Mercurial > repos > bgruening > alevin

changeset 11:e661a3269313 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
author bgruening
date Mon, 05 Dec 2022 15:47:45 +0000
parents e4c01dcece8b
children f2000bc73102
files alevin.xml macros.xml test-data/alevin_mat.mtx 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
diffstat 9 files changed, 1349 insertions(+), 198 deletions(-) [+]
line wrap: on
line diff
--- a/alevin.xml	Thu Jul 22 14:05:58 2021 +0000
+++ b/alevin.xml	Mon Dec 05 15:47:45 2022 +0000
@@ -1,5 +1,5 @@
-<tool id="alevin" name="Alevin" version="@VERSION@+@GALAXY_VERSION@" profile="@PROFILE_VERSION@">
-    <description>Quantification and analysis of 3’ tagged-end single-cell sequencing data</description>
+<tool id="alevin" name="Alevin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">
+    <description>Quantification and analysis of 3-prime tagged-end single-cell sequencing data</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -61,7 +61,10 @@
         #end if
         -o ./output
         -p "\${GALAXY_SLOTS:-4}"
-        ${protocol}
+        ${protocol_cond.protocol}
+        #if $protocol_cond.protocol == '--indropV2'
+            --w1 '${protocol_cond.w1}'
+        #end if
         --tgMap ./alevinmap.tsv
         #if $whitelist:
             --whitelist '${optional.whitelist}'
@@ -85,39 +88,40 @@
             --keepCBFraction '${optional.keepCBFraction}'
         #end if
         ${optional.noDedup}
-        ${optional.dumpBfh}
-        ${optional.dumpFeatures}
-        ${optional.dumpUmiGraph}
+        #if 'dumpBfh' in $output_files:
+            --dumpBfh
+        #end if
+        #if 'dumpFeatures' in $output_files:
+            --dumpFeatures
+        #end if
+        #if 'dumpUmiGraph' in $output_files:
+            --dumpUmiGraph
+        #end if
         ${optional.dumpMtx}
-        #if $optional.lowRegionMinNumBarcodes:
-            --lowregionMinNumBarcodes '${optional.lowRegionMinNumBarcodes}'
-        #end if
         #if $optional.maxNumBarcodes:
             --maxNumBarcodes '${optional.maxNumBarcodes}'
         #end if
         #if $optional.freqThreshold:
             --freqThreshold '${optional.freqThreshold}'
         #end if
-
+        ## && gunzip output/alevin/quants_tier_mat.gz -> the output is binary file
         #if $optional.dumpMtx != "--dumpMtx":
             && python '$__tool_directory__/vpolo_convert.py' -m
         #else:
             && gunzip output/alevin/quants_mat.mtx.gz
         #end if
-        #if $optional.dumpUmiGraph:
+        #if 'dumpUmiGraph' in $output_files:
             && python '$__tool_directory__/vpolo_convert.py' -u
             && sh '$__tool_directory__/umiout.sh'
         #end if
-
-        && gunzip output/alevin/quants_tier_mat.gz
-        #if $optional.numCellBootstraps:
-            && gunzip output/alevin/quants_mean_mat.gz
-            && gunzip output/alevin/quants_var_mat.gz
+        ## those gzip file include binary datasets
+        ## #if $optional.numCellBootstraps:
+        ##    && gunzip output/alevin/quants_mean_mat.gz
+        ##    && gunzip output/alevin/quants_var_mat.gz
+        ## #end if
+        #if 'auxiliar_info' in $output_files
+            && tar -zcvf aux_info.tar.gz output/aux_info
         #end if
-
-        && gunzip output/aux_info/fld.gz
-        && gunzip output/aux_info/observed_bias.gz
-        && gunzip output/aux_info/observed_bias_3p.gz
         ]]>
     </command>
     <inputs>
@@ -128,8 +132,8 @@
                 <option value="unmated">Single-end</option>
             </param>
             <when value="paired">
-                <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="CB+UMI raw sequence file(s)"/>
-                <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="Read-sequence file(s)"/>
+                <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Mate pair 1" help="CB+UMI raw sequence file(s)"/>
+                <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Mate pair 2" help="Read-sequence file(s)"/>
                 <expand macro="stranded_pe"/>
             </when>
             <when value="unmated">
@@ -137,91 +141,136 @@
                 <expand macro="stranded_se"/>
             </when>
         </conditional>
-        <param name="protocol" type="select">
-            <option value="--dropseq">DropSeq Single Cell protocol</option>
