# HG changeset patch
# User iuc
# Date 1636648712 0
# Node ID 204a131e47dbdaea50937e677df739a20e66b168
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
diff -r 000000000000 -r 204a131e47db bbduk.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bbduk.xml Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,356 @@
+
+ decontamination using kmers
+
+ macros.xml
+
+
+ '$ref_name' &&
+ #else:
+ ln -s '$ref' '$ref_name' &&
+ #end if
+ $refs.append(str($ref_name))
+ #end for
+ #set refs = ','.join($refs)
+#else if str($reference_type_cond.reference_type) == 'keywords':
+ #set refs = str($reference_type_cond.reference)
+#end if
+
+bbduk.sh
+in='${read1_file}'
+
+#if str($input_type_cond.input_type) in ['pair', 'paired']:
+ in2='${read2_file}'
+#end if
+#if str($outputs_select).find('outu') >= 0:
+ out='${outputu}'
+ #if str($input_type_cond.input_type) in ['pair', 'paired']:
+ out2='${outputu2}'
+ #end if
+#end if
+#if str($outputs_select).find('outm') >= 0:
+ outm='${outputm}'
+ #if str($input_type_cond.input_type) in ['pair', 'paired']:
+ outm2='${outputm2}'
+ #end if
+#end if
+#if str($outputs_select).find('outs') >= 0:
+ outs='${outputs}'
+#end if
+
+#if str($reference_type_cond.reference_type) != 'no_reference':
+ ref='$refs'
+ #if str($reference_type_cond.ktrim_cond.ktrim_select) == 'yes':
+ ktrim='${reference_type_cond.ktrim_cond.ktrim}'
+ minlength=$reference_type_cond.ktrim_cond.minlength
+ #end if
+#end if
+
+k=$advanced_options.k
+rcomp='${advanced_options.rcomp}'
+maskmiddle='${advanced_options.maskmiddle}'
+minkmerhits='${advanced_options.minkmerhits}'
+minkmerfraction=$advanced_options.minkmerfraction
+mincovfraction=$advanced_options.mincovfraction
+hammingdistance=$advanced_options.hammingdistance
+qhdist=$advanced_options.qhdist
+editdistance=$advanced_options.editdistance
+forbidn='${advanced_options.forbidn}'
+trimfailures='${advanced_options.trimfailures}'
+findbestmatch='${advanced_options.findbestmatch}'
+skipr1='${advanced_options.skipr1}'
+skipr2='${advanced_options.skipr2}'
+
+#if str($output_stats_cond.output_stats) == 'yes':
+ #if str($output_stats_cond.output_stats_select).find('stats') >= 0:
+ stats='${output_stats}'
+ #end if
+ #if str($output_stats_cond.output_stats_select).find('ref') >= 0:
+ refstats='${output_ref}'
+ #end if
+ #if str($output_stats_cond.output_stats_select).find('rpkm') >= 0:
+ rpkm='${output_rpkm}'
+ #end if
+ #if str($output_stats_cond.output_stats_select).find('dump') >= 0:
+ dump='${output_dump}'
+ #end if
+#end if
+#if str($output_hists_cond.output_hists) == 'yes':
+ #if str($output_hists_cond.output_hists_select).find('bhist') >= 0:
+ bhist='${output_bhist}'
+ #end if
+ #if str($output_hists_cond.output_hists_select).find('quhist') >= 0:
+ qhist='${output_quhist}'
+ #end if
+ #if str($output_hists_cond.output_hists_select).find('quchist') >= 0:
+ qchist='${output_quchist}'
+ #end if
+ #if str($output_hists_cond.output_hists_select).find('aqhist') >= 0:
+ aqhist='${output_aqhist}'
+ #end if
+ #if str($output_hists_cond.output_hists_select).find('bqhist') >= 0:
+ bqhist='${output_bqhist}'
+ #end if
+ #if str($output_hists_cond.output_hists_select).find('lhist') >= 0:
+ lhist='${output_lhist}'
+ #end if
+ #if str($output_hists_cond.output_hists_select).find('phist') >= 0:
+ phist='${output_phist}'
+ #end if
+ #if str($output_hists_cond.output_hists_select).find('gchist') >= 0:
+ gchist='${output_gchist}'
+ #end if
+ #if str($output_hists_cond.output_hists_select).find('enthist') >= 0:
+ enthist='${output_enthist}'
+ #end if
+#end if
+t=\${GALAXY_SLOTS:-4}
+]]>
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+ str(outputs_select).find('outu') >= 0
+ 'outu' in outputs_select
+
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+ 'outu' in outputs_select and input_type_cond['input_type'] != 'single'
+
+
+ 'outm' in outputs_select
+
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+ 'outm' in outputs_select and input_type_cond['input_type'] != 'single'
+
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+ 'outs' in outputs_select
+
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+ output_stats_cond['output_stats'] == 'yes' and 'stats' in output_stats_cond['output_stats_select']
+
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+ output_stats_cond['output_stats'] == 'yes' and 'ref' in output_stats_cond['output_stats_select']
+
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+ output_stats_cond['output_stats'] == 'yes' and 'rpkm' in output_stats_cond['output_stats_select']
+
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+ output_stats_cond['output_stats'] == 'yes' and 'dump' in output_stats_cond['output_stats_select']
+
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+ output_hists_cond['output_hists'] == 'yes' and 'bhist' in output_hists_cond['output_hists_select']
+
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+ output_hists_cond['output_hists'] == 'yes' and 'quhist' in output_hists_cond['output_hists_select']
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+ output_hists_cond['output_hists'] == 'yes' and 'quchist' in output_hists_cond['output_hists_select']
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+ output_hists_cond['output_hists'] == 'yes' and 'aqhist' in output_hists_cond['output_hists_select']
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+ output_hists_cond['output_hists'] == 'yes' and 'bqhist' in output_hists_cond['output_hists_select']
+
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+ output_hists_cond['output_hists'] == 'yes' and 'lhist' in output_hists_cond['output_hists_select']
+
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+ output_hists_cond['output_hists'] == 'yes' and 'phist' in output_hists_cond['output_hists_select']
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+ output_hists_cond['output_hists'] == 'yes' and 'gchist' in output_hists_cond['output_hists_select']
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+ output_hists_cond['output_hists'] == 'yes' and 'enthist' in output_hists_cond['output_hists_select']
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+**What it does**
+
+BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single
+high-performance tool. It is capable of quality-trimming and filtering, adapter-trimming, contaminant-filtering via kmer
+matching, sequence masking, GC-filtering, length filtering, entropy-filtering, format conversion, histogram generation,
+subsampling, quality-score recalibration, kmer cardinality estimation, and various other operations in a single pass.
+Specifically, any combination of operations is possible in a single pass with the exception of kmer-based operations (kmer
+trimming, kmer masking, or kmer filtering). At most 1 kmer-based operation can be done in a single pass.
