# HG changeset patch
# User greg
# Date 1677528163 0
# Node ID 491b007eec5dc2ded2e9e96abb52615d5a0cee0a

Uploaded

diff -r 000000000000 -r 491b007eec5d .shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,10 @@
+name: mummer4_dnadiff
+owner: greg
+homepage_url: https://github.com/gregvonkuster/galaxy_tools
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/pima/mummer4_dnadiff
+description: Mummer4 dnadiff
+long_description: |
+  MUMmer is a system for rapidly aligning entire genomes. The current version (release 4.x) can find all 20 base pair maximal exact matches between two bacterial genomes of ~5 million base pairs each in 20 seconds, using 90 MB of memory, on a typical 1.8 GHz Linux desktop computer. 
+categories:
+  - Sequence Analysis
+type: unrestricted
diff -r 000000000000 -r 491b007eec5d all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,15 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the tool-data/genome  directory (a directory that contains a directory
+#for each build).  This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file.
diff -r 000000000000 -r 491b007eec5d dnadiff.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dnadiff.xml	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,133 @@
+<tool id="mummer_dnadiff" name="DNAdiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Evaluate similarities/differences between two sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+<![CDATA[
+    #if $reference_source.reference_source_selector == 'history':
+        ln -f -s '$reference_source.reference_sequence' reference.fa &&
+    #else:
+        ln -f -s '$reference_source.reference_sequence.fields.path' reference.fa &&
+    #end if
+    ln -s $query_sequence query.fa &&
+    dnadiff 'reference.fa' 'query.fa'
+]]>  
+    </command>
+    <inputs>
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Select a reference genome from your history or select a cached reference genome?">
+                <option value="cached">Select a cached reference genome</option>
+                <option value="history">Select a reference genome from the history and build the index</option>
+            </param>
+            <when value="cached">
+                <param name="reference_sequence" type="select" label="Using reference genome" help="Select genome from the list">
+                    <options from_data_table="all_fasta">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="No reference genomes are available"/>
+                    </options>
+                    <validator type="no_options" message="A cached reference genome is not available for the build associated with the selected input file"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="reference_sequence" type="data" format="fasta" label="Use the following dataset as the reference genome" help="You can upload a FASTA or multi-Fasta file to your history and use it as reference"/>
+            </when>
+        </conditional>
+        <param name="query_sequence" type="data" format="fasta" label="Query Sequence(s)" help="FastA or multi-FastA"/>
+        <param name="report_only" type="select" label="Output only the general report file?" help="Select no to output all output files">
+            <option value="yes">YES</option>
+            <option value="no">NO</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="report" format="txt" from_work_dir="out.report" label="${tool.name} on ${on_string}: report"/>
+        <data name="delta" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: delta">
+            <filter> report_only == 'no'</filter>
+        </data>
+        <data name="delta1" format="tabular" from_work_dir="out.1delta" label="${tool.name} on ${on_string}: 1delta" >
+            <filter> report_only == 'no' </filter>
+        </data>
+        <data name="mdelta" format="tabular" from_work_dir="out.mdelta" label="${tool.name} on ${on_string}: mdelta" >
+            <filter> report_only == 'no' </filter>
+        </data>
+        <data name="coords1" format="tabular" from_work_dir="out.1coords" label="${tool.name} on ${on_string}: 1coords" >
+            <filter> report_only == 'no' </filter>
+            <actions>
+                    <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]"/>
+            </actions>
+        </data>
+        <data name="mcoords" format="tabular" from_work_dir="out.mcoords" label="${tool.name} on ${on_string}: mcoords" >
+            <filter> report_only == 'no' </filter>
+            <actions>
+                    <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]"/>
+            </actions>
+        </data>
+        <data name="snps" format="tabular" from_work_dir="out.snps" label="${tool.name} on ${on_string}: snps" >
+            <filter> report_only == 'no' </filter>
+            <actions>
+            	<action name="column_names" type="metadata" default="[P1], [REF SUB], [QUERY SUB], [P2], [BUFF], [DIST], [LEN REF], [LEN QUERY], [REF FRAME], [QUERY FRAME], [REF TAG], [QUERY TAG]"/>
+            </actions>
+        </data>
+        <data name="rdiff" format="tabular" from_work_dir="out.rdiff" label="${tool.name} on ${on_string}: rdiff" >
+            <filter> report_only == 'no' </filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Seq ID, Feature Type, Feature Start, Feature End, Feature Length"/>
+            </actions>
+        </data>
+        <data name="qdiff" format="tabular" from_work_dir="out.qdiff" label="${tool.name} on ${on_string}: qdiff" >
+            <filter> report_only == 'no' </filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Seq ID, Feature Type, Feature Start, Feature End, Feature Length"/>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="reference_source_selector" value="history"/>
+            <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
+            <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta"/>
+            <param name="report_only" value="no"/>
+            <output name="report" ftype="txt" compare="diff" sort="true" lines_diff="2" value="report.txt"/>
+            <output name="delta" ftype="tabular" compare="diff" lines_diff="2" value="delta.txt"/>
+            <output name="delta1" ftype="tabular" compare="diff" lines_diff="2" value="1delta.txt"/>
+            <output name="mdelta" ftype="tabular" compare="diff" lines_diff="2" value="mdelta.txt"/>
+            <output name="coords1" ftype="tabular" compare="diff" value="1coords.txt"/>
+            <output name="mcoords" ftype="tabular" compare="diff" value="mcoords.txt"/>
+            <output name="snps" ftype="tabular" compare="diff" value="snps.txt"/>
+            <output name="rdiff" ftype="tabular" compare="diff" value="rdiff.txt"/>
+            <output name="qdiff" ftype="tabular" compare="diff" value="qdiff.txt"/>
+        </test>
+        <test>
+            <param name="reference_source_selector" value="cached"/>
+            <param name="reference_sequence" ftype="fasta" value="human_aqp3"/>
+            <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta"/>
+            <param name="report_only" value="no"/>
+            <output name="report" ftype="txt" compare="diff" sort="true" lines_diff="2" value="report.txt"/>
+            <output name="delta" ftype="tabular" compare="diff" lines_diff="2" value="delta.txt"/>
+            <output name="delta1" ftype="tabular" compare="diff" lines_diff="2" value="1delta.txt"/>
+            <output name="mdelta" ftype="tabular" compare="diff" lines_diff="2" value="mdelta.txt"/>
+            <output name="coords1" ftype="tabular" compare="diff" value="1coords.txt"/>
+            <output name="mcoords" ftype="tabular" compare="diff" value="mcoords.txt"/>
+            <output name="snps" ftype="tabular" compare="diff" value="snps.txt"/>
+            <output name="rdiff" ftype="tabular" compare="diff" value="rdiff.txt"/>
+            <output name="qdiff" ftype="tabular" compare="diff" value="qdiff.txt"/>
+        </test>
+    </tests>
+     <help><![CDATA[
+This script is a wrapper around nucmer that builds an alignment using default parameters, and runs many of nucmer's helper scripts to process the output and report alignment statistics, SNPs, breakpoints, etc. It is designed for evaluating the sequence and structural similarity of two highly similar sequence sets. E.g. comparing two different assemblies of the same organism, or comparing two strains of the same species.
