changeset 0:6927379c9ede draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
author iuc
date Fri, 27 Nov 2020 21:55:45 +0000
parents
children c784170f3b5e
files 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 16 files changed, 3416 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flair_correct.xml	Fri Nov 27 21:55:45 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 21:55:45 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 21:55:45 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"; transcript_id "ENST00000361390.2"; 
+chrM	hg38_knownGene	exon	3307	4262	0.000000	+	.	gene_id "ENST00000361390.2"; transcript_id "ENST00000361390.2"; 
+chrM	hg38_knownGene	exon	4263	4331	0.000000	+	.	gene_id "ENST00000387365.1"; transcript_id "ENST00000387365.1"; 
+chrM	hg38_knownGene	exon	4329	4400	0.000000	-	.	gene_id "ENST00000387372.1"; transcript_id "ENST00000387372.1"; 
+chrM	hg38_knownGene	exon	4402	4469	0.000000	+	.	gene_id "ENST00000387377.1"; transcript_id "ENST00000387377.1"; 
+chrM	hg38_knownGene	start_codon	4470	4472	0.000000	+	.	gene_id "ENST00000361453.3"; transcript_id "ENST00000361453.3"; 
+chrM	hg38_knownGene	CDS	4470	5508	0.000000	+	0	gene_id "ENST00000361453.3"; transcript_id "ENST00000361453.3"; 
+chrM	hg38_knownGene	stop_codon	5509	5511	0.000000	+	.	gene_id "ENST00000361453.3"; transcript_id "ENST00000361453.3"; 
+chrM	hg38_knownGene	exon	4470	5511	0.000000	+	.	gene_id "ENST00000361453.3"; transcript_id "ENST00000361453.3"; 
+chrM	hg38_knownGene	exon	5512	5579	0.000000	+	.	gene_id "ENST00000387382.1"; transcript_id "ENST00000387382.1"; 
+chrM	hg38_knownGene	exon	5587	5655	0.000000	-	.	gene_id "ENST00000387392.1"; transcript_id "ENST00000387392.1"; 
+chrM	hg38_knownGene	exon	5657	5729	0.000000	-	.	gene_id "ENST00000387400.1"; transcript_id "ENST00000387400.1"; 
+chrM	hg38_knownGene	exon	5761	5826	0.000000	-	.	gene_id "ENST00000387405.1"; transcript_id "ENST00000387405.1"; 
+chrM	hg38_knownGene	exon	5826	5891	0.000000	-	.	gene_id "ENST00000387409.1"; transcript_id "ENST00000387409.1"; 
+chrM	hg38_knownGene	start_codon	5904	5906	0.000000	+	.	gene_id "ENST00000361624.2"; transcript_id "ENST00000361624.2"; 
+chrM	hg38_knownGene	CDS	5904	7442	0.000000	+	0	gene_id "ENST00000361624.2"; transcript_id "ENST00000361624.2"; 
+chrM	hg38_knownGene	stop_codon	7443	7445	0.000000	+	.	gene_id "ENST00000361624.2"; transcript_id "ENST00000361624.2"; 
+chrM	hg38_knownGene	exon	5904	7445	0.000000	+	.	gene_id "ENST00000361624.2"; transcript_id "ENST00000361624.2"; 
+chrM	hg38_knownGene	exon	7446	7514	0.000000	-	.	gene_id "ENST00000387416.2"; transcript_id "ENST00000387416.2"; 
+chrM	hg38_knownGene	exon	7518	7585	0.000000	+	.	gene_id "ENST00000387419.1"; transcript_id "ENST00000387419.1"; 
+chrM	hg38_knownGene	start_codon	7586	7588	0.000000	+	.	gene_id "ENST00000361739.1"; transcript_id "ENST00000361739.1"; 
+chrM	hg38_knownGene	CDS	7586	8266	0.000000	+	0	gene_id "ENST00000361739.1"; transcript_id "ENST00000361739.1"; 
+chrM	hg38_knownGene	stop_codon	8267	8269	0.000000	+	.	gene_id "ENST00000361739.1"; transcript_id "ENST00000361739.1"; 
+chrM	hg38_knownGene	exon	7586	8269	0.000000	+	.	gene_id "ENST00000361739.1"; transcript_id "ENST00000361739.1"; 
+chrM	hg38_knownGene	exon	8295	8364	0.000000	+	.	gene_id "ENST00000387421.1"; transcript_id "ENST00000387421.1"; 
