# HG changeset patch
# User bgruening
# Date 1670255287 0
# Node ID 7e50e8d920dbc42810120f6f5bd767b444012e1b
# Parent  88c07fc4024cd137490412ceeaea988c238e99ca
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042

diff -r 88c07fc4024c -r 7e50e8d920db macros.xml
--- a/macros.xml	Thu Jul 22 14:06:29 2021 +0000
+++ b/macros.xml	Mon Dec 05 15:48:07 2022 +0000
@@ -1,16 +1,17 @@
 <macros>
-    <token name="@VERSION@">1.5.1</token>
-    <token name="@GALAXY_VERSION@">galaxy0</token>
+    <token name="@TOOL_VERSION@">1.9.0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@IDX_VERSION@">q7</token>
     <token name="@PROFILE_VERSION@">20.01</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">salmon</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
             <requirement type="package" version="1.3">seqtk</requirement>
-            <requirement type="package" version="1.12">samtools</requirement>
+            <requirement type="package" version="1.16.1">samtools</requirement>
             <requirement type="package" version="0.2.0">vpolo</requirement>
-            <requirement type="package" version="1.3.0">pandas</requirement>
-            <requirement type="package" version="1.7.0">scipy</requirement>
+            <requirement type="package" version="1.5.2">pandas</requirement>
+            <requirement type="package" version="3.0.0">graphviz</requirement>
+            <requirement type="package" version="1.9.3">scipy</requirement>
         </requirements>
     </xml>
     <xml name="orient">
@@ -72,10 +73,14 @@
             </when>  <!-- build-in -->
             <when value="history">
                 <section name="s_index" title="Salmon index" expanded="true">
-                    <param name="fasta" type="data" format="fasta" label="Transcripts fasta file"/>
+                    <param name="fasta" type="data" format="fasta" label="Transcripts FASTA file"/>
+                    <param name="genome" type="data" format="fasta" optional="true" label="Reference genome" 
+                        help="The reference genome is required for generating a decoy-away index. The decoy sequences are regions of the target genome 
+                            that are sequence similar to annotated transcripts. These are the regions of the genome most likely to cause mismapping." />
                     <param name="kmer" type="integer" value="31" label="Kmer length"/>
                     <param name="phash" type="boolean" label="Perfect Hash" truevalue="--perfectHash" falsevalue="" checked="false"
-                        help="Build the index using a perfect hash rather than a dense hash.  This will require less memory (especially during quantification), but will take longer to construct"/>
+                        help="Build the index using a perfect hash rather than a dense hash.  This will require less memory (especially during quantification), 
+                            but will take longer to construct"/>
                 </section>
             </when>
         </conditional>
@@ -155,9 +160,20 @@
         <param name="dovetail" label="Allow Dovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False" help="Allow dovetail mappings"/>
         <param name="recoverOrphans" label="Recover Orphans" type="boolean" truevalue="--recoverOrphans" falsevalue="" checked="False"
         help="Attempt to recover the mates of orphaned reads. This uses edlib for orphan recovery, and so introduces some computational overhead, but it can improve sensitivity."/>
-        <param name="writeMappings" type="boolean" truevalue="--writeMappings=./output/samout.sam" falsevalue="" checked="False"
-        label="Write Mappings to Bam File"
-        help="If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format.  By default, output will be directed to stdout, but an alternative file name can be provided instead"/>
+        <conditional name="bam_options">
+            <param argument="--writeMappings" type="select" label="Write Mappings to BAM File" help="If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format.  By default, output will be directed to stdout, but an alternative file name can be provided instead">
+                <option value="--writeMappings=./output/samout.sam">Enabled</option>
+                <option value="" selected="true">Disabled</option>
+            </param>
+            <when value="--writeMappings=./output/samout.sam">
+                <param argument="--writeQualities" type="boolean" truevalue="--writeQualities" falsevalue="" checked="false" label="Write qualities" help="If this flag is 
+                provided, then the output SAM file will contain quality strings as well as read sequences." />
+            </when>
+            <when value=""/>
+        </conditional>
