# HG changeset patch
# User iuc
# Date 1678276846 0
# Node ID 29eec6c7bab2a58c1e1c1e58de824884eacd874c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 commit b9fe99d8335825c6c23f569034354323b794127a
diff -r 000000000000 -r 29eec6c7bab2 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Mar 08 12:00:46 2023 +0000
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+ 1.10.0
+ 0
+ 20.09
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+ pbmm2
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+ pbmm2
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diff -r 000000000000 -r 29eec6c7bab2 pbmm2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pbmm2.xml Wed Mar 08 12:00:46 2023 +0000
@@ -0,0 +1,112 @@
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+ map PacBio reads to a reference genome.
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+ macros.xml
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+ `__\ ’s C API. It supports
+native PacBio input. Output can be used directly for polishing using
+`pbgcpp `__.
+
+**Input**: PacBio reads in bam or [gzipped] fasta or fastq format.
+**NOTE**: to use the output of pbmm2 for pbgcpp (GenomicConsensus), you
+have to provide PacBio CLR reads in bam format. You can use pbmm2 to
+align other types of PacBio reads in [gzipped] fasta or fastq format,
+but you can’t use the output for pbgcpp (GenomicConsensus).
+
+**Output**: A **sorted** PacBio BAM file, suitable for use with
+pbgcpp (previously known as GenomicConsensus).
+
+ ]]>
+
+
diff -r 000000000000 -r 29eec6c7bab2 test-data/All4mer.V2.01_Insert.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/All4mer.V2.01_Insert.fa Wed Mar 08 12:00:46 2023 +0000
@@ -0,0 +1,5 @@
+>All4mer.V2.01_Insert
+CATCAGGTAAGAAAGTACGATGCTACAGCTTGTGACTGGTGCGGCACTTTTGGCTGAGTTTCCTGTCCAC
+CTCATGTATTCTGCCCTAACGTCGGTCTTCACGCCATTACTAGACCGACAAAATGGAAGCCGGGGCCTTA
+AACCCCGTTCGAGGCGTAGCAAGGAGATAGGGTTATGAACTCTCCCAGTCAATATACCAACACATCGTGG
+GACGGATTGCAGAGCGAATCTATCCGCGCTCGCATAATTTAGTGTTGATC
diff -r 000000000000 -r 29eec6c7bab2 test-data/all_fasta.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc Wed Mar 08 12:00:46 2023 +0000
@@ -0,0 +1,1 @@
+bnd-ref bnd-ref bnd-ref ${__HERE__}/bnd-ref.fasta
\ No newline at end of file
diff -r 000000000000 -r 29eec6c7bab2 test-data/bnd-ref.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bnd-ref.fasta Wed Mar 08 12:00:46 2023 +0000
@@ -0,0 +1,208 @@
+>indel_ref whatever
+GGAGACTGCGGCTGGGTCTCGGGGCGCGGAGCCTCGGCGGGAGGAGGCGGACACGCTGGC
+AGCGGCGGCGGCAGCGGCCAGCAGCAGCGGCGGCAGCAGCGGCGGCCTCGGTCCGGGGCG
+CCGGCCGTCCTCCTCCTTCCTCCGGCGGCAGCCCTAGTTCCGCCTCTCGGCTCCCCCCGG
+CTCCACTCTCCCCAGCCGGGAGCTGCTCTCTCCTCTTTCTAGTCTCGCCAACATGACCCG
+GCGCGGGCCCGCAGCGCCGCCACCATGGGGAAGGGGGTTGACGAGACAAGTATGAGCCCG
+CAGCTGGTATCAGAACATGGGGACAAGACGAGCAAAAGGCGAAGAAGGAAAGGGACATGG
+ACGAACTCAAGAAGGAAGTGTCTATGGACGACCATAAACTCAGCCATGGATGAACTCCAT
+CGTAAATACGGAACAGATTTGAGCCGAGGCTAACACCCGCAAGGGCCGCTGAGATCCTGG
