# HG changeset patch
# User iuc
# Date 1710765699 0
# Node ID 57f042937ba7d3e79a321392dec1198e12706f34
# Parent  bcd65de9725b6aa747e7674ae5164908764a1b2c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538

diff -r bcd65de9725b -r 57f042937ba7 macros.xml
--- a/macros.xml	Sat Nov 27 09:59:44 2021 +0000
+++ b/macros.xml	Mon Mar 18 12:41:39 2024 +0000
@@ -2,7 +2,7 @@
     <token name="@MUMMER_GNUPLOT_MANUAL@"><![CDATA[&& gnuplot < out.gp]]></token>
     <xml name="bio_tools">
         <xrefs>
-            <xref type="bio.tools">mumer4</xref>
+            <xref type="bio.tools">mummer4</xref>
         </xrefs>
     </xml>
     <xml name="citation">
@@ -10,15 +10,16 @@
             <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="gnuplot_requirement">
-        <requirement type="package" version="5.4.1">gnuplot</requirement>
+        <requirement type="package" version="5.4.8">gnuplot</requirement>
     </xml>
-    <token name="@TOOL_VERSION@">4.0.0rc1</token>
-    <token name="@VERSION_SUFFIX@">2</token>
-    <token name="@PROFILE@">20.05</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement>
+            <requirement type="package" version="1.19.2">samtools</requirement>
             <yield />
         </requirements>
     </xml>
@@ -30,13 +31,13 @@
             <option value="">Color</option>
             <option value="-color">No color (-color)</option>
         </param>
-        <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the defualt dotplot." >
+        <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the default dotplot." >
             <option value="">Dotplot</option>
             <option value="-c">Coverage Plot (-c)</option>
         </param>
-        <param name="filter" type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter"
+        <param type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter"
             help="Only display .delta alignments which represent the 'best' hit to any particular spot on either sequence, i.e. a one-to-one mapping of reference and query subsequences. (--filter)" />
-        <param name="fat" type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" />
+        <param type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" />
         <conditional name="labels" >
             <param name="IDs" type="select" label="Plot a particular reference or query sequence?" help="For alignments that used more than one reference/query." >
                 <option value="no">NO</option>
@@ -54,7 +55,7 @@
             <option value="large">Large</option>
         </param>
         <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" />
-        <param name="title" type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" />
+        <param type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" />
         <conditional name="range" >
             <param name="custom" type="select" label="Choose custom X and Y axis ranges?" >
                 <option value="no">NO</option>
diff -r bcd65de9725b -r 57f042937ba7 mummer.xml
--- a/mummer.xml	Sat Nov 27 09:59:44 2021 +0000
+++ b/mummer.xml	Mon Mar 18 12:41:39 2024 +0000
@@ -9,7 +9,7 @@
     </expand>
     <command detect_errors="exit_code">
         <![CDATA[
-        mummer 
+        mummer
             $anchoring
             -l '$min'
             $direction
@@ -87,9 +87,9 @@
                     <option value="0">No</option>
                     <option value="1">Yes</option>
                 </param>
-                <param name="skip" type="integer" argument="-skip" value="10" label="Sparsify"
+                <param  type="integer" argument="-skip" value="10" label="Sparsify"
                     help="Sparsify the MEM-finding algorithm even more, performing jumps of skip*k [auto (l-10)/k]. (-skip)" />
-                <param name="kmer" type="integer" argument="-kmer" value="1" label="kmer Table"
+                <param  type="integer" argument="-kmer" value="1" label="kmer Table"
                     help="Use kmer table containing sa-intervals (speeds up searching first k characters) in the index and during search. (-kmer)" />
             </when>
             <when value="defaults" />
@@ -112,7 +112,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test  expect_num_outputs="2">
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
             <param name="options|advanced" value="defaults" />
@@ -128,7 +128,7 @@
 
     mummer
 
-    -mumreference    Compute maximal matches that are unique in the reference- sequence but not 
+    -mumreference    Compute maximal matches that are unique in the reference- sequence but not
                      necessarily in the query-sequence (default)
 
     -maxmatch        Compute all maximal matches regardless of their uniqueness
@@ -154,16 +154,16 @@
 
     mummerplot
 
-    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest 
+    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
                    sequence end
 
