| Next changeset 1:dfacabbde112 (2015-11-26) |
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Commit message:
Initial upload |
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added:
je je-clip.xml je_1.0_bundle.jar macros.xml test-data/barcodes_PE.txt test-data/barcodes_SE.txt test-data/clip_barcode_result_file.txt test-data/clip_dataset1_PE.fastq test-data/clip_dataset1_SE.fastq test-data/clip_dataset2_PE.fastq test-data/emb6801m1_CGTACTAGTAGATCGC_1.txt test-data/emb6801m1_CGTACTAGTAGATCGC_2.txt test-data/emb6801m2_AGGCAGAATAGATCGC_1.txt test-data/emb6801m2_AGGCAGAATAGATCGC_2.txt test-data/emb681m1_TAAGGCGACTCTCTAT_1.txt test-data/emb681m1_TAAGGCGACTCTCTAT_2.txt test-data/emb681m4_TCCTGAGCCTCTCTAT_1.txt test-data/emb681m4_TCCTGAGCCTCTCTAT_2.txt test-data/emb681m5_GGACTCCTCTCTCTAT_1.txt test-data/emb681m5_GGACTCCTCTCTCTAT_2.txt test-data/file_1_sequence.txt test-data/file_2_sequence.txt test-data/illu_dualindexing.txt test-data/illu_file_1_index.txt test-data/illu_file_1_sequence.txt test-data/illu_file_2_index.txt test-data/illu_file_2_sequence.txt test-data/illu_summary_PE.txt test-data/illu_unassigned_1_PE.txt test-data/illu_unassigned_2_PE.txt test-data/markdupes_DNase_sorted.bam test-data/markdupes_DNase_sorted_marked.bam test-data/markdupes_metrics.txt test-data/markdupes_umis.txt test-data/picard_MarkDuplicates.bam test-data/picard_MarkDuplicates_test1.bam test-data/sample1_CACTGTGTATAG_1.txt test-data/sample1_CACTGTGTATAG_2.txt test-data/sample2_ATTCCGTCCGTC_1.txt test-data/sample2_ATTCCGTCCGTC_2.txt test-data/sample3_GCTACCTGGTCA_1.txt test-data/sample3_GCTACCTGGTCA_2.txt test-data/sample4_CGAAACCACTGT_1.txt test-data/sample4_CGAAACCACTGT_2.txt test-data/summary_PE.txt test-data/summary_SE.txt test-data/unassigned_1_PE.txt test-data/unassigned_1_SE.txt test-data/unassigned_2_PE.txt |
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| diff -r 000000000000 -r 101525093ba1 je --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/je Wed Nov 25 12:37:01 2015 -0500 |
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| @@ -0,0 +1,15 @@ +#!/bin/sh +# Wrapper around je_1.0_bundle.jar + +# where are we stored ? +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" +# echo $DIR +# path to jar file to execute, this jar is supposed to be in the same dir as this script +JAR_FILE=$DIR"/je_1.0_bundle.jar" + +OPTS="-Xmx2g" +# uncomment to change logging level using your own log4j.xml found in $DIR file +# OPTS=$OPTS" -Dlog4j.configuration=file:$DIR/log4j.xml" + +java $OPTS -jar $JAR_FILE "$@" +exit $? |
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| diff -r 000000000000 -r 101525093ba1 je-clip.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/je-clip.xml Wed Nov 25 12:37:01 2015 -0500 |
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| b'@@ -0,0 +1,245 @@\n+<tool id="je_clip" name="Je-Clip" version="1.0">\n+ <description>clips Unique Molecular Identifiers (UMIs) from fastq files</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Tool exception" />\n+ </stdio>\n+ <version_command>echo \'1.0\'</version_command>\n+ <command interpreter="bash">\n+<![CDATA[\n+ je clip\n+\n+ ## Fastq inputs\n+ @single_or_paired_cmd@\n+ #if str( $library.type ) != "single":\n+ BPOS=${library.BPOS}\n+ #end if\n+\n+ @common_options_cmd@\n+ @barcode_len_cmd@\n+ ADD=${ADD}\n+ #if str($ADD) == "false":\n+ BARCODE_RESULT_FILENAME=$BARCODE_RESULT_FILENAME\n+ #end if\n+\n+ OF1=${OF1}\n+ #if str( $library.type ) != "single":\n+ OF2=${OF2}\n+ #end if\n+\n+ FORCE=true\n+]]>\n+ </command>\n+ <inputs>\n+ <!-- single/paired -->\n+ <expand macro="single_or_paired_general">\n+ <param name="BPOS" type="select" label="Barcode read position (BPOS)" help="where are the barcodes.">\n+ <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option>\n+ <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option>\n+ <option value="BOTH">BOTH (beginning of both reads)</option>\n+ </param>\n+ </expand>\n+ <expand macro="barcode_len_option"/>\n+ <param name="ADD" type="boolean"\n+ label="Add matched barcode at the end of the read header (ADD)"\n+ truevalue="true"\n+ falsevalue="false"\n+ checked="true"\n+ />\n+\n+ <expand macro="common_options"/>\n+\n+\n+ </inputs>\n+ <outputs>\n+ <data name="BARCODE_RESULT_FILENAME" format="tabular" label="Je-Clipped Barcodes"/>\n+ <data name="OF1" format_source="input_1" label="Je-Clipped {on_string}"/>\n+ <data name="OF2" format_source="input_1" label="Je-Clipped {on_string}">\n+ <filter>(type != "single")</filter>\n+ </data>\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <!-- simple test on single end data -->\n+ <param name="type" value="single"/>\n+ <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/>\n+ <param name="LEN" value="6"/>\n+ <param name="ADD" value="false"/>\n+ <output name="BARCODE_RESULT_FILENAME" file="clip_barcode_result_file.txt"/>\n+ <output name="OF1" file="clip_dataset1_SE.fastq"/>\n+ </test>\n+ <test>\n+ <!-- more complex test on paired end data with different barcode for fwd/rev -->\n+ <param name="type" value="paired"/>\n+ <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/>\n+ <param name="input_2" value="file_2_sequence.txt" ftype="fastqsanger"/>\n+ <param name="LEN" value="6"/>\n+ <param name="BPOS" value="BOTH"/>\n+ <output name="OF1" file="clip_dataset1_PE.fastq"/>\n+ <output name="OF2" file="clip_dataset2_PE.fastq"/>\n+ </test>\n+ </tests>\n+\n+\n+ <help>\n+<![CDATA[\n+**What it does**\n+\n+Je clip: Clips barcodes or Unique Molecular Identifiers (UMIs) from the input fastq files\n+Input files are fastq files, and can be in gzip compressed format.\n+\n+Author: Charles Girardot (charles.girardot@embl.de).\n+\n+Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).\n+\n+------\n+\n+**Know what you are doing**\n+\n+.. class:: warningmark\n+\n+ You will want to read the `documentation`__.\n+\n+ .. __: http://gbcs.embl.de/portal/Je\n+\n+------\n+\n+**Parameter list**\n+\n+This is an exhaustive list of options::\n+\n+ FASTQ_FILE1=File\n+ F1=File\n+\n+ Input fastq file (optionally gzipped) for single end data, or first read in paired end data.\n+ Required.\n+\n+ FASTQ_FILE2=File\n+ F2=File\n+\n+ Input fastq file (optionally gzipped) for the second read of paired end data.\n+ '..b"ad name (or headers) will follow the pattern (for both reads of a pair):\n+ @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 CLIPPED_SEQ_FROMREAD1:CLIPPED_SEQ_FROMREAD2\n+ This option only makes sense in paired end mode and ADD=true.Some (if not all) mappers\n+ will indeed complain when read headers of a read pair are not identical.\n+ When SAME_HEADERS=FALSE and the RCHAR is used, read headers look like this:\n+ HISEQ:44:C6KC0ANXX:5:1101:1491:1994:1:N:0:TGGAGTAG\n+ HISEQ:44:C6KC0ANXX:5:1101:1491:1994:3:N:0:CGTTGTAT\n+\n+ SAME_HEADERS=true will instead generates the following identical header for both reads :\n+ HISEQ:44:C6KC0ANXX:5:1101:1491:1994:TGGAGTAG:CGTTGTAT\n+ Note that we also clipped the useless '1:N:0' amd '3:N:0' as they also result in\n+ different headers\n+ Important : this option will force RCHAR=: UNLESS you specify RCHAR=null ; in which case\n+ a space will be preserved i.e.:\n+ HISEQ:44:C6KC0ANXX:5:1101:1491:1994 TAGAACAC:TGGAGTAG:CGTTGTAT\n+\n+ Default value: true.\n+ This option can be set to 'null' to clear the default value. Possible values: {true,\n+ false}\n+\n+ READ_NAME_REPLACE_CHAR=String\n+ RCHAR=String\n+\n+ Replace spaces in read name/header using provided character.\n+ This is needed when you need to retain ADDed barcode in read name/header during mapping\n+ as everything after space in read name is usually clipped in BAM files.\n+ For example, with RCHAR=':':\n+ @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 1:N:0:\n+ becomes\n+ @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965:1:N:0:BARCODE\n+\n+ Default value: ':'. This option can be set to 'null' to clear the default value.\n+\n+ XTRIMLEN=String\n+ XT=String\n+\n+ Optional extra number of base(s) to be trimmed right after the barcode. These extra bases\n+ are not added to read headers.