+
+**Output files:**
+    * report: Summary of alignments, differences and SNPs
+    * delta: Standard nucmer alignment output
+    * 1delta: 1-to-1 alignment from delta-filter -1
+    * mdelta: M-to-M alignment from delta-filter -m
+    * 1coords: 1-to-1 coordinates from show-coords -THrcl .1delta
+    * mcoords: M-to-M coordinates from show-coords -THrcl .mdelta
+    * snps: SNPs from show-snps -rlTHC .1delta
+    * rdiff: Classified ref breakpoints from show-diff -rH .mdelta
+    * qdiff: Classified qry breakpoints from show-diff -qH .mdelta
+    ]]></help>
+    <expand macro="citation"/>
+</tool>
diff -r 000000000000 -r 491b007eec5d macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,22 @@
+<macros>
+    <token name="@MUMMER_GNUPLOT_MANUAL@"><![CDATA[&& gnuplot < out.gp]]></token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">mumer4</xref>
+        </xrefs>
+    </xml>
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1005944</citation>
+        </citations>
+    </xml>
+    <token name="@TOOL_VERSION@">4.0.0rc1</token>
+    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@PROFILE@">20.05</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement>
+            <yield />
+        </requirements>
+    </xml>
+</macros>
diff -r 000000000000 -r 491b007eec5d test-data/1coords.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1coords.txt	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,2 @@
+74	223	43	194	150	152	87.50	6480	5460	2.31	2.78	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5080	5599	4148	4658	520	511	86.18	6480	5460	8.02	9.36	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
diff -r 000000000000 -r 491b007eec5d test-data/1delta.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1delta.txt	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,20 @@
+/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat
+NUCMER
+>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
+74 223 43 194 19 19 0
+-26
+-2
+0
+5080 5599 4148 4658 72 72 0
+-32
+240
+1
+1
+1
+1
+3
+1
+21
+12
+20
+0
diff -r 000000000000 -r 491b007eec5d test-data/all_fasta.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,1 @@
+human_aqp3	human_aqp3	human_aqp3	${__HERE__}/human_aqp3.fasta
diff -r 000000000000 -r 491b007eec5d test-data/delta.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/delta.txt	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,20 @@
+/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat
+NUCMER
+>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
+74 223 43 194 19 19 0
+-26
+-2
+0
+5080 5599 4148 4658 72 72 0
+-32
+240
+1
+1
+1
+1
+3
+1
+21
+12
+20
+0
diff -r 000000000000 -r 491b007eec5d test-data/human_aqp3.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_aqp3.fasta	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,95 @@
+>NG_007476.1:4960-11439 Homo sapiens aquaporin 3 (Gill blood group) (AQP3), RefSeqGene on chromosome 9
+AGCGCTCCTATAAAGGGAGCCACCAGCGCTGGAGGCCGCTGCTCGCTGCGCCACCGCCTCCCGCCACCCC
+TGCCCGCCCGACAGCGCCGCCGCCTGCCCCGCCATGGGTCGACAGAAGGAGCTGGTGTCCCGCTGCGGGG
+AGATGCTCCACATCCGCTACCGGCTGCTCCGACAGGCGCTGGCCGAGTGCCTGGGGACCCTCATCCTGGT
+GGTGAGTGGAGGGAGCCGGGGAAGCCCTTCTCTCTCCAGCCCTTGCACTCCCCAAACTCTCACTTCCCCG
+AAGGGGCTGTGTTTTCCAAGGTAGCCTGGACCCACCTCCCCAGCTGTGACCCCCACGCTTAACCGCGGAG
+GATCAAGCTGACTTCCAAAGTCCTCTTCCCCACGGTTCTAACCCCCTCTCTGACAGCTCCGACTCTTGCC
+AGAATGACAGCTGTTACTCCCCAGTGATAGTGCCGATCGTTTACCCTCCCACAAGTGACTCAGCCAACAG
+GCTGGGGGCAGCGGTCACGCTTGCAGTCTGGGACAGCCAGCCACTTCCCCTGCCTCCCACACCCCTCCAG
+ATTCCCAGAATCCCAGCCCCCAGATGTAGGGGAGGGGGCGGAGGCAAATGAGCCATTATTAGGTTATTTG
+GGTCCTGGGTGTCTGGCCTCTAATGAATAATTAAGCCTCAAAAAGTCCAAAGGTTGAAGTGAGTGAGGAC
+AGTTTGCACGAGTGGGGGCAGAGGGTGCAGGCCACATGGGCTGCGAACAGCGAAGTGGGAAGGGAGGCAG
