" value="1" label="Minimum MAPQ of read assignment to an isoform" help="(Default=1)" /> + </section> + + <section name="additional_outputs" title="Output Options"> + <param name="out_format" type="select" multiple="true" optional="true" display="checkboxes" label="Data types"> + <option value="bed">BED</option> + <option value="fasta">FASTA</option> + </param> + </section> + </inputs> + + <outputs> + <data name="outfile_isoforms_gtf" from_work_dir="flair.collapse.isoforms.gtf" format="gtf" label="${tool.name} on ${on_string}: Isoforms GTF" /> + <data name="outfile_isoforms_bed" from_work_dir="flair.collapse.isoforms.bed" format="bed" label="${tool.name} on ${on_string}: Isoforms BED"> + <filter>additional_outputs['out_format'] and 'bed' in additional_outputs['out_format']</filter> + </data> + <data name="outfile_isoforms_fasta" from_work_dir="flair.collapse.isoforms.fa" format="fasta" label="${tool.name} on ${on_string}: Isoforms FASTA"> + <filter>additional_outputs['out_format'] and 'fasta' in additional_outputs['out_format']</filter> + </data> + </outputs> + + <tests> + <test expect_num_outputs="3"> + <param name="input_query" ftype="bed" value="flair_all_corrected.bed" /> + <param name="input_reads" ftype="fastq.gz" value="chrM.fastq.gz" /> + <param name="ref_selector_genome" value="history" /> + <param name="reffile" ftype="fasta" value="chrM.fa" /> + <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" /> + <param name="out_format" value="bed,fasta" /> + <output name="outfile_isoforms_gtf" ftype="gtf" file="flair.collapse.isoforms.gtf" /> + <output name="outfile_isoforms_bed" ftype="bed" file="flair.collapse.isoforms.bed" /> + <output name="outfile_isoforms_fasta" ftype="fasta" file="flair.collapse.isoforms.fa" /> + </test> + <!-- Test with cached genome --> + <test expect_num_outputs="3"> + <param name="input_query" ftype="bed" value="flair_all_corrected.bed" /> + <param name="input_reads" ftype="fastq.gz" value="chrM.fastq.gz" /> + <param name="ref_selector_genome" value="cached" /> + <param name="reffile" value="chrM" /> + <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" /> + <param name="out_format" value="bed,fasta" /> + <output name="outfile_isoforms_gtf" ftype="gtf" file="flair.collapse.isoforms.gtf" /> + <output name="outfile_isoforms_bed" ftype="bed" file="flair.collapse.isoforms.bed" /> + <output name="outfile_isoforms_fasta" ftype="fasta" file="flair.collapse.isoforms.fa" /> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +------------------- + +@description@ + +**flair collapse** +Defines high-confidence isoforms from corrected reads. + +------------------- + +**Inputs** + +------------------- + +(1) Corrected Reads as Bed12 File. +(2) FASTA/FASTQ file of raw reads. All raw read fastq/fasta files should be concatenated into a single file. +(3) FASTA of Reference Genome. +(4) GTF annotation file. +(5) Promoter regions bed file to identify full-length reads. + +----------- + +**Outputs** + +----------- + +Outputs the high-confidence isoforms in several formats: +(1) bed, +(2) gtf, +(3) FASTA. + +-------------------- + +**More Information** + +-------------------- + +See the excellent `FLAIR documentation`_ + +.. _`FLAIR documentation`: https://github.com/BrooksLabUCSC/flair + + +-------------------- + +**Galaxy Wrapper Development** + +-------------------- + +@citation@ + + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flair_correct.xml Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,137 @@ +<tool id="flair_correct" name="FLAIR correct" version="@TOOL_VERSION@" profile="20.01"> + <description>corrects misaligned splice sites using genome annotations</description> + + <macros> + <import>flair_macros.xml</import> + </macros> + + <expand macro="requirements" /> + <expand macro="version_command" /> + + <command detect_errors="exit_code"><![CDATA[ + +@PREPARE_REF@ + +flair.py correct + +########### +## Input ## +########### + +-q '$input_query' +-g reference.fa +-f '$input_gtf' + +#if $input_shortread: + -j '$input_shortread' +#end if + +######################## +## Additional Options ## +######################## + +$additional_options.strand +-w $additional_options.window + +######### +## END ## +######### + + ]]></command> + <inputs> + <param name="input_query" argument="-q" type="data" format="bed12" label="Uncorrected Bed12 file"/> + <expand macro="reference_interface" /> + <param name="input_gtf" argument="-f" type="data" format="gtf" label="GTF annotation file"/> + <param name="input_shortread" optional="true" argument="-j" type="data" format="bed" label="Splice junction BED file" /> + + <!-- Additional Options --> + <section name="additional_options" title="Additional Options"> + <param name="strand" argument="-n" type="boolean" checked="false" truevalue="-n" falsevalue="" label="Strand Consistency" help="Keep the strand of a read consistent after correction."/> + <param name="window" argument="-w" type="integer" min="1" value="10" label="Window Size" help="Window size for correcting splice sites (Default=10)" /> + </section> + </inputs> + + + <outputs> + <data name="outfile_1" format="bed12" from_work_dir="flair_all_corrected.bed" label="${tool.name} on ${on_string}: Corrected Reads" /> + <data name="outfile_2" format="bed12" from_work_dir="flair_all_inconsistent.bed" label="${tool.name} on ${on_string}: Inconsistent Reads" /> + </outputs> + + <tests> + <test expect_num_outputs="2"> + <param name="input_query" ftype="bed12" value="chrM.bed12" /> + <param name="ref_selector_genome" value="history" /> + <param name="reffile" ftype="fasta" value="chrM.fa" /> + <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" /> + <output name="outfile_1" ftype="bed12" file="flair_all_corrected.bed" /> + <output name="outfile_2" ftype="bed12" file="flair_all_inconsistent.bed" /> + </test> + <!