\n+ When running paired-end, two distinct values can be given using the syntax XT=X:Z where X\n+ and Z are 2 integers to use for read_1 and read_2 respectively. Note that even when\n+ BPOS=READ_1 or BPOS=READ_2, a X:Y synthax can be given to trim the read w/o barcode to\n+ end up with reads of identical length (note that this can also be operated using ZT). If\n+ a unique value is given, e.g. XT=1, while running paired-end the following rule applies :\n+ (1) BPOS=READ_1 or BPOS=READ_2, no trim is applied at the read w/o barcode\n+ (2) BPOS=BOTH, the value is used for both reads.\n+ Note that XT=null is like XT=0.\n+ Default value: 0. This option can be set to 'null' to clear the default value.\n+\n+ ZTRIMLEN=String\n+ ZT=String\n+\n+ Optional extra number of bases to be trimmed from the read end i.e. 3' end. These extra\n+ bases are not added to read headers.\n+ When running paired-end, two distinct values can be given here using the syntax ZT=X:Z\n+ where X and Z are 2 integers to use for read_1 and read_2 respectively. Note that even\n+ when BPOS=READ_1 or BPOS=READ_2, a X:Y synthax can be given to trim the read w/o barcode\n+ as to end up with reads of the same length (note that this can also be operated using\n+ XT). Note that if a single value is passed, the value always applies to both reads in\n+ paired-end mode without further consideration.\n+\n+ Default value: 0. This option can be set to 'null' to clear the default value.\n+\n+ BARCODE_RESULT_FILENAME=String\n+ BF=String\n+\n+ Optional file name where to write clipped barcodes, default name is clipped_barcodes.txt.\n+ This file is automatically created if ADD=FALSE i.e. even if this option is not provided\n+ by user (and always created if this option is given).\n+ File format is tab delimited with:\n+ ``read header (col 1) barcode from read_1 (col 2) barcode quality from read_1 (col 2)``\n+ + barcode + quality from read_2 (col 4 and 5 respectively) when relevant.\n+ Can either be a name (in which case the file will be created in the output dir) or a full path.\n+ Default value: null.\n+\n+]]>\n+ </help>\n+\n+</tool>\n" |
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| diff -r 000000000000 -r 101525093ba1 je_1.0_bundle.jar |
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| Binary file je_1.0_bundle.jar has changed |
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| diff -r 000000000000 -r 101525093ba1 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Nov 25 12:37:01 2015 -0500 |
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| b'@@ -0,0 +1,336 @@\n+<macros>\n+\n+ <token name="@single_or_paired_cmd@">\n+ #if str( $library.type ) == "single":\n+ F1=${library.input_1}\n+ #elif str( $library.type ) == "paired":\n+ F1=${library.input_1}\n+ F2=${library.input_2}\n+ SAME_HEADERS=${library.SAME_HEADERS}\n+ #else\n+ ## prepare paired-end collection\n+ F1=${library.input_1.forward}\n+ F2=${library.input_1.reverse}\n+ SAME_HEADERS=${library.SAME_HEADERS}\n+ #end if\n+ </token>\n+\n+ <xml name="paired_options">\n+ <when value="paired">\n+ <param name="input_1" format="fastq" type="data" label="FASTQ file #1"/>\n+ <param name="input_2" format="fastq" type="data" label="FASTQ file #2"/>\n+ <yield />\n+ <param name="SAME_HEADERS" type="boolean"\n+ label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"\n+ help="Only applies if barcodes are added to the header (option ADD)"\n+ truevalue="true"\n+ falsevalue="false" checked="false"/>\n+ </when>\n+ <when value="paired_collection">\n+ <param name="input_1" format="fastq" type="data_collection" collection_type="paired"\n+ label="FASTQ Paired Dataset"/>\n+ <yield />\n+ <param name="SAME_HEADERS" type="boolean"\n+ label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"\n+ help="Only applies if barcodes are added to the header (option ADD)"\n+ truevalue="true"\n+ falsevalue="false" checked="false"/>\n+ </when>\n+ </xml>\n+\n+ <token name="@single_or_paired_illu_cmd@">\n+ @single_or_paired_cmd@\n+ I1=$library.I1\n+ #if str( $library.type ) != "single":\n+ #if str( $library.I2_CONDITIONAL.I2_AVAILABLE ) == "true":\n+ I2=${library.I2_CONDITIONAL.I2}\n+ BRED=${library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED}\n+ #if str( $library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED ) == "true":\n+ STRICT=${library.I2_CONDITIONAL.BRED_CONDITIONAL.STRICT}\n+ #end if\n+ #end if\n+ #end if\n+ </token>\n+\n+ <xml name="single_or_paired_illu">\n+ <conditional name="library">\n+ <param name="type" type="select" label="Is this single or paired library">\n+ <option value="single">Single-end</option>\n+ <option value="paired">Paired-end</option>\n+ <option value="paired_collection">Paired-end Dataset Collection</option>\n+ </param>\n+ <when value="single">\n+ <param name="input_1" format="fastq" type="data" label="FASTQ file"/>\n+ <param name="I1" type="data" format="fastq" label="First Index File"/>\n+ </when>\n+ <expand macro="paired_options">\n+ <param name="I1" type="data" format="fastq" label="First Index File"/>\n+ <conditional name="I2_CONDITIONAL">\n+ <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?">\n+ <option value="true">Yes</option>\n+ <option value="false" selected="true">No</option>\n+ </param>\n+ <when value="true">\n+ <param name="I2" type="data" format="fastq" label="Second Index File"/>\n+ <expand macro="bred_conditional"/>\n+ </when>\n+ <when value="false"/>\n+ </conditional>\n+ </expand>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="single_or_paired_general">\n+ <conditional name="library">\n+ <param name="type" type="select" label="Is this single or paired library">\n+ <option value="single">Single-end</option>\n+ <option value="pa'..b'T" type="select" label="Fastq Quality Format (V)"\n+ help="How are the quality values encoded in the fastq. Either \'Solexa\' for\n+ pre-pipeline 1.3 style scores (solexa scaling + 66), \'Illumina\' for pipeline 1.3 and\n+ above (phred scaling + 64) or \'Standard\' for phred scaled scores with a character shift\n+ of 33.">\n+ <option value="Standard" selected="true">\n+ Fastq - Illumina Casava v1.8 with Sanger coding quality (phred scaling + 33)\n+ </option>\n+ <option value="Illumina">\n+ Fastq - Illumina v1.3 or above coding of quality (phred scaling + 64)\n+ </option>\n+ <option value="Solexa">\n+ Fastq - Solexa-style quality (solexa scaling + 66)\n+ </option>\n+ <option value="null">\n+ Detect automatically\n+ </option>\n+ </param>\n+ </xml>\n+\n+ <token name="@demultiplexer_common_output_options_cmd@">\n+ KEEP_UNASSIGNED_READ=$KEEP_UNASSIGNED_READ\n+ STATS_ONLY=${adv_options.STATS_ONLY}\n+ #if str( $adv_options.DIAG ) == "true":\n+ BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE\n+ #end if\n+ </token>\n+ <xml name="demultiplexer_common_output_options">\n+ <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"\n+ truealue="true"\n+ falsevalue="false"\n+ checked="true"\n+ />\n+ <section name="adv_options" title="Advanced Options" expanded="False">\n+ <param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)"\n+ truevalue="true" falsevalue="false" checked="false"\n+ help="This file will\n+ contain a line per read pair with the barcode best matching the read subsequence or \'null\' when no\n+ match is found according to matching parameters. This file is useful for debugging or further\n+ processing in case both ends are barcoded."/>\n+ <param name="STATS_ONLY" type="boolean" label="Only produce metric and diagnostic reports (STATS_ONLY)"\n+ truevalue="true" falsevalue="false" checked="false"\n+ help="do not demultiplex." />\n+ </section>\n+ </xml>\n+\n+ <token name="@common_options_cmd@">\n+ XT=${XT}\n+ ZT=${ZT}\n+ #if str( $RCHAR ) != "":\n+ RCHAR=${RCHAR}\n+ #end if\n+ GZ=${GZ}\n+ OUTPUT_DIR=results\n+ </token>\n+ <xml name="common_options">\n+ <param name="XT" type="text" value="0"\n+ label="Extra number of bases to be trimmed right after the barcode (XT)" />\n+ <param name="ZT" type="text" value="0"\n+ label="Extra number of bases to be trimmed from the read end (ZT)" />\n+\n+ <param name="RCHAR" type="text"\n+ label="Replace white space in the read name/header with speficied symbols (RCHAR)"\n+ help="Set to empty for no replacement"\n+ value=":"/>\n+\n+ <param name="GZ" type="boolean" hidden="true" label="Compress output (GZ)"\n+ help="will result in fastq.gz files."\n+ truevalue="true"\n+ falsevalue="false"\n+ checked="false"/>\n+ </xml>\n+\n+ <token name="@demultiplexer_common_outputs_cmd@">\n+ METRICS_FILE_NAME=$METRICS_FILE_NAME\n+ </token>\n+ <xml name="demultiplexer_common_outputs">\n+ <data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex result">\n+ <!--<discover_datasets pattern="(?P<name>.*)\\.txt" ext="fastqsanger"-->\n+ <discover_datasets pattern="(?P<name>.*)\\.txt" directory="results" visible="true" ext="fastqsanger"/>\n+ </data>\n+ <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">\n+ <filter>(adv_options[\'DIAG\'] == \'true\')</filter>\n+ </data>\n+ </xml>\n+\n+</macros>\n' |
