Mercurial > repos > iuc > hal_halstats
changeset 0:25dcde5bf94e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 6244b9d15a5ad97ae20191e2f8fbafe2050c3cac
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hal_halStats.xml Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,492 @@ +<tool id="hal_halstats" name="halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>retrieves basic statistics from a HAL file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command detect_errors="aggressive"><![CDATA[ + set -o pipefail; ## Sets the pipeline’s exit code to halStats’s on failure. + ( ## echo headers for specific numerical data + #if $mode.option == '--baseComp': + echo -e 'fraction_of_As\tfraction_of_Gs\tfraction_of_Cs\tfraction_of_Ts'; + #else if $mode.option == '--numSegments': + echo -e 'numTopSegments\tnumBottomSegments'; + #end if + halStats + #if $mode.option == '--allCoverage': + --allCoverage + #else if $mode.option == '--branches': + --branches + #else if $mode.option == '--genomes': + --genomes + #else if $mode.option == '--metaData': + --metaData + #else if $mode.option == '--root': + --root + #else if $mode.option == '--tree': + --tree + #else if $mode.option == '--baseComp': + --baseComp '$mode.baseComp' + #else if $mode.option == '--bedSequences': + --bedSequences '$mode.bedSequences' + #else if $mode.option == '--bottomSegments': + --bottomSegments '$mode.bottomSegments' + #else if $mode.option == '--branchLength': + --branchLength '$mode.branchLength' + #else if $mode.option == '--children': + --children '$mode.children' + #else if $mode.option == '--chromSizes': + --chromSizes '$mode.chromSizes' + #else if $mode.option == '--coverage': + --coverage '$mode.coverage' + #else if $mode.option == '--genomeMetaData': + --genomeMetaData '$mode.genomeMetaData' + #else if $mode.option == '--numSegments': + --numSegments '$mode.numSegments' + #else if $mode.option == '--parent': + --parent '$mode.parent' + #else if $mode.option == '--percentID': + --percentID '$mode.percentID' + #else if $mode.option == '--sequenceStats': + --sequenceStats '$mode.sequenceStats' + #else if $mode.option == '--sequences': + --sequences '$mode.sequences' + #else if $mode.option == '--span': + --span '$mode.span' + #else if $mode.option == '--spanRoot': + --spanRoot '$mode.spanRoot' + #else if $mode.option == '--topSegments': + --topSegments '$mode.topSegments' + #end if + '$input_hal' + ## Pipes specific output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree. + #if $mode.option == '--allCoverage' or $mode.option == '--sequenceStats' or $mode.option == '--percentID' or $mode.option == '--coverage': + | tr ',' '\t' + #else if $mode.option == '--numSegments': + | tr ' ' '\t' ## Replace spaces + #end if + ) > '$out_file' + ]]></command> + <inputs> + <expand macro="input_hal"/> + <conditional name="mode"> + <param name="option" type="select" label="Select the type of statistics you are interested in"> + <option value="" selected="true">Basic overview</option> + <option value="--genomes">List of genomes in alignment (--genomes)</option> + <option value="--sequences">List of sequences in a given genome (--sequences)</option> + <option value="--bedSequences">List of sequences in a given genome (in BED format) (--bedSequences)</option> + <option value="--sequenceStats">Stats for each sequence in a given genome (--sequenceStats)</option> + <option value="--tree">Newick tree (--tree)</option> + <option value="--branches">List of branches specified by the child genome (--branches)</option> + <option value="--span">Branches on path (or spanning tree) between given list of genomes (--span)</option> + <option value="--spanRoot">Genomes on path (or spanning tree) with spanning tree root between given list of genomes (--spanRoot)</option> + <option value="--children">Names of children of a given genome (--children)</option> + <option value="--root">Root genome name (--root)</option> + <option value="--parent">Parent name of a given genome (--parent)</option> + <option value="--branchLength">Branch length between a given genome and its parent (--branchLength)</option> + <option value="--numSegments">Number of top and of bottom segments of a given genome (--numSegments)</option> + <option value="--topSegments">Coordinates of all top segments of a given genome (in BED format) (--topSegments)</option> + <option value="--bottomSegments">Coordinates of all bottom segments of a given genome (in BED format) (--bottomSegments)</option> + <option value="--baseComp">Base composition by sampling every step bases (--baseComp)</option> + <option value="--genomeMetaData">Metadata for a given genome (--genomeMetaData)</option> + <option value="--metaData">Metadata for the entire alignment (--metaData)</option> + <option value="--chromSizes">Name and length of each sequence in a given genome (in format used by wigToBigWig) (--chromSizes)</option> + <option value="--percentID">Percent ID of a given genome with all other genomes (--percentID)</option> + <option value="--coverage">Histogram of coverage of a given genome with all genomes (--coverage)</option> + <option value="--allCoverage">Histogram of coverage from all genomes to all genomes (--allCoverage)</option> + </param> + <when value=""/> + <when value="--allCoverage"/> + <when value="--baseComp"> + <param name="baseComp" type="text" value="" label="Genome and step" help="Parameter value is of the form genome,step. Ex: human,1000"> + <expand macro="sanitizer_default"/> + <validator type="regex" message="Please enter as genome,step without leading or trailing spaces">^[^\s,](?:[^,]*[^\s,])?,[0-9]+$</validator> + </param> + </when> + <when