# HG changeset patch
# User iuc
# Date 1752606059 0
# Node ID 3db999d4e0c1c231fb9b9450e5f2634dabb8cdb8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5
diff -r 000000000000 -r 3db999d4e0c1 map_damage.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/map_damage.xml Tue Jul 15 19:00:59 2025 +0000
@@ -0,0 +1,555 @@
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+ Tracks and quantifies damage patterns in ancient DNA sequences
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+ 2.2.2
+ 0
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+ mapdamage
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+ mapdamage2
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+ statistics['stats']['no_stats'] == ''
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+ rescale['rescaling']['rescale'] == '--rescale'
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+ fasta
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+ 10.1093/bioinformatics/btt193
+ 10.1093/bioinformatics/btr347
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diff -r 000000000000 -r 3db999d4e0c1 test-data/alignment.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment.fa Tue Jul 15 19:00:59 2025 +0000
@@ -0,0 +1,80 @@
+>minc:123214052
+AGAAAAAGGA
+>minc:123214052:414-495
+TAGATGTGATTTTGAGCAACTGTCAGCTCTGGCTAGTGGCATGGGTTTGTATAGTCATCTGTACGCAAAAGTTGTTGTCTTT
+>simulated_read_1_+
+TAGATGTGATTTTGAGCAACTGTCAGCTCTGGCTAGTGGCATGGGTTTGTATAGTCATCTGTACGCAAAAGTTATTGTCTTT
+>minc:123214052
+AGTAAGGTCC
+>minc:123214052
+TGAGAAGATT
+>minc:123214052:1173-1233
+ACTGGTTGATAGAAATTTGAAAGGTGTAACTCATGTTATTGTTGATGAGATTCATGAGCGT
+>simulated_read_2_+
+ATTGGTTGATAGAAATTTGAAAGGTGTAACTCATGTTATTGTTGATGAGATTCATGAACAT
+>minc:123214052
+GGAATGAATG
+>minc:123214052
+GAGGGAAGAT
+>minc:123214052:3161-3236
+TTGTATTTGGTCGCCAGGTGCTTAAGTCGCTTAAGTCTTCACCTGTGCCATTACAGCCAGCTTTGATTCCACGGAC
+>simulated_read_3_+
+TTGTATTTGGTCGCCAGGTGCTTAAGTCGCTTAAGTCTTCACCTGTGCCATTACAGCCAGCTTTGATTCCACAGAC
+>minc:123214052
+AGAGAGCGGA
+>minc:123224581
+GGGAGAGAAT
+>minc:123224581:211-282
+TTGCAAGCTTTGTGGAGCCCTGATGGAAAATTGATCGCTGTGATTACGTCATCTTTTTTTCTTCACATTTTC
+>simulated_read_4_+
+TTGTAAGCTTTGTGGAGCCCTGATGGAAAATTGATCGCTGTGATTACGTCATCTTTTTTTCTTCACATTTTC
+>minc:123224581
+AAGGTCCAGT
+>minc:123224581
+AGAAAAGGGT
+>minc:123224581:397-472
+TTTTCAGTGAGCAATATTGTGAGCGATAACAAACATATGCTACTTGGACTTTCTGATGGATCTTTATATTGTATCT
+>simulated_read_5_+
+TTTTTAGTGAGTAATATTGTGAGCGATAACAAACATATGCTACTTGGACTTTCTGATAGATCTTTATATTGTATCT
+>minc:123224581
+CATGGAAGGG
+>minc:123224581
+AAGAGCTGGG
+>minc:123224581:765-825
+TTCTGGTGATGTTGTATGTGCTTCAGTGGCGGCAGAGCAACAAATTGTTGCTGTTGGCACC
+>simulated_read_6_+
+TTTTGGTGATGTTGTATGTGCTTCAGTGGCGGCAGAGCAACAAATTGTTGCTATTGACACC
+>minc:123224581
+AGAAGGGGGA
+>minc:123224581
+GAAGATAGGT
+>minc:123224581:1277-1351
+TATTAGTTGTGCAGTCTGAAGATACTGATGAACTTAAGCTTTTACATTTAAACCTTCCAGTTTCTTATATCTCCC
+>simulated_read_7_+
+TATTAGTTGTGCAGTTTGAAGATACTGATGAACTTAAGCTTTTACATTTAAACCTTCCAGTTTCTTATATCTCCC
+>minc:123224581
+AGAATTGGCC