-    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default 
-                   color by match dir) If the plot is very sparse, edit the .gp script to plot with 
+    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default
+                   color by match dir) If the plot is very sparse, edit the .gp script to plot with
                    'linespoints' instead of 'lines'
 
     -c             Generate a reference coverage plot (default for .tiling)
 
-    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on 
+    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on
                    either sequence, i.e. a one-to-one mapping of reference and query subsequences
 
     --fat          Layout sequences using fattest alignment only
diff -r bcd65de9725b -r 57f042937ba7 test-data/1delta.txt
--- a/test-data/1delta.txt	Sat Nov 27 09:59:44 2021 +0000
+++ b/test-data/1delta.txt	Mon Mar 18 12:41:39 2024 +0000
@@ -1,4 +1,4 @@
-/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
+/tmp/tmpmprg208i/files/f/1/b/dataset_f1b7734e-9d42-4c7c-9775-5f18da934854.dat /tmp/tmpmprg208i/files/6/f/5/dataset_6f561e62-f409-4d5b-9469-6080685d3666.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff -r bcd65de9725b -r 57f042937ba7 test-data/delta.txt
--- a/test-data/delta.txt	Sat Nov 27 09:59:44 2021 +0000
+++ b/test-data/delta.txt	Mon Mar 18 12:41:39 2024 +0000
@@ -1,4 +1,4 @@
-/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
+/tmp/tmpmprg208i/files/f/1/b/dataset_f1b7734e-9d42-4c7c-9775-5f18da934854.dat /tmp/tmpmprg208i/files/6/f/5/dataset_6f561e62-f409-4d5b-9469-6080685d3666.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff -r bcd65de9725b -r 57f042937ba7 test-data/mdelta.txt
--- a/test-data/mdelta.txt	Sat Nov 27 09:59:44 2021 +0000
+++ b/test-data/mdelta.txt	Mon Mar 18 12:41:39 2024 +0000
@@ -1,4 +1,4 @@
-/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
+/tmp/tmpmprg208i/files/f/1/b/dataset_f1b7734e-9d42-4c7c-9775-5f18da934854.dat /tmp/tmpmprg208i/files/6/f/5/dataset_6f561e62-f409-4d5b-9469-6080685d3666.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff -r bcd65de9725b -r 57f042937ba7 test-data/nucmer.txt
--- a/test-data/nucmer.txt	Sat Nov 27 09:59:44 2021 +0000
+++ b/test-data/nucmer.txt	Mon Mar 18 12:41:39 2024 +0000
@@ -1,4 +1,4 @@
-reference.fa query.fa
+/tmp/tmpk0v09mol/files/2/f/7/dataset_2f771d7a-b9f1-4fc9-b1ea-d06b84d013a0.dat /tmp/tmpk0v09mol/files/d/1/b/dataset_d1bcd825-fbc8-415a-9896-a6af5fd5ebaa.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff -r bcd65de9725b -r 57f042937ba7 test-data/out.bam
