Mercurial > repos > iuc > vgp_chromosome_assignment

changeset 0:9b52f4e2093b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
author iuc
date Wed, 07 Jan 2026 12:48:42 +0000
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files chromosome_assignment.xml macros.xml test-data/expected_corrected.agp test-data/expected_hap1.agp test-data/expected_hap1_chr_level.fa test-data/expected_hap1_haplotigs.agp test-data/expected_hap1_inter_chr.tsv test-data/expected_hap1_unlocs_no_hapdups.agp test-data/expected_hap2.agp test-data/expected_hap2_haplotigs.agp test-data/expected_hap2_inter_chr.tsv test-data/expected_hap2_unlocs_no_hapdups.agp test-data/expected_orientation.tsv test-data/expected_reversing_renaming.sak test-data/test_hap1_sorted.fa test-data/test_hap1_unlocs_no_hapdups.agp test-data/test_input.agp test-data/test_input.fasta.gz test-data/test_mashmap.out
diffstat 17 files changed, 507 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chromosome_assignment.xml	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,95 @@
+<tool id="vgp_chromosome_assignment" name="VGP Chromosome Assignment" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>Assign chromosome names to scaffolds</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ## Create output directory
+        mkdir -p output_dir &&
+
+        ## Run chromosome_assignment
+        chromosome_assignment
+            -a '$agp'
+            -f '$fasta'
+            -o output_dir
+
+    ]]></command>
+    <inputs>
+        <param name="agp" type="data" format="tabular" label="Haplotype AGP file"
+            help="Input haplotype AGP file without haplotig duplications." />
+        <param name="fasta" type="data" format="fasta" label="Sorted FASTA file"
+            help="Input sorted FASTA file." />
+    </inputs>
+    <outputs>
+        <data name="inter_chr" format="tabular" from_work_dir="output_dir/inter_chr.tsv"
+            label="${tool.name} on ${on_string}: Chromosome Mapping Table"/>
+        <data name="chr_level_fasta" format="fasta" from_work_dir="output_dir/hap.chr_level.fa"
+            label="${tool.name} on ${on_string}: Chromosome-level FASTA"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="agp" value="test_hap1_unlocs_no_hapdups.agp" ftype="tabular"/>
+            <param name="fasta" value="test_hap1_sorted.fa" ftype="fasta"/>
+            <output name="inter_chr" file="expected_hap1_inter_chr.tsv" ftype="tabular"/>
+            <output name="chr_level_fasta" file="expected_hap1_chr_level.fa" ftype="fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+chromosome_assignment substitutes scaffold identifiers with chromosome assignments, generating chromosome-level
+sequences and mapping tables.
+
+The tool processes AGP metadata to:
+
+1. Identify sex chromosomes (X, Y, W, Z) and regular chromosomes
+2. Filter autosomal scaffolds and assign sequential ``SUPER_`` identifiers
+3. Rename sex-linked scaffolds with ``SUPER_X/Y/W/Z`` prefixes
+4. Handle unlocalized contigs by replacing parent scaffold names with chromosomal assignments
+5. Generate documentation mapping original names to new names
+
+**Inputs**
+
+- **Haplotype AGP file**: Tab-delimited AGP file with chromosome assignment metadata (typically hap.unlocs.no_hapdups.agp from split_agp)
+- **Sorted FASTA file**: Sorted sequence file containing scaffolds/contigs (typically sorted using gfastats)
+
+**Outputs**
+
+- **Chromosome Mapping Table (inter_chr.tsv)**: Tab-separated file documenting all scaffold-to-chromosome name transformations
+- **Chromosome-level FASTA**: FASTA file with sequences renamed to chromosome-level assignments
+
+**Workflow Context**
+
+This tool is typically run twice in the VGP curation pipeline, once for each haplotype:
+
+1. Run on Haplotype 1: Use Hap1 AGP and Hap1 sorted FASTA
+2. Run on Haplotype 2: Use Hap2 AGP and Hap2 sorted FASTA
+
+**Input Preparation**
+
+Before running this tool:
+
+1. Run split_agp to split haplotypes and correct AGP files
+2. Use gfastats to sort each haplotype with its corresponding AGP file:
+   - gfastats hap1.fa -a hap1_unlocs_no_hapdups.agp -o hap1.sorted.fa
+   - gfastats hap2.fa -a hap2_unlocs_no_hapdups.agp -o hap2.sorted.fa
+
+**Next Steps**
+
+After running chromosome_assignment on both haplotypes:
+
+1. Run MashMap to align the two chromosome-level haplotypes
+2. Use sak_generation with the two inter_chr.tsv files and MashMap output to generate SAK instructions
+
+.. class:: infomark
+
+**More Information**
+
+This tool is part of the VGP ProcessCuration pipeline for preparing curated genome assemblies for submission.