+
+**Options**
+
+ * **Reference** - if a reference is specified, BBDuk will operate on kmers in one of 4 modes: right-trimming, left-trimming, masking, or filtering. The default is filtering - any read matching a reference kmer will be discarded.
+
+ * **Trim reads to remove bases matching reference kmers** - When trimming to the right, once a reference kmer is matched in a read, that kmer and all the bases to the right will be trimmed, leaving only the bases to the left. When trimming to the left, trimming will be done to the left instead.
+
+**Outputs**
+
+ * **Unmatched** - All the reads that pass all filtering criteria. Reads will be at least as long as **Minimum read length** after any trimming operations and reads will not match any reference kmer if kmer-filtering is being performed. A read’s average quality will be at least as high as the specified **Minimum average quality**.
+ * **Matched** - Reads failing any filter criteria (such as matching a reference kmer). By default, if either read in a pair fails, both will be included in *Matched*.
+ * **Single** - Singleton reads whose mate was trimmed shorter than the value of **Minimum read length**.
+
+
+
+
diff -r 000000000000 -r 204a131e47db macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,96 @@
+
+ 1.0.0
+ 1.0.0
+ 20.09
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+ bbmap
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+ https://doi.org/10.1371/journal.pone.0185056
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diff -r 000000000000 -r 204a131e47db test-data/13-1941-6_S4_L001_R1_600000.fastq.gz
Binary file test-data/13-1941-6_S4_L001_R1_600000.fastq.gz has changed
diff -r 000000000000 -r 204a131e47db test-data/13-1941-6_S4_L001_R2_600000.fastq.gz
Binary file test-data/13-1941-6_S4_L001_R2_600000.fastq.gz has changed
diff -r 000000000000 -r 204a131e47db test-data/NC_002945v4.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_002945v4.fasta Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,101 @@
+>NC_002945.4 Mycobacterium bovis AF2122/97 genome assembly, chromosome: Mycobacterium_bovis_AF2122/97
+TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACC
+CTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAGCAAAGGGCTTG
+GCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTTGCTCTGTTATCCGTGCCGAGCAGCTTTGTC
+CAAAACGAAATCGAGCGCCATCTGCGGGCCCCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGA
+TCCAACTCGGGGTCCGCATCGCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGA
+AAATCCTGCTACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG
+GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCGCAATACCGATTCCGCTACCGCTG
+GCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGCGCCTCCAACCGGTTCGCGCA
+CGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCTTACAACCCCCTGTTCATCTGGGGCGAGTCC
+GGTCTCGGCAAGACACACCTGCTACACGCGGCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGG
+TCAAATATGTCTCCACCGAGGAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGC
+ATTCAAACGCAGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG
+GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATCGTCATCTCAT
+CTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACCCGCTTTGAGTGGGGGCTGAT
+CACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCCATCTTGCGCAAGAAAGCACAGATGGAACGG
+CTCGCGATCCCCGACGATGTCCTCGAACTCATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGG
+GCGCGCTGATCCGGGTCACCGCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGAT
+TGTGCTTCGCGATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC
+GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTGGCCCAGTCAC
+GACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCCAAAATCGGCCAAGCGTTCGG
+CCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATCCTGTCCGAGATGGCCGAGCGCCGTGAGGTC
+TTTGATCACGTCAAAGAACTCACCACTCGCATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCC
+GACAACGTTCTTAAAAAAACTTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCT
+GTGCACAAACCGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG
+ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACCTGCACCAAGA
+CCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCTTCGTCGTTTGTTCTTGGAAA
+GACAGCGCTGGGGATCGTTCGCTGGATACCACCCGCATAACTGGCTCGTCGCGGTGGGTCAGAGGTCAAT
+GATGAACTTTCAAGTTGACGTGAGAAGCTCTACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGG
+GTCACGCGTCATGGGCGTTCGTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTC
+ATCGTGAGGTGAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT
+TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGCCCGCGGTGCC
+GGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTTCCGGATTCGACTACGAGGTT
+TCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTGGAAGCGTTTTAGTTTCTGGCCGATTGTTGT
+CCGATATTACCCGGGCGTTGCCTAACAAGCCCGTAGGCGTTCATGTCGAAGGTAACCGGGTCGCATTGAC
+CTGCGGTAACGCCAGGTTTTCGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCG
+GAAGAGACCGGATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC
+GGGACGACACGCTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGGTTTTGGCCGC
+TACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGTCGCCAGATATCGAAGCGGCT
+GTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAGCGGGCATCGGCGGCTCTGACGTTCGTTTGT
+CGTTGGGTACTGGGCCGGGGGTGGGCAAGGATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCAC
+CACGCGACTTCTTGATGCCGAGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCC
+ACCATGGACGTGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG
+TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGACGAGCCGAGGA
+AGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACCCAACCTATCTAACGGACGGT
+TTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTACGACTGCGGGTAAGCCTGCCTTGCTACGTC
+CGGTGTCCGGGGACGATCGCCCTGTGGCGGGTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGA
+CTATGTCTATCTGTTGATGCCGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCG
+TCATTTGGGGCTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT
+TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACGACGTTAGGTT
+CGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGTGCGGTGATCTCCACGATCGT
+GGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATCGCCACGGGGCGAGTCAACAAAGCGCGATTG
+AATCGATCATCGGTCCGAAGTACACGTGATGTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGG
+ATCTGGGGTTGGTTCGTGGGGATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAG
+GCCTGCGATCGCTGCGGTACGAGCCGAATATGAGAGGGTGGTGCGCCAGCGGACGGCGTTATTGAAGTCC
+GTACCTGGAGCACGGTATCGGGGTGACCGGGGTGTGTTTGACACTCTTGAGGTATGGGACAGTCGTTTGG
+CGGAGCACGGGGCTGAACTGGTGGCCGCCCGCATCGATTTGGTCAACCAGTTGGCACCGGAAGTGAAGAA
+GGCATACCAGCTGTTGGCGCCGGAATCGCGATCGGCGTCTATCGGTTATCGGGCCAGCATGGATGTAACC
+GGTCCCAGCGAGCAGTCAGATACCGATCGGCAATTGTTAGCAGCTCGGCTGTTGGCGGCGCTGGCGGCCC
+GTCGGGATGCCGAACTCGAGCGTGGGGTTTGTCTAGTTGGTCCGCACCGTGACGACCTAATACTGCGACT
+AGGCGATCAACCCGCGAAAGGATTTGCTAGCCATGGGGAGGCGTGGTCGTTGGCGGTGGCACTGCGGTTG
+GCGGCCTATCAACTGTTACGCGTTGATGGTGGTGAGCCGGTGTTGTTGCTCGACGACGTGTTCGCCGAAC
+TGGATGTCATGCGCCGTCGAGCGTTGGCGACGGCGGCCGAGTCCGCCGAACAGGTGTTGGTGACTGCCGC
+GGTGCTCGAGGATATTCCCGCCGGCTGGGACGCCAGGCGGGTGCACATCGATGTGCGTGCCGATGACACC
+GGATCGATGTCGGTGGTTCTGCCATGACGGGTTCTGTTGACCGGCCCGACCAGAATCGCGGTGAGCGATT
+AATGAAGTCACCAGGGTTGGATTTGGTCAGGCGCACCCTGGACGAAGCTCGTGCTGCTGCCCGCGCGCGC
+GGACAAGACGCCGGTCGAGGGCGGGTCGCTTCCGTTGCGTCGGGTCGGGTGGCCGGACGGCGACGAAGCT
+GGTCGGGTCCGGGGCCCGACATTCGTGATCCACAACCGCTGGGTAAGGCCGCTCGTGAGCTGGCAAAGAA
+ACGCGGCTGGTCGGTGCGGGTCGCCGAGGGTATGGTGCTCGGCCAGTGGTCTGCGGTGGTCGGCCACCAG
+ATCGCCGAACATGCACGCCCGACTGCGCTAAACGACGGGGTGTTGAGCGTGATTGCGGAGTCGACGGCGT
+GGGCGACGCAGTTGAGGATCATGCAGGCCCAGCTTCTGGCCAAGATCGCCGCAGCGGTTGGCAACGATGT
+GGTGCGATCGCTAAAGATCACCGGGCCGGCGGCACCATCGTGGCGCAAGGGGCCTCGCCATATTGCCGGT
+AGGGGTCCGCGCGACACCTACGGATAACACGTCGATCGGCCCAGAACAAGGCGCTCCGGTCCCGGCCTGA
+GAGCCTCGAGGACGAAGCGGATCCGTATGCCGGACGTCGGGACGCACCAGGAAGAAAGATGTCCGACGCA
+CGGCGCGGTTAGATGGGTAAAAACGAGGCCAGAAGATCGGCCCTGGCGCCCGATCACGGTACAGTGGTGT
+GCGACCCCCTGCGGCGACTCAACCGCATGCACGCAACCCCTGAGGAGAGTATTCGGATCGTGGCTGCCCA
+GAAAAAGAAGGCCCAAGACGAATACGGCGCTGCGTCTATCACCATTCTCGAAGGGCTGGAGGCCGTCCGC
+AAACGTCCCGGCATGTACATTGGCTCGACCGGTGAGCGCGGTTTACACCATCTCATTTGGGAGGTGGTCG
+ACAACGCGGTCGACGAGGCGATGGCCGGTTATGCAACCACAGTGAACGTAGTGCTGCTTGAGGATGGCGG
+TGTCGAGGTCGCCGACGACGGCCGCGGCATTCCGGTCGCCACCCACGCCTCCGGCATACCGACCGTCGAC
+GTGGTGATGACACAACTACATGCCGGCGGCAAGTTCGACTCGGACGCGTATGCGATATCTGGTGGTCTGC
+ACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCGGCTCGAAGTCGAGATCAAGCGCGACGGGTA
+CGAGTGGTCTCAGGTTTATGAGAAGTCGGAACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACG
+GGGTCAACGGTACGGTTCTGGGCCGACCCCGCTGTTTTCGAAACCACGGAATACGACTTCGAAACCGTCG
+CCCGCCGGCTGCAAGAGATGGCGTTCCTCAACAAGGGGCTGACCATCAACCTGACCGACGAGAGGGTGAC
+CCAAGACGAGGTCGTCGACGAAGTGGTCAGCGACGTCGCCGAGGCGCCGAAGTCGGCAAGTGAACGCGCA
+GCCGAATCCACTGCACCGCACAAAGTTAAGAGCCGCACCTTTCACTATCCGGGTGGCCTGGTGGACTTCG
+TGAAACACATCAACCGCACCAAGAACGCGATTCATAGCAGCATCGTGGACTTTTCCGGCAAGGGCACCGG
+GCACGAGGTGGAGATCGCGATGCAATGGAACGCCGGGTATTCGGAGTCGGTGCACACCTTCGCCAACACC
+ATCAACACCCACGAGGGCGGCACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGT
+ACGCCAAGGACCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT
+GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAAGTTGGGCAAC
+ACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAATGAACAGCTGACCCACTGGTTTGAAGCCAACCCCA
+CCGACTCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGCGCAAGCCCGTATCGCGGCACGTAAGGCACG
+AGAGTTGGTGCGGCGTAAGAGCGCCACCGACATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCC
+ACGGATCCGCGCAAGTCCGAACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTC
+GCGATTCGATGTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA
+CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCACGACGAGTTC
+GATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGATGTTGACGGCCAACATATTT
+CCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCCGCTCATCGAGAACGGGCATGTGTTTTTGGC
+ACAACCGCCGCTGTACAAACTCAAGTGGCAGCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGC
diff -r 000000000000 -r 204a131e47db test-data/adapters.fa.gz
Binary file test-data/adapters.fa.gz has changed
diff -r 000000000000 -r 204a131e47db test-data/bduk_output_dump1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bduk_output_dump1.fasta Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,100 @@
+>116
+GAGATGGAACTGTAACTGGAGTTCCTT
+>7
+TGCCTAAGTGACTAGAGTTCAGACGTG
+>28
+TGAACTCCAGTCAAATTCCTTTATCTC
+>141
+GCATACGAGATGTATAGGTGACTGGAG
+>3
+GTTCAGCAGGAATACCGAGACCGATCT
+>126
+GGTAGCATCTCGTATGCCGTCTTCTGC
+>123
+GCCAAGGAACTCCAGTCACGTTTCGAT
+>126
+ATACGAGATGCTAACGTGACTGGAGTT
+>18
+CCGTATCTCGTATACCGTCTTCTGCTT
+>26
+TCTGAACTCCAGTAACGAGTGGATATC
+>17
+GAAGACGGCATACAAGATTGTTGACTG
+>22
+TGAACTCCAGTCAAGTGAAACGATCTC
+>50
+ACGCTACGCTATCACGTATGCCGTCTT
+>103
+TCGGGTGCCAAGGAACTCCAGTCACAT
+>141
+ATACATCTCGTATACCGTCTTCTGCTT
+>113
+TCGGGTGCCAAGGAACTCCAGTCACGG
+>84
+GAGATTACTACGCATCTCGTGGGCTCG
+>122
+CGTGGCCATCTCGAATGCCGTCTTCTG
+>139
+TCCAGTCACCGGAATATCTCGTATGCC
+>42
+CAGAAGACGGCATACGAGATTCGCCTT
+>107
+TGTGTGACTGGAGATCCTTGGCACCCG
+>140
+CATACGAGATAGCAAGGTGACTGGAGT
+>6
+GGTGACTGGAGTTAAGACGTGTGCTCT
+>30
+TCTCTTATACACAACTCCGAGCCCACG
+>122
+CAGTCACGTGGCCATCTCGTATGCCGT
+>19
+GTCACATGTCAGAATCTCGTATGCCGT
+>41
+GCGTGTAGATCTCAGTGGTCGCCGTAT
+>1
+GTGACTGGAGTTCAGACGTGTGCTCTT
+>15
+GTCTGAACTCCAGACACGGCTACATCT
+>4
+TCCGATCTCAAGCAGAAGACGGCATAC
+>119
+GAAGACGGCATACAAGATCTCTACGTG
+>129
+GTCACATTCCTATATCGTATGCCGTCT
+>107
+GATCACTGTGTGAATGGAGTTCCTTGG
+>9
+ATACGAGATCACTATGTGACTGGAGTT
+>24
+CTGAACTCCAGTCACGTTTCGGAATCT
+>116
+TGGAACTGTGACTAGAGTTCCTTGGCA
+>13
+GAAGACGGCATACAAGATCTGATCGTG
+>30
+TCTTATACACATCACCGAGCCCACGAG
+>49
+CAGAGAGGATCTCATATGCCGTCTTCT
+>133
+TCGTGGTGACTGGAGTTCCTTGGCACC
+>8
+CAGTCACTGACCAATCTCGTATGCCGT
+>33
+TCTAGTGTAGATCACGGTGGTCGCCGT
+>21
+TGCGGACGTGACTAGAGTTCAGACGTG
+>37
+GACGACTCCTTACATGTAGATCTCGGT
+>124
+GTACGGTGACTGGAGTTCCTTGGCACC
+>69
+TACACTTATGCGAACGTCGGCAGCGTC
+>149
+GCATACGAGATCTACGAGTGACTGGAG
+>124
+GAGATCGTACGGTAACTGGAGTTCCTT
+>105
+GCCAAGGAACTCCAGTCACTTAGGCAT
+>150
+CAGTCACTCGGCAATCTCGTATGCCGT
diff -r 000000000000 -r 204a131e47db test-data/bduk_output_quhist1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bduk_output_quhist1.tabular Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,101 @@
+#BaseNum Read1_linear Read1_log Read2_linear Read2_log
+1 16.400 4.332 32.940 32.694
+2 24.580 19.293 32.680 30.545
+3 29.880 28.913 32.720 32.218
+4 35.400 35.023 35.740 28.139
+5 35.610 35.076 35.980 34.688
+6 36.070 35.819 36.130 35.232
+7 36.030 35.134 35.750 28.304
+8 36.210 35.891 35.760 30.427
+9 37.770 36.724 37.550 36.174
+10 37.770 36.627 37.890 36.829
+11 38.130 34.528 37.720 35.825
+12 38.120 37.610 37.930 36.724
+13 37.600 29.816 37.860 33.975
+14 39.600 38.822 39.490 29.436
+15 39.240 37.118 39.430 34.527
+16 39.370 37.815 39.670 29.527
+17 39.230 35.062 39.310 34.199
+18 39.410 38.456 39.700 38.264
+19 39.470 38.621 38.680 28.791
+20 39.170 36.390 39.340 38.126
+21 39.340 38.280 39.320 37.141
+22 38.870 32.580 38.480 25.015
+23 39.370 37.125 38.850 32.436
+24 38.940 36.347 39.200 37.110
+25 38.560 36.248 39.000 28.586
+26 38.810 33.655 38.460 29.005
+27 38.930 35.395 38.560 25.539
+28 39.090 37.259 38.190 23.947
+29 38.610 25.879 38.730 30.749
+30 38.540 33.271 38.520 32.796
+31 38.840 33.517 38.040 30.447
+32 38.730 36.053 38.530 27.397
+33 38.340 34.385 38.880 35.605
+34 38.470 28.217 38.430 32.167
+35 37.350 30.035 38.560 26.684
+36 37.380 20.434 38.900 32.524
+37 37.810 32.591 38.450 34.632