+>minc:123230223
+CAGAAGGAGA
+>minc:123230223:288-341
+TATTGTGATACCATATTTTCTGGCAGATTGTAGTGAATGTGTCGATTGCAAGTC
+>simulated_read_8_+
+TATTGTGATATCATATTTTCTGGCAGATTGTAGTGAATGTGTCGATTGCAAATC
+>minc:123230223
+AAAGAAGAGC
+>minc:123230223
+GAGGTGCAGA
+>minc:123230223:822-880
+TTACTGCTTTGAGTGTGTTGGTTCTTCATCCTTGGTGCAAGAAGCGTATGCTTGCTGTC
+>simulated_read_9_+
+TTATTGTTTTGAGTGTGTTGGTTCTTCATCCTTGGTGCAAAAAGCGTATGCTTACTATC
+>minc:123230223
+GAAAGGGATG
+>minc:123230223
+CTAAAACTGA
+>minc:123230223:1017-1080
+CATTCCAATTCTGCTGAAACGTTACATGGACAAGGAATTACAATTAGATGAATTTGTGACACAT
+>simulated_read_10_+
+TATTCTAATTCTGCTGAAACGTTACATGGACAAGGAATTACAATTAGATGAATTTGTAACACAT
+>minc:123230223
+GAGATGAAGT
diff -r 000000000000 -r 3db999d4e0c1 test-data/all_fasta.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc Tue Jul 15 19:00:59 2025 +0000
@@ -0,0 +1,1 @@
+test test_reference Reference file for planemo tests ${__HERE__}/ref.fa
diff -r 000000000000 -r 3db999d4e0c1 test-data/ref.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref.fa Tue Jul 15 19:00:59 2025 +0000
@@ -0,0 +1,140 @@
+>minc:123214052 K14442 ATP-dependent RNA helicase DHX36 [EC:5.6.2.6] | (RefSeq) DExH-box ATP-dependent RNA helicase DExH5, mitochondrial (N)
+atgccccttctctctccactttttcaaatccctcccaaactcatcatgaaggatcggcct
+cccccgtcctacggcgccgtttacgttcctcctcaccaacgtctccgctcggtcatcgcc
+agtcgcgcctcaattccttcgcttcctcacttaccagcactacaacaacaaaataataat
+aatttcagtaataatcataataaaaatattaatgatgataataaaaagagactgaagtat
+aactcaggttcagcgtacagtggagtatccgaggaaggctctgatcgggagctggatacg
+tggctgctaccgggtgcttacccctctgataatgtggaggagtggagaaggaagttgact
+gcgtttttatgtgacaagtcaaagcaagagttgatctcaagggagaaaaaggatagatgt
+gattttgagcaactgtcagctctggctagtggcatgggtttgtatagtcatctgtacgca
+aaagttgttgtctttagtaaggtcccactgccaaactacagatttgatttagatgatagg
+cggccacagagggaggtgaccttatcccttgggttgctcagacgaattgattactatctt
+ggagaatacttctctcaaaagtataggaataagggaagttttgtggatctatccgtctca
+aggtctagcagtagtagtagtcttgctactgaagaaggtctttttgaacaaccagatcaa
+tcagtatccagtaattctgtcatggataaaattttgcagcgacgaagtttacaactgcgt
+gatcagcagcaagcttggcaggaatctccagatggtagaaaaatgcttgaatttcgaaga
+agtctccctgcttataaggagaaggacgctattctgacagccatttcacaaaatcaggtc
+ataattatatcaggtgaaactggctgtggcaagaccacacaaattcctcagttcatattt
+gagtccgaaatagaatctgttcgtggagctgtttgtagtgttatttgtacacaaccaaga
+agaatatctgcaatttctgtttctgagagagttgcttcagagagaggggagacattgggt
+gaatctgttgggtataaagttcggctggagggcgtgaaagggaaggatacccatcttctc
+ttctgcaccacaggcattttgttgagaagattactggttgatagaaatttgaaaggtgta
+actcatgttattgttgatgagattcatgagcgtggaatgaatgaggattttctgcttatt
+gtccttaaagatctcctccctcgccggcctgaattgaagctgattctgatgagtgcaaaa
+ctagatgcagagctttttttgtcctactttggtggagctatgataattcacattccgggt
+ttcacataccctgtcagaactcattttctggaaaatatattggaagtgacgggttacaga
+ttgaccccatttaatcaaattgatgattatggcgaagaaaaaatgtggaaaatgagcaaa
+caagcaccaagaaaaaggaagagccaaattgcatctttagttgaggatgcacttagagtg
+gccaatttcaaggagtatagcccccagactaaggagtcattgtcatgttggaatcctgat
+tgtattggttttaatctcattgaatacctcctatgtcatatttgtgagaaggaaagacct
+ggtgctgttctagtctttatgactggttgggatgacataaattctcttaaggataaacta