-            <option value="--chromium">10x chromium v2 Single Cell protocol</option>
-            <option value="--chromiumV3">10x chromium v3 Single Cell protocol</option>
-            <option value="--gemcode">Gemcode v1 Single Cell protocol</option>
-            <option value="--celseq">CEL-Seq Single Cell protocol</option>
-            <option value="--celseq2">CEL-Seq2 Single Cell protocol</option>
-        </param>
+        <conditional name="protocol_cond">
+            <param name="protocol" type="select" label="Type of single-cell protocol" help="In cases where single-cell protocol supports variable length cellbarcodes, alevin adds nucleotide padding to make the lengths uniform. Furthermore, the padding scheme ensures that there are no collisions added in the process.">
+                <option value="--dropseq">DropSeq Single Cell protocol</option>
+                <option value="--chromium">10x chromium v2 Single Cell protocol</option>
+                <option value="--chromiumV3">10x chromium v3 Single Cell protocol</option>
+                <option value="--gemcode">Gemcode v1 Single Cell protocol</option>
+                <option value="--celseq">CEL-Seq Single Cell protocol</option>
+                <option value="--celseq2">CEL-Seq2 Single Cell protocol</option>
+                <option value="--sciseq3">Sci-RNA-seq3 protocol</option>
+                <option value="--indropV2">InDrop v2 protocol</option>
+                <option value="--splitSeqV1">SplitSeqV1 protocol</option>
+                <option value="--splitSeqV2">SplitSeqV2 protocol</option>
+            </param>
+            <when value="--dropseq"/>
+            <when value="--chromium"/>
+            <when value="--chromiumV3"/>
+            <when value="--gemcode"/>
+            <when value="--celseq"/>
+            <when value="--celseq2"/>
+            <when value="--sciseq3"/>
+            <when value="--indropV2">
+                <param argument="--w1" type="text" value="" label="w1 adapters">
+                    <sanitizer invalid_char="">
+                        <valid initial="string.letters"/>
+                    </sanitizer>
+                    <validator type="regex">[ATGC]+</validator>
+                </param>
+            </when>
+            <when value="--splitSeqV1"/>
+            <when value="--splitSeqV2"/>
+        </conditional>
         <param name="tgmap" type="data" format="tsv,tabular" label="Transcript to gene map file" help="Tsv with no header, containing two columns mapping each transcript present in the reference to the corresponding gene (the first column is a transcript and the second is the corresponding gene)."/>
-        <param name="allout" type="boolean" label="Retrieve all output files" truevalue="Yes" falsevalue="No" checked="false" help="If not selected, all log, info.txt, and json files output by Alevin will not be retrieved"/>
-        <section name="optional" title="Optional commands" expanded="false">
-            <param name="whitelist" type="data" format="tsv,tabular" optional="true" label="Whitelist file" help="Explicitly specify whitelist CP for cell detection and CB sequence correction. If not specified, putative CBs generated."/>
-            <param name="noDedup" type="boolean" truevalue="--noDedup" falsevalue="" checked="false" help="Causes pipeline to only perform CB correction, then maps the read-sequences to the transcriptome generating the interim data-structure of CB-EqClass-UMI-count. Used in parallel with --dumpBarcodeEq or --dumpBfh for the purposes of obtaining raw information or debugging."/>
-            <param name="mrna" type="data" format="tsv" optional="true" help="Single column tsv of mitochondrial genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
-            <param name="rrna" type="data" format="tsv" optional="true" help="Single column tsv of ribosomal genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
-            <param name="dumpBfh" type="boolean" truevalue="--dumpBfh" falsevalue="" checked="false" help="Dumps the full CB-EqClass-UMI-count data-structure for the purposed of allowing raw data analysis and debugging."/>
-            <param name="dumpFeatures" type="boolean" truevalue="--dumpFeatures" falsevalue="" checked="false" help="Dumps all features used by the CB classification and their counts at each cell level. Generally, this is used for the purposes of debugging."/>