+38 38.150 33.133 38.750 35.749
+39 37.660 31.924 38.420 26.003
+40 38.040 34.153 38.730 36.080
+41 37.970 35.596 39.020 37.708
+42 37.240 31.069 39.380 33.973
+43 37.740 29.175 38.840 35.607
+44 38.070 34.040 38.400 23.939
+45 37.690 30.131 38.160 26.507
+46 37.160 26.236 37.990 32.407
+47 37.820 35.168 37.330 29.388
+48 37.920 35.623 37.850 31.413
+49 38.150 34.322 37.830 27.255
+50 38.250 34.017 38.260 36.442
+51 38.060 36.455 36.270 30.125
+52 37.240 34.726 37.000 33.291
+53 37.700 32.804 37.210 34.667
+54 37.740 33.699 37.520 34.736
+55 37.780 33.713 37.880 35.604
+56 37.470 31.063 37.880 35.326
+57 36.680 26.593 36.810 22.646
+58 36.390 26.714 37.140 31.327
+59 35.960 29.732 36.900 20.404
+60 35.500 27.738 36.440 21.355
+61 35.800 28.761 36.200 20.579
+62 34.880 22.760 36.570 21.483
+63 35.560 30.716 36.180 21.372
+64 35.460 30.521 35.970 20.108
+65 35.090 25.249 35.450 20.127
+66 35.240 31.736 35.330 20.499
+67 35.230 25.003 35.410 21.618
+68 34.870 25.901 35.400 21.693
+69 34.560 24.095 35.200 21.684
+70 34.670 29.988 34.730 21.372
+71 35.010 32.741 34.710 21.582
+72 33.750 21.148 34.060 18.014
+73 34.130 29.634 34.040 18.342
+74 34.080 21.493 33.840 17.025
+75 33.590 20.367 33.380 16.366
+76 31.930 18.529 33.300 17.088
+77 32.400 18.486 32.360 15.307
+78 32.840 18.708 32.170 15.246
+79 33.190 18.732 32.130 15.504
+80 32.680 17.826 32.770 15.850
+81 32.690 17.578 32.640 15.552
+82 32.510 16.664 32.800 15.822
+83 31.640 15.134 32.350 15.209
+84 31.220 15.026 32.320 15.547
+85 31.270 14.413 32.170 15.387
+86 31.310 14.436 32.520 15.576
+87 32.130 14.923 32.070 15.354
+88 31.610 14.417 31.780 15.361
+89 31.240 14.665 32.290 15.854
+90 31.130 14.606 31.730 15.508
+91 31.350 14.867 32.120 14.926
+92 31.270 14.282 32.040 14.910
+93 31.790 14.879 31.770 14.676
+94 31.010 13.468 31.380 14.768
+95 30.280 12.737 31.220 14.847
+96 30.310 12.852 31.050 14.129
+97 30.390 12.411 31.160 13.935
+98 30.150 12.394 30.960 13.893
+99 30.300 11.964 30.610 13.166
+100 29.860 11.945 30.460 12.397
diff -r 000000000000 -r 204a131e47db test-data/bduk_outputu1.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bduk_outputu1.fastqsanger Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,102 @@
+@XXXXXXXXXX:7:1101:1582:1835#/1
+NGCTTCAGTTGGTACAGGTGTGTCACCCGTAGTTTGTAGGCTTGGAAGCCTGTAAGCTGTAGGGAACGTGGCAAGAACCAGATCTGGCCTTCCATATCTC
++
+!1=DDDDDAFFDDEFFG@AGHBCFHIFIEGIC?DBFGIFF?FGDFIBFFII8BCFIEEF.@FFIIEFFCE=??B@>A@@@BBBAD>A:?BBBBB@>>>B:
+@XXXXXXXXXX:7:1101:1610:1859#/1
+NTTATGTGTTACGTGAATCTCCTGAAGACAGCAGAAACTAGGTTGGTGAATTCTTATCCATTCTGCCATTCTGTATCTTTTAAGTGGAGCATTTAGGCTA
++
+!1=DDFDFHHHHHHJJIJJJJJJJJJJJIJIIJJJIJIJJJJIJJJIIJJJIJJJIIJJJJIIJJJJGIJJJIHJHHHHHHHFFFFFFDDDEEDEDDCDD
+@XXXXXXXXXX:7:1101:1743:1871#/1
+NCGGGATGGAGGCAGGGCAAGCGGATGCAGGCCCAGCCCTGCCCTTACAGGTAGCTGGAAGTGACGAAGGAGTGGGGCCCCCGGACTCTGCTCAGGTGGA
++
+!1=DDDFFHHHHHIJJJEGGGIHIGIIGGGIIIJEHHHGGCCHIIIFHHFHADDCDDC@CECECCDDB7?BB9?BA>9<@DDB>>9>CD>:>CA9A:A@A
+@XXXXXXXXXX:7:1101:1536:1878#/1
+NGGCCTTTTTGGACAGGTGGTGTGTGGTGGCCTTGGTATGTGCTTTCTCGTGTTACATCGCGCCATCATTGGTATATGGTTAGTGTGTTGGTTAGTAGGC
++
+!1=DDDFEHHHHCGGIJFHIECHEFHIGGGGIJI:95>@ABCAACDCC
+@XXXXXXXXXX:7:1101:2990:100153#/1
+GCCAGGAGTGACTGTGTTGTTCTTTGCTTTATATACATAAGCGCATCTCTTGCCCAAATAGAATTCTGTTTCATCTCGGGCGTAAACACCTTCAATTTTA
++
+@@@DDDFDBFHDFH<@D>CDDDDCCB
+@XXXXXXXXXX:7:1101:1624:1906#/1
+NCCAGGTTTAAGGCATTACATCGAGGGGCTGAACTTGAGACAGTCCCTGAAAATGTAAGAACAGGAGCTAGAACTTGCTTATGGGAAGGGCCTAGGGAGA
++
+!1=DDFFFHHHHHJJJJJIJJJJJJJJJJJJJJJJJIJJIJIIJJJJJJJGIJJIIJIECGIHHHHFFFFEECEECEDDDDDDCDCDDDDDDDDDDDDD@
+@XXXXXXXXXX:7:1101:1666:1926#/1
+NGCAAACTGGTCAGGACCTGGAGCTGCTTGCCTGGCCTTGGCACAAGAGGCCGACATATGCCCAGCCCCTAGGAGTGACAGATCCGTCCTCTGTGGGAAC
++
+!1BDFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJIJJJJJJIJJJJJJJJJJJJJJJHHHHHHFFFFDDDDDDCCDBDDDDDDDDDDDDDDDDDDDDBCD
+@XXXXXXXXXX:7:1101:2921:100163#/1
+CTCCGGATGCCAAAGGATCTGACAGTGTATCTAGCTTTGGAAAACACAGGGGTCTGCCCTGTGAGCTGCTCCAACACCTTGGCTGCTCGCGTCAGTCTGT
++
+CCBFFFFFHHHHHJJJIJIIIJJJJHIFFHGIIHEIJIIIIIJIIGIIIICHHHHIJIIEHHJIHHFHHFFFFFFBDDDDDCDDDDDDDDD@B@@CCDDD
+@XXXXXXXXXX:7:1101:1513:1929#/1
+NCACTATCAAGGTTAGTGTCTATATCTACTTGAGANAAAATACTGAAAATTCAGTGTATGAAGCCAAATCCTGATTTAACAAGTTATTGGTAGTATAAGT
++
+!1:ABDDDDFFF:ACGFGFHHFIFAHEEHDFI@F8!1:CFEFFIGEFGIII>GIFICGGII@FFFIEFEADGIIEIFFFFFFFEEDDDDBDAC>>;;BA5
+@XXXXXXXXXX:7:1101:2759:100170#/1
+CTGCTCATCACATTCCAGATGCCATCACAGGCAATGACCATGAATTCATGGTCGTCAGTGAGAGTCAGCACCTTGATGTCAGGAAGGGCTGAAATCATCT