+CTCGGGATGGCCCAACGCCCTCACGCCCCTCTCCCACTACTCCCGAGTGGGTCAAATTCT
+GTAGGCAGCTGTTCGGTGGCTTCTCCATGTTACTGTGGATTGGAGCCATTCTTGGTTTCT
+TGGCTTATGGCATCCGAAGTGGCTACAGGAAGAGGAACCACCAAATGATGATCTGTACCA
+TCGGGGTCGTGCTGTCTGCTGTCTCGATCCATTAACTGGCTGTTTCTCCTATTATCAAGA
+AGCAAAAAAGCTCCAAGTCAATGGAATTCCTTCAAGAACATGGGTCCCTCAGCAAGCCCT
+CGTGATTCGAAATGGAGAGAAGATGAGCATCAACGGCAGAGGAGTTCGTCGTTGGTGATC
+TGGTGGAGGTGAAGGGCGGAGACCGAATCCCTGCTGATCTCAGAATCATATCTGCAAATG
+GGCTGCAAGGTGGATAACTCCTCACTCACTGGTGAATCAGAACCCCAGACTCCGGTCCCC
+GGATTTCACAAACGAGAACCCTTGGAGACAAGGAACATTGCCTCTTCTCAACCAACTGTG
+TTGAAGGAACTGCACGTGGCATCGTTGTGTACACTGGGGATCGCACCGTGATGGGCAGGA
+TCGCCACACCCTTGCTTCTGGGCTGGAATGCGGCCAGACCCCCATTGCTGAAGAAATCGA
+GCACTTTCATCCACCTCATCACGGGGTGGCCGTGTTCCTGGGGGGTGTCTTTCTTCATGT
+CTCTCTCTGATCCTTGAGTACACCTGGCTCGAGGCTGTTCATCTTTCCCCATTGGTATCA
+>bnd_ref_U [moreinfo]
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+GATGCCGACTTTAGCAAAAAATGAGAATGAGTTGATCGATAGTTGTGATTACTCCTGCGA
+AACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATATCCGGATAACGCAATGGATC
+AAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAATGGTATGAAC
+CACAGGCGAGAGCAGTAAAATGGCGGTCAAATTGGTAATAGCCATGCAGGCCATTATGAT
+ATCTGCCAGTTGCCACATCAGCGGAAGGCTTAGCAAGGTGCCGCCGATGACCGTTGCGAA
+GGTGCAGATCCGCAAACACCAGATCGCTTTAGGGTTGTTCAGGCGTAAAAAGAAGAGATT
+GTTTTCGGCATAAATGTAGTTGGCAACGATGGAGCTGAAGGCAAACAGAATAACCACAAG
+GGTAACAAACTCAGCACCCCAGGAACCCATTAGCACCCGCATCGCCTTCTGGATAAGCTG
+AATACCTTCCAGCGGCATGTAGGTTGTGCCGTTACCCGCCAGTAATATCAGCATGGCGCT
+TGCCGTACAGATGACCAGGGTGTCGATAAAAATGCCAATCATCTGGACAATCCCTTGCGC
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>bnd_ref_V
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+GACTGACATTGCTTTTGCACTTGGTGTACTGGCGCTGTTGGGAAGTCGTGTTCCGTTAGC
+GCTGAAGATCTTTTTGATGGCTCTGGCTATTATCGACGATCTTGGGGCCATCATTATCAT
+CGCATTGTTCTACACTAATGACTTATCGATGGCCTCTCTTGGCGTCGCGGCTGTAGCAAT
+TGCGGTACTCGCGGTATTGAATCTGTGTGGTGCACGCCGCACGGGCGTCTATATTCTTGT
+TGGCGTGGTGTTGTGGACTGCGGTGTTGAAATCGGGGGTTCACGCAACTCTGGCGGGGGT
+AATTGTCGGCTTCTTTATTCCTTTGAAAGAGAAGCATGGGCGTTCTCCAGCGAAGCGACT
+GGAGCATGTGTTGCACCCGTGGGTGGCGTATCTGATTTTGCCGCTGTTTGCATTTGCTAA
+TGCTGGCGTTTCACTGCAAGGCGTCACGCTGGATGGCTTGACCTCCATTCTGCCATTGGG
+GATCATCGCTGGCTTGCTGATTGGCAAACCGCTGGGGATTAGTCTGTTCTGCTGGTTGGC
+GCTGCGTTTGAAACTGGCGCATCTGCCTGAGGGAACGACTTATCAGCAAATTATGGTGGG
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>bnd_ref_W
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+CTGGATAACACCGTGCGGCTGCCGGGGCTGGCGAATCTGTGGGTGCCGCCAATTCGTAAC
+CGTATCGATATGCTCTCAACCGGCATTAAAAGCCCCATCGGCATTAAAGTTTCCGGCACT
+GTGCTGGCGGATATCGACGCGATGGCTGAGCAAATTGAAGAAGTAGCGCGAACGGTGCCA
+GGCGTAGCTTCTGCGCTTGCCGAGCGGCTGGAAGGTGGGCGCTATATCAACGTTGAGATT
+AACCGTGAAAAAGCCGCACGTTACGGTATGACGGTGGCGGATGTGCAGTTGTTTGTGACT
+TCTGCGGTGGGCGGGGCGATGGTTGGCGAAACGGTGGAAGGGATTGCCCGTTATCCAATT
+AATCTGCGTTATCCGCAAAGCTGGCGCGATAGTCCGCAGGCACTGCGCCAGCTGCCGATC
+CTGACGCCGATGAAGCAGCAAATCACCCTGGCAGACGTGGCCGACATTAAAGTCTCTACC