-            <param name="dumpUmiGraph" type="boolean" truevalue="--dumpUmiGraph" falsevalue="" checked="false" help="Dump the per-cell level umi graph"/>
-            <param name="dumpMtx" type="boolean" truevalue="--dumpMtx" falsevalue="" checked="false" help="Converts the default binary format of alevin for gene-count matrix into a human readable mtx (matrix market exchange) sparse format."/>
-            <param name="forceCells" type="integer" optional="true" help="Explicitly specify the number of cells."/>
-            <param name="expectCells" type="integer" optional="true" help="define a close upper bound on expected number of cells."/>
-            <param name="numCellBootstraps" type="integer" optional="true" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/>
-            <param name="minScoreFraction" type="float" optional="true" help="This value controls the minimum allowed score for a mapping to be considered valid. It matters only when --validateMappings has been passed to Salmon. The maximum possible score for a fragment is ms = read_len * ma (or ms = (left_read_len + right_read_len) * ma for paired-end reads).
+        <param name="output_files" type="select" multiple="true" display="checkboxes" label="Extra output files">
+            <option value="salmon_log">Salmon Quant log file</option>
+            <option value="fragment_length">Observed fragment length distribution</option>
+            <option value="auxiliar_info">Auxiliar info files</option>
+            <option value="dumpUmiGraph">Per cell level parsimonious Umi graph (--dumpUmiGraph)</option>
+            <option value="dumpFeatures">Features used by the CB classification and their counts at each cell level (--dumpFeatures)</option>
+            <option value="dumpBfh">Full CB-EC-UMI-count data-structure (--dumpBfh)</option>
+            <option value="commands">Commands info file</option>
+        </param>
+        <section name="optional" title="Advanced options" expanded="false">
+            <param argument="--whitelist" type="data" format="tsv,tabular" optional="true" label="Whitelist file" help="Explicitly specify whitelist CP for cell detection and CB sequence correction. If not specified, putative CBs generated."/>
+            <param argument="--noDedup" type="boolean" truevalue="--noDedup" falsevalue="" checked="false" label="Skip deduplication step" help="Causes pipeline to only perform CB correction, then maps the read-sequences to the transcriptome generating the interim data-structure of CB-EqClass-UMI-count. Used in parallel with --dumpBarcodeEq or --dumpBfh for the purposes of obtaining raw information or debugging."/>
+            <param argument="--mrna" type="data" format="tsv" optional="true" label="Mito-RNA genes file" help="Single column tsv of mitochondrial genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
+            <param argument="--rrna" type="data" format="tsv" optional="true" label="Ribosomal RNA file" help="Single column tsv of ribosomal genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
+            <param argument="--dumpMtx" type="boolean" truevalue="--dumpMtx" falsevalue="" checked="false" label=" Dump cell v transcripts count matrix in MTX format" help="Converts the default binary format of alevin for gene-count matrix into a human readable mtx (matrix market exchange) sparse format."/>
+            <param argument="--forceCells" type="integer" min="0" optional="true" label="Number of cells" help="Explicitly specify the number of cells."/>
+            <param argument="--expectCells" type="integer" min="0" optional="true" label="Upper bound on expected number of cells" help="define a close upper bound on expected number of cells."/>
+            <param argument="--numCellBootstraps" type="integer" min="0" value="0" optional="true" label="Generate mean and variance for cell x gene matrix by boostrap" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/>
+            <param argument="--minScoreFraction" type="float" optional="true" label="Minimum allowed score for a mapping" help="This value controls the minimum allowed score for a mapping to be considered valid. It matters only when --validateMappings has been passed to Salmon. The maximum possible score for a fragment is ms = read_len * ma (or ms = (left_read_len + right_read_len) * ma for paired-end reads).