-- Test with cached genome --> + <test expect_num_outputs="2"> + <param name="input_query" ftype="bed12" value="chrM.bed12" /> + <param name="ref_selector_genome" value="cached" /> + <param name="reffile" value="chrM" /> + <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" /> + <output name="outfile_1" ftype="bed12" file="flair_all_corrected.bed" /> + <output name="outfile_2" ftype="bed12" file="flair_all_inconsistent.bed" /> + </test> + </tests> + + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +------------------- + +@description@ + +**flair correct** +Corrects misaligned splice sites using genome annotations and/or short-read splice junctions. Based on common user issues we have encountered, for flair-correct to run properly, please ensure/note that (1) the genome annotation and genome sequences are compatible, (2) gtf is preferred over gff for annotation and annotations that do not split single exons into multiple entries are ideal. + +------------------- + +**Inputs** + +------------------- + +(1) Uncorreced bed12 file. +(2) FASTA file of the reference genome. +(3) GTF annotation file. +(4) BED format splice junctions from short-read sequencing or GTF annotation file. + +----------- + +**Outputs** + +----------- + +(1) bed12 of corrected reads, +(2) bed12 of reads that weren't able to be corrected, +(3) psl of corrected reads if the -c chromsizes file is provided. + +Either (1) or (3) can be supplied to flair-collapse as the query. + +-------------------- + +**More Information** + +-------------------- + +See the excellent `FLAIR documentation`_ + +.. _`FLAIR documentation`: https://github.com/BrooksLabUCSC/flair + + +-------------------- + +**Galaxy Wrapper Development** + +-------------------- + +@citation@ + + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flair_macros.xml Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,60 @@ +<macros> + <token name="@TOOL_VERSION@">1.5</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">flair</requirement> + <yield /> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>flair.py --version</version_command> + </xml> + + <token name="@PREPARE_REF@"><![CDATA[ + #if str($reference_source_genome.ref_selector_genome) == 'history': + ln -s '$reference_source_genome.reffile' reference.fa && + samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for indexing fasta reference for flair" >&2 && + #else + ln -s '${reference_source_genome.reffile.fields.path}' reference.fa && + #end if + ]]></token> + + <xml name="reference_interface"> + <conditional name="reference_source_genome"> + <param name="ref_selector_genome" type="select" label="Choose the source for the reference genome"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="reffile" argument="-g" type="select" label="Reference genome"> + <options from_data_table="fasta_indexes"> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> + </options> + </param> + </when> + <when value="history"> + <param name="reffile" argument="-g" type="data" format="fasta" label="Reference" help="Reference sequence" /> + </when> + </conditional> + </xml> + + <token name="@description@"> + +**FLAIR** FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads. +FLAIR can be run optionally with short-read data to help increase splice site accuracy of the long read splice junctions. FLAIR uses multiple alignment steps and splice site filters to increase confidence in the set of isoforms defined from noisy data. FLAIR was designed to be able to sense subtle splicing changes in nanopore data from Tang et al. (2018). +It is recommended to combine all samples together prior to running flair-collapse for isoform assembly by concatenating corrected read psl or bed files together. Following the creation of an isoform reference from flair-collapse, consequent steps will assign reads from each sample individually to isoforms of the combined assembly for downstream analyses. + + </token> + + <token name="@citation@"> + +Author: Florian Heyl + + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41467-020-15171-6</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/UCSC_Main_on_Human_knownGene_region_chrM.gtf Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,76 @@ +chrM hg38_knownGene exon 577 647 0.000000 + . gene_id "ENST00000387314.1"; transcript_id "ENST00000387314.1"; +chrM hg38_knownGene exon 648 1601 0.000000 + . gene_id "ENST00000389680.2"; transcript_id "ENST00000389680.2"; +chrM hg38_knownGene exon 1602 1670 0.000000 + . gene_id "ENST00000387342.1"; transcript_id "ENST00000387342.1"; +chrM hg38_knownGene exon 1671 3229 0.000000 + . gene_id "ENST00000387347.2"; transcript_id "ENST00000387347.2"; +chrM hg38_knownGene exon 3230 3304 0.000000 + . gene_id "ENST00000386347.1"; transcript_id "ENST00000386347.1"; +chrM hg38_knownGene start_codon 3307 3309 0.000000 + . gene_id "ENST00000361390.2"; transcript_id "ENST00000361390.2"; +chrM hg38_knownGene CDS 3307 4259 0.000000 + 0 gene_id "ENST00000361390.2"; transcript_id "ENST00000361390.2"; +chrM hg38_knownGene stop_codon 4260 4262 0.000000 + . gene_id "ENST00000361390.2"; 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transcript_id "ENST00000361789.2"; +chrM hg38_knownGene CDS 14747 15884 0.000000 + 0 gene_id "ENST00000361789.2"; transcript_id "ENST00000361789.2"; +chrM hg38_knownGene stop_codon 15885 15887 0.000000 + . gene_id "ENST00000361789.2"; transcript_id "ENST00000361789.2"; +chrM hg38_knownGene exon 14747 15887 0.000000 + . gene_id "ENST00000361789.2"; transcript_id "ENST00000361789.2"; +chrM hg38_knownGene exon 15888 15953 0.000000 + . gene_id "ENST00000387460.2"; transcript_id "ENST00000387460.2"; +chrM hg38_knownGene exon 15956 16023 0.000000 - . gene_id "ENST00000387461.2"; transcript_id "ENST00000387461.2";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.bed12 Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,1348 @@ +chrM 569 1461 1fb96112-b5ee-46ac-9ca4-c3e170512e4d;0 60 + 569 1461 99,99,99 1 892, 0, +chrM 570 1631 ca7655f0-1077-4546-850f-be0f10f50a81;0 60 + 570 1631 99,99,99 1 1061, 0, +chrM 570 3149 07a2d20a-8f33-4283-87e2-ee2b28b771f2;0 60 + 570 3149 99,99,99 1 2579, 0, +chrM 571 1180 fd4b26fc-72f9-4060-8c6d-deca2e55cceb;0 60 + 571 1180 99,99,99 1 609, 0, +chrM 571 1041 ec1423b2-49e7-4751-81b6-39614fd8991d;0 60 + 571 1041 99,99,99 1 470, 0, +chrM 578 1601 550708cd-84a1-40c0-aed9-b6b38faca411;0 49 + 578 1601 99,99,99 1 1023, 0, +chrM 658 1215 2dc80131-77c9-4dd4-b6ab-26de0d91afc5;0 60 + 658 1215 99,99,99 1 557, 0, +chrM 660 1118 31d34648-3f54-4a65-9878-2ae72795dba4;0 58 + 660 1118 99,99,99 1 458, 0, +chrM 661 1258 f7ee2b0a-5e47-4c55-a70b-60fc2a8d9d5f;0 52 + 661 1258 99,99,99 1 597, 0, +chrM 661 1191 385a6115-47fa-45f1-a64e-6bf9e9e8f716;0 60 + 661 1191 99,99,99 1 530, 0, +chrM 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5dac3f00-ff98-4945-944e-71670bc92587;0 60 + 14757 15869 99,99,99 1 1112, 0, +chrM 14758 15887 d69cbde2-2d60-4e19-ac83-817b0c69f28e;0 60 + 14758 15887 99,99,99 1 1129, 0, +chrM 14758 15886 016bc55b-7a52-4f24-b3d6-9132df099d80;0 60 + 14758 15886 99,99,99 1 1128, 0, +chrM 14758 15883 64e15f2e-0069-43b5-9dab-7940ef61c849;0 60 + 14758 15883 99,99,99 1 1125, 0, +chrM 14758 15887 6f6d8722-287e-4445-a9c8-94238428138f;0 60 + 14758 15887 99,99,99 1 1129, 0, +chrM 14758 15879 c072360c-3ac0-4097-8733-362a494a988e;0 60 + 14758 15879 99,99,99 1 1121, 0, +chrM 14760 15887 45bb9527-2be5-4272-b819-48a7971c6fbe;0 60 + 14760 15887 99,99,99 1 1127, 0, +chrM 14760 15883 7f6ec223-0a7f-415e-bdd8-0b2e2c4985ff;0 60 + 14760 15883 99,99,99 1 1123, 0, +chrM 14761 15847 95cb889c-4a97-4c29-a77c-3312a219a6ad;0 60 + 14761 15847 99,99,99 1 1086, 0, +chrM 14766 15887 f81dd59c-c08b-4c7d-8c23-1e47857afb92;0 60 + 14766 15887 99,99,99 1 1121, 0, +chrM 14766 15887 4a1cc098-aa5d-4ad9-87a6-fba57c10c7d7;0 