+ATTCTGACGGTAGAAGGGTGGGAGGAAGCTAGGCCCAGGCACAGAGGACGCGTGTCTAAAGTTGCTCACC
+TGGTGCTCAGCGACTCCCAGGCCCTGTCTGTTATCCAGACAGATGCTGTCAGCGTCTGTGCAGAAGACGA
+CAAGCATTCTGGTTACTCCCTGGCCTCTTGGTTACTCTGTGGGTTCTCTGAGTGAGCATTTCCCTGCCTG
+AGTTACTCCTCAGTCCTAGTTACTCCTTGGTCACACCAGTTTCACCCTGGTTTTGTTCTGAGTGACTCTG
+TTTGCACTTCTTAGGTCTGGCAGACCCACCAGTTATGTTCTATTTCCTGTCCCAGTTACTCTGATTTTTC
+AGCCGCTCATGTGGTTACACCTGTTTTCCTCTGTGTTCAGTTGCTACATTGCAGTGAGTGGGTTACTCCG
+TTCCTGCCCCAGCCCTGGGTAGTACAGACCAGCTGGCCCACTGTGGACTAGGAAGCCTAACTAAGGGCAA
+GTAGGGATCCCCAAATGGTTGAGGATCAGGATCTATGGGCAGAGGAGGGCTGAAACCCACTTCTGGCTTC
+CAAGAATAGGAAGTGGGGAAGCCACAGGGGGCATTTTATCCACAGCCTCCCATAAGATTAGTCGTCCTAT
+CAGCCAGCCCTAGCCCCTCTCTCCTGTGCCAAGAAGGCAATAGGAGGTGGCCTTTATCACTCTCCTGCCT
+CGGAGCCCTCACTCCTATCGGAGTCCTGAGTCCAGCCACCTGTTTTAGAGCAGCCAGGCTAGGGGAGGAT
+GATGTCTTCTATTTTCCTAGAGGGGCCTCCTCATTCCCTCCCAAGTCTCAGTTCACTCTCTCACAAAGGA
+GCCGTTAGTCCTCCCACTGAGCCCCAGGATCATCAGGCTTATCCCAGACCACAAAAGAAGAGTGTTAAAT
+TTTAGGGGAAGGGTTGCAGACTCAGATGGATGTGAGGTATTGGATATCAGTGAGAAGCAGAACTTCAAGG
+ACTGCATGAACTGGAGGGGCAGGCCTGGGGATCCCTTTGTAGTGGGTGAGTGCCTGCCTGCCTACCTGCG
+TGTTGGGAGCCTAGGCCTGCAGTGGCAGAATCAGGGTTGGCTTTGGGGTGAGGAAAGCCCCTTTCTCTGA
+GATACCTGGTGTGAGGGCAGGGGGCGGTGCTGGCCGAGAACTCAGGGCAGGGGTTGGGGGAGGAAGAGGA
+AGATTAGCCCCAAGGTGGTGGAACTGGCTCTGACAGCTCCTCCCTCCAAGGCGTCCTGGGATGGAGCCAG
+GTCTGAGCCTTTGGCAGGCAAGGAGCTGCTGCCAGGGCCTCCCAAGCAGGGCAGGGCGCCTCAGACCCTC
+ACGTGCCTGTCTCCCACCACCCCTCCTCACACATACACCTGCAATCTCTGATCTTTGCTCTCACCTGCCT
+GCACACCTTTGCCCCATGTCATTGCCGCTGGCTTCTCCGTTATCTCTTGGTCTTTCTGGGATGATAATCA
+AAATGCTTAACTATCCAGTACAACAGGCACTGACCCGTCAGAATAAACAAGGTCTGTAGCACAGGTCCTG
+GAAACTGCCTGCTCTGTGGGCATAAAACCTTTAGTTATGGGCAGGTGGGAGAGGAGACCAGGGCAAGGCA
+TTGGAGCAGCTTTGAGGGACACTCAGGGGGCTCAGGGCAACAATGCTTTACAGCTGCTGCAGAAGTATTT
+TCAGGCTTGAACAAGGGGAACAGACATAGTACGTTCTTTTTCTTTTTTAAATAGAGACAAAGTCTCACTA
+TGTTGCCCAGGCTGTTCTCAAACTCCTGGGTTCAAGATCCTCCCATCTCAGCCTCCAAAGTGCTGGGATT
+ACAGGTGTGAGCCACCACAGCTGGCTCCAGTATGTTCTATATTTGTAGAACACCAGGGCTCTTAGTCTCT
+TTTAGTTCCCCCATTTTTGGCAGAAAGTTTAGAACCGATCTCCCCATTTCTACAGCCCTGGGTCCCGGGC
+TGGGGATAGTGAGAGGAGCCACACAGATCCCTGTCTGTAGGACCTCCAAATCTGAGTGGGGAATCTGGAC
+CCCTGAGAGCAGAGAGGTCATGGGTGGAGAGAGGAGACGCTGGGACAGGGACAGGTAAAGGAAGGGGAGG
+TTGTTGAGGGGGACATGGTGAAGGCTGGGGCTCTGGCATCCTGGACTCAGGAGAAGTGGATTCAACCTCA
+CTTCTGGTCTCCTCCCTATTTATTTATGCCGCCCATTGCCACCACTACCACCACCACATGAGCTTTTCTT
+TTCAACTCTTTTTTTTTTTTTTTTGAGATGGAGTCCCGCTCTGTCGCCCAGGCTGAAGTGCAGTGGCGCA
+ATCTTGGCTCACTGCAACATCTGCCTCCCATTTTCAAGTGATTCTCCTGCCTCAGCCTCCCGAGTAGCTG
+GGATTACAGGCACCTGCCACCACGCCTGGCTAATTTTTGTACTTTTAGTAGAGATGGGGTTTCACTATGT
+TGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCACCTCGGCCTACCAAAGTGCTGGGATT
+ACAGTGTGAGCCACTGCACCGGGCCTACATGAGCTTTTCTTTGGGGCAGCTGGGGGATGAGTGAGAGGCT
+TCCCACCTTTATGGTCCAGGCCTGAAGGGCTGTGGAGAAACTTGTGCTAAGGTGAAAGCTGTTCCCCTAC
+ACCTACGCCTGCTGAAATTCAAGGAAAATCAGTGAAGATGGTTCAGTCATCTTCTAGGATCCCAGTCGCA
+GACCCTGCTTCCAGCCCTTTCCATAGGGCCCTCTCATATTAGAGTTGGGACAGTGGGGTGGGAAGGCATG
+TGTCCTTTTTCTGGAAAGTGCAATTACAGCAGAAGGGGTTTGGGCTGGGTTCCAGGAAGCGCCTCTAGTC
+CTCCCAGTGGTGGCGAGTGGGCATGTTGCTGGCTTCACCCCTTCCTTCTGGAGTGAGAGTTGCTGGTCCT
+CACCCTCCCTGCCTGTTCTTCTTCCTGACAGATGTTTGGCTGTGGCTCCGTGGCCCAGGTTGTGCTCAGC
+CGGGGCACCCACGGTGGTTTCCTCACCATCAACCTGGCCTTTGGCTTTGCTGTCACTCTGGGCATCCTCA
+TCGCTGGCCAGGTCTCTGGTAAGGCCTTAACCCTGCCCCCAGCCCTTGGCCCTCAATAGCATTCCCACTA
+GGTGTCCTGGCATTCCTAAGGGCAGGTCACAGCTGTGGCCTCTGCTTTGGCCCCTTGGGAAAGGAGGGTG
+GAGAAGAAACTTGACACTTAGAACTTTCGACTCTCACCTTGGAATCAGAGATTATCAGCTGACCTGTTAC
+ATAGACCAACCGCCATCCTGTGCAAGAAACCCCTCTCTGCACCCCTTCTCAGGGGACCCTAGCCTGCCGA
+CTGTGGCAGGCTGCAGCTAATAGGTCCCTTGTCCCCTCTGCCCAGGGGCCCACCTGAACCCTGCCGTGAC
+CTTTGCCATGTGCTTCCTGGCTCGTGAGCCCTGGATCAAGCTGCCCATCTACACCCTGGCACAGACGCTG
+GGAGCCTTCTTGGGTGCTGGAATAGTTTTTGGGCTGTATTATGGTAAGCATTCCCCACCCTGTCCTCCTC