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| diff -r 000000000000 -r 101525093ba1 test-data/barcodes_PE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcodes_PE.txt Wed Nov 25 12:37:01 2015 -0500 |
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| @@ -0,0 +1,4 @@ +sample1 CACTGT:GTATAG sample1_1_PE.txt sample1_2_PE.txt +sample2 ATTCCG:TCCGTC sample2_1_PE.txt sample2_2_PE.txt +sample3 GCTACC:TGGTCA sample3_1_PE.txt sample3_2_PE.txt +sample4 CGAAAC:CACTGT sample4_1_PE.txt sample4_2_PE.txt \ No newline at end of file |
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| diff -r 000000000000 -r 101525093ba1 test-data/barcodes_SE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcodes_SE.txt Wed Nov 25 12:37:01 2015 -0500 |
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| @@ -0,0 +1,4 @@ +sample1 CACTGT sample1_SE.txt +sample2 ATTCCG sample2_SE.txt +sample3 GCTACC sample3_SE.txt +sample4 CGAAAC sample4_SE.txt \ No newline at end of file |
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| diff -r 000000000000 -r 101525093ba1 test-data/clip_barcode_result_file.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clip_barcode_result_file.txt Wed Nov 25 12:37:01 2015 -0500 |
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| @@ -0,0 +1,26 @@ +READ_HEADER BC_SEQ_READ1 BC_QUAL_READ1 +1:N:0: CACTGT CCCFFF +1:N:0: CACTGT BBCFFF +1:N:0: CACTGT CCCFFF +1:N:0: CACTGT =?@D;D +1:N:0: CACTGT BB=DDD +1:N:0: CACTGT CCCFFF +1:N:0: ATTCCG @BCFFF +1:N:0: ATTCCG @BCFFF +1:N:0: ATTCCG @@CFFF +1:N:0: ATTCCG CCCFFF +1:N:0: ATTCCG 1?8ADD +1:N:0: ATTCCG CCCFFF +1:N:0: ATTCCG @@CFFF +1:N:0: GCTACC CCCFFF +1:N:0: GCTACC CC@FFF +1:N:0: GCTACC CCCFFF +1:N:0: GCTACC CCCFFF +1:N:0: GCTACC CCCFFF +1:N:0: GCTACC CCCFFF +1:N:0: CGAAAC CCCFFF +1:N:0: CGAAAC CCCFFF +1:N:0: CGAAAC ?@@FFD +1:N:0: CGAAAC @@@DAD +1:N:0: CGAAAC ;@@BDD +1:N:0: CGAAAC CCCFFF |
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| diff -r 000000000000 -r 101525093ba1 test-data/clip_dataset1_PE.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clip_dataset1_PE.fastq Wed Nov 25 12:37:01 2015 -0500 |
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| @@ -0,0 +1,100 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097:1:N:0:CACTGT +TCAATGCCAATAGCAATGAAACCACCCATANAANNNNNACGGCTGAACANNNNNNNACNNGATATAGCATAAATGNANNNTNNNNANTNNNNNN ++ +FFHHHHHJJJJJJJJJJJIJJJIJJJJJJI#1?#####00?FHIJJJJI#######--##,,=A=CDDDDDDDEE################### +@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140:1:N:0:CACTGT +AATTTATCTCTTTTCATATAACTCTCTGGTAATNNNNAACATAAAACCGANCGCACATGATAATTCTTCCAAATTTATATATNAATTTTATANN ++ +DFHHHGHHIJJJJJJIJIJIGHHHIJJJJGGIJ####11?DHHIIIIGHI#-<FEHGIJIJHGHFHHHHHFFFFFFEFEEEE#,;?BDDFDE## +@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170:1:N:0:CACTGT +TGTAAAGTAGCTAATCAACTAAAAATTTTAATTCCAGTAGGAACTGCAATNATTATAGTAGCTGAGGTAAAATAAGCTCGAGTATCTACATCTA ++ +FFHHHHHIJJJJJJJJJJJJIJJJJJJJJJJJJIJJJIIJJJJJJJJJJI#0?FHIJJJJJJJJGIJHIIJJJHHHHHHFFD@CEEEFDDDDDC +@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179:1:N:0:CACTGT +ACCAGACTTGTGGGGCGACTGTTCAGGCCGTGTAGGGCATTCAGGGGTAGCATGGGAGCAGCTAGATTAGATGCAGATCTCTGAGAAGCTGTCT ++ +BDDBFDFIIEF??8@EFGFHFGAFFGGIHH;5.=CEE),7.;(;ACB9>?CAAC??9?B@9??C:(:@A::@CC:4+:>@C@AAC(>9?CCCC@ +@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184:1:N:0:CACTGT +GTGGGAAAGGGAAGGGCAAGGGGGAGGGGAAGAATTTAACCGGGCGGGAGGAGAATCGGGCAGGGAAGAATGGTTGGTTGGTGGAACAACTGAA ++ +EDHHHDHJJGIGIJCBDHEHGJJJBGEHIBGGHFGFFGGHFFDD>?BDBBDDDDDD@ADD;>@D98AB?CCDD:CBB<ADD8<?<@?B?ACDCA +@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193:1:N:0:CACTGT +GCGAGTGTTTGCACGATTATCTCATATTCAAACTGGTCAACATGGGCATACGATTTCTTGCGCTCCTTGCTTTCAAACAGCCTGTCTCTTATAC ++ +F+CFHFHIIJJJJJJIJJIJJJJJJJJJJIJJJJJJBGIJJJJJJJJJJJJJJJJIJJJJHHFFFDEEEDDDDDDDDDDDBBDDDDDDDDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204:1:N:0:ATTCCG +CATCTGTTGCTCATATAGGAATTGTTCTATCAGGACTTTTAACTATAACTTATTGAGGTTTATGTGGTTCTTATACATTAATAATTGCTCATGG ++ +DFHHHGHJJIJJJJJJJJJJJJJJJJJJIJJJJJJJIJJJIJJJJJJIJJJJJJIJJJHIJJJJHIIHHHHIJJJIJJHHHHHHFFFFEFCEEE +@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207:1:N:0:ATTCCG +GTCGTTGTGATACTAAACTTTCTCAAATAATAAAAAAAAAGAATAAAATTCCTAATAATGAAATAGTTGATCCAATAGTTGATACAATATTTCA ++ +FFHHHGHIIGIJJIIJJJJJJIIHIIJHGIHGJIJIJJJHGCCHIGGEHH>EEFFFFFFFACCEACEDCDCCCCCDCDEEDDDE(:ACCD:@D@ +@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211:1:N:0:ATTCCG +AGTAAATTAAATGCGAAAATAAAAGGCAGCATGAGNTANTTACTNAAANGGGGTCATNAACAGTACTTGTGCTCCNCCANGTCGNCGNTNCNCT ++ +FFFHHHHJJJIJJJJJJJIJIJJJJJJJJJJJJJJ#0?#0?DHI#-;F#-;DH?EFH#,;BCDEEEEEDDCCCDD#,8?#,5?B########## +@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222:1:N:0:ATTCCG +ATAGTAATAATATTACCTAATACAAATAATGAAATATCATATTGATGAAATCATTTTACTATACCTGATACAGTTGTTATAGCTCCGATAGCTC ++ +FDFHHHHJJIIJJJGJIIJJIIJHIJIJIJIIJJJJJJJIIJJIGGHIJJJIJGJJIIIHIIHJ>GHIIIIIIGGGIIJJJJIH)=ABDDDDEE +@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233:1:N:0:ATTCCG +AATTTAATGCAATTACCAATCTTACAAGTTATTATACCAATAATTGCATCTATGTTTTGCTTTCTTGACAAGAAACACAAGGTAACTTGGGTTA ++ +DD<DFDFB<?:EIBHHIIFF:AHI?HC<*:1:EF@G49D<B3?@F4?BDD*BG*?B??B<B8888@F)).@;@;@;=6?############### +@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240:1:N:0:ATTCCG +GGCATCGTTGCTGCTCTTAACGTCCAAATGGACGGGCGACTCCCCGAACATTGCCTCGAGTCGTGTCTCCACGGATTTCTGGACGTCCGAATCG ++ +FFHHHHHJJJIIIJIHGIJJIHHJJJHIJJJFHIJJBHGGHHHHFEDDDDDDDDDDDDDDCCBDDDDDDDDDDDDDDDDEDD@BDDDDBB@BBD +@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245:1:N:0:ATTCCG +AAATATAAAGTATAAGCAGCTCTAAAAAAAGATAAAAAAGATAATAAAATTATAGAAATTCAAGATCAAGAAACAATTCTATTTAATAAAGAAA ++ +FFFBDFHGIGHGJIJJJJJIIDHHIJJIGGHEEGGIIIIGGDHIGE@FHHIIJJFGGHGHCAHH@D;CD;CCCECDDCCDDDCD3>ACAA:@?C +@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088:1:N:0:GCTACC +AAGTTTATAAATGGCAACCTTAAGTGTAANNNANNNNNTATGCACAGNANNNNNNNNANNNATGCAAAACGACTCNNNNNNNNNNNNCNNNNNN ++ +FFHHHHHJJJJJJJJJJJJJJJJJIIHIJ###1#####20?FHJJJJ#.########-###--;BDFEEECDDDD################### +@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095:1:N:0:GCTACC +ACGTTCATAAGATACATTAGCTAAACAAAANAANNNNNAAGAACATAAANNNNNNNCANNTATTAATGTATAAGANCNNNANNNNCNTNNNNNN ++ +FFHHHHHJJJJJJIJJJJIJJJJIJJJJJJ#1C#####00?FIJJJJJJ#######--##,5?DDEEEFCFFEDD################### +@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114:1:N:0:GCTACC +CGTTGGAGGAGGAGCCGCCATGAATGCCCTGCGNNNNTTCTACCTGGAGANNNCGGTGGTCACACGAGCCTACACCACGGTCNNCGTGCTNNNN ++ +FFHHHHGJJGHJGHIJJJJJJJJJJJJJJJJJJ####.-;DHIJJHHHHH###,,=?BDBDDDDDDDDDDDDDDDDDDDDDD##+28@DD#### +@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119:1:N:0:GCTACC +TGGACTCAAGACCTAATTGCATTAACCGTCTGTNNNNTACGTAGCGTATGNNATTGCGCACTTCTTCTGCGGATAGTCCTTCNNCATCTCNNNN ++ +FFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJIJ####20?GHIJJJIJIJ##-5CEFHFFDDEEDDDDDDDDDDDDDEDDDD##+2?BDD#### +@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124:1:N:0:GCTACC +TACATATACTTATAGGCATACTTATACGACTTCNNNNCCCGGTTAATATGNNGTGGCCCGTATAAGTTAATGGGCACAACCGNNTGGGACNNNN ++ +FFHHHHHIJJJJJJJJJJJIJJJJJJJJJJJJJ####00BFHGIIJJJJJ##--BEHJJHDFFEDEEFEEEDDDDDDDDDDD##+2<B@B#### +@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150:1:N:0:GCTACC +TCCACTCGCATGTGTATCTAATGAATGCCTCAANACGCTCCTGAACGCAANCAGGTATGTGTGGTAGACCAAAAAAAAAAAANCGGCAGGTANN ++ +FFHHHHHJJJJJJJHIJJJJJJJJJJJJJJJJJ#2?FHIJJJJHIJJJJJ#.;DHCHHHHHHHFDFFEEEEDDDDDDDDDDD############ +@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151:1:N:0:CGAAAC +AACTTAAGGCTGAAAATTATTTATTTGACTTGTGTCAAATATAAAAATGTNTTGTGTAGAAACGGTAATGTGAAATTAATGTNAAATATTCTNN ++ +FFHHHHHJJJJJJJJJJJJJJJJJJIIIJJJJHIJJJJIJIJJJIJIJJI#0?FGIIJJJJJJIIEIJJHHHGHHHFFFFFF#,;ABDEDEE## +@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159:1:N:0:CGAAAC +TGCAATGCAAGTGGATTAGAGGATTGCAGCTGGAGGGGTAACAGCAGTGCNTTCGAAATATGTATCTTACAGCATTTCTGGGNTCCTCGTCCGN ++ +FFHHHHHJJJJHIIIIJIJIJJJJJJJJJJJJJFHJJJ?FHCFFHGIGHC#-5;DHHFHHHFCDFFFFFEEEECEDCDCCDC#,8<BBDABB## +@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170:1:N:0:CGAAAC +CTCTTGGGTGTATTGGTTGGCCGTTTTACTCTTTTGTTGGAGACTGAGAANCTTAGCTGATATAACTTCTACCGATTCTCCTTTAACTGCACTT ++ +FFHFHHHI?FEEEHHIHHGIEGHHIJJHIIGIIIJFGIJJHIIIEHIIHG#-;CEHHHHDFFFFFDEEC@CECDD?