+chrM	hg38_knownGene	start_codon	8366	8368	0.000000	+	.	gene_id "ENST00000361851.1"; transcript_id "ENST00000361851.1"; 
+chrM	hg38_knownGene	CDS	8366	8569	0.000000	+	0	gene_id "ENST00000361851.1"; transcript_id "ENST00000361851.1"; 
+chrM	hg38_knownGene	stop_codon	8570	8572	0.000000	+	.	gene_id "ENST00000361851.1"; transcript_id "ENST00000361851.1"; 
+chrM	hg38_knownGene	exon	8366	8572	0.000000	+	.	gene_id "ENST00000361851.1"; transcript_id "ENST00000361851.1"; 
+chrM	hg38_knownGene	start_codon	8527	8529	0.000000	+	.	gene_id "ENST00000361899.2"; transcript_id "ENST00000361899.2"; 
+chrM	hg38_knownGene	CDS	8527	9204	0.000000	+	0	gene_id "ENST00000361899.2"; transcript_id "ENST00000361899.2"; 
+chrM	hg38_knownGene	stop_codon	9205	9207	0.000000	+	.	gene_id "ENST00000361899.2"; transcript_id "ENST00000361899.2"; 
+chrM	hg38_knownGene	exon	8527	9207	0.000000	+	.	gene_id "ENST00000361899.2"; transcript_id "ENST00000361899.2"; 
+chrM	hg38_knownGene	start_codon	9207	9209	0.000000	+	.	gene_id "ENST00000362079.2"; transcript_id "ENST00000362079.2"; 
+chrM	hg38_knownGene	CDS	9207	9987	0.000000	+	0	gene_id "ENST00000362079.2"; transcript_id "ENST00000362079.2"; 
+chrM	hg38_knownGene	stop_codon	9988	9990	0.000000	+	.	gene_id "ENST00000362079.2"; transcript_id "ENST00000362079.2"; 
+chrM	hg38_knownGene	exon	9207	9990	0.000000	+	.	gene_id "ENST00000362079.2"; transcript_id "ENST00000362079.2"; 
+chrM	hg38_knownGene	exon	9991	10058	0.000000	+	.	gene_id "ENST00000387429.1"; transcript_id "ENST00000387429.1"; 
+chrM	hg38_knownGene	start_codon	10059	10061	0.000000	+	.	gene_id "ENST00000361227.2"; transcript_id "ENST00000361227.2"; 
+chrM	hg38_knownGene	CDS	10059	10401	0.000000	+	0	gene_id "ENST00000361227.2"; transcript_id "ENST00000361227.2"; 
+chrM	hg38_knownGene	stop_codon	10402	10404	0.000000	+	.	gene_id "ENST00000361227.2"; transcript_id "ENST00000361227.2"; 
+chrM	hg38_knownGene	exon	10059	10404	0.000000	+	.	gene_id "ENST00000361227.2"; transcript_id "ENST00000361227.2"; 
+chrM	hg38_knownGene	exon	10405	10469	0.000000	+	.	gene_id "ENST00000387439.1"; transcript_id "ENST00000387439.1"; 
+chrM	hg38_knownGene	start_codon	10470	10472	0.000000	+	.	gene_id "ENST00000361335.1"; transcript_id "ENST00000361335.1"; 
+chrM	hg38_knownGene	CDS	10470	10763	0.000000	+	0	gene_id "ENST00000361335.1"; transcript_id "ENST00000361335.1"; 
+chrM	hg38_knownGene	stop_codon	10764	10766	0.000000	+	.	gene_id "ENST00000361335.1"; transcript_id "ENST00000361335.1"; 
+chrM	hg38_knownGene	exon	10470	10766	0.000000	+	.	gene_id "ENST00000361335.1"; transcript_id "ENST00000361335.1"; 
+chrM	hg38_knownGene	start_codon	10760	10762	0.000000	+	.	gene_id "ENST00000361381.2"; transcript_id "ENST00000361381.2"; 
+chrM	hg38_knownGene	CDS	10760	12134	0.000000	+	0	gene_id "ENST00000361381.2"; transcript_id "ENST00000361381.2"; 
+chrM	hg38_knownGene	stop_codon	12135	12137	0.000000	+	.	gene_id "ENST00000361381.2"; transcript_id "ENST00000361381.2"; 
+chrM	hg38_knownGene	exon	10760	12137	0.000000	+	.	gene_id "ENST00000361381.2"; transcript_id "ENST00000361381.2"; 
+chrM	hg38_knownGene	exon	12138	12206	0.000000	+	.	gene_id "ENST00000387441.1"; transcript_id "ENST00000387441.1"; 
+chrM	hg38_knownGene	exon	12207	12265	0.000000	+	.	gene_id "ENST00000387449.1"; transcript_id "ENST00000387449.1"; 
+chrM	hg38_knownGene	exon	12266	12336	0.000000	+	.	gene_id "ENST00000387456.1"; transcript_id "ENST00000387456.1"; 