                 The argument to --minScoreFraction determines what fraction of the maximum score s a mapping must achieve to be potentially retained. For a minimum score fraction of f, only mappings with a score less than (f * s) will be kept. Mappings with lower scores will be considered as low-quality, and will be discarded."/>
-            <param name="keepCBFraction" type="float" optional="true" help="Fraction of cellular barcodes to keep (Between 0 and 1)."/>
-            <param name="lowRegionMinNumBarcodes" type="integer" optional="true" help="Minimum number of cell barcodes to use fo learning low confidence region (defaults to 200)"/>
-            <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/>
-            <param name="freqThreshold" type="integer" optional="true" help="Minimum frequency for a barcode to be considered. Defaults to 10"/>
+            <param argument="--keepCBFraction" type="float" min="0" max="1" optional="true" label="Fraction of cellular barcodes to keep" help="Use 1 to quantify all"/>
+            <param argument="--maxNumBarcodes" type="integer" min="0" value="100000" label="Maximum allowable limit to process the cell barcodes" help="Default: 100000"/>
+            <param argument="--freqThreshold" type="integer" min="0" value="10" optional="true" label="Minimum frequency for a barcode to be considered" help="Default: 10"/>
         </section>
     </inputs>
     <outputs>
-        <data name="quants_mat_tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv">
+        <data name="quants_mat_tsv" label="${tool.name} on ${on_string}: per-cell gene-count matrix (tabular)" format="txt" from_work_dir="quants_mat.tsv">
             <filter>optional["dumpMtx"] is not True</filter>
         </data>
-        <data name="quants_mat_mtx" label="quants_mat.mtx" format="mtx" from_work_dir="output/alevin/quants_mat.mtx">
+        <data name="quants_mat_mtx" label="${tool.name} on ${on_string}: per-cell gene-count matrix (MTX)" format="mtx" from_work_dir="output/alevin/quants_mat.mtx">
             <filter>optional["dumpMtx"]</filter>
         </data>
-        <data name="raw_cb_frequency_txt" label="raw_cb_frequency.txt" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt">
-            <filter>optional["dumpFeatures"]</filter>
+        <data name="quants_mat_gz" label="${tool.name} on ${on_string}: per-cell level gene-count matrix (binary)" format="gz" from_work_dir="output/alevin/quants_mat.gz"/>
+        <data name="quants_mat_cols_txt" label="${tool.name} on ${on_string}: column headers (gene-ids)" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
+        <data name="quants_mat_rows_txt" label="${tool.name} on ${on_string}: row index (CB-ids)" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
+        <data name="quants_tier_mat" label="${tool.name} on ${on_string}: tier categorization" format="gz" from_work_dir="output/alevin/quants_tier_mat.gz"/>
+        <data name="featureDump_txt" label="${tool.name} on ${on_string}: cell-level information (featureDump)" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
+        <data name="raw_cb_frequency_txt" label="${tool.name} on ${on_string}: raw CB classification frequencies" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt">
+            <filter>output_files and 'dumpFeatures' in output_files</filter>
         </data>
-        <data name="quants_mat_cols_txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
-        <data name="quants_mat_rows_txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
-        <data name="quants_tier_mat" label="quants_tier_mat" format="mtx" from_work_dir="output/alevin/quants_tier_mat"/>
-        <data name="alevin_log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">
-            <filter>allout</filter>
+        <data name="whitelist_txt" label="${tool.name} on ${on_string}: whitelist" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
+
+        <data name="auxiliar_files" label="${tool.name} on ${on_string}: auxiliar info files" format="tgz" from_work_dir="aux_info.tar.gz">
+            <filter>output_files and 'auxiliar_info' in output_files</filter>
         </data>