@CDD@CACDCDDDDCDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174:1:N:0:CGAAAC +AAATGACCAAATCCTAGGTGTTTGAGCGCGGACTGGAGGCGATTCCGCTGTCCGTGGATCTGTGGATCCACTACCTAATGCACGTTAAGTCCAA ++ +DDHHAHHGGB@BHIIIFE<AHHI;4?9DHGE@A;AHGEHEE>AC@@CB@BBA@?BBBBA@CCDCCCCC<493?CCCCCC>:>A<8???AC#### +@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176:1:N:0:CGAAAC +GGAAGAGAAAAAAATATAAAGTGTCAAGGGGCGTGTGCAGCGACACTTCGCCGACCCCTCCCCACATTATTTTTTTGCCGCCCGCTGGTAGCAG ++ +DA:DBFDF;A<A@EGGB@:?D1:D?9:BGIDGE4@########################################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187:1:N:0:CGAAAC +AAATAATCAAACTACATCGACAAAATGTCAATATCATGCAGCTGCTTCAAAACCAAAATGATGATTTTTTGAGAAGTGATTATTTAAATGTCGT ++ +FFHHHHHJJJJJJJJJJJJJJJJJIJJIJJJJJJJJJJJJJJJJJJJJJJJJJJIJIJJJJJJJJJJHHFFDDDEDCDDFEEDFEEEDEEFEDD |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/clip_dataset1_SE.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clip_dataset1_SE.fastq Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,100 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097 1:N:0: +TCAATGCCAATAGCAATGAAACCACCCATANAANNNNNACGGCTGAACANNNNNNNACNNGATATAGCATAAATGNANNNTNNNNANTNNNNNN ++ +FFHHHHHJJJJJJJJJJJIJJJIJJJJJJI#1?#####00?FHIJJJJI#######--##,,=A=CDDDDDDDEE################### +@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140 1:N:0: +AATTTATCTCTTTTCATATAACTCTCTGGTAATNNNNAACATAAAACCGANCGCACATGATAATTCTTCCAAATTTATATATNAATTTTATANN ++ +DFHHHGHHIJJJJJJIJIJIGHHHIJJJJGGIJ####11?DHHIIIIGHI#-<FEHGIJIJHGHFHHHHHFFFFFFEFEEEE#,;?BDDFDE## +@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170 1:N:0: +TGTAAAGTAGCTAATCAACTAAAAATTTTAATTCCAGTAGGAACTGCAATNATTATAGTAGCTGAGGTAAAATAAGCTCGAGTATCTACATCTA ++ +FFHHHHHIJJJJJJJJJJJJIJJJJJJJJJJJJIJJJIIJJJJJJJJJJI#0?FHIJJJJJJJJGIJHIIJJJHHHHHHFFD@CEEEFDDDDDC +@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179 1:N:0: +ACCAGACTTGTGGGGCGACTGTTCAGGCCGTGTAGGGCATTCAGGGGTAGCATGGGAGCAGCTAGATTAGATGCAGATCTCTGAGAAGCTGTCT ++ +BDDBFDFIIEF??8@EFGFHFGAFFGGIHH;5.=CEE),7.;(;ACB9>?CAAC??9?B@9??C:(:@A::@CC:4+:>@C@AAC(>9?CCCC@ +@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184 1:N:0: +GTGGGAAAGGGAAGGGCAAGGGGGAGGGGAAGAATTTAACCGGGCGGGAGGAGAATCGGGCAGGGAAGAATGGTTGGTTGGTGGAACAACTGAA ++ +EDHHHDHJJGIGIJCBDHEHGJJJBGEHIBGGHFGFFGGHFFDD>?BDBBDDDDDD@ADD;>@D98AB?CCDD:CBB<ADD8<?<@?B?ACDCA +@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193 1:N:0: +GCGAGTGTTTGCACGATTATCTCATATTCAAACTGGTCAACATGGGCATACGATTTCTTGCGCTCCTTGCTTTCAAACAGCCTGTCTCTTATAC ++ +F+CFHFHIIJJJJJJIJJIJJJJJJJJJJIJJJJJJBGIJJJJJJJJJJJJJJJJIJJJJHHFFFDEEEDDDDDDDDDDDBBDDDDDDDDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204 1:N:0: +CATCTGTTGCTCATATAGGAATTGTTCTATCAGGACTTTTAACTATAACTTATTGAGGTTTATGTGGTTCTTATACATTAATAATTGCTCATGG ++ +DFHHHGHJJIJJJJJJJJJJJJJJJJJJIJJJJJJJIJJJIJJJJJJIJJJJJJIJJJHIJJJJHIIHHHHIJJJIJJHHHHHHFFFFEFCEEE +@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207 1:N:0: +GTCGTTGTGATACTAAACTTTCTCAAATAATAAAAAAAAAGAATAAAATTCCTAATAATGAAATAGTTGATCCAATAGTTGATACAATATTTCA ++ +FFHHHGHIIGIJJIIJJJJJJIIHIIJHGIHGJIJIJJJHGCCHIGGEHH>EEFFFFFFFACCEACEDCDCCCCCDCDEEDDDE(:ACCD:@D@ +@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 1:N:0: +AGTAAATTAAATGCGAAAATAAAAGGCAGCATGAGNTANTTACTNAAANGGGGTCATNAACAGTACTTGTGCTCCNCCANGTCGNCGNTNCNCT ++ +FFFHHHHJJJIJJJJJJJIJIJJJJJJJJJJJJJJ#0?#0?DHI#-;F#-;DH?EFH#,;BCDEEEEEDDCCCDD#,8?#,5?B########## +@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222 1:N:0: +ATAGTAATAATATTACCTAATACAAATAATGAAATATCATATTGATGAAATCATTTTACTATACCTGATACAGTTGTTATAGCTCCGATAGCTC ++ +FDFHHHHJJIIJJJGJIIJJIIJHIJIJIJIIJJJJJJJIIJJIGGHIJJJIJGJJIIIHIIHJ>GHIIIIIIGGGIIJJJJIH)=ABDDDDEE +@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233 1:N:0: +AATTTAATGCAATTACCAATCTTACAAGTTATTATACCAATAATTGCATCTATGTTTTGCTTTCTTGACAAGAAACACAAGGTAACTTGGGTTA ++ +DD<DFDFB<?:EIBHHIIFF:AHI?HC<*:1:EF@G49D<B3?@F4?BDD*BG*?B??B<B8888@F)).@;@;@;=6?############### +@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240 1:N:0: +GGCATCGTTGCTGCTCTTAACGTCCAAATGGACGGGCGACTCCCCGAACATTGCCTCGAGTCGTGTCTCCACGGATTTCTGGACGTCCGAATCG ++ +FFHHHHHJJJIIIJIHGIJJIHHJJJHIJJJFHIJJBHGGHHHHFEDDDDDDDDDDDDDDCCBDDDDDDDDDDDDDDDDEDD@BDDDDBB@BBD +@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245 1:N:0: +AAATATAAAGTATAAGCAGCTCTAAAAAAAGATAAAAAAGATAATAAAATTATAGAAATTCAAGATCAAGAAACAATTCTATTTAATAAAGAAA ++ +FFFBDFHGIGHGJIJJJJJIIDHHIJJIGGHEEGGIIIIGGDHIGE@FHHIIJJFGGHGHCAHH@D;CD;CCCECDDCCDDDCD3>ACAA:@?C +@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 1:N:0: +AAGTTTATAAATGGCAACCTTAAGTGTAANNNANNNNNTATGCACAGNANNNNNNNNANNNATGCAAAACGACTCNNNNNNNNNNNNCNNNNNN ++ +FFHHHHHJJJJJJJJJJJJJJJJJIIHIJ###1#####20?FHJJJJ#.########-###--;BDFEEECDDDD################### +@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 1:N:0: +ACGTTCATAAGATACATTAGCTAAACAAAANAANNNNNAAGAACATAAANNNNNNNCANNTATTAATGTATAAGANCNNNANNNNCNTNNNNNN ++ +FFHHHHHJJJJJJIJJJJIJJJJIJJJJJJ#1C#####00?FIJJJJJJ#######--##,5?DDEEEFCFFEDD################### +@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 1:N:0: +CGTTGGAGGAGGAGCCGCCATGAATGCCCTGCGNNNNTTCTACCTGGAGANNNCGGTGGTCACACGAGCCTACACCACGGTCNNCGTGCTNNNN ++ +FFHHHHGJJGHJGHIJJJJJJJJJJJJJJJJJJ####.-;DHIJJHHHHH###,,=?BDBDDDDDDDDDDDDDDDDDDDDDD##+28@DD#### +@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 1:N:0: +TGGACTCAAGACCTAATTGCATTAACCGTCTGTNNNNTACGTAGCGTATGNNATTGCGCACTTCTTCTGCGGATAGTCCTTCNNCATCTCNNNN ++ +FFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJIJ####20?GHIJJJIJIJ##-5CEFHFFDDEEDDDDDDDDDDDDDEDDDD##+2?BDD#### +@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 1:N:0: +TACATATACTTATAGGCATACTTATACGACTTCNNNNCCCGGTTAATATGNNGTGGCCCGTATAAGTTAATGGGCACAACCGNNTGGGACNNNN ++ +FFHHHHHIJJJJJJJJJJJIJJJJJJJJJJJJJ####00BFHGIIJJJJJ##--BEHJJHDFFEDEEFEEEDDDDDDDDDDD##+2<B@B#### +@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150 1:N:0: +TCCACTCGCATGTGTATCTAATGAATGCCTCAANACGCTCCTGAACGCAANCAGGTATGTGTGGTAGACCAAAAAAAAAAAANCGGCAGGTANN ++ +FFHHHHHJJJJJJJHIJJJJJJJJJJJJJJJJJ#2?FHIJJJJHIJJJJJ#.;DHCHHHHHHHFDFFEEEEDDDDDDDDDDD############ +@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151 1:N:0: +AACTTAAGGCTGAAAATTATTTATTTGACTTGTGTCAAATATAAAAATGTNTTGTGTAGAAACGGTAATGTGAAATTAATGTNAAATATTCTNN ++ +FFHHHHHJJJJJJJJJJJJJJJJJJIIIJJJJHIJJJJIJIJJJIJIJJI#0?FGIIJJJJJJIIEIJJHHHGHHHFFFFFF#,;ABDEDEE## +@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159 1:N:0: +TGCAATGCAAGTGGATTAGAGGATTGCAGCTGGAGGGGTAACAGCAGTGCNTTCGAAATATGTATCTTACAGCATTTCTGGGNTCCTCGTCCGN ++ +FFHHHHHJJJJHIIIIJIJIJJJJJJJJJJJJJFHJJJ?FHCFFHGIGHC#-5;DHHFHHHFCDFFFFFEEEECEDCDCCDC#,8<BBDABB## +@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170 1:N:0: +CTCTTGGGTGTATTGGTTGGCCGTTTTACTCTTTTGTTGGAGACTGAGAANCTTAGCTGATATAACTTCTACCGATTCTCCTTTAACTGCACTT ++ +FFHFHHHI?FEEEHHIHHGIEGHHIJJHIIGIIIJFGIJJHIIIEHIIHG#-;CEHHHHDFFFFFDEEC@CECDD?@CDD@CACDCDDDDCDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174 1:N:0: +AAATGACCAAATCCTAGGTGTTTGAGCGCGGACTGGAGGCGATTCCGCTGTCCGTGGATCTGTGGATCCACTACCTAATGCACGTTAAGTCCAA ++ +DDHHAHHGGB@BHIIIFE<AHHI;4?9DHGE@A;AHGEHEE>AC@@CB@BBA@?BBBBA@CCDCCCCC<493?CCCCCC>:>A<8???AC#### +@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176 1:N:0: +GGAAGAGAAAAAAATATAAAGTGTCAAGGGGCGTGTGCAGCGACACTTCGCCGACCCCTCCCCACATTATTTTTTTGCCGCCCGCTGGTAGCAG ++ +DA:DBFDF;A<A@EGGB@:?D1:D?9:BGIDGE4@########################################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187 1:N:0: +AAATAATCAAACTACATCGACAAAATGTCAATATCATGCAGCTGCTTCAAAACCAAAATGATGATTTTTTGAGAAGTGATTATTTAAATGTCGT ++ +FFHHHHHJJJJJJJJJJJJJJJJJIJJIJJJJJJJJJJJJJJJJJJJJJJJJJJIJIJJJJJJJJJJHHFFDDDEDCDDFEEDFEEEDEEFEDD |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/clip_dataset2_PE.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clip_dataset2_PE.fastq Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,100 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097:4:N:0:GTATAG +AGAATGGTGNNNNTGTNNNNNTCCTAATATTCCATTTATGCTATATCCAGTCGTTCTNNNNNNNNNNNNNNNNNNNNNNNNNGTGGTTTCATNN ++ +2@>@@@@@@####43@#####11=?????????>?????????????????????@?##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140:4:N:0:GTATAG +TTATATGAAAGNAATATAAAATTTATATATAAATTTGGAAGAATTATCATGTGCGCTCNNNNNNNNNTTANANATNNNNNNAGAGTTATATGAN ++ +2@@@@@@@?@@#3=>?@@?@@@?@?@>?????>????????????>??????@?????