+caagctcatcctatattaggagattcaagccgagtattgttacttacctgccatggttct
+atggctagttcagagcagagtttaatatttgacgagcctgaaggtggagtgaggaaaata
+gtgcttactactaacatagctgagactagtatcaccattaatgatgttgtttttgtcatt
+gactgtgggaaagcaaaggagacatcttatgatgcactgaataacacttcttgtctgctt
+ccttcctggatttccaaggtttctgctcaacaaagaagaggaagggctggccgtgttcaa
+ccaggagaatgttaccatctgtatcctaggtctgtgtatgatgcttttgcagaatatcag
+cttcctgaaattttaaggacacctttgcagtctctatgcttgcaaattaaaagtttaaaa
+cttgggagtatttctgagttcttatccagggctctgcagtcacctgagttgctagctgtc
+caaaatgctattgaatatttaaaaatcactggggccttggaccagaatgaagacttgact
+gtcttagggcggtacttgaccatgcttccaatggaacccaaacttggaaagatgctaata
+ttaggtgccatcttcaaatgtctggaaccagtattaacaattgttgctggccttaatgtc
+agagatcctttcttagcaccagtggacaaaaaggatcttgctgaggctgcaaagtctcag
+ttttcctgtgatcatagtgaccatcttgcacttgtacgggcttacgagggatggaaagat
+gctgaaagagaccttgctggatacgaatactgttggaaaaactttctctcatttcaatca
+atgaaagctatcgattctcttcgggatgagttcttctctttgctcagggatactggtctt
+gttgattgcaacacaaccatttgcaatgcatggagctatgatgatcatcttgttcgagca
+gttatttgttatggtctttaccctggaatttgctccgttgtgaacaatgtgaagtccttt
+tcactgaaaactatggaagacggccatgtgcttctatactctaattctatcaatgctcgg
+caacctgaaattccatacccatggctggttttcaatgagaagataaaagtgaactctatt
+tttctaagggattcaacagctatctgtgattcagtgttgctcctgtttggtggtagcatc
+tctcaaggaaacactgatgggggacacttgaaaatgatgggaggatatttagaattcttc
+atggaacctgcactttctgatatgtatcaatgtttaaggagagaacttgatgagctgatt
+cagaataagttactcaatcccagaatggaaatgcacatgtatcgtgatctcctatctgca
+gttcgattgcttgtttcagaagatcgttgcgagggaagatttgtatttggtcgccaggtg
+cttaagtcgcttaagtcttcacctgtgccattacagccagctttgattccacggacagag
+agcggacctgggggcgataatcctaagagtcagctccaaacattgctcaccagggcagga
+tatgctgcccccagctacaaatcaagacaattgaagaacaaccagttcttggctacagtg
+gagttcaatggaattcaaattatgggtcggccttgcaacaataagaagagcgcagagaag
+gatgccgcagctgaggcactgcagtggctaatgggagggacccagacaagccttgaatgt
+ataaatcaaatgtcactgttactgaagaaagcaagaaggatcacttctgaatcagcacca
+ccctcaagttcatag
+>minc:123224581 K20476 RAB6A-GEF complex partner protein 1 | (RefSeq) guanine nucleotide exchange factor subunit RIC1-like (N)
+atgtacatgtcgtacggatggccacaggtgatcccaatagagcaagggcagtgttcgtcg
+tctcaacggatcatatacttgaaagttatcaatggcttattactcgttgtctctccttca
+catgtcgagctgtggagttcctcgcggcataaagtgaggttagggaaatataagagggat
+tcagagtcgctgcagagagagggagagaatttgcaagctttgtggagccctgatggaaaa
+ttgatcgctgtgattacgtcatctttttttcttcacattttcaaggtccagtttacagaa
+aaaagaatacaaattggagcaaagcatccttctggtttgtttttggcaaatatatttctt
+gttctcagtgagcaggtgccttttgcagaaaagggtttttcagtgagcaatattgtgagc
+gataacaaacatatgctacttggactttctgatggatctttatattgtatctcatggaag
+ggggagttctgtggagcttttgaactcaatgactttcgatatgatagcagctcagtgaca
+ctactaccaaattccctgagtaatggctttgcttctgcagagacttcaggagcttttgtt
+tctggtcacaaattctccagaaagtgcgctattgtccagctggagctttgctttctaatg
+agactgcttcttattgtatattctgatggaaaactgatatcatgctctataagtaagaaa
+ggtttaaagcaacctgaatttattaaagttgaaaaagagctgggttctggtgatgttgta
+tgtgcttcagtggcggcagagcaacaaattgttgctgttggcaccagaagggggattgtt
+gagctatatgacctggcagaatctgcatcactcattcgtactgtgtctttgtacgactgg
+ggatactcaatggatgatactggttctgtcagttatattgcatggacacctgataattct
