Galaxy |

Changeset 11:e661a3269313 (2022-12-05)

Previous changeset 10:e4c01dcece8b (2021-07-22) Next changeset 12:f2000bc73102 (2022-12-07)

Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042

modified:
alevin.xml
macros.xml
test-data/alevin_mat.mtx

added:
test-data/alevin_mat_01.mtx
test-data/alevin_mat_02.mtx
test-data/alevin_mat_indropV2.mtx
test-data/full_data_structure.txt
test-data/genome.fasta
test-data/length_distribution.txt

diff -r e4c01dcece8b -r e661a3269313 alevin.xml
--- a/alevin.xml Thu Jul 22 14:05:58 2021 +0000
+++ b/alevin.xml Mon Dec 05 15:47:45 2022 +0000

[

b'@@ -1,5 +1,5 @@\n-<tool id="alevin" name="Alevin" version="@VERSION@+@GALAXY_VERSION@" profile="@PROFILE_VERSION@">\n- <description>Quantification and analysis of 3\xe2\x80\x99 tagged-end single-cell sequencing data</description>\n+<tool id="alevin" name="Alevin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">\n+ <description>Quantification and analysis of 3-prime tagged-end single-cell sequencing data</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n@@ -61,7 +61,10 @@\n #end if\n -o ./output\n -p "\\${GALAXY_SLOTS:-4}"\n- ${protocol}\n+ ${protocol_cond.protocol}\n+ #if $protocol_cond.protocol == \'--indropV2\'\n+ --w1 \'${protocol_cond.w1}\'\n+ #end if\n --tgMap ./alevinmap.tsv\n #if $whitelist:\n --whitelist \'${optional.whitelist}\'\n@@ -85,39 +88,40 @@\n --keepCBFraction \'${optional.keepCBFraction}\'\n #end if\n ${optional.noDedup}\n- ${optional.dumpBfh}\n- ${optional.dumpFeatures}\n- ${optional.dumpUmiGraph}\n+ #if \'dumpBfh\' in $output_files:\n+ --dumpBfh\n+ #end if\n+ #if \'dumpFeatures\' in $output_files:\n+ --dumpFeatures\n+ #end if\n+ #if \'dumpUmiGraph\' in $output_files:\n+ --dumpUmiGraph\n+ #end if\n ${optional.dumpMtx}\n- #if $optional.lowRegionMinNumBarcodes:\n- --lowregionMinNumBarcodes \'${optional.lowRegionMinNumBarcodes}\'\n- #end if\n #if $optional.maxNumBarcodes:\n --maxNumBarcodes \'${optional.maxNumBarcodes}\'\n #end if\n #if $optional.freqThreshold:\n --freqThreshold \'${optional.freqThreshold}\'\n #end if\n-\n+ ## && gunzip output/alevin/quants_tier_mat.gz -> the output is binary file\n #if $optional.dumpMtx != "--dumpMtx":\n && python \'$__tool_directory__/vpolo_convert.py\' -m\n #else:\n && gunzip output/alevin/quants_mat.mtx.gz\n #end if\n- #if $optional.dumpUmiGraph:\n+ #if \'dumpUmiGraph\' in $output_files:\n && python \'$__tool_directory__/vpolo_convert.py\' -u\n && sh \'$__tool_directory__/umiout.sh\'\n #end if\n-\n- && gunzip output/alevin/quants_tier_mat.gz\n- #if $optional.numCellBootstraps:\n- && gunzip output/alevin/quants_mean_mat.gz\n- && gunzip output/alevin/quants_var_mat.gz\n+ ## those gzip file include binary datasets\n+ ## #if $optional.numCellBootstraps:\n+ ## && gunzip output/alevin/quants_mean_mat.gz\n+ ## && gunzip output/alevin/quants_var_mat.gz\n+ ## #end if\n+ #if \'auxiliar_info\' in $output_files\n+ && tar -zcvf aux_info.tar.gz output/aux_info\n #end if\n-\n- && gunzip output/aux_info/fld.gz\n- && gunzip output/aux_info/observed_bias.gz\n- && gunzip output/aux_info/observed_bias_3p.gz\n ]]>\n </command>\n <inputs>\n@@ -128,8 +132,8 @@\n <option value="unmated">Single-end</option>\n </param>\n <when value="paired">\n- <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="CB+UMI raw sequence file(s)"/>\n- <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="Read-sequence file(s)"/>\n+ <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Mate pair 1" help="CB+UMI raw sequence file(s)"/>\n+ <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Mate pair 2" help="Read-sequence file(s)"/>\n <expand macro="stranded_pe"/>\n </when>\n <when value="unmated">\n@@ -137,91 +141,136 @@\n <expand macro="stranded_se"/>\n </when>\n </conditional>\n- <param name="protocol" type="select">\n- <op'..b'value="Yes"/>\n+ <param name="dumpMtx" value="true"/>\n </section>\n- <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true" lines_diff="62"/>\n+ <output name="quants_mat_mtx" file="alevin_mat_02.mtx" ftype="mtx" sort="true"/>\n+ </test>\n+ <test expect_num_outputs="8">\n+ <conditional name="refTranscriptSource">\n+ <param name="TranscriptSource" value="history"/>\n+ <section name="s_index">\n+ <param name="fasta" value="minitranscript.fa"/>\n+ </section>\n+ </conditional>\n+ <conditional name="pairstraight">\n+ <param name="readselect" value="paired"/>\n+ <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>\n+ <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>\n+ <param name="orientation" value="I"/>\n+ <param name="strandedness" value="SR"/>\n+ </conditional>\n+ <conditional name="protocol_cond">\n+ <param name="protocol" value="-\\-indropV2"/>\n+ <param name="w1" value="ATCAT"/>\n+ </conditional>\n+ <param name="tgmap" value="minitxp.tsv"/>\n+ <param name="output_files" value="dumpFeatures"/>\n+ <section name="optional">\n+ <param name="keepCBFraction" value="1"/>\n+ <param name="freqThreshold" value="5"/>\n+ <param name="dumpMtx" value="true"/>\n+ </section>\n+ <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx" ftype="mtx" sort="true"/>\n </test>\n <test expect_num_outputs="14">\n <conditional name="refTranscriptSource">\n@@ -260,16 +339,35 @@\n <param name="orientation" value="I"/>\n <param name="strandedness" value="SR"/>\n </conditional>\n- <param name="protocol" value="--chromium"/>\n+ <conditional name="protocol_cond">\n+ <param name="protocol" value="--chromium"/>\n+ </conditional>\n <param name="tgmap" value="minitxp.tsv"/>\n+ <param name="output_files" value="dumpFeatures,salmon_log,fragment_length,auxiliar_info,dumpUmiGraph,dumpBfh,commands"/>\n <section name="optional">\n- <param name="keepCBFraction" value="1"/>\n- <param name="dumpFeatures" value="Yes"/>\n- <param name="numCellBootstraps" value="2"/>\n- <param name="freqThreshold" value="5"/>\n- <param name="dumpMtx" value="Yes"/>\n+ <param name="dumpMtx" value="true"/>\n </section>\n- <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true" lines_diff="62"/>\n+ <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true"/>\n+ <output name="salmon_quant_log" ftype="txt">\n+ <assert_contents>\n+ <has_text text="Index contained 322 targets"/>\n+ <has_text text="Counted 14 total reads in the equivalence classes"/>\n+ </assert_contents>\n+ </output>\n+ <output name="flenDist_txt" file="length_distribution.txt" ftype="txt"/>\n+ <output name="auxiliar_files" ftype="tgz">\n+ <assert_contents>\n+ <has_size value="1898" delta="100"/>\n+ </assert_contents>\n+ </output>\n+ <output_collection name="umigraphs" type="list" count="14">\n+ <element name="AGTGGGATCTTAACCT">\n+ <assert_contents>\n+ <has_size value="4017" delta="1000"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output name="bfh_txt" file="full_data_structure.txt" ftype="txt"/>\n </test>\n </tests>\n <help><![CDATA[\n'

diff -r e4c01dcece8b -r e661a3269313 macros.xml
--- a/macros.xml Thu Jul 22 14:05:58 2021 +0000
+++ b/macros.xml Mon Dec 05 15:47:45 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>  
             <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 e4c01dcece8b -r e661a3269313 test-data/alevin_mat.mtx
--- a/test-data/alevin_mat.mtx Thu Jul 22 14:05:58 2021 +0000
+++ b/test-data/alevin_mat.mtx Mon Dec 05 15:47:45 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 e4c01dcece8b -r e661a3269313 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 15:47:45 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
+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 56 0.500000
+50 57 0.500000
+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 38 1.000000
+70 21 1.000000
+71 38 1.000000
+72 38 1.000000
+73 16 1.000000
+74 30 1.000000
+75 16 1.000000
+76 30 1.000000
+77 40 1.000000
+78 52 0.500000
+78 53 0.500000
+79 53 1.000000
+80 42 0.500000
+80 44 0.500000
+81 34 1.000000
+82 9 1.000000
+83 15 1.000000
+84 45 1.000000
+85 47 1.000000
+86 40 1.000000
+87 56 1.000000
+88 56 1.000000
+89 34 1.000000
+90 56 1.000000
+91 38 1.000000
+92 53 1.000000
+93 56 1.000000
+94 53 1.000000
+95 38 1.000000
+96 53 1.000000

diff -r e4c01dcece8b -r e661a3269313 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 15:47:45 2022 +0000

diff -r e4c01dcece8b -r e661a3269313 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 15:47:45 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 16 1.000000
+16 9 1.000000
+17 43 0.500000
+17 45 0.500000
+18 28 1.000000
+19 42 0.500000
+19 44 0.500000
+20 40 1.000000
+21 46 1.000000
+22 38 1.000000
+23 19 1.000000
+24 9 1.000000
+25 56 1.000000
+26 8 1.000000
+27 9 1.000000
+28 28 1.000000
+29 53 1.000000
+30 56 1.000000
+31 28 1.000000
+32 30 1.000000
+33 34 1.000000
+34 38 1.000000
+35 28 1.000000
+36 30 1.000000
+37 30 1.000000
+38 28 1.000000
+39 34 1.000000
+40 19 1.000000
+41 47 1.000000
+42 38 1.000000
+43 28 1.000000
+44 19 1.000000
+45 56 1.000000
+46 28 1.000000
+47 23 1.000000
+48 43 0.500000
+48 45 0.500000
+49 38 1.000000
+50 56 0.500000
+50 57 0.500000
+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 23 1.000000
+58 30 1.000000
+59 53 1.000000
+60 30 1.000000
+61 9 1.000000
+62 34 1.000000
+63 24 1.000000
+64 30 1.000000
+65 56 1.000000
+66 9 1.000000
+67 61 1.000000
+68 21 1.000000
+69 38 1.000000
+70 38 1.000000
+71 16 1.000000
+72 38 1.000000
+73 38 1.000000
+74 30 1.000000
+75 53 1.000000
+76 16 1.000000
+77 30 1.000000
+78 40 1.000000
+79 52 0.500000
+79 53 0.500000
+80 42 0.500000
+80 44 0.500000
+81 34 1.000000
+82 9 1.000000
+83 15 1.000000
+84 45 1.000000
+85 47 1.000000
+86 40 1.000000
+87 56 1.000000
+88 34 1.000000
+89 56 1.000000
+90 56 1.000000
+91 38 1.000000
+92 53 1.000000
+93 56 1.000000
+94 53 1.000000
+95 38 1.000000
+96 53 1.000000

diff -r e4c01dcece8b -r e661a3269313 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 15:47:45 2022 +0000