#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170:4:N:0:GTATAG +GCTATTGGATTATTAGGATTTATTGTATGAGCTCATCATATATTTACCGTTGGAATAGATNTAGATACTCGAGCTTATTTTACCTCAGCTACTA ++ +FFHHHHHJEHIHHJIJJHIJJIJJJIJJJIJJJJIJJJJIJIIJIGJJJJJJJJJJJJJJ#-;CFHIJJJHHHFFFFFEEEEEEEDDDDDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179:4:N:0:GTATAG +AGAGATCTGCATCTAATCTAGCTGCTCCCATGCTACCCCTGAATACCCTACACGGCCTGAACAGTCGCCCCACAAGTCTGGCGTGGGGCTGTCT ++ +DFHF?HHGBHHIJJIGIIIJGIJBEHIGID<9EHIIJJI@;?BGGHIIIIIIIIIIIAGE@HHH?EDFDDB?B?9?:ACCC(85>>B>>@BBD@ +@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184:4:N:0:GTATAG +CATTCTGTATGCCCTTCCCTCTCGCACACTCGACCCAATGACCCGCTTTGCTCTGTTTACCTCTCCGCTCTGTTTTTGCACTTGGAAATTGCTA ++ +FFHGDHHGGIJJIJJJGHIIIGFHHIIGIIIJIJJEHGEGGIJJIIIIGGGHGGFHHFEC@BCEDECDDDDDDDDDD?AC>ACCCCACADCCDD +@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193:4:N:0:GTATAG +TGAAAGCAAGGAGCGCAAGAAATCGTATGCCCATGTTGACCAGTTTGAATATGAGATAATCGTGCAAACACTCCCAAGGAACTGTCTCTTATAC ++ +FFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJHJJJJJGHIIIIIJJIJIJEEEEHHFFFEEEEDED3=CDDDDDDDDCDDDDDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204:4:N:0:TCCGTC +TTCTTCGACTTCCAAGACGTTCATAAGATACATTAGCTAAACAAAATAACCCAGAAGAACATAAACCATGAGCAATTATTAATGTATAAGAACC ++ +FFHHHFHIJJJJJJJJJJIIGIIIJJIIGHJJJJIJJIIJIJJJIJJIJJJJJJJJIGIJIIJJHHFHHFFFFFEDEEEFFFEDDDEFEDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207:4:N:0:TCCGTC +TATATTTATTGGAGTTAATTTAACATTTTTTCCTCAACATTTTTTAGGATTGGCTGGAATACCTCGACGTTATTCAGATTACCCAGATGCTTAC ++ +FDHDHHHIJJJJEHHHIIIIJIJHIHIJJJJIGHEIIIJJIJJJHHGIIIJIJIJIJEHGHGFHFH8?ABC?BC>>AADDCACDDDDD<@CD>> +@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211:4:N:0:TCCGTC +GGCATAGCCATCGAGGTGTGTCCGGTGTCAAATCAAGTGCTGCAACTGGGCGTGGACTATCGGAATCATCCGGCGGCACTGCTGTTGGCCGCCA ++ +FFHHHHGJJJJJJIJJAGHHGIHHIDFGHIJJJGIJJGIJJIIJIJJIJJJJHHFEFEECACDDBB@CCD@?BDDDDDDDDDDDDCDB:@>BBD +@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222:4:N:0:TCCGTC +GACCATTAACAGGAGCTATCGGAGCTATAACAACTGTATCAGGTATAGTAAAATGATTTCATCAATATGATATTTCATTATTTGTATTAGGTAA ++ +FFHHFHGJJJJJJIIJJGJIIJGHGHIIIJIJJIGIHIIGIIJBFDIIGHJJIJJGIEIEGHIJCH@EHFHGHHHGFFFFFFFFFDDEEDCAC@ +@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233:4:N:0:TCCGTC +AACCAAGATACCTTGTGTTTCTTGGCAAGAAAGCAAAACATTGATGCAATTATTGGTATAATAACTTGTAAGATTGGTAATTGCATTAAATTGT ++ +D4DB?:3E3+2AEAHHFIIIIIIIE9?9?3DGFF>;;F;D9BD9?@DCFFICFGF@FCF@@F@C@DF<7C@E3?ECC>7@DDBAADA;;;>A:A +@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240:4:N:0:TCCGTC +CAGCAATCGCAGCAACAACTAAATGGAAACCAACAGCATCTGCCCATCAATCGTCAACCGGCGCCACAGCAATCACACTTCCTGGACAATTCAA ++ +FDHDHHHIGJIJJJJJJJIJJIJJJJJIJJJIIJJJJJJIIJJJHHGGGEGIJEHIJGHFFDDDDD@BBDCDDDDDDDDDDDDDDBDDBDDDDE +@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245:4:N:0:TCCGTC +TTTATTAAATAGAATTGTTTCTTGATCTTGAATTTCTATAATTTTATTATCTTTTTTATCTTTTTTTAGAGCTGCTTATACTTTATATTTATAT ++ +EDHFHHGJIIHIEEHIIIIJIJJJ?FFHGHFGHIJHGGIGDFFIG9EHGHEHIJJJJGIFHIGIJJA=;?>CEBBEECCC;>CDCA;BDD>@;C +@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088:4:N:0:TGGTCA +TAATTTGTTNNNNNNNNNNNNTTCACAATTTGGTCAATAGCTTGCATAGAAAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNTAATCCAGCNN ++ +2@>@@@@@@############11=???????????????????????>????@@@@@##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095:4:N:0:TGGTCA +TTCTATCAGNNNNTTTNNNNNTAACTTATTGAGGTTTATGTGGTTCTTATACATTAANNNNNNNNNNNNNNNNNNNNNNNNNTGGGTTATTTNN ++ +2@@@?@@@@####43@#####11=???????8??>??>??????????????@@@@@##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114:4:N:0:TGGTCA +AAGTTGGCANNNNATATNNNCGAAGATAATACACGTACACGTCATCCGCGATTTAGAANNNNNNNNNNNNNNNNNNNNNNNNCGCCAAGGTGNN ++ +2@@@@@@@?####33@@###14=???????????????????????????????????#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119:4:N:0:TGGTCA +CACACCAATNNNATTATNATGTTATTTAATACATTTATTAAAGAGAATAATGAAATTTNNNNNNNNNANNNNNNNNNNNNNNTATATTCTGCNN ++ +2@@@@@@@?###34@@@#1@????????????????????????????????@@@@@@#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124:4:N:0:TGGTCA +AAGAGAGTANNNATAAGATACTCCAAGCAAAAGCAGAGTATCTGTAAACACTTCGCTCNNNNNNNNNGNNNNNNNNNNNNNCCGTGCAAGTCNN ++ +2@??@?@??###44@@@@?@?@@@????????????>?<?????????????@@???@#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150:4:N:0:TGGTCA +AAGACAGTGACAATTCAAATTACACATGCGCGTTGCGCACTCACAGATACAAAGATACANNNANNNNCGGGCATACNTNNNAACAGAGCGACTG ++ +<@@@@@??@@@@?@@@@@@@@@@@@@@@???????????????????????????????################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151:4:N:0:CACTGT +ACATACTCAATATGTTTTACATATTTATGACAGACCTTCTCAAACAGAATATTTTACATNNNTTNNNCATTACCGTTTNNNCACAACACATTTT ++ +:@?@?@@@?????@@@@@@?@??@@@???@@?????????????????????@@@@@@@###-8###--=?????==?################ +@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159:4:N:0:CACTGT +GGCATACCTGCTGCCATTGGTCACACTGGCAGATTACGCGATTATTTTTTTTACGGAAANNNTGNNNTTTCCCTTCCGGNNTGAATTGCCTGGA ++ +:@@?@@@@@@@@@?@?@??@??@@@@??????<????????<?????????=<?######################################## +@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170:4:N:0:CACTGT +GACCTACTAAACCTAACAATTCCAGCTATATTAACATTAGCTGAAGACACTAATCAGGAANAATTTAAAACAGAAAACATAATGGCACAGTCCA ++ +AACCCCCCBCCCBBB7CCCCCCBCCBBAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB#.;AAABBAAAAA@AA@@@@@@B>==?AA????A +@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174:4:N:0:CACTGT +AAGTCTTTGCGCAGACGGATCACCTCCTCGTTTGCAAGTGTGATAGGTACATCATGCTTTNTGTTCAAATCTTGGAAAATGAAATGTGCATGTA ++ +BB?FCBFG4?@@1<?A:6EF:?9)?00??:BDD1<B########################################################## +@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176:4:N:0:CACTGT +GACCGTTAGTCGGCGGGCGGTACCTGGTACCAGCGGGCGGCAAAAAAATAATGTGGGGAGGGGTCGGCGAAGTGTCGCTGAAAACGCCCCTTGC ++ +DDDD:@AE@AED@E?############################################################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187:4:N:0:CACTGT +GGATCAACATTTTTTATAGCAACAGGATTTCACGGAATTCATGTATTAATCGGAACAACTTTTTTATTAGTATGTTTACTACGACATTTAAATA ++ +FFHHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJJJIJJJJJJJIHGIGIIJJJIJJJJHHHHHHDDEEEEDEFEFEEDDDEDDDDDDDEEEDEE |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/emb6801m1_CGTACTAGTAGATCGC_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emb6801m1_CGTACTAGTAGATCGC_1.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179:1:N:0:CGTACTAG:TAGATCGC:CCCCACAC +CAGACTTGTGGGGCGACTGTTCAGGCCGTGTAGGGCATTCAGGGGTAGCATGGGAGCAGCTAGATTAGATGCAGATCTCTGAGAAGC ++ +DBFDFIIEF??8@EFGFHFGAFFGGIHH;5.=CEE),7.;(;ACB9>?CAAC??9?B@9??C:(:@A::@CC:4+:>@C@AAC(>9? +@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240:1:N:0:CGTACTAG:TAGATCGC:GTCGTTGG +CATCGTTGCTGCTCTTAACGTCCAAATGGACGGGCGACTCCCCGAACATTGCCTCGAGTCGTGTCTCCACGGATTTCTGGACGTCCG ++ +HHHHHJJJIIIJIHGIJJIHHJJJHIJJJFHIJJBHGGHHHHFEDDDDDDDDDDDDDDCCBDDDDDDDDDDDDDDDDEDD@BDDDDB |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/emb6801m1_CGTACTAGTAGATCGC_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emb6801m1_CGTACTAGTAGATCGC_2.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179:4:N:0:CGTACTAG:TAGATCGC:CTTCTCAG +AGATCTGCATCTAATCTAGCTGCTCCCATGCTACCCCTGAATACCCTACACGGCCTGAACAGTCGCCCCACAAGTCTGGCGTGGGG ++ +HF?HHGBHHIJJIGIIIJGIJBEHIGID<9EHIIJJI@;?BGGHIIIIIIIIIIIAGE@HHH?EDFDDB?B?9?:ACCC(85>>B> +@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240:4:N:0:CGTACTAG:TAGATCGC:CATATGCA +GCAATCGCAGCAACAACTAAATGGAAACCAACAGCATCTGCCCATCAATCGTCAACCGGCGCCACAGCAATCACACTTCCTGGACA ++ +HDHHHIGJIJJJJJJJIJJIJJJJJIJJJIIJJJJJJIIJJJHHGGGEGIJEHIJGHFFDDDDD@BBDCDDDDDDDDDDDDDDBDD |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/emb6801m2_AGGCAGAATAGATCGC_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emb6801m2_AGGCAGAATAGATCGC_1.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193:1:N:0:AGGCAGAA:TAGATCGC:TTCCTTGC +GAGTGTTTGCACGATTATCTCATATTCAAACTGGTCAACATGGGCATACGATTTCTTGCGCTCCTTGCTTTCAAACAGCCTGTCTCT ++ +CFHFHIIJJJJJJIJJIJJJJJJJJJJIJJJJJJBGIJJJJJJJJJJJJJJJJIJJJJHHFFFDEEEDDDDDDDDDDDBBDDDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245:1:N:0:AGGCAGAA:TAGATCGC:GAATATAA +ATATAAAGTATAAGCAGCTCTAAAAAAAGATAAAAAAGATAATAAAATTATAGAAATTCAAGATCAAGAAACAATTCTATTTAATAA ++ +FBDFHGIGHGJIJJJJJIIDHHIJJIGGHEEGGIIIIGGDHIGE@FHHIIJJFGGHGHCAHH@D;CD;CCCECDDCCDDDCD3>ACA |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/emb6801m2_AGGCAGAATAGATCGC_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emb6801m2_AGGCAGAATAGATCGC_2.