| Next changeset 1:f880686a9194 (2019-10-23) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a |
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added:
paralyzer.xml readme.rst test-data/input.2bit test-data/input.fa test-data/input.ini test-data/input.sam test-data/out.clusters test-data/out.distribution test-data/out.groups test-data/out_PARalyzer_Utilized.sam tool-data/lastz_seqs.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 4dbe81be8b81 paralyzer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paralyzer.xml Tue Dec 06 03:28:59 2016 -0500 |
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| b'@@ -0,0 +1,387 @@\n+<tool id="paralyzer" name="PARalyzer" version="1.5">\n+\n+ <description>A method to map interaction sites between RNA-binding proteins\n+ and their targets</description>\n+\n+ <requirements>\n+ <!-- conda dependency -->\n+ <requirement type="package" version="1.5">paralyzer</requirement>\n+ <requirement type="package" version="324">ucsc-fatotwobit</requirement>\n+ </requirements>\n+\n+ <command>\n+<![CDATA[\n+ #if $refGenomeSource.genomeSource == "history":\n+ faToTwoBit \'$refGenomeSource.ownFile\' ownFile.2bit\n+ &&\n+ #end if\n+\n+ ## execute paralyzer\n+ ## note the 2nd argument is the memory parameter\n+ ## the parameter can be override in job_conf.xml e.g.\n+ ## <env id="_JAVA_OPTIONS">-Xmx12G</env>\n+ PARalyzer 2G $input_ini\n+\n+]]>\n+ </command>\n+ <inputs>\n+ <param name="input_sam" type="data"\n+ format="sam" label="Alignment"\n+ help="The sam file containing alignment of the read data."/>\n+\n+ <param name="collapse" type="boolean" truevalue="=COLLAPSED"\n+ falsevalue="" checked="True"\n+ label="Incorporate the read copy number"\n+ help="If reads were collapse before alignment and you want\n+ to incorporate the read copy number, please select Yes,\n+ otherwise select No" />\n+\n+ <!-- Genome source. -->\n+ <conditional name="refGenomeSource">\n+ <param name="genomeSource" type="select"\n+ label="Will you select a reference genome from your\n+ history or use a built-in genome?"\n+ help="The version of genome against which the reads were aligned.">\n+ <option value="2bit" selected="True">\n+ Use a built-in genome</option>\n+ <option value="history">\n+ Use a genome from my current history</option>\n+ </param>\n+ <when value="2bit">\n+ <param name="builtin" type="select"\n+ label="Select a reference genome">\n+ <options from_data_table="lastz_seqs">\n+ <filter type="sort_by" column="1" />\n+ <validator type="no_options"\n+ message="A built-in reference genome is not available\n+ for the build associated with the selected input file"/>\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="ownFile" type="data" format="fasta"\n+ label="Select the reference genome" />\n+ </when>\n+ </conditional>\n+\n+ <conditional name="methods">\n+ <param name="choice" type="select"\n+ label="Please select one of the approaches"\n+ help="">\n+ <option value="EXTEND_BY_READ">\n+ EXTEND_BY_READ\n+ </option>\n+ <option value="HAFFNER_APPROACH">\n+ HAFFNER_APPROACH\n+ </option>\n+ <option value="ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL">\n+ ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL\n+ </option>\n+ </param>\n+ <when value="EXTEND_BY_READ" />\n+ <when value="HAFFNER_APPROACH" />\n+ <when value="ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL">\n+ <param name="max_num" type="integer"\n+ value="0" label="The maximum number"\n+ help="\n+ The maximum number of reads to extend beyond the positive\n+ signal in each direction (default 0) the cluster is defined\n+ ">\n+ <validator type="in_range"\n+ message="Minimum allowed value is 0" min="0"/>\n+ </param>\n+ </when>\n+ </conditional>\n+\n+ <conditional name="conversion">\n+ <param name="selection" type="select"\n+ label="Conversion"\n+ help="Please specify char'..b'f crosslinking, providing for\n+single-nucleotide resolution binding information. PARalyzer utilizes this\n+nucleotide substition in a kernel density estimate classifier to generate\n+the high resolution set of Protein-RNA interaction sites.\n+\n+.. _paralyzer: https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/\n+.. _PAR-CLIP: http://www.ncbi.nlm.nih.gov/pubmed/20371350\n+\n+.. class:: infomark\n+\n+**Approaches**\n+\n+``EXTEND_BY_READ``: including this line means that the cluster will be extended\n+beyond the signal to include a region such that it extends to\n+the end of any read that falls within the cluster and contained\n+a conversion, or until the minimum read depth\n+(MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION parameter) is no longer met\n+\n+``HAFNER_APPROACH``: identifies the location with the largest number of conversion\n+events and extends the cluster up to\n+( parameter ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL)nt\n+in each direction from that point, or until the minimum\n+read depth (MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION parameter) is no longer met\n+\n+``ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL``: the maximum number of reads to\n+extend beyond the positive signal in each direction (default 0)\n+the cluster is defined as the region where the conversion KDE is above\n+the background KDE and then extended up to #integer#, or until the minimum\n+read depth (MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION parameter) is no longer met\n+\n+.. class:: infomark\n+\n+**Outputs**\n+\n+DISTRIBUTIONS: contains the signal KDE, background KDE, read count & conversion for all locations within each group\n+ * The data will be in blocks of four lines for each group\n+ * groups on the reverse strand do not need to be reversed; the values always equal nucleotdies from GroupStart to GroupEnd, regardless of Strand\n+ * First Column = Chromosome = chromosome on which the group resides\n+ * Second Column = Strand = orientation in which the group resides\n+ * Third Column = GroupStart = beginning coordinate on the chromosome of the group\n+ * Fourth Column = GroupEnd = ending coordinate on the chromosome of the group\n+ * Fifth Column = GroupID = unique ID for the group\n+ * Sixth Column = Information = reports if the current line contains the Signal, Background, Conversion Percent, or ReadCount\n+ * All nucleotides that do not have any possibility of having a conversion event are given a value of -1\n+ * All Subsequent Columns: the values for each nucleotide from GroupStart until GroupEnd\n+\n+\n+GROUPS: a comma separated file containing the information about the resulting groups\n+ * Chromosome = chromosome on which the group resides\n+ * Strand = orientation in which the group resides\n+ * GroupStart = beginning coordinate on the chromosome of the group\n+ * GroupEnd = ending coordinate on the chromosome of the