+
+<expand macro="help_common"/>
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,56 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">vgp-processcuration</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">1.0</token>
+    <token name="@PROFILE@">21.09</token>
+    <xml name="edam_ontology">
+        <edam_topics>
+            <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
+            <edam_topic>topic_3797</edam_topic> <!-- Genome assembly -->
+        </edam_topics>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">vgp-processcuration</xref>
+        </xrefs>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+@misc{vgl_curation,
+    author = {VGL-Hub},
+    title = {VGL Curation - ProcessCuration toolkit for genome assembly submission},
+    year = {2025},
+    url = {https://github.com/vgl-hub/vgl-curation},
+}
+            </citation>
+        </citations>
+    </xml>
+    <xml name="help_common">
+        <![CDATA[
+**About ProcessCuration**
+
+ProcessCuration is a Python-based toolkit designed to process manually curated genome assemblies for submission.
+It reconciles AGP files (A Golden Path) created in PretextView with genome assembly FASTAs, preparing them for
+database submission through renaming, reorienting, and sorting operations.
+
+The toolkit is part of the VGP (Vertebrate Genomes Project) curation pipeline and works in conjunction with
+tools like gfastats and MashMap.
+
+**Input Naming Convention**
+
+Scaffolds must follow the naming pattern before curation:
+- Haplotype 1: H1.scaffold_X
+- Haplotype 2: H2.scaffold_X
+
+**More Information**
+
+- GitHub repository: https://github.com/vgl-hub/vgl-curation
+- VGP Genome Assembly Pipeline: https://vertebrategenomesproject.org/
+        ]]>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expected_corrected.agp	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,4 @@
+Scaffold_33	1	4414	1	W	scaffold_16.hap1	1	4414	+	Painted	Hap_1	
+Scaffold_34	1	4303	1	W	scaffold_17.hap2	1	4303	+	Painted	Hap_2	
+Scaffold_35	1	4409	1	W	scaffold_17.hap1	1	4409	+	Painted	Hap_1	
+Scaffold_36	1	4299	1	W	scaffold_16.hap2	1	4299	+	Painted	Hap_2	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expected_hap1.agp	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,2 @@
+Scaffold_33	1	4414	1	W	scaffold_16.hap1	1	4414	+	Painted	Hap_1	
+Scaffold_35	1	4409	1	W	scaffold_17.hap1	1	4409	+	Painted	Hap_1	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expected_hap1_chr_level.fa	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,310 @@
+>SUPER_1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+>SUPER_2
+AACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGT
+TAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTC
+CGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTG
+TCATAGAATGACATTTCCACTTTAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCA
+TGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTG
+CTTTTCTCGCTCAAAAAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGA
+TTTTATTTGTCAAACTGTCATAGAATGACGCGCTAATTTCCACTTGAGTAAACATCAATT
+CTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAA
+AGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAA
+ATGACAGAATATGAGTATTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGA
+CATTTCCACTTGAGAAACATCAATTCTTTGCATGTTTTTGAAGGACAGCATGGTTTATTT
+TGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGC
+TCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTA
+TTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATG
+TTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGT
+ACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGA
+ATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCC
+ACTTTAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCG
+TGTTGAGTTAGTGTGAAAAGTGAGGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAG
+CGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTG
+TCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAA
+GGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGACATGTTCA
+TTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTA
+TTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAA
+ACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTT
+AGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCC
+GACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGT
+CATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCAT
+GGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGC
+TTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGAT
+TCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTTAGAAACATCAAT
+TCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAA
+AAGTGAGGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAA
+AATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAAT
+GACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATT
+TTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCG
+CTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGT
+ATTTATTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATG
+TTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGT
+ATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGA
+ATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCC
+ACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCG
+TGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAG
+CGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTG
+TCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAA
+GGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTC
+ATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGT
+ATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGA
+AACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGT
+TAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGAGTTATTC
+CGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTG
+TCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCA
+TGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTG
+CTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGA
+TTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAA
+TTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGA
+AAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGA
+AAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAA
+TGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTAT
+TTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTC
+GCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTG
+TATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCA
+TGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCA
+GTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACA
+GAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTT
+CCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATT
+CGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAAT
+AGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATT
+TGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTG
+AAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGT
+TCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGA
+GTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATCACATTTCCACTTGA
+GAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGA
+GTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGAGTTAT
+TCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAAC
+TGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAG
+CATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTG
+TGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTA
+GATTCATTTGTATTTATTTGTCAAACTGTCATAGAATTATTCCGACCTGAAAATGACAGA
+ATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCC
+ACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCG
+TGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAG
+CGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTG
+TCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAA
+GGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTC
+ATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGT
+ATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGA
+AACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGT
+TAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTC
+CGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTG
+TCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCA
+TGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTG
+CTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGA
+TTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAA
+TTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGA
+AAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGA
+AAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAA
+TGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTAT
+TTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTC
+GCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTG
+TATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCA
+TGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCA
+GTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGAGTTATTCCGACCTGAAAATGACA
+GAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTT
+CCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATT
+CGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAAT
+AGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATT
+TGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTG
+AAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGT
+TCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGA
+GTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGA
+GAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGA
+GTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTAT
+TCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAAC
+TGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAG
+CATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTG
+TGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTA
+GATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTTAGAAACATC
+AATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGT
+GAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCT
+GAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAG
+AATGACATTTCCACTTTAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTT
+ATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGAGGTACATGTTCATTTTGTGCTTTTC
+TCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATT
+TGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTG
+CATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTG
+CAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGA
+CAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACAT
+TTCCACTTTAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAA
+TTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAA
+ATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTA
+TTTGTCAAACTGTCATAGAATGACATTTCCACTTTAGAAACATCAATTCTTGCATGTTTT
+TGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGAGGTACAT
+GTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATAT
+GAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTT
+TAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTT
+GAGTTAGTGTGAAAAGTGAGGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTT
+ATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAA
+ACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGAC
+AGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTT
+TGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expected_hap1_inter_chr.tsv	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,2 @@
+Scaffold_33	SUPER_1
+Scaffold_35	SUPER_2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expected_hap1_unlocs_no_hapdups.agp	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,2 @@
+Scaffold_33	1	4414	1	W	scaffold_16.hap1	1	4414	+	Painted	Hap_1	
+Scaffold_35	1	4409	1	W	scaffold_17.hap1	1	4409	+	Painted	Hap_1	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expected_hap2.agp	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,2 @@
+Scaffold_34	1	4303	1	W	scaffold_17.hap2	1	4303	+	Painted	Hap_2	
+Scaffold_36	1	4299	1	W	scaffold_16.hap2	1	4299	+	Painted	Hap_2	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expected_hap2_inter_chr.tsv	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,2 @@
+Scaffold_36	SUPER_1
+Scaffold_34	SUPER_2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expected_hap2_unlocs_no_hapdups.agp	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,2 @@
+Scaffold_34	1	4303	1	W	scaffold_17.hap2	1	4303	+	Painted	Hap_2	
+Scaffold_36	1	4299	1	W	scaffold_16.hap2	1	4299	+	Painted	Hap_2	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expected_orientation.tsv	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,3 @@
+	Hap_1	Hap_2	Main Orientation
+0	SUPER_1	SUPER_2	-
+1	SUPER_2	SUPER_1	-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expected_reversing_renaming.sak	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,4 @@
+RVCP	SUPER_2_oldname	
+RVCP	SUPER_1_oldname	
+RENAME	SUPER_2_oldname	SUPER_1
+RENAME	SUPER_1_oldname	SUPER_2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_hap1_sorted.fa	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,4 @@
+>Scaffold_33
+CCCACACCCACCCCACCCCACCCCCACCCCCACCCCCCACACCCCACCCCACCCCACCCCCACCCCTACCCCCCCACCCCCAACCCACCCCCACCCACCCACCCCTCACCCCACCCTACCCCCAACCCCTCCCCCACCCCACCCAACCCACCCCTACCCTAACCCTAACCCTAACCCTACCCCTAACCTACCCTACCCTACCCTACCCACCCTAACCCTACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTACCCAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCCTAACCCTAACCCTAACCCTACCCTACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCCCCCCCCCTAACCCTACCCTAACCCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCCCTAACCCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCCTAACCCACTCGCCAGGAATACTGGGGCCGGGGGGACAGGCGGTATGCGGGTTGGATGGACCGTGCACCTTCCTTCCCTGCTTGGGGAGGGACTCGGACCCGATTCCCTAACCCTAACCCTAACCCTTAATCTAACCCTAACCCCCCTAACCCTAACCCGCCACTGACACTAACCCTCTCCCTGACACTAACCCTGACCATAACCACTTACTACCCACTTGCCAAACCATAACCCTTACCTTTGCCTAAGGTTACTACCCACAAGGGTTACCATTTTCAGACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGCCTTTGCCCAAGCGTAACCCTTACCTTTGCCTACCTTTACTACCCACAAGGTTTACCATTTTCATACATTCAAAGGGGGGTCCAAACGACTCAGGGGGCTCTGAAACGTGCTCCTAGACACTTTCTGGGGGACACTTTTGGGCTATGCCACTTTGTCATATTATCACACTTTTCCATATTCCCATACACATACATGGGAATATTAATATGGCCATAACTTTTGAACGGAACATCACAGAGCTTCAGGACCACCACCGTTGGACTCAGGGTACATCAAATAGGGGGGGTAGACAAACTTTCAACCTTCTAGCTCCAAAAAAAATCTTCAGCATTTTTGCTGACATCAGCCTTTTCACCCTTAATCTACCCCCCCCGCACCCCCCCCAACGCCGCCACTGACACTAACCCTCTCCCTGACACTAACCCTGACCATAACCACTTACTACCCACTTGCCAAACCGTAACCCTTACCTTTGCCTAAGGTTACTACCCACAAGGGTTACCATTTTCAGACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGCCTTTGCCCAAGCGTAACCCTTACCTTTGCCTACCTTTACTACCCACAAGCTTTACCATTTTCATACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGGCTATGGCACTTTGTCATATTATCACACTTTTCCATATTCCCATACACATACATGGGAATATTAATATGGCCATAACTTTTGAACGGAACATCACAGAGCTTCAGGACCACCACCGTTGGACTCAGGGTACATCAAATAGGGGGGGTAGACAAACTTTCAACCTTCTAGCTCCAAATAAAAAGTTCGGCAACTTTTGCCGAATCAGCCTTTTCACCCTTAATCTAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCCCCCCCCTAACCCTAACCCTAACCCTAACCCCCTAACCCAAAAACAGTACTAAACTTAAAGAACTACAAACAAACTATGTATCCCTGGACTGGGTGGCGTAGGGACTGGTGTCCCCAACGCACTCGCCAGGAATACTGGGGCCGGGGGGACAGGCGGTATGCGGGTTGGATGGACCGTGCACCTTCCTTCCCTGCTTGGGGAGGGACTCGGACCCGATTCCCTAACCCTAACCCTAACCCTTAATCTAACCCTAACCCCCCTAACCCTAACCCGCCACTGACACTAACCCTCTCCCTGACACTAACCCTGACCATAACCACTTACTACCCACTTGCCAAACCATAACCCTTACCTTTGCCTAAGGTTACTACCCACAAGGGTTACCATTTTCAGACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGCCTTTGCCCAAGCGTAACCCTTACCTTTGCCTACCTTTACTACCCACAAGGTTTACCATTTTCATACATTCAAAGGGGGGTCCAAACGACTCAGGGGGCTCTGAAACGTGCTCCTAGACACTTTCTGGGGGACACTTTTGGGCTATGCCACTTTGTCATATTATCACACTTTTCCATATTCCCATACACATACATGGGAATATTAATATGGCCATAACTTTTGAACGGAACATCACAGAGCTTCAGGACCACCACCGTTGGACTCAGGGTACATCAAATAGGGGGGGTAGACAAACTTTCAACCTTCTAGCTCCAAAAAAAATCTTCAGCATTTTTGCTGACATCAGCCTTTTCACCCTTAATCTACCCCCCCCGCACCCCCCCCAACGCCGCCACTGACACTAACCCTCTCCCTGACACTAACCCTGACCATAACCACTTACTACCCACTTGCCAAACCGTAACCCTTACCTTTGCCTAAGGTTACTACCCACAAGGGTTACCATTTTCAGACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGCCTTTGCCCAAGCGTAACCCTTACCTTTGCCTACCTTTACTACCCACAAGCTTTACCATTTTCATACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGGCTATGGCACTTTGTCATATTATCACACTTTTCCATATTCCCATACACATACATGGGAATATTAATATGGCCATAACTTTTGAACGGAACATCACAGAGCTTCAGGACCACCACCGTTGGACTCAGGGTACATCAAATAGGGGGGGTAGACAAACTTTCAACCTTCTAGCTCCAAATAAAAAGTTCGGCAACTTTTGCCGAATCAGCCTTTTCACCCTTAATCTAACCCTACCCTAACTTTTGCCGAATCAGCCTTTTCACCCTTAATCTAACCCTAACCCTAACCCCTAACCCTAACCCTACCCCCCCCCACACCCCCCCAACGCCACCACTGACACTAACCCTCTCCCTGACACTAACCCTGACCATAACCACTTACTACCCACTTGCCAAACCGTAACCCTTACCTTTGCCTAAGGTTACTACCCACAAGGGTTACCATTTTCAGACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGCCTTTGCCCAAGCGTAACCCTTACCTTTGCCTAGGTTTACTACCCACAAGGTTTACAATTTTCATACATTCAAAGGGGGGTCCAAACGACTCAGGGGGCTCTGAAACGTGCTCCTAGACACTTTCTGGGGGACACTTTTGGGCTATGCCACTTTGTCATATTATCACACTTTTCCATATTCCCATACACATACATGGGAATATTAATATGGCCATAACTTTTGAACGGAACATCACAGAGCTTCAGGACCACCACCGTTGGACTCAGGGTACATCAAATAGGGGGGGTAGACAAACTTTCAACCTTCTAGCTCCAAAAAAAATCTTCAGCATTTTTGCTGACATCAGCCTTTTCACCCTTAATCTAACGGAACATCACAGAGCTTCAGGACCACCACCGTTGGACTCAGGGTACATCAAATAGGGGGGGTAGACAAACTTTCAACCTTCTAGCTCCAAATAAAAAGTTTGTCCCTTTTTGCCCGAATCAGCCTTTTCACCCTTAATCTAACCCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTGACCACCACCGTTGGACTCAGGGTACATCAAATAGGGGGGGTAGACAAACTTTCAACCTTCTAGCTCCAAATAAAAAGTTTGTCCCTTTTTGCCCGAATCAGCCTTTTCACCCTTAATCTAACCCTAACCCTAACCCAAACTTTCAACCTTCTAGCTCCAAATAAAAAGTTCGGCAACTTTTGCCGAATCAGCCTTTTCACCCTTAATCTAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCCCCCCCCTAACCCTAACCCTAACCCTAACCCCCTAACCCAAAAACAGTACTAAACTTAAAGAACTACAAACAAACTATGTATCCCTGGACTGGGTGGCGTAGGGACTGGTGTCCCCAACGCACTCGCCAGGAATACTGGGGCCGGGGGGACAGGCGGTATGCGGGTTGGATGGACCGTGCACCTTCCTTCCCTGCTTGGGGAGGGACTCGGACCCGATTCCCTAACCCTAACCCTAACCCTTAATCTAACCCTAACCCCCCTAACCCTAACCCGCCACTGACACTAACCCTCTCCCTGACACTAACCCTGACCATAACCACTTACTACCCACTTGCCAAACCATAACCCTTACCTTTGCCTAAGGTTACTACCCACAAGGGTTACCATTTTCAGACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGCCTTTGCCCAAGCGTAACCCTTACCTTTGCCTACCTTTACTACCCACAAGGTTTACCATTTTCATACATTCAAAGGGGGGTCCAAACGACTCAGGGGGCTCTGAAACGTGCTCCTAGACACTTTCTGGGGGACACTTTTGGGCTATGCCACTTTGTCATATTATCACACTTTTCCATATTCCCATACACATACATGGGAATATTAATATGGCCATAACTTTTGAACGGAACATCACAGAGCTTCAGGACCACCACCGTTGGACTCAGGGTACATCAAATAGGGGGGGTAGACAAACTTTCAACCTTCTAGCTCCAAAAAAAATCTTCAGCATTTTTGCTGACATCAGCCTTTTCACCCTTAATCTACCCCCCCCGCACCCCCCCCAACGCCGCCACTGACACTAACCCTCTCCCTGACACTAACCCTGACCATAACCACTTACTACCCACTTGCCAAACCGTAACCCTTACCTTTGCCTAAGGTTACTACCCACAAGGGTTACCATTTTCAGACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGCCTTTGCCCAAGCGTAACCCTTACCTTTGCCTACCTTTACTACCCACAAGCTTTACCATTTTCATACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGGCTATGGCACTTTGTCATATTATCACACTTTTCCATATTCCCATACACATACATGGGAATATTAATATGGCCATAACTTTTGAACGGAACATCACAGAGCTTCAGGACCACCACCGTTGGACTCAGGGTACATCAAATAGGGGGGGTAGACAAACTTTCAACCTTCTAGCTCCAAATAAAAAGTTCGGCAACTTTTGCCGAATCAGCCTTTTCACCCTTAATCTAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCCCCCCCCTAACCCTAACCCTAACCCTAACCCCCTAACCCAAAAACAGTACTAAACTTAAAGAACTACAAACAAACTATGTATCCCTGGACTGGGTGGCGTAGGGACTGGTGTCCCCAACGCACTCGCCAGGAATACTGGGGCCGGGGGGACAGGCGGTATGCGGGTTGGATGGACCGTGCACCTTCCTTCCCTGCTTGGGGAGGGACTCGGACCCGATTCCCTAACCCTAACCCTAACCCTTAATCTAACCCTAACCCCCCTAACCCTAACCCGCCACTGACACTAACCCTCTCCCTGACACTAACCCTGACCATAACCACTTACTACCCACTTGCCAAACCATAACCCTTACCTTTGCCTAAGGTTACTACCCACAAGGGTTACCATTTTCAGACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGCCTTTGCCCAAGCGTAACCCTTACCTTTGCCTACCTTTACTACCCACAAGGTTTACCATTTTCATACATTCAAAGGGGGGTCCAAACGACTCAGGGGGCTCTGAAACGTGCTCCTAGACACTTTCTGGGGGACACTTTTGGGCTATGCCACTTTGTCATATTATCACACTTTTCCATATTCCCATACACATACATGGGAATATTAATATGGCCATAACTTTTGAACGGAACATCACAGAGCTTCAGGACCACCACCGTTGGACTCAGGGTACATCAAATAGGGGGGGTAGACAAACTTTCAACCTTCTAGCTCCAAAAAAAATCTTCAGCATTTTTGCTGACATCAGCCTTTTCACCCTTAATCTAACCCTAACCCCCTAACCCAAAAACAGTACTAAACTTAAAGAACTACAAACAAACTATGTATCCCTGGACTGGGTGGCGTAGGGACTGGTGTCCCCAACGCACTCGCCAGGAATACTGGGGCCGGGGGGACAGGCGGTATGCGGGTTGGATGGACCGTGCACCTTCCTTCCCTGCTTGGGGAGGGACTCGGACCCGATTCCCTAACCCTAACCCTAACCCTTAATCTAACCCTAACCCCCCTAACCCTAACCCGCCACTGACACTAACCCTCTCCCTGACACTAACCCTGACCATAACCACTTACTACCCACTTGCCAAACCATAACCCTTACCTTTGCCTAAGGTTACTACCCACAAGGGTTACCATTTTCAGACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGCCTTTGCCCAAGCGTAACCCTTACCTTTGCCTACCTTTACTACCCACAAGGTTTACCATTTTCATACATTCAAAGGGGGGTCCAAACGACTCAGGGGGCTCTGAAACGTGCTCCTAGACACTTTCTGGGGGACACTTTTGGGCTATGCCACTTTGTCATATTATCACACTTTTCCATATTCCCATACACATACATGGGAATATTAATATGGCCATAACTTTTGAACGGAACATCACAGAGCTTCAGGACCACCACCGTTGGACTCAGGGTACATCAAATAGGGGGGTAGACAAACTTTCAACCTTCTAGCTCCAAAAAAAATCTTCAGCATTTTTGCTGACATCAGCCTTTTCACCCTTAATCTACCCCCCCCGCACCCCCCCCAACGCCGCCACTGACACTAACCCTCTCCCTGACACTAACCCTGACCATAACCACTTACTACCCACTTGCCAAACCGTAACCCTTACCTTTGCCTAAGGTTACTACCCACAAGGGTTACCATTTTCAGACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGCCTTTGCCCAAGCGTAACCCTTACCTTTGCCTACCTTTACTACCCACAAGCTTTACCATTTTCATACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGGCTATGGCACTTTGTCATATTATCACACTTTTCCATATTCCCATACACATACATGGGAATATTAATATGGCCATAACTTTTGAACGGAACATCACAGAGCTTCAGGACCACCACCGTTGGACTCAGGGTACATCAAATAGGGGGGGTAGACAAACTTTCAACCTTCTAGCTCCAAATAAAAAGTTCGGCAACTTTTGCCGAATCAGCCTTTTCACCCTTAATCTAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCCCCCCCCTAACCCTAACCCTAACCCTAACCCCCTAACCCAAAAACAGTACTAAACTTAAAGAACTACAAACAAACTATGTATCCCTGGACTGGGTGGCGTAGGGACTGGTGTCCCCAACGCACTCGCCAGGAATACTGGGGCCGGGGGGACAGGCGGTATGCGGGTTGGATGGACCGTGCACCTTCCTTCCCTGCTTGGGGAGGGACTCGGACCCGATTCCCTAACCCTAACCCTAACCCTTAATCTAACCCTAACCCCCCTAACCCTAACCCGCCACTGACACTAACCCTCTCCCTGACACTAACCCTGACCATAACCACTTACTACCCACTTGCCAAACCATAACCCTTACCTTTGCCTAAGGTTACTACCCACAAGGGTTACCATTTTCAGACATCGGAAGGGGGGTCCAAACCACTCGGGGGACCATGAAACGTGCTCCTACACACTTTCTGGGGGACACTTTTGGCCTTTGCCCAAGCGTAACCCTTACCTTTGCCTACCTTTACTACCCACAAGGTTTACCATTTTCATACATTCAAAGGGGGGTCCAAACGACTCAGGGGGCTCTGAAACGTGCTCCTAGACACTTTCTGGGGGACACTTTTGGGCTATGCCACTTTGTCATATTATCACACTTTTCCATATTCCCATACACATACATGGGAATATTAATATGGCCATAACTTTTGAACGGAACATCACAGAGCTTCAGGACCACCACCGTTGGACTCAGGGTACATCAAATAGGGGGGGTAGACAAACTTTCAACCTTCTAGCTCCAAAAAAAATCTTCAGCATTTTTGCTGACATCAGCCTTTTCACCCTTAATCTACCCCCCCCGCACCCCCCCCAACGCCGCCACTGACACTAACCCTCTCCCTGACACTAACCCTGACCATAACCACTTACTACCCACTTGCCAAACCGTAACCCTTACCTTTGCCTAAGGTTACT
