| Previous changeset 3:b16228ec1540 (2017-11-09) Next changeset 5:daf29b40670f (2022-10-22) |
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Commit message:
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3 |
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modified:
hicup_filter.xml hicup_macros.xml test-data/HiCUP_summary_report.txt test-data/dataset1.fastq test-data/dataset1.mapper_barchart.svg test-data/dataset1.truncation_barchart.svg test-data/dataset2.fastq test-data/dataset2.mapper_barchart.svg test-data/dataset2.truncation_barchart.svg test-data/digester_file.txt test-data/hicup_deduplicator_summary.txt test-data/hicup_filter_summary.txt test-data/hicup_mapper_summary.txt test-data/hicup_truncater_summary.txt |
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added:
test-data/HiCUP_summary_report.html test-data/chr21And22FromHg38.fasta test-data/dataset1.trunc.fastq.gz test-data/dataset1_2.ditag_size_distribution.svg test-data/dataset1_2.filt.bam test-data/dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg test-data/dataset1_2.filt.bam.deduplicator_uniques_barchart.svg test-data/dataset1_2.hicup.bam test-data/dataset1_2.pair.bam test-data/dataset1_2.pair.bam.filter_piechart.svg test-data/dataset1_2_contiguous.filter.bam test-data/dataset1_2_invalid.filter.bam test-data/dataset1_2_re_ligation.filter.bam test-data/dataset1_2_same_circularised.filter.bam test-data/dataset1_2_same_dangling_ends.filter.bam test-data/dataset1_2_same_internal.filter.bam test-data/dataset2.trunc.fastq.gz |
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removed:
test-data/chr1.fa test-data/dataset.contiguous.filter.sam test-data/dataset.filt.sam test-data/dataset.hicup.sam test-data/dataset.invalid.filter.sam test-data/dataset.re_ligation.filter.sam test-data/dataset.same_circularised.filter.sam test-data/dataset.same_dangling_ends.filter.sam test-data/dataset.same_internal.filter.sam test-data/dataset1.trunc.fastq test-data/dataset2.trunc.fastq test-data/deduplicator_cis_trans_piechart.svg test-data/deduplicator_uniques_barchart.svg test-data/filter_piechart.svg test-data/result.pair.sam test-data/results.html |
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| diff -r b16228ec1540 -r a7bbbf32da62 hicup_filter.xml --- a/hicup_filter.xml Thu Nov 09 11:16:04 2017 -0500 +++ b/hicup_filter.xml Fri May 25 17:49:27 2018 -0400 |
| [ |
| @@ -1,59 +1,64 @@ -<tool id="hicup_filter" name="Hicup Filter" version="@VERSION@.0"> - <description>classifies read pairs, identifying valid Hi-C di-tags.</description> +<tool id="hicup_filter" name="Hicup Filter" version="@VERSION@.0" profile="18.01"> + <description>classifies read pairs, identifying valid Hi-C di-tags</description> <macros> <import>hicup_macros.xml</import> </macros> - <expand macro="requirements_hicup" /> - <expand macro="stdio" /> - <command><![CDATA[ - hicup_filter --digest '$digest' + <expand macro="requirements_hicup"/> + <command detect_errors="exit_code"><![CDATA[ + #for $i, $file in enumerate($inputFiles): + #if $file.ext != 'sam': + ln -s '$file' ./${i}.bam && + #end if + #end for + hicup_filter --zip --digest '$digest' #if $advanced_options.longest: --longest '$advanced_options.longest' #end if #if $advanced_options.shortest: --shortest '$advanced_options.shortest' #end if - #for $file in $inputFiles: - $file + #for $i, $file in enumerate($inputFiles): + #if $file.ext != 'sam': + ./${i}.bam + #else: + '$file' + #end if #end for - && mv hicup_filter_ditag_rejects* hicup_filter_ditag_rejects - && mv *filt.sam dataset.filt.sam - && mv hicup_filter_summary* hicup_filter_summary.txt - && mv hicup_filter_ditag_rejects/*contiguous.filter.sam hicup_filter_ditag_rejects/dataset.contiguous.filter.sam - && mv hicup_filter_ditag_rejects/*re_ligation.filter.sam hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam - && mv hicup_filter_ditag_rejects/*same_dangling_ends.filter.sam hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam - && mv hicup_filter_ditag_rejects/*invalid.filter.sam hicup_filter_ditag_rejects/dataset.invalid.filter.sam - && mv hicup_filter_ditag_rejects/*same_circularised.filter.sam hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam - && mv hicup_filter_ditag_rejects/*same_internal.filter.sam hicup_filter_ditag_rejects/dataset.same_internal.filter.sam - #if $advanced_options.longest or $advanced_options.shortest: - && mv hicup_filter_ditag_rejects/*wrong_size.filter.sam hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam - #end if - - && mv *filter_piechart.svg filter_piechart.svg ]]></command> <inputs> - <param name="inputFiles" type="data" multiple="true" format="bam,sam" label="Input"/> + <param name="inputFiles" type="data" multiple="true" format="sam,qname_sorted.bam" label="Input files in BAM or SAM fomat"/> <param argument="--digest" type="data" format="txt" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/> <section name="advanced_options" title="Advanced options"> <expand macro="filter_longest_shortest" /> </section> </inputs> <outputs> - <expand macro="filter_output" /> + <data name="dataset_filt" format="qname_sorted.bam" from_work_dir="*.filt.bam" label="filt.bam" /> + <data name="hicup_filter_summary" format="txt" from_work_dir="hicup_filter_summary*.txt" label="hicup_filter_summary.txt" /> + <data name="contiguous_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*contiguous.filter.bam" label="contiguous.filter.bam" /> + <data name="re_ligation_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*re_ligation.filter.bam" label="re_ligation.filter.bam" /> + <data name="same_dangling_ends_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_dangling_ends.filter.bam" label="same_dangling_ends.filter.bam" /> + <data name="invalid_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*invalid.filter.bam" label="invalid.filter.bam" /> + <data name="same_circularised_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_circularised.filter.bam" label="same_circularised.filter.bam" /> + <data name="same_internal_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_internal.filter.bam" label="same_internal.filter.bam" /> + <data name="wrong_size_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*wrong_size.filter.bam" label="wrong_size.filter.bam"/> + <data name="filter_piechart" format="svg" from_work_dir="*filter_piechart.svg" label="Filter piechart" /> + <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" /> </outputs> <tests> <test> + <param name="inputFiles" value="dataset1_2.pair.bam" ftype="qname_sorted.bam" /> <param name="digest" value="digester_file.txt" ftype="txt" /> - <param name="inputFiles" value="result.pair.sam" ftype="sam" /> <output name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/> - <output name="dataset_filt" file="dataset.filt.sam" lines_diff="8" /> - <output name="contiguous_filter" file="dataset.contiguous.filter.sam" lines_diff="8" /> - <output name="re_ligation_filter" file="dataset.re_ligation.filter.sam" lines_diff="8" /> - <output name="same_dangling_ends_filter" file="dataset.same_dangling_ends.filter.sam" lines_diff="8" /> - <output name="invalid_filter" file="dataset.invalid.filter.sam" lines_diff="8" /> - <output name="same_circularised_filter" file="dataset.same_circularised.filter.sam" lines_diff="8" /> - <output name="same_internal_filter" file="dataset.same_internal.filter.sam" lines_diff="8" /> - <output name="filter_piechart" file="filter_piechart.svg" ftype="svg" lines_diff="1000" /> + <output name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" lines_diff="1000" /> + <output name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" lines_diff="1000" /> </test> </tests> <help><![CDATA[ |
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| diff -r b16228ec1540 -r a7bbbf32da62 hicup_macros.xml --- a/hicup_macros.xml Thu Nov 09 11:16:04 2017 -0500 +++ b/hicup_macros.xml Fri May 25 17:49:27 2018 -0400 |