value="--bedSequences"> + <param name="bedSequences" type="text" value="" label="Genome name"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </when> + <when value="--topSegments"> + <param name="topSegments" type="text" value="" label="Genome name"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </when> + <when value="--bottomSegments"> + <param name="bottomSegments" type="text" value="" label="Genome name"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </when> + <when value="--branchLength"> + <param name="branchLength" type="text" value="" label="Genome name"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </when> + <when value="--branches"/> + <when value="--children"> + <param name="children" type="text" value="" label="Genome name"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </when> + <when value="--chromSizes"> + <param name="chromSizes" type="text" value="" label="Genome name"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </when> + <when value="--coverage"> + <param name="coverage" type="text" value="" label="Genome name"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </when> + <when value="--genomeMetaData"> + <param name="genomeMetaData" type="text" value="" label="Genome name"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </when> + <when value="--genomes"/> + <when value="--metaData"/> + <when value="--numSegments"> + <param name="numSegments" type="text" value="" label="Genome name"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </when> + <when value="--parent"> + <param name="parent" type="text" value="" label="Genome name"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </when> + <when value="--percentID"> + <param name="percentID" type="text" value="" label="Genome name" help="Only non-duplicated and unambiguous sites are considered"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </when> + <when value="--root"/> + <when value="--sequenceStats"> + <param name="sequenceStats" type="text" value="" label="Genome name"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </when> + <when value="--sequences"> + <param name="sequences" type="text" value="" label="Genome name"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </when> + <when value="--span"> + <param name="span" type="text" value="" label="List of genomes" help="Enter a comma-separated (no spaces) list of genomes"> + <expand macro="sanitizer_default"/> + <expand macro="validator_comma_list"/> + </param> + </when> + <when value="--spanRoot"> + <param name="spanRoot" type="text" value="" label="List of genomes" help="Enter a comma-separated (no spaces) list of genomes"> + <expand macro="sanitizer_default"/> + <expand macro="validator_comma_list"/> + </param> + </when> + <when value="--tree"/> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="txt" label="${tool.name} on ${on_string}: Stats"> + <change_format> + <when input="mode.option" value="--numSegments" format="tabular"/> + <when input="mode.option" value="--allCoverage" format="tabular"/> + <when input="mode.option" value="--sequenceStats" format="tabular"/> + <when input="mode.option" value="--percentID" format="tabular"/> + <when input="mode.option" value="--coverage" format="tabular"/> + <when input="mode.option" value="--chromSizes" format="tabular"/> + <when input="mode.option" value="--baseComp" format="tabular"/> + <when input="mode.option" value="--metaData" format="tabular"/> + <when input="mode.option" value="--genomeMetaData" format="tabular"/> + <when input="mode.option" value="--bedSequences" format="bed"/> + <when input="mode.option" value="--topSegments" format="bed"/> + <when input="mode.option" value="--bottomSegments" format="bed"/> + </change_format> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <output name="out_file" ftype="txt"> + <assert_contents> + <has_line line="(Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/> + <has_line line="GenomeName, NumChildren, Length, NumSequences, NumTopSegments, NumBottomSegments"/> + <has_line line="Genome_0, 3, 1758, 1, 0, 8"/> + <has_n_lines n="10"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--allCoverage"/> + </conditional> + <output name="out_file" ftype="tabular"> + <assert_contents> + <has_line line="FromGenome	 ToGenome	 sitesCovered1Times	 sitesCovered2Times	 sitesCovered3Times	 sitesCovered4Times	 sitesCovered5Times"/> + <has_line line="Genome_1	 Genome_1	 5472	 4688	 3516	 2637	 1465"/> + <has_n_lines n="10"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--bedSequences"/> + <param name="bedSequences" value="Genome_0"/> + </conditional> + <output name="out_file" ftype="bed"> + <assert_contents> + <has_line line="Genome_0_seq	0	1758"/> + <has_n_lines n="1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--topSegments"/> + <param name="topSegments" value="Genome_1"/> + </conditional> + <output name="out_file" ftype="bed"> + <assert_contents> + <has_line line="Genome_1_seq	0	293"/> + <has_line line="Genome_1_seq	3223	3399"/> + <has_line line="Genome_1_seq	5274	5472"/> + <has_n_lines n="28"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--bottomSegments"/> + <param name="bottomSegments" value="Genome_0"/> + </conditional> + <output name="out_file" ftype="bed"> + <assert_contents> + <has_line line="Genome_0_seq	0	293"/> + <has_line line="Genome_0_seq	1033	1172"/> + <has_line line="Genome_0_seq	1465	1758"/> + <has_n_lines n="8"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--tree"/> + </conditional> + <output name="out_file" ftype="txt"> + <assert_contents> + <has_line line="(Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/> + <has_n_lines