Binary file test-data/out.bam has changed
diff -r bcd65de9725b -r 57f042937ba7 test-data/out.cram
Binary file test-data/out.cram has changed
diff -r bcd65de9725b -r 57f042937ba7 test-data/out.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.sam	Mon Mar 18 12:41:39 2024 +0000
@@ -0,0 +1,6 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:NG_007476.1:4960-11439	LN:6480	M5:dcb745df791cdf1218f74d62ab4e1507	UR:file:///tmp/tmp885k3_3o/files/8/f/5/dataset_8f5d35c8-47ee-4bac-87e6-449833607f46.dat
+@PG	ID:samtools	PN:samtools	VN:1.19.2	CL:samtools sort -o outsamheadsort outsamhead
+@PG	ID:samtools.1	PN:samtools	PP:samtools	VN:1.19.2	CL:samtools calmd outsamheadsort reference.fa
+NC_000070.6:c41098183-41092724	0	NG_007476.1:4960-11439	74	10	42S25M1I1M1I124M5266S	*	0	0	ACCGCTCTCGGTGCCTTGCGCTAGCTACTTTGCACTCGTACGCCGCCGGACCTCGCCGCTGCCTGCCTCGCGCCATGGGTCGACAGAAGGAGTTGATGAATCGTTGTGGGGAGATGCTTCACATCCGCTACCGGCTGCTTCGCCAGGCGCTGGCGGAGTGCCTGGGGACCCTCATCCTTGTGGTGAGTGCAGGGTAGTGAGCAGTCCTATCTATTTCAGGCCCCGTGGTCCCCAACTCCTTATTCACTCCAGGGACAGTTTTCCAGGCAGACACGACCAGTTCCCCAGCTCTGCTCCCGAGGCTTAACCCTCAGGGTCAAGCTGACCTCCAAAGCCTTCAACAGTCTTGACAGTTCTAACTCAACTTGTGACAGTGCTACTTACCCAAGAACAGCTCTGCTATTTTGCCTTTCCCCCTGGAGACAGAGACCAAGGCTGCGGAGGGTCACCCCTTAGTGTGGGACCTCCCACACGTTTCCTGGCTTCCCAACTTTCCCAGGGCTCCAACCTCAGGACACAGCAGAGAAAGGCAAATGGACACCCCTATTAAGTTATTTGGGTCTTGGGTGTCTGGCCCCTAATGAATAATTAAGCCTCAGAAAGTCCAAAAGTTGCAGTGAAGTGAGGGCGGATTACGGCAGGTAGGGGCAGAGGGCGCAGATTTCTTGGGCTGTAAGCAGCAAAATCGGAAGAACGGAGATTGTGGAAGGAAACAGAGCCTAACAGAACAGTGGGCGCGTCTAAATGTGTTGTGCACACGCTGTAGGAGTCCTTCGGATCCTGCGACCCAGATGCTTCCAGCGTCTTTGCTGGCCTTTTGATCCCCCCTCTGCCTCTCCTCTCAATGGCCCCTGGTGAACCCCCAGATCTCAGGCTTCTGCAGTTTTGCCCCGAGTTCTGGTTAACTTGGCGCACTTCTTGATCAGACAGACACTATGGCTTTCATTTCCTGTCCCAGTTACTCTGATTTTCAGCCACTGACTTGTTTTTCTGAGTCTCTTCTCAATTCCGGTGTCCCTTTTTGCAGTGGGGTGGGTTACTTGAGTTCCAGCAACAGCCTCAGTCTTGGGTAGTGCAGATCAGTCAACTGGCGAGGGAACATGGTGGGGCAGGCTACACATGGAGAAAGGGGGCCCAAATGTGCCTCTGACTTCATAGACTAGTGGCCTATCAGTTGTCCCCACTCCCTCCTGCCTCGGTGGTTCCCTGTTTCCTATCTTGATTTGTGAGTCTGGCCACCTGTTCGGTTGAGAGCAGCAAGAGGACAAGGGAGGGTGTCTTACAGTTTCAAAATGGGGCCCCCTCATCCCGTCCCAGTTCTCAGAGCCTATTCCTCTGTAAAAGAACAGTCAGTCCCCCCACTGAGTCCCAGGATCACTTGGCTTAGCCTAGACCACAAAAAGAGGGTTCTGGATTTGTGGTGAAGGCTTTCAGGCTCAGGTAGATGCGAGAGATCAGGTGTCAGGGAAAAGCTTGAGGAGAGGGGAGAGCAAGCCTAGTGGATCCCCTGATGACTGAGGGCCTGCTCGTGTCCCTGTGTTGGGGACTTGAGACCTCTGTGTCAGGATCCAGGTTGACTTTGGGGTGAGGAAAGCCCCCTTTTTTCTGAGGTATATAGTTGGGTGGTATATGGGGTGAGGGGCTGGCTAAGAACCTGCAGCTGGGTGAAAGTGCAGGATAAGGAAGAGGAAAGATTAGCCCCAAGGTGGTGGAACTGGCTTTGACAGCCTCCTCCTCCGGAGGCCCCTTGGCACGGAGCCAAGTCTGGGCCTCAGGCAAAGAGCTCAGGCCAGGGTCTGACTGGACATAGTGCCCGGGACGGCCACATGCCTCCACCCCTTGCTCTTACAATCTCTGACCTTTGCTCTCACCTGCCGGAACACCTTTGACCTACATCGCTGCCACTGGCCTCCCTGCCTCATCTTCCCGAGTGATAATAATCAGTGCTTAACAACCCAGCACCCAGGCTTGGACCCATTAGAGTTAATGAGGCACAGCTTGCTGCTGGCCAGCGTAGCACTTACTTGTTTGTGAGACCCCGGGTCTCCTTCGCCCTAGTCCTTGGCTGTTCTAGAACTCACTCTGTAGACCAGGCTGGTCTCTCTGCCTCGAGAGTGCAGGGATCAGGCCTGGCTCAGCATAGCACTGGTTCAGTTATGGAGAACTGAGAAAGGAGTCCCAGGGCCGGGCTGGAGGAGCGTGGAGGGCCACTAGAGACTTGAGGCAACAGCACTTAACAGTTGGTGGAGAGTATTCACACTTGAACATATGTCTGTCTGTCCCTGCCGATCCTGAGGCACCTTTTAGTCCCTCTATCCCAGGGTTAGAACAGATCTCACGGGACCTAGAGGGAAGAGCTGCTTAAAACCTTCTATTTAGGACTCTACAGATCAGAGTGGAAATCCTGGAGACAGCGGGCTGGAGAAGGAAGAGGAAAAGTGGCCTGGGGAGGGACCGGCAGGGACAGATGTGAACAGGGAGGCTATAATGAGGAACACGTGAGGACCAGATACGCAGACATTTCTCCATGCAGGAGTAGATTCAACTTCTCTTTTGATCTCTCTCCGTGGCCCCCACCTCCTCCACTATGACCTGGGCTTTGGAAGAGTCCAGGACGATGGGGTATTTCCTACCTCTGTGTGCCAAATCTGGAGGACGGGCAGAAACTGCTGTAGTGATAGCTCCCTTCTGTGCCCTTCCCGGATTCAAGAAAAACCAGTGGATGTCATTTAACCACCTGGGTCCCCAGTCATGTACCCATTACTGATTCCCCCCCATCCCCCCATGAGGCTCTGCACGTCTCCTCTTTCTGGGACTTAAGGAGGGATTTGGGTTATATCCCAGGAAGCACCTTCAGTGGTGTCAGGCATGTCTGATCTCAGTGGGACTTCACTTGCTTTGTTTTCCGACAGATGTTTGGCTGTGGCTCCGTGGCTCAGGTGGTGCTCAGCCGTGGCACCCATGGTGGCTTCCTCACCATCAACTTGGCTTTTGGCTTCGCTGTCACCCTTGGCATCTTGGTGGCTGGCCAGGTGTCTGGTAAGGCCTCAACCCCAGCTTCAGTTTTCAGCCCTCACCAGCATTTCCAACAAGTATCTGCCTAGAGAGCAGAGGGGGAGGAACAACTCCAACCAAGGACGCACACTAACAGCACCTCAGCTTTGGGCCCTTTGGAGGCAAGGGTGGAAGAGACTTCACAGAACCTTTGACTTTCACCTTGGAATCAAAGATCAGTCTGTGACATAGTCCAACTGCCATCCAGGCTAAGAAAACCTACCTACACCCCAGAAAGGAAGAGCCCAAGGTGGCAGGCTGTAACTAATGGATGCTATCTCCTCTTCGCAGGTGCCCACTTGAACCCCGCTGTGACCTTCGCAATGTGCTTCCTGGCACGAGAGCCCTGGATCAAGCTGCCCATCTATGCACTGGCACAGACACTGGGGGCCTTCTTGGGCGCTGGGATTGTTTTTGGGCTGTACTACGGTAAGCATTCCCCATCCCGCCCTCCCTTCTCCACACTTTCCCTCTTTAAGTACTTGTTGGCACCAAGCCCACTGATGACAACCGGGGCCTGCCCAGGCCCAGGGCCCGTGACTCATTCACGAACACTCAGGCCCAGGTTGGGGGCCTAGGGGAAAGAAACGAGTTGGGCAACAACAGAATCTCAGGTCCTCCACCCCGCCCCACCCCCTGAGCCTCTACAGTCATATGCTTACCCATGACCCCTGGCGGGGTGGGGAGGGCAGCTCTGAGAGGAGAGGCTCTGCCCTCACTCACAATGGCTCTAATCTGTCACCAGATGCAATCTGGGCCTTTGCCAACAATGAGCTTTTCGTCTCTGGCCCCAACGGCACAGCTGGAATCTTTGCCACCTATCCCTCTGGACACTTGGACATGGTCAATGGCTTCTTTGATCAGGTATGGACTAGGGACATGTGAAGTAAAGGTAGAGGGAGGAACAGTCTTGTTTTGGACAACGCTCCTTGATTGTAGCAGGATTTCTTCTCAGTTCGTGAGAACCCCAACCTCAGAACATGGTGGTGGCGTTGTCTTTTATAAAGCATGGCGCTTCCCAGTGAGTTCTTGGTTTTGCGATCATCCTAGAGTCAGGATGGTCTCTAGCGTGGAGGACTGGAGCGTGGGAGAAGGAGCTGGCCCTCACCGTGCTCTCTCCCCTCTCCCAGTTCATAGGCACAGCCGCCCTTATTGTGTGTGTACTGGCCATCGTTGACCCTTATAACAACCCTGTGCCCCGTGGCCTGGAGGCTTTCACTGTGGGCCTGGTGGTCCTGGTCATTGGAACCTCCATGGGCTTCAATTCTGGCTATGCCGTCAACCCTGCCCGTGACTTTGGACCTCGCCTCTTCACCGCCCTGGCTGGCTGGGGCTCAGAAGTCTTCACGTGAGTACAGTCCCCACTCCCCAGCTTGCCTCCCCTCTTCCTGCCGACCTGTCTCTGATTTCCGGTGTTCTCCCTCCAGGACTGGCCGGCACTGGTGGTGGGTACCCATTGTCTCCCCACTCCTGGGTTCCATCGCTGGTGTCTTCGTGTACCAGCTCATGATTGGTTGCCACCTGGAGCAGCCCCCACCCTCCACCGAGGAAGAGAATGTGAAGCTGGCCCACATGAAACACAAGGAGCAGATCTGAGTGGGCAGCAGCCCCCCTCCCCCACTGTGCACTCTCCTGAGTGTCCACTGACTGTGTGGGGACCAGTCCCCGAAAGCCCTTTGTGATGCCTCTCTCGGGCTAAACCGCTCCCTGTGTCCACCCCTGCTGGATGGGCCCTCCAGAATTTCTATGAACTCTGCCCATTAGGGCATTAGGTTCCCACCCACCTTTAAGCCAAGGTAGGATAGCAAATAAGATGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATGAATGTGTACATGTGTGCTGTTTTCTAAGCTGAATGATGCAAAGGCAAGGGACCAAGTTTTCAAAACAAACTGTAGCAGCTCAGGGGAAGGGAGCCCAGGGGAAGGGAGAAAGTGAGTCAGGAATGTGCCAGAGTGTGCATGCTTCAGGGACTCCTCCATGTGGAGGTGGACCCAGAAGTGAGTTTCTAAGTATGCGTGTGCCTACTGTTTTTTTTTTTTTTTTTGAAATGGACTTCTAGGCTTGGGGAGGGGGAAGGGATAAGAAGGGTGTAGCTCACATCTGGAGCTATGACCCTTGACTGGGGGCTGTGTAATATGTTTCTGTTATAAGATAGACATTGGGAGGGGCTGAAGTCCAGGTCGTAAGTTTCATAATTTGTTTTTTAAATATATAAATATATACATACATATATGTTACAGCCCTAGGAATAGGGGTGGGAAACTCCACTTTTTAAAAGGGGTTTCCTTTCTTTAATCCTCCAATCAACAATGTACTGTTGCCTTTTATATATAAAAAAGAATAAAACGTATACATGCTACAGG	*	NM:i:19	MD:Z:5C3A0G6C30C2G2T0C0C2C2C11C20C2A11C23G10G4
+NC_000070.6:c41098183-41092724	2048	NG_007476.1:4960-11439	5080	10	4147H31M1I239M5D2M2D20M1D11M1D19M1D188M802H	*	0	0	GGAGCTGGCCCTCACCGTGCTCTCTCCCCTCTCCCAGTTCATAGGCACAGCCGCCCTTATTGTGTGTGTACTGGCCATCGTTGACCCTTATAACAACCCTGTGCCCCGTGGCCTGGAGGCTTTCACTGTGGGCCTGGTGGTCCTGGTCATTGGAACCTCCATGGGCTTCAATTCTGGCTATGCCGTCAACCCTGCCCGTGACTTTGGACCTCGCCTCTTCACCGCCCTGGCTGGCTGGGGCTCAGAAGTCTTCACGTGAGTACAGTCCCCACTCCCCAGCTTGCCTCCCCTCTTCCTGCCGACCTGTCTCTGATTTCCGGTGTTCTCCCTCCAGGACTGGCCGGCACTGGTGGTGGGTACCCATTGTCTCCCCACTCCTGGGTTCCATCGCTGGTGTCTTCGTGTACCAGCTCATGATTGGTTGCCACCTGGAGCAGCCCCCACCCTCCACCGAGGAAGAGAATGTGAAGCTGGCCCACATGAAACACAAGGAGCAGATCTGAGTGGGCAG	*	NM:i:72	MD:Z:7C0A0G6C2T4C2A23T7C8G8T8C2C8C2C5A11C5C26C17C2C23G8C2C5T2T2A5T2G11T1C19C5^CCCAG2^CA7C6T5^G0C6C0C2^A4C4C1A0T0G0A4^C1G4C7C4A3T11G5C2G14C5T2G20G5C2C28A27T0G4G26
diff -r bcd65de9725b -r 57f042937ba7 test-data/report.txt
--- a/test-data/report.txt	Sat Nov 27 09:59:44 2021 +0000
+++ b/test-data/report.txt	Mon Mar 18 12:41:39 2024 +0000
@@ -1,4 +1,4 @@
-/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
+/tmp/tmpmprg208i/files/f/1/b/dataset_f1b7734e-9d42-4c7c-9775-5f18da934854.dat /tmp/tmpmprg208i/files/6/f/5/dataset_6f561e62-f409-4d5b-9469-6080685d3666.dat
 NUCMER
 