group\n+ * GroupID = unique ID for the group\n+ * ReadCount = number of reads within the group\n+\n+CLUSTERS: a comma separated file containing the information about the resulting clusters\n+ * Chromosome = chromosome on which the cluster resides\n+ * Strand = orientation in which the cluster resides\n+ * ClusterStart = beginning coordinate on the chromosome of the cluster\n+ * ClusterEnd = ending coordinate on the chromosome of the cluster\n+ * ClusterID = unique ID for the cluster\n+ * ClusterSequence = sequence of the cluster\n+ * ReadCount = number of reads that overlap the cluster by at least 1 nucleotide\n+ * ModeLocation = coordinate of the location with the highest signal / (signal + background) value\n+ * ModeScore = score of the highest signal / (signal + background) value\n+ * ConversionLocationCount = number of unique location where at least 1 conversion occurred\n+ * ConversionEventCount = total number of conversions that occurred within the cluster\n+ * NonConversionEventCount = total number of possible conversion events that did not occur\n+\n+]]></help>\n+ <citations>\n+ <citation type="doi">10.1186/gb-2011-12-8-r79</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 4dbe81be8b81 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Tue Dec 06 03:28:59 2016 -0500 |
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| @@ -0,0 +1,5 @@ +Important notes +---------------- + +The default memory usage is 2G which can be override in job_conf.xml e.g. +<env id="_JAVA_OPTIONS">-Xmx12G</env> |
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| diff -r 000000000000 -r 4dbe81be8b81 test-data/input.2bit |
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| Binary file test-data/input.2bit has changed |
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| diff -r 000000000000 -r 4dbe81be8b81 test-data/input.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fa Tue Dec 06 03:28:59 2016 -0500 |
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| b'@@ -0,0 +1,333 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT\n+TTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTG\n+GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATC\n+CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTA\n+AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT\n+GTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA\n+AACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTT\n+TATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATT\n+ATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCCGC\n+CCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCA\n+ACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAA\n+GCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAAT\n+AGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGA\n+ACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCAC\n+ACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTT\n+AACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGC\n+GGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTA\n+GATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACT\n+CCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCC\n+TAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGC\n+CACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGG\n+AGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTC\n+AGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAA\n+GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTG\n+GCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGC\n+TTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTC\n+AAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGA\n+GGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAA\n+CCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCA\n+ACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCACCT\n+TACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATG\n+AAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCT\n+GCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGA\n+CCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGT\n+CTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTAC\n+CGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTA\n+AATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGT\n+AAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAA\n+GCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGA\n+ACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATG\n+TTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGA\n+TTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAAC\n+AAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTA\n+CCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCA\n+GTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAAAGGTAGCATA\n+ATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTC\n+AGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCG\n+GGCATAACACAGCAAGACGAGAAGACCCTATGGAGCTTTAATTTATTAAT\n+GCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGT\n+ACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCC\n+AATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCT\n+ATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCA\n+GGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATT\n+AAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCT\n+ATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATT\n+ATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATGGCAGAGCCCGGT\n+AATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAATTCCTCTTCTT\n+AACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAAT\n+CGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATAC\n+AACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCC\n+TTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCG\n+CTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTC\n+AACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTC\n+AATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCG\n+CACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATC\n+ATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCT\n+TATCACAACACAAGAACACCT'..b'CTTAGTTACCGCTAACAACCTATTC\n+CAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCAT\n+CAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAA\n+TCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGA\n+TTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAG\n+GCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAA\n+GGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGC\n+AGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCAC\n+TAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCA\n+GCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTC\n+CACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATA\n+CTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGA\n+TATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCT\n+CCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGT\n+TTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAA\n+CGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCT\n+ATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAA\n+ACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACA\n+TTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTC\n+ACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAA\n+CTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATT\n+TCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCC\n+TATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCT\n+CCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTC\n+CTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACC\n+TATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTT\n+CAACCAGTAACTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGC\n+ACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTA\n+TTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAAC\n+ACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAA\n+TAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAA\n+ATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAAT\n+AACACACCCGACCACACCGCTAACAATCAATACTAAACCCCCATAAATAG\n+GAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTC\n+AACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGA\n+CCCCAATACGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTC\n+ATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTC\n+ACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAG\n+CCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCAC\n+ATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAA\n+TGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATC\n+CTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGTG\n+AGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCCG\n+CCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTAC\n+TCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTT\n+GCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACG\n+AAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTT\n+CCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGCG\n+ACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACATC\n+AAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCC\n+TAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAG\n+CAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGC\n+CCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGAC\n+AAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAACT\n+ATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTAT\n+AAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGG\n+ACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAG\n+ATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGT\n+ACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCAC\n+CTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTA\n+CAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCAACTGCAACTC\n+CAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAA\n+CAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAA\n+ATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGAC\n+CACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACAT\n+CTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCT\n+TAAATAAGACATCACGATG\n' 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| diff -r 000000000000 -r 4dbe81be8b81 test-data/input.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.ini Tue Dec 06 03:28:59 2016 -0500 |
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| @@ -0,0 +1,22 @@ +#all values are the default ones +BANDWIDTH=3 +CONVERSION=T>C +MINIMUM_READ_COUNT_PER_GROUP=5 +MINIMUM_READ_COUNT_PER_CLUSTER=2 +MINIMUM_READ_COUNT_FOR_KDE=3 +MINIMUM_CLUSTER_SIZE=11 +MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=2 +MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=2 +MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=1 +MINIMUM_READ_LENGTH=20 +MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=1 + +EXTEND_BY_READ + +GENOME_2BIT_FILE=input.2bit +SAM_FILE=input.sam=COLLAPSED + +OUTPUT_DISTRIBUTIONS_FILE=out.distribution +OUTPUT_GROUPS_FILE=out.groups +OUTPUT_CLUSTERS_FILE=out.clusters +#OUTPUT_READS_FILE=out_PARalyzer_Utilized.sam |
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| diff -r 000000000000 -r 4dbe81be8b81 test-data/input.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.sam Tue Dec 06 03:28:59 2016 -0500 |
| b |
| b'@@ -0,0 +1,953 @@\n+@SQ\tSN:chrM\tLN:16569\n+3122-56\t0\tchrM\t720\t255\t21M\t*\t0\t0\tTTCACCCTCTAAATCACCACG\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+4366-41\t0\tchrM\t3197\t255\t23M\t*\t0\t0\tCATTATACCCACACCCACCCAAG\tIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:0T22\tNM:i:1\n+4748-37\t0\tchrM\t1450\t255\t20M\t*\t0\t0\tCTTAGTTGAACAGGGCCCTG\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\tNM:i:0\n+5000-35\t0\tchrM\t1645\t255\t25M\t*\t0\t0\tATTTCAACTTAACTTGACCGCTCTG\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:25\tNM:i:0\n+7405-24\t0\tchrM\t1450\t255\t25M\t*\t0\t0\tCTTAGTTGAACAGGGCCCTGAAGCG\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:25\tNM:i:0\n+8670-21\t0\tchrM\t1423\t255\t20M\t*\t0\t0\tATTTAGCAGTAAACTGAGAG\tIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:15A4\tNM:i:1\n+11115-17\t0\tchrM\t1114\t255\t24M\t*\t0\t0\tTTAAATCAACAAAACTGCTCGCCA\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:24\tNM:i:0\n+11953-16\t0\tchrM\t1253\t255\t21M\t*\t0\t0\tCCTATATACCGCCATCTTCAG\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+13131-15\t0\tchrM\t1539\t255\t21M\t*\t0\t0\tCATTTATATAGAGGAGACAAG\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+15971-12\t0\tchrM\t1423\t255\t23M\t*\t0\t0\tATTTAGCAGTAAACTGAGAGTAG\tIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:15A7\tNM:i:1\n+19590-10\t0\tchrM\t1025\t255\t21M\t*\t0\t0\tAAAGTGGCTTTAACATATCTG\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+19914-10\t0\tchrM\t8670\t255\t28M\t*\t0\t0\tACTAATCAAACTAACCTCAAAACAAATG\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:28\tNM:i:0\n+20885-10\t0\tchrM\t11800\t255\t26M\t*\t0\t0\tACTTCAAACTCTACTCCCACTAATAG\tIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:26\tNM:i:0\n+21266-9\t0\tchrM\t1093\t255\t21M\t*\t0\t0\tCTTAGCCCTAAACCTCAACAG\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+22033-9\t0\tchrM\t4422\t255\t20M\t*\t0\t0\tCTATCGGGCCCATACCCCGA\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\tNM:i:0\n+24420-8\t0\tchrM\t992\t255\t27M\t*\t0\t0\tTAAAAAACTCCAGTTGACACAAAATAG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+24637-8\t0\tchrM\t741\t255\t26M\t*\t0\t0\tATCAAAAGGGACAAGCATCAAGCACG\tIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:9A16\tNM:i:1\n+25285-8\t0\tchrM\t12207\t255\t21M\t*\t0\t0\tGAGAAAGCTCACAAGAACTGC\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+25854-8\t0\tchrM\t3197\t255\t22M\t*\t0\t0\tCATTATACCCACACCCACCCAA\tIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:0T21\tNM:i:1\n+26165-8\t0\tchrM\t1682\t255\t28M\t*\t0\t0\tCCCCAAACCCACTCCACCTTACTACCAG\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:28\tNM:i:0\n+26412-8\t0\tchrM\t587\t255\t25M\t*\t0\t0\tCTTACCTCCTCAAAGCAATACACTG\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:25\tNM:i:0\n+26513-8\t0\tchrM\t1517\t255\t22M\t*\t0\t0\tACATTTAACTAAAACCCCTACG\tIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:22\tNM:i:0\n+26793-8\t0\tchrM\t623\t255\t26M\t*\t0\t0\tACGGGCTCACATCACCCCATAAACAC\tIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:25A0\tNM:i:1\n+29748-7\t0\tchrM\t1477\t255\t27M\t*\t0\t0\tTACACACCGCCCGTCACCCTCCTCAAG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+32129-7\t0\tchrM\t11658\t255\t22M\t*\t0\t0\tCCATTCTCATCCAAACCCCCTG\tIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:22\tNM:i:0\n+32919-6\t0\tchrM\t10538\t255\t27M\t*\t0\t0\tCTCACACCTCATATCCTCCCTACTATG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+34500-6\t0\tchrM\t1539\t255\t20M\t*\t0\t0\tCATTTATATAGAGGAGACAA\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\tNM:i:0\n+37673-6\t16\tchrM\t4371\t255\t30M\t*\t0\t0\tTCTCCGTGCCACCTATCACACCCCATCCTA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:30\tNM:i:0\n+38072-6\t0\tchrM\t13146\t255\t27M\t*\t0\t0\tCCCACTAATCCAAACTCTAACACTATG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+39034-5\t0\tchrM\t1228\t255\t20M\t*\t0\t0\tATCAACCTCACCACCTCTTG\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\tNM:i:0\n+39340-5\t0\tchrM\t15624\t255\t27M\t*\t0\t0\tCCCTATTACTATCCATCCTCATCCTAG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+40359-5\t0\tchrM\t1448\t255\t27M\t*\t0\t0\tTGCTTAGTTGAACAGGGCCCTGAAGCG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+42562-5\t0\tchrM\t587\t255\t22M\t*\t0\t0\tCTTACCTCCTCAAAGCAATACA\tIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:22\tNM:i:0\n+42853-5\t0\tchrM\t903\t255\t28M\t*\t0\t0\tTCACACGATTAACCCAAGTCAATAGAAG\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:28\tNM:i:0\n+43258-5\t0\tchrM\t1416\t255\t25M\t*\t0\t0\tAAGGTGGATTTAGCAGTAAACTGAG\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:22A2\tNM:i:1\n+43464-5\t0\tchrM\t6542\t255\t23M\t*\t0\t0\tCAACCTCAACACCACCTTCTTCG\tIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:23\tNM:i:0\n+44314-5\t0\tchrM\t1253\t255\t20M\t*\t0\t0\tCCTATATACCGCCATCTTCA\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\t'..b'ATTCCTCTTCTTAACACCA\tIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:20A2\tNM:i:1\n+1291753-1\t0\tchrM\t910\t255\t21M\t*\t0\t0\tATTAACCCAAGTCAATAGAAG\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+1294271-1\t0\tchrM\t8698\t255\t22M\t*\t0\t0\tATAACCATACACAACACCAAAG\tIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:17T4\tNM:i:1\n+1294286-1\t0\tchrM\t1402\t255\t24M\t*\t0\t0\tAAACTTAAGGGTCGAAGGGGGATT\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:18T5\tNM:i:1\n+1295492-1\t0\tchrM\t4302\t255\t24M\t*\t0\t0\tATAATAGGAGCTTAAACCCCCTTA\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:24\tNM:i:0\n+1298968-1\t0\tchrM\t5055\t255\t27M\t*\t0\t0\tTACAACCCTAACATAACCATTCTTAAT\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+1300275-1\t0\tchrM\t1619\t255\t28M\t*\t0\t0\tCAAAGCACCCAACTTACACTTAGGAGAT\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:28\tNM:i:0\n+1300703-1\t0\tchrM\t3032\t255\t20M\t*\t0\t0\tGTTCGTTTGTTCAACGATTA\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\tNM:i:0\n+1301615-1\t0\tchrM\t7139\t255\t28M\t*\t0\t0\tCCATTTCACTATCATATTCATCGGCGTA\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:28\tNM:i:0\n+1302286-1\t0\tchrM\t1218\t255\t27M\t*\t0\t0\tATAAACCCCGATCAACATCACCACCTC\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:16C10\tNM:i:1\n+1303593-1\t0\tchrM\t787\t255\t27M\t*\t0\t0\tCTTAGCCTAGCCACACCCCCATGGGAA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:21C5\tNM:i:1\n+1304414-1\t0\tchrM\t10022\t255\t20M\t*\t0\t0\tCCAATTAACTAGTTTTGACA\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\tNM:i:0\n+1306285-1\t0\tchrM\t10327\t255\t36M\t*\t0\t0\tCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:36\tNM:i:0\n+1307553-1\t0\tchrM\t11193\t255\t30M\t*\t0\t0\tCCGGCACATACTTCCTATTCTACACCCTAG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:1A28\tNM:i:1\n+1315185-1\t16\tchrM\t4377\t255\t24M\t*\t0\t0\tTGCCACCTATCACACACCATCCTA\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:15C8\tNM:i:1\n+1315758-1\t16\tchrM\t4328\t255\t21M\t*\t0\t0\tGCTAGGACTATGAGAATCGAA\tIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:0T20\tNM:i:1\n+1316317-1\t0\tchrM\t11923\t255\t26M\t*\t0\t0\tCTCAAATATCACTCTCCTACTTACAG\tIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:0A25\tNM:i:1\n+1316768-1\t0\tchrM\t1904\t255\t25M\t*\t0\t0\tCCGAAACCAGACGAGCTACCTAAGA\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:25\tNM:i:0\n+1320780-1\t0\tchrM\t4687\t255\t25M\t*\t0\t0\tCTATCCTCTTCAACAATATACTCTC\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:25\tNM:i:0\n+1321276-1\t0\tchrM\t2032\t255\t25M\t*\t0\t0\tGAATCGTAGTTCAACTTTAAATTTG\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:5T19\tNM:i:1\n+1321453-1\t0\tchrM\t2114\t255\t27M\t*\t0\t0\tCTCTTTGGACACTAGGAAAAAACCTAG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:25T1\tNM:i:1\n+1322102-1\t0\tchrM\t8038\t255\t28M\t*\t0\t0\tTATAATAATTACATCACAAGACGTCTTG\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:28\tNM:i:0\n+1323531-1\t0\tchrM\t6518\t255\t20M\t*\t0\t0\tCATCACTATACCACTAACAG\tIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:11T8\tNM:i:1\n+1324159-1\t0\tchrM\t3180\t255\t24M\t*\t0\t0\tATATCATCTCAACTTAGCATTATA\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:17T6\tNM:i:1\n+1324512-1\t16\tchrM\t5803\t255\t24M\t*\t0\t0\tCAATATGAAAATCACCTCGGAGCG\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:23T0\tNM:i:1\n+1324879-1\t0\tchrM\t2656\t255\t29M\t*\t0\t0\tTCTCTTACTTTTAACCAGTGAAATTGACC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:29\tNM:i:0\n+1328459-1\t0\tchrM\t10234\t255\t20M\t*\t0\t0\tCTATTACCTTCTTATTATTC\tIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:19T0\tNM:i:1\n+1329464-1\t0\tchrM\t732\t255\t29M\t*\t0\t0\tATCACCACGATCAAAAGGGACAAGCATCA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:18A10\tNM:i:1\n+1330044-1\t0\tchrM\t8309\t255\t21M\t*\t0\t0\tCTTGGCATTAACCTTTTAAGT\tIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:3A17\tNM:i:1\n+1334311-1\t0\tchrM\t4179\t255\t23M\t*\t0\t0\tCAACTTCCTACCACTCACCCTAG\tIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:0A22\tNM:i:1\n+1337331-1\t16\tchrM\t5672\t255\t24M\t*\t0\t0\tTTAAACCCACAAACACATAGTTAA\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:16T7\tNM:i:1\n+1337660-1\t0\tchrM\t3110\t255\t31M\t*\t0\t0\tCAAATTCCTCCCTGTACAAAAGGACAAGAGA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:17G13\tNM:i:1\n+1338772-1\t0\tchrM\t12145\t255\t23M\t*\t0\t0\tTAGTTTAACCAAAACATCAGATT\tIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:23\tNM:i:0\n+1345449-1\t0\tchrM\t1517\t255\t21M\t*\t0\t0\tACATCTAACTAAAACCCCTAC\tIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:4T16\tNM:i:1\n+1350032-1\t0\tchrM\t7398\t255\t22M\t*\t0\t0\tCCCCCACCCTACCACACATTCG\tIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:22\tNM:i:0\n+1350956-1\t16\tchrM\t10954\t255\t26M\t*\t0\t0\tCCTAATACTAACTACCTGACTCCTAC\tIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:26\tNM:i:0\n' |