-        <data name="featureDump_txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
-        <data name="whitelist_txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
-        <data name="bfh_txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt">
-            <filter>optional["dumpBfh"]</filter>
+        <data name="salmon_quant_log" format="txt" label="${tool.name} on ${on_string}: Salmon log file" from_work_dir="output/logs/salmon_quant.log">
+            <filter>output_files and 'salmon_log' in output_files</filter>
+        </data>
+        <data name="cmd_info" label="${tool.name} on ${on_string}: command info (JSON)" format="json" from_work_dir="output/cmd_info.json">
+            <filter>output_files and 'commands' in output_files</filter>
         </data>
-        <data name="quants_mean_mat" label="quants_mean_mat" format="mtx" from_work_dir="output/alevin/quants_mean_mat">
-            <filter>optional["numCellBootstraps"]</filter>
+        <data name="flenDist_txt" format="txt" label="${tool.name} on ${on_string}: observed fragment length distribution" from_work_dir="output/libParams/flenDist.txt">
+            <filter>output_files and 'fragment_length' in output_files</filter>
         </data>
-        <data name="quants_var_mat" label="quants_var_mat" format="mtx" from_work_dir="output/alevin/quants_var_mat">
+        <data name="bfh_txt" label="${tool.name} on ${on_string}: full CB-EC-UMI-count data-structure" format="txt" from_work_dir="output/alevin/bfh.txt">
+            <filter>output_files and 'dumpBfh' in output_files</filter>
+        </data>
+        <data name="quants_mean_mat" label="${tool.name} on ${on_string}: count matrix mean file" format="gz" from_work_dir="output/alevin/quants_mean_mat.gz">
             <filter>optional["numCellBootstraps"]</filter>
         </data>
-        <data name="quants_boot_rows_txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">
+        <data name="quants_var_mat" label="${tool.name} on ${on_string}: count matrix variance file" format="gz" from_work_dir="output/alevin/quants_var_mat.gz">
+            <filter>optional["numCellBootstraps"]</filter>
+        </data>
+        <data name="quants_boot_rows_txt" label="${tool.name} on ${on_string}: bootstraps rows" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">
             <filter>optional["numCellBootstraps"]</filter>
         </data>
-        <data name="alevinmeta_info_json" format="json" label="meta_info.json" from_work_dir="output/aux_info/alevin_meta_info.json">
-            <filter>allout</filter>
-        </data>
-        <data name="ambig_info_tsv" format="tsv" label="ambig_info.tsv" from_work_dir="output/aux_info/ambig_info.tsv">
-            <filter>allout</filter>
-        </data>
-        <data name="meta_info_json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json">
-            <filter>allout</filter>
-        </data>
-        <data name="expected_bias" format="txt" label="expected_bias" from_work_dir="output/aux_info/fld"/>
-        <data name="observed_bias" format="txt" label="observed_bias" from_work_dir="output/aux_info/observed_bias"/>
-        <data name="observed_bias_3p" format="txt" label="observed_bias_3p" from_work_dir="output/aux_info/observed_bias_3p"/>
-        <data name="flenDist_txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/>
-        <data name="salmon_quant_log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log">
-            <filter>allout</filter>
-        </data>
-        <collection name="umigraphs" type="list" label="Umi graph PDFs">
-            <filter>optional["dumpUmiGraph"]</filter>
-            <discover_datasets pattern="__name_and_ext__" ext="pdf" directory="fixed"/>
+        <collection name="umigraphs" type="list" label="${tool.name} on ${on_string}: UMI graph PDFs">
+            <filter>output_files and 'dumpUmiGraph' in output_files</filter>
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf" format="pdf" directory="fixed"/>
         </collection>
-        <data name="cmd_info.json" label="cmd_info.json" format="json" from_work_dir="output/cmd_info.json">
-            <filter>allout</filter>
-        </data>
     </outputs>
     <tests>
+        <test expect_num_outputs="8">