n="1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--spanRoot"/> + <param name="spanRoot" value="Genome_0,Genome_1"/> + </conditional> + <output name="out_file" ftype="txt"> + <assert_contents> + <has_text text="Genome_0 Genome_1"/> + <has_n_lines n="1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--sequences"/> + <param name="sequences" value="Genome_0"/> + </conditional> + <output name="out_file" ftype="txt"> + <assert_contents> + <has_line line="Genome_0_seq"/> + <has_n_lines n="1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--sequenceStats"/> + <param name="sequenceStats" value="Genome_0"/> + </conditional> + <output name="out_file" ftype="tabular"> + <assert_contents> + <has_line line="SequenceName	 Length	 NumTopSegments	 NumBottomSegments"/> + <has_line line="Genome_0_seq	 1758	 0	 8"/> + <has_n_lines n="3"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--root"/> + </conditional> + <output name="out_file" ftype="txt"> + <assert_contents> + <has_line line="Genome_0"/> + <has_n_lines n="1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--parent"/> + <param name="parent" value="Genome_1"/> + </conditional> + <output name="out_file" ftype="txt"> + <assert_contents> + <has_line line="Genome_0"/> + <has_n_lines n="1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--percentID"/> + <param name="percentID" value="Genome_0"/> + </conditional> + <output name="out_file" ftype="tabular"> + <assert_contents> + <has_line line="Genome	 % ID	 numID	 numSites"/> + <has_line line="Genome_0	 1	 1758	 1758"/> + <has_n_lines n="5"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--numSegments"/> + <param name="numSegments" value="Genome_1"/> + </conditional> + <output name="out_file" ftype="tabular"> + <assert_contents> + <has_line line="numTopSegments	numBottomSegments"/> + <has_line line="28	0"/> + <has_n_lines n="2"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--genomes"/> + </conditional> + <output name="out_file" ftype="txt"> + <assert_contents> + <has_line line="Genome_0 Genome_1 Genome_2 Genome_3"/> + <has_n_lines n="1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--children"/> + <param name="children" value="Genome_0"/> + </conditional> + <output name="out_file" ftype="txt"> + <assert_contents> + <has_line line="Genome_1 Genome_2 Genome_3"/> + <has_n_lines n="1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--chromSizes"/> + <param name="chromSizes" value="Genome_1"/> + </conditional> + <output name="out_file" ftype="tabular"> + <assert_contents> + <has_line line="Genome_1_seq	5472"/> + <has_n_lines n="1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--branches"/> + </conditional> + <output name="out_file" ftype="txt"> + <assert_contents> + <has_line line="Genome_1 Genome_2 Genome_3"/> + <has_n_lines n="1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--branchLength"/> + <param name="branchLength" value="Genome_1"/> + </conditional> + <output name="out_file" ftype="txt"> + <assert_contents> + <has_line line="1"/> + <has_n_lines n="1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="option" value="--baseComp"/> + <param name="baseComp" value="Genome_0,1000"/> + </conditional> + <output name="out_file" ftype="tabular"> + <assert_contents> + <has_line line="fraction_of_As	fraction_of_Gs	fraction_of_Cs	fraction_of_Ts"/> + <has_line line="0.5	0	0.5	0"/> + <has_n_lines n="2"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +halStats prints structural and summary information from a HAL file, which must be provided as input. +It can list genomes, sequences, sizes, and relationships, provides sequence level statistics such as coverage histograms and percent ID, and can export sequence or segment information in BED format. + +It is useful for quick inspection of a HAL file and for extracting per genome or per sequence summaries. + +----- + +**Output** + +The tool generates different output formats based on the selected type of statistic: + +- **Tabular** for --coverage, --allCoverage, --sequenceStats, --percentID, --baseComp, --chromSizes, --metaData, --numSegments, or --genomeMetaData +- **BED** for --bedSequences, --topSegments, or --bottomSegments +- Plain **text** for all other type of statistics + + ]]></help> + <expand macro="citation"/> + <expand macro="creator"/> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,191 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">cactus</requirement> + </requirements> + </xml> + <token name="@TOOL_VERSION@">2.9.9</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">25.1</token> + <xml name="stdio"> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <!-- In case the return code has not been set properly check stderr too --> + <regex source="stderr" match="Error:"/> + <regex source="stderr" match="Exception:"/> + <regex match="terminate called after throwing"/> + <regex match="hal_exception"/> + </stdio> + </xml> + <xml name="input_hal"> + <param name="input_hal" type="data" format="hal" label="HAL file"/> + </xml> + <xml name="input_mapping"> + <param name="input_mapping" type="data" format="txt,tsv" label="File for renaming" help="Tab-separated file. First column: existing name, second column: new name. Any names not provided will stay the same"/> + </xml> + <xml name="hal_backend_format"> + <conditional name="backend"> + <param name="format" type="select" label="Back-end storage format for new HAL file" help="Select the back-end storage format for the new HAL file (--format)"> + <option value="hdf5" selected="true">HDF5</option> + <!