# HG changeset patch
# User iuc
# Date 1770374123 0
# Node ID a84e089a22f87c4fa4ae349d0fa05bf2d4295e40

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 6244b9d15a5ad97ae20191e2f8fbafe2050c3cac

diff -r 000000000000 -r a84e089a22f8 hal_halBranchMutations.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hal_halBranchMutations.xml	Fri Feb 06 10:35:23 2026 +0000
@@ -0,0 +1,156 @@
+<tool id="hal_halbranchmutations" name="halBranchMutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>identifies mutations on a branch between given genome and its parent</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/> 
+    <expand macro="stdio"/>
+    <command detect_errors="aggressive"><![CDATA[
+        halBranchMutations
+            #if $support.file == 'true':
+                --refTargets '$support.refTargets'
+            #end if
+            #if $mode.export == 'sequence':
+                --refSequence '$mode.sequence'
+            #end if
+            --start $start
+            --length $length
+            --maxGap $maxGap
+            --maxNFraction $maxNFraction
+            --refFile stdout
+            --snpFile stdout
+            --delBreakFile stdout
+            --parentFile '$output_parentFile'
+            '$input_hal' '$refGenome' > '$output_file'
+    ]]></command>
+    <inputs>
+        <expand macro="input_hal"/>
+        <param name="refGenome" type="text" value="" label="Reference genome" help="To be analyzed branch and its according parent. Must denote bottom node in a branch, and therefore cannot be the root itself">
+            <expand macro="sanitizer_default"/>
+            <expand macro="validator_trim"/>
+        </param> 
+        <conditional name="support">
+            <param name="file" type="select" label="Use a BED file for coordinates" help="Use a BED file to define intervals in the reference genome to process">
+                <option value="false" selected="true">No, don't use a BED file (default)</option>
+                <option value="true">Yes, use a BED file (--refTargets)</option>
+            </param>
+            <when value="false"/>
+            <when value="true">
+                <param name="refTargets" type="data" format="bed" label="BED file"/>
+            </when>
+        </conditional>
+        <conditional name="mode">
+            <param name="export" type="select" label="Sequence process options">
+                <option value="default" selected="true">Process all sequences (default)</option>
+                <option value="sequence">Process a reference sequence (--refSequence)</option>
+            </param>
+            <when value="default"/>
+            <when value="sequence">
+                <expand macro="params_sequence"/>
+            </when>
+        </conditional>
+        <expand macro="params_start"/>
+        <expand macro="params_length"/>
+        <expand macro="params_maxGap"/>
+        <expand macro="params_maxNFraction"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="bed" label="${tool.name} on ${on_string}"/>
+        <data name="output_parentFile" format="bed" label="${tool.name} on ${on_string}: Rearrangements in reference's parent genome"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="refGenome" value="Genome_1"/>
+            <output name="output_file" ftype="bed">
+                <assert_contents>
+                    <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
+                    <has_line line="Genome_1_seq&#009;1465&#009;1758&#009;I&#009;Genome_0&#009;Genome_1"/>
+                    <has_line line="Genome_1_seq&#009;4395&#009;4688&#009;P&#009;Genome_0&#009;Genome_1"/>
+                    <has_n_lines n="5"/>
+                </assert_contents>
+            </output>
+            <output name="output_parentFile" ftype="bed">
+                <assert_contents>
+                    <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
+                    <has_line line="Genome_0_seq&#009;293&#009;879&#009;U&#009;Genome_0&#009;Genome_1"/>
+                    <has_line line="Genome_0_seq&#009;586&#009;879&#009;U&#009;Genome_0&#009;Genome_1"/>
+                    <has_n_lines n="13"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="refGenome" value="Genome_1"/>
+            <param name="start" value="10"/>
+            <param name="length" value="500"/>
+            <output name="output_file" ftype="bed">
+                <assert_contents>
+                    <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+            <output name="output_parentFile" ftype="bed">