60 + 14766 15887 99,99,99 1 1121, 0, +chrM 14770 15887 ce4659c3-382a-4361-b5ea-28c442883218;0 60 + 14770 15887 99,99,99 1 1117, 0, +chrM 14770 16075 90808752-db98-4215-b707-b0944c0a7272;0 60 + 14770 16075 99,99,99 1 1305, 0, +chrM 14778 14984 774ce748-fca6-4046-8daa-da7c6e91765a;0 60 + 14778 14984 99,99,99 1 206, 0, +chrM 14846 15115 76dc9f46-8b7b-48a8-9225-bca23777bda2;0 60 + 14846 15115 99,99,99 1 269, 0, +chrM 14924 15659 79eea848-d3ff-4e7b-9c01-9a3710c20732;0 60 + 14924 15659 99,99,99 1 735, 0, +chrM 14982 15842 dd484c35-375e-47a8-b9e8-31c0b4d39b4b;0 60 + 14982 15842 99,99,99 1 860, 0, +chrM 15009 15887 3bd3e3d3-132c-43e2-872a-8a41e25d8805;0 60 + 15009 15887 99,99,99 1 878, 0, +chrM 15169 15886 cdb71c09-5f6e-4145-99c6-3e0cbfd90739;0 60 + 15169 15886 99,99,99 1 717, 0, +chrM 15194 15883 2622775b-65c9-4cae-9a3b-c6be3e0faa17;0 60 + 15194 15883 99,99,99 1 689, 0, +chrM 15213 15876 3b1ef952-41fe-4d83-808c-76caa7f7b83d;0 60 + 15213 15876 99,99,99 1 663, 0, +chrM 15461 15887 9f0d3300-a9c3-41aa-af9b-00403ffbeacb;0 60 + 15461 15887 99,99,99 1 426, 0, +chrM 15496 15876 fbd51668-5fe6-431a-ad8b-fe1165eebf19;0 60 + 15496 15876 99,99,99 1 380, 0, +chrM 15587 15887 3c97e997-9eed-405b-b40e-28122064980c;0 60 + 15587 15887 99,99,99 1 300, 0, +chrM 15589 15887 32c06f69-94bc-4023-8ae7-f66dc584d355;0 30 + 15589 15887 99,99,99 1 298, 0, +chrM 15670 15874 4a827e6b-259e-4723-8860-f978ceaaa5f7;0 58 + 15670 15874 99,99,99 1 204, 0, +chrM 15695 15877 7e44209b-aae3-4993-91e4-fe5b37ab2eb2;0 55 + 15695 15877 99,99,99 1 182, 0, +chrM 15800 16569 a78fb847-612c-42c0-9b73-d59b91a9e9df;0 60 + 15800 16569 99,99,99 1 769, 0, +chrM 15963 16569 f6bd411a-d419-4197-a525-324568f7944a;0 60 + 15963 16569 99,99,99 1 606, 0, +chrM 15963 16540 ccdfb0ae-54fb-4e3d-8f92-587d4cdc7141;0 60 + 15963 16540 99,99,99 1 577, 0, +chrM 15968 16271 37432238-4f0a-4817-b648-73cb476a71d7;0 60 + 15968 16271 99,99,99 1 303, 0, +chrM 15970 16311 a446bc9e-f22d-40ca-a502-d78b06fc8dd4;0 60 + 15970 16311 99,99,99 1 341, 0, +chrM 15970 16557 2f14a1a9-c356-4568-9a4e-150c8d2038d0;0 60 + 15970 16557 99,99,99 1 587, 0, +chrM 15970 16296 19cc5328-7604-445f-b261-7e71a02273c6;0 60 + 15970 16296 99,99,99 1 326, 0, +chrM 15971 16569 46a0710f-c426-4f83-902b-a99be8273b34;0 60 + 15971 16569 99,99,99 1 598, 0, +chrM 15971 16569 d52a572f-79ca-4109-a247-55ab7b0ceda6;0 60 + 15971 16569 99,99,99 1 598, 0, +chrM 15972 16569 8bf3eb49-3aeb-4bc6-9bcc-1cfb1a896618;0 60 + 15972 16569 99,99,99 1 597, 0, +chrM 15976 16291 f051705e-4230-4631-84e3-7e014eb98f35;0 48 + 15976 16291 99,99,99 1 315, 0,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,333 @@ +>chrM +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT +TTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTG +GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATC +CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTA +AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT +GTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA +AACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA +AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTT +TATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATT +ATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCCGC +CCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCA +ACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAA +GCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAAT +AGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA +GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGA +ACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCAC +ACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTT +AACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGC +GGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTA +GATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACT +CCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC +ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCC +TAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGC +CACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGG +AGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTC +AGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAA +GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTG +GCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT +GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGC +TTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTC +AAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGA +GGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAA +CCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCA +ACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCACCT +TACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG +ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATG +AAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCT +GCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGA +CCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGT +CTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTAC +CGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTA +AATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC +CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGT +AAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAA +GCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGA +ACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATG +TTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGA +TTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAAC +AAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA +AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTA +CCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCA +GTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagcata +atcacttgttccttaaatagggacctgtatgaatggctccacgagggttc +agctgtctcttacttttaaccagtgaaattgacctgcccgtgaagaggcg +ggcataacacagcaagacgagaagaccctatggagctttaatttaTTAAT +GCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT +AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGT +ACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCC +AATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCT +ATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCA +GGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATT +AAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCT +ATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT +ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATT +ATACCCACACCCACCCAAGAACAGGGTTTgttaagatggcagagcccggt +aatcgcataaaacttaaaactttacagtcagaggttcaattcctcttctt +aacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAAT +CGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATAC +AACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCC +TTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC +ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCG +CTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTC +AACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTC +AATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCG +CACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATC +ATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCT +TATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG +CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTC +GACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATA +CGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTA +TTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGAC +GCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTACT +TCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGCT +ACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA +GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCC +CCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTA +AATAATAGGAGCTTAAACCCCCTTATTTctaggactatgagaatcgaacc +catccctgagaatccaaaattctccgtgccacctatcacaccccatccta +AAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGG +TTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTACT +CTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT +TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCT +AACCAAAAAAATAAACCCTCGTTCCACAGAAGCTGCCATCAAGTATTTCC +TCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTTCAAC +AATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTC +ATCATTAATAATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCT +TTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGC +CTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA +AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTAT +CCATCATAGCAGGCAGTTGAGGTGGATTAAACCAAACCCAGCTACGCAAA +ATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTCT +ACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCC +TAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACC +CTACTACTATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAAT +TCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT +TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATC +ATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACCT +ACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAACG +TAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCC +ACACTCATCGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACT +AATAATCTTATAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGC +CCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA +CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAG +CCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCT +AAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAA +AAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAA +TTCAATATGAAAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGT +CTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACCTCACCCCCA +CTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG +AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTC +TAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGT +AACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAAT +CTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAG +TTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAAC +ATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTGC +TATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG +CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCC +TTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCAC +AACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCCC +TCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTC +CCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAA +CACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAAC +ACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA +GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGA +ACCATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTCC +TAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGTA +GACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCAC +CGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGA +AATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACC +GTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT +ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAA +TAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCTA +TTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTAT +CATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCC +TATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACA +TGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAAT +ATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC +TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCC +CCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTAGACAaaa +aaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggcc +tccatgactttttcAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTC +AAAGTTAAATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCG +CAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCAC +CTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC +TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATC +TCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCAT +CCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACG +AGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTAC +TGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACAT +ACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTG +ACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA +TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAAC +AGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGAC +CGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGT +TTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGG +GCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGT +AAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACA +CCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT +AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATAT +TAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAA +AATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTCA +TTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCT +ATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGAC +TAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGATA +ACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT +AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCAT +TTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTA +TGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCT +AGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAG +TTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTA +CGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGG +AAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA +TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTA +ATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAA +CACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCCC +ATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAG +CCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTA +ACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAG +CACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG +GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTC +TGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCA +CTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCC +TAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCAC +CATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTAT +TACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTACT +TCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT +GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCT +CACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATC +ACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTT +TGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAG +TATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAA +AAAGAGTAATAAACTTCGCCTTAATTTTAATAATCAACACCCTCCTAGCC +TTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT +AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCC +GCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTA +TTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAAC +AACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCC +TAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACC +GAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATTA +TGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG +CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATA +TCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGC +TACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCTA +TTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTA +CTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAAA +CCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCACT +GACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA +GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAAC +AACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCCC +CCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGCC +AACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCT +ATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGA +ACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGG +CTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA +TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACT +AATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACTC +TCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACTA +GCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTT +ATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTAC +TTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACA +CTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT +ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAG +ACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGTA +GTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCAT +TCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAA +ACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGA +CTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCT +CGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG +TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGA +CTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAAC +ACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCA +CACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTA +TCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTT +AACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCCTTA +TTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC +AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAG +GCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACAC +TACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCA +CCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCC +ATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCAT +GTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCC +AAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA +TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACT +GTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTAC +TCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATTC +CAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCAT +CAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAA +TCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGA +TTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA +CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAG +GCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAA +GGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGC +AGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCAC +TAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCA +GCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTC +CACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC +CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATA +CTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGA +TATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCT +CCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGT +TTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAA +CGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCT +ATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC +ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAA +ACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACA +TTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTC +ACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAA +CTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATT +TCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCC +TATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT +AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCT +CCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTC +CTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACC +TATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTT +CAACCAGTAACTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGC +ACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTA +TTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC +TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAAC +ACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAA +TAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAA +ATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAAT +AACACACCCGACCACACCGCTAACAATCAATACTAAACCCCCATAAATAG +GAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTC +AACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC +CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGA +CCCCAATACGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTC +ATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTC +ACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAG +CCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCAC +ATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAA +TGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC +TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATC +CTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGTG +AGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCCG +CCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTAC +TCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTT +GCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACG +AAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC +ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTT +CCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGCG +ACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACATC +AAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCC +TAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAG +CAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGC +CCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT +AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGAC +AAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAACT +ATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTAT +AAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGG +ACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAG +ATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGT +ACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA +TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCAC +CTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTA +CAAGcaagtacagcaatcaaccctcaactatcacacatcaactgcaactC +CAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAA +CAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAA +ATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGAC +CACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG +CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACAT +CTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCT +TAAATAAGACATCACGATG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa.fai Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,1 @@ +chrM 16569 6 50 51
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,1 @@ +chrM hg19 human mitochondrial genome ${__HERE__}/chrM.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair.collapse.isoforms.bed Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,14 @@ +chrM 661 1341 ca7655f0-1077-4546-850f-be0f10f50a81_chrM:000 60 + 661 1341 14 1 680, 0, +chrM 1274 1601 07a2d20a-8f33-4283-87e2-ee2b28b771f2_chrM:1000 60 + 1274 1601 11 1 327, 0, +chrM 1681 3211 7739a708-0dd8-4e16-856c-0488b9378738_ENST00000387347.2 60 + 1681 3211 31 1 1530, 0, +chrM 3315 4220 13557349-20c1-42e2-8477-a31c29e524a3_ENST00000361390.2 60 + 3315 4220 58 1 905, 0, +chrM 4482 5439 7c64296d-12c2-49bd-a404-70478fff9a62_ENST00000361453.3 60 - 4482 5439 33 1 957, 0, +chrM 5591 5865 272f11a9-f8b7-4c23-8526-a36936b8527f_chrM:5000 29 + 5591 5865 66 1 274, 0, +chrM 5911 7518 1804a832-0ae7-4760-bd8c-2b8250455c48_ENST00000361624.2 60 + 5911 7518 167 1 1607, 0, +chrM 7596 8294 3065b2ed-affa-4e42-8c6e-b385487325f6_ENST00000361739.1 45 + 7596 8294 116 1 698, 0, +chrM 8377 9207 08c5eaa2-47a2-4813-ae6d-e579904d6416_ENST00000361899.2 42 + 8377 9207 77 1 830, 0, +chrM 9221 9991 29af7e32-7b11-4c36-ae11-25b54575faea_ENST00000362079.2 60 + 9221 9991 148 1 770, 0, +chrM 10070 10404 7258b7cf-cbd2-4dab-928d-bbb5bc115c4c_ENST00000361227.2 60 + 10070 10404 78 1 334, 0, +chrM 10482 12053 ccdaa81a-848a-4da0-abef-6411c5c3a01e_ENST00000361381.2 60 + 10482 12053 54 1 1571, 0, +chrM 12350 14748 81c2d0d9-44c7-4f0a-bb58-7b0ab49220a5_ENST00000361567.2 60 + 12350 14748 20 1 2398, 0, +chrM 15971 16569 2f14a1a9-c356-4568-9a4e-150c8d2038d0_chrM:15000 60 + 15971 16569 3 1 598, 0,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair.collapse.isoforms.fa Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,28 @@ +>ca7655f0-1077-4546-850f-be0f10f50a81_chrM:000 +TAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCC +>07a2d20a-8f33-4283-87e2-ee2b28b771f2_chrM:1000 +AAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAAC +>7739a708-0dd8-4e16-856c-0488b9378738_ENST00000387347.2 +CCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagcataatcacttgttccttaaatagggacctgtatgaatggctccacgagggttcagctgtctcttacttttaaccagtgaaattgacctgcccgtgaagaggcgggcataacacagcaagacgagaagaccctatggagctttaatttaTTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACC +>13557349-20c1-42e2-8477-a31c29e524a3_ENST00000361390.2 +GCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTAGCATTACTTATATGATATGT +>7c64296d-12c2-49bd-a404-70478fff9a62_ENST00000361453.3 +GGGTGGGTTTTGTATGTTCAAACTGTCATTTTATTTTTACGTTGTTAGATATGGGGAGTAGTGTGATTGAGGTGGAGTAGATTAGGCGTAGGTAGAAGTAGAGGTTAAGGAGGGTGATGGTGGCTATGATGGTGGGGATGATGAGGCTATTGTTTTTTGTGAATTCTTCGATAATGGCCCATTTGGGCAAAAAGCCGGTTAGCGGGGGCAGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTTAGCTTGTTTCAGGTGCGAGATAGTAGTAGGGTCGTGGTGCTGGAGTTTAAGTTGAGTAGTAGGAATGCGGTAGTAGTTAGGATAATATAAATAGTTAAATTAAGAATGGTTATGTTAGGGTTGTACGGTAGAACTGCTATTATTCATCCTATGTGGGTAATTGAGGAGTATGCTAAGATTTTGCGTAGCTGGGTTTGGTTTAATCCACCTCAACTGCCTGCTATGATGGATAAGATTGAGAGAGTGAGGAGAAGGCTTACGTTTAGTGAGGGAGAGATTTGGTATATGATTGAGATGGGGGCTAGTTTTTGTCATGTGAGAAGAAGCAGGCCGGATGTCAGAGGGGTGCCTTGGGTAACCTCTGGGACTCAGAAGTGAAAGGGGGCTATTCCTAGTTTTATTGCTATAGCTATTATGATTATTAATGATGAGTATTGATTGGTAGTATTGGTTATGGTTCATTGTCCGGAGAGTATATTGTTGAAGAGGATAGCTATTAGAAGGATTATGGATGCGGTTGCTTGCGTGAGGAAATACTTGATGGCAGCTTCTGTGGAACGAGGGTTTATTTTTTTGGTTAGAACTGGAATAAAAGCTAGCATGTTTATTTCTAGGCCTACTCAGGTAAAAAATCAGTGCGAGCTTAGCGCTGTGATGAGTGTGCCTGCAAAGATGGTAGAGTAGATGACGGGTTGGG +>272f11a9-f8b7-4c23-8526-a36936b8527f_chrM:5000 +ACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGT +>1804a832-0ae7-4760-bd8c-2b8250455c48_ENST00000361624.2 +CGACCGTTGACTATTCTCTACAAACCACAAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTAGACAaaaaaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggcctccatgactttttcAAAA +>3065b2ed-affa-4e42-8c6e-b385487325f6_ENST00000361739.1 +AGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCC +>08c5eaa2-47a2-4813-ae6d-e579904d6416_ENST00000361899.2 +AATACTACCGTATGGCCCACCATAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAACACATAA +>29af7e32-7b11-4c36-ae11-25b54575faea_ENST00000362079.2 +CATGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTA +>7258b7cf-cbd2-4dab-928d-bbb5bc115c4c_ENST00000361227.2 +TTAATTTTAATAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACCGAAT +>ccdaa81a-848a-4da0-abef-6411c5c3a01e_ENST00000361381.2 +ACATAAATATTATACTAGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCACTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACAGCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACAC +>81c2d0d9-44c7-4f0a-bb58-7b0ab49220a5_ENST00000361567.2 +TACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGACCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAAT +>2f14a1a9-c356-4568-9a4e-150c8d2038d0_chrM:15000 +TAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTACAAGcaagtacagcaatcaaccctcaactatcacacatcaactgcaactCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair.collapse.isoforms.gtf Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,28 @@ +chrM FLAIR transcript 662 1341 . + . gene_id "chrM:000"; transcript_id "ca7655f0-1077-4546-850f-be0f10f50a81"; +chrM FLAIR exon 662 1341 . + 60 gene_id "chrM:000"; transcript_id "ca7655f0-1077-4546-850f-be0f10f50a81"; exon_number "0"; +chrM FLAIR transcript 1275 1601 . + . gene_id "chrM:1000"; transcript_id "07a2d20a-8f33-4283-87e2-ee2b28b771f2"; +chrM FLAIR exon 1275 1601 . + 60 gene_id "chrM:1000"; transcript_id "07a2d20a-8f33-4283-87e2-ee2b28b771f2"; exon_number "0"; +chrM FLAIR transcript 1682 3211 . + . gene_id "ENST00000387347.2"; transcript_id "7739a708-0dd8-4e16-856c-0488b9378738"; +chrM FLAIR exon 1682 3211 . + 60 gene_id "ENST00000387347.2"; transcript_id "7739a708-0dd8-4e16-856c-0488b9378738"; exon_number "0"; +chrM FLAIR transcript 3316 4220 . + . gene_id "ENST00000361390.2"; transcript_id "13557349-20c1-42e2-8477-a31c29e524a3"; +chrM FLAIR exon 3316 4220 . + 60 gene_id "ENST00000361390.2"; transcript_id "13557349-20c1-42e2-8477-a31c29e524a3"; exon_number "0"; +chrM FLAIR transcript 4483 5439 . - . gene_id "ENST00000361453.3"; transcript_id "7c64296d-12c2-49bd-a404-70478fff9a62"; +chrM FLAIR exon 4483 5439 . - 60 gene_id "ENST00000361453.3"; transcript_id "7c64296d-12c2-49bd-a404-70478fff9a62"; exon_number "0"; +chrM FLAIR transcript 5592 5865 . + . gene_id "chrM:5000"; transcript_id "272f11a9-f8b7-4c23-8526-a36936b8527f"; +chrM FLAIR exon 5592 5865 . + 29 gene_id "chrM:5000"; transcript_id "272f11a9-f8b7-4c23-8526-a36936b8527f"; exon_number "0"; +chrM FLAIR transcript 5912 7518 . + . gene_id "ENST00000361624.2"; transcript_id "1804a832-0ae7-4760-bd8c-2b8250455c48"; +chrM FLAIR exon 5912 7518 . + 60 gene_id "ENST00000361624.2"; transcript_id "1804a832-0ae7-4760-bd8c-2b8250455c48"; exon_number "0"; +chrM FLAIR transcript 7597 8294 . + . gene_id "ENST00000361739.1"; transcript_id "3065b2ed-affa-4e42-8c6e-b385487325f6"; +chrM FLAIR exon 7597 8294 . + 45 gene_id "ENST00000361739.1"; transcript_id "3065b2ed-affa-4e42-8c6e-b385487325f6"; exon_number "0"; +chrM FLAIR transcript 8378 9207 . + . gene_id "ENST00000361899.2"; transcript_id "08c5eaa2-47a2-4813-ae6d-e579904d6416"; +chrM FLAIR exon 8378 9207 . + 42 gene_id "ENST00000361899.2"; transcript_id "08c5eaa2-47a2-4813-ae6d-e579904d6416"; exon_number "0"; +chrM FLAIR transcript 9222 9991 . + . gene_id "ENST00000362079.2"; transcript_id "29af7e32-7b11-4c36-ae11-25b54575faea"; +chrM FLAIR exon 9222 9991 . + 60 gene_id "ENST00000362079.2"; transcript_id "29af7e32-7b11-4c36-ae11-25b54575faea"; exon_number "0"; +chrM FLAIR transcript 10071 10404 . + . gene_id "ENST00000361227.2"; transcript_id "7258b7cf-cbd2-4dab-928d-bbb5bc115c4c"; +chrM FLAIR exon 10071 10404 . + 60 gene_id "ENST00000361227.2"; transcript_id "7258b7cf-cbd2-4dab-928d-bbb5bc115c4c"; exon_number "0"; +chrM FLAIR transcript 10483 12053 . + . gene_id "ENST00000361381.2"; transcript_id "ccdaa81a-848a-4da0-abef-6411c5c3a01e"; +chrM FLAIR exon 10483 12053 . + 60 gene_id "ENST00000361381.2"; transcript_id "ccdaa81a-848a-4da0-abef-6411c5c3a01e"; exon_number "0"; +chrM FLAIR transcript 12351 14748 . + . gene_id "ENST00000361567.2"; transcript_id "81c2d0d9-44c7-4f0a-bb58-7b0ab49220a5"; +chrM FLAIR exon 12351 14748 . + 60 gene_id "ENST00000361567.2"; transcript_id "81c2d0d9-44c7-4f0a-bb58-7b0ab49220a5"; exon_number "0"; +chrM FLAIR transcript 15972 16569 . + . gene_id "chrM:15000"; transcript_id "2f14a1a9-c356-4568-9a4e-150c8d2038d0"; +chrM FLAIR exon 15972 16569 . + 60 gene_id "chrM:15000"; transcript_id "2f14a1a9-c356-4568-9a4e-150c8d2038d0"; exon_number "0";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair_all_corrected.bed Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,1340 @@ +chrM 569 1461 1fb96112-b5ee-46ac-9ca4-c3e170512e4d;0 60 + 569 1461 99,99,99 1 892, 0, +chrM 570 1631 ca7655f0-1077-4546-850f-be0f10f50a81;0 60 + 570 1631 99,99,99 1 1061, 0, +chrM 570 3149 07a2d20a-8f33-4283-87e2-ee2b28b771f2;0 60 + 570 3149 99,99,99 1 2579, 0, +chrM 571 1180 fd4b26fc-72f9-4060-8c6d-deca2e55cceb;0 60 + 571 1180 99,99,99 1 609, 0, +chrM 571 1041 ec1423b2-49e7-4751-81b6-39614fd8991d;0 60 + 571 1041 99,99,99 1 470, 0, +chrM 578 1601 550708cd-84a1-40c0-aed9-b6b38faca411;0 49 + 578 1601 99,99,99 1 1023, 0, +chrM 658 1215 2dc80131-77c9-4dd4-b6ab-26de0d91afc5;0 60 + 658 1215 99,99,99 1 557, 0, +chrM 660 1118 31d34648-3f54-4a65-9878-2ae72795dba4;0 58 + 660 1118 99,99,99 1 458, 0, +chrM 661 1258 f7ee2b0a-5e47-4c55-a70b-60fc2a8d9d5f;0 52 + 661 1258 99,99,99 1 597, 0, +chrM 661 1191 385a6115-47fa-45f1-a64e-6bf9e9e8f716;0 60 + 661 1191 99,99,99 1 530, 0, +chrM 661 1341 f3b281ca-2587-46ce-8f37-4019909debad;0 6 + 661 1341 99,99,99 1 680, 0, +chrM 661 1214 0dea8b5d-78d3-42d6-9284-458c574f8e26;0 60 + 661 1214 99,99,99 1 553, 0, +chrM 661 1223 3f02c2e6-10dc-426b-b9dd-dd180be4d84d;0 55 + 661 1223 99,99,99 1 562, 0, +chrM 661 1236 4d24b700-6645-44a4-bdeb-c8f1f82fd43a;0 60 + 661 1236 99,99,99 1 575, 0, +chrM 661 1215 a3113469-53e5-4399-8dd1-3e80e6cd4840;0 42 + 661 1215 99,99,99 1 554, 0, +chrM 661 1562 c2ac6756-bf06-40ee-b116-629cb06dc938;0 60 + 661 1562 99,99,99 1 901, 0, +chrM 661 1365 36639f99-fc00-48ae-9e41-a716f3c85183;0 60 + 661 1365 99,99,99 1 704, 0, +chrM 661 1218 16c2c9d6-4694-4810-9277-dcfb6c0bf1be;0 60 + 661 1218 99,99,99 1 557, 0, +chrM 661 1300 f189c761-c080-4b56-a655-f9510205a098;0 60 + 661 1300 99,99,99 1 639, 0, +chrM 661 1476 56c4f0a0-919a-47d7-9301-efedea78d911;0 58 + 661 1476 99,99,99 1 815, 0, +chrM 661 1319 1eac4a10-986b-4f42-b3dd-3e2b607fea06;0 60 + 661 1319 99,99,99 1 658, 0, +chrM 661 1042 6ba621b6-fd6c-4796-adbf-067fcf2e5056;0 60 + 661 1042 99,99,99 1 381, 0, +chrM 661 1231 94ed9dc9-c718-4cb6-a1a1-9d09589a85de;0 60 + 661 1231 99,99,99 1 570, 0, +chrM 661 1000 3978ce5e-977d-4ba4-9f8c-3964a85eb6a2;0 51 + 661 1000 99,99,99 1 339, 0, +chrM 663 1119 3364bed4-f737-4e16-a4ff-4e040854792a;0 60 + 663 1119 99,99,99 1 456, 0, +chrM 667 1479 bb9afd60-09db-421c-ab2e-82246c288f76;0 60 + 667 1479 99,99,99 1 812, 0, +chrM 670 1191 8645727c-31ca-40c3-ba14-b55aceeaaf24;0 60 + 670 1191 99,99,99 1 521, 0, +chrM 670 1188 e1e06242-962d-4c16-adf2-b9c2d04393e7;0 60 + 670 1188 99,99,99 1 518, 0, +chrM 671 1033 becad4cf-9e68-43ac-b445-50c77d90599b;0 24 + 671 1033 99,99,99 1 362, 0, +chrM 672 1237 5f0a6f3e-08b6-43fb-b2fe-6a22d69b9f13;0 20 + 672 1237 99,99,99 1 565, 0, +chrM 682 1229 f7783e60-4446-471d-be7a-768b6076b0b1;0 60 + 682 1229 99,99,99 1 547, 0, +chrM 683 1157 e874ce99-235c-4fc9-8d00-1917eda2b03f;0 56 + 683 1157 99,99,99 1 474, 0, +chrM 709 1003 6570595e-650e-4b85-9e7e-723b9a727b28;0 60 + 709 1003 99,99,99 1 294, 0, +chrM 722 1001 78fd7765-20aa-4906-b329-cbeef0a1a84b;0 60 + 722 1001 99,99,99 1 279, 0, +chrM 736 1027 