+        <param name="writeMappings" type="boolean" truevalue="" falsevalue="" checked="False"
+            label="Write Mappings to Bam File"
+            help="If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format.  By default, output will be directed to stdout, but an alternative file name can be provided instead"/>
         <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
         label="Consistent Hits"
         help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/>
@@ -315,10 +331,21 @@
         mkdir ./index &&
         mkdir ./output &&
         #if $quant_type.refTranscriptSource.TranscriptSource != "indexed":
+            #if $quant_type.refTranscriptSource.s_index.genome
+                cat '${quant_type.refTranscriptSource.s_index.genome}' | grep "^>" | cut -d " " -f 1 > 'decoys.txt' &&
+                sed -i.bak -e 's/>//g' 'decoys.txt' &&
+                cat '${quant_type.refTranscriptSource.s_index.fasta}' '${quant_type.refTranscriptSource.s_index.genome}' > 'input_index.fasta' &&
+            #else
+                ln -s '${quant_type.refTranscriptSource.s_index.fasta}' 'input_index.fasta' &&
+            #end if
             salmon index -i ./index
                 --kmerLen '${quant_type.refTranscriptSource.s_index.kmer}'
                 --gencode
-                --transcripts '${quant_type.refTranscriptSource.s_index.fasta}'
+                --threads "\${GALAXY_SLOTS:-4}"
+                --transcripts 'input_index.fasta'
+                #if $quant_type.refTranscriptSource.s_index.genome
+                    --decoy 'decoys.txt'
+                #end if
             &&
             #set $index_path = './index'
         #else
@@ -453,7 +480,10 @@
             #end if
             ${quant_type.dovetail}
             ${quant_type.recoverOrphans}
-            ${quant_type.writeMappings}
+            ${quant_type.bam_options.writeMappings}
+            #if $quant_type.bam_options.writeMappings:
+                ${quant_type.bam_options.writeQualities}
+            #end if
             ${quant_type.consistentHits}
             #if $quant_type.quasiCoverage:
                 --quasiCoverage '${quant_type.quasiCoverage}'
diff -r 88c07fc4024c -r 7e50e8d920db salmonquantmerge.xml
--- a/salmonquantmerge.xml	Thu Jul 22 14:06:29 2021 +0000
+++ b/salmonquantmerge.xml	Mon Dec 05 15:48:07 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="salmonquantmerge" name="Salmon quantmerge" version="@VERSION@+@GALAXY_VERSION@" profile="@PROFILE_VERSION@">
+<tool id="salmonquantmerge" name="Salmon quantmerge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">
     <description>Merge multiple quantification results into a single file</description>
     <macros>
         <import>macros.xml</import>
diff -r 88c07fc4024c -r 7e50e8d920db test-data/alevin_mat.mtx
--- a/test-data/alevin_mat.mtx	Thu Jul 22 14:06:29 2021 +0000
+++ b/test-data/alevin_mat.mtx	Mon Dec 05 15:48:07 2022 +0000
@@ -1,5 +1,5 @@
 %%MatrixMarket	matrix	coordinate	real	general
-95	61	99
+14	61	15
 1	9	1.000000
 2	28	1.000000
 3	38	1.000000
@@ -11,91 +11,7 @@
 9	28	1.000000
 10	30	1.000000
 11	53	1.000000
-12	4	1.000000
+12	3	0.500000
+12	4	0.500000
 13	28	1.000000
 14	56	1.000000
-15	9	1.000000
-16	43	0.500000
-16	45	0.500000
-17	42	0.500000
-17	44	0.500000
-18	28	1.000000
-19	46	1.000000
-20	38	1.000000
-21	40	1.000000
-22	19	1.000000
-23	9	1.000000
-24	56	1.000000
-25	8	1.000000
-26	28	1.000000
-27	53	1.000000
-28	56	1.000000
-29	28	1.000000
-30	30	1.000000
-31	38	1.000000
-32	28	1.000000
-33	30	1.000000
-34	34	1.000000
-35	30	1.000000
-36	28	1.000000
-37	34	1.000000
-38	16	1.000000
-39	19	1.000000
-40	47	1.000000
-41	38	1.000000
-42	28	1.000000
-43	56	1.000000
-44	28	1.000000
-45	9	1.000000
-46	19	1.000000
-47	23	1.000000
-48	43	0.500000
-48	45	0.500000
-49	38	1.000000
-50	57	1.000000
-51	40	1.000000
-52	38	1.000000
-53	19	1.000000
-54	16	1.000000
-55	15	1.000000
-56	56	1.000000
-57	53	1.000000
-58	30	1.000000
-59	9	1.000000
-60	34	1.000000
-61	30	1.000000
-62	24	1.000000
-63	30	1.000000
-64	56	1.000000
-65	9	1.000000
-66	23	1.000000
-67	61	1.000000
-68	38	1.000000
-69	21	1.000000
-70	38	1.000000
-71	38	1.000000
-72	16	1.000000
-73	30	1.000000
-74	16	1.000000
-75	30	1.000000
-76	40	1.000000
-77	52	1.000000
-78	53	1.000000
-79	42	0.500000
-79	44	0.500000
-80	34	1.000000
-81	9	1.000000
-82	15	1.000000
-83	45	1.000000
-84	47	1.000000
-85	40	1.000000
-86	56	1.000000
-87	56	1.000000
-88	34	1.000000
-89	56	1.000000
-90	38	1.000000
-91	53	1.000000
-92	56	1.000000
-93	53	1.000000
-94	38	1.000000
-95	53	1.000000
diff -r 88c07fc4024c -r 7e50e8d920db test-data/alevin_mat_01.mtx
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alevin_mat_01.mtx	Mon Dec 05 15:48:07 2022 +0000
@@ -0,0 +1,105 @@