| b |
| diff -r 000000000000 -r 4dbe81be8b81 test-data/out.clusters --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.clusters Tue Dec 06 03:28:59 2016 -0500 |
| b |
| @@ -0,0 +1,12 @@ +Chromosome,Strand,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ModeScore,ConversionLocationCount,ConversionEventCount,NonConversionEventCount +chrM,+,587,611,G1.1,CTTACCTCCTCAAAGCAATACACTG,35,611,0.7144525084717777,3,3,193 +chrM,+,1011,1046,G7.1,CAAAATAGACTACGAAAGTGGCTTTAACATATCTGA,59,1014,0.766829880927257,4,6,293 +chrM,+,1356,1380,G11.1,AAATGGGCTACATTTTCTACCCCAG,8,1356,0.9528781135391861,2,4,45 +chrM,+,1504,1538,G13.1,TATACTTCAAAGGACATTTAACTAAAACCCCTACG,29,1504,0.7008871509609117,3,4,187 +chrM,+,3644,3668,G28.1,TTTACTCAATCCTCTGATCAGGGTG,6,3668,0.8442721693981579,2,2,49 +chrM,+,4687,4709,G33.1,CTATCCTCTTCAACAATATACTC,10,4701,0.685344790998179,2,2,77 +chrM,+,10099,10126,G44.1,CCTTACTACTAATAATTATTACATTTTG,20,10126,0.7036352727446128,9,18,198 +chrM,+,10234,10253,G45.1,CTATTACCTTCTTATTATTT,15,10242,0.628246444540548,6,13,167 +chrM,+,11800,11825,G54.1,ACTTCAAACTCTACTCCCACTAATAG,17,11811,0.6746533466968669,2,4,114 +chrM,+,15624,15650,G61.1,CCCTATTACTATCCATCCTCATCCTAG,11,15650,0.8565998761927102,2,2,94 +chrM,-,5656,5682,G66.1,TGTGGGTTTAAGTCCCATTGGTCTAGT,15,5672,0.7398246560751324,2,3,105 |
| b |
| diff -r 000000000000 -r 4dbe81be8b81 test-data/out.distribution --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.distribution Tue Dec 06 03:28:59 2016 -0500 |
| b |
| b'@@ -0,0 +1,280 @@\n+chrM,+,578,611,G1,Signal,0.002215647350437845,0.0025486490996327505,0.0033512306533325857,0.005059926789592,0.008260756395008636,0.013505626784301462,0.020954059234529792,0.0299782652199515,0.03902923011456293,0.04603875436594269,0.04932580211518826,0.048549865619717206,0.04507348177805402,0.04138678690001441,0.03983936113740914,0.04138679170454176,0.04507351237933689,0.04855003695006115,0.049326660206632095,0.04604260006541274,0.03904465287539063,0.030033612204165668,0.021131793374589248,0.014016358479580942,0.009574043926603193,0.008081769737601222,0.009573216446614694,0.01401251767427011,0.021116371313953223,0.029978265309591256,0.03886691874560019,0.04553186837118595,0.04801337267513411,0.04552819400205986\n+chrM,+,578,611,G1,Background,1.2209048315730615E-4,3.603238285450243E-4,9.559550867440201E-4,0.0022779221908931983,0.004876088785336435,0.009382835444954649,0.016249985649528738,0.025379874349871386,0.03586215677280685,0.04608121943793897,0.05427979312372392,0.05931572711065931,0.0611219767112613,0.060536792404385836,0.058631311609363024,0.056029645033997225,0.0526765212803818,0.04813534596942365,0.042138060399237634,0.03500734640599324,0.027718228641336412,0.021596812771857963,0.017825436503422994,0.016980490259316434,0.018791842691639787,0.02222709251884686,0.025887063882603797,0.02855187683822939,0.029601733952503588,0.02907822833494162,0.027388045408612983,0.02491204781067512,0.02182373115482499,0.01819639715298444\n+chrM,+,578,611,G1,ConversionPercent,0.0,0.0,0.0,-1.0,0.0,-1.0,0.0,-1.0,-1.0,-1.0,0.029411764705882353,0.0,-1.0,-1.0,-1.0,0.0,-1.0,-1.0,0.02857142857142857,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,0.0,-1.0,-1.0,-1.0,-1.0,0.043478260869565216,-1.0\n+chrM,+,578,611,G1,ReadCount,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,31.0,34.0,35.0,35.0,35.0,35.0,35.0,35.0,35.0,35.0,35.0,35.0,35.0,35.0,35.0,34.0,34.0,34.0,34.0,34.0,32.0,32.0,27.0,23.0,18.0\n+chrM,+,618,648,G2,Signal,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN\n+chrM,+,618,648,G2,Background,0.02036593717344964,0.021545016307393333,0.02075732208426233,0.0185385704974925,0.016058912714066974,0.014760904679190731,0.01587828157972765,0.01998982972281574,0.02675320351637033,0.034960239754755124,0.04297654071640097,0.049405220789464195,0.0535841168786108,0.05557022229372446,0.05566645347184046,0.05396985366953199,0.05040911572029058,0.045246285093177935,0.039518458485473036,0.03488986269786294,0.032873809743312964,0.0339156693702837,0.03697349270669586,0.03992163497504548,0.0405773797250822,0.03775485498814145,0.031740787708163055,0.02397583483668845,0.016233937121823184,0.00984391561814854,0.005344335360713711\n+chrM,+,618,648,G2,ConversionPercent,0.0,0.0,0.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,0.0,-1.0,-1.0,-1.0,-1.0,0.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,0.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0\n+chrM,+,618,648,G2,ReadCount,3.0,3.0,3.0,3.0,3.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,16.0,15.0,15.0,15.0,15.0,12.0,8.0\n+chrM,+,654,686,G3,Signal,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN\n+chrM,+,654,686,G3,Background,9.953220102971815E-6,1.530861346254756E-5,3.4459806098020246E-5,9.56647447663998E-5,2.703927121931167E-4,7.156912204090039E-4,0.0017279294897960494,0.0037779223946685474,0.007470826216486843,0.013375154593952448,0.021727452676785997,0.03213384667308052,0.04347354298646796,0.05415125272851285,0.06262891229168409,0.0679435512978882,0.06990212205245414,0.06888842192866376,0.06551603097147045,0.06043232198241675,0.054358735453526506,0.04817522015940096,0.04280950214078691,0.03891328055327392,0.0365574417508949,0.03520259290589588,0.033987762494036323,0.032142988084991456,0.0292760506293448,0.025420689661975606,0.020909335909571714,0.01620204530591941,0.011753596349020758\n+chrM,+,654,686,G3,ConversionPercent,0.0,0.0,0.0,-1.0,-1.0,'..b'9097391205,0.033429949757332385,0.02562379870962735,0.01795848213827771,0.011468225361533217,0.006650105326922155,0.003490804270966266,0.001654570637333493\n+chrM,-,7451,7514,G69,ConversionPercent,0.0,0.0,-1.0,-1.0,0.0,0.0,-1.0,-1.0,0.0,0.0,-1.0,-1.0,-1.0,0.0,0.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,0.0,0.5,0.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,0.0,0.0,-1.0,-1.0,-1.0,0.0,0.0,-1.0,-1.0,-1.0,-1.0,0.