b'@@ -0,0 +1,551 @@\n+322\n+218\n+8\n+ENST00000641515.2\n+ENST00000335137.4\n+ENST00000426406.3\n+ENST00000420190.6\n+ENST00000437963.5\n+ENST00000342066.8\n+ENST00000618181.4\n+ENST00000622503.4\n+ENST00000618323.4\n+ENST00000616016.4\n+ENST00000618779.4\n+ENST00000616125.4\n+ENST00000620200.4\n+ENST00000617307.4\n+ENST00000341065.8\n+ENST00000455979.1\n+ENST00000327044.7\n+ENST00000338591.8\n+ENST00000622660.1\n+ENST00000466300.1\n+ENST00000379410.7\n+ENST00000379409.6\n+ENST00000379407.7\n+ENST00000491024.1\n+ENST00000341290.6\n+ENST00000433179.3\n+ENST00000428771.6\n+ENST00000304952.10\n+ENST00000484667.2\n+ENST00000624697.4\n+ENST00000624652.1\n+ENST00000649529.1\n+ENST00000379370.7\n+ENST00000620552.4\n+ENST00000652369.1\n+ENST00000651234.1\n+ENST00000453464.3\n+ENST00000379339.5\n+ENST00000379325.7\n+ENST00000421241.6\n+ENST00000477196.5\n+ENST00000467751.5\n+ENST00000379320.5\n+ENST00000379319.5\n+ENST00000434641.5\n+ENST00000462097.5\n+ENST00000475119.5\n+ENST00000442117.5\n+ENST00000427787.5\n+ENST00000480643.1\n+ENST00000379290.5\n+ENST00000379289.5\n+ENST00000379288.3\n+ENST00000486379.1\n+ENST00000328596.10\n+ENST00000379268.7\n+ENST00000486728.5\n+ENST00000379265.5\n+ENST00000379236.4\n+ENST00000360001.11\n+ENST00000660930.1\n+ENST00000465727.5\n+ENST00000263741.12\n+ENST00000655486.1\n+ENST00000403997.2\n+ENST00000379198.5\n+ENST00000330388.2\n+ENST00000450390.6\n+ENST00000347370.6\n+ENST00000349431.10\n+ENST00000400929.6\n+ENST00000464036.5\n+ENST00000360466.6\n+ENST00000400930.8\n+ENST00000473215.5\n+ENST00000435198.5\n+ENST00000509720.5\n+ENST00000466752.5\n+ENST00000503294.5\n+ENST00000477894.5\n+ENST00000422076.5\n+ENST00000502382.1\n+ENST00000488418.2\n+ENST00000379116.9\n+ENST00000379101.8\n+ENST00000338555.6\n+ENST00000400928.7\n+ENST00000470022.1\n+ENST00000325425.12\n+ENST00000379099.3\n+ENST00000354700.10\n+ENST00000353662.4\n+ENST00000354980.7\n+ENST00000379031.10\n+ENST00000467712.1\n+ENST00000540437.5\n+ENST00000545578.5\n+ENST00000620829.4\n+ENST00000618806.4\n+ENST00000435064.5\n+ENST00000411962.5\n+ENST00000421495.6\n+ENST00000458452.7\n+ENST00000419704.5\n+ENST00000532772.5\n+ENST00000450926.6\n+ENST00000527098.5\n+ENST00000528879.5\n+ENST00000531377.5\n+ENST00000527383.5\n+