+GGACCGTCGATGCTGAAAACCGAGAATGCGCGCCCGACGAGCTGGATTTATATCGATGCC
+CGCGATCGTGACATGGTGTCGGTGGTTCACGATTTGCAAAAAGCGATAGCTGAAAAAGTG
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>bnd_ref_Y
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+GCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTA
+TACCGCCAATAGACTTTATTTACCTTCCTACTATAAAGCGGATATAAGTTAGGGACTGAA
+ACATTATTCTTACGCGGTCTGGCTGCCATTACTCAAAATCCGTTGCAAAAGTAATGAGTC
+ATTTTTCTTGATTACAGGTGTTACCAACTCCCCAACTAACTCGGCGTCCTCACGCACTCG
+CCATAACCGGCCTTGTTTCATGGCCGGTGGACAAAATAAATTCTGCTTAGCATAACGACG
+CAATGTGGACACACTTGGAGGATTACTTCTGTATTTTTCAGCAGCCCATTCTTCAAGAGT
+TAACATTTGAAGCATATGCGATCACCTTATTACTACACTAACTGCTTAGTCTCAGCATAT
+CGACCCTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGC
+TATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAA
+AAGGGCGGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCAC
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>bnd_ref_X
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+GGAATACCCAGCACATCGGCGATCGCGTGGATCGCACCATCCGGCACCCAGCCACGCTGC
+TTCTGAACGATTTTCAGCGCTTCAATGGACGCCGCACGCGGGTCTTCGTAGTGGTGCATC
+TCGTGCTCGATCGCTTCACGCTCTGCCGCACTCAGCTCAAAAGCCTCGGTTTGTGGTTGT
+TGATTCTCGTGCATAATTAGCGGTCCACATCTGACATAACAAAATCGATACTGCCCAGAT
+AAACAATCAGGTCAGACACCAGGCTGCCGCGGATCGCCGCCGGAATTTGCTGCAAATGCG
+CAAAGCTCGGGGTACGAACACGGGTGCGGTAACTCATGGTGCTGCCGTCGCTGGTCAGGT
+AGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCATTGGCAGGCATCA
+CCGGACCCCACGACACTTGCAGGAAGTGGGTGATCAGGGTTTCGATATGTTGCAGCGTGC
+GCTCTTTCGGCGGCGGCGTGGTCAGCGGGTGATCCGCTTTGAACGGGCCTTCCGGCATGT
+TGTTGAGGCACTGCTCAAGAATGCGCAGACTCTGGCGCAGCTCTTCCACTTTAAGCATTG
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>bnd_ref_Z #appendix
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+CTAAAAACGTGGCGAACGGTTTGCTTTTCAGATCCTGCAATGCGCCGTGGAAGGCATAGC
+GCACCTGTTCGTTGAAAACGTTGGTTTTGCGATTTACCGGTTTTGGCGAGGATTTCGCGC
+GTTTTGGTGCGTTACGACCGCCGTCGCCTGAGCCGCCGACCGATTTACGGAAGCGATCAA
+GACGCCCGCCAAACTGCCGAATATGATTGATTGCATCGCGCTTATTCATGGCCCACGCCT
+CCATGCAAGTGACCATCGCTCAGGGTGAGCATGCGATAGGAACGCCGCGAGATCAGGTTG
+ATGTCGTGCGTTGCCATCAATACGGTTACCCCAACGCGGTTAAACTCTTCAAACAGACGT
+AAAATGCCTTCCGACAGCGCGTCGTCCAGGTTACCAGTCGGTTCGTCCGCCAGCAGTACC
+GCGGGCTTGTTCACCACCGCGCGGGCAATGCCAACACGCTGTTGTTCACCGCCCGAAAGC
+TGAATAGGGAAGTTCTTCGCTTTGTCCAGTAGCCCGACTTTATCCAGCGCCGCCGACACC
+CGGCGACGAATATCGTCACCGCTGGCACCGGCGATAATCAGCGGGATCGCCACGTTATCG
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
diff -r 000000000000 -r 29eec6c7bab2 test-data/bnd.bam
Binary file test-data/bnd.bam has changed
diff -r 000000000000 -r 29eec6c7bab2 test-data/out.aligned_subreads.bam
Binary file test-data/out.aligned_subreads.bam has changed
diff -r 000000000000 -r 29eec6c7bab2 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Wed Mar 08 12:00:46 2023 +0000
@@ -0,0 +1,7 @@
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+ value, dbkey, name, path
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