+                <assert_contents>
+                    <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
+                    <has_line line="Genome_0_seq&#009;293&#009;879&#009;U&#009;Genome_0&#009;Genome_1"/>
+                    <has_n_lines n="3"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="refGenome" value="Genome_1"/>
+            <conditional name="mode">
+                <param name="export" value="sequence"/>
+                <param name="sequence" value="Genome_1_seq"/>
+            </conditional>
+            <output name="output_file" ftype="bed">
+                <assert_contents>
+                    <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
+                    <has_line line="Genome_1_seq&#009;1465&#009;1758&#009;I&#009;Genome_0&#009;Genome_1"/>
+                    <has_line line="Genome_1_seq&#009;4395&#009;4688&#009;P&#009;Genome_0&#009;Genome_1"/>
+                    <has_n_lines n="5"/>
+                </assert_contents>
+            </output>
+            <output name="output_parentFile" ftype="bed">
+                <assert_contents>
+                    <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
+                    <has_line line="Genome_0_seq&#009;293&#009;879&#009;U&#009;Genome_0&#009;Genome_1"/>
+                    <has_line line="Genome_0_seq&#009;586&#009;879&#009;U&#009;Genome_0&#009;Genome_1"/>
+                    <has_n_lines n="13"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="refGenome" value="Genome_1"/>
+            <conditional name="support">
+                <param name="file" value="true"/>
+                <param name="refTargets" value="halBranchMutations.bed"/>
+            </conditional>
+            <output name="output_file" ftype="bed">
+                <assert_contents>
+                    <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
+                    <has_line line="Genome_1_seq&#009;1465&#009;1758&#009;I&#009;Genome_0&#009;Genome_1"/>
+                    <has_line line="Genome_1_seq&#009;4395&#009;4688&#009;P&#009;Genome_0&#009;Genome_1"/>
+                    <has_n_lines n="5"/>
+                </assert_contents>
+            </output>
+            <output name="output_parentFile" ftype="bed">
+                <assert_contents>
+                    <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
+                    <has_line line="Genome_0_seq&#009;586&#009;879&#009;U&#009;Genome_0&#009;Genome_1"/>
+                    <has_line line="Genome_0_seq&#009;1172&#009;1465&#009;U&#009;Genome_0&#009;Genome_1"/>
+                    <has_n_lines n="13"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+halBranchMutations detects mutations that occurred on the branch between a chosen genome and its parent in a HAL alignment. 
+It reports point mutations, deletions, duplications, and other structural changes in an output BED file. 
+    ]]></help>
+    <expand macro="citation"/>
+    <expand macro="creator"/>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r a84e089a22f8 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Feb 06 10:35:23 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
diff -r 000000000000 -r a84e089a22f8 test-data/hal2fasta_output.fasta.bz2
Binary file test-data/hal2fasta_output.fasta.bz2 has changed
diff -r 000000000000 -r a84e089a22f8 test-data/hal2fasta_output.fasta.gz
Binary file test-data/hal2fasta_output.fasta.gz has changed
diff -r 000000000000 -r a84e089a22f8 test-data/hal2maf.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hal2maf.bed	Fri Feb 06 10:35:23 2026 +0000
@@ -0,0 +1,2 @@
+Genome_0_seq	0	293
+Genome_0_seq	586	879
diff -r 000000000000 -r a84e089a22f8 test-data/hal2maf_append.maf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hal2maf_append.maf	Fri Feb 06 10:35:23 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-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
diff -r 000000000000 -r a84e089a22f8 test-data/hal2maf_output.maf.bz2
Binary file test-data/hal2maf_output.maf.bz2 has changed
diff -r 000000000000 -r a84e089a22f8 test-data/hal2maf_output.maf.gz
Binary file test-data/hal2maf_output.maf.gz has changed
diff -r 000000000000 -r a84e089a22f8 test-data/hal2paf_output.paf.gz
Binary file test-data/hal2paf_output.paf.gz has changed
diff -r 000000000000 -r a84e089a22f8 test-data/hal2vg_noAncestors_output.pg
Binary file test-data/hal2vg_noAncestors_output.pg has changed
diff -r 000000000000 -r a84e089a22f8 test-data/hal2vg_output.hg
Binary file test-data/hal2vg_output.hg has changed
diff -r 000000000000 -r a84e089a22f8 test-data/hal2vg_output.pg