-- + At the moment, creating a HAL file in mmap format is disabled. The creation in HDF5 format is enforced. + <option value="mmap">mmap</option> + --> + </param> + <when value="hdf5"/> + <!-- + <when value="mmap"> + <param argument="- -mmapFileSize" type="integer" label="Initial file size" value="64" min="1" help="Initial mmap HAL file size in gigabytes"/> + </when> + --> + </conditional> + </xml> + <xml name="params_mmap_size"> + <param argument="--mmapFileSize" type="integer" label="Initial file size" value="64" min="1" help="Initial mmap HAL file size in gigabytes"/> + </xml> + <xml name="params_start"> + <param argument="--start" type="integer" value="0" label="Start coordinate" help="Coordinate within reference genome (or reference sequence if set) to start at"/> + </xml> + <xml name="params_length"> + <param argument="--length" type="integer" min="0" value="0" label="Length to process" help="Length of the reference genome (or reference sequence if set) to process. If set to 0, the entire thing is processed"/> + </xml> + <xml name="params_onlySequenceNames"> + <param argument="--onlySequenceNames" type="boolean" truevalue="--onlySequenceNames" falsevalue="" checked="false" label="Only sequence names" help="Use only sequence names for output names. By default, the UCSC convention of Genome.Sequence is used"/> + </xml> + <xml name="params_root_optional"> + <param argument="--root" type="text" value="" optional="true" label="Root genome" help="Process only genomes belonging to the subtree rooted at the root genome"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </xml> + <xml name="params_refGenome"> + <param name="refGenome" type="text" value="" label="Reference genome" help="Reference genome to process"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </xml> + <xml name="params_genomeNoRoot"> + <param name="genome" type="text" value="" label="Genome name" help="Name of genome to process (can't be root)"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </xml> + <xml name="params_rootGenome"> + <param name="rootGenome" type="text" value="" label="Root genome" help="Process only genomes belonging to the subtree rooted at the root genome"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </xml> + <xml name="params_rootGenome_optional"> + <param argument="--rootGenome" type="text" value="" optional="true" label="Root genome" help="Process only genomes belonging to the subtree rooted at the root genome"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </xml> + <xml name="params_targetGenomes"> + <param name="targetGenomes" type="text" value="" label="Target genomes" help="Comma-separated (no spaces) list of target genomes (others are excluded)"> + <expand macro="sanitizer_default"/> + <expand macro="validator_comma_list"/> + </param> + </xml> + <xml name="params_targetGenomes_optional"> + <param argument="--targetGenomes" type="text" value="" optional="true" label="Target genomes" help="Comma-separated (no spaces) list of target genomes (others are excluded) (vist all if empty)"> + <expand macro="sanitizer_default"/> + <expand macro="validator_comma_list"/> + </param> + </xml> + <xml name="params_sequence"> + <param name="sequence" type="text" value="" label="Reference sequence" help="Reference sequence in reference genome to process"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </xml> + <xml name="params_srcGenome"> + <param name="srcGenome" type="text" label="Source genome" help="Source genome present in both input files from which coordinates should be mapped from"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </xml> + <xml name="params_tgtGenome"> + <param name="tgtGenome" type="text" label="Target genome" help="Target genome present in HAL file to which coordinates should be mapped to"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </xml> + <xml name="params_conditional_refGenome"> + <conditional name="genome"> + <param name="reference" type="select" label="Reference genome" help="Select the genome to use as reference"> + <option value="" selected="true">Use HAL tree root (default)</option> + <option value="custom">Specific reference genome (--refGenome)</option> + </param> + <when value=""/> + <when value="custom"> + <param name="refGenome" type="text" value="" label="Reference genome"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + <param argument="--noAncestors" type="boolean" truevalue="--noAncestors" falsevalue="" checked="false" label="Exclude ancestors" help="Should only be enabled when the chosen reference genome is a non-ancestral genome"/> + </when> + </conditional> + </xml> + <xml name="params_conditional_compression"> + <conditional name="compression"> + <param name="type" type="select" label="Compress output file"> + <option value="" selected="true">Don't compress output file (default)</option> + <option value="gz">Compress output file to .gz</option> + <option value="bz2">Compress output file to .bz2</option> + </param> + <when value=""/> + <when value="gz"/> + <when value="bz2"/> + </conditional> + </xml> + <xml name="params_numSamples"> + <param argument="--numSamples" type="integer" min="1" value="1000000" label="Number of bases" help="Number of bases to sample for calculation"/> + </xml> + <xml name="params_seed"> + <param argument="--seed" type="integer" value="0" label="Random seed" help="Set a seed for reproducibility"/> + </xml> + <xml name="params_maxGap"> + <param argument="--maxGap" type="integer" min="0" value="20" label="Max gap" help="Maximum indel length to be considered a gap. Gaps can be nested within other rearrangements"/> + </xml> + <xml name="params_maxNFraction"> + <param argument="--maxNFraction" type="float" min="0" value="1" label="Maximum