+CACTACCCCCGTCCCTCTGTTCAGGACCTGCTGGCACCAGGCCTTTTGATGACAGACGGCTAGGACCTGC
+CCAGGCCCCGGGCTCATGACTCACTCATTCACGCACAGGGTCAAGGTAGGGGGCACGAAGGGAAAGAAAC
+AAGTTGGGCAATAACAGAGTCTCAGGCCCTCCACCCCACCCCACGCCACCCCCTCTGCCTGCTGCAATAC
+AGCAGTATTGCTACTTACCCATAACTCATGGGAGGGTGGGGAGGGCACACCTGAGAGGGAAGTCTGGGCT
+CAGGCCTCTCCCCCGACTCACTGTGTGTCTAATCTGTCACCAGATGCAATCTGGCACTTCGCCGACAACC
+AGCTTTTTGTTTCGGGCCCCAATGGCACAGCCGGCATCTTTGCTACCTACCCCTCTGGACACTTGGATAT
+GATCAATGGCTTCTTTGACCAGGTATGGGCTGGGGACGTGTGAGGGGAACGCAGGGAGGGGACCGAGTTG
+CCTTGGTAGCTCATGGGCTGGTTGGGGGACAGGACTCCTCGACTGTAGCAGGGTTTCTCCAATCTGTGGG
+GTAACCCGCATCAGAACATGGTGGCAAGTACTTACAAAACATGCGGCTCTCCAGCGGGTTCTTGTCACGC
+AGACATTCTAGCACCATTGCTTTCAGGAGAAGAGCATGGGCGGGCGCTGACAAGAGTTTAAGAGCTAGAG
+GGAAGACGGGGGATGGAAGGAGGGGTCAGAGAAAGGGAGGGAGCTGCAGCTCACCCTGTTCTCCCCACTC
+CCCAGTTCATAGGCACAGCCTCCCTTATCGTGTGTGTGCTGGCCATTGTTGACCCCTACAACAACCCCGT
+CCCCCGAGGCCTGGAGGCCTTCACCGTGGGCCTGGTGGTCCTGGTCATTGGCACCTCCATGGGCTTCAAC
+TCCGGCTATGCCGTCAACCCTGCCCGGGACTTTGGCCCCCGCCTTTTTACAGCCCTTGCGGGCTGGGGCT
+CTGCAGTCTTCACGTGAGTACAGCCCCCACCCAGCTCACCCCAGCCTGCCTCTCCTCTGCCCTGCCCCCC
+ATGTCCCTGACTATGAGTGTCTGTCCCCCCAGGACCGGCCAGCATTGGTGGTGGGTGCCCATCGTGTCCC
+CACTCCTGGGCTCCATTGCGGGTGTCTTCGTGTACCAGCTGATGATCGGCTGCCACCTGGAGCAGCCCCC
+ACCCTCCAACGAGGAAGAGAATGTGAAGCTGGCCCATGTGAAGCACAAGGAGCAGATCTGAGTGGGCAGG
+GGCCATCTCCCCACTCCGCTGCCCTGGCCTTGAGCATCCACTGACTGTCCAAGGGCCACTCCCAAGAAGC
+CCCCTTCACGATCCACCCTTTCAGGCTAAGGAGCTCCCTATCTACCCTCACCCCACGAGACAGCCCCTTC
+AGGATTTCCACTGGACCTTGCCCAAATAGCACCTTAGGCCACTGCCCCTAAGCTGGGGTGGAACCGGAAT
+TTGGGTCAATACATCCTTTTGTCTCCCAAGGGAAGAGAATGGGCAGCAGGTATGTGTGTGTGTGCATGTG
+TGTGCATGTGTGTGCATGTGTGTGCAGGGGTGTGTGTGTGTGGGGGGGGTTCCCAGATATTCAGGGCAAG
+GGACCAGTCGGAAGGGATTCTGGCTATTGGGGGAGCCCAGAGACAGGGGAAGGCAGCCTGTCCATCTGTG
+CATAAGGAGAGGAAAGTTCCAGGGTGTGTATGTTTCAGGGGCTTCACATGGAGGAGCTGCAGATAGATAT
+GTGTTTCTGTGTATGTGTATGTCTGCCTTTTTTTCTAAGTGGGGGCTTCTACAGGCTTTTGGGAAGTAGG
+GTGGATGTGGGTAGGGCTGGGAGGAGGGGGCCACAGCTTAGGTTTGGAGCTCTGGATGTACATACATAAG
+TAGGAGCAGTGGGACGTGTTTCTGTCATAATGCAGGCATGAAGGGTGGAGTGAAGTCAGGTCATAAGTTT
+CATGTTTGCTTTTGTTTTGTTTTGTTTTTAATGTATGTAGCAGATGTTACAGTCTTAGGGATCCGGGATG
+GGAGACCCCACTTTAGAAAGGGTCGTCACTCCTTTAATCCTCTACTCAACAATGTACTCTTTTACTTTTA
+TATTAAAAAAAATAAAATAAATATGTGCCTAAAACCTCCA
+
diff -r 000000000000 -r 491b007eec5d test-data/mcoords.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mcoords.txt	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,2 @@
+74	223	43	194	150	152	87.50	6480	5460	2.31	2.78	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5080	5599	4148	4658	520	511	86.18	6480	5460	8.02	9.36	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
diff -r 000000000000 -r 491b007eec5d test-data/mdelta.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mdelta.txt	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,20 @@
+/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat
+NUCMER
+>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
+74 223 43 194 19 19 0
+-26
+-2
+0
+5080 5599 4148 4658 72 72 0
+-32
+240
+1
+1
+1
+1
+3
+1
+21
+12
+20
+0
diff -r 000000000000 -r 491b007eec5d test-data/mouse_aqp3.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mouse_aqp3.fasta	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,80 @@
+>NC_000070.6:c41098183-41092724 Mus musculus strain C57BL/6J chromosome 4, GRCm38.p4 C57BL/6J
+ACCGCTCTCGGTGCCTTGCGCTAGCTACTTTGCACTCGTACGCCGCCGGACCTCGCCGCTGCCTGCCTCG
+CGCCATGGGTCGACAGAAGGAGTTGATGAATCGTTGTGGGGAGATGCTTCACATCCGCTACCGGCTGCTT
+CGCCAGGCGCTGGCGGAGTGCCTGGGGACCCTCATCCTTGTGGTGAGTGCAGGGTAGTGAGCAGTCCTAT
+CTATTTCAGGCCCCGTGGTCCCCAACTCCTTATTCACTCCAGGGACAGTTTTCCAGGCAGACACGACCAG
+TTCCCCAGCTCTGCTCCCGAGGCTTAACCCTCAGGGTCAAGCTGACCTCCAAAGCCTTCAACAGTCTTGA
+CAGTTCTAACTCAACTTGTGACAGTGCTACTTACCCAAGAACAGCTCTGCTATTTTGCCTTTCCCCCTGG