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| @@ -1,22 +1,19 @@ <macros> - <token name="@VERSION@">0.5.10</token> + <token name="@VERSION@">0.6.1</token> <xml name="requirements_hicup"> <requirements> <requirement type="package" version="@VERSION@">hicup</requirement> <requirement type="package" version="2.2.6">bowtie2</requirement> <requirement type="package" version="1.2">samtools</requirement> <requirement type="package" version="0.13.1">docutils</requirement> + <yield/> </requirements> - </xml> - <xml name="stdio"> - <stdio> - <exit_code range="1:" /> - </stdio> + <version_command>hicup --version</version_command> </xml> <xml name="citation_hicup"> - <citations> - <citation type="doi">10.12688/f1000research.7334.1</citation> - </citations> + <citations> + <citation type="doi">10.12688/f1000research.7334.1</citation> + </citations> </xml> <xml name="reference_genome_macro"> <conditional name="reference_genome"> @@ -38,56 +35,23 @@ </when> </conditional> </xml> - <xml name="filter_output"> - <data name="dataset_filt" format="sam" from_work_dir="dataset.filt.sam" label="filt.sam" /> - <data name="hicup_filter_summary" format="txt" from_work_dir="hicup_filter_summary.txt" label="hicup_filter_summary.txt" /> - <data name="contiguous_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.contiguous.filter.sam" label="contiguous.filter.sam" /> - <data name="re_ligation_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam" label="re_ligation.filter.sam" /> - <data name="same_dangling_ends_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam" label="same_dangling_ends.filter.sam" /> - <data name="invalid_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.invalid.filter.sam" label="invalid.filter.sam" /> - <data name="same_circularised_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam" label="same_circularised.filter.sam" /> - <data name="same_internal_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_internal.filter.sam" label="same_internal.filter.sam" /> - <data name="wrong_size_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam" label="wrong_size.filter.sam"/> - <data name="filter_piechart" format="svg" from_work_dir="filter_piechart.svg" label="Filter piechart.svg" /> - </xml> - <xml name="mapper_output"> - <data name="hicup_mapper_summary" format="txt" from_work_dir="hicup_mapper_summary.txt" label="hicup_mapper_summary.txt"/> - <data name="result_pair" format="sam" from_work_dir="result.pair.sam" label="pair.sam"/> - <data name="dataset1_mapper_barchart" format="svg" from_work_dir="dataset1.mapper_barchart.svg" label="Mapper Dataset1 Barchart.svg" /> - <data name="dataset2_mapper_barchart" format="svg" from_work_dir="dataset2.mapper_barchart.svg" label="Mapper Dataset2 Barchart.svg" /> - </xml> - <xml name="truncater_output"> - <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary.txt" /> - <data name="dataset1_trunc" format="fastq" label="Hicup Dataset1 Truncation" from_work_dir="dataset1.trunc.fastq" /> - <data name="dataset2_trunc" format="fastq" label="Hicup Dataset2 Truncation" from_work_dir="dataset2.trunc.fastq" /> - <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1.truncation_barchart.svg" /> - <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2.truncation_barchart.svg" /> - </xml> <xml name="input_files"> - <param name="input_first_sequence" type="data" format="fastq" label="First input sequence" help="The first sequence:"/> - <param name="input_second_sequence" type="data" format="fastq" label="Second input sequence" help="The second sequence:"/> + <param name="input_first_sequence" type="data" format="fastq,fastq.gz" label="First input sequence" help="The first sequence:"/> + <param name="input_second_sequence" type="data" format="fastq,fastq.gz" label="Second input sequence" help="The second sequence:"/> </xml> <xml name="re1"> <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme recognition sequence"/> </xml> <xml name="re2"> - <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags." help="To specify a restriction enzyme instead of sonication to shorten di-tags. This restriction site does NOT form a Hi-C ligation junction. 2 .g. AG^CT,AluI. Typically the sonication protocol is followed."/> - </xml> - <xml name="digester_input"> - <param name="input_files_digest" type="data" multiple="true" format="fasta" label="Input DNA sequence files that should be digested"/> - <param argument="--genome" type="text" label="Genome" help="Name of the genome to be digested (not the path to the genome - file or files, but the genome name to include in the output file)"/> + <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags." + help="To specify a restriction enzyme instead of sonication to shorten di-tags. This restriction site does NOT form a Hi-C ligation junction. 2 .g. AG^CT,AluI. Typically the sonication protocol is followed."/> </xml> <xml name="filter_longest_shortest"> <param argument="--longest" type="text" value="" label="Max insert size" help="Maximum allowable insert size (bps)"/> <param argument="--shortest" type="text" value="" label="Min insert size" help="Minimum allowable insert size (bps)"/> </xml> <xml name="no_fill"> - <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill" help="Hi-C protocol did NOT include a fill-in of sticky ends prior to re-ligation and therefore reads shall be truncated at the restriction site sequence"/> - </xml> - <xml name="deduplicator_output"> - <data name="cis_trans_piechart" format="svg" from_work_dir="deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/> - <data name="uniques_barchart" format="svg" from_work_dir="deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" /> - <data name="hicup_deduplicator_summary" format="txt" from_work_dir="hicup_deduplicator_summary.txt" label="Hicup Deduplicator Summary" /> + <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill" + help="Hi-C protocol did NOT include a fill-in of sticky ends prior to re-ligation and therefore reads shall be truncated at the restriction site sequence"/> </xml> </macros> |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/HiCUP_summary_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HiCUP_summary_report.html Fri May 25 17:49:27 2018 -0400 |
| [ |
| b'@@ -0,0 +1,661 @@\n+\xef\xbb\xbf<!DOCTYPE html>\n+<html>\n+<head>\n+\t<meta http-equiv="content-type" content="text/html; charset=UTF-8">\n+\t<title>HiCUP Processing Report - dataset1_2</title>\n+\t<style type="text/css">\n+\t\tbody {\n+\t\t\tfont-family: Arial, sans-serif;\n+\t\t\tfont-size:14px;\n+\t\t\tpadding:0 20px 20px;\n+\t\t}\n+\t\t.container {\n+\t\t\tmargin:0 auto;\n+\t\t\tmax-width:1200px;\n+\t\t}\n+\t\t.header_title {\n+\t\t\tfloat:left;\n+\t\t}\n+\t\t.header_subtitle {\n+\t\t\tfloat:right;\n+\t\t\ttext-align:right;\n+\t\t\tmargin-top:40px;\n+\t\t}\n+\t\t.header_subtitle h4,\n+\t\t.header_subtitle p {\n+\t\t\tmargin:0;\n+\t\t}\n+\t\th1 {\n+\t\t\tfont-size: 3.2em;\n+\t\t}\n+\t\th2 {\n+\t\t\tfont-size:2.2em;\n+\t\t}\n+\t\th3 {\n+\t\t\tfont-size:1.8em;\n+\t\t}\n+\t\th4 {\n+\t\t\tfont-size:1.4em;\n+\t\t}\n+\t\th3, h4, hr {\n+\t\t\tclear:both;\n+\t\t}\n+\t\thr {\n+\t\t\tborder-top:1px solid #CCC;\n+\t\t\tborder-bottom:1px solid #F3F3F3;\n+\t\t\tborder-left:0;\n+\t\t\tborder-right:0;\n+\t\t\theight:0;\n+\t\t}\n+\t\ta img {\n+\t\t\tborder:0;\n+\t\t}\n+\t\t.data {\n+\t\t\tfloat:left;\n+\t\t\twidth:500px;\n+\t\t\tmax-width:100%;\n+\t\t\tmargin-right:30px;\n+\t\t}\n+\t\t.data_table {\n+\t\t\tborder:1px solid #CCC;\n+\t\t\tborder-collapse:separate;\n+\t\t\tborder-spacing: 0;\n+\t\t\tborder-left:0;\n+\t\t\t-webkit-border-radius:4px;\n+\t\t\t-moz-border-radius:4px;\n+\t\t\tborder-radius:4px;\n+\t\t\tmargin-bottom:30px;\n+\t\t}\n+\t\t.data_table th, .data_table td {\n+\t\t\tborder-left:1px solid #CCC;\n+\t\t\tborder-top:1px solid #CCC;\n+\t\t\tpadding:5px 7px;\n+\t\t}\n+\t\t.data_table thead tr th,\n+\t\t.data_table thead tr td {\n+\t\t\ttext-align:right;\n+\t\t\tborder-top:0;\n+\t\t\tborder-bottom: 2px solid #666;\n+\t\t}\n+\t\t.data_table tbody tr:first-child th,\n+\t\t.data_table tbody tr:first-child td {\n+\t\t\tborder-top:0;\n+\t\t}\n+\t\t\n+\t\t.data_table th {\n+\t\t\ttext-align:left;\n+\t\t}\n+\t\t.data_table td {\n+\t\t\ttext-align:right;\n+\t\t}\n+\t\t.data_table tfoot th,\n+\t\t.data_table tfoot td {\n+\t\t\tborder-top: 2px solid #666;\n+\t\t}\n+\t\t\n+\t\t.plot {\n+\t\t\twidth:650px;\n+\t\t\tmax-width:100%;\n+\t\t\tfloat:left;\n+\t\t\tmargin-bottom:30px;\n+\t\t}\n+\t\t#ditag_length_plot {\n+\t\t\twidth:100%;\n+\t\t\theight:600px;\n+\t\t}\n+\t\t\n+\t\tfooter {\n+\t\t\tcolor:#999;\n+\t\t}\n+\t\tfooter a {\n+\t\t\tcolor:#999;\n+\t\t}\n+\t</style>\n+</head>\n+<body>\n+\t<script>\n+\t\t/*! jQuery v1.10.2 | (c) 2005, 2013 jQuery Foundation, Inc. | jquery.org/license\n+\t\t//@ sourceMappingURL=jquery-1.10.2.min.map\n+\t\t*/\n+\t\t(function(e,t){var n,r,i=typeof t,o=e.location,a=e.document,s=a.documentElement,l=e.jQuery,u=e.