fraction of Ns" help="Maximum fraction of Ns in a rearranged segment for it to not be ignored as missing data"/> + </xml> + <xml name="params_noDupes"> + <param argument="--noDupes" type="boolean" truevalue="--noDupes" falsevalue="" checked="false" label="No duplicates" help="Do not map between duplications in graph"/> + </xml> + <xml name="params_noMarkAncestors"> + <param argument="--noMarkAncestors" type="boolean" truevalue="--noMarkAncestors" falsevalue="" checked="false" label="Don't mark ancestors" help="Don't mark ancestors for update"/> + </xml> + <xml name="sanitizer_default"> + <sanitizer invalid_char=""> + <valid initial="string.ascii_letters,string.digits,string.punctuation"> + <add value=" "/> + </valid> + </sanitizer> + </xml> + <xml name="validator_trim"> + <validator type="regex" message="Enter without leading or trailing spaces">^\S(?:.*\S)?$</validator> + </xml> + <xml name="validator_comma_list"> + <validator type="regex" message="Enter a comma separated list of genomes, without leading or trailing spaces">^\S(?:[^,]*\S)?(?:,\S(?:[^,]*\S)?)*$</validator> + </xml> + <xml name="validator_newick"> + <validator type="regex" message="Enter a Newick tree">^.*;$</validator> + </xml> + <xml name="creator"> + <creator> + <person givenName="Niklas" familyName="Mayle" url="https://github.com/Maed0x"/> + <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12"/> + <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/> + </creator> + </xml> + <xml name="citation"> + <citations> + <citation type="doi">10.1093/bioinformatics/btt128</citation> + </citations> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hal2maf.bed Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,2 @@ +Genome_0_seq 0 293 +Genome_0_seq 586 879
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hal2maf_append.maf Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,90 @@ +##maf version=1 scoring=N/A +# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0; + +a +s Genome_0.Genome_0_seq 0 293 + 1758 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGTGAGGTTGACACTCCGTTCGTGTTACATGTCCGACAGGCCGCTGTGCTAGCGCCTGGGCCGCCGCCGTAACGATCCAATCGCACCTTAGCGTCAATCCACACGTGCCCCCCTTGGGGAGTCGTGTGCCCGCTGAACTTGGTGCGGGCCTACTTGCGACCTGCCGCTCTCGAGGCCGGGCCGCTCAAGAGACGGACCGAGAGTGCGGGGCCTCGCGCTCGTTGTGACCCCCATCGCGCCCCGTCT +s Genome_1.Genome_1_seq 0 293 + 5472 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGTGAGGTTGACACTCCGTTCGTGTTACATGTCCGACAGGCCGCTGTGCTAGCGCCTGGGCCGCCGCCGTAACGATCCAATCGCACCTTAGCGTCAATCCACACGTGCCCCCCTTGGGGAGTCGTGTGCCCGCTGAACTTGGTGCGGGCCTACTTGCGACCTGCCGCTCTCGAGGCCGGGCCGCTCAAGAGACGGACCGAGAGTGCGGGGCCTCGCGCTCGTTGTGACCCCCATCGCGCCCCGTCT +s Genome_1.Genome_1_seq 1758 293 + 5472 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGTGAGGTTGACACTCCGTTCGTGTTACATGTCCGACAGGCCGCTGTGCTAGCGCCTGGGCCGCCGCCGTAACGATCCAATCGCACCTTAGCGTCAATCCACACGTGCCCCCCTTGGGGAGTCGTGTGCCCGCTGAACTTGGTGCGGGCCTACTTGCGACCTGCCGCTCTCGAGGCCGGGCCGCTCAAGAGACGGACCGAGAGTGCGGGGCCTCGCGCTCGTTGTGACCCCCATCGCGCCCCGTCT +s Genome_2.Genome_2_seq 0 293 + 4270 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGTGAGGTTGACACTCCGTTCGTGTTACATGTCCGACAGGCCGCTGTGCTAGCGCCTGGGCCGCCGCCGTAACGATCCAATCGCACCTTAGCGTCAATCCACACGTGCCCCCCTTGGGGAGTCGTGTGCCCGCTGAACTTGGTGCGGGCCTACTTGCGACCTGCCGCTCTCGAGGCCGGGCCGCTCAAGAGACGGACCGAGAGTGCGGGGCCTCGCGCTCGTTGTGACCCCCATCGCGCCCCGTCT +s Genome_3.Genome_3_seq 1758 293 + 6139 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGTGAGGTTGACACTCCGTTCGTGTTACATGTCCGACAGGCCGCTGTGCTAGCGCCTGGGCCGCCGCCGTAACGATCCAATCGCACCTTAGCGTCAATCCACACGTGCCCCCCTTGGGGAGTCGTGTGCCCGCTGAACTTGGTGCGGGCCTACTTGCGACCTGCCGCTCTCGAGGCCGGGCCGCTCAAGAGACGGACCGAGAGTGCGGGGCCTCGCGCTCGTTGTGACCCCCATCGCGCCCCGTCT +s Genome_3.Genome_3_seq 0 293 + 6139 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGTGAGGTTGACACTCCGTTCGTGTTACATGTCCGACAGGCCGCTGTGCTAGCGCCTGGGCCGCCGCCGTAACGATCCAATCGCACCTTAGCGTCAATCCACACGTGCCCCCCTTGGGGAGTCGTGTGCCCGCTGAACTTGGTGCGGGCCTACTTGCGACCTGCCGCTCTCGAGGCCGGGCCGCTCAAGAGACGGACCGAGAGTGCGGGGCCTCGCGCTCGTTGTGACCCCCATCGCGCCCCGTCT + +a +s Genome_0.Genome_0_seq 293 293 + 1758 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_1.Genome_1_seq 293 293 + 5472 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_1.Genome_1_seq 2637 293 + 5472 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_2.Genome_2_seq 2051 293 + 4270 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_2.Genome_2_seq 3223 293 + 4270 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_2.Genome_2_seq 293 293 + 4270 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_3.Genome_3_seq 2637 293 + 6139 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_3.Genome_3_seq 293 293 + 6139 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG + +a +s Genome_0.Genome_0_seq 586 293 + 1758 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_1.Genome_1_seq 2930 293 + 5472 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_1.Genome_1_seq 3809 293 + 5472 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_1.Genome_1_seq 586 293 + 5472 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_2.Genome_2_seq 3516 293 + 4270 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_2.Genome_2_seq 3809 293 + 4270 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_2.Genome_2_seq 586 293 + 4270 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_3.Genome_3_seq 3809 293 + 6139 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_3.Genome_3_seq 5633 293 + 6139 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_3.Genome_3_seq 586 293 + 6139 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_3.Genome_3_seq 2930 293 + 6139 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC + +a +s Genome_0.Genome_0_seq 879 154 + 1758 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_1.Genome_1_seq 4102 154 + 5472 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_1.Genome_1_seq 4981 154 + 5472 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_1.Genome_1_seq 879 154 + 5472 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_1.Genome_1_seq 2344 154 + 5472 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_2.Genome_2_seq 2344 154 + 4270 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_2.Genome_2_seq 2930 154 + 4270 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_2.Genome_2_seq 879 154 + 4270 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_2.Genome_2_seq 1758 154 + 4270 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_3.Genome_3_seq 4102 154 + 6139 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_3.Genome_3_seq 5926 154 + 6139 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_3.Genome_3_seq 879 154 + 6139 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_3.Genome_3_seq 2344 154 + 6139 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC + +a +s Genome_0.Genome_0_seq 1033 139 + 1758 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_1.Genome_1_seq 4256 139 + 5472 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_1.Genome_1_seq 5135 139 + 5472 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_1.Genome_1_seq 1033 139 + 5472 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_1.Genome_1_seq 2498 139 + 5472 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_2.Genome_2_seq 2498 139 + 4270 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_2.Genome_2_seq 3084 139 + 4270 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_2.Genome_2_seq 1033 139 + 4270 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_2.Genome_2_seq 1912 139 + 4270 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_3.Genome_3_seq 4256 139 + 6139 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_3.Genome_3_seq 1033 139 + 6139 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_3.Genome_3_seq 2498 139 + 6139 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC + +a +s Genome_0.Genome_0_seq 1172 176 + 1758 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATG +s Genome_1.Genome_1_seq 4395 176 + 5472 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATG +s Genome_1.Genome_1_seq 4688 176 + 5472 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATG +s Genome_1.Genome_1_seq 1172 176 + 5472 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATG +s Genome_1.Genome_1_seq 2051 176 + 5472 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATG +s Genome_1.Genome_1_seq 3223 176 + 5472 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATG +s Genome_2.Genome_2_seq 1172 176 + 4270 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATG +s Genome_3.Genome_3_seq 4688 176 + 6139 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATG +s Genome_3.Genome_3_seq 1172 176 + 6139 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATG +s Genome_3.Genome_3_seq 2051 176 + 6139 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATG +s Genome_3.Genome_3_seq 3223 176 + 6139 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATG +s Genome_3.Genome_3_seq 4395 176 + 6139 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATG + +a +s Genome_0.Genome_0_seq 1348 410 + 1758 GTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCCGCGCCGCTCGTTCGCGATAGCCCTAAGGCTGGGACCCATGGAGACTGGGCATGGGGCTCCGGCACCGAGAGCTCCGTGACCCACCCCTGGGCCCGTAGGCGCCCGACCGCGACGGCCAGACCGTCGGAGGGACCCAGAAGCTGGCGTGACGTCAGGCTATAGTCATCGGCTGGAGTCCTTCGTACGGATGTGGTGCGGACCAAACCGTACGAGCGCAACGCGGCAGTCTGCGCACTGGCCGGTATTCATCCCCCCGAGATGAACGAGGCCAGGAGCCCGGCCACGCGTCGGCG +s Genome_1.Genome_1_seq 4571 117 + 5472 GTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_1.Genome_1_seq 4864 117 + 5472 GTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_1.Genome_1_seq 1348 117 + 5472 GTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_1.Genome_1_seq 2227 117 + 5472 GTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_1.Genome_1_seq 3399 117 + 5472 GTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_2.Genome_2_seq 1348 117 + 4270 GTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_3.Genome_3_seq 4571 117 + 6139 GTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_3.Genome_3_seq 1348 117 + 6139 GTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_3.Genome_3_seq 2227 117 + 6139 GTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_3.Genome_3_seq 3399 117 + 6139 GTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/halBranchMutations.bed Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,2 @@ +Genome_1_seq 0 293 +Genome_1_seq 586 5400
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/halLiftover.bed Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,3 @@ +Genome_0_seq 0 243 Region_A +Genome_0_seq 243 586 Region_B +Genome_0_seq 1000 1100 Region_C
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/halLiftover_append.bed Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,9 @@ +Genome_1_seq 0 243 Region_A +Genome_1_seq 1758 2001 Region_A +Genome_1_seq 243 586 Region_B +Genome_1_seq 2001 2051 Region_B +Genome_1_seq 2637 2930 Region_B +Genome_1_seq 1000 1100 Region_C +Genome_1_seq 2465 2565 Region_C +Genome_1_seq 4223 4323 Region_C +Genome_1_seq 5102 5202 Region_C