+AGACAGAGACCAAGGCTGCGGAGGGTCACCCCTTAGTGTGGGACCTCCCACACGTTTCCTGGCTTCCCAA
+CTTTCCCAGGGCTCCAACCTCAGGACACAGCAGAGAAAGGCAAATGGACACCCCTATTAAGTTATTTGGG
+TCTTGGGTGTCTGGCCCCTAATGAATAATTAAGCCTCAGAAAGTCCAAAAGTTGCAGTGAAGTGAGGGCG
+GATTACGGCAGGTAGGGGCAGAGGGCGCAGATTTCTTGGGCTGTAAGCAGCAAAATCGGAAGAACGGAGA
+TTGTGGAAGGAAACAGAGCCTAACAGAACAGTGGGCGCGTCTAAATGTGTTGTGCACACGCTGTAGGAGT
+CCTTCGGATCCTGCGACCCAGATGCTTCCAGCGTCTTTGCTGGCCTTTTGATCCCCCCTCTGCCTCTCCT
+CTCAATGGCCCCTGGTGAACCCCCAGATCTCAGGCTTCTGCAGTTTTGCCCCGAGTTCTGGTTAACTTGG
+CGCACTTCTTGATCAGACAGACACTATGGCTTTCATTTCCTGTCCCAGTTACTCTGATTTTCAGCCACTG
+ACTTGTTTTTCTGAGTCTCTTCTCAATTCCGGTGTCCCTTTTTGCAGTGGGGTGGGTTACTTGAGTTCCA
+GCAACAGCCTCAGTCTTGGGTAGTGCAGATCAGTCAACTGGCGAGGGAACATGGTGGGGCAGGCTACACA
+TGGAGAAAGGGGGCCCAAATGTGCCTCTGACTTCATAGACTAGTGGCCTATCAGTTGTCCCCACTCCCTC
+CTGCCTCGGTGGTTCCCTGTTTCCTATCTTGATTTGTGAGTCTGGCCACCTGTTCGGTTGAGAGCAGCAA
+GAGGACAAGGGAGGGTGTCTTACAGTTTCAAAATGGGGCCCCCTCATCCCGTCCCAGTTCTCAGAGCCTA
+TTCCTCTGTAAAAGAACAGTCAGTCCCCCCACTGAGTCCCAGGATCACTTGGCTTAGCCTAGACCACAAA
+AAGAGGGTTCTGGATTTGTGGTGAAGGCTTTCAGGCTCAGGTAGATGCGAGAGATCAGGTGTCAGGGAAA
+AGCTTGAGGAGAGGGGAGAGCAAGCCTAGTGGATCCCCTGATGACTGAGGGCCTGCTCGTGTCCCTGTGT
+TGGGGACTTGAGACCTCTGTGTCAGGATCCAGGTTGACTTTGGGGTGAGGAAAGCCCCCTTTTTTCTGAG
+GTATATAGTTGGGTGGTATATGGGGTGAGGGGCTGGCTAAGAACCTGCAGCTGGGTGAAAGTGCAGGATA
+AGGAAGAGGAAAGATTAGCCCCAAGGTGGTGGAACTGGCTTTGACAGCCTCCTCCTCCGGAGGCCCCTTG
+GCACGGAGCCAAGTCTGGGCCTCAGGCAAAGAGCTCAGGCCAGGGTCTGACTGGACATAGTGCCCGGGAC
+GGCCACATGCCTCCACCCCTTGCTCTTACAATCTCTGACCTTTGCTCTCACCTGCCGGAACACCTTTGAC
+CTACATCGCTGCCACTGGCCTCCCTGCCTCATCTTCCCGAGTGATAATAATCAGTGCTTAACAACCCAGC
+ACCCAGGCTTGGACCCATTAGAGTTAATGAGGCACAGCTTGCTGCTGGCCAGCGTAGCACTTACTTGTTT
+GTGAGACCCCGGGTCTCCTTCGCCCTAGTCCTTGGCTGTTCTAGAACTCACTCTGTAGACCAGGCTGGTC
+TCTCTGCCTCGAGAGTGCAGGGATCAGGCCTGGCTCAGCATAGCACTGGTTCAGTTATGGAGAACTGAGA
+AAGGAGTCCCAGGGCCGGGCTGGAGGAGCGTGGAGGGCCACTAGAGACTTGAGGCAACAGCACTTAACAG
+TTGGTGGAGAGTATTCACACTTGAACATATGTCTGTCTGTCCCTGCCGATCCTGAGGCACCTTTTAGTCC
+CTCTATCCCAGGGTTAGAACAGATCTCACGGGACCTAGAGGGAAGAGCTGCTTAAAACCTTCTATTTAGG
+ACTCTACAGATCAGAGTGGAAATCCTGGAGACAGCGGGCTGGAGAAGGAAGAGGAAAAGTGGCCTGGGGA
+GGGACCGGCAGGGACAGATGTGAACAGGGAGGCTATAATGAGGAACACGTGAGGACCAGATACGCAGACA
+TTTCTCCATGCAGGAGTAGATTCAACTTCTCTTTTGATCTCTCTCCGTGGCCCCCACCTCCTCCACTATG
+ACCTGGGCTTTGGAAGAGTCCAGGACGATGGGGTATTTCCTACCTCTGTGTGCCAAATCTGGAGGACGGG
+CAGAAACTGCTGTAGTGATAGCTCCCTTCTGTGCCCTTCCCGGATTCAAGAAAAACCAGTGGATGTCATT
+TAACCACCTGGGTCCCCAGTCATGTACCCATTACTGATTCCCCCCCATCCCCCCATGAGGCTCTGCACGT
+CTCCTCTTTCTGGGACTTAAGGAGGGATTTGGGTTATATCCCAGGAAGCACCTTCAGTGGTGTCAGGCAT
+GTCTGATCTCAGTGGGACTTCACTTGCTTTGTTTTCCGACAGATGTTTGGCTGTGGCTCCGTGGCTCAGG
+TGGTGCTCAGCCGTGGCACCCATGGTGGCTTCCTCACCATCAACTTGGCTTTTGGCTTCGCTGTCACCCT
+TGGCATCTTGGTGGCTGGCCAGGTGTCTGGTAAGGCCTCAACCCCAGCTTCAGTTTTCAGCCCTCACCAG
+CATTTCCAACAAGTATCTGCCTAGAGAGCAGAGGGGGAGGAACAACTCCAACCAAGGACGCACACTAACA
+GCACCTCAGCTTTGGGCCCTTTGGAGGCAAGGGTGGAAGAGACTTCACAGAACCTTTGACTTTCACCTTG
+GAATCAAAGATCAGTCTGTGACATAGTCCAACTGCCATCCAGGCTAAGAAAACCTACCTACACCCCAGAA
+AGGAAGAGCCCAAGGTGGCAGGCTGTAACTAATGGATGCTATCTCCTCTTCGCAGGTGCCCACTTGAACC
+CCGCTGTGACCTTCGCAATGTGCTTCCTGGCACGAGAGCCCTGGATCAAGCTGCCCATCTATGCACTGGC
+ACAGACACTGGGGGCCTTCTTGGGCGCTGGGATTGTTTTTGGGCTGTACTACGGTAAGCATTCCCCATCC
+CGCCCTCCCTTCTCCACACTTTCCCTCTTTAAGTACTTGTTGGCACCAAGCCCACTGATGACAACCGGGG
+CCTGCCCAGGCCCAGGGCCCGTGACTCATTCACGAACACTCAGGCCCAGGTTGGGGGCCTAGGGGAAAGA
+AACGAGTTGGGCAACAACAGAATCTCAGGTCCTCCACCCCGCCCCACCCCCTGAGCCTCTACAGTCATAT
+GCTTACCCATGACCCCTGGCGGGGTGGGGAGGGCAGCTCTGAGAGGAGAGGCTCTGCCCTCACTCACAAT
+GGCTCTAATCTGTCACCAGATGCAATCTGGGCCTTTGCCAACAATGAGCTTTTCGTCTCTGGCCCCAACG
+GCACAGCTGGAATCTTTGCCACCTATCCCTCTGGACACTTGGACATGGTCAATGGCTTCTTTGATCAGGT
+ATGGACTAGGGACATGTGAAGTAAAGGTAGAGGGAGGAACAGTCTTGTTTTGGACAACGCTCCTTGATTG
