Mercurial > repos > iuc > hal_halvalidate
changeset 0:13917eec61b1 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_halValidate.xml Fri Feb 06 10:34:22 2026 +0000 @@ -0,0 +1,55 @@ +<tool id="hal_halvalidate" name="halValidate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>checks if a HAL file is valid</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command detect_errors="aggressive"><![CDATA[ + halValidate + #if $genome: + --genome '$genome' + #end if + '$input_hal' > '$out_file' + ]]></command> + <inputs> + <expand macro="input_hal"/> + <param argument="--genome" type="text" value="" optional="true" label="Specific genome" help="Specific genome to validate instead of entire file"> + <expand macro="sanitizer_default"/> + <expand macro="validator_trim"/> + </param> + </inputs> + <outputs> + <data name="out_file" format="txt" label="${tool.name} on ${on_string}: Validation ${genome}"/> + </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="File valid"/> + <has_n_lines n="2"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <param name="genome" value="Genome_0"/> + <output name="out_file" ftype="txt"> + <assert_contents> + <has_line line="File valid"/> + <has_n_lines n="2"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +halValidate checks the structural and metadata integrity of a HAL file. +A HAL file is needed as input, and the tool reports a simple text message indicating whether the file is valid or not. +It can run a full file scan or limit the check to a single genome. + +Use it to confirm that a HAL database is readable, consistent, and not corrupted before running downstream analyses. + ]]></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 10:34:22 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 10:34:22 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 10:34:22 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 10:34:22 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 10:34:22 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 10:34:22 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 10:34:22 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 10:34:22 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 10:34:22 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 10:34:22 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 10:34:22 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 10:34:22 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 10:34:22 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 10:34:22 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 10:34:22 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