+chrM	hg38_knownGene	start_codon	12337	12339	0.000000	+	.	gene_id "ENST00000361567.2"; transcript_id "ENST00000361567.2"; 
+chrM	hg38_knownGene	CDS	12337	14145	0.000000	+	0	gene_id "ENST00000361567.2"; transcript_id "ENST00000361567.2"; 
+chrM	hg38_knownGene	stop_codon	14146	14148	0.000000	+	.	gene_id "ENST00000361567.2"; transcript_id "ENST00000361567.2"; 
+chrM	hg38_knownGene	exon	12337	14148	0.000000	+	.	gene_id "ENST00000361567.2"; transcript_id "ENST00000361567.2"; 
+chrM	hg38_knownGene	stop_codon	14149	14151	0.000000	-	.	gene_id "ENST00000361681.2"; transcript_id "ENST00000361681.2"; 
+chrM	hg38_knownGene	CDS	14152	14673	0.000000	-	0	gene_id "ENST00000361681.2"; transcript_id "ENST00000361681.2"; 
+chrM	hg38_knownGene	start_codon	14671	14673	0.000000	-	.	gene_id "ENST00000361681.2"; transcript_id "ENST00000361681.2"; 
+chrM	hg38_knownGene	exon	14149	14673	0.000000	-	.	gene_id "ENST00000361681.2"; transcript_id "ENST00000361681.2"; 
+chrM	hg38_knownGene	exon	14674	14742	0.000000	-	.	gene_id "ENST00000387459.1"; transcript_id "ENST00000387459.1"; 
+chrM	hg38_knownGene	start_codon	14747	14749	0.000000	+	.	gene_id "ENST00000361789.2"; 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 21:55:45 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	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,
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+chrM	13607	14678	27d0e30a-e65c-423d-992b-5483d5565923;0	60	+	13607	14678	99,99,99	1	1071,	0,
+chrM	13624	14538	b9308c6b-1169-48d8-a657-89ae33060235;0	60	+	13624	14538	99,99,99	1	914,	0,
+chrM	13682	14507	59fea62b-afca-4ff2-860b-d993a0659919;0	60	+	13682	14507	99,99,99	1	825,	0,
+chrM	13688	14674	3e7180dd-ea32-4deb-8129-d4f807e1efc8;0	60	+	13688	14674	99,99,99	1	986,	0,
+chrM	14536	14748	78f8ac46-b6ce-4b75-b744-2276333f79ea;0	60	+	14536	14748	99,99,99	1	212,	0,
+chrM	14541	14728	2e4d800c-7943-493e-8525-6caf58bbc02f;0	60	+	14541	14728	99,99,99	1	187,	0,
+chrM	14552	14738	595b9542-db2b-47fc-aaa5-5fee9b7b3c16;0	60	+	14552	14738	99,99,99	1	186,	0,
+chrM	14757	15887	22eceb47-b528-4c39-8254-0d60a604bd3f;0	60	+	14757	15887	99,99,99	1	1130,	0,
+chrM	14757	15887	cf24a281-b665-4b8f-a3a3-528576c3067c;0	60	+	14757	15887	99,99,99	1	1130,	0,
+chrM	14757	16045	fb76bcd3-041c-4e20-9175-ae434cbb3210;0	60	+	14757	16045	99,99,99	1	1288,	0,
+chrM	14757	15670	f993603f-03f0-4fe4-9de0-4de82f7a0d0d;0	60	+	14757	15670	99,99,99	1	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/chrM.fa	Fri Nov 27 21:55:45 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 21:55:45 2020 +0000
@@ -0,0 +1,1 @@
+chrM	16569	6	50	51
Binary file test-data/chrM.fastq.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc	Fri Nov 27 21:55:45 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 21:55:45 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 21:55:45 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 21:55:45 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 21:55:45 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,
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+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 21:55:45 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 21:55:45 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 21:55:45 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 21:55:45 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>