+TAGCAGGATTTCTTCTCAGTTCGTGAGAACCCCAACCTCAGAACATGGTGGTGGCGTTGTCTTTTATAAA
+GCATGGCGCTTCCCAGTGAGTTCTTGGTTTTGCGATCATCCTAGAGTCAGGATGGTCTCTAGCGTGGAGG
+ACTGGAGCGTGGGAGAAGGAGCTGGCCCTCACCGTGCTCTCTCCCCTCTCCCAGTTCATAGGCACAGCCG
+CCCTTATTGTGTGTGTACTGGCCATCGTTGACCCTTATAACAACCCTGTGCCCCGTGGCCTGGAGGCTTT
+CACTGTGGGCCTGGTGGTCCTGGTCATTGGAACCTCCATGGGCTTCAATTCTGGCTATGCCGTCAACCCT
+GCCCGTGACTTTGGACCTCGCCTCTTCACCGCCCTGGCTGGCTGGGGCTCAGAAGTCTTCACGTGAGTAC
+AGTCCCCACTCCCCAGCTTGCCTCCCCTCTTCCTGCCGACCTGTCTCTGATTTCCGGTGTTCTCCCTCCA
+GGACTGGCCGGCACTGGTGGTGGGTACCCATTGTCTCCCCACTCCTGGGTTCCATCGCTGGTGTCTTCGT
+GTACCAGCTCATGATTGGTTGCCACCTGGAGCAGCCCCCACCCTCCACCGAGGAAGAGAATGTGAAGCTG
+GCCCACATGAAACACAAGGAGCAGATCTGAGTGGGCAGCAGCCCCCCTCCCCCACTGTGCACTCTCCTGA
+GTGTCCACTGACTGTGTGGGGACCAGTCCCCGAAAGCCCTTTGTGATGCCTCTCTCGGGCTAAACCGCTC
+CCTGTGTCCACCCCTGCTGGATGGGCCCTCCAGAATTTCTATGAACTCTGCCCATTAGGGCATTAGGTTC
+CCACCCACCTTTAAGCCAAGGTAGGATAGCAAATAAGATGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA
+GAGAGAGAGAGAGAATGAATGTGTACATGTGTGCTGTTTTCTAAGCTGAATGATGCAAAGGCAAGGGACC
+AAGTTTTCAAAACAAACTGTAGCAGCTCAGGGGAAGGGAGCCCAGGGGAAGGGAGAAAGTGAGTCAGGAA
+TGTGCCAGAGTGTGCATGCTTCAGGGACTCCTCCATGTGGAGGTGGACCCAGAAGTGAGTTTCTAAGTAT
+GCGTGTGCCTACTGTTTTTTTTTTTTTTTTTGAAATGGACTTCTAGGCTTGGGGAGGGGGAAGGGATAAG
+AAGGGTGTAGCTCACATCTGGAGCTATGACCCTTGACTGGGGGCTGTGTAATATGTTTCTGTTATAAGAT
+AGACATTGGGAGGGGCTGAAGTCCAGGTCGTAAGTTTCATAATTTGTTTTTTAAATATATAAATATATAC
+ATACATATATGTTACAGCCCTAGGAATAGGGGTGGGAAACTCCACTTTTTAAAAGGGGTTTCCTTTCTTT
+AATCCTCCAATCAACAATGTACTGTTGCCTTTTATATATAAAAAAGAATAAAACGTATACATGCTACAGG
+
diff -r 000000000000 -r 491b007eec5d test-data/qdiff.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/qdiff.txt	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,3 @@
+NC_000070.6:c41098183-41092724	BRK	1	42	42
+NC_000070.6:c41098183-41092724	GAP	195	4147	3953	4856	-903
+NC_000070.6:c41098183-41092724	BRK	4659	5460	802
diff -r 000000000000 -r 491b007eec5d test-data/rdiff.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rdiff.txt	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,3 @@
+NG_007476.1:4960-11439	BRK	1	73	73
+NG_007476.1:4960-11439	GAP	224	5079	4856	3953	903
+NG_007476.1:4960-11439	BRK	5600	6480	881
diff -r 000000000000 -r 491b007eec5d test-data/report.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/report.txt	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,87 @@
+/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat
+NUCMER
+
+                               [REF]                [QRY]
+[Sequences]
+TotalSeqs                          1                    1
+AlignedSeqs              1(100.0000%)          1(100.0000%)
+UnalignedSeqs             0(0.0000%)           0(0.0000%)
+
+[Bases]
+TotalBases                      6480                 5460
+AlignedBases           670(10.3395%)        663(12.1429%)
+UnalignedBases        5810(89.6605%)       4797(87.8571%)
+
+[Alignments]
+1-to-1                             2                    2
+TotalLength                      670                  663
+AvgLength                   335.0000             331.5000
+AvgIdentity                  86.4791              86.4791
+
+M-to-M                             2                    2
+TotalLength                      670                  663
+AvgLength                   335.0000             331.5000
+AvgIdentity                  86.4791              86.4791
+
+[Feature Estimates]
+Breakpoints                        4                    4
+Relocations                        0                    0
+Translocations                     0                    0
+Inversions                         0                    0
+
+Insertions                         3                    3
+InsertionSum                    5810                 4797