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193:4:N:0:AGGCAGAA:TAGATCGC:GCTGTTTG +AAAGCAAGGAGCGCAAGAAATCGTATGCCCATGTTGACCAGTTTGAATATGAGATAATCGTGCAAACACTCCCAAGGAACTGTCTC ++ +HHHHHJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJHJJJJJGHIIIIIJJIJIJEEEEHHFFFEEEEDED3=CDDDDDDDDCDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245:4:N:0:AGGCAGAA:TAGATCGC:AATTTCTT +TATTAAATAGAATTGTTTCTTGATCTTGAATTTCTATAATTTTATTATCTTTTTTATCTTTTTTTAGAGCTGCTTATACTTTATAT ++ +HFHHGJIIHIEEHIIIIJIJJJ?FFHGHFGHIJHGGIGDFFIG9EHGHEHIJJJJGIFHIGIJJA=;?>CEBBEECCC;>CDCA;B |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/emb681m1_TAAGGCGACTCTCTAT_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emb681m1_TAAGGCGACTCTCTAT_1.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207:1:N:0:TAAGGCGA:CTCTCTAT:TTACTTGT +CGTTGTGATACTAAACTTTCTCAAATAATAAAAAAAAAGAATAAAATTCCTAATAATGAAATAGTTGATCCAATAGTTGATACAATA ++ +HHHGHIIGIJJIIJJJJJJIIHIIJHGIHGJIJIJJJHGCCHIGGEHH>EEFFFFFFFACCEACEDCDCCCCCDCDEEDDDE(:ACC +@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222:1:N:0:TAAGGCGA:CTCTCTAT:GTTAAAAT +AGTAATAATATTACCTAATACAAATAATGAAATATCATATTGATGAAATCATTTTACTATACCTGATACAGTTGTTATAGCTCCGAT ++ +FHHHHJJIIJJJGJIIJJIIJHIJIJIJIIJJJJJJJIIJJIGGHIJJJIJGJJIIIHIIHJ>GHIIIIIIGGGIIJJJJIH)=ABD |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/emb681m1_TAAGGCGACTCTCTAT_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emb681m1_TAAGGCGACTCTCTAT_2.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207:4:N:0:TAAGGCGA:CTCTCTAT:CATTATTA +TATTTATTGGAGTTAATTTAACATTTTTTCCTCAACATTTTTTAGGATTGGCTGGAATACCTCGACGTTATTCAGATTACCCAGAT ++ +HDHHHIJJJJEHHHIIIIJIJHIHIJJJJIGHEIIIJJIJJJHHGIIIJIJIJIJEHGHGFHFH8?ABC?BC>>AADDCACDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222:4:N:0:TAAGGCGA:CTCTCTAT:GTCCATGA +CCATTAACAGGAGCTATCGGAGCTATAACAACTGTATCAGGTATAGTAAAATGATTTCATCAATATGATATTTCATTATTTGTATT ++ +HHFHGJJJJJJIIJJGJIIJGHGHIIIJIJJIGIHIIGIIJBFDIIGHJJIJJGIEIEGHIJCH@EHFHGHHHGFFFFFFFFFDDE |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/emb681m4_TCCTGAGCCTCTCTAT_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emb681m4_TCCTGAGCCTCTCTAT_1.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184:1:N:0:TCCTGAGC:CTCTCTAT:GGTAGAGT +GGGAAAGGGAAGGGCAAGGGGGAGGGGAAGAATTTAACCGGGCGGGAGGAGAATCGGGCAGGGAAGAATGGTTGGTTGGTGGAACAA ++ +HHHDHJJGIGIJCBDHEHGJJJBGEHIBGGHFGFFGGHFFDD>?BDBBDDDDDD@ADD;>@D98AB?CCDD:CBB<ADD8<?<@?B? +@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233:1:N:0:TCCTGAGC:CTCTCTAT:AACAACAA +TTTAATGCAATTACCAATCTTACAAGTTATTATACCAATAATTGCATCTATGTTTTGCTTTCTTGACAAGAAACACAAGGTAACTTG ++ +<DFDFB<?:EIBHHIIFF:AHI?HC<*:1:EF@G49D<B3?@F4?BDD*BG*?B??B<B8888@F)).@;@;@;=6?########## |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/emb681m4_TCCTGAGCCTCTCTAT_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emb681m4_TCCTGAGCCTCTCTAT_2.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184:4:N:0:TCCTGAGC:CTCTCTAT:CTTTTCCA +TTCTGTATGCCCTTCCCTCTCGCACACTCGACCCAATGACCCGCTTTGCTCTGTTTACCTCTCCGCTCTGTTTTTGCACTTGGAAA ++ +HGDHHGGIJJIJJJGHIIIGFHHIIGIIIJIJJEHGEGGIJJIIIIGGGHGGFHHFEC@BCEDECDDDDDDDDDD?AC>ACCCCAC +@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233:4:N:0:TCCTGAGC:CTCTCTAT:GAAATAAA +CCAAGATACCTTGTGTTTCTTGGCAAGAAAGCAAAACATTGATGCAATTATTGGTATAATAACTTGTAAGATTGGTAATTGCATTA ++ +DB?:3E3+2AEAHHFIIIIIIIE9?9?3DGFF>;;F;D9BD9?@DCFFICFGF@FCF@@F@C@DF<7C@E3?ECC>7@DDBAADA; |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/emb681m5_GGACTCCTCTCTCTAT_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emb681m5_GGACTCCTCTCTCTAT_1.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204:1:N:0:GGACTCCT:CTCTCTAT:CTTATTCA +TCTGTTGCTCATATAGGAATTGTTCTATCAGGACTTTTAACTATAACTTATTGAGGTTTATGTGGTTCTTATACATTAATAATTGCT ++ +HHHGHJJIJJJJJJJJJJJJJJJJJJIJJJJJJJIJJJIJJJJJJIJJJJJJIJJJHIJJJJHIIHHHHIJJJIJJHHHHHHFFFFE +@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187:1:N:0:GGACTCCT:CTCTCTAT:ATATAAAA +ATAATCAAACTACATCGACAAAATGTCAATATCATGCAGCTGCTTCAAAACCAAAATGATGATTTTTTGAGAAGTGATTATTTAAAT ++ +HHHHHJJJJJJJJJJJJJJJJJIJJIJJJJJJJJJJJJJJJJJJJJJJJJJJIJIJJJJJJJJJJHHFFDDDEDCDDFEEDFEEEDE |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/emb681m5_GGACTCCTCTCTCTAT_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emb681m5_GGACTCCTCTCTCTAT_2.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204:4:N:0:GGACTCCT:CTCTCTAT:TTAATATT +CTTCGACTTCCAAGACGTTCATAAGATACATTAGCTAAACAAAATAACCCAGAAGAACATAAACCATGAGCAATTATTAATGTATA ++ +HHHFHIJJJJJJJJJJIIGIIIJJIIGHJJJJIJJIIJIJJJIJJIJJJJJJJJIGIJIIJJHHFHHFFFFFEDEEEFFFEDDDEF +@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187:4:N:0:GGACTCCT:CTCTCTAT:ATTTATGG +ATCAACATTTTTTATAGCAACAGGATTTCACGGAATTCATGTATTAATCGGAACAACTTTTTTATTAGTATGTTTACTACGACATT ++ +HHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJJJIJJJJJJJIHGIGIIJJJIJJJJHHHHHHDDEEEEDEFEFEEDDDEDDDDDDD |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/file_1_sequence.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/file_1_sequence.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,100 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097 1:N:0: +CACTGTTCAATGCCAATAGCAATGAAACCACCCATANAANNNNNACGGCTGAACANNNNNNNACNNGATATAGCATAAATGNANNNTNNNNANTNNNNNN ++ +CCCFFFFFHHHHHJJJJJJJJJJJIJJJIJJJJJJI#1?#####00?FHIJJJJI#######--##,,=A=CDDDDDDDEE################### +@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140 1:N:0: +CACTGTAATTTATCTCTTTTCATATAACTCTCTGGTAATNNNNAACATAAAACCGANCGCACATGATAATTCTTCCAAATTTATATATNAATTTTATANN ++ +BBCFFFDFHHHGHHIJJJJJJIJIJIGHHHIJJJJGGIJ####11?DHHIIIIGHI#-<FEHGIJIJHGHFHHHHHFFFFFFEFEEEE#,;?BDDFDE## +@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170 1:N:0: +CACTGTTGTAAAGTAGCTAATCAACTAAAAATTTTAATTCCAGTAGGAACTGCAATNATTATAGTAGCTGAGGTAAAATAAGCTCGAGTATCTACATCTA ++ +CCCFFFFFHHHHHIJJJJJJJJJJJJIJJJJJJJJJJJJIJJJIIJJJJJJJJJJI#0?FHIJJJJJJJJGIJHIIJJJHHHHHHFFD@CEEEFDDDDDC +@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179 1:N:0: +CACTGTACCAGACTTGTGGGGCGACTGTTCAGGCCGTGTAGGGCATTCAGGGGTAGCATGGGAGCAGCTAGATTAGATGCAGATCTCTGAGAAGCTGTCT ++ +=?@D;DBDDBFDFIIEF??8@EFGFHFGAFFGGIHH;5.=CEE),7.;(;ACB9>?CAAC??9?B@9??C:(:@A::@CC:4+:>@C@AAC(>9?CCCC@ +@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184 1:N:0: +CACTGTGTGGGAAAGGGAAGGGCAAGGGGGAGGGGAAGAATTTAACCGGGCGGGAGGAGAATCGGGCAGGGAAGAATGGTTGGTTGGTGGAACAACTGAA ++ +BB=DDDEDHHHDHJJGIGIJCBDHEHGJJJBGEHIBGGHFGFFGGHFFDD>?BDBBDDDDDD@ADD;>@D98AB?CCDD:CBB<ADD8<?<@?B?ACDCA +@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193 1:N:0: +CACTGTGCGAGTGTTTGCACGATTATCTCATATTCAAACTGGTCAACATGGGCATACGATTTCTTGCGCTCCTTGCTTTCAAACAGCCTGTCTCTTATAC ++ +CCCFFFF+CFHFHIIJJJJJJIJJIJJJJJJJJJJIJJJJJJBGIJJJJJJJJJJJJJJJJIJJJJHHFFFDEEEDDDDDDDDDDDBBDDDDDDDDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204 1:N:0: +ATTCCGCATCTGTTGCTCATATAGGAATTGTTCTATCAGGACTTTTAACTATAACTTATTGAGGTTTATGTGGTTCTTATACATTAATAATTGCTCATGG ++ +@BCFFFDFHHHGHJJIJJJJJJJJJJJJJJJJJJIJJJJJJJIJJJIJJJJJJIJJJJJJIJJJHIJJJJHIIHHHHIJJJIJJHHHHHHFFFFEFCEEE +@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207 1:N:0: +ATTCCGGTCGTTGTGATACTAAACTTTCTCAAATAATAAAAAAAAAGAATAAAATTCCTAATAATGAAATAGTTGATCCAATAGTTGATACAATATTTCA ++ +@BCFFFFFHHHGHIIGIJJIIJJJJJJIIHIIJHGIHGJIJIJJJHGCCHIGGEHH>EEFFFFFFFACCEACEDCDCCCCCDCDEEDDDE(:ACCD:@D@ +@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 1:N:0: +ATTCCGAGTAAATTAAATGCGAAAATAAAAGGCAGCATGAGNTANTTACTNAAANGGGGTCATNAACAGTACTTGTGCTCCNCCANGTCGNCGNTNCNCT ++ +@@CFFFFFFHHHHJJJIJJJJJJJIJIJJJJJJJJJJJJJJ#0?#0?DHI#-;F#-;DH?EFH#,;BCDEEEEEDDCCCDD#,8?#,5?B########## +@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222 1:N:0: +ATTCCGATAGTAATAATATTACCTAATACAAATAATGAAATATCATATTGATGAAATCATTTTACTATACCTGATACAGTTGTTATAGCTCCGATAGCTC ++ +CCCFFFFDFHHHHJJIIJJJGJIIJJIIJHIJIJIJIIJJJJJJJIIJJIGGHIJJJIJGJJIIIHIIHJ>GHIIIIIIGGGIIJJJJIH)=ABDDDDEE +@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233 1:N:0: +ATTCCGAATTTAATGCAATTACCAATCTTACAAGTTATTATACCAATAATTGCATCTATGTTTTGCTTTCTTGACAAGAAACACAAGGTAACTTGGGTTA ++ +1?8ADDDD<DFDFB<?:EIBHHIIFF:AHI?HC<*:1:EF@G49D<B3?@F4?BDD*BG*?B??B<B8888@F)).@;@;@;=6?############### +@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240 1:N:0: +ATTCCGGGCATCGTTGCTGCTCTTAACGTCCAAATGGACGGGCGACTCCCCGAACATTGCCTCGAGTCGTGTCTCCACGGATTTCTGGACGTCCGAATCG ++ +CCCFFFFFHHHHHJJJIIIJIHGIJJIHHJJJHIJJJFHIJJBHGGHHHHFEDDDDDDDDDDDDDDCCBDDDDDDDDDDDDDDDDEDD@BDDDDBB@BBD +@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245 1:N:0: +ATTCCGAAATATAAAGTATAAGCAGCTCTAAAAAAAGATAAAAAAGATAATAAAATTATAGAAATTCAAGATCAAGAAACAATTCTATTTAATAAAGAAA ++ +@@CFFFFFFBDFHGIGHGJIJJJJJIIDHHIJJIGGHEEGGIIIIGGDHIGE@FHHIIJJFGGHGHCAHH@D;CD;CCCECDDCCDDDCD3>ACAA:@?C +@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 1:N:0: +GCTACCAAGTTTATAAATGGCAACCTTAAGTGTAANNNANNNNNTATGCACAGNANNNNNNNNANNNATGCAAAACGACTCNNNNNNNNNNNNCNNNNNN ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJIIHIJ###1#####20?FHJJJJ#.