90fef919-6bc3-48f9-85c8-87d8a5251967;0 60 + 736 1027 99,99,99 1 291, 0, +chrM 743 1194 038a94b2-8d27-48e9-b319-8f5afab370de;0 47 + 743 1194 99,99,99 1 451, 0, +chrM 843 1182 11555bed-0cd5-466b-bc33-e1471c67069f;0 60 + 843 1182 99,99,99 1 339, 0, +chrM 853 1601 bd1bd54a-7196-440b-a210-9049b19561f2;0 60 + 853 1601 99,99,99 1 748, 0, +chrM 873 1371 a470bde4-ddda-452d-9960-34ae9bb8d8cd;0 42 + 873 1371 99,99,99 1 498, 0, +chrM 883 1601 8fef762f-f8ee-4493-afcf-3876480619d9;0 60 + 883 1601 99,99,99 1 718, 0, +chrM 899 1514 75c7d0bb-b9c9-44f4-a7cc-0c90b2939b1a;0 41 + 899 1514 99,99,99 1 615, 0, +chrM 905 1480 91067ece-d6e2-4755-9d58-7ce8c5e1269d;0 47 + 905 1480 99,99,99 1 575, 0, +chrM 906 1600 2a2aa7e2-9392-4d18-80c2-6ecb196f0c3a;0 21 + 906 1600 99,99,99 1 694, 0, +chrM 916 1404 88e10926-72ef-44e0-8aea-3087ae881943;0 60 + 916 1404 99,99,99 1 488, 0, +chrM 933 1340 4eca6002-439f-4e4c-985d-49836304090a;0 41 + 933 1340 99,99,99 1 407, 0, +chrM 1002 1183 a98eb040-7def-41e7-875f-869f697626e0;0 28 + 1002 1183 99,99,99 1 181, 0, +chrM 1013 1534 24a31559-977b-469a-8322-7eebcf717043;0 42 + 1013 1534 99,99,99 1 521, 0, +chrM 1015 1244 5fb65ab7-b06e-47c8-bfab-adab22e2e6cd;0 16 + 1015 1244 99,99,99 1 229, 0, +chrM 1021 1254 64d410ad-1910-4986-bd37-1f095480884b;0 15 - 1021 1254 217,95,2 1 233, 0, +chrM 1239 1601 f08d4285-b69f-489c-99e6-ab9745ea4e41;0 60 + 1239 1601 99,99,99 1 362, 0, +chrM 1274 1481 d1fdb276-6f96-4a3f-897e-c96a301cb13a;0 56 + 1274 1481 99,99,99 1 207, 0, +chrM 1286 1601 6dc7c596-b85e-4fc6-b710-b100dfc96594;0 56 + 1286 1601 99,99,99 1 315, 0, +chrM 1401 1558 380f5644-b809-4794-94ee-ad8fa6a9a8c2;0 44 + 1401 1558 99,99,99 1 157, 0, +chrM 1453 1601 86b4b1b2-2a5d-45f8-9aac-a108282ae669;0 29 + 1453 1601 99,99,99 1 148, 0, +chrM 1681 3186 4dbf4903-6d11-4ab5-9ab8-ed3dd4fb8d4b;0 60 + 1681 3186 99,99,99 1 1505, 0, +chrM 1681 1892 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913, 0, +chrM 14757 15822 a6f7c93a-69a7-494b-a49a-eb8a64ce3918;0 60 + 14757 15822 99,99,99 1 1065, 0, +chrM 14757 15856 01c13ab7-ef27-4e62-ac39-638653276f7e;0 60 + 14757 15856 99,99,99 1 1099, 0, +chrM 14757 15869 5dac3f00-ff98-4945-944e-71670bc92587;0 60 + 14757 15869 99,99,99 1 1112, 0, +chrM 14758 15887 d69cbde2-2d60-4e19-ac83-817b0c69f28e;0 60 + 14758 15887 99,99,99 1 1129, 0, +chrM 14758 15886 016bc55b-7a52-4f24-b3d6-9132df099d80;0 60 + 14758 15886 99,99,99 1 1128, 0, +chrM 14758 15883 64e15f2e-0069-43b5-9dab-7940ef61c849;0 60 + 14758 15883 99,99,99 1 1125, 0, +chrM 14758 15887 6f6d8722-287e-4445-a9c8-94238428138f;0 60 + 14758 15887 99,99,99 1 1129, 0, +chrM 14758 15879 c072360c-3ac0-4097-8733-362a494a988e;0 60 + 14758 15879 99,99,99 1 1121, 0, +chrM 14760 15887 45bb9527-2be5-4272-b819-48a7971c6fbe;0 60 + 14760 15887 99,99,99 1 1127, 0, +chrM 14760 15883 7f6ec223-0a7f-415e-bdd8-0b2e2c4985ff;0 60 + 14760 15883 99,99,99 1 1123, 0, +chrM 14761 15847 95cb889c-4a97-4c29-a77c-3312a219a6ad;0 60 + 14761 15847 99,99,99 1 1086, 0, +chrM 14766 15887 f81dd59c-c08b-4c7d-8c23-1e47857afb92;0 60 + 14766 15887 99,99,99 1 1121, 0, +chrM 14766 15887 4a1cc098-aa5d-4ad9-87a6-fba57c10c7d7;0 60 + 14766 15887 99,99,99 1 1121, 0, +chrM 14770 15887 ce4659c3-382a-4361-b5ea-28c442883218;0 60 + 14770 15887 99,99,99 1 1117, 0, +chrM 14770 16075 90808752-db98-4215-b707-b0944c0a7272;0 60 + 14770 16075 99,99,99 1 1305, 0, +chrM 14778 14984 774ce748-fca6-4046-8daa-da7c6e91765a;0 60 + 14778 14984 99,99,99 1 206, 0, +chrM 14846 15115 76dc9f46-8b7b-48a8-9225-bca23777bda2;0 60 + 14846 15115 99,99,99 1 269, 0, +chrM 14924 15659 79eea848-d3ff-4e7b-9c01-9a3710c20732;0 60 + 14924 15659 99,99,99 1 735, 0, +chrM 14982 15842 dd484c35-375e-47a8-b9e8-31c0b4d39b4b;0 60 + 14982 15842 99,99,99 1 860, 0, +chrM 15009 15887 3bd3e3d3-132c-43e2-872a-8a41e25d8805;0 60 + 15009 15887 99,99,99 1 878, 0, +chrM 15169 15886 cdb71c09-5f6e-4145-99c6-3e0cbfd90739;0 60 + 15169 15886 99,99,99 1 717, 0, +chrM 15194 15883 2622775b-65c9-4cae-9a3b-c6be3e0faa17;0 60 + 15194 15883 99,99,99 1 689, 0, +chrM 15213 15876 3b1ef952-41fe-4d83-808c-76caa7f7b83d;0 60 + 15213 15876 99,99,99 1 663, 0, +chrM 15461 15887 9f0d3300-a9c3-41aa-af9b-00403ffbeacb;0 60 + 15461 15887 99,99,99 1 426, 0, +chrM 15496 15876 fbd51668-5fe6-431a-ad8b-fe1165eebf19;0 60 + 15496 15876 99,99,99 1 380, 0, +chrM 15587 15887 3c97e997-9eed-405b-b40e-28122064980c;0 60 + 15587 15887 99,99,99 1 300, 0, +chrM 15589 15887 32c06f69-94bc-4023-8ae7-f66dc584d355;0 30 + 15589 15887 99,99,99 1 298, 0, +chrM 15670 15874 4a827e6b-259e-4723-8860-f978ceaaa5f7;0 58 + 15670 15874 99,99,99 1 204, 0, +chrM 15695 15877 7e44209b-aae3-4993-91e4-fe5b37ab2eb2;0 55 + 15695 15877 99,99,99 1 182, 0, +chrM 15800 16569 a78fb847-612c-42c0-9b73-d59b91a9e9df;0 60 + 15800 16569 99,99,99 1 769, 0, +chrM 15963 16569 f6bd411a-d419-4197-a525-324568f7944a;0 60 + 15963 16569 99,99,99 1 606, 0, +chrM 15963 16540 ccdfb0ae-54fb-4e3d-8f92-587d4cdc7141;0 60 + 15963 16540 99,99,99 1 577, 0, +chrM 15968 16271 37432238-4f0a-4817-b648-73cb476a71d7;0 60 + 15968 16271 99,99,99 1 303, 0, +chrM 15970 16311 a446bc9e-f22d-40ca-a502-d78b06fc8dd4;0 60 + 15970 16311 99,99,99 1 341, 0, +chrM 15970 16557 2f14a1a9-c356-4568-9a4e-150c8d2038d0;0 60 + 15970 16557 99,99,99 1 587, 0, +chrM 15970 16296 19cc5328-7604-445f-b261-7e71a02273c6;0 60 + 15970 16296 99,99,99 1 326, 0, +chrM 15971 16569 46a0710f-c426-4f83-902b-a99be8273b34;0 60 + 15971 16569 99,99,99 1 598, 0, +chrM 15971 16569 d52a572f-79ca-4109-a247-55ab7b0ceda6;0 60 + 15971 16569 99,99,99 1 598, 0, +chrM 15972 16569 8bf3eb49-3aeb-4bc6-9bcc-1cfb1a896618;0 60 + 15972 16569 99,99,99 1 597, 0, +chrM 15976 16291 f051705e-4230-4631-84e3-7e014eb98f35;0 48 + 15976 16291 99,99,99 1 315, 0,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair_all_inconsistent.bed Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,8 @@ +chrM 1692 16233 8e95941f-3681-40f9-98c2-f5dee4c29acd;0 60 + 1692 16233 27,158,119 2 881,20, 0,14521, +chrM 2011 10881 4d2c4cb6-5652-4bff-aeaa-1a7501b9203e;0 60 + 2011 10881 99,99,99 2 1237,30, 0,8840, +chrM 3258 4226 a6aa00e3-7d42-431e-aa9b-f974416c184b;0 60 - 3258 4226 217,95,2 2 563,338, 0,630, +chrM 3328 4257 c2a3dfdd-b7b9-4af8-b933-d7042384d0cc;0 60 - 3328 4257 217,95,2 2 187,628, 0,301, +chrM 4482 9899 d49d098d-20e2-471c-b621-aea607dcf717;0 58 - 4482 9899 217,95,2 2 1016,46, 0,5371, +chrM 4737 8145 8c9e8a40-b47d-43f7-bc54-d15976e27c0c;0 60 - 4737 8145 217,95,2 2 725,15, 0,3393, +chrM 5911 12712 78cc6deb-e14a-479f-a24e-7941deded72c;0 60 + 5911 12712 27,158,119 2 1609,72, 0,6729, +chrM 11384 12143 af53d265-544a-420b-ae7b-8b56aebe1ac7;0 60 - 11384 12143 217,95,2 2 65,642, 0,117,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,7 @@ +<tables> + <!-- Location of SAMTools indexes for FASTA files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,6 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> +</tables>