+%%MatrixMarket	matrix	coordinate	real	general
+96	61	103
+1	9	1.000000
+2	28	1.000000
+3	38	1.000000
+4	28	1.000000
+5	42	1.000000
+6	9	1.000000
+7	56	1.000000
+8	28	1.000000
+9	28	1.000000
+10	30	1.000000
+11	53	1.000000
+12	3	0.500000
+12	4	0.500000
+13	28	1.000000
+14	56	1.000000
+15	9	1.000000
+16	43	0.500000
+16	45	0.500000
+17	42	0.500000
+17	44	0.500000
+18	28	1.000000
+19	46	1.000000
+20	38	1.000000
+21	40	1.000000
+22	19	1.000000
+23	9	1.000000
+24	56	1.000000
+25	8	1.000000
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+27	53	1.000000
+28	56	1.000000
+29	28	1.000000
+30	30	1.000000
+31	38	1.000000
+32	28	1.000000
+33	30	1.000000
+34	34	1.000000
+35	30	1.000000
+36	28	1.000000
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+40	47	1.000000
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+42	28	1.000000
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+44	28	1.000000
+45	9	1.000000
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+48	43	0.500000
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+49	38	1.000000
+50	56	0.500000
+50	57	0.500000
+51	40	1.000000
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+78	52	0.500000
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+80	42	0.500000
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+81	34	1.000000
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+95	38	1.000000
+96	53	1.000000
diff -r 88c07fc4024c -r 7e50e8d920db test-data/alevin_mat_02.mtx
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alevin_mat_02.mtx	Mon Dec 05 15:48:07 2022 +0000
@@ -0,0 +1,105 @@
+%%MatrixMarket	matrix	coordinate	real	general
+96	61	103
+1	9	1.000000
+2	28	1.000000
+3	38	1.000000
+4	28	1.000000
+5	42	1.000000
+6	9	1.000000
+7	56	1.000000
+8	28	1.000000
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+10	30	1.000000
+11	53	1.000000
+12	3	0.500000
+12	4	0.500000
+13	28	1.000000
+14	56	1.000000
+15	9	1.000000
+16	43	0.500000
+16	45	0.500000
+17	42	0.500000
+17	44	0.500000
+18	28	1.000000
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+20	38	1.000000
+21	40	1.000000
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+48	43	0.500000
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diff -r 88c07fc4024c -r 7e50e8d920db test-data/alevin_mat_indropV2.mtx
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alevin_mat_indropV2.mtx	Mon Dec 05 15:48:07 2022 +0000
@@ -0,0 +1,105 @@
+%%MatrixMarket	matrix	coordinate	real	general
+96	61	103
+1	9	1.000000
+2	28	1.000000
+3	38	1.000000
+4	28	1.000000
+5	42	1.000000
+6	9	1.000000
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+12	3	0.500000
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diff -r 88c07fc4024c -r 7e50e8d920db test-data/full_data_structure.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/full_data_structure.txt	Mon Dec 05 15:48:07 2022 +0000
@@ -0,0 +1,551 @@
+322
+218
+8
+ENST00000641515.2
+ENST00000335137.4
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+ENST00000343938.9
+ENST00000488011.1
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+ENST00000378891.9
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+ENST00000400809.8
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+ENST00000408918.8
+ENST00000425598.2
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+ENST00000492508.1
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+ENST00000520296.5
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+ENST00000537107.5
+ENST00000454272.2
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+ENST00000476993.2
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+ENST00000378756.7
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+ENST00000536055.5
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+ENST00000520777.5
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+ENST00000479814.5
+ENST00000435358.5
+ENST00000503792.1
+ENST00000490017.1
+ENST00000341832.10
+ENST00000407249.7
+ENST00000615951.4
+ENST00000340677.9
+ENST00000611150.3
+ENST00000629289.2
+ENST00000626918.2
+ENST00000629312.2
+ENST00000614300.4
+ENST00000617444.4
+ENST00000611123.1
+ENST00000404249.8
+ENST00000356200.7
+ENST00000378638.6
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+ENST00000498806.1
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+ENST00000610897.4
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+ENST00000378609.9
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+ENST00000640067.1
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+ENST00000414253.5
+ENST00000400918.7
+ENST00000378543.2
+ENST00000378546.9
+ENST00000440825.6
+ENST00000420515.1
+ENST00000378536.5
+ENST00000378531.8
+ENST00000378529.7
+ENST00000449373.2
+ENST00000378525.2
+ENST00000494279.2
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+ENST00000605895.6