########-###--;BDFEEECDDDD################### +@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 1:N:0: +GCTACCACGTTCATAAGATACATTAGCTAAACAAAANAANNNNNAAGAACATAAANNNNNNNCANNTATTAATGTATAAGANCNNNANNNNCNTNNNNNN ++ +CC@FFFFFHHHHHJJJJJJIJJJJIJJJJIJJJJJJ#1C#####00?FIJJJJJJ#######--##,5?DDEEEFCFFEDD################### +@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 1:N:0: +GCTACCCGTTGGAGGAGGAGCCGCCATGAATGCCCTGCGNNNNTTCTACCTGGAGANNNCGGTGGTCACACGAGCCTACACCACGGTCNNCGTGCTNNNN ++ +CCCFFFFFHHHHGJJGHJGHIJJJJJJJJJJJJJJJJJJ####.-;DHIJJHHHHH###,,=?BDBDDDDDDDDDDDDDDDDDDDDDD##+28@DD#### +@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 1:N:0: +GCTACCTGGACTCAAGACCTAATTGCATTAACCGTCTGTNNNNTACGTAGCGTATGNNATTGCGCACTTCTTCTGCGGATAGTCCTTCNNCATCTCNNNN ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJIJ####20?GHIJJJIJIJ##-5CEFHFFDDEEDDDDDDDDDDDDDEDDDD##+2?BDD#### +@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 1:N:0: +GCTACCTACATATACTTATAGGCATACTTATACGACTTCNNNNCCCGGTTAATATGNNGTGGCCCGTATAAGTTAATGGGCACAACCGNNTGGGACNNNN ++ +CCCFFFFFHHHHHIJJJJJJJJJJJIJJJJJJJJJJJJJ####00BFHGIIJJJJJ##--BEHJJHDFFEDEEFEEEDDDDDDDDDDD##+2<B@B#### +@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150 1:N:0: +GCTACCTCCACTCGCATGTGTATCTAATGAATGCCTCAANACGCTCCTGAACGCAANCAGGTATGTGTGGTAGACCAAAAAAAAAAAANCGGCAGGTANN ++ +CCCFFFFFHHHHHJJJJJJJHIJJJJJJJJJJJJJJJJJ#2?FHIJJJJHIJJJJJ#.;DHCHHHHHHHFDFFEEEEDDDDDDDDDDD############ +@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151 1:N:0: +CGAAACAACTTAAGGCTGAAAATTATTTATTTGACTTGTGTCAAATATAAAAATGTNTTGTGTAGAAACGGTAATGTGAAATTAATGTNAAATATTCTNN ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJIIIJJJJHIJJJJIJIJJJIJIJJI#0?FGIIJJJJJJIIEIJJHHHGHHHFFFFFF#,;ABDEDEE## +@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159 1:N:0: +CGAAACTGCAATGCAAGTGGATTAGAGGATTGCAGCTGGAGGGGTAACAGCAGTGCNTTCGAAATATGTATCTTACAGCATTTCTGGGNTCCTCGTCCGN ++ +CCCFFFFFHHHHHJJJJHIIIIJIJIJJJJJJJJJJJJJFHJJJ?FHCFFHGIGHC#-5;DHHFHHHFCDFFFFFEEEECEDCDCCDC#,8<BBDABB## +@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170 1:N:0: +CGAAACCTCTTGGGTGTATTGGTTGGCCGTTTTACTCTTTTGTTGGAGACTGAGAANCTTAGCTGATATAACTTCTACCGATTCTCCTTTAACTGCACTT ++ +?@@FFDFFHFHHHI?FEEEHHIHHGIEGHHIJJHIIGIIIJFGIJJHIIIEHIIHG#-;CEHHHHDFFFFFDEEC@CECDD?@CDD@CACDCDDDDCDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174 1:N:0: +CGAAACAAATGACCAAATCCTAGGTGTTTGAGCGCGGACTGGAGGCGATTCCGCTGTCCGTGGATCTGTGGATCCACTACCTAATGCACGTTAAGTCCAA ++ +@@@DADDDHHAHHGGB@BHIIIFE<AHHI;4?9DHGE@A;AHGEHEE>AC@@CB@BBA@?BBBBA@CCDCCCCC<493?CCCCCC>:>A<8???AC#### +@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176 1:N:0: +CGAAACGGAAGAGAAAAAAATATAAAGTGTCAAGGGGCGTGTGCAGCGACACTTCGCCGACCCCTCCCCACATTATTTTTTTGCCGCCCGCTGGTAGCAG ++ +;@@BDDDA:DBFDF;A<A@EGGB@:?D1:D?9:BGIDGE4@########################################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187 1:N:0: +CGAAACAAATAATCAAACTACATCGACAAAATGTCAATATCATGCAGCTGCTTCAAAACCAAAATGATGATTTTTTGAGAAGTGATTATTTAAATGTCGT ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJIJJIJJJJJJJJJJJJJJJJJJJJJJJJJJIJIJJJJJJJJJJHHFFDDDEDCDDFEEDFEEEDEEFEDD \ No newline at end of file |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/file_2_sequence.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/file_2_sequence.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,100 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097 4:N:0: +GTATAGAGAATGGTGNNNNTGTNNNNNTCCTAATATTCCATTTATGCTATATCCAGTCGTTCTNNNNNNNNNNNNNNNNNNNNNNNNNGTGGTTTCATNN ++ +#####22@>@@@@@@####43@#####11=?????????>?????????????????????@?##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140 4:N:0: +GTATAGTTATATGAAAGNAATATAAAATTTATATATAAATTTGGAAGAATTATCATGTGCGCTCNNNNNNNNNTTANANATNNNNNNAGAGTTATATGAN ++ +#####22@@@@@@@?@@#3=>?@@?@@@?@?@>?????>????????????>??????@?????#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170 4:N:0: +GTATAGGCTATTGGATTATTAGGATTTATTGTATGAGCTCATCATATATTTACCGTTGGAATAGATNTAGATACTCGAGCTTATTTTACCTCAGCTACTA ++ +#4=DFFFFHHHHHJEHIHHJIJJHIJJIJJJIJJJIJJJJIJJJJIJIIJIGJJJJJJJJJJJJJJ#-;CFHIJJJHHHFFFFFEEEEEEEDDDDDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179 4:N:0: +GTATAGAGAGATCTGCATCTAATCTAGCTGCTCCCATGCTACCCCTGAATACCCTACACGGCCTGAACAGTCGCCCCACAAGTCTGGCGTGGGGCTGTCT ++ +@@CDFFDFHF?HHGBHHIJJIGIIIJGIJBEHIGID<9EHIIJJI@;?BGGHIIIIIIIIIIIAGE@HHH?EDFDDB?B?9?:ACCC(85>>B>>@BBD@ +@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184 4:N:0: +GTATAGCATTCTGTATGCCCTTCCCTCTCGCACACTCGACCCAATGACCCGCTTTGCTCTGTTTACCTCTCCGCTCTGTTTTTGCACTTGGAAATTGCTA ++ +B@CFFFFFHGDHHGGIJJIJJJGHIIIGFHHIIGIIIJIJJEHGEGGIJJIIIIGGGHGGFHHFEC@BCEDECDDDDDDDDDD?AC>ACCCCACADCCDD +@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193 4:N:0: +GTATAGTGAAAGCAAGGAGCGCAAGAAATCGTATGCCCATGTTGACCAGTTTGAATATGAGATAATCGTGCAAACACTCCCAAGGAACTGTCTCTTATAC ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJHJJJJJGHIIIIIJJIJIJEEEEHHFFFEEEEDED3=CDDDDDDDDCDDDDDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204 4:N:0: +TCCGTCTTCTTCGACTTCCAAGACGTTCATAAGATACATTAGCTAAACAAAATAACCCAGAAGAACATAAACCATGAGCAATTATTAATGTATAAGAACC ++ +CCCFFFFFHHHFHIJJJJJJJJJJIIGIIIJJIIGHJJJJIJJIIJIJJJIJJIJJJJJJJJIGIJIIJJHHFHHFFFFFEDEEEFFFEDDDEFEDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207 4:N:0: +TCCGTCTATATTTATTGGAGTTAATTTAACATTTTTTCCTCAACATTTTTTAGGATTGGCTGGAATACCTCGACGTTATTCAGATTACCCAGATGCTTAC ++ +@?@DDDFDHDHHHIJJJJEHHHIIIIJIJHIHIJJJJIGHEIIIJJIJJJHHGIIIJIJIJIJEHGHGFHFH8?ABC?BC>>AADDCACDDDDD<@CD>> +@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 4:N:0: +TCCGTCGGCATAGCCATCGAGGTGTGTCCGGTGTCAAATCAAGTGCTGCAACTGGGCGTGGACTATCGGAATCATCCGGCGGCACTGCTGTTGGCCGCCA ++ +C#1ADDFFHHHHGJJJJJJIJJAGHHGIHHIDFGHIJJJGIJJGIJJIIJIJJIJJJJHHFEFEECACDDBB@CCD@?BDDDDDDDDDDDDCDB:@>BBD +@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222 4:N:0: +TCCGTCGACCATTAACAGGAGCTATCGGAGCTATAACAACTGTATCAGGTATAGTAAAATGATTTCATCAATATGATATTTCATTATTTGTATTAGGTAA ++ +@BCFFFFFHHFHGJJJJJJIIJJGJIIJGHGHIIIJIJJIGIHIIGIIJBFDIIGHJJIJJGIEIEGHIJCH@EHFHGHHHGFFFFFFFFFDDEEDCAC@ +@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233 4:N:0: +TCCGTCAACCAAGATACCTTGTGTTTCTTGGCAAGAAAGCAAAACATTGATGCAATTATTGGTATAATAACTTGTAAGATTGGTAATTGCATTAAATTGT ++ +@@<DDAD4DB?:3E3+2AEAHHFIIIIIIIE9?9?3DGFF>;;F;D9BD9?@DCFFICFGF@FCF@@F@C@DF<7C@E3?ECC>7@DDBAADA;;;>A:A +@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240 4:N:0: +TCCGTCCAGCAATCGCAGCAACAACTAAATGGAAACCAACAGCATCTGCCCATCAATCGTCAACCGGCGCCACAGCAATCACACTTCCTGGACAATTCAA ++ +@@?DFFFDHDHHHIGJIJJJJJJJIJJIJJJJJIJJJIIJJJJJJIIJJJHHGGGEGIJEHIJGHFFDDDDD@BBDCDDDDDDDDDDDDDDBDDBDDDDE +@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245 4:N:0: +TCCGTCTTTATTAAATAGAATTGTTTCTTGATCTTGAATTTCTATAATTTTATTATCTTTTTTATCTTTTTTTAGAGCTGCTTATACTTTATATTTATAT ++ +?@@DFBEDHFHHGJIIHIEEHIIIIJIJJJ?FFHGHFGHIJHGGIGDFFIG9EHGHEHIJJJJGIFHIGIJJA=;?>CEBBEECCC;>CDCA;BDD>@;C +@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 4:N:0: +TGGTCATAATTTGTTNNNNNNNNNNNNTTCACAATTTGGTCAATAGCTTGCATAGAAAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNTAATCCAGCNN ++ +#####42@>@@@@@@############11=???????????????????????>????@@@@@##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 4:N:0: +TGGTCATTCTATCAGNNNNTTTNNNNNTAACTTATTGAGGTTTATGTGGTTCTTATACATTAANNNNNNNNNNNNNNNNNNNNNNNNNTGGGTTATTTNN ++ +#####42@@@?@@@@####43@#####11=???????8??>??>??????????????@@@@@##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 4:N:0: +TGGTCAAAGTTGGCANNNNATATNNNCGAAGATAATACACGTACACGTCATCCGCGATTTAGAANNNNNNNNNNNNNNNNNNNNNNNNCGCCAAGGTGNN ++ +#####22@@@@@@@?####33@@###14=???????????????????????????????????#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 4:N:0: +TGGTCACACACCAATNNNATTATNATGTTATTTAATACATTTATTAAAGAGAATAATGAAATTTNNNNNNNNNANNNNNNNNNNNNNNTATATTCTGCNN ++ +#####22@@@@@@@?###34@@@#1@????????????????????????????????@@@@@@#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 4:N:0: +TGGTCAAAGAGAGTANNNATAAGATACTCCAAGCAAAAGCAGAGTATCTGTAAACACTTCGCTCNNNNNNNNNGNNNNNNNNNNNNNCCGTGCAAGTCNN ++ +#####22@??@?@??###44@@@@?@?@@@????????????>?<?????????????@@???@#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150 4:N:0: +TGGTCAAAGACAGTGACAATTCAAATTACACATGCGCGTTGCGCACTCACAGATACAAAGATACANNNANNNNCGGGCATACNTNNNAACAGAGCGACTG ++ +###2#4<@@@@@??@@@@?@@@@@@@@@@@@@@@???????????????????????????????