                                [REF]                [QRY]
@@ -39,49 +39,49 @@
 
 [SNPs]
 TotalSNPs                         78                   78
+AT                        2(2.5641%)           2(2.5641%)
+AC                        6(7.6923%)           5(6.4103%)
+AG                        2(2.5641%)           5(6.4103%)
+TA                        2(2.5641%)           2(2.5641%)
 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%)
+GT                        5(6.4103%)           2(2.5641%)
+GA                        5(6.4103%)           2(2.5641%)
+GC                        6(7.6923%)           6(7.6923%)
 
 TotalGSNPs                         1                    1
-TA                        0(0.0000%)           0(0.0000%)
+GT                        0(0.0000%)           0(0.0000%)
+GA                        0(0.0000%)           0(0.0000%)
+GC                        0(0.0000%)           0(0.0000%)
+CG                        0(0.0000%)           0(0.0000%)
+CT                        0(0.0000%)           0(0.0000%)
+CA                        0(0.0000%)          1(100.0000%)
+TC                        0(0.0000%)           0(0.0000%)
 TG                        0(0.0000%)           0(0.0000%)
-TC                        0(0.0000%)           0(0.0000%)
+TA                        0(0.0000%)           0(0.0000%)
+AT                        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
+A.                       3(23.0769%)           0(0.0000%)
 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%)
+G.                       2(15.3846%)           1(7.6923%)
 .A                        0(0.0000%)          3(23.0769%)
 .T                       2(15.3846%)           0(0.0000%)
+.C                        0(0.0000%)          5(38.4615%)
+.G                        1(7.6923%)          2(15.3846%)
 
 TotalGIndels                       0                    0
+G.                        0(0.0000%)           0(0.0000%)
+C.                        0(0.0000%)           0(0.0000%)
 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%)
+.A                        0(0.0000%)           0(0.0000%)
 .T                        0(0.0000%)           0(0.0000%)