+InsertionAvg               1936.6667            1599.0000
+
+TandemIns                          0                    0
+TandemInsSum                       0                    0
+TandemInsAvg                  0.0000               0.0000
+
+[SNPs]
+TotalSNPs                         78                   78
+TG                        2(2.5641%)           5(6.4103%)
+TC                       9(11.5385%)         28(35.8974%)
+TA                        2(2.5641%)           2(2.5641%)
+GC                        6(7.6923%)           6(7.6923%)
+GA                        5(6.4103%)           2(2.5641%)
+GT                        5(6.4103%)           2(2.5641%)
+CT                      28(35.8974%)          9(11.5385%)
+CA                        5(6.4103%)           6(7.6923%)
+CG                        6(7.6923%)           6(7.6923%)
+AT                        2(2.5641%)           2(2.5641%)
+AG                        2(2.5641%)           5(6.4103%)
+AC                        6(7.6923%)           5(6.4103%)
+
+TotalGSNPs                         1                    1
+TA                        0(0.0000%)           0(0.0000%)
+TG                        0(0.0000%)           0(0.0000%)
+TC                        0(0.0000%)           0(0.0000%)
+AG                        0(0.0000%)           0(0.0000%)
+AC                       1(100.0000%)           0(0.0000%)
+AT                        0(0.0000%)           0(0.0000%)
+GC                        0(0.0000%)           0(0.0000%)
+GA                        0(0.0000%)           0(0.0000%)
+GT                        0(0.0000%)           0(0.0000%)
+CT                        0(0.0000%)           0(0.0000%)
+CG                        0(0.0000%)           0(0.0000%)
+CA                        0(0.0000%)          1(100.0000%)
+
+TotalIndels                       13                   13
+T.                        0(0.0000%)          2(15.3846%)
+G.                       2(15.3846%)           1(7.6923%)
+C.                       5(38.4615%)           0(0.0000%)
+A.                       3(23.0769%)           0(0.0000%)
+.G                        1(7.6923%)          2(15.3846%)
+.C                        0(0.0000%)          5(38.4615%)
+.A                        0(0.0000%)          3(23.0769%)
+.T                       2(15.3846%)           0(0.0000%)
+
+TotalGIndels                       0                    0
+T.                        0(0.0000%)           0(0.0000%)
+A.                        0(0.0000%)           0(0.0000%)
+G.                        0(0.0000%)           0(0.0000%)
+C.                        0(0.0000%)           0(0.0000%)
+.A                        0(0.0000%)           0(0.0000%)
+.C                        0(0.0000%)           0(0.0000%)
+.G                        0(0.0000%)           0(0.0000%)
+.T                        0(0.0000%)           0(0.0000%)
diff -r 000000000000 -r 491b007eec5d test-data/snps.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snps.txt	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,91 @@
+79	C	G	48	4	48	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+83	A	C	52	1	52	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+84	G	T	53	1	53	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+91	C	T	60	7	60	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+98	.	T	68	1	68	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+99	.	