+gcttttgctgttgggtggaagtcaagaggacttactgtgtggtctgtttcggggtgtcgt
+ttgatgtcaacaatccgtcagattggcttaagttctgtgtcttctccagttgcaaagcca
+aaccaagactttaaatatgagccactaatgagcggcacctctctggttcagtgggatgaa
+tatggatataggctttacgcaattgaggaagaatcgtcagagcaaattcttgcattttcc
+tttggcaaatgttgtattagcagaggagtatctggcatgacttatgcccgtcaagtaatt
+tatggtgaagataggttattagttgtgcagtctgaagatactgatgaacttaagctttta
+catttaaaccttccagtttcttatatctcccagaattggcctgtccaacatgtggcagct
+agcaaggatggaatgtacttagcagttgctggtcttcatgggttaatattatatgatata
+aggctgaaaaagtggcgagtatttggagatatcacgcaggaacaaaagattcagtgcaaa
+ggtttgctgtggctgggaaagattattgttgtctgcaactacattgattcttctaacatg
+tatgaactgcttttttatcctagatatcatcttgatcagagctcactactctgtcggaaa
+cctttgcttgcaaaaccaatggtgatggatgtctaccaagattatatattggtgacctat
+cgcccatttgatgtccacatattccatgtgaaattatttggtgaattgacaccttcaaac
+actccagacctacaactttctacagtacgagaactttcaatcatgactgcgaagagccac
+ccagctgctatgcgctttatccctgatcaggttactggtgaaagtacattaaacaatcga
+gtttcatctgaagaagatttgtctgagagggagcctgcaagatgtttgatattaagagca
+aatggggagctttcacttctggatttagatgatggaagggaaagggagcttaccgattct
+gttgaattattttgggttacttgtggacaatcagaggagaagatgagtctaattgaggaa
+gtttcatggttggattatggctttcgagggatgcaggtttggtatccgtcttcgggtgtt
+gacccttttaagcaggaggactttttgcatttggacccggagttggagtttgaccgtgag
+gtgtatcctttgggtcttcttccaaatgctggtattgttgttggcgtttcgcagagactg
+tcgttttcagcatgcacagagtttccttgttttgaaccaactcctcaagcccaaactata
+ttgcattgcctacttcggcatcttcttcagagggacaaaattgtggaggctttacggttg
+gcacagttgtctgcagaaaagcctcatttttcacattgtctggagtggcttctttttact
+gtatttgaagctgaaatttccaggcaaaatataaacaagaaccaaatctcaacccttaaa
+cgtgctgccaacttttctcttttggagaagacttgcaatttaattagaaattttcctgag
+taccttagtgttgttgtcagtgttgctagaaagactgatggtcgacattggtcagatttg
+ttctctgctgctggaagatctacagagttgtttgaggactgcttccagcggagatggtat
+cgcactgcggctggctatattcttgtgattgctaaacttgaaggtcccgctgtcagtcaa
+tattgtgccttacgtttattacaggcaacacttgatgaatgtttatatgaacttgctggg
+gaactggtgagattcttactgagatctggaagggaatttgaaccagcatcaactgattca
+gaaaaattatcacccagattcttgggctattttctttttcctcctagttacaggaggtca
+tctttggataaaagcacctctctcaaggagcagagtcctaatgttgcttctgttaagaac
+atcttagaaaatcatgctagctatttgatgtcggggaaagaactttccaagcttgttgca
+tttgtaaagggcactcagtttgatttagtggaatatcttcaacgagaaagatatggtagt
+gctcgcttagagaattttgcttcagcgcttgaactgattgcgcaaaagcttcacatgggt
+acactgcagagcaggttggatgcagaatttctcttggctcatatgtgctctgtcaagttc
+aaagaatggatagttgtacttgccactcttttaagacgatctgagattctttttgatctt
+ttctgtcatgatacacggttatggaaagcttatgccattacattacagtctcattccacg
+ttcgccgagtaccaagatcttcttgaatccttggaggagagacttacatctgttttgaat
+acagaagacaaatga
+>minc:123230223 K00121 S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase [EC:1.1.1.284 1.1.1.1] | (RefSeq) alcohol dehydrogenase-like 7 (N)
+atggatagcgacaatttgttaagggaaaccgcagggaagccgattcgatgcagagctgcc
+atagctcgagtgccaggggagtctctggtaatagaggagattctagtggaccctccgagt
+tcccatgaagttcggattcgaatcatctgtacaggtctctgtcacagcgatatcactttc
+tggaaaatgaaggattttcctgctgttttcccaagaattctgggtcatgaggctattggg
+aaggtggaaagtgtgggggagaatgtaaaagatgtagcagaaggagatattgtgatacca
+tattttctggcagattgtagtgaatgtgtcgattgcaagtcaaagaagagcaacctatgt