ENST00000434694.6\n+ENST00000526797.5\n+ENST00000526332.5\n+ENST00000430786.5\n+ENST00000527719.5\n+ENST00000530031.5\n+ENST00000429572.5\n+ENST00000534345.5\n+ENST00000531019.5\n+ENST00000498476.6\n+ENST00000470679.3\n+ENST00000525285.1\n+ENST00000343938.9\n+ENST00000488011.1\n+ENST00000339381.6\n+ENST00000378891.9\n+ENST00000378888.10\n+ENST00000610709.2\n+ENST00000632445.1\n+ENST00000631679.1\n+ENST00000342753.8\n+ENST00000309212.10\n+ENST00000445648.5\n+ENST00000477278.3\n+ENST00000338370.7\n+ENST00000338338.9\n+ENST00000321751.9\n+ENST00000378853.3\n+ENST00000400809.8\n+ENST00000482621.5\n+ENST00000408952.8\n+ENST00000481223.6\n+ENST00000488340.5\n+ENST00000408918.8\n+ENST00000425598.2\n+ENST00000497013.1\n+ENST00000344843.12\n+ENST00000492508.1\n+ENST00000482352.1\n+ENST00000520296.5\n+ENST00000427211.3\n+ENST00000537107.5\n+ENST00000454272.2\n+ENST00000442470.1\n+ENST00000378821.3\n+ENST00000495558.1\n+ENST00000338660.5\n+ENST00000476993.2\n+ENST00000471398.1\n+ENST00000378785.6\n+ENST00000475091.2\n+ENST00000308647.7\n+ENST00000378756.7\n+ENST00000378755.9\n+ENST00000339113.8\n+ENST00000536055.5\n+ENST00000400830.3\n+ENST00000378733.9\n+ENST00000425828.1\n+ENST00000624426.1\n+ENST00000291386.4\n+ENST00000359060.5\n+ENST00000422725.4\n+ENST00000520777.5\n+ENST00000355826.9\n+ENST00000518681.5\n+ENST00000505820.6\n+ENST00000489635.5\n+ENST00000514363.1\n+ENST00000487053.5\n+ENST00000502470.5\n+ENST00000378712.5\n+ENST00000510793.5\n+ENST00000504599.5\n+ENST00000503789.5\n+ENST00000378708.5\n+ENST00000506488.5\n+ENST00000514234.5\n+ENST00000486072.1\n+ENST00000483015.1\n+ENST00000356026.9\n+ENST00000472264.1\n+ENST00000512731.5\n+ENST00000378675.7\n+ENST00000479814.5\n+ENST00000435358.5\n+ENST00000503792.1\n+ENST00000490017.1\n+ENST00000341832.10\n+ENST00000407249.7\n+ENST00000615951.4\n+ENST00000340677.9\n+ENST00000611150.3\n+ENST00000629289.2\n+ENST00000626918.2\n+ENST00000629312.2\n+ENST00000614300.4\n+ENST00000617444.4\n+ENS'..b'AAACA\n+GAACGGAGTCGTCTTC\n+CATGACAGTACCGAGA\n+CACATAGTCATGTGGT\n+TACTTACTCAAAGTAG\n+GGGCATCGTAGCTTGT\n+GACAGAGAGGGTGTGT\n+AGCCTAATCATTCACT\n+CATCGAATCTGCGGCA\n+GCTTCCAAGAGCTGGT\n+CATGACAGTAGCCTCG\n+CAGCATAAGACTTGAA\n+TTGTAGGCACCATCCT\n+GACTACACAACGATGG\n+CGAATGTGTACCATCA\n+