Mercurial > repos > iuc > hal_halreplacegenome
changeset 0:de9294f0826f 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_halReplaceGenome.xml Fri Feb 06 10:36:13 2026 +0000 @@ -0,0 +1,115 @@ +<tool id="hal_halreplacegenome" name="halReplaceGenome" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>replaces a genome in a HAL file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command detect_errors="aggressive"><![CDATA[ + ## Copy input HAL to ensure that it is not modified. + cp '$input_hal' writable_hal.hal && + halReplaceGenome + #if $replaceTop.useTopAlignment == 'true': + --topAlignmentFile '$replaceTop.topAlignmentFile' + #else: + --noTopAlignment + #end if + #if $replaceBottom.useBottomAlignment == 'true': + --bottomAlignmentFile '$replaceBottom.bottomAlignmentFile' + #else: + --noBottomAlignment + #end if + $noMarkAncestors + writable_hal.hal '$refGenome' && + ## echo 'ok' to check it with assert_stdout. This is needed because there is no other stdout output, + ## and the output HAL file checksum always changes even with identical inputs. + echo 'ok' + ]]></command> + <inputs> + <expand macro="input_hal"/> + <expand macro="params_refGenome"/> + <conditional name="replaceTop"> + <param name="useTopAlignment" type="select" label="Top alignment" help="A top alignment file is required if the reference genome to be replaced is not the root. If none is provided, all top segments are removed even for the non-root reference genome. This produces an invalid HAL file, at least temporarily"> + <option value="true" selected="true">Yes, provide top alignment (default)</option> + <option value="false">No, remove all top segments (--noTopAlignment)</option> + </param> + <when value="true"> + <param name="topAlignmentFile" type="data" format="hal" label="Top alignment file" help="HAL file containing an alignment of the reference genome, its parent, and its siblings (--topAlignmentFile)"/> + </when> + <when value="false"/> + </conditional> + <conditional name="replaceBottom"> + <param name="useBottomAlignment" type="select" label="Bottom alignment" help="A bottom alignment file is required if the reference genome to be replaced is not a leaf. If none is provided, all bottom segments are removed even for the non-leaf reference genome. This produces an invalid HAL file, at least temporarily"> + <option value="true" selected="true">Yes, provide bottom alignment (default)</option> + <option value="false">No, remove all bottom segments (--noBottomAlignment)</option> + </param> + <when value="true"> + <param name="bottomAlignmentFile" type="data" format="hal" label="Bottom alignment file" help="HAL file containing an alignment of the reference genome and its children (--bottomAlignmentFile)"/> + </when> + <when value="false"/> + </conditional> + <expand macro="params_noMarkAncestors"/> + </inputs> + <outputs> + <data name="out_file" format="hal" label="${tool.name} on ${on_string}" from_work_dir="writable_hal.hal"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <param name="refGenome" value="Genome_2"/> + <conditional name="replaceTop"> + <param name="useTopAlignment" value="true"/> + <param name="topAlignmentFile" value="halReplaceGenome_top_input.hal"/> + </conditional> + <conditional name="replaceBottom"> + <param name="useBottomAlignment" value="false"/> + </conditional> + <output name="out_file" ftype="hal"> + <assert_contents> + <has_size min="55000"/> + </assert_contents> + </output> + <assert_stdout> + <has_line line="ok"/> + </assert_stdout> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTestExtended.hal"/> + <param name="refGenome" value="Insert"/> + <conditional name="replaceTop"> + <param name="useTopAlignment" value="true"/> + <param name="topAlignmentFile" value="halReplaceGenome2_top_input.hal"/> + </conditional> + <conditional name="replaceBottom"> + <param name="useBottomAlignment" value="true"/> + <param name="bottomAlignmentFile" value="halReplaceGenome2_bot_input.hal"/> + </conditional> + <param name="noMarkAncestors" value="true"/> + <output name="out_file" ftype="hal"> + <assert_contents> + <has_size min="80000"/> + </assert_contents> + </output> + <assert_stdout> + <has_line line="ok"/> + </assert_stdout> + </test> + </tests> + <help><![CDATA[ +halReplaceGenome replaces an existing genome from an input HAL file while keeping the overall tree topology intact. +Depending on whether the genome is a root, leaf, or internal node, separate top and bottom alignment files may be required to reconnect the genome correctly to its parent and children. +Options exist to remove top or bottom alignment segments explicitly. +By default, ancestor nodes are marked for update to ensure consistency of the alignment after replacement. +This behavior can be disabled when ancestor updates are not required. + +A new HAL file is created as output instead of modifying the input HAL file. + +----- + +.. class:: warningmark + +Running the tool on a HAL file in mmap format may fail or generate an invalid new HAL file, while the HDF5 format can run successfully. It is recommended to convert the input to HDF5 format first using halExtract. + ]]></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 10:36:13 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 10:36:13 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 10:36:13 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 10:36:13 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 10:36:13 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 10:36:13 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 10:36:13 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 10:36:13 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 10:36:13 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 10:36:13 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 10:36:13 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 10:36:13 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 10:36:13 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 10:36:13 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 10:36:13 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