$,c={},p=[],f="1.10.2",d=p.concat,h=p.push,g=p.slice,m=p.indexOf,y=c.toString,v=c.hasOwnProperty,b=f.trim,x=function(e,t){return new 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/></a>\n+\t\t<p>Analysis produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/hicup/"><strong>HiCUP</strong></a> (0.6.1) - a tool for mapping and performing quality control on Hi-C data.</p>\n+\t\t<p>Report graphs rendered using <a href="http://jquery.com/">jQuery</a> and <a href="http://www.highcharts.com/">Highcharts</a>.</p>\n+\t</footer>\n+</div>\n+</body>\n+</html>\n+\n' |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/HiCUP_summary_report.txt --- a/test-data/HiCUP_summary_report.txt Thu Nov 09 11:16:04 2017 -0500 +++ b/test-data/HiCUP_summary_report.txt Fri May 25 17:49:27 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ File Total_Reads_1 Total_Reads_2 Not_Truncated_Reads_1 Not_Truncated_Reads_2 Truncated_Read_1 Truncated_Read_2 Average_Length_Truncated_1 Average_Length_Truncated_2 Too_Short_To_Map_Read_1 Too_Short_To_Map_Read_2 Unique_Alignments_Read_1 Unique_Alignments_Read_2 Multiple_Alignments_Read_1 Multiple_Alignments_Read_2 Failed_To_Align_Read_1 Failed_To_Align_Read_2 Paired_Read_1 Paired_Read_2 Valid_Pairs Invalid_Pairs Same_Circularised Same_Dangling_Ends Same_Fragment_Internal Re_Ligation Contiguous_Sequence Wrong_Size Deduplication_Read_Pairs_Uniques Deduplication_Cis_Close_Uniques Deduplication_Cis_Far_Uniques Deduplication_Trans_Uniques Percentage_Mapped Percentage_Valid Percentage_Uniques Percentage_Unique_Trans Percentage_Ditags_Passed_Through_HiCUP -dataset_1265_4.dat.hicup.sam 1000 1000 923 939 77 61 21.39 22.21 35 24 14 23 13 7 938 946 1 1 1 0 0 0 0 0 0 0 1 0 1 0 0.10 100.00 100.00 0.00 0.10 +dataset1_2.hicup.bam 99742 99742 92512 92628 7230 7114 22.45 22.63 2658 2476 3885 3725 12437 12679 80762 80862 1143 1143 543 600 22 75 474 29 0 0 543 43 440 60 1.15 47.51 100.00 11.05 0.54 |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/chr1.fa --- a/test-data/chr1.fa Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,4000 +0,0 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NNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n' 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| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/chr21And22FromHg38.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr21And22FromHg38.fasta Fri May 25 17:49:27 2018 -0400 |
| b |
| b'@@ -0,0 +1,1950572 @@\n+>chr21\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNN'..b'NNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNN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|
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset.contiguous.filter.sam --- a/test-data/dataset.contiguous.filter.sam Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -@HD VN:1.0 SO:unsorted -@SQ SN:chr1 LN:199950 -@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" -@PG ID:HiCUP Mapper VN:0.5.9 -@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" -@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset.filt.sam --- a/test-data/dataset.filt.sam Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -@HD VN:1.0 SO:unsorted -@SQ SN:chr1 LN:199950 -@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" -@PG ID:HiCUP Mapper VN:0.5.9 -@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" -@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" -SRR071233.43293 83 chr1 35433 3 40M = 75323 0 GAGTCCAGGAGTTCAAGACCAGCCTGGGTAACATAGTGAG CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-15 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:3G22A1C11 YT:Z:UU CT:Z:FAR -SRR071233.43293 163 chr1 75323 23 40M = 35433 0 CTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCG CCBCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-10 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:20A18A0 YT:Z:UU CT:Z:FAR |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset.hicup.sam --- a/test-data/dataset.hicup.sam Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -@HD VN:1.0 SO:unsorted -@SQ SN:chr1 LN:199950 -@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" -@PG ID:HiCUP Mapper VN:0.5.9 -@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" -@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" -@PG HiCUP Deduplicator VN:0.5.9 -SRR071233.43293 83 chr1 35433 3 40M = 75323 0 GAGTCCAGGAGTTCAAGACCAGCCTGGGTAACATAGTGAG CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-15 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:3G22A1C11 YT:Z:UU CT:Z:FAR -SRR071233.43293 163 chr1 75323 23 40M = 35433 0 CTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCG CCBCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-10 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:20A18A0 YT:Z:UU CT:Z:FAR |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset.invalid.filter.sam --- a/test-data/dataset.invalid.filter.sam Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -@HD VN:1.0 SO:unsorted -@SQ SN:chr1 LN:199950 -@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" -@PG ID:HiCUP Mapper VN:0.5.9 -@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" -@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset.re_ligation.filter.sam --- a/test-data/dataset.re_ligation.filter.sam Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -@HD VN:1.0 SO:unsorted -@SQ SN:chr1 LN:199950 -@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" -@PG ID:HiCUP Mapper VN:0.5.9 -@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" -@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset.same_circularised.filter.sam --- a/test-data/dataset.same_circularised.filter.sam Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -@HD VN:1.0 SO:unsorted -@SQ SN:chr1 LN:199950 -@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" -@PG ID:HiCUP Mapper VN:0.5.9 -@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" -@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset.same_dangling_ends.filter.sam --- a/test-data/dataset.same_dangling_ends.filter.sam Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -@HD VN:1.0 SO:unsorted -@SQ SN:chr1 LN:199950 -@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" -@PG ID:HiCUP Mapper VN:0.5.9 -@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" -@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset.same_internal.filter.sam --- a/test-data/dataset.same_internal.filter.sam Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -@HD VN:1.0 SO:unsorted -@SQ SN:chr1 LN:199950 -@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" -@PG ID:HiCUP Mapper VN:0.5.9 -@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" -@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1.fastq --- a/test-data/dataset1.fastq Thu Nov 09 11:16:04 2017 -0500 +++ b/test-data/dataset1.fastq Fri May 25 17:49:27 2018 -0400 |
| b |
| b'@@ -3998,3 +3998,394971 @@\n TCATAAAATCATTTGTAGATTGAAGCTAGCTTCTCAGTTG\n +SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n CCCACCCCCCCCCCCCCCCCCCCCBCC?CCCCCCCCCCCC\n+@SRR071233.158001 NRTG514-16_0001:3:2:1462:11875 length=40\n+CCTTTCTCCAGTATTAATTACCAGCATCACAAATGCTGTG\n++SRR071233.158001 NRTG514-16_0001:3:2:1462:11875 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.158159 NRTG514-16_0001:3:2:1478:16327 length=40\n+AACTTGGGGACCAAGCCTGAACCATGTTTGTGGTATCCCC\n++SRR071233.158159 NRTG514-16_0001:3:2:1478:16327 length=40\n+CCCCCCBCCCCCCCCCCCCCCCCCCBCBCCCCCACCCCCC\n+@SRR071233.158317 NRTG514-16_0001:3:2:1497:20254 length=40\n+CAAAGAGCTTGCATTACTTCAACCTTAAAGCCTAATGTGC\n++SRR071233.158317 NRTG514-16_0001:3:2:1497:20254 length=40\n+CCCCABCCCCCCCCCCCCCCCCCCCCCCCC@ACCCCB@CC\n+@SRR071233.158475 NRTG514-16_0001:3:2:1518:10673 length=40\n+GCAATAGTCACTGCGGCTGGCCTGCTTATATTTTTTGACT\n++SRR071233.158475 NRTG514-16_0001:3:2:1518:10673 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCBB:ACC\n+@SRR071233.158633 NRTG514-16_0001:3:2:1537:20891 length=40\n+AATTGGCTGAGGGTTAATTGGCTCACTTTTCTGCAAGCCG\n++SRR071233.158633 NRTG514-16_0001:3:2:1537:20891 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.158791 NRTG514-16_0001:3:2:1558:6652 length=40\n+TATGCCTATACTTGCCAAAGAACTCACTCTTTACTTGAAG\n++SRR071233.158791 NRTG514-16_0001:3:2:1558:6652 length=40\n+CCC3CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CC\n+@SRR071233.158949 NRTG514-16_0001:3:2:1574:16012 length=40\n+TGTCAATGGATCTACCATTCTGGGATCTGGAAGACAGTGA\n++SRR071233.158949 NRTG514-16_0001:3:2:1574:16012 length=40\n+CCCCCC>CCCCCCCCCCCCCCCBC@CCCCCCCCCCCCACC\n+@SRR071233.159107 NRTG514-16_0001:3:2:1593:8997 length=40\n+ATGGAACGGAATGGAATGGAATGGAATGGAATGGAATGGA\n++SRR071233.159107 NRTG514-16_0001:3:2:1593:8997 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.159265 NRTG514-16_0001:3:2:1614:8008 length=40\n+CCCACTGCACAGACAAAATAAATCTACTGAGATCATGGCA\n++SRR071233.159265 NRTG514-16_0001:3:2:1614:8008 length=40\n+CCCCCCCCCCCCCCCCCCCCBBBCCCCCCCCCCCCCCCCC\n+@SRR071233.159423 NRTG514-16_0001:3:2:1633:17035 length=40\n+TTTGAAGGCAGGGGTCTTTCCTGGTGTCCCTACAATCTTA\n++SRR071233.159423 NRTG514-16_0001:3:2:1633:17035 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCC\n+@SRR071233.159581 NRTG514-16_0001:3:2:1649:18359 length=40\n+ACCTCTGCCTCCATGCCTCTCCCCCATCCCATTCCCACAG\n++SRR071233.159581 NRTG514-16_0001:3:2:1649:18359 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCB>CCCCCCCCCCCC@?