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/halRenameGenomes_input.tsv Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,2 @@ +Genome_0 Genome_test_0 +Genome_1 Genome_test_1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/halRenameGenomes_input.txt Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,2 @@ +Genome_0 Genome_test_0 +Genome_1 Genome_test_1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/halRenameSequences_input.tsv Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,1 @@ +Genome_1_seq Genome_test_1_seq \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/halRenameSequences_input.txt Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,1 @@ +Genome_1_seq Genome_test_1_seq \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/halSynteny.psl Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,8 @@ +243 0 0 0 0 0 0 0 ++ Genome_0_seq 1758 0 243 Genome_1_seq 5472 0 243 1 243, 0, 0, +243 0 0 0 0 0 0 0 ++ Genome_0_seq 1758 0 243 Genome_1_seq 5472 1758 2001 1 243, 0, 1758, +343 0 0 0 0 0 0 0 ++ Genome_0_seq 1758 243 586 Genome_1_seq 5472 243 586 1 343, 243, 243, +343 0 0 0 0 0 1 586 ++ Genome_0_seq 1758 243 586 Genome_1_seq 5472 2001 2930 2 50,293, 243,293, 2001,2637, +100 0 0 0 0 0 0 0 ++ Genome_0_seq 1758 1000 1100 Genome_1_seq 5472 1000 1100 1 100, 1000, 1000, +100 0 0 0 0 0 0 0 ++ Genome_0_seq 1758 1000 1100 Genome_1_seq 5472 2465 2565 1 100, 1000, 2465, +100 0 0 0 0 0 0 0 ++ Genome_0_seq 1758 1000 1100 Genome_1_seq 5472 4223 4323 1 100, 1000, 4223, +100 0 0 0 0 0 0 0 ++ Genome_0_seq 1758 1000 1100 Genome_1_seq 5472 5102 5202 1 100, 1000, 5102,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/halWiggleLiftover.wig Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,5 @@ +variableStep chrom=Genome_0_seq +1 0.5 +293 1.0 +586 1.5 +879 2.0 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/halWiggleLiftover_append.wig Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,8 @@ +fixedStep chrom=Genome_1_seq start=2 step=1 +0.5 +fixedStep chrom=Genome_1_seq start=294 step=1 +1 +fixedStep chrom=Genome_1_seq start=2931 step=1 +1.5 +fixedStep chrom=Genome_1_seq start=4103 step=1 +2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maf2halTest.maf Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,77 @@ +##maf version=1 scoring=N/A +# hal ((Genome_3:0)Genome_1:0,Genome_2:0)Genome_0; + +a +s Genome_0.Genome_0_seq 0 293 + 1758 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGTGAGGTTGACACTCCGTTCGTGTTACATGTCCGACAGGCCGCTGTGCTAGCGCCTGGGCCGCCGCCGTAACGATCCAATCGCACCTTAGCGTCAATCCACACGTGCCCCCCTTGGGGAGTCGTGTGCCCGCTGAACTTGGTGCGGGCCTACTTGCGACCTGCCGCTCTCGAGGCCGGGCCGCTCAAGAGACGGACCGAGAGTGCGGGGCCTCGCGCTCGTTGTGACCCCCATCGCGCCCCGTCT +s Genome_1.Genome_1_seq 1758 293 + 5472 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGTGAGGTTGACACTCCGTTCGTGTTACATGTCCGACAGGCCGCTGTGCTAGCGCCTGGGCCGCCGCCGTAACGATCCAATCGCACCTTAGCGTCAATCCACACGTGCCCCCCTTGGGGAGTCGTGTGCCCGCTGAACTTGGTGCGGGCCTACTTGCGACCTGCCGCTCTCGAGGCCGGGCCGCTCAAGAGACGGACCGAGAGTGCGGGGCCTCGCGCTCGTTGTGACCCCCATCGCGCCCCGTCT +s Genome_1.Genome_1_seq 0 293 + 5472 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGTGAGGTTGACACTCCGTTCGTGTTACATGTCCGACAGGCCGCTGTGCTAGCGCCTGGGCCGCCGCCGTAACGATCCAATCGCACCTTAGCGTCAATCCACACGTGCCCCCCTTGGGGAGTCGTGTGCCCGCTGAACTTGGTGCGGGCCTACTTGCGACCTGCCGCTCTCGAGGCCGGGCCGCTCAAGAGACGGACCGAGAGTGCGGGGCCTCGCGCTCGTTGTGACCCCCATCGCGCCCCGTCT +s Genome_2.Genome_2_seq 0 293 + 4270 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGTGAGGTTGACACTCCGTTCGTGTTACATGTCCGACAGGCCGCTGTGCTAGCGCCTGGGCCGCCGCCGTAACGATCCAATCGCACCTTAGCGTCAATCCACACGTGCCCCCCTTGGGGAGTCGTGTGCCCGCTGAACTTGGTGCGGGCCTACTTGCGACCTGCCGCTCTCGAGGCCGGGCCGCTCAAGAGACGGACCGAGAGTGCGGGGCCTCGCGCTCGTTGTGACCCCCATCGCGCCCCGTCT +s Genome_3.Genome_3_seq 0 293 + 6139 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGTGAGGTTGACACTCCGTTCGTGTTACATGTCCGACAGGCCGCTGTGCTAGCGCCTGGGCCGCCGCCGTAACGATCCAATCGCACCTTAGCGTCAATCCACACGTGCCCCCCTTGGGGAGTCGTGTGCCCGCTGAACTTGGTGCGGGCCTACTTGCGACCTGCCGCTCTCGAGGCCGGGCCGCTCAAGAGACGGACCGAGAGTGCGGGGCCTCGCGCTCGTTGTGACCCCCATCGCGCCCCGTCT +s Genome_3.Genome_3_seq 1758 293 + 6139 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGTGAGGTTGACACTCCGTTCGTGTTACATGTCCGACAGGCCGCTGTGCTAGCGCCTGGGCCGCCGCCGTAACGATCCAATCGCACCTTAGCGTCAATCCACACGTGCCCCCCTTGGGGAGTCGTGTGCCCGCTGAACTTGGTGCGGGCCTACTTGCGACCTGCCGCTCTCGAGGCCGGGCCGCTCAAGAGACGGACCGAGAGTGCGGGGCCTCGCGCTCGTTGTGACCCCCATCGCGCCCCGTCT + +a +s Genome_0.Genome_0_seq 293 293 + 1758 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_1.Genome_1_seq 2637 293 + 5472 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_1.Genome_1_seq 293 293 + 5472 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_2.Genome_2_seq 3223 293 + 4270 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_2.Genome_2_seq 293 293 + 4270 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_2.Genome_2_seq 2051 293 + 4270 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_3.Genome_3_seq 293 293 + 6139 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG +s Genome_3.Genome_3_seq 2637 293 + 6139 AGCTCGGCGGCACGCCCGCTCGGAGCTGCAATAGTGCCTCCCCGGAAGGCAAAGATAGTACCGGAGGACCGTGAGTATAAGTTCGGCACCGTGGGAAAACTGGGGAGGCCTCCACGGGCCGAGCGTTCCGGCTCCGCTCCGTACCCTCCTAGACCGGGCTCGGCGGCAAAGGGGCGCATAATACCGTCTATGCTAGCTCTCTGGCGTTGGGCATGCCAGCGACTATGACGGCCCTTTGCGGATGTCGCGGTTCCGGCGAGCAAACCGTGGCGACGCTTCGCCCCGGCAGGATG + +a +s Genome_0.Genome_0_seq 586 293 + 1758 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_1.Genome_1_seq 3809 293 + 5472 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_1.Genome_1_seq 586 293 + 5472 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_1.Genome_1_seq 2930 293 + 5472 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_2.Genome_2_seq 3809 293 + 4270 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_2.Genome_2_seq 586 293 + 4270 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_2.Genome_2_seq 