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,0.0,-1.0,-1.0,0.047619047619047616,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0\n+chrM,-,7451,7514,G69,ReadCount,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,10.0,10.0,12.0,18.0,18.0,19.0,19.0,21.0,21.0,21.0,23.0,23.0,23.0,23.0,23.0,23.0,23.0,23.0,23.0,23.0,23.0,21.0,21.0,19.0,19.0,19.0,19.0,19.0,18.0,16.0\n+chrM,-,14671,14729,G70,Signal,6.790172814387105E-4,6.790176204912454E-4,6.790199494931065E-4,6.790342308940637E-4,6.791123755632963E-4,6.794937478165981E-4,6.81152828911359E-4,6.875818129080967E-4,7.097525681164913E-4,7.777167122569575E-4,9.626372105322135E-4,0.0014083132307271427,0.002357109742838275,0.004134215911407174,0.00704514291562569,0.01117498405876473,0.016164143390529916,0.021122369114592737,0.024829983852440316,0.026209674109281496,0.02482998385265352,0.02112236911693099,0.01616414341334034,0.01117498425788014,0.007045144470951239,0.0041342267827401665,0.0023571777397750964,0.0014086938063408952,9.645432751591733E-4,7.86259101262961E-4,7.440108931094448E-4,8.105231587346287E-4,0.0010759507512997561,0.0018139736633060192,0.0035962963718324343,0.007391404275607729,0.014499814668482368,0.026143520356354574,0.042662884589858195,0.06261952187284268,0.08245242476397563,0.09728288371483014,0.10280164474208038,0.09728288371477685,0.08245242476339106,0.06261952186714008,0.04266288454007934,0.02614351996752319,0.014499811950649118,0.007391387276373524,0.003596201227928996,0.0018134971471492794,0.0010738151540482554,8.019585774863904E-4,7.132755566528118E-4,6.875596206658617E-4,6.809232962868179E-4,6.793978072736109E-4,6.790852285966797E-4\n+chrM,-,14671,14729,G70,Background,0.0021886785503851813,0.003234984469373231,0.004290855302994767,0.0051274583569229076,0.0055717735777897496,0.005622348623005156,0.005493655402569303,0.005544445917423097,0.006117341795906193,0.007377725205161006,0.00924654455675428,0.011466978284900335,0.013761847030135638,0.015982915166130946,0.01816648188278695,0.020479126391088388,0.023100848102688445,0.026103856126156805,0.029364065545125554,0.032536021887763715,0.03512742632736429,0.03667743522356292,0.036965149046051644,0.03612306926700893,0.034576628425249535,0.03284863249555021,0.03135092440094212,0.030266916116775098,0.029545816189600765,0.028969513676197108,0.028252659136569745,0.02715768456929971,0.02560258158850639,0.0237179530176939,0.02181623297966202,0.02028251195630798,0.01943959432020946,0.01943865983052428,0.02019764833268929,0.021396094513783267,0.022541281710240113,0.023108593100962086,0.022714294574895422,0.021241280284484056,0.01885415169287598,0.015905001553728648,0.012793719538045855,0.009859491451874926,0.0073406255537767666,0.005385151826186241,0.004067600839354729,0.0033828284152757075,0.0032253885041158953,0.0033884424640267374,0.0036089819998165176,0.003652202815899496,0.0033936926989137127,0.0028520395639691264,0.002154147822948095\n+chrM,-,14671,14729,G70,ConversionPercent,-1.0,0.0,-1.0,-1.0,0.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,0.0,-1.0,-1.0,-1.0,0.0,-1.0,-1.0,0.09090909090909091,-1.0,0.0,0.0,-1.0,-1.0,0.0,-1.0,-1.0,0.0,-1.0,-1.0,0.0,0.0,-1.0,-1.0,0.0,-1.0,0.0,-1.0,-1.0,0.0,0.0,0.6666666666666666,0.0,0.0,-1.0,-1.0,0.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,0.0,-1.0,-1.0,-1.0\n+chrM,-,14671,14729,G70,ReadCount,1.0,1.0,2.0,3.0,6.0,6.0,8.0,8.0,8.0,9.0,9.0,9.0,10.0,11.0,11.0,11.0,11.0,11.0,11.0,11.0,11.0,12.0,13.0,13.0,13.0,13.0,13.0,13.0,13.0,10.0,9.0,10.0,8.0,6.0,6.0,6.0,5.0,5.0,5.0,7.0,7.0,7.0,6.0,5.0,5.0,4.0,4.0,4.0,4.0,4.0,4.0,4.0,4.0,4.0,4.0,4.0,4.0,4.0,4.0\n' |
| b |
| diff -r 000000000000 -r 4dbe81be8b81 test-data/out.groups --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.groups Tue Dec 06 03:28:59 2016 -0500 |
| b |
| @@ -0,0 +1,71 @@ +Chromosome,Strand,GroupStart,GroupEnd,GroupID,GroupSequence,ReadCount,ConversionLocationCount,ConversionEventCount +chrM,+,578,611,G1,TTTATGTAGCTTACCTCCTCAAAGCAATACACTG,35,3,3 +chrM,+,618,648,G2,TTTAGACGGGCTCACATCACCCCATAAACAA,16,0,0 +chrM,+,654,686,G3,TTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAA,5,0,0 +chrM,+,698,769,G4,CAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAG,108,1,2 +chrM,+,787,817,G5,CTTAGCCTAGCCACACCCCCACGGGAAACAG,7,0,0 +chrM,+,856,934,G6,AGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAATAGAAGCCGG,16,0,0 +chrM,+,987,1057,G7,AGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACACACAATAG,60,4,6 +chrM,+,1080,1198,G8,ATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA,51,1,2 +chrM,+,1218,1275,G9,ATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATACCGCCATCTTCAGCA,43,0,0 +chrM,+,1286,1355,G10,AAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAG,11,0,0 +chrM,+,1356,1476,G11,AAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCG,169,4,7 +chrM,+,1477,1503,G12,TACACACCGCCCGTCACCCTCCTCAAG,10,0,0 +chrM,+,1504,1569,G13,TATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAAGTCGTAACATG,56,4,6 +chrM,+,1578,1771,G14,ACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAACCTGGCGC,99,2,2 +chrM,+,1777,1873,G15,ATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATA,19,1,1 +chrM,+,1878,1937,G16,TGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAA,6,0,0 +chrM,+,1959,1990,G17,CAAAATAGTGGGAAGATTTATAGGTAGAGGCG,5,0,0 +chrM,+,1991,2019,G18,ACAAACCTACCGAGCCTGGTGATAGCTGG,5,0,0 +chrM,+,2032,2108,G19,GAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTCCAAAGAGG,14,0,0 +chrM,+,2109,2187,G20,AACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCC,11,0,0 +chrM,+,2203,2306,G21,GTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTA,29,1,2 +chrM,+,2323,2461,G22,ATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAAAAA,52,2,2 +chrM,+,2497,2527,G23,TTTACCAAAAACATCACCTCTAGCATCACCA,5,1,1 +chrM,+,2644,2684,G24,AGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACC,8,1,1 +chrM,+,2778,2923,G25,TCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAG,16,1,1 +chrM,+,2944,3052,G26,CAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAA,20,1,1 +chrM,+,3110,3277,G27,CAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAG,84,3,64 +chrM,+,3636,3670,G28,CCTAGCCGTTTACTCAATCCTCTGATCAGGGTGAG,6,2,2 +chrM,+,3671,3698,G29,CATCAAACTCAAACTACGCCCTGATCGG,6,0,0 +chrM,+,3746,3776,G30,CCATCATTCTACTATCAACATTACTAATAAG,9,0,0 +chrM,+,4293,4330,G31,ATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCT,8,1,1 +chrM,+,4402,4463,G32,AGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCC,25,0,0 +chrM,+,4687,4715,G33,CTATCCTCTTCAACAATATACTCTCCGGA,10,2,2 +chrM,+,5055,5093,G34,TACAACCCTAACATAACCATTCTTAATTTAACTATTTAT,5,1,2 +chrM,+,5113,5140,G35,CATTCCTACTACTCAACTTAAACTCCAG,6,0,0 +chrM,+,6250,6276,G36,CTATAGTGGAGGCCGGAGCAGGAACAG,6,1,1 +chrM,+,6334,6360,G37,ACCTAACCATCTTCTCCTTACACCTAG,10,1,3 +chrM,+,6478,6505,G38,CAGTCCTACTTCTCCTATCTCTCCCAGT,12,0,0 +chrM,+,6518,6564,G39,CATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCG,7,1,1 +chrM,+,8295,8364,G40,CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA,10,1,1 +chrM,+,8365,8387,G41,AATGCCCCAACTAAATACTACCG,5,1,1 +chrM,+,8670,8719,G42,ACTAATCAAACTAACCTCAAAACAAATGATAACCATACACAACACTAAAG,23,2,2 +chrM,+,9991,10048,G43,ACTCTTTTAGTATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCA,14,1,1 +chrM,+,10099,10126,G44,CCTTACTACTAATAATTATTACATTTTG,20,9,18 +chrM,+,10234,10254,G45,CTATTACCTTCTTATTATTTG,15,6,13 +chrM,+,10291,10318,G46,CCCTACAAACAACTAACCTGCCACTAAT,5,0,0 +chrM,+,10405,10467,G47,TGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATTATGATAATCATATTTACC,10,0,0 +chrM,+,10538,10564,G48,CTCACACCTCATATCCTCCCTACTATG,11,0,0 +chrM,+,10696,10730,G49,CCCTACTAGTCTCAATCTCCAACACATATGGCCTA,6,1,2 +chrM,+,10972,10993,G50,ACTCCTACCCCTCACAATCATG,9,1,1 +chrM,+,11193,11222,G51,CAGGCACATACTTCCTATTCTACACCCTAG,5,0,0 +chrM,+,11378,11425,G52,ATACCTCTTTACGGACTCCACTTATGACTCCCTAAAGCCCATGTCGAA,7,1,1 +chrM,+,11643,11679,G53,CCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTG,10,1,1 +chrM,+,11800,11825,G54,ACTTCAAACTCTACTCCCACTAATAG,17,2,4 +chrM,+,12138,12242,G55,GTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCA,47,0,0 +chrM,+,12266,12325,G56,ACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCC,19,0,0 +chrM,+,12584,12610,G57,ACTACTTCTCCATAATATTCATCCCTG,7,0,0 +chrM,+,12900,12923,G58,ATTTATCCTACACTCCAACTCATG,5,1,1 +chrM,+,13146,13172,G59,CCCACTAATCCAAACTCTAACACTATG,14,0,0 +chrM,+,14839,14865,G60,AAACTTCGGCTCACTCCTTGGCGCCTG,7,1,1 +chrM,+,15624,15650,G61,CCCTATTACTATCCATCCTCATCCTAG,11,2,2 +chrM,+,15919,15954,G62,TGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAA,16,1,1 +chrM,-,4328,4364,G63,GATTCTCAGGGATGGGTTCGATTCTCATAGTCCTAGA,10,0,0 +chrM,-,4365,4400,G64,TAGGATGGGGTGTGATAGGTGGCACGGAGAATTTTG,20,0,0 +chrM,-,5585,5655,G65,AAGGGCTTAGCTTAATTAAAGTGGCTGATTTGCGTTCAGTTGATGCAGAGTGGGGTTTTGCAGTCCTTAGC,12,0,0 +chrM,-,5656,5695,G66,TTAACTAAGTGTTTGTGGGTTTAAGTCCCATTGGTCTAGT,15,2,3 +chrM,-,5756,5789,G67,AAGAAGCAGCTTCAAACCTGCCGGGGCTTCTCCC,6,0,0 +chrM,-,5795,5853,G68,AAGACAGGGGTTAGGCCTCTTTTTACCAGCTCCGAGGTGATTTTCATATTGAATTGCAA,9,0,0 +chrM,-,7451,7514,G69,GAAAAAGTCATGGAGGCCATGGGGTTGGCTTGAAACCAGCTTTGGGGGGTTCGATTCCTTCCTT,25,2,2 +chrM,-,14671,14729,G70,AAATACAACGATGGTTTTTCATATCATTGGTCGTGGTTGTAGTCCGTGCGAGAATAATG,17,2,5 |
| b |
| diff -r 000000000000 -r 4dbe81be8b81 test-data/out_PARalyzer_Utilized.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_PARalyzer_Utilized.sam Tue Dec 06 03:28:59 2016 -0500 |
| b |
| b'@@ -0,0 +1,953 @@\n+@SQ\tSN:chrM\tLN:16569\n+3122-56\t0\tchrM\t720\t255\t21M\t*\t0\t0\tTTCACCCTCTAAATCACCACG\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+4366-41\t0\tchrM\t3197\t255\t23M\t*\t0\t0\tCATTATACCCACACCCACCCAAG\tIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:0T22\tNM:i:1\n+4748-37\t0\tchrM\t1450\t255\t20M\t*\t0\t0\tCTTAGTTGAACAGGGCCCTG\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\tNM:i:0\n+5000-35\t0\tchrM\t1645\t255\t25M\t*\t0\t0\tATTTCAACTTAACTTGACCGCTCTG\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:25\tNM:i:0\n+7405-24\t0\tchrM\t1450\t255\t25M\t*\t0\t0\tCTTAGTTGAACAGGGCCCTGAAGCG\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:25\tNM:i:0\n+8670-21\t0\tchrM\t1423\t255\t20M\t*\t0\t0\tATTTAGCAGTAAACTGAGAG\tIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:15A4\tNM:i:1\n+11115-17\t0\tchrM\t1114\t255\t24M\t*\t0\t0\tTTAAATCAACAAAACTGCTCGCCA\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:24\tNM:i:0\n+11953-16\t0\tchrM\t1253\t255\t21M\t*\t0\t0\tCCTATATACCGCCATCTTCAG\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+13131-15\t0\tchrM\t1539\t255\t21M\t*\t0\t0\tCATTTATATAGAGGAGACAAG\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+15971-12\t0\tchrM\t1423\t255\t23M\t*\t0\t0\tATTTAGCAGTAAACTGAGAGTAG\tIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:15A7\tNM:i:1\n+19590-10\t0\tchrM\t1025\t255\t21M\t*\t0\t0\tAAAGTGGCTTTAACATATCTG\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+19914-10\t0\tchrM\t8670\t255\t28M\t*\t0\t0\tACTAATCAAACTAACCTCAAAACAAATG\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:28\tNM:i:0\n+20885-10\t0\tchrM\t11800\t255\t26M\t*\t0\t0\tACTTCAAACTCTACTCCCACTAATAG\tIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:26\tNM:i:0\n+21266-9\t0\tchrM\t1093\t255\t21M\t*\t0\t0\tCTTAGCCCTAAACCTCAACAG\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+22033-9\t0\tchrM\t4422\t255\t20M\t*\t0\t0\tCTATCGGGCCCATACCCCGA\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\tNM:i:0\n+24420-8\t0\tchrM\t992\t255\t27M\t*\t0\t0\tTAAAAAACTCCAGTTGACACAAAATAG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+24637-8\t0\tchrM\t741\t255\t26M\t*\t0\t0\tATCAAAAGGGACAAGCATCAAGCACG\tIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:9A16\tNM:i:1\n+25285-8\t0\tchrM\t12207\t255\t21M\t*\t0\t0\tGAGAAAGCTCACAAGAACTGC\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+25854-8\t0\tchrM\t3197\t255\t22M\t*\t0\t0\tCATTATACCCACACCCACCCAA\tIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:0T21\tNM:i:1\n+26165-8\t0\tchrM\t1682\t255\t28M\t*\t0\t0\tCCCCAAACCCACTCCACCTTACTACCAG\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:28\tNM:i:0\n+26412-8\t0\tchrM\t587\t255\t25M\t*\t0\t0\tCTTACCTCCTCAAAGCAATACACTG\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:25\tNM:i:0\n+26513-8\t0\tchrM\t1517\t255\t22M\t*\t0\t0\tACATTTAACTAAAACCCCTACG\tIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:22\tNM:i:0\n+26793-8\t0\tchrM\t623\t255\t26M\t*\t0\t0\tACGGGCTCACATCACCCCATAAACAC\tIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:25A0\tNM:i:1\n+29748-7\t0\tchrM\t1477\t255\t27M\t*\t0\t0\tTACACACCGCCCGTCACCCTCCTCAAG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+32129-7\t0\tchrM\t11658\t255\t22M\t*\t0\t0\tCCATTCTCATCCAAACCCCCTG\tIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:22\tNM:i:0\n+32919-6\t0\tchrM\t10538\t255\t27M\t*\t0\t0\tCTCACACCTCATATCCTCCCTACTATG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+34500-6\t0\tchrM\t1539\t255\t20M\t*\t0\t0\tCATTTATATAGAGGAGACAA\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\tNM:i:0\n+37673-6\t16\tchrM\t4371\t255\t30M\t*\t0\t0\tTCTCCGTGCCACCTATCACACCCCATCCTA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:30\tNM:i:0\n+38072-6\t0\tchrM\t13146\t255\t27M\t*\t0\t0\tCCCACTAATCCAAACTCTAACACTATG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+39034-5\t0\tchrM\t1228\t255\t20M\t*\t0\t0\tATCAACCTCACCACCTCTTG\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\tNM:i:0\n+39340-5\t0\tchrM\t15624\t255\t27M\t*\t0\t0\tCCCTATTACTATCCATCCTCATCCTAG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+40359-5\t0\tchrM\t1448\t255\t27M\t*\t0\t0\tTGCTTAGTTGAACAGGGCCCTGAAGCG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+42562-5\t0\tchrM\t587\t255\t22M\t*\t0\t0\tCTTACCTCCTCAAAGCAATACA\tIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:22\tNM:i:0\n+42853-5\t0\tchrM\t903\t255\t28M\t*\t0\t0\tTCACACGATTAACCCAAGTCAATAGAAG\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:28\tNM:i:0\n+43258-5\t0\tchrM\t1416\t255\t25M\t*\t0\t0\tAAGGTGGATTTAGCAGTAAACTGAG\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:22A2\tNM:i:1\n+43464-5\t0\tchrM\t6542\t255\t23M\t*\t0\t0\tCAACCTCAACACCACCTTCTTCG\tIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:23\tNM:i:0\n+44314-5\t0\tchrM\t1253\t255\t20M\t*\t0\t0\tCCTATATACCGCCATCTTCA\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\t'..b'ATTCCTCTTCTTAACACCA\tIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:20A2\tNM:i:1\n+1291753-1\t0\tchrM\t910\t255\t21M\t*\t0\t0\tATTAACCCAAGTCAATAGAAG\tIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:21\tNM:i:0\n+1294271-1\t0\tchrM\t8698\t255\t22M\t*\t0\t0\tATAACCATACACAACACCAAAG\tIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:17T4\tNM:i:1\n+1294286-1\t0\tchrM\t1402\t255\t24M\t*\t0\t0\tAAACTTAAGGGTCGAAGGGGGATT\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:18T5\tNM:i:1\n+1295492-1\t0\tchrM\t4302\t255\t24M\t*\t0\t0\tATAATAGGAGCTTAAACCCCCTTA\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:24\tNM:i:0\n+1298968-1\t0\tchrM\t5055\t255\t27M\t*\t0\t0\tTACAACCCTAACATAACCATTCTTAAT\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:27\tNM:i:0\n+1300275-1\t0\tchrM\t1619\t255\t28M\t*\t0\t0\tCAAAGCACCCAACTTACACTTAGGAGAT\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:28\tNM:i:0\n+1300703-1\t0\tchrM\t3032\t255\t20M\t*\t0\t0\tGTTCGTTTGTTCAACGATTA\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\tNM:i:0\n+1301615-1\t0\tchrM\t7139\t255\t28M\t*\t0\t0\tCCATTTCACTATCATATTCATCGGCGTA\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:28\tNM:i:0\n+1302286-1\t0\tchrM\t1218\t255\t27M\t*\t0\t0\tATAAACCCCGATCAACATCACCACCTC\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:16C10\tNM:i:1\n+1303593-1\t0\tchrM\t787\t255\t27M\t*\t0\t0\tCTTAGCCTAGCCACACCCCCATGGGAA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:21C5\tNM:i:1\n+1304414-1\t0\tchrM\t10022\t255\t20M\t*\t0\t0\tCCAATTAACTAGTTTTGACA\tIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:20\tNM:i:0\n+1306285-1\t0\tchrM\t10327\t255\t36M\t*\t0\t0\tCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:36\tNM:i:0\n+1307553-1\t0\tchrM\t11193\t255\t30M\t*\t0\t0\tCCGGCACATACTTCCTATTCTACACCCTAG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:1A28\tNM:i:1\n+1315185-1\t16\tchrM\t4377\t255\t24M\t*\t0\t0\tTGCCACCTATCACACACCATCCTA\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:15C8\tNM:i:1\n+1315758-1\t16\tchrM\t4328\t255\t21M\t*\t0\t0\tGCTAGGACTATGAGAATCGAA\tIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:0T20\tNM:i:1\n+1316317-1\t0\tchrM\t11923\t255\t26M\t*\t0\t0\tCTCAAATATCACTCTCCTACTTACAG\tIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:0A25\tNM:i:1\n+1316768-1\t0\tchrM\t1904\t255\t25M\t*\t0\t0\tCCGAAACCAGACGAGCTACCTAAGA\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:25\tNM:i:0\n+1320780-1\t0\tchrM\t4687\t255\t25M\t*\t0\t0\tCTATCCTCTTCAACAATATACTCTC\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:25\tNM:i:0\n+1321276-1\t0\tchrM\t2032\t255\t25M\t*\t0\t0\tGAATCGTAGTTCAACTTTAAATTTG\tIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:5T19\tNM:i:1\n+1321453-1\t0\tchrM\t2114\t255\t27M\t*\t0\t0\tCTCTTTGGACACTAGGAAAAAACCTAG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:25T1\tNM:i:1\n+1322102-1\t0\tchrM\t8038\t255\t28M\t*\t0\t0\tTATAATAATTACATCACAAGACGTCTTG\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:28\tNM:i:0\n+1323531-1\t0\tchrM\t6518\t255\t20M\t*\t0\t0\tCATCACTATACCACTAACAG\tIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:11T8\tNM:i:1\n+1324159-1\t0\tchrM\t3180\t255\t24M\t*\t0\t0\tATATCATCTCAACTTAGCATTATA\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:17T6\tNM:i:1\n+1324512-1\t16\tchrM\t5803\t255\t24M\t*\t0\t0\tCAATATGAAAATCACCTCGGAGCG\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:23T0\tNM:i:1\n+1324879-1\t0\tchrM\t2656\t255\t29M\t*\t0\t0\tTCTCTTACTTTTAACCAGTGAAATTGACC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:29\tNM:i:0\n+1328459-1\t0\tchrM\t10234\t255\t20M\t*\t0\t0\tCTATTACCTTCTTATTATTC\tIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:19T0\tNM:i:1\n+1329464-1\t0\tchrM\t732\t255\t29M\t*\t0\t0\tATCACCACGATCAAAAGGGACAAGCATCA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:18A10\tNM:i:1\n+1330044-1\t0\tchrM\t8309\t255\t21M\t*\t0\t0\tCTTGGCATTAACCTTTTAAGT\tIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:3A17\tNM:i:1\n+1334311-1\t0\tchrM\t4179\t255\t23M\t*\t0\t0\tCAACTTCCTACCACTCACCCTAG\tIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:0A22\tNM:i:1\n+1337331-1\t16\tchrM\t5672\t255\t24M\t*\t0\t0\tTTAAACCCACAAACACATAGTTAA\tIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:16T7\tNM:i:1\n+1337660-1\t0\tchrM\t3110\t255\t31M\t*\t0\t0\tCAAATTCCTCCCTGTACAAAAGGACAAGAGA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:17G13\tNM:i:1\n+1338772-1\t0\tchrM\t12145\t255\t23M\t*\t0\t0\tTAGTTTAACCAAAACATCAGATT\tIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:23\tNM:i:0\n+1345449-1\t0\tchrM\t1517\t255\t21M\t*\t0\t0\tACATCTAACTAAAACCCCTAC\tIIIIIIIIIIIIIIIIIIIII\tXA:i:1\tMD:Z:4T16\tNM:i:1\n+1350032-1\t0\tchrM\t7398\t255\t22M\t*\t0\t0\tCCCCCACCCTACCACACATTCG\tIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:22\tNM:i:0\n+1350956-1\t16\tchrM\t10954\t255\t26M\t*\t0\t0\tCCTAATACTAACTACCTGACTCCTAC\tIIIIIIIIIIIIIIIIIIIIIIIIII\tXA:i:0\tMD:Z:26\tNM:i:0\n' |
| b |
| diff -r 000000000000 -r 4dbe81be8b81 tool-data/lastz_seqs.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/lastz_seqs.loc.sample Tue Dec 06 03:28:59 2016 -0500 |
| b |
| @@ -0,0 +1,30 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of 2bit genome files for use with Lastz. You will +#need to supply these files and then create a lastz_seqs.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The lastz_seqs.loc +#file has this format (white space characters are TAB characters): +# +#<unique_build_id> <display_name> <file_path> +# +#So, for example, if your lastz_seqs.loc began like this: +# +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit +# +#then your /depot/data2/galaxy/twobit/ directory +#would need to contain the following 2bit files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit +# +#Your lastz_seqs.loc file should include an entry per line for +#each file you have stored that you want to be available. Note that +#your files should all have the extension '2bit'. +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. +# |
| b |
| diff -r 000000000000 -r 4dbe81be8b81 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Dec 06 03:28:59 2016 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="lastz_seqs" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/lastz_seqs.loc" /> + </table> +</tables> |