\n+@SRR071233.159739 NRTG514-16_0001:3:2:1666:17689 length=40\n+AGGTGTGAGCCACTGCACCCAGCCCCAAACTTTATTTCAA\n++SRR071233.159739 NRTG514-16_0001:3:2:1666:17689 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCBBCB\n+@SRR071233.159897 NRTG514-16_0001:3:2:1688:5846 length=40\n+CAAGCCTTGCATTTAAATTTACTTTCAGACTCACTTCCTA\n++SRR071233.159897 NRTG514-16_0001:3:2:1688:5846 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.160055 NRTG514-16_0001:3:2:1707:16043 length=40\n+AGCTAGAAGCTAGTGATAAAGATACAAAGCAGAGAATACG\n++SRR071233.160055 NRTG514-16_0001:3:2:1707:16043 length=40\n+CCCCCCCCBCCCCCCCACACCCC=CCCCCCCC<CBCCCCC\n+@SRR071233.160213 NRTG514-16_0001:3:2:1725:16894 length=40\n+GCTTCTACTGCTCTCTCCCTCGTTCCCCTCCTGGGGCCCA\n++SRR071233.160213 NRTG514-16_0001:3:2:1725:16894 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@CCCCCCC;\n+@SRR071233.160371 NRTG514-16_0001:3:2:1745:6576 length=40\n+ACTCATCACTTCTACTCATGCAAAGATGACTAAGCAGGAA\n++SRR071233.160371 NRTG514-16_0001:3:2:1745:6576 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC\n+@SRR071233.160529 NRTG514-16_0001:3:2:1764:16215 length=40\n+ATCTCCTCAGATGAGAGTTTCACTTGATTTCTGTCAGTCT\n++SRR071233.160529 NRTG514-16_0001:3:2:1764:16215 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.160687 NRTG514-16_0001:3:2:1785:5070 length=40\n+TTATATTTTAAAGCTATCTGTCCTTGCCGGCACGAACTCT\n++SRR071233.160687 NRTG514-16_0001:3:2:1785:5070 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.160845 NRTG514-16_0001:3:2:1800:8076 length=40\n+TAGTTGTTATTTTATGCTTACATTATGCTTACATTAGACA\n++SRR071233.160845 NRTG514-16_0001:3:2:1800:8076 length=40\n+CCCCCCC'..b'ngth=40\n+CCCAGGCTCGTCTTAAACTCCTGGGATCAAGCGATTCTCC\n++SRR071233.15756235 NRTG514-16_0001:3:120:19400:13419 length=40\n+CCCCCCCCCCCBCCCCCCCCCCCCC@CCCCCCCCCCCCCC\n+@SRR071233.15756393 NRTG514-16_0001:3:120:19423:16561 length=40\n+CAGAACCAAAGACAAAAACCACATGATTATCTCAATAAAT\n++SRR071233.15756393 NRTG514-16_0001:3:120:19423:16561 length=40\n+CCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.15756551 NRTG514-16_0001:3:120:19443:11373 length=40\n+TGCCTCTTAGTGAGAGAATAATATATATTCTTGTATTTAT\n++SRR071233.15756551 NRTG514-16_0001:3:120:19443:11373 length=40\n+CCCCCCCCBCDCCCCCCCCCCCCCCCCCCCCCCCCDCCCC\n+@SRR071233.15756709 NRTG514-16_0001:3:120:19466:16073 length=40\n+TAATGCTTTCTACATTCAAAACACTGTGCTAAAACTAAAT\n++SRR071233.15756709 NRTG514-16_0001:3:120:19466:16073 length=40\n+77795:9;9<<?B<?<636:>>>><AA@AA##########\n+@SRR071233.15756867 NRTG514-16_0001:3:120:19487:14719 length=40\n+AGCTTCTTGCAGGATGCTTCCATAATTATGGGGAGGGGAA\n++SRR071233.15756867 NRTG514-16_0001:3:120:19487:14719 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCBBBB=\n+@SRR071233.15757025 NRTG514-16_0001:3:120:19507:5307 length=40\n+CCTTTAGAATTGTCCACATTGATGATAGAGAGACAAATGT\n++SRR071233.15757025 NRTG514-16_0001:3:120:19507:5307 length=40\n+CCCCCCCBCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCC\n+@SRR071233.15757183 NRTG514-16_0001:3:120:19528:12801 length=40\n+CATATTATTTAGAAACAGCAAGCTAGCTTCAAGACCCTGG\n++SRR071233.15757183 NRTG514-16_0001:3:120:19528:12801 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.15757341 NRTG514-16_0001:3:120:19549:13328 length=40\n+AAAACAACTAAGAATGAGACCTACACTGTCAAAGGTAGCT\n++SRR071233.15757341 NRTG514-16_0001:3:120:19549:13328 length=40\n+CCCCCCBBCCCCCCCCCCCCCCCCCCCDCCCBBCCACCCC\n+@SRR071233.15757499 NRTG514-16_0001:3:120:19569:4795 length=40\n+TATAGGCTTCCATTATCTTGGCTTTTCCCCAGATGTAAAT\n++SRR071233.15757499 NRTG514-16_0001:3:120:19569:4795 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCBCBCCCC\n+@SRR071233.15757657 NRTG514-16_0001:3:120:19591:16400 length=40\n+GGAGCCATGGTGGCATCTGGCTGTTGGAAAGCACACAGGG\n++SRR071233.15757657 NRTG514-16_0001:3:120:19591:16400 length=40\n+AC=CCCCCCCCBBCCBBBBB?BBBBBBBB=BB=B>BB@BB\n+@SRR071233.15757815 NRTG514-16_0001:3:120:19610:20289 length=40\n+GAAGTGGAGATGAATCAGAAGACTGTTGGGGTATCGTTCT\n++SRR071233.15757815 NRTG514-16_0001:3:120:19610:20289 length=40\n+CCCCCCCCCCCCCCCCCCACCCCCCCCCCBC@CCCCCBCA\n+@SRR071233.15757973 NRTG514-16_0001:3:120:19632:19403 length=40\n+TTTGATATATGTTAGGTGCTATCTGGCATTTTAAGTATAT\n++SRR071233.15757973 NRTG514-16_0001:3:120:19632:19403 length=40\n+CC?CCC?=CBCCCC?B4AABB;*B2B;BB5-;>9:B<B7:\n+@SRR071233.15758131 NRTG514-16_0001:3:120:19651:11249 length=40\n+TTGTTCTGTACTTGGTTCATTGATAATAGGATGCCCCGTC\n++SRR071233.15758131 NRTG514-16_0001:3:120:19651:11249 length=40\n+CCCCCBCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.15758289 NRTG514-16_0001:3:120:19675:17150 length=40\n+AGCAGAAAGGAAGCTAGCTTTAGCACTCTGCAATGCCCAC\n++SRR071233.15758289 NRTG514-16_0001:3:120:19675:17150 length=40\n+CCCCCCCBACCCCCCCCCCCBCCACCCCCCCCCCCCCCCC\n+@SRR071233.15758447 NRTG514-16_0001:3:120:19696:1737 length=40\n+ACAAATACTAGGCTGAGAATAAAAGCTAGCTTTATAGTGG\n++SRR071233.15758447 NRTG514-16_0001:3:120:19696:1737 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCC\n+@SRR071233.15758605 NRTG514-16_0001:3:120:19717:8653 length=40\n+AAGTTAGCATTCACCTTGTTATAGTGACACAGCATACAGT\n++SRR071233.15758605 NRTG514-16_0001:3:120:19717:8653 length=40\n+CBCCCCCCCCCCCCCCACCCBCCCCCBCCCCCCCBCC@CC\n+@SRR071233.15758763 NRTG514-16_0001:3:120:19738:11060 length=40\n+TTTAGAACTTGAAATTTTGATTTTGGAAAATTTGTCAAAT\n++SRR071233.15758763 NRTG514-16_0001:3:120:19738:11060 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCC\n+@SRR071233.15758921 NRTG514-16_0001:3:120:19762:15127 length=40\n+GGGGCAATGGAGCCCCGACCCGGCGGGCACAATCTCTGGC\n++SRR071233.15758921 NRTG514-16_0001:3:120:19762:15127 length=40\n+?48<?<;><>BA:?A<<>>3B###################\n+@SRR071233.15759079 NRTG514-16_0001:3:120:19785:6316 length=40\n+CCAGAGTTCTTGCTAAAATTGGATTTTACAGGTGCATAAA\n++SRR071233.15759079 NRTG514-16_0001:3:120:19785:6316 length=40\n+CC?CCCCCBBCCCCACCBCCACCCCCCCCBCCCCCACCCC\n' |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1.mapper_barchart.svg --- a/test-data/dataset1.mapper_barchart.svg Thu Nov 09 11:16:04 2017 -0500 +++ b/test-data/dataset1.mapper_barchart.svg Fri May 25 17:49:27 2018 -0400 |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1.trunc.fastq --- a/test-data/dataset1.trunc.fastq Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,4000 +0,0 @@\n-@SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n-NAAGATACCTTGACCGCTCATCCCCTGNNTTCATGAAAGA\n-+SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n-!##########################!!###########\n-@SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n-AGCTTTCTCCTTCTTTTGTCTTTCCCTCCTTTCTGTTGGG\n-+SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n-:BBBBBA??BABBB@<:;A?@B@BBB?BB?6;9<9AA?:0\n-@SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n-CATAGACAATACAATGGCAGCATTGAATAGTTGTGGCAGA\n-+SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n-C@CCB@CCCCCCCACC@BCAC?CC@?;:?BAAC@A=A<A5\n-@SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n-AGATCAAGCTCAGGACAGTCTTGATCTCCTGACCTCATGA\n-+SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n-ACCAACCCACCCCCCCCCCCCBCCCCCCCCCCCCCBCCCC\n-@SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n-ATACTGGCAAACTGAATCCAGCAGCACATCAAAAAGCTAG\n-+SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n-CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCC@C@CBCACC\n-@SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n-AGAAAACTGGAGAAGAAAGAGCCAGGGTAGTCAAAGGACT\n-+SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n-C?<CCCCCCCCCCCCCBCCCCCCCCCCC?CCCCC@CCCCC\n-@SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n-AAAAAACCCTTCCTATTTGAAGAGCAAGCTACATAAGCAA\n-+SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n-CCCCBCCCCCCCCCBCCCCCCABCCC?BCCCCACCCBCC?