| Next changeset 1:e5b18909f73d (2021-04-08) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" |
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added:
macros.xml meryl.xml test-data/child.fasta test-data/maternal.fasta test-data/output_02.read-db.meryldb test-data/output_03.read-db.meryldb test-data/output_23.mat.hist test-data/output_23.pat.hist test-data/output_23.read-db.hist test-data/output_24.read-db.hist test-data/paternal.fasta test-data/read-db.meryldb |
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| diff -r 000000000000 -r 068920e730f4 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Apr 05 15:04:36 2021 +0000 |
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| @@ -0,0 +1,33 @@ +<macros> + <token name="@TOOL_VERSION@">1.2</token> + <token name="@GALAXY_TOOL_VERSION@">galaxy0</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0196</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0525</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.1">merqury</requirement> + <requirement type="package" version="1.2">meryl</requirement> + <requirement type="package" version="1.34">tar</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{githubMeryl, + author = {Arang Rhie, Brian P. Walez, Sergey Koren, Adam M. Phillippy}, + year = {2020}, + title = {Meryl}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/marbl/meryl}, + } + </citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 068920e730f4 meryl.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/meryl.xml Mon Apr 05 15:04:36 2021 +0000 |
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| b"@@ -0,0 +1,629 @@\n+<tool id='meryl' name='Meryl' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'>\n+ <description>a genomic k-mer counter and sequence utility</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro='edam_ontology' />\n+ <expand macro='requirements' />\n+ <version_command>meryl --version</version_command>\n+ <command detect_errors='exit_code'><![CDATA[\n+ #if $operation_type.command_type == 'count-kmers'\n+ meryl\n+ #if $operation_type.options_kmer_size.kmer_size == 'estimate'\n+ #from math import log\n+ $operation_type.options_kmer_size.input_kmer_size = int(log(int($operation_type.options_kmer_size.genome_size)*(1-float($operation_type.options_kmer_size.collision_rate))/float($operation_type.options_kmer_size.collision_rate))/log(4))\n+ #end if\n+ $operation_type.count_operations\n+ k=$operation_type.options_kmer_size.input_kmer_size\n+ $operation_type.input_reads\n+ output read-db.meryl &&\n+ echo 'K-mer size: ${$operation_type.options_kmer_size.input_kmer_size}' &&\n+ tar -zcf read-db.meryldb read-db.meryl\n+ #elif $operation_type.command_type == 'filter-kmers'\n+ mkdir -p ./temp_db/ &&\n+ tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&\n+ mv ./temp_db/* tmp.meryl &&\n+ meryl\n+ $operation_type.filter_operations\n+ $operation_type.N\n+ tmp.meryl\n+ output read-db.meryl &&\n+ tar -zcf read-db.meryldb read-db.meryl\n+ #elif $operation_type.command_type == 'arithmetic-kmers'\n+ mkdir -p ./temp_db/ &&\n+ tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&\n+ mv ./temp_db/* tmp.meryl &&\n+ meryl\n+ $operation_type.arithmetic_operations\n+ $operation_type.X\n+ tmp.meryl\n+ output read-db.meryl &&\n+ tar -zcf read-db.meryldb read-db.meryl\n+ #elif $operation_type.command_type == 'groups-kmers'\n+ mkdir -p ./temp_db/ &&\n+ tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&\n+ mv ./temp_db/* tmp_01.meryl &&\n+ tar -zxf $operation_type.input_meryldb_03 -C ./temp_db/ &&\n+ mv ./temp_db/* tmp_02.meryl &&\n+ meryl\n+ $operation_type.groups_operations\n+ tmp_01.meryl\n+ tmp_02.meryl\n+ output read-db.meryl &&\n+ tar -zcf read-db.meryldb read-db.meryl\n+ #elif $operation_type.command_type == 'histogram-kmers'\n+ mkdir -p ./temp_db/ &&\n+ tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&\n+ mv ./temp_db/* tmp.meryl &&\n+ meryl histogram tmp.meryl > read-db.hist\n+ #elif $operation_type.command_type == 'trio-mode'\n+ export MERQURY=\\$(dirname \\$(command -v merqury.sh))/../share/merqury/ &&\n+ #for $i, $read in enumerate($paternal_reads):\n+ mkdir 'paternal{$i}.meryl' &&\n+ meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'paternal{$i}.meryl' &&\n+ #end for\n+ meryl union-sum paternal*.meryl output pat.meryl &&\n+ #for $i, $read in enumerate($maternal_reads):\n+ mkdir 'maternal{$i}.meryl' &&\n+ meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'maternal{$i}.meryl' &&\n+ #end for\n+ meryl union-sum maternal*.meryl output mat.meryl &&\n+ #for $i, $read in enumerate($child_reads):\n+ mkdir 'child{$i}.meryl' &&\n+ meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'child{$i}.meryl' &&\n+ #end for\n+ meryl union-sum child*.meryl output child.meryl &&\n+ ## mat specific"..b'\n+ </output>\n+ <output name="read_db_hist" file="output_23.read-db.hist" />\n+ <output name="pat_db" ftype="meryldb">\n+ <assert_contents>\n+ <has_size value="1779" delta="300" />\n+ </assert_contents>\n+ </output>\n+ <output name="pat_db_hist" file="output_23.pat.hist" />\n+ <output name="mat_db" ftype="meryldb">\n+ <assert_contents>\n+ <has_size value="1569" delta="300" />\n+ </assert_contents>\n+ </output>\n+ <output name="mat_db_hist" file="output_23.mat.hist" />\n+ </test>\n+ <test expect_num_outputs="1">\n+ <conditional name="operation_type">\n+ <param name="command_type" value="histogram-kmers" />\n+ <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />\n+ </conditional>\n+ <output name="read_db_hist" file="output_24.read-db.hist" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+**Purpose**\n+\n+Meryl is the k-mer counter. It is built into the Celera assembler and is also available as a stand-alone application.\n+Meryl uses a sorting-based approach that sorts the k-mers in lexicographical order.\n+\n+In addition of generating count-databases, meryl can perform simple operations on it. \n+\n+-----\n+ \n+.. class:: infomark\n+ \n+**Basic functions**\n+\n+The functions that meryl includes are described below: \n+\n+ ::\n+\n+ COUNT OPERATIONS\n+ - Count: count the occurrences of canonical k-mers\n+ - Count-forward: count the occurreces of forward k-mers\n+ - Count-reverse: count the occurreces of reverse k-mers\n+ FILTERING OPERATIONS\n+ - Less-than: return k-mers that occur fewer than N times in the input\n+ - Greater-than: return k-mers that occur more than N times in the input\n+ - Equal-to: return k-mers that occur exactly N times in the input\n+ - Not-equal-to: return k-mers that do not occur exactly N times in the input\n+ ARITHMETIC OPERATIONS\n+ - Increase: add x to the count of each k-mer\n+ - Decrease: subsctract x from the count of each k-mer\n+ - Multiply: multiply the count of each k-mer by x\n+ - Divide: divide the count of each k-mer by x\n+ - Divide-round: divide the count of each k-mer by x and round th results\n+ - Modulo: set the count of each k-mer to the remainder of the count divided by x\n+ OPERATIONS ON SETS\n+ - Union-min: return k-mers that occur in any input, set the count to the minimum count\n+ - Union-max: return k-mers that occur in any input, set the count to the maximum count\n+ - Union-sum: return k-mers that occur in any input, set the count to the sum of the counts\n+ - Intersect: return k-mers that occur in all inputs, set the count to the count in the first input\n+ - Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count\n+ - Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count\n+ - Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts\n+ - Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs\n+ - Difference: return k-mers that occur in the first input, but none of the other inputs\n+ - Symmetric-difference: return k-mers that occur in exactly one input\n+\n+-----\n+ \n+.. class:: infomark\n+ \n+**Additional function: build hap-mers dbs for trios**\n+\n+In addition of the basic operations, this wrapper allows to build the hap-mers databases for trios, in accordance\n+with `merqury\'s recommended guidelines. <https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs#3-build-hap-mer-dbs-for-trios>`_\n+\n+ ]]> </help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 068920e730f4 test-data/child.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/child.fasta Mon Apr 05 15:04:36 2021 +0000 |
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| b'@@ -0,0 +1,898 @@\n+>K12_1\n+GGCGGCGAAAAGCTCATCTTTATCACTGCGAGCTACAGGGGGGGACCTTTGCCTGGCTTGGCGCTTATCAGTTAGCGAAGAGCGTGACAAATATACGGCGTGGAGGCCGCGGAATATGATGAAGGTTCCAACCAGCTTAATGAGGAGGAAACCCGCATCATGTAGTATTTCAGCCGTGAAACGTCTGCCAGGGCAGCAGAGCATAGATTTGTATATAGGAATCAGGCCTGTAGGCTATAATACTCGTTTCACTGCTGGTACTTACGTATTGCGCGTTGCAGCGGGCCGTTGTATAATTCTTTTTATCAGAGACTATCACGATGTGGTTTGTGTGAAAAGGGAAGATGGTAAGAATTTATTATTGCTGAGATATTCCCTTTATAATCCACTAGCATACAATATTGAACCCTAAATGGAGTTAGTATATGCGTTAGAATCTTTGGAATGATGCGCAGATACTGGTAAATGGCTACATAGCAGTACTGGGTGGTGAGGTTTTGTGGTGTTCTTTCACGTATAATGAGGACCAAGTAAAGTTATGATAGTAACTGCAGAACATTTTGTTGTCGTTATGTATGCTTTGGAAAGAAACGCCAGAATAAGAAGACTTCTATAGTAGAATATTTGATAATAGGAAATATTCTGGTATTAGTCTGTAAAGAACAATGAAAATATTTGCATCTAGGGCAAAAGCTGATCTAATTTAAGAAAGGAGTCATATCCTCTTGATAATGAATTTTAAATGTCCCACATGTGTTAGGGGATAGAGTGTGCTATTTGCTTATCATAACTCCACAGGATGAGATGTATGTCCATTTGGCGAATGATGTTGATGAATATTTTTTGCAAGTTAGCTGATAAATACTTTGTATAGATTATAGTTAGAAGATATGTATCCTAAATGCCATTTTTATCTCACGCACACCTATGATGGTATGCGATTTCGATTCATATTGAGGCGGCTAATAATCAGTATGGATGACATATATATTATTTATCAGAAATTAGTTAATGTTCGCTCAGGGATTGAGTTTAGTGAATTAGTCATTATCCAAGATTCCTATTGTTGATCTAATCGTATTATAATTATTAGTTTGTTTTTAATATAATGATAGTGGAAGCTATAAGTTTATGTAGGGATTTTGCAATTTTATGAAAAATATTATGTCTAATTTATTTTTCGATGCTTGTCACCATTTTTTTATTGAATTTTTTTTTTTTAAATAACTGATTTTGCCTGTAAATGAGACAAGCTGTTTACGGTGTTCTGATGGAAACAGTTATTTTGGATGTGAGTTTTGTCAAGTAAATACATTAGATGTATCATCTCTCACTATGCATTACTGTTCTCTGTTTAAAAATAATACGGTAAAACTGAAACAATGGCGATACAATTAGCTGAAATATATGATTAGGTAGTCGGCTAATGTGCGAACGGATTGGGCAGAAGAAGAAAACACCATATTTAAATTACGGAACTATGCTCAGATAGTTGGGTTTCTGAGGGGAGGCAAAGTTACGCGTATGAAGTTGCCGGGTGGGTATTTATATATAGAAATTAACTAAGAAAAATGGATGTGTTTTGAATTTCCTACATATGTAACATAATGCTAGGCGCTGAGGATGCGGATGGAAACATTGGCGTGGAGCGGGAGTATGATGGAGTGGGGCAACCAGCCTGAATGAAGAGAAACCCGCATGCACCCTGCACCAGCCCGTAGCCGGCTGCCGGGGGCAGGCAGTAATGATAATGGAGTCGGGCCCTGTACTCACAAACCGGAACGCCGGTACTACGATCCGTTGCAGAGGGGGCGGTATATCACCAGGGACCCGATAGGGCTGGAGGGGGGGAATGGAGTCTGTATGGCGTATCCGCTGAATCCCGGTGAATGGTATTGAGTCCATTAGGGTTAAGTCTCCGCAGATGTAGGCGCTAATAGAAGAAAAGATCAACGTAAACCATCAAAAGAGGGCATCGGGATAGATTAGTCTGATACTTATGGAACGATATGAAGAGAATTAAATTTAGGTGTCTCTGATCAATTTTTGCTCCATTGTATGCATTTGTCGAGTGTCTAAATTAAATGACGCCTGGTGTTCAGCCGATCGGCGAAAGGGCTGGTTTGAAGAACAGAGAATTAGAGATTTAGCGGTTAACTCTGTTCGGATGTACGCGCAGAAAAGTACACGCTACTCCCATTTCTGAATGATTGAAGATAAATAAGACACAACAAGAAAAGACTTGGCTGTAAATGACCGATGGCGTTTCATGTCCATCAATCCAAGCAGATCTGCTCAGATCAGACTGTAGTCGATGTATATTAATCGCAGAGCCACTAAAAAACGATACAATGGGCTTTACAAAGATGCTGGCTAGTCTCAAAGTAAACTCTATCAAAGATGATAATATTGTATTTTGCTATTAATACATCACTGTGGTTGTTTTTATGCGTAAATTTAACTTATCTTTATTTATACAAAGATGAATCTCTTGTAAAGTAAAGCATTACATATAACTATATGGCAATACCAGAAAAATGAGGAGTTTTTTACATGGGCTCCCGTATTTTTTCCCGCAGCGTGCGGTGGATATATCAATATACGCACAAATGTAGAAGATGATTATTTTTCTATTTTTCCTAAGCAAAATGATCGGATGGGGGTAGGTTTAAAGAAAAGCATTGACAGTGAGGGCGCAGGGAACAAGTGGCGAAAATCGTATCAAAGAATGATCCAGATAGGCAAAAAAAGTGTGGTGTAAATAGTGGTAAGATACCAGGGCAAGGGATGGTGTAAACTTTTTTTTGTTGGTGAAATTAATGTTACGCATTATTTTATCCAACAAATATTGGAGCCTGGATTGCCTGATGCGTTGTGGCAGAGTAATTGCTTGAATTAAGAGTCTATCCCATATCGAAGTCGTCAACTTCGTAGTGAGGAAACAAGGTCAAAATTCCTGACTGAGAAAAGAGCATGTGGCATGATCTGTGTAAAGCCCATATAAGCTCAGACAGATGAATATGCTACTCGTATTGCAGTTGTTTATTGAGGGTGAGTTTCCGACCCTGGAAAGGCAACAAATAACATATGAACAGTCAGAGAGTTTAACATAGAATTGCAGCTGGTCTTTTAGCGATGTCTGACCATTGTGTCAATCACATATTCAGCCATGGCATTAAGTTAAAATGTTAGCGTGTTTAATGTGAGTCCCTATCTGAAATAAATAATCGCTTACCGGATTAAAATAAATTTGCTTGCCCGGGAAGAAAGAGGAAATAAATCGCATTAGCGGGAAAACCAGCGGGCAGGCGCCAGGGGACATGCCCCAGTACGGCGGCCCGATGTCCAGGGTTCAGGGCGGGGGCTAGCTGATAGCTCGCGCGACTGCAATCGAGGACTCATACAACTCTTTTACGTGGAAGCGTCACCTGAATAAAATTTGTTCAGTATCGTCTTTGAGAGTTCTCAAGGTTATTGGATGTACAGACAGAAGCGGAGCACCACTGTCGGGAGATATAAAACCCCCTGTTTACGGCAGCTCGTTGCTGGCCACGGGCTGACCATTGTGTCGGGAAAGCGAGCGGGCGTATCAAACCAACAGCCTGTTCAGTTGCCTCATGCCGGTACGTGTTCTAAGTTTAGGAGCGCGCGGCGACCCTACGATTAATGCTGGCGCATGCCACAGCCCGCCTTCAGCGACCAGGTTCGCGGTAACGATAAGACGTATCACGCGAAACGCCCATGATTTTAGCAGGCTTTGATACGTGTGCTTGAGTTTTCTTGTCAGGCCAGATTGAGCAAACCGGGCTTTTGTTCATGATGGACGGGATTGGCAGTATGAGAGCATGAGAGTCTACCTCTTGTTTTGGATACAAGGATTCGACCCACTCCATATCAAAACGCGGTACTCTCAACCTTTCAAGGCATGTGTCCAGATCAAGCCCTCGCGAGAGCCGCGCTAATACAAAGACG'..b'GAAAACCGCAGCGGGGCCGACATAAACTCTACAAGAAGTACAACATAGGTTAACTGCACAGACGCGAACCATGTCTTCCATCTATGTCACCCAGCAAAAAAACCCCCGCTGCGGACGATACCACTCGATGTCCACAACCAGATCGCAAAGCTATATCACTCATGCTATCATTTTTGCAGGTAGCGGCTATACTTGCAAGAGTTACAAGGGCACCGCACAAGCATGCGTCACCCGGATAATGCCAAAAGCGGCGGTTGTGCGTGATTATGGGTTCCACCTGAAAGAAAAGGGAGGCCCTGGAGGCGGCATCAGTGAAAAATTC\n+>K12_895\n+AACGCGAGCGCGCCCGCCTCGAAACGGAAAAGTAACGCTATCGAAGGCTGGGAACTGGCCCGGTAGCGCACATCGCGACCGCCTAGATCCAAGGTAAGAAAATTATCAGTTGTGCCAATTCGGCGTGCGGTCTTGTATTGATGGACGGTGTGCTGGAAAACGTTCCGAGCGCCGCGCATGCAGCGTTGTCGGTATGTACCGTAATGAAGAAAGCTCGGAGCAGGTACCGTACTTCCAGATACCTGGTTTCTAGAGCATCGATGAGCTTATGCGCTTTGATCGTTGAACCCAATGCTGGCAACCGGTGGTTCCGTTATCGCGACCATCGACCTGCCGAAAAAAAAGCGGGCTGCCAGCAGGCATCAAAGTTCTGGTGCTGGTAGCTGCGCCAGAAGGTATCGCTGCGTGGAAAAAGCGCACCCGGACGTCGAACTGTAATACCGCATCGATTGATCAGGGGACTGAACGAGCACGGATACCATTATTCCGGGCCTCGGCGTGCCGGTGACAGAAATCTTTGCTACGAATAAAGAATAAAAATAATTAAATGCCGACTTTAAGAGTCGGCTTTTTTCTGAAGTACTACAGCCGCCTATAACACATAATACAGAGGATAATACTATGACGCGCCGTGCTATCGGGGTTGAGTGAAAGACCGCCACTTTACAGACAATCCCCGCTTAAGTTTGCAACATTTGTTCGCCATGTTTGGTGCACCGTCCTGGTCCCGTTCTTATTTCATATTAACCCCGGCGACTGTACTGTTATTTAACCGGTATTGGAACGCTGCTGTATCTCTTCATCTGTAAAACGCGAAAATTCCGAGCTTATCTTGGTTCCACGCTTTGCTTTATTCACACGGAATTGTGTACTGTTGCCGTTAGGGTAATGAAGTCGCGCTGGGCGCGCTTTATTATGTCGCGGGCGTTGCTGTTCTGCCTGGTTCCTTTATCGTGAACGAAAGCGGGGCGGTGGCTGGACGTCTGTTTCCACCTGCGGCAGTGGGCGCAATCGTTGTCCGTCATCGGTCTGGAGGCTGGCGGCGTAGCTGCCGGTATGGCGGGTTTACTCCGGCTGAAGGCAAACGCCAGACTCCAAAACCATCATCATCTCTAATTACCACCCTGGCGGTCACGGTTTGTAGGTTCCGTGCTGTTCCGTGGTTTCTGGCAATTTCCGCCGATTTATTGGCGCTGGTGGGGGTACGCGCGTCTCTTTCGCAATGGGAATTGTCCGATCACCACGCCGATTAATTAATGCTCACTGGTTTGCGCTGCCCACCCTCTATACGCCCGGCTTCGAGTGGCCTTTGCCATTCTGACTATTCTGCCAGCGGCGTTAGTGGTTATTGCCGAACACGTAGGGGCACTTGGTAGTAACGGCTAATATCGTCCCAAAAAAGATCTGCTGCCGCGATTCCAGGTCTGCACACGTTTCGATGTTTGCTAATGGCTTGTTTCGACGTGATTTCCGCTTCTTTGGCTCTACGCCAATACTAGTTACGAGAAAACATTGGCGGTGATGCGATCACCGTGTTTCAGTACCTGGGCTTATCGGCGGGGGCGCGATTTTCGCTATCCGGCTTTCCTGCACCTTGGCGTCGGGTAAACTGGATGCCGCTATCAATGATCCCATTGCGGTGATGGGCGGCGTTTCGCTGCTGCTTTATGGTGTCATCGGTGCTTCCGGTATTCGTGTTTTCGATCGAATCGAAAGTGGATACAAAAAAGCAGCAGAACCTGATCCTGATTCGTGATTTTGAATCATCGGCGTCATGGCGCGAAGGTAAACATCGGCGCGGCGGAGTTAAAAGGTATGGCGCTTGGCGACCATCGTCGGTATCCGGCTTAAGTTTGATCTTCAAACTGATTCAGTGTGCTGCGCCCCTGAAGAAGTGGTCTGAGCCAGAAGACGCGGATAATAACAGAAATAATGTAGCCGGGCAGTGGGTTGCTGCCCGGTTCAACATATGGGATTCTGGGGTAAACTCTCCGCGATTTTGTGAAATCCTGGTTGAGGTATTCTGAACAACACCCGCACACTCTCTTTGCACTTTAATCTTCCTGACGACGAAACCTTTGCAAGTTTCTGGCCGTGGGATAACTCCTTCTTTACTGGACGCGCTGCAAACGTGCTGCCGTCAGGACATAGCGGTTACATCTATCCTCTGGTCACGCGAAGGCGCGGGGCGCAGCCATCTGCTGCACGCGGCTTGCCGGATTGTCGCAGCGTGGCGATGCGGTGGCTATGTCCCCGCTGGAATAACGCACCTGGTTTGTTCCGGAAGTGCTCGACGGTATGGAGCATTTGGTCGCTGGTCTGTAATGCGACAACATTGAGTTATTGAGGCGATGAGCTTGTGGGAGATGGCGATTTCGATCTTACAATGAACTTCTGGAATCGGGCAAACACGGTTGTTGATCACCGGCGATCGTCCACCGCGGCAGTTGAATCTTGGATTACGGCATCTCGCGTCGGGACTCGACTGGGGGCAGACCTCTACAAATTGCAGCCACTTTCTGATGAAGATAAGTTGCAGCGCTACAGTTACGCGCGCGTTTGCGTGGTTTTGACTGCCGGAAGATGTGGGGCGTTTCTGCTGAAGCGGCTCGACAGAGAAATGCG\n+>K12_897\n+ATGTCTAACCACAATCTCTAAACGGTAAATATTACCAACAGGCACTCAAAAACAAAAGCAGTGAACTGGTACGCGAACAGCGGTTTTAACGAGTATTCTCGAGAAATACAGGAAATTCATGCGATCACATGAAACCAACGTCATTCGCAAAGAGGAGACTATGCAGAATGTTGCCGGCTGCGCCGGGCTTGCTTCACAGCCCCAACACAAAAGCGACTGAGGCAATTACGCTACCAGTACTTTGAAGAAATGAAATGCTTTAGCAACTAACTATTGAAAAGCATTCTGTATCTGTAAAAAAACGGCCCGCAGTTTCTATGGGTTGATCCGATACAAAACAAGACACATTCATGTAAAGAGAACTGGTACGATGAAGAGCCTAACAGGTTGCATAGGAAAGACATATCGCACTGACTGATTGACGAAATATCGCTGAGTGCCATTCCTCAAAGAACCGAAGAAAGAAGCGGTAACAAAGTAATCTGGATACCGAAAATTAAATACAAATAAAAAATCGTAGACTATTCCATGTTGTCATGATTAAAGATTATTTACAGTATAATAAAAAAAAATAAACCAGTATAAGAAGAATCAACAGCGAGGGCTATGATATGCGAATAATGAAGATCAGCCATAAAAGCGAAAACTTCTCCATTAGACACAGCGAGGAGCTATATTGAGTAGACCCTGAACTGGCGAACTTTCACCGCTCGTAATCAGATATTGAGCAAGTTTTCCTAGAAAAAAATAAGAAAAAATGGCTCAAACAGTATCGGAATACGAAAACAAATTATGCGCAGCGAATAATTTATCATATCGGTGTTATGGCCAGACAAATAGAAGATAAGACACGCATAGTGAAATTCTCAGCAGGAAACGTGGGAATAAGCTCGCGATGACTAATGGTTTTGTCAGGCGAATAATAAATATGCAGTGATTTTTTTTTGCCGGTGTCGACCCCGAAGCCTTTTTATTTTTACTAATACGAAATTTTGAGTA\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 068920e730f4 test-data/maternal.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maternal.fasta Mon Apr 05 15:04:36 2021 +0000 |
| b |
| b'@@ -0,0 +1,15649 @@\n+>110000000001_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CGCCAGTNATGCATAGGTCTGGCGAACGCGGGATCCCTCAATTCCCCGTAGCTGATCCACTGAACGGCGAGCTGGCGGTG\n+GCTCACGAAAACGTAATTCATACATTTTGCGCACCACCTTCAGGCGTAGATCTTCCGTTAAAGCCAG\n+>120000000001_clr=0,146_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CTTCCGGACAACCCGGAGGGGCGCGGGCAGATAAATTACTCTACCAGGCAAAGCTGGCTTTAACGGAAGATCTACGCCTG\n+AAGGTGGTGCGCAAAATGTATGAATTACGTTTTCGTGAGCCACCGCCAGCTCGCCGTTCAGTGGAT\n+>110000000005_clr=0,146_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+ATCCATCNCCACATTCAACCCGGCATCCCGTGCCAGTACTGCCGCTTGCTCATTAATCACCCCCAGTTGCATCCAGAGGG\n+TTTTCGCGCCAATGGCGATAGCTTCCTGCGCTACGCCCCACGCCGCTTCTGAATTACGGAAAACAT\n+>120000000005_clr=0,146_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CCGCGCAGCAGAGAGCTGGGAACCTTCTTGCCGTCGAGTACCAGAAGATCGACATCGGTTGAAAGCCGCAGCGTGGTGGC\n+AAAAACGGATACCGGCAAACATAATGCAATCAAGGGGGTCACGATGCCGGTTTTCATAGGTAGCTC\n+>110000000007_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GTCTACGNTTACTCAAAATTCCTGTTTGATGAATATGTTCGCCAAATCCTGCCGGAAGCGAACTCGCAGATTGTTGGCTT\n+CCGCTATTTCAACGTTTATGGACCGCGTGAAGGCCATAAAGGCAGCATGGCGAGCGTCGCTTTCCAT\n+>120000000007_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+ACATAGACGAAGTCGCGTTTAAAGTTCTCGCTACCTTCGAACAGCTTCGGTGATTCACCGTTATTAAGCTGGGTGTTGAG\n+ATGGAAAGCGACGCTCGCCATGCTGCCTTTATGGCCTTCACGCGGTCCATAAACGTTGAAATAGCGG\n+>110000000009_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CTCATGCNCTGTTTACCCGTGACGTCGACTACATCGTTAAAGATGGTGAAGTTATCATCGTTGACGAACACACCGGTCGT\n+ACCATGCAGGGCCGTCGCTGGTCCGATGGTCTGCACCAGGCTGTGGAAGCGAAAGAAGGTGTGCAGA\n+>120000000009_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CGTTCTGGATCTGCACACCTTCTTTCGCTTCCACAGCCTGGTGCAGACCATCGGACCAGCGACGGCCCTGCATGGTACGA\n+CCGGTGTGTTCGTCAACGATGATAACTTCACCATCTTTAACGATGTAGTCGACGTCACGGGTAAACA\n+>110000000013_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+AGGCGTAGGCGGCATCGACATCTTTGGTCTGGCACAGCGTCGAGAAAATCGAACTGTAAGAGCGGGCATGAACCGCTTCC\n+ATAAAGCTGATATTCGATAATACCGCTTCTTCATGAGGCGTGAGTGCATCGGGCATCAGCGAAGGCG\n+>120000000013_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GGCAGACATTAACTGTCGTAGAACAACAACTGACGATGCGCGTTTTTACTGGCCTGACGCTGCTCGACACGCTGCAAAAT\n+GTTATCGGCGCGCCTTCGCTGATGCCCGATGCACTCACGCCTCATGAAGAAGCGGGATTATCGAATA\n+>110000000015_clr=0,139_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GTGAAGAACACCGAGTTCCGCAAACTCTAAAACGCAATCCCAAACAGTGTTTTGACATTAGCATCCGTGGTGGCAGCCAG\n+CCATGCGGCATCTTCTCCACGCCAGTGCGCAATACGTTGCAAAATATGGGGCAGATGGG\n+>120000000015_clr=0,146_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GTATTTATGCACTGTCGCGATGCCCACGAGCGGTTTATGACATTACTGGAGCCGTGGCTGGATAAACTGCCTGGTGCGGT\n+TCTTCATTGCTTTACCGGCACACGCGAAGAGATGCAGGCGTGCGTGGCGCATGGAATTTATATCGG\n+>110000000017_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GGTTGGTTTTGACCTGGTGAAAGCCTGTAAAGAGGCTTTCGCGGCCGCGAATGTACTGCTGAAAGTGATCATCGAAACCG\n+GCGAACTGAAAGACGAAGCGCTGATCCGTAAAGCGTCTGAAATCTCCATCAAAGCGGGTGCGGGCTT\n+>120000000017_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CCTGATAAGCGCAGCGCATCAGGCGTAAAGCATCTTACTTAGTAGCTGCTGGCGCTCTTACCGTCGCCGTGACCCAGCGC\n+TTTCAGCAGGCTTGCCAGCAGGCTGGAAGCACCAAAGCGGTAGTGACGCGCATCAGCCCAGTCAGCA\n+>110000000019_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CCTCTCTGGCGGTAGATCCCTGCCGCCAAAATTGCGCTAAATCAATCTCCCTTAAAGTTGCATGAAAAATCCCTTTTATC\n+CCCGCGTTAAGCGTCTTAACCTTAAACATGTATATTAAATATAACTTTAAAAGGTGTGATCATGTTT\n+>120000000019_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GCCAGGCATTGTGCTTTCAGCGCCTCGCGCAAGGCAATCGCTTCACGAGCGTAGCCGACAATACGCGGAGAATCGAAGTT\n+AACGTTGGTCAGGGTTGAGAAAAAGGCACGTGGCGCGAAGCTGTCGACATCGTGGTTGATGATGCCG\n+>110000000021_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CGGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTG\n+GATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGACAATGCCAGTAAGA\n+>120000000021_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CGGTAAAACTTAGCGTCCAGGAGGTATACAGTGACGGTTCATCTTTTTTCTTACTGGCATTGTCATCAACCGCTTTCATT\n+TTTTCGCTCAATGCGACAATTGCGCGATGCAAATCCAGTTCGTCGATTTTCGCCTCTTTTAATTGGT\n+>110000000023_clr=0,146_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GCCATATATCATGCTTAACCTTGGTATCCTGGGTCGCCGCTACAAAGTCTTTATGGGTGATGCGGGCAGTACGCTGATTG\n+GTTTTACCGTGATCTGGATCCTGCTCGAAACGACCCAAGGCAAAACCCATCCCATCAGCCCGGTTA\n+>120000000023_clr=0,143_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CCACCATATCCATTAGCGGAAT'..b'GTTGCAACCGTTCTGCCACCGCTTCCACAATATCGGTTTCCGCCA\n+>110000006160_clr=0,146_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GTCCCGCATCCTGTCATGCTGATTTCCGGTTCCGAAAATATCGTGAAAGAAAGCGAATGCGTTTCTCTCCCGGGGCTGCG\n+CTGAATTTTCTTCCTCCAGCATTTGCTGTTCTTTGCGTTTACCGCTTCTGAAATAGTCGTTCAGCT\n+>120000006160_clr=0,145_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GTCACTACAGGCGCATATTACCAGCCTGCTGGCGGATATCCAGGAGATTGAGGAATGTCAGAATCAGGTGACCGGTGATG\n+TCAGAATGGCCATGGAGGACATCAATACCAAAACCGGGGAATTACTGACGAAGGTCTGTGCCTCA\n+>110000006162_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GGGTACACCTGCTGCGCTATACCTGGCGGGCGCTGGCGTCGGGACGCTGGTACTGGCAGATGACGACGATGTGCATTTAA\n+GCAATCTGCAACGACAAATCCTCTTTACCACTGAAGATATCGATCGCCCGAAATCGCAGGTCAGCCA\n+>120000006162_clr=0,146_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+TCTCTATACCGCTTAATAACTTAATGGCTTCCAGTGCCTGCAAAGTGCCCATAACCCCGACCACCGGGCCAACCACGCCC\n+GCCGTGCGGCAGTTGCGTTCTGGCTCCTGGTTTTCTGGCCACAGGCAGCGGTAACAACCCTGCCCC\n+>110000006164_clr=0,146_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CCCATAAACCGTTTATTGTGTTCATCACCGCGTGGAAAGAACATGCGGTAGAAGCGTTTGAACTGGAGGCGTTTGACTAC\n+ATTCTAAAACCGTATCAGGAGTCACGCATTACCGGGATGCTGCAAAAACTGGAAGCAGCCTGGCAA\n+>120000006164_clr=0,146_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GCATTAACTGGCGGAATTCTTTAACTTTGCTGCGGCTGACCGGCACTTCAAAATCCAGATCTTTCAGCCGCAGAATATAG\n+GTGTTATTAAACCACGGTTCGATTTCGCGGATTTTGTTCAGATTGACACAAAATGAGCGATGGCAG\n+>110000006166_clr=0,145_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GTACCCACTTGAGCACGCAGTGCGGCAAAGCTGCTGATCGGCTTACCGTTCAGTGAGGTGATCACATCACCCGCTTTAAT\n+GCCCGCTTTTGCAGCGGAGGAATTAGGCAGAACCTGGCTCACGAAAGCACCGCGCTGGGCGGCAA\n+>120000006166_clr=0,146_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+AGTATATGGTGACCTACACCCGGCGGATGATTTCTTCACCGAAACCACGCCGTATGCGCCGAGCAGCCCTTATTCCGCGT\n+CAAAAACCATCAGCGACCATCTGGTGCGCGCCTGGCTGCGAACCTATGGTCATACAACTCTTATCA\n+>110000006168_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GTCATGTCTAACGCTTTATATTTTGGCTCTGTTCTGTCTCTGCGTTTTTGGGTCATTTCTCGCAACCTCTCACTTTTTCG\n+CCTCACTTTTTCAAGCGTCTCACTTCGTCGCAGTTGGGATTTTCGGTTTTTCTATGTGTGTGTTTCA\n+>120000006168_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GGGTTATTCGAATCGATGGGGATGATGTAGCGCCGCTATAAAAGGGAGGAGAAAAAAAGAGGGGGCTAGAAAGAGGGCCA\n+CAATTAGCCAGCTCTCCCTCCCTTTTAGCCCTGTATACATCCTCACAAGTGAGGGGTAAAAAAATAA\n+>110000006170_clr=0,146_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GAACATCCACTCGATCTTCGCCTTCTTCCGGTTTATTGTGTTTTAACCACCTGCCCGTAAACCTGGAGAACCATCGCGTG\n+TTTCAAAAAGTTGACGCCTACGCTGGCGACCCGATTCTTACGCTTATGGAGCGTTTTAAAGAAGAC\n+>120000006170_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GGCGATAGCTGTTAAGCCCTTCCATCGGTAAATAAAGCGAAGCGCCATGAGGCACCGCATTCAGGCGCGCTTCCGCCTCC\n+GCCACGGCTTTCAATTGTGGAATAATTCCGTCTTCGTTGTAGTACAGACCGATACTTAAATTCACTT\n+>110000006172_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CCTGCATGCCGTTAATGTAATCCAGACGTTGCTGAAAGCGCAGTTGTTGTGCAGGGGTGTAAGAGCTCTGGCAATCACGA\n+ACCATCATGGGGTCAGGCATCACACCGGATTCATCCAGAATCATACGATAATCCCCGGTAATTTCAG\n+>120000006172_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+ATGCTCGACAGCTCGAATTACAGCGGGAACATCTGGATGTGCTGAAATGGCAAATTAACTGTGCTGCGCGCGAATGCATT\n+TACTCGCAGCATCAACTGATGGAGGCCTGCACAGAAGACGCTCTCAGCAATTTTATGCAGGCGAATG\n+>110000006176_clr=0,108_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CCACAGGAAGTTGTACCGTCATCGCGCAGTTGGGCAAACGAGCTAAGTTGTTGGCCTTTCTTGACGATAACCGCACCGGT\n+TGCCGGATCGGTAATATCGGCCAGCGCC\n+>120000006176_clr=0,108_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GGCGCTGGCCGATATTACCGATCCGGCAACCGGTGCGGTTATCGTCAAGAAAGGCCAACAACTTAGCTCGTTTGCCCAAC\n+TGCGCGATGACGGTACAACTTCCTGTGG\n+>110000006178_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+ACATTGATGTACTGCATGTATGCAAAGGACGTCACATTACCGTGCAGTACAGTTGATAGCCCCTTCCCAGGTAGCGGGAA\n+GCATATTTCGGCAATCCAGAGACAGCGGCGTTATCTGGCTCTGGAGAAAGCTTATAACAGAGGATAA\n+>120000006178_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+TAGGAGAGGATCATTTCTTTACCCTCTTCGTCTTTGATCAGCACAGCCACAGAGCCTTTAACGATGTAGTACAGCGTTTC\n+CGCTTTTTCACCCTGGTGAATAAGCGTGCTCTTGGATGGGTACTTATGAATGTGGCAATGAGACAAG\n+>110000006180_clr=0,147_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+GCTCTGGAACACGAACATCGATCCAGTGTTCAGCGGCGAAAACGGGCAGTGAAAACACCAGTGCCAGAGCAAGTAAGCCT\n+TTTTTAAACATGTAAGCGTCCTTCTATGGATGAATATTGCTATCCATTATACGCCTGAGATTTAACA\n+>120000006180_clr=0,143_clv=1,0_max=1,0_tnt=1,0_rnd=t\n+CGTTTACGCGAGATGGAACGTTATGTCACTTCCGATACATTC\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 068920e730f4 test-data/output_02.read-db.meryldb |
| b |
| Binary file test-data/output_02.read-db.meryldb has changed |
| b |
| diff -r 000000000000 -r 068920e730f4 test-data/output_03.read-db.meryldb |
| b |
| Binary file test-data/output_03.read-db.meryldb has changed |
| b |
| diff -r 000000000000 -r 068920e730f4 test-data/output_23.pat.hist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_23.pat.hist Mon Apr 05 15:04:36 2021 +0000 |
| b |
| @@ -0,0 +1,5 @@ +10 1 +11 1 +14 1 +15 1 +19 1 |
| b |
| diff -r 000000000000 -r 068920e730f4 test-data/output_24.read-db.hist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_24.read-db.hist Mon Apr 05 15:04:36 2021 +0000 |
| b |
| @@ -0,0 +1,422 @@ +4 1 +6 1 +7 1 +8 5 +9 5 +10 5 +11 6 +12 2 +13 10 +14 10 +15 8 +16 6 +17 6 +18 9 +19 13 +20 10 +21 7 +22 16 +23 18 +24 11 +25 16 +26 14 +27 12 +28 15 +29 15 +30 11 +31 12 +32 18 +33 20 +34 21 +35 23 +36 20 +37 23 +38 32 +39 31 +40 27 +41 25 +42 22 +43 33 +44 27 +45 29 +46 35 +47 31 +48 38 +49 45 +50 30 +51 53 +52 54 +53 39 +54 43 +55 38 +56 47 +57 48 +58 53 +59 54 +60 49 +61 54 +62 45 +63 47 +64 41 +65 55 +66 61 +67 44 +68 51 +69 55 +70 57 +71 68 +72 51 +73 66 +74 56 +75 57 +76 52 +77 47 +78 48 +79 58 +80 50 +81 53 +82 55 +83 53 +84 51 +85 63 +86 52 +87 56 +88 65 +89 56 +90 51 +91 58 +92 58 +93 73 +94 53 +95 59 +96 56 +97 47 +98 58 +99 65 +100 54 +101 43 +102 56 +103 60 +104 53 +105 54 +106 40 +107 52 +108 54 +109 57 +110 43 +111 45 +112 46 +113 45 +114 46 +115 48 +116 47 +117 60 +118 58 +119 60 +120 46 +121 45 +122 42 +123 48 +124 51 +125 36 +126 59 +127 57 +128 48 +129 44 +130 59 +131 60 +132 53 +133 45 +134 51 +135 49 +136 45 +137 43 +138 46 +139 38 +140 34 +141 53 +142 38 +143 39 +144 34 +145 43 +146 37 +147 33 +148 34 +149 39 +150 40 +151 31 +152 35 +153 31 +154 34 +155 41 +156 19 +157 32 +158 42 +159 22 +160 28 +161 20 +162 32 +163 28 +164 28 +165 25 +166 27 +167 29 +168 23 +169 29 +170 28 +171 32 +172 31 +173 30 +174 31 +175 34 +176 32 +177 27 +178 23 +179 21 +180 31 +181 23 +182 17 +183 21 +184 19 +185 22 +186 26 +187 16 +188 29 +189 16 +190 16 +191 23 +192 23 +193 23 +194 22 +195 18 +196 18 +197 15 +198 15 +199 23 +200 17 +201 13 +202 16 +203 13 +204 16 +205 18 +206 20 +207 23 +208 9 +209 15 +210 14 +211 13 +212 18 +213 7 +214 15 +215 18 +216 17 +217 10 +218 16 +219 16 +220 5 +221 16 +222 12 +223 11 +224 9 +225 16 +226 14 +227 15 +228 13 +229 7 +230 13 +231 11 +232 13 +233 8 +234 4 +235 15 +236 13 +237 6 +238 8 +239 7 +240 6 +241 3 +242 11 +243 14 +244 4 +245 7 +246 11 +247 4 +248 6 +249 7 +250 12 +251 10 +252 4 +253 7 +254 11 +255 10 +256 9 +257 5 +258 5 +259 8 +260 5 +261 7 +262 9 +263 7 +264 6 +265 8 +266 5 +267 6 +268 10 +269 5 +270 6 +271 8 +272 4 +273 3 +274 7 +275 7 +276 7 +277 6 +278 4 +279 8 +280 6 +281 5 +282 7 +283 7 +284 2 +285 4 +286 2 +287 7 +288 5 +289 3 +290 3 +291 1 +292 2 +293 9 +294 4 +295 4 +296 3 +297 5 +298 4 +299 1 +300 2 +301 4 +302 3 +303 1 +304 2 +305 2 +306 3 +307 2 +308 4 +309 3 +310 3 +311 4 +312 1 +313 3 +314 3 +315 1 +316 2 +317 4 +318 5 +319 5 +320 2 +321 4 +322 3 +323 5 +324 2 +325 2 +326 2 +327 4 +329 3 +330 2 +331 4 +332 2 +333 3 +334 3 +336 1 +337 4 +338 2 +340 3 +341 1 +342 4 +343 1 +344 1 +345 3 +346 1 +347 5 +350 3 +351 1 +353 1 +354 2 +356 1 +357 1 +358 1 +359 3 +360 1 +361 1 +362 2 +363 3 +364 2 +365 2 +368 1 +369 3 +371 2 +372 4 +373 2 +375 1 +376 1 +377 2 +378 1 +379 1 +380 3 +381 2 +383 1 +384 3 +385 1 +388 1 +389 1 +390 2 +393 1 +395 1 +396 1 +397 1 +398 2 +399 2 +400 2 +401 2 +403 1 +408 1 +409 1 +411 1 +412 1 +415 1 +417 1 +421 1 +422 1 +423 1 +424 1 +428 1 +429 1 +430 1 +435 1 +438 1 +439 1 +450 1 +451 1 +452 1 +454 1 +457 3 +467 1 +472 1 +475 2 +484 1 +486 1 +490 1 +491 1 +500 1 +504 1 +510 1 +525 1 +529 1 +549 1 +559 1 +572 1 +582 1 +588 1 +647 1 +774 1 +2127 1 |
| b |
| diff -r 000000000000 -r 068920e730f4 test-data/paternal.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paternal.fasta Mon Apr 05 15:04:36 2021 +0000 |
| b |
| b'@@ -0,0 +1,14642 @@\n+>M00141:217:000000000-A55DC:1:1101:20444:1000_1:N:0:1\n+NGGGCTTTAAAATCCACTTTTTCCATATCGATAGTCACGTTTTCCTGCGCGTAGGTATCGGTATAGGTTAATTTTTCTTC\n+AACACCCGCGATGTTTTTGTATTTGGCGCTTAACGGCTCAAGTGTCTTGGCAGCATCTTCTTTGGTGGTTGCACCAATGG\n+AGGCAAATTGAATTTTGGTTTCAGAAGATTGCTTAAGCACCTTGTCACCTTTGTAGACATAGGTAATGGCAATTTCAGTG\n+CCGTTCAGATTGGCGCTGAATTTCTTCGATTCTTCTTTGTCACCGCAGCCAGCAAGAG\n+>M00141:217:000000000-A55DC:1:1101:20444:1000_2:N:0:1\n+GTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAA\n+CGGTGTTTTGCTTTGCGAACAATTATTCCCCATGCTTCAGCAACAAGGATGAAATAGTGCTTTTTACTAAGAGTTCTACT\n+CCCGTTCCGGACTGCTCACGCCACGGTATTAGGCATATCCTATATAGCCCCTGGTGAGAGTCACCAGTTCCTTGATTAAA\n+TAAAATGGAGTTTTACATGAAGGCTTTCAATACGCTGTTTTCCCTCGTTGTTTCATCTGTT\n+>M00141:217:000000000-A55DC:1:1101:10937:1000_1:N:0:1\n+NTGAACTCCACATCCTGCGGATCGTAAACCGTCACCTCTTCTTCGTGATACAAACGCCACAACACTTCGTTTGCCGGTAA\n+GGTCAGCAGTTCTTCGGTTTTGATGGTTTCGGTTAGCGTCGCCAGGTGGTCAAAGTCGTCCTGCTGGGCATTTTGCGCAG\n+GCATTACCTGCAACAACATACCGCCTGCAGCCGGTTTGCCGTCTACGTCGCCGGTGCGAATAAACAGGCGCGTCGGCAGC\n+TGTTCAGAACGCATAAAGTAATCTTCCAGGCAGGCCGCCAGGGTATCACCTTCCAGACCA\n+>M00141:217:000000000-A55DC:1:1101:10937:1000_2:N:0:1\n+GATGAATCTGGCGGTTATTAACGGTAACAATAACCAGCAGATGCGCGGTGTGGCGCGCGTGCAGGGCGAAATTCCAGAAA\n+ATGCCGACCTGAAAACGCTGGTCGGCAATGGTTACGTGGTGATCACCATTACCCCGAGCGAAGGCGAACGCTATCAGGGC\n+GTAGTTGGTCTGGAAGGTGATACCCTGGCGGCCTGCCTGGAAGATTACTTTATGCGTTCTGAACAGCTGCCGACGCGCCT\n+GTTTATTCGCACCGGCGACGTAGACGGCAAACCGGCTGCAGGCGGTAGGTTGTTGCAGGT\n+>M00141:217:000000000-A55DC:1:1101:20798:1000_1:N:0:1\n+NACATGCACTTCAACGGCATTACTGGTGACCTCTTCGTCCCAGGTATACAGTTTCTCTTCAATCAGTTTGCGCGACAGTA\n+CCCGACCAGCGTTACGCATCAGTAATTCCAGCAGGGCAAATTCTTTTGGTTTCAGTGTTAAGGGTTCGCCAGCCAGCGTG\n+GCGATACGTTTGCCGGGGTCGAGCATGACGTTACCGTGGCGCAGCTCGTTGCTGGCCTGGCCGTTGGTTCGGCGCATCAG\n+AGCTTCCAGCCTGGCGGCGACTTCTATCAACGCAAAAGGGTTACACAGATAATCGTCAGCT\n+>M00141:217:000000000-A55DC:1:1101:20798:1000_2:N:0:1\n+ATTACTGCGATTACTGCTGCGAATTTTTTCATGTTTATTACTCCCTTTAATGTCTGTTTCCGAGCATTTAACAAGATAGT\n+CCTTAACAACTTCTTAAGGGAAAAAAATAAAATTTAGTGCTGTACAGAGCGCGTTACAACACGGTTTACTGGCAGCAAAT\n+ACGGTTATCGCAGGGATGAAACAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGC\n+CTTAGTAAAATGGGTTTTAGCGTCCACTGGTTTACACAAGGTCGTAAGGGAAAAGAGGCGG\n+>M00141:217:000000000-A55DC:1:1101:13535:1000_1:N:0:1\n+NCGGTTGAGTTCAAAGGCAAAGATTTGCTTGCGCTGTCGCCGGAAGATCGCGCGGGCGAAGGCATCTTTATGGCCTTCCA\n+GTATCCGGTGGAGATTCCAGGTGTCAGTAACCAGTTTTTCCTGCAAACGGCACTTAATGCGGTGCGCAGCTATCGCGGCC\n+AGGAAACGCTCGACCGCTTTGATTTTCAGGATTTGATGGAAGAGAAAATCGCTCTCCTGAAGATGCCGGAAGATTTATTA\n+ACCCGTTCGGTAAACGTTGGTTTTTCCGGCGGCGAGAAAAAGCGCAACGATTTTTTGCAA\n+>M00141:217:000000000-A55DC:1:1101:13535:1000_2:N:0:1\n+TTCGTCCCTGATATAGCACATGAACGTAATCAGGCTTGATGTAGTCGAGAATGCGTTGGTAGTGCGTAACAATGATGAAT\n+GAGCGCTTGCCATCACGCAGCGAGTTCACGCCATCGGCGACCACTTTTAATGCGTCAATATCCAGCCCGGAGTCCGACTC\n+ATCAAGAATGCATAACTCCGGTTCCAGCACCGCCATTTGCAAAATATCGTTGCGCTTTTTCTCGCCGCCGGAAAAACCAA\n+CGTTTACCGAACGGGTTAATAAATCTTCCGGCATCTTCAGGAGAGCGATTTTCTCTTCCAT\n+>M00141:217:000000000-A55DC:1:1101:20536:1000_1:N:0:1\n+NACGACACATTACCGGAAATTCAGGCCGACCCGGACAGGCTGACTCAGGTCCTGTTGAATCTCTATCTCAATGCTATTCA\n+GGCGATTGGTCAGCATGGCGTGATTAGCGTGACGGCCAGCGAAAGCGGCGCGGGCGTGAAAATCAGCGTTACCGACAGCG\n+GTAAGGGAATTGCGGCAGATCAGCTTGATGCCATCTTCACTCCGTACTTCACCACTAAAGCCGAAGGCACCGGATTGGGG\n+CTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGG\n+>M00141:217:000000000-A55DC:1:1101:20536:1000_2:N:0:1\n+TCCACCACCAGAATATCGATATTATCGTGCGTCATCCTTGTGGGTCCTTACGCGTAATATTGACCGGAAGCCAGAGGGTG\n+AACGTTGAGCCTTTTCCCTCCTGGCTTGCGACCTGAATTGTACCACCGTGTTGTTCAACAATATTATGCACGACCGCCAG\n+CCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTAC\n+CGCTGTCGGTAACGCTGATTTTCACGCCCGCGCCGCTTTCGCTGGCCGTCACGCTAATCAC\n+>M00141:217:000000000-A55DC:1:1101:20871:1000_1:N:0:1\n+NCGTAACTTTATTCATATCTCTTCCCCCTCCCTGTACTTCGATTATCACCACCATCGCGATATTAAAGAAGATTTTCGCC\n+CTCACCGCTTCGCCAACGAGTTTGCCCGCAGCAAAGCAGCCAGCGAAGAAGTGATCAATATGCTTTCGCAGGCGAATCCA\n+CAAACGCGCTTTACTATTCTGCGCCCACAAAGTCTGTTCGGACCGCACGATAAAGTCTTTATTCCCCGTCTGGCGCATAT\n+GATGCACCACTACGGCAGTATTCTGTTACCGCATGGCGGCAGT'..b'CTGAGCGCCGGTCGCTACCATTACCAGTTGGTCTGGTGTCAAAAATAATAATAA\n+>M00141:217:000000000-A55DC:1:1101:12440:1102_1:N:0:1\n+CGAGCAGATCACCCGCGAAACCTACAAATATGCCGATATGCTGGCGATGTCCGCCAAGAAAGATGCGATGGTGCCGATGG\n+GCGGCCTGCTGTGCATGAAAGACGACAGCTTCTTTGATGTGTACACCGAGTGCAGAACCCTTTGCGTGGTGCAGGAAGGC\n+TTCCCGACATATGGCGGCCTGGAAGGCGGCGCGATGGAGCGTCTGGCGGTAGGTCTGTATGACGGCATGAATCTCGACTG\n+GCTGGCTTATCGTATCGCGCAGGTACAGTACCTGGTCGACGGTCTGGAAGAGATTGGCGTT\n+>M00141:217:000000000-A55DC:1:1101:12440:1102_2:N:0:1\n+ATAACACCCCAAAATGCAGAGTGCTTTTTTTCAGCTTGATCAGTCATGATGCCACCTTTAGAGGAAGGCTATTTTTGTTA\n+TTGAGGATGTAGGGTAAGAGAGTGGCTAACATCCTTATAGCCACTCTGTAGTATTAATTAAACTTCTTTAAGTTTTGCGG\n+TGAAGTGACGCAATACTTTCGGTTCGTACGTAAAGGTTAATCCTTTAATATTCGCCGCGTTCTCTTTCACATGTTTAAAG\n+GCTTCACTAATGAAGTCCATTTGTGTTTGAGTATATGTTGCGCGCGGAATGGTTAAACGG\n+>M00141:217:000000000-A55DC:1:1101:10934:1102_1:N:0:1\n+TCCCAGACAATCAATACGCGCCAGCCGAGTTCCTGCAAGCGACTGATATCGCGGCGATCGCGCTCAACATTTTTACCTAT\n+CTTCTCCAGCCAGAACTCGGTTCGAGTCGCAGGCACTTTAAACAGATAGCAGTGATGATGATGCCAGAAGTAGCCATGGG\n+TAAATATCACGCAGCGATATTCAACAACGACAAAATCCGGACGTCCGGGAAGACTGGCGTCCTGCACGCGAAATGCCAGG\n+CCCTGCCTGGTTAACCGACCGGCTAGGGGATATCATTACGCAGTGCCACGCATGTCAAACG\n+>M00141:217:000000000-A55DC:1:1101:10934:1102_2:N:0:1\n+ACGCCGGTGCTGTGGAAGTACCTCTATCGATATGCGAAAAAACATCAGGCGCGCGGTAACGGCTTCGGTTATGGAATGGT\n+TTATCCGAACAATCCGCAAAGCGTCACGCGTACGCTGTCTGCGCGTTATTACAAAGATGGCGCGGAAATTTTAATCGATC\n+GCGGCTGGGATATGGCCAAGGGTGAGAAAGACTTTGACGAACCGCTGAATCAGCAACATCGTCCACGTCGGATAAAGCAT\n+CGGGAATGCGCGCGCCTAACGGGTGTTAAAGCGCCGGGAGCAGCGAACTTCCGTTTTCCGG\n+>M00141:217:000000000-A55DC:1:1101:17905:1102_1:N:0:1\n+GGTTGATGTGGGGGCTTATTTTTGTCGGGCCGTTGATCGTGCCGGAATACCCGGCGATGTTGCAGTCGATGGGGCGTTAT\n+CTGGCGTTAGGGTTAATTGCGCTGCCCATTGCCTGGCTGGGACGCGTGCGTCTGCGTCAGTTGGCGCGTCGCGACTGGCT\n+TACCGCCTTGATGCTCACTATGATGGGCAACCTCATCTATTACTTCTGCCTTGCCAGTGCCATTCAACTTACTGGCGCGC\n+CTGTTTCCACGATGATTATCGGCACCCTGCCGGTGGTCGTTCTTGTCTTTTCCCATCTGCT\n+>M00141:217:000000000-A55DC:1:1101:17905:1102_2:N:0:1\n+GTTTCGAAAACAATCAGCGGCCCGAGAATCACTGTCGGTAATAGCTGGCTGGCTACGTTCCAGCAGCGTGCGCCCACCCC\n+TGAGCAAACCACGCCTATCGCAACCATCAGACTAATAAACACCAGCGGCAGGGGGCCAACGGGTCGGGAGAAGTCCGGCG\n+TTTGCGTACTAGGCCAGTAACAAGCGACGAGATAGCCGATAAGTGAAACCGGCAGTGTTACCAGCGCCTGCGCTGTTCCC\n+CCCCCCCTCTGACTTTTGTCGGCTTCTTCCCCCCGACTGCCGGCTTTCCCCCCGCCATACC\n+>M00141:217:000000000-A55DC:1:1101:21867:1103_1:N:0:1\n+CCGCATTGATGGCAGTGCACTGCGTGGTTCCTCCACATCCGGCTGCTTTATATGTTGCCAATAAGCTGGGCGCAGATATC\n+GGTTCGGTGATCGTCTACGGTTTGCTGGTTGGGCTGATGGCATCACTGATCGGTGGCCCACTTTTCCTTAAATTTCTGGG\n+TCAACGACTGCCCTTTAAACCTGTACCCACAGAGTTTGCAGATCTCAAAGTTCGCGATGAAAAAACACTACCGTCATTAG\n+GCGCAACGTTATTCACCATACTGCTACCCATTGCGCTGATGTTGGTTAAACCGATTGCCG\n+>M00141:217:000000000-A55DC:1:1101:21867:1103_2:N:0:1\n+TAAATGTCGCTGTCGTATAGTATTTAGATGATTCATTGAGCGTAGCGCCGCAATATTTCTTCACTAGCCAGAAAAGCGAG\n+TCCGTCACGATAGTGCAGCCAATTGCACCTGAACCGATAGCAATCGCAATAATTTCCGGGTTGATGTCGGGATACAGCGG\n+CAGCATTGGTGCAAACATTGCCGTTGCCCCCATCATTGCCACGGTAGTGTAGCCCACTGCCGCATACATACTAAGACACA\n+CAAACAAGGACCGACGAGCAGGGTGCATCTGCCAATAGGAGCGAATACACCCCAACGGATC\n+>M00141:217:000000000-A55DC:1:1101:18689:1103_1:N:0:1\n+TTTGCAGGCGCTGAACCGCCTTTCGAGCACGGTCTACGTGATGATGATCCTGAGCGTAACGAAGCAGCCGCTAACGGTGA\n+AGCAGATCCAACAACGACTGGGGGAAACGCAATGATTATTGAACGTTGTCGTGAACTGGCGTTGCGAGCGCCCGCCAGAG\n+TGGTTTTTCCGGATGCGTTAGACCAACGTGTGCTGAAAGCCGCGCAATATTTACATCAACAAGGTCTGGCAACGCCCATT\n+CTGGTCGCCAATCCGTTTGAACTTCGTCAGTTTGCGCTCAGTCACGGCGTGGCGATGGACG\n+>M00141:217:000000000-A55DC:1:1101:18689:1103_2:N:0:1\n+GTTTCGGCACTGGCAAGCGCGATATCCGCCAGCTGCGCCGCCGTCGGCTGTGGCACCACGCTGCAATCGGCAAAGCCCAA\n+CGCCGGGCCGCTGTACTGTGGCAACATCAGGAAAATGGAAGAGAGCGTTTTACAGCCTGGCTGCAAGCCGATAATGCGTA\n+ATCCGGCACGCAGCACATTTGCCGTGGAAGAGAGGTTGCCCGCGATACAGACATCCGCTTTACCGGCGCCGACCATTGCT\n+GCGGCGCACACCAGAGGGTCGGTAAGTTTTTCCAGCGCATCCTGCGGCGTGTTCTGGCCCC\n+>M00141:217:000000000-A55DC:1:1101:18899:1103_1:N:0:1\n+CAATGTATTAGACCCGTATATTGTTCGACCGGTCGCTGTCGCCTGGCGTGATTATGTTCCGCAACCGGCGCGTAACGGTT\n+TGAGCAACTTTACTGGCAACCTTGAAGAACCTGCGGTGATGGTTAACTACTTCTTGCAGGGCGACCCTTATCAGGGGATG\n+GTCCACTTTACCCGCTTTTTCCTGAACACCATTTTGGGGATGGGCGGTTTTATTGAT\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 068920e730f4 test-data/read-db.meryldb |
| b |
| Binary file test-data/read-db.meryldb has changed |