+ENST00000306256.13
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+ENST00000443438.5
+ENST00000488353.2
+ENST00000288774.7
+ENST00000650293.1
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+ENST00000507596.5
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+ENST00000419816.6
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+ENST00000378466.8
+ENST00000435556.8
+ENST00000505228.5
+ENST00000651094.1
+ENST00000502512.1
+ENST00000468002.2
+ENST00000486396.1
+ENST00000502770.2
+ENST00000378453.4
+ENST00000426449.5
+ENST00000434817.5
+ENST00000435221.6
+ENST00000451778.5
+ENST00000409119.5
+ENST00000355716.4
+GGATTACCATAGGATA
+CTCTGGTAGGAGTAGA
+GCTTGAAGTCGGATCC
+CTGCTGTGTTACGTCA
+TTAACTCAGCTAACAA
+CATTATCTCAACTCTT
+CTCGAGGGTCGCCATG
+CGAACATGTTACAGAA
+AAGGCAGCACCATCCT
+TCATTACGTCTCATCC
+GGTATTGTCTGACCTC
+GACGTTACAAGAAGAG
+TGTTCCGAGCGCTCCA
+CGCTATCTCTTAACCT
+GTATTCTGTAGTGAAT
+GTCGGGTGTGCAGTAG
+ATCATGGCAGCCAATT
+AGTTGGTTCGCGATCG
+AGAATAGTCCTATTCA
+TTGCGTCAGCTAAACA
+GAACGGAGTCGTCTTC
+CATGACAGTACCGAGA
+CACATAGTCATGTGGT
+TACTTACTCAAAGTAG
+GGGCATCGTAGCTTGT
+GACAGAGAGGGTGTGT
+AGCCTAATCATTCACT
+CATCGAATCTGCGGCA
+GCTTCCAAGAGCTGGT
+CATGACAGTAGCCTCG
+CAGCATAAGACTTGAA
+TTGTAGGCACCATCCT
+GACTACACAACGATGG
+CGAATGTGTACCATCA
+ATAGACCTCTCACATT
+AGTGGGATCTTAACCT
+TGGACGCGTAGAAGGA
+CCGTGGAAGTAGGCCA
+CTCACACTCGCCTGTT
+AGTAGTCGTAACGACG
+GTCTCGTGTGATGTGG
+GTAACTGGTTCACGGC
+CTTAGGAGTCTCCATC
+GGTGAAGCAATGACCT
+ACGATACAGCCCAGCT
+TGTTCCGCAGCATGAG
+TTAGGCAAGCCGCCTA
+TGACTTTTCGCTAGCG
+GGACATTCACTCTGTC
+GATCGTATCGCACTCT
+TACACGAGTGCACTTA
+GTACTCCCAACTTGAC
+GCGACCACAGTCGATT
+CTGTTTAGTCCGTCAG
+CCGGGATCATGAGCGA
+ACTGAACTCTTTAGTC
+AACCATGAGAGTACCG
+TAGAGCTCACGAGAGT
+ACGCAGCCATAAAGGT
+CTCGAGGCATGCCTTC
+AGCGTATAGATACACA
+ACGCCAGAGGGTATCG
+TGATTTCAGTGGGCTA
+TTCTCAAAGTACGTAA
+TCATTTGTCCATGAGT
+AGAATAGCAGTGGGAT
+AAAGTAGAGTCAAGGC
+TACTTGTAGGGAACGG
+TACCTATCAGATGGGT
+CTGAAGTTCCACGTGG
+ACCAGTATCTCATTCA
+AAACGGGAGCGGCTTC
+AAACCTGCAGGCGATA
+CACAGGCGTGATGTCT
+CACAAACGTGCTTCTC
+TGACTAGAGTACGCGA
+CGACCTTAGGAGCGTT
+ATAGACCTCTCGATGA
+AACCGCGAGACACTAA
+TCGAGGCGTCTACCTC
+TACGGATAGATGTTAG
+CAGTCCTCACGAAGCA
+GTGCTTCAGGCTAGAC
+GCGCCAAGTCATGCAT
+CCACGGAGTAATAGCA
+CAAGTTGAGATCCTGT
+ATCCGAAGTAACGCGA
+AATCCAGAGCCAACAG
+TTCGGTCCATTGTGCA
+TCTCTAACAACACCCG
+TCATTACCACAGAGGT
+GCATGTAAGTACGTAA
+ACGGGCTAGTTCGATC
+GTCCTCATCACAATGC
+GGCCGATAGGTACTCT
+GACGTTAAGGGAAACA
+CGAATGTCATACAGCT
+CATGGCGAGCTGAAAT
+CACACCTAGTGAACGC
+TTTATGCAGGCCCTTG
+GTACTTTCACGTCAGC
+GGATGTTTCAGTCAGT
+GAAATGAGTAGCGTAG
+CATGCCTCAGACAAAT
+AGCATACTCTTGCAAG
+AAAGCAATCTGCCCTA
+GTCGGGTTCACGGTTA
+GGTGCGTGTCAGGACA
+CTGTGCTGTAAACCTC
+CGATGTAAGTTCGCGC
+ATGGGAGCAGCTCGCA
+GCTCTGTAGTTTCCTT
+CACAGGCCACGAAAGC
+GTGCTTCGTTGTCTTT
+GTGCTTCAGGCTCTTA
+GAAATGAAGACAGACC
+CTCGGAGGTCGACTGC
+CAACCAACACAGACAG
+TTCTCAAAGCTCCTCT
+GTACTTTAGTCCTCCT
+TGTGGTAGTTACGACT
+TAGAGCTGTGGACGAT
+GTCTTCGGTTTCCACC
+GGTGCGTTCAAACCGT
+GGACATTCATTGCGGC
+GCTGCGACATAACCTG
+TCTCATAAGTTAGCGG
+TAGTGGTAGAAGGTGA
+GCGAGAACAAGTTGTC
+GACTACAGTTGTACAC
+CCTAGCTGTCGCGTGT
+ATTACTCGTACTCAAC
+AGCAGCCAGATGTCGG
+AGATCTGTCTGCGTAA
+ACGCCAGTCAAGCCTA
+AAGGCAGGTAGTGAAT
+TTAACTCGTCTGATTG
+TGACGGCCATGCTGGC
+GGAAAGCTCGAATGCT
+CTCGTACCATTAACCG
+CATGGCGTCCATGAGT
+CAGCATACAAGTTAAG
+CACCTTGGTGGTCCGT
+ACTGAGTCATCCCATC
+AAGCCGCCAATCTGCA
+TTAGGCACAACGATGG
+GTACGTACACACGCTG
+CTGTGCTTCCGCGGTA
+ACCAGTAAGGGCTCTC
+AACTTTCTCATCGGAT
+AACACGTCACCTGGTG
+TCAATCTCATGCCACG
+GTCATTTAGGCAGTCA
+GTCACAAGTATTCGTG
+GGAGCAATCGCTTGTC
+GATGAGGTCCATTCTA
+GATGAAAGTGATGTCT
+GATCAGTAGGGTTTCT
+GAAACTCAGTACTTGC
+CTACATTGTCACTGGC
+CGATTGACATACGCCG
+AGTTGGTGTACCGGCT
+TTAGGACTCGTGACAT
+GTGCATAGTAACGACG
+GTACGTAGTAAGTTCC
+GTAACGTTCCACGTGG
+GGACAAGTCTCAAGTG
+GGAAAGCAGGAGTAGA
+CTCCTAGAGCAGACTG
+AGCGTCGGTGTTCGAT
+TTTGTCACAGGTCCAC
+GTCACGGGTAAGTTCC
+GTATCTTTCATCATTC
+GACGTGCGTAGCAAAT
+GAACATCGTATAAACG
+CTGTTTATCAGTCAGT
+CTCGGGACACATCCAA
+CTAACTTTCAGCTTAG
+CGATCGGAGGTGGGTT
+CGACCTTCATTGGGCC
+AATCCAGCAGCCTGTG
+TTAGTTCCATGTAAGA
+TGGCTGGCAATTGCTG
+GTATTCTGTAGGCTGA
+GTAGTCATCCAGTATG
+GGGATGAAGAGGGATA
+GCTTCCAAGGAATCGC
+CTTTGCGCACAGGAGT
+CCGGGATTCTTGTCAT
+CCATTCGGTAGCCTAT
+CAGCCGACAGATTGCT
+CACAAACTCTTAACCT
+CAACTAGTCCTCTAGC
+ATCGAGTGTACAGCAG
+TTATGCTAGAGATGAG
+TGGCGCAGTCTCGTTC
+TCAGCTCTCTGCTTGC
+GTTACAGAGTTATCGC
+GTAGTCATCAGCTCTC
+GGGAGATGTGCTTCTC
+GCGCCAAGTACGAAAT
+CTGCGGAAGTACGCGA
+CCATTCGAGCTAACTC
+ATCTACTTCTGAGTGT
+AACTCAGGTTTGACAC
+AACCGCGGTAAGTGTA
+TGCCCTATCCACTCCA
+TCATTTGAGCAAATCA
+GTGAAGGAGCCAGAAC
+CTCTGGTGTTAAGGGC
+CCTTCGACACTATCTT
+CATCCACAGGCTATCT
+CACCACTTCATCGGAT
+ATCATCTCATCCAACA
+AGGTCATTCCGCGGTA
+AGACGTTAGACCACGA
+AACGTTGCAGTTAACC
+AAAGCAAAGTGTCCAT
+8	198	199	200	201	202	203	204	205	1	1	32	1	TACGGGCTGC	1
+1	170	1	1	21	1	GAACATTTGT	1
+3	29	30	31	2	2	34	1	CGGCGTCCGG	1	1	1	AGCGGCTGGT	1
+11	5	6	7	8	9	10	11	12	13	14	16	1	1	93	1	TTGACACCAT	1
+1	146	1	1	46	1	AACACAGATA	1