\n-@SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n-GGACTGAATGAAATAATATATGCATAAAGTACATAAAAAT\n-+SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n-CCCCCCCCCCCBACC<7<<:CCCCCCCCC@CCCCBCCC=>\n-@SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n-GCTTTCATCAAATGCCTTTGTCTTGGCATCTGAATTCCAG\n-+SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCACCACCCCCCBCCCC\n-@SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n-CTATGAAAAGAAAAGAAGAAAAGCTT\n-+SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n-CCCCCCCCCCCBBBBCBBCCCBBCCC\n-@SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n-AGAAGAGACACCTGCACACTTCCCTCCAAGAAGCTT\n-+SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n-CCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCC\n-@SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n-CGCATCACAAAGCTT\n-+SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n-CACCCCCCDCCCCCC\n-@SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n-CATGCACACAATGGACAATCCCAGCAGAATTTGCTTTTCA\n-+SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n-@SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n-AGTTTTTCCTTGCATATGTGAAGCTT\n-+SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCC\n-@SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n-GGCTTGGCTTAACCAATAACTTTTGTAGAAACCTTTATGA\n-+SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n-@SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n-AGCTTGGGCAGGAAGATGACCTACATGAATGAGGTGAGGA\n-+SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCC\n-@SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n-TTGGTGTGTGGCCAGTGCTGACAACAGCATTTTGAACTAC\n-+SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n-CCCCCCCCCCCCCBCCCCCCACCCCCCCCCCCCCCCCCCC\n-@SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n-ATAATTCTGCAAAAGGCCATAAGCTT\n-+SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCC\n-@SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n-TGTGTTCCATTTGATGTCAAACAATAGGTTGAAAAATTAG\n-+SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n-00///9;<;;BBBBBB@@B@BABBBBBB@BBBBBBBBBBB\n-@SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n-TGTGGGACCAGTGCAGCATTTAGTCTAGGAATAAATTTGT\n-+SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n-@SRR071233.3161 NRTG514-16_0001:3:1:1426:3923 length=40\n-TGAAAAAGCCAAACATAGAAAACGAAACTTTAAAACAGCA\n-+SRR071233.3161 NRTG514-16_0001:3:1:1426:3923 length'..b'===:\n-@SRR071233.154841 NRTG514-16_0001:3:2:1055:18658 length=40\n-TGTGGAGGGTTTTTTCCTCGCTTGGGTTCATTAAGCTAGC\n-+SRR071233.154841 NRTG514-16_0001:3:2:1055:18658 length=40\n-CBCCCCCCACCCCCCBC@?CBB@BB@BBBBBB<B>B9BBB\n-@SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n-AGCTTAGAATATACTATTATTGAAGAAGGAAAGCCTTAGA\n-+SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n-CCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n-@SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n-TCTGAGAGTTCCAGTAGCTTCACATGCTCCAGTAATTGGT\n-+SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCC>\n-@SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n-CATGGAAGACAGCCCTGCAGAGCTAAATTTAGGCAGAGAC\n-+SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n-CCCCCCBCCCCCCCCCCDCCCACCCCACCCCCCCDCDCCB\n-@SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n-ATCCACCCACCTTGGCCTCCCAAAGTGCTAGAATTACAGG\n-+SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCC?CCCACCCCCCCCCC\n-@SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n-ACTCATCTTGGACCTTGTTCTTCTTCTAATTCCACCATCA\n-+SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n-@SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n-AGCAGTGGTTCTCCCAGCACAGCATTTGAGCTCCAACAAC\n-+SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n-CCCCCCCBCCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCC\n-@SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n-CCTCTGAGACAAAGCTT\n-+SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n-CCCCCCDCCCBCCCCCC\n-@SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n-TCTTTAAAGTTCGCACAGAGTTTGGGGTATTCATTTTCAG\n-+SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCACCCBCCCB\n-@SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n-TAGGTAGAGGGATTAGTTGAGGCCAAGGCCTTGATCTGGG\n-+SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n-CCCCBCCACCC@CCCCCCCCCCCCCCCCCCCBCC@CCC@=\n-@SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n-TCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAG\n-+SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n-CCCCCBCCCCCCBACCCCCCC@BCCBCCCCCCCCCCCCCC\n-@SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n-TTGGGGAGGTGGCTGGGGAAGACCAGGGGCTACCTAAAAA\n-+SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n-DCCCCCCCBBCCDCCCCBCCBCCCBABCCC@CCCBCC?CC\n-@SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n-GGAGAGATGAAAGAGTCAGACAGCTCTACAAAGCCTCTTT\n-+SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n-CCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCBCC\n-@SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n-TAAACACTATGACCATTTCCATCTTTCAGCCCTCTTGATT\n-+SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CC\n-@SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n-TTAAAGACTAAATGCTTACCATGTGTATGCTAGGTGTACA\n-+SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n-CC@CCBCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCDCCC\n-@SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n-ACGTTACACAGTGCATGACTATGCATGGTTTTTGGATTAA\n-+SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCC\n-@SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n-AAAGTTTTCCCGTTTAATATTATAAAATGGAATCATGTAA\n-+SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n-00//0+AAAACCCCCCBCCCCCCCCCCCCCCCCCCCCCCC\n-@SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n-TTTGGTAAGATTCTGAATGATTTTTCTGGTTTTATTTTTT\n-+SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n-CCCCCCCCCCCCCCCCCCC@CCCCCCBBCCCCCCCBBBBB\n-@SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n-TCATTAAATGTACTCTAATGGAATCATGGAATGGACTCGA\n-+SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n-ABCCBCC@CCCCCCCCCBCCCACCCCCCCC=B@B@CCCCC\n-@SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n-TCATAAAATCATTTGTAGATTGAAGCTT\n-+SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n-CCCACCCCCCCCCCCCCCCCCCCCBCC?\n' |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1.trunc.fastq.gz |
| b |
| Binary file test-data/dataset1.trunc.fastq.gz has changed |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1.truncation_barchart.svg --- a/test-data/dataset1.truncation_barchart.svg Thu Nov 09 11:16:04 2017 -0500 +++ b/test-data/dataset1.truncation_barchart.svg Fri May 25 17:49:27 2018 -0400 |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1_2.ditag_size_distribution.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset1_2.ditag_size_distribution.svg Fri May 25 17:49:27 2018 -0400 |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1_2.filt.bam |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1_2.pair.bam.filter_piechart.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset1_2.pair.bam.filter_piechart.svg Fri May 25 17:49:27 2018 -0400 |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1_2_contiguous.filter.bam |
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| Binary file test-data/dataset1_2_contiguous.filter.bam has changed |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1_2_invalid.filter.bam |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1_2_re_ligation.filter.bam |
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| Binary file test-data/dataset1_2_re_ligation.filter.bam has changed |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1_2_same_circularised.filter.bam |
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| Binary file test-data/dataset1_2_same_circularised.filter.bam has changed |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1_2_same_dangling_ends.filter.bam |
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| Binary file test-data/dataset1_2_same_dangling_ends.filter.bam has changed |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset1_2_same_internal.filter.bam |
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| Binary file test-data/dataset1_2_same_internal.filter.bam has changed |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset2.fastq --- a/test-data/dataset2.fastq Thu Nov 09 11:16:04 2017 -0500 +++ b/test-data/dataset2.fastq Fri May 25 17:49:27 2018 -0400 |