3516 293 + 4270 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_3.Genome_3_seq 586 293 + 6139 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_3.Genome_3_seq 2930 293 + 6139 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_3.Genome_3_seq 5633 293 + 6139 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC +s Genome_3.Genome_3_seq 3809 293 + 6139 CCTCCGTCTGCGCGGGCATCTGCGTACAGAACTCCCGTTAGTGCGCTAAGCATTCCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGACGATCCGGGGCGTGCGTCCTGACATGGCGGGTCTAGCGGGGCCCGCTCAGTGCACTCCTGGATGCAATGGGGCGGCGCACACGCGGACACCAGGACGGTGAAAGGACGGGGTGCGCTTAGATTGAGCGGACGCCGGCGGGCGCCTACGCCGGTTTCACCC + +a +s Genome_0.Genome_0_seq 879 154 + 1758 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_1.Genome_1_seq 4981 154 + 5472 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_1.Genome_1_seq 879 154 + 5472 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_1.Genome_1_seq 2344 154 + 5472 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_1.Genome_1_seq 4102 154 + 5472 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_2.Genome_2_seq 2930 154 + 4270 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_2.Genome_2_seq 879 154 + 4270 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_2.Genome_2_seq 1758 154 + 4270 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_2.Genome_2_seq 2344 154 + 4270 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_3.Genome_3_seq 879 154 + 6139 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_3.Genome_3_seq 2344 154 + 6139 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_3.Genome_3_seq 5926 154 + 6139 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC +s Genome_3.Genome_3_seq 4102 154 + 6139 ACTGCTGCCGCGTGGAGCACGGCTGTGGAAGGCTGCGCGGGCTTAGTCCGTGCCGGCTTGCCGGGCAGCTATCACTCTCCGCAGGGAAGGGCGCCCAATGCAACGTTCTGGCACACGTGAGATGCCGTCATGTCACCAGCCCTCTAGCCCCCCC + +a +s Genome_0.Genome_0_seq 1033 139 + 1758 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_1.Genome_1_seq 5135 139 + 5472 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_1.Genome_1_seq 1033 139 + 5472 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_1.Genome_1_seq 2498 139 + 5472 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_1.Genome_1_seq 4256 139 + 5472 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_2.Genome_2_seq 3084 139 + 4270 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_2.Genome_2_seq 1033 139 + 4270 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_2.Genome_2_seq 1912 139 + 4270 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_2.Genome_2_seq 2498 139 + 4270 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_3.Genome_3_seq 1033 139 + 6139 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_3.Genome_3_seq 2498 139 + 6139 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC +s Genome_3.Genome_3_seq 4256 139 + 6139 CAATCGCCTACACGGGGATGGATACTACGGGCCCCTGTCTCAGTAACGGTACCGATGTTGCCTCCGGATCCCTGCCACGCCGGCATGCCCCATGCCCACCGGCAGCTGTTAATAGCAAGTCCCAGGGTGGGGCGTGTTC + +a +s Genome_0.Genome_0_seq 1172 586 + 1758 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATGGTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCCGCGCCGCTCGTTCGCGATAGCCCTAAGGCTGGGACCCATGGAGACTGGGCATGGGGCTCCGGCACCGAGAGCTCCGTGACCCACCCCTGGGCCCGTAGGCGCCCGACCGCGACGGCCAGACCGTCGGAGGGACCCAGAAGCTGGCGTGACGTCAGGCTATAGTCATCGGCTGGAGTCCTTCGTACGGATGTGGTGCGGACCAAACCGTACGAGCGCAACGCGGCAGTCTGCGCACTGGCCGGTATTCATCCCCCCGAGATGAACGAGGCCAGGAGCCCGGCCACGCGTCGGCG +s Genome_1.Genome_1_seq 4688 293 + 5472 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATGGTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_1.Genome_1_seq 1172 293 + 5472 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATGGTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_1.Genome_1_seq 2051 293 + 5472 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATGGTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_1.Genome_1_seq 3223 293 + 5472 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATGGTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_1.Genome_1_seq 4395 293 + 5472 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATGGTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_2.Genome_2_seq 1172 293 + 4270 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATGGTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_3.Genome_3_seq 1172 293 + 6139 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATGGTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_3.Genome_3_seq 2051 293 + 6139 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATGGTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_3.Genome_3_seq 3223 293 + 6139 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATGGTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_3.Genome_3_seq 4395 293 + 6139 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATGGTTGGGGGCGGTTACTCACCGCGGGGGAGCTGGCAGCCTAGTGACAATCCGGTTAATCATATGCAGGAGGTCGTCCTCGCCCGCGAGGCAGATTCACCATGCGTGGGCGAACAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +s Genome_3.Genome_3_seq 4688 176 + 6139 GGCGGGAGGGGACGCGGCCGGGCATAAGATTATGAGCTCCATAGCAGGACGCGCGGCCCTCCATCTGAGTGCACTGTGTGCCTTGACCGACGCCCTGACTCCCCCCTGATGTCGTAGCGCGGAGGGCCAGGGGCATTCCGGCCGAAGCCGCTGCAACGGCGAAGGGCGCGAAGATG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maf2halTestAppend.maf Fri Feb 06 10:39:34 2026 +0000 @@ -0,0 +1,6 @@ +##maf version=1 scoring=N/A +# hal ((Genome_NEW:0)Genome_3:0)Ancestor; + +a +s Genome_3.Genome_3_seq 100 50 + 6139 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGT +s Genome_NEW.Genome_NEW_seq 500 50 + 4000 GCTATCGGGGGGGACCGCACACCTCGTATGCCGGCAGTGGTGCCGCGCGT \ No newline at end of file