++
+CCCFFFFFHHHHHJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJIJJJIJJJIJJJJJJHIIJJJIJJJJJJJHHHHHHHFFFFFEEDDDDDBCDDDDDDD
+@XXXXXXXXXX:7:1101:1708:1937#/1
+NGGTCGGTGTCCTTTTTTGGCGTCAAACTTATAGAGGGAAGCAGGGAATCTACCCAACCAAAGCCAATGAACAGTCAGTCAGTCCATCTAGTTAAGGTTC
++
+!1=BDDDDFDHHHIJJIJIJGIJIGGIJIGAGFHGHIGA=FCDFGHJJHEHFHHEFFFDABCDCDCCCDCDDDDDACDDCDDCAAACCDDDDDDACCACD
+@XXXXXXXXXX:7:1101:2981:100211#/1
+GGGGTCAGTGGGAAAGGTGTCAATGGGACTTCGGTCTCCATGCCGAAACACCAAAGTCACAAACTTCAACTCCTTGGCTAGTACACTTCGGTCTAGCCAG
++
+@@CFDDDFFFFHHEIGGHIIIIJJIIDHIGGIJFGBHIIIGGGGGGGIIJJHJGIG=DECEEEFFFFCDCCE@CC@?CDCBDDCDCCCCBB?B@>CACAB
+@XXXXXXXXXX:7:1101:1688:1946#/1
+NCCGCCTTCTTTCTCTACTTCGTGACCTTTTGTGGTCCCGAGACCTGCTGCATCTTCTGTCTGATGTTCGGCTTGAGTGTCTACTTCCTGAACGACTTCT
++
+!1:BDAADDBEEFEEFIIIIIEADEC?C>DDCE?CCC6=?###########################
+@XXXXXXXXXX:7:1101:2767:100225#/1
+CGCCTGGTGTCAATGCGCACATCTGGAGTTCCCATCTCCTTCATGGCAAATTTCCGAATCTCTTTGAGTGCCCGAGGTGCACGCTTCTTGAAGCCCACTC
++
+@@@FDFFFGHHHFJJIJIIIIJIJIJIGHBD@DFGGGJIFIJJJJIIIIIGHIIGIJFIJJIJIG@EECCHEEDCAD>ACCCDDDDDACCAC@CDDDDDD
+@XXXXXXXXXX:7:1101:1536:1959#/1
+NGATACTGTTGGGTCAGGACCAGGGCCTGCACCACCGAAATTCTGTCTTTTACAAACTGGACCAAGCGGTTGAGAATACAGGGGCCGAAGAGTAGGATTA
++
+!4:BB?DDHHDHAE?ECB@=GGI=<;CG@B;==AEC?DECA<;8;3CCCC8&-5>@@59?4::>>>CC
+@XXXXXXXXXX:7:1101:2797:100234#/1
+GTGCTGGTCTCTCTCCACGATCTCTTACGTGCTAGCAGGGTGAACAAGGACGCCTCGCTGTCATTGCACTCACGCCACAGGAGCCTGGCACATTTCCGCT
++
++:?BDD8DFFFB8ED;@GF8A3?FH?B<)11?@FG;@CBB?=88?5(95983?(8<>88=@?C##################
+@XXXXXXXXXX:7:1101:1593:1980#/1
+NGGCACCAGAAGCATGAGCATAGGCAGAGCCATTTCCACCATGCTGACGGCAGGCAAGAAGAAGACAAAAATGAACCCCTTTCATGCTTGTTTAGAAATG
++
+!1=DFFFFHHHHGJJJJJJJJIJJIJJJIGJIIJJJJGIIIJJJJJIIJJJJJJIIJHHHHHFFFFFEEDDDDDDDDDDDDDDDEDDDEDDDDDDDDDDD
+@XXXXXXXXXX:7:1101:2946:100242#/1
+TGGGGATGTTGTTAAAAAAAATACAGGCTCCCCCACAACTGGGGTGCCTGGGGGGAACTTGGTCTGCTTCAGCCCAAGAGGAATCAAAAGATCAAAAGCA
++
+@@@FFDDDHHHHHJIIGIJIGEGIIJJIIJJGJJEECDEA=FHI-=?B?CEDDDD5583:AC3::94:CAACCDBABD8?BA?CCDDDDD@CCACCDCBD
+@XXXXXXXXXX:7:1101:1987:1781#/1
+NTTAGCAGGTCCTCGTAGCGTTTCCGCAACTCTCGGAATCTGGAGTCTTCGGAGTGCAACTCTGAGGGTCCCGGGAAACTTGCGCGGCTCGCCTCGGCCA
++
+!1=DDFFFHHHHHJJJJJIJJJJIJJJJJJJJJJJJJJJGJJJJIIHIJJJIJHHGHFFFFFFCEEDDDDDDDDDBDDDDDDDDDDDDDDBBDDD9B?B<
+@XXXXXXXXXX:7:1101:3046:100006#/1
+CTGTACAGCATGGATGTGGACAGGGAAAACAGCAAGTGCACACAGTGGGACAGGCCACAGGACAGGCTGGGAGTGAATAAAGAGTTCACACTGCTTCCCT
++
+CCCFFFFFHHHHHJJJIJJJJJJJJJJJJJJJIJJJFHIJJIIJIGGHIJJJJJJIJJIIJJJHHHHFFFD=C;?CDCDDD@>?>@CACDACCDDCDDDD
+@XXXXXXXXXX:7:1101:1900:1788#/1
+NCCCGCTGCCCACGCCACTGTCCCGGCGCTGCCCTGGGCGCGGAATGCGCGTTAGGCAATCCCCGGTCTGCGCGTCCCACACGCAGATGTGGCCTGCCAG
++
+!1=DFFFFGHHGHJJJIJJIJJJJGIIJJJIIJJIJJJIHFFDDDDDDDDDBDDDDDDDDDDDDBD@BDDDB>BB:(98CA>98
+@XXXXXXXXXX:7:1101:1848:1879#/1
+NCTTCTTCTTCCTCATGTTTTTTGATCAACTGCTCCACTTCTTTTTGTTTGAGAACTCTGATTACTGTCTTTCCATTCTCTCTTGTTAGTGTTGCAATTT
diff -r 000000000000 -r 204a131e47db test-data/bduk_outputu2.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bduk_outputu2.fastqsanger Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,102 @@
+@XXXXXXXXXX:7:1101:1582:1835#/2
+GCAATGATGGGGCCGCTCCCGGGGCCACACCTGCTTCTGGATCCGCTGCTTCCAAGTTCCTTTGCCTCCCTCCTGGCATCACTGTCTGCGACTCAGGCCG
++
+@@@DDDADHFHGFEGIGIIIGEGFD@FHA@GIGIJJIJJEAHHEBEDACEAC@CDDDC@@CCCCDCD@AD9?BCCDDCCDDDDDDDDCC99BBDDCACBB
+@XXXXXXXXXX:7:1101:1610:1859#/2
+CAATAACACAGTCCAAAATATATGTATGTATGTATATATATATGCAGGCAACAAATAGCACAATGAATAAAATAGTACTTCATCTCAGTACTAACATTGA
++
+C@BFFFFFHHGHDIIJJJJJJIIJHIJJHIJIJJIGIJIJJJJJFIIJJIIIIIJJJIJJJJJJJJIJJJIJJJJEGIIJJIJHHHHHCDFFFFFFEEEE
+@XXXXXXXXXX:7:1101:1743:1871#/2
+GCTTCCAAGGGACAAAGTCCTGCCCTTGGGTGTGGAAGACACCGTGGACAAGCTCAAGATGCTGGAAGGCCGCAAGACCAGCATCCGCAAGTCAGTGCAG
++
+CCCFFFFFHHHHHJJJJJIIJHEHJIJJJIEDGIIIJIGGGIJIGEIIIIJIIIIIHGHHHHFFFFFFFDB>B@BDDCDDDDDDDCB?@BDCCDDDDDDD
+@XXXXXXXXXX:7:1101:1536:1878#/2
+TGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCC
++
+@@@DFFFFHGFHGIJJJJJJJAFDHICDFHGIJIIJEEIJGIJGHJIJJIFAAAFGBGGFFFHGHFDFDFBCBDDDDCDDCC
+@XXXXXXXXXX:7:1101:2990:100153#/2
+TGGAGGCCTGCTGGGAACGGGACTTCTAAAAGGAACTATGTCTGGAAGGCTGTGGTCCAAGGCCATTTTTGCTGGCTATAAGCGGGGTCTCCGGAACCAA
++
+@@@DDDDFHHFDHJJIGGHIJHIJJJJJGGGHJEGIIJJJIJJJIJJII?=FFHIHGGIJIHHHHFFC@BBCCEDDDDDECCDBDBD09CDDDDBBB??1
+@XXXXXXXXXX:7:1101:1624:1906#/2
+GGCTGGTCTGTCCCCTCTGCATCTGGGGCTCCTCCTGGCCCTTCTCCCGCTGCCTGTCCTGCCTCCTGGCCCTGCAGCAGCACCTTGCCCAGTGATCTTT
++
+CCCFFFFFHGHHHJJJJJJJIJJJIJJJIJIJJIJJIJIJJJJJJGGIJJFGIJGHHIFHHHHHFFDFDEEDDDD?CDDDDDDDDDCCDCDDCCCDCCCD