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| b'@@ -3998,3 +3998,394971 @@\n AGGATGTATTGGCAAGAGGAACTATTAAGACCATTGTTAC\n +SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n CCCBCCCCCCCCCCCCCCC?CCBCCCCCCCCCCCCCCCCC\n+@SRR071233.158001 NRTG514-16_0001:3:2:1462:11875 length=40\n+ACTGTTCCGGGCATCGGGAGGGACGTGCCTTGGCATGCCA\n++SRR071233.158001 NRTG514-16_0001:3:2:1462:11875 length=40\n+CCCCCCCCCCCCCCCCCDCCCB@CCCCCCA@CCCCCCCCC\n+@SRR071233.158159 NRTG514-16_0001:3:2:1478:16327 length=40\n+ACAGCTGCTTGTTATTGGCTGTGCTGCTATTTGCTGTATC\n++SRR071233.158159 NRTG514-16_0001:3:2:1478:16327 length=40\n+CCCCCCCCCCCCC@CCCCCCC=CC@773.8BB/?==>AAA\n+@SRR071233.158317 NRTG514-16_0001:3:2:1497:20254 length=40\n+AAAGAGCATTATGCTAGCTTTTCAACTCCAGTGAATTGTT\n++SRR071233.158317 NRTG514-16_0001:3:2:1497:20254 length=40\n+CCCCCCC@CCCCCCACCCAACCCCCCCCCCCBC>C@AAA@\n+@SRR071233.158475 NRTG514-16_0001:3:2:1518:10673 length=40\n+AATGGGAGAAGTGGTGTGTTGGAGCAAAGCTAGCTTGAGT\n++SRR071233.158475 NRTG514-16_0001:3:2:1518:10673 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.158633 NRTG514-16_0001:3:2:1537:20891 length=40\n+CAGTGGCTGGGACTGGTTGTTTCTTTCCATGTTTAGTGCT\n++SRR071233.158633 NRTG514-16_0001:3:2:1537:20891 length=40\n+CCCCCCCCCC##############################\n+@SRR071233.158791 NRTG514-16_0001:3:2:1558:6652 length=40\n+CGCAGGGATGCAACAGGATTTGGGAGAAAAGCTTAATCTC\n++SRR071233.158791 NRTG514-16_0001:3:2:1558:6652 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.158949 NRTG514-16_0001:3:2:1574:16012 length=40\n+AGTCAGTTAAGCTAGCTTTGGAAACGTCCACCTAGATTTC\n++SRR071233.158949 NRTG514-16_0001:3:2:1574:16012 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCC\n+@SRR071233.159107 NRTG514-16_0001:3:2:1593:8997 length=40\n+CCATTCCATTCCATTCCATTCCATTCCTTTCCATTCCATT\n++SRR071233.159107 NRTG514-16_0001:3:2:1593:8997 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.159265 NRTG514-16_0001:3:2:1614:8008 length=40\n+ATGGAAATGTATGGAACAGTTATTACATATTTGGTGCTGC\n++SRR071233.159265 NRTG514-16_0001:3:2:1614:8008 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.159423 NRTG514-16_0001:3:2:1633:17035 length=40\n+CAGATGTTTAAGTCTGCAGAAGTTTCTGCTGCCTTTTGTT\n++SRR071233.159423 NRTG514-16_0001:3:2:1633:17035 length=40\n+CCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCCCC@\n+@SRR071233.159581 NRTG514-16_0001:3:2:1649:18359 length=40\n+TACAGAGTTGGACCTTCCTTTGATTGAGCAGTTTGGAAAC\n++SRR071233.159581 NRTG514-16_0001:3:2:1649:18359 length=40\n+CCCCCBCCCCCCCCCCCCCCCCCCCBCDCCCCCCCCCCCC\n+@SRR071233.159739 NRTG514-16_0001:3:2:1666:17689 length=40\n+CGTGTACCTAATACACAATATTGTAATATTGTAATATTGT\n++SRR071233.159739 NRTG514-16_0001:3:2:1666:17689 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.159897 NRTG514-16_0001:3:2:1688:5846 length=40\n+ACTTTGGGAAGCTAGCTTTATATGAGTTCCACATATACAT\n++SRR071233.159897 NRTG514-16_0001:3:2:1688:5846 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCC\n+@SRR071233.160055 NRTG514-16_0001:3:2:1707:16043 length=40\n+GATGCTAGAGCTAAAAGATACTGGAGCTGCAGCCAAAACC\n++SRR071233.160055 NRTG514-16_0001:3:2:1707:16043 length=40\n+CCCC?CCCCCCCCCCCCCCCCCC@BCCCCCCCC@ABCC:C\n+@SRR071233.160213 NRTG514-16_0001:3:2:1725:16894 length=40\n+AGAATGAAGGTTTTAAAAAAAAAAAACATTGAGTTATCAC\n++SRR071233.160213 NRTG514-16_0001:3:2:1725:16894 length=40\n+CCCCCCCCCCCCCCCCCCCCBBBBBBBBBCCBCCCCCC@B\n+@SRR071233.160371 NRTG514-16_0001:3:2:1745:6576 length=40\n+AGCTTCTAGATAGAAATTGGGGTTGGAGAGGACAATTTAA\n++SRR071233.160371 NRTG514-16_0001:3:2:1745:6576 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.160529 NRTG514-16_0001:3:2:1764:16215 length=40\n+AGCTTATAATGAACATCACCCAGACTGGATTTTAAGACAA\n++SRR071233.160529 NRTG514-16_0001:3:2:1764:16215 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCC\n+@SRR071233.160687 NRTG514-16_0001:3:2:1785:5070 length=40\n+AGCTTCAGACTCTTTCTGGTCTTACTCCTTCTGACCGTGC\n++SRR071233.160687 NRTG514-16_0001:3:2:1785:5070 length=40\n+CCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.160845 NRTG514-16_0001:3:2:1800:8076 length=40\n+CACAGCCTCCCAAAGTGCTGGGATTACAGGAATGAGTCAC\n++SRR071233.160845 NRTG514-16_0001:3:2:1800:8076 length=40\n+CCCCCCC'..b'ngth=40\n+AATAAGTAAAGACAAAGCTATCTTAGCATTTTGGGAGGCT\n++SRR071233.15756235 NRTG514-16_0001:3:120:19400:13419 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCBACCCCC\n+@SRR071233.15756393 NRTG514-16_0001:3:120:19423:16561 length=40\n+ATTGGTTTTCAAAAGGAATGCTTCCAGCTTTTGCCCATTC\n++SRR071233.15756393 NRTG514-16_0001:3:120:19423:16561 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.15756551 NRTG514-16_0001:3:120:19443:11373 length=40\n+GTACAGAAGCTACCTTGCTGGCTTGTACTGTGCTAGAATT\n++SRR071233.15756551 NRTG514-16_0001:3:120:19443:11373 length=40\n+CCCCBBC@CCCCCCCCCCCDCCCC@CACCB@ACCCBCC@C\n+@SRR071233.15756709 NRTG514-16_0001:3:120:19466:16073 length=40\n+TTTAACCACCAGGCTAGGCTGCCTCCTAAGCAGAAAGCTC\n++SRR071233.15756709 NRTG514-16_0001:3:120:19466:16073 length=40\n+@@@@@:AAA?@4>@@7:<><A6@:A52>27AAA2A:???=\n+@SRR071233.15756867 NRTG514-16_0001:3:120:19487:14719 length=40\n+CTGTGCTTGTCCTTTCACTGTAATAAATCATAGCCATGAG\n++SRR071233.15756867 NRTG514-16_0001:3:120:19487:14719 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.15757025 NRTG514-16_0001:3:120:19507:5307 length=40\n+GAAAATTTAGGTTCAAGGAAGGTAGCTTACCATAAATGTA\n++SRR071233.15757025 NRTG514-16_0001:3:120:19507:5307 length=40\n+CBCCCCCCCCCBCCCCCCCCCC@CCCCCCCCCCCCCCCAC\n+@SRR071233.15757183 NRTG514-16_0001:3:120:19528:12801 length=40\n+TTACTGAGATTCAGGGAGGGTACATTGGACATTGCTCTGG\n++SRR071233.15757183 NRTG514-16_0001:3:120:19528:12801 length=40\n+CCCCCCCCCCCCCCCCCCCB<CCCCCCCCCCCCCCCCCCC\n+@SRR071233.15757341 NRTG514-16_0001:3:120:19549:13328 length=40\n+TTCCTTCATGATTCTATTCAGAAAACTTTTCCCTTTTCAT\n++SRR071233.15757341 NRTG514-16_0001:3:120:19549:13328 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACBC\n+@SRR071233.15757499 NRTG514-16_0001:3:120:19569:4795 length=40\n+TGTGAATTCAGGTTTTACTTGGTGCATCACAACTGTCAGG\n++SRR071233.15757499 NRTG514-16_0001:3:120:19569:4795 length=40\n+CCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCDCCCCCC\n+@SRR071233.15757657 NRTG514-16_0001:3:120:19591:16400 length=40\n+GACTCTCAGCCTTCCTTTCCTTCTCTGGGGTCTGTCTGTT\n++SRR071233.15757657 NRTG514-16_0001:3:120:19591:16400 length=40\n+?BAAB=B=@@BBBB@BBB>BB@9BB@@=>B>BBBBBBBB>\n+@SRR071233.15757815 NRTG514-16_0001:3:120:19610:20289 length=40\n+AACCTCTTACTAGGTTATGGAACCAGCCCAGTAGTTCAGC\n++SRR071233.15757815 NRTG514-16_0001:3:120:19610:20289 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCC?CCCCCBC\n+@SRR071233.15757973 NRTG514-16_0001:3:120:19632:19403 length=40\n+ATTGTGATCCTCTCTGATTTAGCTGTGTTTAGTTTCATAT\n++SRR071233.15757973 NRTG514-16_0001:3:120:19632:19403 length=40\n+?7/:<?<?<??<8??3<=AA9?4><???<2B@BB<B:::B\n+@SRR071233.15758131 NRTG514-16_0001:3:120:19651:11249 length=40\n+CTTCCCCAGAATCATTGCATGAGCTCCCACCTGCAGCCTC\n++SRR071233.15758131 NRTG514-16_0001:3:120:19651:11249 length=40\n+CCCCCCCCCCBCCBCCCCCBCBCCCCCCCBCCCCCCCCCC\n+@SRR071233.15758289 NRTG514-16_0001:3:120:19675:17150 length=40\n+CAAGAAAACAATAGCATATTTCAACTCACTTTGATGATCT\n++SRR071233.15758289 NRTG514-16_0001:3:120:19675:17150 length=40\n+?????<B;;@>>ACCCCCACCCBBC@CBBCCCCCCCCCBC\n+@SRR071233.15758447 NRTG514-16_0001:3:120:19696:1737 length=40\n+CATAAAAAGAGAACTCTGACCCACAATCTGCAGCAATTAG\n++SRR071233.15758447 NRTG514-16_0001:3:120:19696:1737 length=40\n+CCCCCCCBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.15758605 NRTG514-16_0001:3:120:19717:8653 length=40\n+GATGCTGGTTCAGAACAGAAGACTCAGACCAACGCTAAGA\n++SRR071233.15758605 NRTG514-16_0001:3:120:19717:8653 length=40\n+CCACCBCACCCCCCBBBBBCCCCCCBCBCCC@CCCCC@CC\n+@SRR071233.15758763 NRTG514-16_0001:3:120:19738:11060 length=40\n+TGTGACGATGACACGTTTGAGAGTGCTCCCGGGACAGCAT\n++SRR071233.15758763 NRTG514-16_0001:3:120:19738:11060 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.15758921 NRTG514-16_0001:3:120:19762:15127 length=40\n+CGGGGGACCAATANCTTGGGGGCGTCCGGCTGGGGNCAGG\n++SRR071233.15758921 NRTG514-16_0001:3:120:19762:15127 length=40\n+#############!#####################!####\n+@SRR071233.15759079 NRTG514-16_0001:3:120:19785:6316 length=40\n+GCAGGANNNNNNNNNTCAAAGATTCTTNANNNNNNNNNAC\n++SRR071233.15759079 NRTG514-16_0001:3:120:19785:6316 length=40\n+CCCCC#!!!!!!!!!############!#!!!!!!!!!##\n' |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset2.mapper_barchart.svg --- a/test-data/dataset2.mapper_barchart.svg Thu Nov 09 11:16:04 2017 -0500 +++ b/test-data/dataset2.mapper_barchart.svg Fri May 25 17:49:27 2018 -0400 |
| b |