ATAGACCTCTCACATT\n+AGTGGGATCTTAACCT\n+TGGACGCGTAGAAGGA\n+CCGTGGAAGTAGGCCA\n+CTCACACTCGCCTGTT\n+AGTAGTCGTAACGACG\n+GTCTCGTGTGATGTGG\n+GTAACTGGTTCACGGC\n+CTTAGGAGTCTCCATC\n+GGTGAAGCAATGACCT\n+ACGATACAGCCCAGCT\n+TGTTCCGCAGCATGAG\n+TTAGGCAAGCCGCCTA\n+TGACTTTTCGCTAGCG\n+GGACATTCACTCTGTC\n+GATCGTATCGCACTCT\n+TACACGAGTGCACTTA\n+GTACTCCCAACTTGAC\n+GCGACCACAGTCGATT\n+CTGTTTAGTCCGTCAG\n+CCGGGATCATGAGCGA\n+ACTGAACTCTTTAGTC\n+AACCATGAGAGTACCG\n+TAGAGCTCACGAGAGT\n+ACGCAGCCATAAAGGT\n+CTCGAGGCATGCCTTC\n+AGCGTATAGATACACA\n+ACGCCAGAGGGTATCG\n+TGATTTCAGTGGGCTA\n+TTCTCAAAGTACGTAA\n+TCATTTGTCCATGAGT\n+AGAATAGCAGTGGGAT\n+AAAGTAGAGTCAAGGC\n+TACTTGTAGGGAACGG\n+TACCTATCAGATGGGT\n+CTGAAGTTCCACGTGG\n+ACCAGTATCTCATTCA\n+AAACGGGAGCGGCTTC\n+AAACCTGCAGGCGATA\n+CACAGGCGTGATGTCT\n+CACAAACGTGCTTCTC\n+TGACTAGAGTACGCGA\n+CGACCTTAGGAGCGTT\n+ATAGACCTCTCGATGA\n+AACCGCGAGACACTAA\n+TCGAGGCGTCTACCTC\n+TACGGATAGATGTTAG\n+CAGTCCTCACGAAGCA\n+GTGCTTCAGGCTAGAC\n+GCGCCAAGTCATGCAT\n+CCACGGAGTAATAGCA\n+CAAGTTGAGATCCTGT\n+ATCCGAAGTAACGCGA\n+AATCCAGAGCCAACAG\n+TTCGGTCCATTGTGCA\n+TCTCTAACAACACCCG\n+TCATTACCACAGAGGT\n+GCATGTAAGTACGTAA\n+ACGGGCTAGTTCGATC\n+GTCCTCATCACAATGC\n+GGCCGATAGGTACTCT\n+GACGTTAAGGGAAACA\n+CGAATGTCATACAGCT\n+CATGGCGAGCTGAAAT\n+CACACCTAGTGAACGC\n+TTTATGCAGGCCCTTG\n+GTACTTTCACGTCAGC\n+GGATGTTTCAGTCAGT\n+GAAATGAGTAGCGTAG\n+CATGCCTCAGACAAAT\n+AGCATACTCTTGCAAG\n+AAAGCAATCTGCCCTA\n+GTCGGGTTCACGGTTA\n+GGTGCGTGTCAGGACA\n+CTGTGCTGTAAACCTC\n+CGATGTAAGTTCGCGC\n+ATGGGAGCAGCTCGCA\n+GCTCTGTAGTTTCCTT\n+CACAGGCCACGAAAGC\n+GTGCTTCGTTGTCTTT\n+GTGCTTCAGGCTCTTA\n+GAAATGAAGACAGACC\n+CTCGGAGGTCGACTGC\n+CAACCAACACAGACAG\n+TTCTCAAAGCTCCTCT\n+GTACTTTAGTCCTCCT\n+TGTGGTAGTTACGACT\n+TAGAGCTGTGGACGAT\n+GTCTTCGGTTTCCACC\n+GGTGCGTTCAAACCGT\n+GGACATTCATTGCGGC\n+GCTGCGACATAACCTG\n+TCTCATAAGTTAGCGG\n+TAGTGGTAGAAGGTGA\n+GCGAGAACAAGTTGTC\n+GACTACAGTTGTACAC\n+CCTAGCTGTCGCGTGT\n+ATTACTCGTACTCAAC\n+AGCAGCCAGATGTCGG\n+AGATCTGTCTGCGTAA\n+ACGCCAGTCAAGCCTA\n+AAGGCAGGTAGTGAAT\n+TTAACTCGTCTGATTG\n+TGACGGCCATGCTGGC\n+GGAAAGCTCGAATGCT\n+CTCGTACCATTAACCG\n+CATGGCGTCCATGAGT\n+CAGCATACAAGTTAAG\n+CACCTTGGTGGTCCGT\n+ACTGAGTCATCCCATC\n+AAGCCGCCAATCTGCA\n+TTAGGCACAACGATGG\n+GTACGTACACACGCTG\n+CTGTGCTTCCGCGGTA\n+ACCAGTAAGGGCTCTC\n+AACTTTCTCATCGGAT\n+AACACGTCACCTGGTG\n+TCAATCTCATGCCACG\n+GTCATTTAGGCAGTCA\n+GTCACAAGTATTCGTG\n+GGAGCAATCGCTTGTC\n+GATGAGGTCCATTCTA\n+GATGAAAGTGATGTCT\n+GATCAGTAGGGTTTCT\n+GAAACTCAGTACTTGC\n+CTACATTGTCACTGGC\n+CGATTGACATACGCCG\n+AGTTGGTGTACCGGCT\n+TTAGGACTCGTGACAT\n+GTGCATAGTAACGACG\n+GTACGTAGTAAGTTCC\n+GTAACGTTCCACGTGG\n+GGACAAGTCTCAAGTG\n+GGAAAGCAGGAGTAGA\n+CTCCTAGAGCAGACTG\n+AGCGTCGGTGTTCGAT\n+TTTGTCACAGGTCCAC\n+GTCACGGGTAAGTTCC\n+GTATCTTTCATCATTC\n+GACGTGCGTAGCAAAT\n+GAACATCGTATAAACG\n+CTGTTTATCAGTCAGT\n+CTCGGGACACATCCAA\n+CTAACTTTCAGCTTAG\n+CGATCGGAGGTGGGTT\n+CGACCTTCATTGGGCC\n+AATCCAGCAGCCTGTG\n+TTAGTTCCATGTAAGA\n+TGGCTGGCAATTGCTG\n+GTATTCTGTAGGCTGA\n+GTAGTCATCCAGTATG\n+GGGATGAAGAGGGATA\n+GCTTCCAAGGAATCGC\n+CTTTGCGCACAGGAGT\n+CCGGGATTCTTGTCAT\n+CCATTCGGTAGCCTAT\n+CAGCCGACAGATTGCT\n+CACAAACTCTTAACCT\n+CAACTAGTCCTCTAGC\n+ATCGAGTGTACAGCAG\n+TTATGCTAGAGATGAG\n+TGGCGCAGTCTCGTTC\n+TCAGCTCTCTGCTTGC\n+GTTACAGAGTTATCGC\n+GTAGTCATCAGCTCTC\n+GGGAGATGTGCTTCTC\n+GCGCCAAGTACGAAAT\n+CTGCGGAAGTACGCGA\n+CCATTCGAGCTAACTC\n+ATCTACTTCTGAGTGT\n+AACTCAGGTTTGACAC\n+AACCGCGGTAAGTGTA\n+TGCCCTATCCACTCCA\n+TCATTTGAGCAAATCA\n+GTGAAGGAGCCAGAAC\n+CTCTGGTGTTAAGGGC\n+CCTTCGACACTATCTT\n+CATCCACAGGCTATCT\n+CACCACTTCATCGGAT\n+ATCATCTCATCCAACA\n+AGGTCATTCCGCGGTA\n+AGACGTTAGACCACGA\n+AACGTTGCAGTTAACC\n+AAAGCAAAGTGTCCAT\n+8\t198\t199\t200\t201\t202\t203\t204\t205\t1\t1\t32\t1\tTACGGGCTGC\t1\n+1\t170\t1\t1\t21\t1\tGAACATTTGT\t1\n+3\t29\t30\t31\t2\t2\t34\t1\tCGGCGTCCGG\t1\t1\t1\tAGCGGCTGGT\t1\n+11\t5\t6\t7\t8\t9\t10\t11\t12\t13\t14\t16\t1\t1\t93\t1\tTTGACACCAT\t1\n+1\t146\t1\t1\t46\t1\tAACACAGATA\t1\n+4\t287\t289\t291\t293\t2\t2\t140\t1\tCCGTACGGGG\t1\t35\t1\tGGATTCAGTA\t1\n+3\t273\t274\t275\t1\t1\t86\t1\tCCGACTCGTT\t1\n+4\t134\t135\t136\t137\t5\t5\t30\t1\tACGAATGTTT\t1\t95\t1\tACAGAGCTAA\t1\t45\t1\tAGTTTACACT\t1\t3\t1\tACCTATGTTC\t1\t41\t1\tGACTATGGAT\t1\n'

diff -r e4c01dcece8b -r e661a3269313 test-data/genome.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fasta Mon Dec 05 15:47:45 2022 +0000

b'@@ -0,0 +1,239 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n'

diff -r e4c01dcece8b -r e661a3269313 test-data/length_distribution.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/length_distribution.txt Mon Dec 05 15:47:45 2022 +0000

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