+@XXXXXXXXXX:7:1101:1666:1926#/2
+GGCTGTGGGAACTCTAGCTGCTGTCAGCCCCTCCTGTAGGAGCTGGCCCTGCCCAGGCTCCTGACTTCCCTCAGGAAGTCTTTCTGTCTTTCTCCATCAG
++
+CCCFFFFFHHFHHJJIJJJJJJIJJJJJJJJJJJJJJJJIIJJJJIJJJJIJJIJJIIJJJIHCHHGHFFFFBEE>@B>CDDDCDDDDDDDDDACDDCCD
+@XXXXXXXXXX:7:1101:2921:100163#/2
+GAAAAGGAGAACCCCATGCGGGAACTTCGCATCCGCAAACTCTGTCTCAACATCTGTGTTGGGGAGAGTGGAGACAGACTGACGCGAGCAGCCAAGGTGT
++
+CCCFFFFFHHGHHJJIJJJJJJIIJJJIIIGDHIGIJJJIJJ>HHGEHHGEHFFFFCDEEDCBDDDBB>C@DDCDDDDDDDDDDB@BD@BDDDBDDD:@@
+@XXXXXXXXXX:7:1101:1513:1929#/2
+AAAATGAGGGCCCGTAACAGAACCAGTGTGTGTATAACGAAAACCATGTATAAAATGGGCCTATCACCCTTGTCAGAGATATAAATTACCACATTTGCCT
++
+?@@;;D>DFH:;?EFD:FCAADACDDCDCCCCABCDCDDCACDCCAA?@CD4:<@AC
+@XXXXXXXXXX:7:1101:1688:1946#/2
+GAGAAAGGGAAGAAAGAGAAAGGAAAAGACGAAGGGAAGAGGAAGAAAGAGAAAAAGAAAGGGCTCGTGACAGAGAAAGAAGAAAGAGAAGTCGTTCACG
++
+BB@ADFFFHDDHAGGHGHGGHEHGIJJIIJIIJJJJ):?FF:FGGGIJIJIHCHHHFBCE;ACDDDDDCA@<@DBDDCDDCDDDDDDDDD@CCCDAA@>ACC>>A@@C1<
+@XXXXXXXXXX:7:1101:1536:1959#/2
+GAGACAAAAATTGTTTGAATCAGGACAAGGGAGGTTTGAGGGACTGTTTAACAGGTCCCCATGGTTCACGACCCTGATATCCACCATTATGGGCCCTCTG
++
+@8@1:?:=DD>D;5>BBAA:>CCD?8@BD9A
+@XXXXXXXXXX:7:1101:2797:100234#/2
+GGAAACGCTGGAGAAGACAGTGTTGCTAGTCTGTTCCTGTTCGTGAGAATGCTTTGAATGGAGGCTCACTGTGCTGCGGCGGCTGCGGCCGTAGCGGGCG
++
+B1=+:A+0A::A2+2A2A3A<+28E=<)/8@@@6C(6==737==>>@########################
+@XXXXXXXXXX:7:1101:1552:1976#/2
+TGTGAGCACACCATATATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAGT
++
+CCCFFFFFHHHHHIIGIGGIHJIGHHJIECGGGHJIJJJJJJJJJGHIJJGGHGIIEHIIJDIJFHFFFFF@CCCEECDDDDDCDDDB@BDDBBBDDCD>
+@XXXXXXXXXX:7:1101:1748:1978#/2
+CAAGGAGCTGTTCTGTCGTGGCTTTGGAATTCAGATGCTCTCACTGTGATAGAGATGGGGTCTTGGGGGGCTGGGAGCTGTTCTGTCGTGGCTTTGGAGT
++
+B@@FFFFFHHHHHJJIIJHIJIJJJJJIIJJIJJJJJIJJJJIJJJGHFGGHHIIIJIJJ@GIIJJIHFDDDDDDABBDCCDDEDDDB?BDDDDCCDCDA
+@XXXXXXXXXX:7:1101:2779:100239#/2
+GCTGTGGTTACCTGTCCCCTGCCCCTGGCCTCCAGCCAGCTGCCAGTGGCCCCTCAGCTGCCTGTGGTGAGGCAATACTTAGCTAGGTTCTTAGACGGCC
++
+?GDHFGGGAFEHE?F@8?>F;CFCEADEEG@EEHAEFBDEEED7A>CACDECD>C@A(5>>C@>A#####
+@XXXXXXXXXX:7:1101:1593:1980#/2
+GGCTGTTCTCGAACTCCTGACCTCAGGTGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCGCCTAGCCGTCACATTTC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJJJFHIIJJJJJIIJJJJJJJJJJJJJJJIHIJJJJJHIJJJJJJJHEEEFEEEEDECDDDDDDDDDBDDDCDDEE
+@XXXXXXXXXX:7:1101:2946:100242#/2
+AATCCCTTCACCCCAGTTGCCAAACAGACCCCCCACCCCCTGGATTTTCCTTCTCCCTCCATCCCTTGACGGTTCTGGCCTTCCCAAACTGCTTTTGATC
++
+C@CFFFFFHHHFFHBHHHEIJJIIIJIIJCGGIIGIHHIJIG@D;DCE>>?AEEFF@@DB(.;>?;CC@>=',5ADCDCCDA>B?CDD>ACCC0>C
+@XXXXXXXXXX:7:1101:1987:1781#/2
+GCCGCAACCTGCACAGCCATGCCCGGGCAAGAACTCAGGACGCTGAATGGCTCTCAGATGCTCCTGGTGTTGCTGGTGCTCTCGTGGCTGCCGCATGGGG
++
+CCCFFFFFHHHHHJJJJJJIJJJJJJJJJJJJJJJJJJIIJIJJJJJHHHHHFFFFFFEEEEEEDDDCCBDDDDDDDDDDDDDDDDDDDDDD<@BBDBBD
+@XXXXXXXXXX:7:1101:3046:100006#/2
+GACGAGATGGAGTTCACCGAGGCCGAGAGCAACATGAATGACCTGGTGTCCGAGTACCAGCAGTACCAGGATGCCACAGCCGAGGAGGAGGGCGAGTTCG
++
+CCCFFFFFHHHHFIJJJJJIIJIJJIHIIIJJJIIJJJGIJJJIJJIJHGEHFFFEEEEEDDDDDDDDDDDCDDDDDDDDDDDDDDDDBDDBDD
+@XXXXXXXXXX:7:1101:1848:1879#/2
+GGAGAAATGACCTTGAAGTCAGCACTTGCTTTAGCTATCAAAGTACTAAATAAGACCATGGATGTTAGTAAACTCTCTGCTGAAAAAGTGGAAATTGCAA
diff -r 000000000000 -r 204a131e47db test-data/cv_input.bam
Binary file test-data/cv_input.bam has changed
diff -r 000000000000 -r 204a131e47db test-data/cv_output.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_output.gff Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,18 @@
+##gff-version
+#BBMapVersion
+#ploidy 2
+#rarity 1.00000
+#minAlleleFraction 0.1000
+#reads 2207
+#pairedReads 0
+#properlyPairedReads 0
+#readLengthAvg
+#properPairRate 0.0000
+#totalQualityAvg
+#mapqAvg
+#reference
+#seqid source type start end score strand phase attributes
+NC_002945.4 . sequence_variant_obs 976327 976327
+NC_002945.4 . sequence_variant_obs 1501932 1501932
+NC_002945.4 . sequence_variant_obs 3380579 3380579
+NC_002945.4 . sequence_variant_obs 3646293 3646293
diff -r 000000000000 -r 204a131e47db test-data/cv_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_output.txt Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,18 @@
+#fileformat
+#BBMapVersion
+#ploidy 2
+#rarity 1.00000
+#minAlleleFraction 0.1000
+#reads 2207
+#pairedReads 0
+#properlyPairedReads 0
+#readLengthAvg
+#properPairRate
+#totalQualityAvg
+#mapqAvg
+#reference
+#scaf start stop type call r1p r1m r2p r2m paired lengthSum mapq mapqMax baseq baseqMax edist edistMax id idMax cov minusCov nearbyVarCount flagged contigEndDist phredScore readCount alleleFraction revisedAF strandRatio baseqAvg mapqAvg edistAvg identityAvg edistScore identityScore qualityScore pairedScore biasScore coverageScore homopolymerScore score