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| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset2.trunc.fastq --- a/test-data/dataset2.trunc.fastq Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,4000 +0,0 @@\n-@SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n-AGAACCCATTCACACTCCCGCCAGCAGCAGGTTCGTGCCA\n-+SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n-@BABA@BBBBBBBB?BBBB@:?AAAB5<BAA92A=2:;77\n-@SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n-GTTGGAAACGGGATAAACCGCACAGAACTAAACAGAAGCA\n-+SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n-?????<B???A:5>-794<4<7>>97?9?;BAB@@7895;\n-@SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n-GATGCAGCTAGCAAGCAGGAGGGCCAGGTTTCCAACCGCG\n-+SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n-BCCCBCC@CCCCCCC=CBBACCAACCCCCBCCB;CCCCC?\n-@SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n-GACCATGCTCCCTATTATTCTTGTTGAGTAACTGTAAGAC\n-+SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n-CCCCCCCB8CCCCCCCCCCCCCCCCBCCCCBBACCCBCCC\n-@SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n-CTAGTGGGAAAGTGAAATGGTGTTGCATGTATGCAAGCTT\n-+SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n-CCCC>CCCCCCCBCC@CCCC@CCCCCCCCCCCCCCCCC@C\n-@SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n-GCAAGAGGCCTAGCTTTAAGGCTATCTCAGTTTTTGACAT\n-+SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n-CCC@CCCCCCCCCB?CCCCC@CC?@@@@@?C@CC?C?CC@\n-@SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n-GGTAGCCATCCCAACAGCCTTGGACCTCACTGCAGATCTA\n-+SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n-CCCCCCC>CCCCACCBCBACBCCCCCCCBCCCCCCCCC@B\n-@SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n-GCTCCCAACTCAGAGGAGTTGGCCGGGTAAGCTGTTTTCA\n-+SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n-BCCCCC@CBBCC@?@C?C=@BBBB>CC;?CC@CC=CB>C@\n-@SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n-GAATTTCATATCCAGCCAAACTAAGCTACCTTTGCTATCA\n-+SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n-CCCCCCCCDCCCCCCDCCCCCCCCCBACCCCC@CCCCCCC\n-@SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n-GCCATGGTGAGCATTTACACCATGGACACTGGCAAACTCC\n-+SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n-CCCCCCCCCBCC@CCCCCCCCCCCCACCCCCCC@CCDCCC\n-@SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n-TAGTATTTTTATCATTTTATCTAAAGATCTTTACTTTTCG\n-+SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n-CCCCCCCCCBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCC\n-@SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n-TAAAAGACTTGGGTGGCATGTGGTTTTTAGAAGAAATTTA\n-+SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n-@CCCCCCCCCCBCBCCCCCCCCCBCCCCCCC:CCC?BCCC\n-@SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n-AACCCCAGGAAAGCTT\n-+SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n-CCCCCCCCCCCCCCCC\n-@SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n-AGCTTTTCGGAGCTAAATCATGCCCCAACAAAGGATAGCA\n-+SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC\n-@SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n-TACTAACTGTTTTAGTTTACCTCTTAGTTTTCCGCATGTC\n-+SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n-CCCCCCCCCCCCCACCCCCCCCCCCDCCCCCCCCCCCCCC\n-@SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n-CGCATTTAAGCTTCTCAAAGATGGTCATGCCTCCCTCACC\n-+SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n-CCCCCCCCCCCCCCCCC6CCCCCCCCCCCCCCCCCCCCCC\n-@SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n-GGTCAAATCTAAGCTT\n-+SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n-CCCCCCCCCCCCCCCC\n-@SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n-AATAAATAAAGTATTTAGGAAACAGATCTTACCTCACTTG\n-+SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n-CCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n-@SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n-CAAGGCTCTGATTTATCTCTTGATTTTTATTCTTACTTTT\n-+SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n-BBBBBBBBBB>BBBBBAB@B?@3>@BBBB===BBBBBBAB\n-@SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n-AATAGTTTGTGCCTCTAAAAACAGGCAGGCTAAATAAGCT\n-+SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n-CDCCCCCCCCCCCCCCCCCCCCBBCCCCCCCACCCCCCCC\n-@SRR071233.3161 NRTG514-16_0001:3:1:1426:3923 length=40\n-AACAAGGACTCCTGGGTTGATCTCCAGCCTCAAAAATCCT\n-+SRR07'..b'AAGGGCAAGGAAGACTTTTACAGGTGCTGGATCCGG\n-+SRR071233.154841 NRTG514-16_0001:3:2:1055:18658 length=40\n->>6>>@<@?@B>BBBBBBBBBB>BBBBBBBBBBBB8@B@B\n-@SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n-TCTCATATTTTTTGAAGTAAACATCAAAATCACCATCCAG\n-+SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n-CCCCCCCCCCC@@@CCCCCCCCCACCCCCCCCCCCCCCCC\n-@SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n-AATGAGAGAAAACTTCAGTAATCACCTAACCCCAAAAAAT\n-+SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n-CCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCC@CCCCC\n-@SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n-CACACCACTGCCCTGCACACAAACCCTCCAGGAGGTTTAT\n-+SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCB>CCBC\n-@SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n-TGGATTTCTCATGAATGGTTGAGTACTATCCTTTTGCTAC\n-+SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n-CCCCCCBCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCC\n-@SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n-GGTGACGGATGTCCCAGGAGGACGACCCAAGCCCACCCGC\n-+SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n-CCCCCCCCCBCCCCCBCCCCCCCCCCCCCCCCCB<CBB@?\n-@SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n-GGCCTTGATAAATTGTAACTACCATGATTAGACTTTTGTA\n-+SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n-CCCCCBCCCCCACCCCCCCCCCCCCCCACCCCCCCCCCCC\n-@SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n-AGTCTCCTTACTAGGGCAGTTCAACTTCATAGTGGTGCAG\n-+SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n-CCCCCCCCC;CBCCCCCCCCCCCCCCCDBCCCBCCCCCCC\n-@SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n-CCTACAATGCTCCCATCCAAGCTAGGGTGAAGGCAGATCC\n-+SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n-CCCCCCCCCCCCCCCBCCCCCCCCCCA@CCCCC>@CACCC\n-@SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n-ATGCTCCTTTCTCAGTACTTTCATAGCACCTTCTTCATAC\n-+SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n-CCACCCCCCCCCBCC@BCCCACBCCCCCCCACCCC@BCCC\n-@SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n-AAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGG\n-+SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n-CCCCC?@@CBCCCCCCCBCCCCCCCCC@CCCC@CCCCCC?\n-@SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n-ACAGAGCGCAGGACAGAAAGTAAGGCATTTCAAGCAGAGA\n-+SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n-CCCCCCCCCCCCCCCCCACB@CCCCCCCCCCCCC?A8AAA\n-@SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n-AACACTTAAAAAAAAAAAAAAAAAACCAAACCCCAGGCTC\n-+SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n-BBCCCCCDCCCCC@BBBBBBBBBB################\n-@SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n-CTAAAACTGGACTGAGAAAAGGTGATCCCATTTGGCTTCA\n-+SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n-CCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCC\n-@SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n-TATAATTTCTGTTCTTTTACATTTGCTGAGGAGTGCTTTA\n-+SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n-CCCCCCCCCCCCCCCCC@@CCCCCCCCCCCCCCCCCCCCC\n-@SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n-CTATCCTAAGGTTATGAATGTATTCTCCTATATTATATTC\n-+SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n-CCCCCCCCCCCCCCCCCACCDCCCCCCCCCCACCCCCCCC\n-@SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n-TAAAATTCAAAATTTCTGCTCCCCTATCCAGACCACTGGC\n-+SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n-@SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n-AGCTTTGCCCATCATGAGGAATGAACCTAGCTCCTATTGC\n-+SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n-CCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCDCADCCCC\n-@SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n-ATTTGATTCCATTCAATGATGATTCCATTCTATTCCATTC\n-+SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n-@BABAACCCCCCCCCCCCBB@=@AACBCCCCCCBCCC?CC\n-@SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n-AGGATGTATTGGCAAGAGGAACTATTAAGACCATTGTTAC\n-+SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n-CCCBCCCCCCCCCCCCCCC?CCBCCCCCCCCCCCCCCCCC\n' |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset2.trunc.fastq.gz |
| b |
| Binary file test-data/dataset2.trunc.fastq.gz has changed |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/dataset2.truncation_barchart.svg --- a/test-data/dataset2.truncation_barchart.svg Thu Nov 09 11:16:04 2017 -0500 +++ b/test-data/dataset2.truncation_barchart.svg Fri May 25 17:49:27 2018 -0400 |
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| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/deduplicator_uniques_barchart.svg --- a/test-data/deduplicator_uniques_barchart.svg Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/digester_file.txt --- a/test-data/digester_file.txt Thu Nov 09 11:16:04 2017 -0500 +++ b/test-data/digester_file.txt Fri May 25 17:49:27 2018 -0400 |