+tcaaaattccccttcaaggtctctccttggatggctagatctgagacaagcagattcaga
+gatctcaagggacaaactttgcatcattttttatttgtttcaagttttagtgagtatact
+gtggtagacattgctaatatagtaaagattgaccccgacgtccctccaagtaaggcatgc
+ctcctaagttgtggggtatcaacaggggttggagctgcttggagaacagcaaacgtggag
+gctggatcaactgttgtcatatttgggctaggatcaattggattagctgtcgcagaggga
+gcaagactttgtggtgctactagaattataggtgtcgatgtgattccagagaaatttgaa
+ataggaaaaaagtttggagtcacagaatttgttaatgctaaaagttgtggggataaatca
+gtaagccaggtaatcaatgagatgactgatggaggtgcagattactgctttgagtgtgtt
+ggttcttcatccttggtgcaagaagcgtatgcttgctgtcgaaagggatggggaaagaca
+gttgtgttgggagtggacaagccaggagcacaggtgagcttaagctctcttgatgtcctt
+gagagtggaaaaattctgaagggatcattgtttggaggactcaaagctaaaactgacatt
+ccaattctgctgaaacgttacatggacaaggaattacaattagatgaatttgtgacacat
+gagatgaagtttgaagagatcaataaagcctttgatttacttattcaaggaaagtgtcta
+cggtgtgtcatttggatggacaaataa
diff -r 000000000000 -r 3db999d4e0c1 test-data/ref.fa.fai
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref.fa.fai Tue Jul 15 19:00:59 2025 +0000
@@ -0,0 +1,3 @@
+minc:123214052 3555 141 60 61
+minc:123224581 3375 3883 60 61
+minc:123230223 1167 7472 60 61
diff -r 000000000000 -r 3db999d4e0c1 test-data/reference_lgdistribution.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference_lgdistribution.txt Tue Jul 15 19:00:59 2025 +0000
@@ -0,0 +1,12 @@
+# table produced by mapDamage version 2.2.2
+# using mapped file test_align.bam and ref.fa as reference file
+# Std: strand of reads
+Std Length Occurences
++ 82 1
++ 61 2
++ 76 2
++ 72 1
++ 75 1
++ 54 1
++ 59 1
++ 64 1
diff -r 000000000000 -r 3db999d4e0c1 test-data/reference_misincorporation.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference_misincorporation.txt Tue Jul 15 19:00:59 2025 +0000
@@ -0,0 +1,844 @@
+# table produced by mapDamage version 2.2.2
+# using mapped file test_align.bam and ref.fa as reference file
+# Chr: reference from sam/bam header, End: from which termini of DNA sequences, Std: strand of reads
+Chr End Std Pos A C G T Total G>A C>T A>G T>C A>C A>T C>G C>A T>G T>A G>C G>T A>- T>- C>- G>- ->A ->T ->C ->G S
+minc:123214052 3p + 1 0 1 0 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+minc:123214052 3p + 2 1 0 1 1 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+minc:123214052 3p + 3 0 1 1 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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diff -r 000000000000 -r 3db999d4e0c1 test-data/test_align.bam
Binary file test-data/test_align.bam has changed
diff -r 000000000000 -r 3db999d4e0c1 test-data/test_align.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_align.sam Tue Jul 15 19:00:59 2025 +0000
@@ -0,0 +1,15 @@
+@HD VN:1.5 SO:unsorted GO:query
+@SQ SN:minc:123214052 LN:3555
+@SQ SN:minc:123224581 LN:3375
+@SQ SN:minc:123230223 LN:1167
+@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/home/taulagnon/miniconda3/envs/ancientDNA/bin/bowtie2-align-s --wrapper basic-0 -x index -S test_align.sam -U reads.fa"