G	70	1	70	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+122	C	T	93	3	93	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+125	G	A	96	3	96	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+128	T	A	99	1	99	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+129	C	A	100	1	100	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+130	C	T	101	1	101	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+133	C	T	104	3	104	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+136	C	T	107	3	107	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+148	C	T	119	12	119	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+169	C	T	140	3	140	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+172	A	C	143	3	143	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+184	C	G	155	12	155	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+208	G	T	179	11	179	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+219	G	C	190	5	190	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5087	C	G	4155	1	1306	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5088	A	C	4156	1	1305	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5089	G	C	4157	1	1304	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5096	C	G	4164	3	1297	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5099	T	C	4167	3	1294	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5104	C	T	4172	3	1289	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5107	A	C	4175	3	1286	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5110	.	T	4179	3	1282	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5131	T	G	4200	8	1261	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5139	C	T	4208	8	1253	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5148	G	A	4217	9	1244	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5157	T	C	4226	9	1235	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5166	C	T	4235	3	1226	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5169	C	T	4238	3	1223	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5178	C	T	4247	3	1214	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5181	C	G	4250	3	1211	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5187	A	T	4256	6	1205	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5199	C	T	4268	6	1193	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5205	C	T	4274	6	1187	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5232	C	A	4301	18	1160	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5250	C	T	4319	3	1142	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5253	C	T	4322	3	1139	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5277	G	T	4346	9	1115	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5286	C	A	4355	3	1106	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5289	C	T	4358	3	1103	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5295	T	C	4364	3	1097	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5298	T	C	4367	3	1094	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5301	A	C	4370	3	1091	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5307	T	G	4376	3	1085	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5310	G	T	4379	3	1082	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5322	T	A	4391	2	1070	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5324	C	A	4393	2	1068	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5344	C	T	4413	6	1048	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5350	C	.	4418	1	1043	6480	5460	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
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diff -r 000000000000 -r 491b007eec5d tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under tool-data/genome directory -->
+    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r 491b007eec5d tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Mon Feb 27 20:02:43 2023 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under tool-data/genome directory -->
+    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+</tables>