+            <conditional name="refTranscriptSource">
+                <param name="TranscriptSource" value="history"/>
+                <section name="s_index">
+                    <param name="fasta" value="minitranscript.fa"/>
+                </section>
+            </conditional>
+            <conditional name="pairstraight">
+                <param name="readselect" value="paired"/>
+                <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
+                <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
+                <param name="orientation" value="I"/>
+                <param name="strandedness" value="SR"/>
+            </conditional>
+            <conditional name="protocol_cond">
+                <param name="protocol" value="--chromium"/>
+            </conditional>
+            <param name="tgmap" value="minitxp.tsv"/>
+            <param name="output_files" value="dumpFeatures"/>
+            <section name="optional">
+                <param name="keepCBFraction" value="1"/>
+                <param name="freqThreshold" value="5"/>
+                <param name="dumpMtx" value="true"/>
+            </section>
+            <output name="quants_mat_mtx" file="alevin_mat_01.mtx" ftype="mtx" sort="true"/>
+        </test>
         <test expect_num_outputs="11">
             <conditional name="refTranscriptSource">
                 <param name="TranscriptSource" value="history"/>
@@ -236,15 +285,45 @@
                 <param name="orientation" value="I"/>
                 <param name="strandedness" value="SR"/>
             </conditional>
-            <param name="protocol" value="--chromium"/>
+            <conditional name="protocol_cond">
+                <param name="protocol" value="--chromium"/>
+            </conditional>
             <param name="tgmap" value="minitxp.tsv"/>
+            <param name="output_files" value="dumpFeatures"/>
             <section name="optional">
                 <param name="keepCBFraction" value="1"/>
-                <param name="dumpFeatures" value="Yes"/>
+                <param name="numCellBootstraps" value="2"/>
                 <param name="freqThreshold" value="5"/>
-                <param name="dumpMtx" value="Yes"/>
+                <param name="dumpMtx" value="true"/>
             </section>
-            <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true" lines_diff="62"/>
+            <output name="quants_mat_mtx" file="alevin_mat_02.mtx" ftype="mtx" sort="true"/>
+        </test>
+        <test expect_num_outputs="8">
+            <conditional name="refTranscriptSource">
+                <param name="TranscriptSource" value="history"/>
+                <section name="s_index">
+                    <param name="fasta" value="minitranscript.fa"/>
+                </section>
+            </conditional>
+            <conditional name="pairstraight">
+                <param name="readselect" value="paired"/>
+                <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
+                <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
+                <param name="orientation" value="I"/>
+                <param name="strandedness" value="SR"/>
+            </conditional>
+            <conditional name="protocol_cond">
+                <param name="protocol" value="-\-indropV2"/>
+                <param name="w1" value="ATCAT"/>
+            </conditional>
+            <param name="tgmap" value="minitxp.tsv"/>
+            <param name="output_files" value="dumpFeatures"/>
+            <section name="optional">
+                <param name="keepCBFraction" value="1"/>
+                <param name="freqThreshold" value="5"/>
+                <param name="dumpMtx" value="true"/>
+            </section>
+            <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx" ftype="mtx" sort="true"/>
         </test>
         <test expect_num_outputs="14">
             <conditional name="refTranscriptSource">
@@ -260,16 +339,35 @@
                 <param name="orientation" value="I"/>
                 <param name="strandedness" value="SR"/>
             </conditional>
-            <param name="protocol" value="--chromium"/>
+            <conditional name="protocol_cond">
+                <param name="protocol" value="--chromium"/>
+            </conditional>
             <param name="tgmap" value="minitxp.tsv"/>
+            <param name="output_files" value="dumpFeatures,salmon_log,fragment_length,auxiliar_info,dumpUmiGraph,dumpBfh,commands"/>
             <section name="optional">
-                <param name="keepCBFraction" value="1"/>
-                <param name="dumpFeatures" value="Yes"/>
-                <param name="numCellBootstraps" value="2"/>
-                <param name="freqThreshold" value="5"/>
-                <param name="dumpMtx" value="Yes"/>
+                <param name="dumpMtx" value="true"/>
             </section>
-            <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true" lines_diff="62"/>
+            <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true"/>
+            <output name="salmon_quant_log" ftype="txt">
+                <assert_contents>
+                    <has_text text="Index contained 322 targets"/>
+                    <has_text text="Counted 14 total reads in the equivalence classes"/>
+                </assert_contents>
+            </output>
+            <output name="flenDist_txt" file="length_distribution.txt" ftype="txt"/>
+            <output name="auxiliar_files" ftype="tgz">
+                <assert_contents>
+                    <has_size value="1898" delta="100"/>
+                </assert_contents>
+            </output>
+            <output_collection name="umigraphs" type="list" count="14">
+                <element name="AGTGGGATCTTAACCT">
+                    <assert_contents>
+                        <has_size value="4017" delta="1000"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="bfh_txt" file="full_data_structure.txt" ftype="txt"/>
         </test>
     </tests>
     <help><![CDATA[
--- 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>  <!-- 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}'
--- 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
--- /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
--- /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
@@ -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
--- /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
--- /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
@@ -0,0 +1,551 @@
+322
+218
+8
+ENST00000641515.2
+ENST00000335137.4
+ENST00000426406.3
+ENST00000420190.6
+ENST00000437963.5
+ENST00000342066.8
+ENST00000618181.4
+ENST00000622503.4
+ENST00000618323.4
+ENST00000616016.4
+ENST00000618779.4
+ENST00000616125.4
+ENST00000620200.4
+ENST00000617307.4
+ENST00000341065.8
+ENST00000455979.1
+ENST00000327044.7
+ENST00000338591.8
+ENST00000622660.1
+ENST00000466300.1
+ENST00000379410.7
+ENST00000379409.6
+ENST00000379407.7
+ENST00000491024.1
+ENST00000341290.6
+ENST00000433179.3
+ENST00000428771.6
+ENST00000304952.10
+ENST00000484667.2
+ENST00000624697.4
+ENST00000624652.1
+ENST00000649529.1
+ENST00000379370.7
+ENST00000620552.4
+ENST00000652369.1
+ENST00000651234.1
+ENST00000453464.3
+ENST00000379339.5
+ENST00000379325.7
+ENST00000421241.6
+ENST00000477196.5
+ENST00000467751.5
+ENST00000379320.5
+ENST00000379319.5
+ENST00000434641.5
+ENST00000462097.5
+ENST00000475119.5
+ENST00000442117.5
+ENST00000427787.5
+ENST00000480643.1
+ENST00000379290.5
+ENST00000379289.5
+ENST00000379288.3
+ENST00000486379.1
+ENST00000328596.10
+ENST00000379268.7
+ENST00000486728.5
+ENST00000379265.5
+ENST00000379236.4
+ENST00000360001.11
+ENST00000660930.1
+ENST00000465727.5
+ENST00000263741.12
+ENST00000655486.1
+ENST00000403997.2
+ENST00000379198.5
+ENST00000330388.2
+ENST00000450390.6
+ENST00000347370.6
+ENST00000349431.10
+ENST00000400929.6
+ENST00000464036.5
+ENST00000360466.6
+ENST00000400930.8
+ENST00000473215.5
+ENST00000435198.5
+ENST00000509720.5
+ENST00000466752.5
+ENST00000503294.5
+ENST00000477894.5
+ENST00000422076.5
+ENST00000502382.1
+ENST00000488418.2
+ENST00000379116.9
+ENST00000379101.8
+ENST00000338555.6
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+ENST00000470022.1
+ENST00000325425.12
+ENST00000379099.3
+ENST00000354700.10
+ENST00000353662.4
+ENST00000354980.7
+ENST00000379031.10
+ENST00000467712.1
+ENST00000540437.5