+>Scaffold_35
+AACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTTAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAAAAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTTTATTTGTCAAACTGTCATAGAATGACGCGCTAATTTCCACTTGAGTAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTTAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGAGGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTTAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGAGGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGAGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATCACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGAGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGAGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTTAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTTAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGAGGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTATATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTTAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTTAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGAGGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTTAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGAGGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTTTAGATTCATTTGTATTTATTTGTCAAACTGTCATAGAATGACATTTCCACTTGAGAAACATCAATTCTTGCATGTTTTTGAAGGACAGCATGGTTTATTTTGAATTCGTGTTGAGTTAGTGTGAAAAGTGCAGTACATGTTCATTTTGTGCTTTTCTCGCTCAAATAGCGTTATTCCGACCTGAAAATGACAGAATATGAGTATTT
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_hap1_unlocs_no_hapdups.agp	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,2 @@
+Scaffold_33	1	24739779	1	W	scaffold_16.hap1	1	24739779	+	Painted	Hap_1	
+Scaffold_35	1	24437540	1	W	scaffold_17.hap1	1	24437540	+	Painted	Hap_1	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_input.agp	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,7 @@
+##agp-version	2.1
+# DESCRIPTION: Generated by PretextViewAI Version 1.0.0
+# HiC MAP RESOLUTION: 39904.841797 bp/texel
+Scaffold_33	1	24741001	1	W	scaffold_16.hap1	1	24741001	+	Painted	Hap_1	
+Scaffold_34	1	24461668	1	W	scaffold_17.hap2	1	24461668	+	Painted	Hap_2	
+Scaffold_35	1	24461668	1	W	scaffold_17.hap1	1	24461668	+	Painted	Hap_1	
+Scaffold_36	1	24581382	1	W	scaffold_16.hap2	1	24581382	+	Painted	Hap_2	
Binary file test-data/test_input.fasta.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_mashmap.out	Wed Jan 07 12:48:42 2026 +0000
@@ -0,0 +1,10 @@
+SUPER_1	24569333	0	24150000	-	SUPER_2	24437540	419743	24421883	41	24150000	22	id:f:0.994373	kc:f:0.991464
+SUPER_1	24569333	24150000	24569333	-	SUPER_2	24437540	12170	362135	5	419333	17	id:f:0.978691	kc:f:0.509185
+SUPER_2	24463642	0	10750000	-	SUPER_1	24739779	13979195	24724929	41	10750000	22	id:f:0.994281	kc:f:0.996774
+SUPER_2	24463642	10750000	10800000	-	SUPER_1	24739779	13806614	13856614	18	50000	15	id:f:0.967081	kc:f:0.518457
+SUPER_2	24463642	10800000	10850000	-	SUPER_1	24739779	13929079	13979079	16	50000	14	id:f:0.962616	kc:f:0.645041
+SUPER_2	24463642	10850000	15200000	-	SUPER_1	24739779	9359376	13681754	43	4350000	22	id:f:0.99353	kc:f:0.970742
+SUPER_2	24463642	15200000	19950000	-	SUPER_1	24739779	4612591	9293719	37	4750000	23	id:f:0.99447	kc:f:0.999766
+SUPER_2	24463642	20000000	24250000	-	SUPER_1	24739779	306879	4608250	44	4301371	23	id:f:0.995415	kc:f:0.990297
+SUPER_2	24463642	24250000	24300000	+	SUPER_1	24739779	272287	322287	28	50000	18	id:f:0.982711	kc:f:0.859448
+SUPER_2	24463642	24300000	24463642	-	SUPER_1	24739779	86973	246795	43	163642	25	id:f:0.996852	kc:f:0.926126