| [ |
| b"@@ -1,56 +1,19943 @@\n-Genome:genome\tRestriction_Enzyme1:re1_unspecified [A^AGCTT]\tRestriction_Enzyme2:None\tHicup digester version 0.5.9\n+Genome:chr21And22FromHg38\tRestriction_Enzyme1:re1_unspecified [A^AGCTT]\tRestriction_Enzyme2:None\tHicup digester version 0.6.1\n 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5\t8595\t8595\tRe1\tRe1\n+chr22\t50363436\t50363511\t8596\t8596\tRe1\tRe1\n+chr22\t50363512\t50367080\t8597\t8597\tRe1\tRe1\n+chr22\t50367081\t50379288\t8598\t8598\tRe1\tRe1\n+chr22\t50379289\t50397379\t8599\t8599\tRe1\tRe1\n+chr22\t50397380\t50401722\t8600\t8600\tRe1\tRe1\n+chr22\t50401723\t50401984\t8601\t8601\tRe1\tRe1\n+chr22\t50401985\t50421256\t8602\t8602\tRe1\tRe1\n+chr22\t50421257\t50426383\t8603\t8603\tRe1\tRe1\n+chr22\t50426384\t50428909\t8604\t8604\tRe1\tRe1\n+chr22\t50428910\t50444665\t8605\t8605\tRe1\tRe1\n+chr22\t50444666\t50450724\t8606\t8606\tRe1\tRe1\n+chr22\t50450725\t50450736\t8607\t8607\tRe1\tRe1\n+chr22\t50450737\t50450804\t8608\t8608\tRe1\tRe1\n+chr22\t50450805\t50458364\t8609\t8609\tRe1\tRe1\n+chr22\t50458365\t50466498\t8610\t8610\tRe1\tRe1\n+chr22\t50466499\t50482637\t8611\t8611\tRe1\tRe1\n+chr22\t50482638\t50485316\t8612\t8612\tRe1\tRe1\n+chr22\t50485317\t50486417\t8613\t8613\tRe1\tRe1\n+chr22\t50486418\t50491090\t8614\t8614\tRe1\tRe1\n+chr22\t50491091\t50493790\t8615\t8615\tRe1\tRe1\n+chr22\t50493791\t50495968\t8616\t8616\tRe1\tRe1\n+chr22\t50495969\t50500513\t8617\t8617\tRe1\tRe1\n+chr22\t50500514\t50501346\t8618\t8618\tRe1\tRe1\n+chr22\t50501347\t50509861\t8619\t8619\tRe1\tRe1\n+chr22\t50509862\t50514002\t8620\t8620\tRe1\tRe1\n+chr22\t50514003\t50535493\t8621\t8621\tRe1\tRe1\n+chr22\t50535494\t50555553\t8622\t8622\tRe1\tRe1\n+chr22\t50555554\t50560973\t8623\t8623\tRe1\tRe1\n+chr22\t50560974\t50566738\t8624\t8624\tRe1\tRe1\n+chr22\t50566739\t50574082\t8625\t8625\tRe1\tRe1\n+chr22\t50574083\t50576569\t8626\t8626\tRe1\tRe1\n+chr22\t50576570\t50578973\t8627\t8627\tRe1\tRe1\n+chr22\t50578974\t50598031\t8628\t8628\tRe1\tRe1\n+chr22\t50598032\t50618927\t8629\t8629\tRe1\tRe1\n+chr22\t50618928\t50626366\t8630\t8630\tRe1\tRe1\n+chr22\t50626367\t50628581\t8631\t8631\tRe1\tRe1\n+chr22\t50628582\t50629592\t8632\t8632\tRe1\tRe1\n+chr22\t50629593\t50630215\t8633\t8633\tRe1\tRe1\n+chr22\t50630216\t50630812\t8634\t8634\tRe1\tRe1\n+chr22\t50630813\t50633886\t8635\t8635\tRe1\tRe1\n+chr22\t50633887\t50634576\t8636\t8636\tRe1\tRe1\n+chr22\t50634577\t50640196\t8637\t8637\tRe1\tRe1\n+chr22\t50640197\t50640456\t8638\t8638\tRe1\tRe1\n+chr22\t50640457\t50643142\t8639\t8639\tRe1\tRe1\n+chr22\t50643143\t50645738\t8640\t8640\tRe1\tRe1\n+chr22\t50645739\t50657934\t8641\t8641\tRe1\tRe1\n+chr22\t50657935\t50666016\t8642\t8642\tRe1\tRe1\n+chr22\t50666017\t50668885\t8643\t8643\tRe1\tRe1\n+chr22\t50668886\t50669931\t8644\t8644\tRe1\tRe1\n+chr22\t50669932\t50671729\t8645\t8645\tRe1\tRe1\n+chr22\t50671730\t50676679\t8646\t8646\tRe1\tRe1\n+chr22\t50676680\t50694482\t8647\t8647\tRe1\tRe1\n+chr22\t50694483\t50696303\t8648\t8648\tRe1\tRe1\n+chr22\t50696304\t50713988\t8649\t8649\tRe1\tRe1\n+chr22\t50713989\t50716566\t8650\t8650\tRe1\tRe1\n+chr22\t50716567\t50724541\t8651\t8651\tRe1\tRe1\n+chr22\t50724542\t50726541\t8652\t8652\tRe1\tRe1\n+chr22\t50726542\t50726987\t8653\t8653\tRe1\tRe1\n+chr22\t50726988\t50733406\t8654\t8654\tRe1\tRe1\n+chr22\t50733407\t50735950\t8655\t8655\tRe1\tRe1\n+chr22\t50735951\t50736155\t8656\t8656\tRe1\tRe1\n+chr22\t50736156\t50746610\t8657\t8657\tRe1\tRe1\n+chr22\t50746611\t50749091\t8658\t8658\tRe1\tRe1\n+chr22\t50749092\t50752511\t8659\t8659\tRe1\tRe1\n+chr22\t50752512\t50754396\t8660\t8660\tRe1\tRe1\n+chr22\t50754397\t50760974\t8661\t8661\tRe1\tRe1\n+chr22\t50760975\t50763868\t8662\t8662\tRe1\tRe1\n+chr22\t50763869\t50764496\t8663\t8663\tRe1\tRe1\n+chr22\t50764497\t50765215\t8664\t8664\tRe1\tRe1\n+chr22\t50765216\t50769525\t8665\t8665\tRe1\tRe1\n+chr22\t50769526\t50771588\t8666\t8666\tRe1\tRe1\n+chr22\t50771589\t50773285\t8667\t8667\tRe1\tRe1\n+chr22\t50773286\t50777600\t8668\t8668\tRe1\tRe1\n+chr22\t50777601\t50783896\t8669\t8669\tRe1\tRe1\n+chr22\t50783897\t50786637\t8670\t8670\tRe1\tRe1\n+chr22\t50786638\t50787146\t8671\t8671\tRe1\tRe1\n+chr22\t50787147\t50791313\t8672\t8672\tRe1\tRe1\n+chr22\t50791314\t50791700\t8673\t8673\tRe1\tRe1\n+chr22\t50791701\t50793839\t8674\t8674\tRe1\tRe1\n+chr22\t50793840\t50798861\t8675\t8675\tRe1\tRe1\n+chr22\t50798862\t50799224\t8676\t8676\tRe1\tRe1\n+chr22\t50799225\t50818468\t8677\t8677\tRe1\tNone\n' |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/filter_piechart.svg --- a/test-data/filter_piechart.svg Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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| diff -r b16228ec1540 -r a7bbbf32da62 test-data/hicup_deduplicator_summary.txt --- a/test-data/hicup_deduplicator_summary.txt Thu Nov 09 11:16:04 2017 -0500 +++ b/test-data/hicup_deduplicator_summary.txt Fri May 25 17:49:27 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ File Read_pairs_processed Unique_di-tags Cis_<10kbp_of_uniques Cis_>10kbp_of_uniques Trans_of_uniques -dataset_1265_4.dat.filt.sam 1 1 0 1 0 +dataset1_2.filt.bam 543 543 43 440 60 |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/hicup_filter_summary.txt --- a/test-data/hicup_filter_summary.txt Thu Nov 09 11:16:04 2017 -0500 +++ b/test-data/hicup_filter_summary.txt Fri May 25 17:49:27 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ File Total_pairs Valid_pairs Cis_<10kbp Cis_>10kbp Trans Invalid_pairs Same_circularised Same_dangling_ends Same_internal Re-ligation Contiguous_sequence Wrong_size -dataset_1265_4.dat.pair.sam 1 1 0 1 0 0 0 0 0 0 0 0 +dataset1_2.pair.bam 1143 543 43 440 60 600 22 75 474 29 0 0 |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/hicup_mapper_summary.txt --- a/test-data/hicup_mapper_summary.txt Thu Nov 09 11:16:04 2017 -0500 +++ b/test-data/hicup_mapper_summary.txt Fri May 25 17:49:27 2018 -0400 |
| b |
| @@ -1,3 +1,3 @@ File Total_reads_processed Reads_too_short_to_map %Reads_too_short_to_map Unique_alignments %Unique_alignments Multiple_alignments %Multiple_alignments Failed_to_align %failed_to_align Paired %Paired -dataset_1265.dat.trunc.fastq 1000 35 3.5 14 1.4 13 1.3 938 93.8 1 0.1 -dataset_1264.dat.trunc.fastq 1000 24 2.4 23 2.3 7 0.7 946 94.6 1 0.1 +dataset1.trunc.fastq.gz 99742 2658 2.7 3885 3.9 12437 12.5 80762 81.0 1143 1.1 +dataset2.trunc.fastq.gz 99742 2476 2.5 3725 3.7 12679 12.7 80862 81.1 1143 1.1 |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/hicup_truncater_summary.txt --- a/test-data/hicup_truncater_summary.txt Thu Nov 09 11:16:04 2017 -0500 +++ b/test-data/hicup_truncater_summary.txt Fri May 25 17:49:27 2018 -0400 |
| b |
| @@ -1,3 +1,3 @@ File Total_Reads_Processed Truncated %Truncated Not_truncated %Not_truncated Average_length_truncated_sequence -dataset_1265.dat 1000 77 7.70 923 92.30 21.39 -dataset_1264.dat 1000 61 6.10 939 93.90 22.21 +dataset1.fastq 99742 7230 7.25 92512 92.75 22.45 +dataset2.fastq 99742 7114 7.13 92628 92.87 22.63 |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/result.pair.sam --- a/test-data/result.pair.sam Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -@HD VN:1.0 SO:unsorted -@SQ SN:chr1 LN:199950 -@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" -@PG ID:HiCUP Mapper VN:0.5.9 -@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" -SRR071233.43293 83 chr1 35433 3 40M = 75323 0 GAGTCCAGGAGTTCAAGACCAGCCTGGGTAACATAGTGAG CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-15 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:3G22A1C11 YT:Z:UU -SRR071233.43293 163 chr1 75323 23 40M = 35433 0 CTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCG CCBCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-10 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:20A18A0 YT:Z:UU |
| b |
| diff -r b16228ec1540 -r a7bbbf32da62 test-data/results.html --- a/test-data/results.html Thu Nov 09 11:16:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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/></a>\n-\t\t<p>Analysis produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/hicup/"><strong>HiCUP</strong></a> (0.5.9) - a tool for mapping and performing quality control on Hi-C data.</p>\n-\t\t<p>Report graphs rendered using <a href="http://jquery.com/">jQuery</a> and <a href="http://www.highcharts.com/">Highcharts</a>.</p>\n-\t</footer>\n-</div>\n-</body>\n-</html>\n-\n' |