+ENST00000545578.5
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+ENST00000618806.4
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+ENST00000421495.6
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+ENST00000419704.5
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+ENST00000527098.5
+ENST00000528879.5
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+ENST00000526797.5
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+ENST00000530031.5
+ENST00000429572.5
+ENST00000534345.5
+ENST00000531019.5
+ENST00000498476.6
+ENST00000470679.3
+ENST00000525285.1
+ENST00000343938.9
+ENST00000488011.1
+ENST00000339381.6
+ENST00000378891.9
+ENST00000378888.10
+ENST00000610709.2
+ENST00000632445.1
+ENST00000631679.1
+ENST00000342753.8
+ENST00000309212.10
+ENST00000445648.5
+ENST00000477278.3
+ENST00000338370.7
+ENST00000338338.9
+ENST00000321751.9
+ENST00000378853.3
+ENST00000400809.8
+ENST00000482621.5
+ENST00000408952.8
+ENST00000481223.6
+ENST00000488340.5
+ENST00000408918.8
+ENST00000425598.2
+ENST00000497013.1
+ENST00000344843.12
+ENST00000492508.1
+ENST00000482352.1
+ENST00000520296.5
+ENST00000427211.3
+ENST00000537107.5
+ENST00000454272.2
+ENST00000442470.1
+ENST00000378821.3
+ENST00000495558.1
+ENST00000338660.5
+ENST00000476993.2
+ENST00000471398.1
+ENST00000378785.6
+ENST00000475091.2
+ENST00000308647.7
+ENST00000378756.7
+ENST00000378755.9
+ENST00000339113.8
+ENST00000536055.5
+ENST00000400830.3
+ENST00000378733.9
+ENST00000425828.1
+ENST00000624426.1
+ENST00000291386.4
+ENST00000359060.5
+ENST00000422725.4
+ENST00000520777.5
+ENST00000355826.9
+ENST00000518681.5
+ENST00000505820.6
+ENST00000489635.5
+ENST00000514363.1
+ENST00000487053.5
+ENST00000502470.5
+ENST00000378712.5
+ENST00000510793.5
+ENST00000504599.5
+ENST00000503789.5
+ENST00000378708.5
+ENST00000506488.5
+ENST00000514234.5
+ENST00000486072.1
+ENST00000483015.1
+ENST00000356026.9
+ENST00000472264.1
+ENST00000512731.5
+ENST00000378675.7
+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
+ENST00000509982.5
+ENST00000460465.5
+ENST00000357760.6
+ENST00000358779.9
+ENST00000378633.5
+ENST00000479362.1
+ENST00000401096.2
+ENST00000355439.7
+ENST00000643905.1
+ENST00000341426.9
+ENST00000341991.7
+ENST00000378625.5
+ENST00000342348.9
+ENST00000498806.1
+ENST00000469045.5
+ENST00000489538.1
+ENST00000497186.5
+ENST00000610897.4
+ENST00000615252.4
+ENST00000378609.9
+ENST00000439272.6
+ENST00000434686.6
+ENST00000437146.1
+ENST00000378604.3
+ENST00000307786.8
+ENST00000378602.3
+ENST00000310991.8
+ENST00000378598.4
+ENST00000470931.2
+ENST00000416272.1
+ENST00000642590.1
+ENST00000493964.5
+ENST00000378590.4
+ENST00000638411.1
+ENST00000378585.7
+ENST00000639045.1
+ENST00000640067.1
+ENST00000638771.1
+ENST00000640949.1
+ENST00000640030.1
+ENST00000640981.1
+ENST00000638763.1
+ENST00000638804.1
+ENST00000378567.8
+ENST00000468310.5
+ENST00000503297.1
+ENST00000400921.6
+ENST00000495347.5
+ENST00000461106.6
+ENST00000461465.5
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+ENST00000481140.5
+ENST00000482686.5
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+ENST00000470986.5
+ENST00000470511.5
+ENST00000471018.6
+ENST00000466352.5
+ENST00000497183.5
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+ENST00000400919.7
+ENST00000428120.5
+ENST00000414253.5
+ENST00000400918.7
+ENST00000378543.2
+ENST00000378546.9
+ENST00000440825.6
+ENST00000420515.1
+ENST00000378536.5
+ENST00000378531.8
+ENST00000378529.7
+ENST00000449373.2
+ENST00000378525.2
+ENST00000494279.2
+ENST00000378513.7
+ENST00000378518.5
+ENST00000605895.6
+ENST00000306256.13
+ENST00000378512.5
+ENST00000443438.5
+ENST00000488353.2
+ENST00000288774.7
+ENST00000650293.1
+ENST00000447513.6
+ENST00000507596.5
+ENST00000510434.1
+ENST00000508384.5
+ENST00000502666.1
+ENST00000514502.1
+ENST00000609981.5
+ENST00000449969.5
+ENST00000378486.8
+ENST00000419816.6
+ENST00000278878.6
+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fasta	Mon Dec 05 15:47:45 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
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/length_distribution.txt	Mon Dec 05 15:47:45 2022 +0000
@@ -0,0 +1,2 @@
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