Binary file test-data/hal2vg_output.pg has changed
diff -r 000000000000 -r a84e089a22f8 test-data/hal2vg_refGenomes_output.pg
Binary file test-data/hal2vg_refGenomes_output.pg has changed
diff -r 000000000000 -r a84e089a22f8 test-data/hal2vg_targetGenomes_chop_output.pg
Binary file test-data/hal2vg_targetGenomes_chop_output.pg has changed
diff -r 000000000000 -r a84e089a22f8 test-data/halAddToBranch_bot_input.hal
Binary file test-data/halAddToBranch_bot_input.hal has changed
diff -r 000000000000 -r a84e089a22f8 test-data/halAddToBranch_top_input.hal
Binary file test-data/halAddToBranch_top_input.hal has changed
diff -r 000000000000 -r a84e089a22f8 test-data/halBranchMutations.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/halBranchMutations.bed	Fri Feb 06 10:35:23 2026 +0000
@@ -0,0 +1,2 @@
+Genome_1_seq	0	293
+Genome_1_seq	586	5400
diff -r 000000000000 -r a84e089a22f8 test-data/halLiftover.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/halLiftover.bed	Fri Feb 06 10:35:23 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
diff -r 000000000000 -r a84e089a22f8 test-data/halLiftover_append.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/halLiftover_append.bed	Fri Feb 06 10:35:23 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
diff -r 000000000000 -r a84e089a22f8 test-data/halRenameGenomes_input.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/halRenameGenomes_input.tsv	Fri Feb 06 10:35:23 2026 +0000
@@ -0,0 +1,2 @@
+Genome_0	Genome_test_0
+Genome_1	Genome_test_1
diff -r 000000000000 -r a84e089a22f8 test-data/halRenameGenomes_input.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/halRenameGenomes_input.txt	Fri Feb 06 10:35:23 2026 +0000
@@ -0,0 +1,2 @@
+Genome_0	Genome_test_0
+Genome_1	Genome_test_1
diff -r 000000000000 -r a84e089a22f8 test-data/halRenameSequences_input.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/halRenameSequences_input.tsv	Fri Feb 06 10:35:23 2026 +0000
@@ -0,0 +1,1 @@
+Genome_1_seq	Genome_test_1_seq
\ No newline at end of file
diff -r 000000000000 -r a84e089a22f8 test-data/halRenameSequences_input.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/halRenameSequences_input.txt	Fri Feb 06 10:35:23 2026 +0000
@@ -0,0 +1,1 @@
+Genome_1_seq	Genome_test_1_seq
\ No newline at end of file
diff -r 000000000000 -r a84e089a22f8 test-data/halReplaceGenome2_bot_input.hal
Binary file test-data/halReplaceGenome2_bot_input.hal has changed
diff -r 000000000000 -r a84e089a22f8 test-data/halReplaceGenome2_top_input.hal
Binary file test-data/halReplaceGenome2_top_input.hal has changed
diff -r 000000000000 -r a84e089a22f8 test-data/halReplaceGenome_top_input.hal
Binary file test-data/halReplaceGenome_top_input.hal has changed
diff -r 000000000000 -r a84e089a22f8 test-data/halSynteny.psl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/halSynteny.psl	Fri Feb 06 10:35:23 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,
diff -r 000000000000 -r a84e089a22f8 test-data/halTest.hal
Binary file test-data/halTest.hal has changed
diff -r 000000000000 -r a84e089a22f8 test-data/halTestExtended.hal
Binary file test-data/halTestExtended.hal has changed
diff -r 000000000000 -r a84e089a22f8 test-data/halTestIndels.hal
Binary file test-data/halTestIndels.hal has changed
diff -r 000000000000 -r a84e089a22f8 test-data/halWiggleLiftover.wig
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/halWiggleLiftover.wig	Fri Feb 06 10:35:23 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
diff -r 000000000000 -r a84e089a22f8 test-data/halWiggleLiftover_append.wig
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/halWiggleLiftover_append.wig	Fri Feb 06 10:35:23 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
diff -r 000000000000 -r a84e089a22f8 test-data/maf2halTest.maf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maf2halTest.maf	Fri Feb 06 10:35:23 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--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
diff -r 000000000000 -r a84e089a22f8 test-data/maf2halTest.maf.bz2
Binary file test-data/maf2halTest.maf.bz2 has changed
diff -r 000000000000 -r a84e089a22f8 test-data/maf2halTest.maf.gz
Binary file test-data/maf2halTest.maf.gz has changed
diff -r 000000000000 -r a84e089a22f8 test-data/maf2halTestAppend.hal
Binary file test-data/maf2halTestAppend.hal has changed
diff -r 000000000000 -r a84e089a22f8 test-data/maf2halTestAppend.maf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maf2halTestAppend.maf	Fri Feb 06 10:35:23 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