+0 976326 976327 SUB T
+0 1501931 1501932 SUB C
+0 3380578 3380579 SUB G
+0 3646292 3646293 SUB A
diff -r 000000000000 -r 204a131e47db test-data/cv_output.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_output.vcf Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,60 @@
+##fileformat=VCFv4.2
+##BBMapVersion=
+##ploidy=2
+##rarity=1.00000
+##minallelefraction=0.10000
+##reads=2207
+##pairedReads=0
+##properlyPairedReads=0
+##readLengthAvg=
+##properPairRate=0.00000
+##totalQualityAvg=
+##mapqAvg=43.348
+##reference=
+##contig=
+##FILTER=
+##FILTER=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
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+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
+NC_002945.4 976327 . N T 22.21 PASS SN=0;STA=976326;STO=976327;TYP=SUB;R1P=2;R1M=0;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=77;MQM=40;BQS=48;BQM=24;EDS=111;EDM=65;IDS=1930;IDM=972;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1.0000:1.0000:0:0:0.9980:22.21:PASS
+NC_002945.4 1501932 . N C 27.20 PASS SN=0;STA=1501931;STO=1501932;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=88;MQM=44;BQS=64;BQM=39;EDS=74;EDM=38;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1.0000:1.0000:0:0:0.9980:27.20:PASS
+NC_002945.4 3380579 . N G 27.85 PASS SN=0;STA=3380578;STO=3380579;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=289;MQS=87;MQM=44;BQS=75;BQM=38;EDS=105;EDM=63;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1.0000:1.0000:0:0:0.9980:27.85:PASS
+NC_002945.4 3646293 . N A 23.34 PASS SN=0;STA=3646292;STO=3646293;TYP=SUB;R1P=1;R1M=1;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=291;MQS=86;MQM=44;BQS=76;BQM=38;EDS=44;EDM=31;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=1.0000 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1.0000:1.0000:0:0:1.0000:23.34:PASS
diff -r 000000000000 -r 204a131e47db test-data/cv_qualityhist_output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_qualityhist_output.tabular Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,46 @@
+#BaseQualityHist
+#Vars
+#Mean
+#Median
+#Mode
+#Quality AvgCount MaxCount
+0 0 0
+1 0 0
+2 0 0
+3 0 0
+4 0 0
+5 0 0
+6 0 0
+7 0 0
+8 0 0
+9 0 0
+10 0 0
+11 0 0
+12 0 0
+13 0 0
+14 0 0
+15 0 0
+16 0 0
+17 0 0
+18 0 0
+19 0 0
+20 0 0
+21 0 0
+22 0 0
+23 0 0
+24 1 1
+25 0 0
+26 0 0
+27 0 0
+28 0 0
+29 0 0
+30 0 0
+31 0 0
+32 1 0
+33 0 0
+34 0 0
+35 0 0
+36 0 0
+37 1 0
+38 1 2
+39 0 1
diff -r 000000000000 -r 204a131e47db test-data/cv_scorehist_output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_scorehist_output.tabular Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,34 @@
+#ScoreHist
+#Vars
+#Mean
+#Median
+#Mode
+#Quality Count
+0 0
+1 0
+2 0
+3 0
+4 0
+5 0
+6 0
+7 0
+8 0
+9 0
+10 0
+11 0
+12 0
+13 0
+14 0
+15 0
+16 0
+17 0
+18 0
+19 0
+20 0
+21 0
+22 1
+23 1
+24 0
+25 0
+26 0
+27 2
diff -r 000000000000 -r 204a131e47db test-data/cv_zygosityhist_output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_zygosityhist_output.tabular Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,8 @@
+#ZygoHist
+#Vars
+#Mean
+#HomozygousFraction
+#Zygosity Count
+0 0
+1 0
+2 4
diff -r 000000000000 -r 204a131e47db test-data/fasta_indexes.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,1 @@
+89 89 Mycobacterium_AF2122 ${__HERE__}/NC_002945v4.fasta
diff -r 000000000000 -r 204a131e47db test-data/output1.bam
Binary file test-data/output1.bam has changed
diff -r 000000000000 -r 204a131e47db test-data/output2.bam
Binary file test-data/output2.bam has changed
diff -r 000000000000 -r 204a131e47db test-data/output3.bam
Binary file test-data/output3.bam has changed
diff -r 000000000000 -r 204a131e47db tool-data/fasta_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files. You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored. The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file. For example:
+#
+#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 000000000000 -r 204a131e47db tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,8 @@
+
+
+
+
+ value, dbkey, name, path
+
+
+
diff -r 000000000000 -r 204a131e47db tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Thu Nov 11 16:38:32 2021 +0000
@@ -0,0 +1,6 @@
+
+
+ value, dbkey, name, path
+
+
+