+simulated_read_1 0 minc:123214052 414 42 82M * 0 0 TAGATGTGATTTTGAGCAACTGTCAGCTCTGGCTAGTGGCATGGGTTTGTATAGTCATCTGTACGCAAAAGTTATTGTCTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGFGFFFCCCC AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:73G8 YT:Z:UU
+simulated_read_2 0 minc:123214052 1173 23 61M * 0 0 ATTGGTTGATAGAAATTTGAAAGGTGTAACTCATGTTATTGTTGATGAGATTCATGAACAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGFGG AS:i:-16 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C55G1G1 YT:Z:UU
+simulated_read_3 0 minc:123214052 3161 42 76M * 0 0 TTGTATTTGGTCGCCAGGTGCTTAAGTCGCTTAAGTCTTCACCTGTGCCATTACAGCCAGCTTTGATTCCACAGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFGFFCC AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:72G3 YT:Z:UU
+simulated_read_4 0 minc:123224581 211 42 72M * 0 0 TTGTAAGCTTTGTGGAGCCCTGATGGAAAATTGATCGCTGTGATTACGTCATCTTTTTTTCTTCACATTTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGFGFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:3C68 YT:Z:UU
+simulated_read_5 0 minc:123224581 397 24 76M * 0 0 TTTTTAGTGAGTAATATTGTGAGCGATAACAAACATATGCTACTTGGACTTTCTGATAGATCTTTATATTGTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGFGCCCC AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:4C6C45G18 YT:Z:UU
+simulated_read_6 0 minc:123224581 765 23 61M * 0 0 TTTTGGTGATGTTGTATGTGCTTCAGTGGCGGCAGAGCAACAAATTGTTGCTATTGACACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:2C49G3G4 YT:Z:UU
+simulated_read_7 0 minc:123224581 1277 42 75M * 0 0 TATTAGTTGTGCAGTTTGAAGATACTGATGAACTTAAGCTTTTACATTTAAACCTTCCAGTTTCTTATATCTCCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGFGGFFGFFFCC AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15C59 YT:Z:UU
+simulated_read_8 0 minc:123230223 288 24 54M * 0 0 TATTGTGATATCATATTTTCTGGCAGATTGTAGTGAATGTGTCGATTGCAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:10C40G2 YT:Z:UU
+simulated_read_9 0 minc:123230223 822 0 59M * 0 0 TTATTGTTTTGAGTGTGTTGGTTCTTCATCCTTGGTGCAAAAAGCGTATGCTTACTATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGGGGGFGF AS:i:-28 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:3C2C33G12G2G2 YT:Z:UU
+simulated_read_10 0 minc:123230223 1017 23 64M * 0 0 TATTCTAATTCTGCTGAAACGTTACATGGACAAGGAATTACAATTAGATGAATTTGTAACACAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGFFGFFFFFFFCCCCCCCCC AS:i:-17 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:0C4C51G6 YT:Z:UU
diff -r 000000000000 -r 3db999d4e0c1 tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Tue Jul 15 19:00:59 2025 +0000
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#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. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 000000000000 -r 3db999d4e0c1 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Jul 15 19:00:59 2025 +0000
@@ -0,0 +1,8 @@
+
+
+
+
+ value, dbkey, name, path
+
+
+
diff -r 000000000000 -r 3db999d4e0c1 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Tue Jul 15 19:00:59 2025 +0000
@@ -0,0 +1,8 @@
+
+
+
+
+ value, dbkey, name, path
+
+
+