+4	287	289	291	293	2	2	140	1	CCGTACGGGG	1	35	1	GGATTCAGTA	1
+3	273	274	275	1	1	86	1	CCGACTCGTT	1
+4	134	135	136	137	5	5	30	1	ACGAATGTTT	1	95	1	ACAGAGCTAA	1	45	1	AGTTTACACT	1	3	1	ACCTATGTTC	1	41	1	GACTATGGAT	1
diff -r 88c07fc4024c -r 7e50e8d920db test-data/genome.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fasta	Mon Dec 05 15:48:07 2022 +0000
@@ -0,0 +1,239 @@
+>chrM
+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG
+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC
+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA
+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC
+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA
+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC
+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA
+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC
+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC
+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA
+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC
+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA
+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA
+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT
+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC
+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC
+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC
+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA
+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC
+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT
+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA
+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA
+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA
+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA
+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG
+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA
+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC
+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA
+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT
+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC
+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG
+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC
+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG
+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC
+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA
+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC
+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA
+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT
+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA
+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT
+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG
+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA
+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG
+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG
+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT
+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA
+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT
+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA
+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC
+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC
+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC
+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG
+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC
+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC
+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG
+CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTC
+CGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATAC
+ACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCC
+CTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAAC
+AGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA
+GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATAT
+GTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTAGGACTATGA
+GAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAAGTAAGGTC
+AGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCT
+GGCCCAACCCGTCATCTACTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT
+TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTC
+GTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTAT
+CCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTCATCATTAATA
+ATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAG
+GCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA
+AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGA
+GGTGGATTAAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAA
+TAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCCTAACTACTAC
+CGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACTATCTCGCACCTGAAACAAGCTA
+ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT
+TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCAC
+CATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATA
+TCTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCG
+CCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATTTAGGTTAAATAC
+AGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA
+CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGA
+CTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCC
+GCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGA
+AAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCA
+GCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG
+AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCC
+GAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCAT
+TTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAAT
+AATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTC
+CTACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG
+CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTC
+CTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATAC
+CAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAG
+CTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGG
+AGACCCCATTCTATACCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA
+GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTA
+TGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGG
+AATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAA
+GTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAG
+GATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT
+ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATC
+ATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCC
+ATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAAT
+GCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTC
+ATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC
+TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGA
+AGAACCCGTATACATAAAATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAA
+CCCCATGGCCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAAT
+TATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCT
+ATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC
+TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGA
+AACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTAC
+ATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACG
+AGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGA
+CCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA
+TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTC
+TAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGC
+AAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTT
+ACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTT
+AAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT
+AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTA
+CCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCT
+GTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCT
+CTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAAC
+TAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT
+AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTA
+TCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTA
+AAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGA
+AACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCAC
+CTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA
+TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCAC
+ACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAA
+AACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATT
+TCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGG
+CGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG
+GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAG
+CCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAA
+GTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAA
+TAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCT
+CCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT
+GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCC
+AACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGT
+AGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGT
+ACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTAA
+TAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT
+AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAA
+TTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAG
+CCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAG
+TCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAAT
+GATTTCGACTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG
+CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGA
+AGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAAT
+ATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAA
+TCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCA
+ACAATTATATTACTACCACTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA
+GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCC
+AACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATC
+ATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCT
+CCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAAC
+CACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA
+TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCC
+TAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTT
+AATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCT
+AAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCT
+ATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT
+ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCA
+TACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCG
+GCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTA
+CGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTT
+TGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG
+TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGC
+CCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAA
+CCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACC
+CCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAA
+CAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC
+AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCA
+ACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCC
+ATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCAT
+CCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAA
+CTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA
+TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACC
+CAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA
+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA
+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT
+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA
+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT
+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA
+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC
+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC
+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC
+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC
+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC
+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA
+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC
+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC
+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC
+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA
+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC
+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA
+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT
+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA
+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA
+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA
+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA
+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC
+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC
+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC
+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG
+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC
+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC
+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC
+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA
+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA
+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC
+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC
+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC
+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC
+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA
+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT
+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC
+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT
+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC
+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA
+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC
+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT
+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC
+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC
+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA
+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC
+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA
+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA
+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA
+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG
+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG
+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC
+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG
+
diff -r 88c07fc4024c -r 7e50e8d920db test-data/length_distribution.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/length_distribution.txt	Mon Dec 05 15:48:07 2022 +0000
@@ -0,0 +1,2 @@
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