################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151 4:N:0: +CACTGTACATACTCAATATGTTTTACATATTTATGACAGACCTTCTCAAACAGAATATTTTACATNNNTTNNNCATTACCGTTTNNNCACAACACATTTT ++ +###2#2:@?@?@@@?????@@@@@@?@??@@@???@@?????????????????????@@@@@@@###-8###--=?????==?################ +@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159 4:N:0: +CACTGTGGCATACCTGCTGCCATTGGTCACACTGGCAGATTACGCGATTATTTTTTTTACGGAAANNNTGNNNTTTCCCTTCCGGNNTGAATTGCCTGGA ++ +###2#2:@@?@@@@@@@@@?@?@??@??@@@@??????<????????<?????????=<?######################################## +@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170 4:N:0: +CACTGTGACCTACTAAACCTAACAATTCCAGCTATATTAACATTAGCTGAAGACACTAATCAGGAANAATTTAAAACAGAAAACATAATGGCACAGTCCA ++ +#4=AAAAACCCCCCBCCCBBB7CCCCCCBCCBBAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB#.;AAABBAAAAA@AA@@@@@@B>==?AA????A +@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174 4:N:0: +CACTGTAAGTCTTTGCGCAGACGGATCACCTCCTCGTTTGCAAGTGTGATAGGTACATCATGCTTTNTGTTCAAATCTTGGAAAATGAAATGTGCATGTA ++ +#+1=BBBB?FCBFG4?@@1<?A:6EF:?9)?00??:BDD1<B########################################################## +@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176 4:N:0: +CACTGTGACCGTTAGTCGGCGGGCGGTACCTGGTACCAGCGGGCGGCAAAAAAATAATGTGGGGAGGGGTCGGCGAAGTGTCGCTGAAAACGCCCCTTGC ++ +???DDDDDDD:@AE@AED@E?############################################################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187 4:N:0: +CACTGTGGATCAACATTTTTTATAGCAACAGGATTTCACGGAATTCATGTATTAATCGGAACAACTTTTTTATTAGTATGTTTACTACGACATTTAAATA ++ +BBCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJJJIJJJJJJJIHGIGIIJJJIJJJJHHHHHHDDEEEEDEFEFEEDDDEDDDDDDDEEEDEE |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/illu_dualindexing.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illu_dualindexing.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,5 @@ +emb6801m2 AGGCAGAA:TAGATCGC +emb6801m1 CGTACTAG:TAGATCGC +emb681m5 GGACTCCT:CTCTCTAT +emb681m1 TAAGGCGA:CTCTCTAT +emb681m4 TCCTGAGC:CTCTCTAT |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/illu_file_1_index.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illu_file_1_index.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,100 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097 2:N:0: +NNNNNNNN ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140 2:N:0: +NGNNNNNN ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170 2:N:0: +NCNNNNGC ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179 2:N:0: +CGTANTAG ++ +BCCF#2=B +@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184 2:N:0: +TCCTGAGC ++ +B@@FFFFD +@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193 2:N:0: +AGGCAGAA ++ +@C@BDDDF +@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204 2:N:0: +GGACTCCT ++ +@@@;DDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207 2:N:0: +TAAGGCGA ++ +CBCFFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 2:N:0: +CGTNNNNG ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222 2:N:0: +TAAGGCGA ++ +@@@FFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233 2:N:0: +TCCTGAGC ++ +???DDBA# +@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240 2:N:0: +CGTACTAG ++ +BBBADDAD +@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245 2:N:0: +AGGCAGAA ++ +?@@D??=B +@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 2:N:0: +NNNNNNNN ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 2:N:0: +NNNNNNNN ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 2:N:0: +NNNNNNNN ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 2:N:0: +NNNNNNNN ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 2:N:0: +NNNNNNNN ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150 2:N:0: +NGNNNNNN ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151 2:N:0: +NCNNNNNN ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159 2:N:0: +NGNNNNNG ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170 2:N:0: +NGNNNNAG ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174 2:N:0: +NCCNNNGC ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176 2:N:0: +NGGNNGAA ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187 2:N:0: +GGACTCCT ++ +CCBFFFFF |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/illu_file_1_sequence.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illu_file_1_sequence.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,100 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097 1:N:0: +GTCATATCAATGCCAATAGCAATGAAACCACCCATANAANNNNNACGGCTGAACANNNNNNNACNNGATATAGCATAAATGNANNNTNNNNANTNNNNNN ++ +CCCFFFFFHHHHHJJJJJJJJJJJIJJJIJJJJJJI#1?#####00?FHIJJJJI#######--##,,=A=CDDDDDDDEE################### +@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140 1:N:0: +ATTTAAAATTTATCTCTTTTCATATAACTCTCTGGTAATNNNNAACATAAAACCGANCGCACATGATAATTCTTCCAAATTTATATATNAATTTTATANN ++ +BBCFFFDFHHHGHHIJJJJJJIJIJIGHHHIJJJJGGIJ####11?DHHIIIIGHI#-<FEHGIJIJHGHFHHHHHFFFFFFEFEEEE#,;?BDDFDE## +@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170 1:N:0: +GTTCCATGTAAAGTAGCTAATCAACTAAAAATTTTAATTCCAGTAGGAACTGCAATNATTATAGTAGCTGAGGTAAAATAAGCTCGAGTATCTACATCTA ++ +CCCFFFFFHHHHHIJJJJJJJJJJJJIJJJJJJJJJJJJIJJJIIJJJJJJJJJJI#0?FHIJJJJJJJJGIJHIIJJJHHHHHHFFD@CEEEFDDDDDC +@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179 1:N:0: +CCCCACACCAGACTTGTGGGGCGACTGTTCAGGCCGTGTAGGGCATTCAGGGGTAGCATGGGAGCAGCTAGATTAGATGCAGATCTCTGAGAAGCTGTCT ++ +=?@D;DBDDBFDFIIEF??8@EFGFHFGAFFGGIHH;5.=CEE),7.;(;ACB9>?CAAC??9?B@9??C:(:@A::@CC:4+:>@C@AAC(>9?CCCC@ +@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184 1:N:0: +GGTAGAGTGGGAAAGGGAAGGGCAAGGGGGAGGGGAAGAATTTAACCGGGCGGGAGGAGAATCGGGCAGGGAAGAATGGTTGGTTGGTGGAACAACTGAA ++ +BB=DDDEDHHHDHJJGIGIJCBDHEHGJJJBGEHIBGGHFGFFGGHFFDD>?BDBBDDDDDD@ADD;>@D98AB?CCDD:CBB<ADD8<?<@?B?ACDCA +@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193 1:N:0: +TTCCTTGCGAGTGTTTGCACGATTATCTCATATTCAAACTGGTCAACATGGGCATACGATTTCTTGCGCTCCTTGCTTTCAAACAGCCTGTCTCTTATAC ++ +CCCFFFF+CFHFHIIJJJJJJIJJIJJJJJJJJJJIJJJJJJBGIJJJJJJJJJJJJJJJJIJJJJHHFFFDEEEDDDDDDDDDDDBBDDDDDDDDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204 1:N:0: +CTTATTCATCTGTTGCTCATATAGGAATTGTTCTATCAGGACTTTTAACTATAACTTATTGAGGTTTATGTGGTTCTTATACATTAATAATTGCTCATGG ++ +@BCFFFDFHHHGHJJIJJJJJJJJJJJJJJJJJJIJJJJJJJIJJJIJJJJJJIJJJJJJIJJJHIJJJJHIIHHHHIJJJIJJHHHHHHFFFFEFCEEE +@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207 1:N:0: +TTACTTGTCGTTGTGATACTAAACTTTCTCAAATAATAAAAAAAAAGAATAAAATTCCTAATAATGAAATAGTTGATCCAATAGTTGATACAATATTTCA ++ +@BCFFFFFHHHGHIIGIJJIIJJJJJJIIHIIJHGIHGJIJIJJJHGCCHIGGEHH>EEFFFFFFFACCEACEDCDCCCCCDCDEEDDDE(:ACCD:@D@ +@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 1:N:0: +ATTCAAAGTAAATTAAATGCGAAAATAAAAGGCAGCATGAGNTANTTACTNAAANGGGGTCATNAACAGTACTTGTGCTCCNCCANGTCGNCGNTNCNCT ++ +@@CFFFFFFHHHHJJJIJJJJJJJIJIJJJJJJJJJJJJJJ#0?#0?DHI#-;F#-;DH?EFH#,;BCDEEEEEDDCCCDD#,8?#,5?B########## +@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222 1:N:0: +GTTAAAATAGTAATAATATTACCTAATACAAATAATGAAATATCATATTGATGAAATCATTTTACTATACCTGATACAGTTGTTATAGCTCCGATAGCTC ++ +CCCFFFFDFHHHHJJIIJJJGJIIJJIIJHIJIJIJIIJJJJJJJIIJJIGGHIJJJIJGJJIIIHIIHJ>GHIIIIIIGGGIIJJJJIH)=ABDDDDEE +@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233 1:N:0: +AACAACAATTTAATGCAATTACCAATCTTACAAGTTATTATACCAATAATTGCATCTATGTTTTGCTTTCTTGACAAGAAACACAAGGTAACTTGGGTTA ++ +1?8ADDDD<DFDFB<?:EIBHHIIFF:AHI?HC<*:1:EF@G49D<B3?@F4?BDD*BG*?B??B<B8888@F)).@;@;@;=6?############### +@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240 1:N:0: +GTCGTTGGCATCGTTGCTGCTCTTAACGTCCAAATGGACGGGCGACTCCCCGAACATTGCCTCGAGTCGTGTCTCCACGGATTTCTGGACGTCCGAATCG ++ +CCCFFFFFHHHHHJJJIIIJIHGIJJIHHJJJHIJJJFHIJJBHGGHHHHFEDDDDDDDDDDDDDDCCBDDDDDDDDDDDDDDDDEDD@BDDDDBB@BBD +@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245 1:N:0: +GAATATAAATATAAAGTATAAGCAGCTCTAAAAAAAGATAAAAAAGATAATAAAATTATAGAAATTCAAGATCAAGAAACAATTCTATTTAATAAAGAAA ++ +@@CFFFFFFBDFHGIGHGJIJJJJJIIDHHIJJIGGHEEGGIIIIGGDHIGE@FHHIIJJFGGHGHCAHH@D;CD;CCCECDDCCDDDCD3>ACAA:@?C +@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 1:N:0: +CTATAAAAGTTTATAAATGGCAACCTTAAGTGTAANNNANNNNNTATGCACAGNANNNNNNNNANNNATGCAAAACGACTCNNNNNNNNNNNNCNNNNNN ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJIIHIJ###1#####20?FHJJJJ#.########-###--;BDFEEECDDDD################### +@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 1:N:0: +TCCAAGACGTTCATAAGATACATTAGCTAAACAAAANAANNNNNAAGAACATAAANNNNNNNCANNTATTAATGTATAAGANCNNNANNNNCNTNNNNNN ++ +CC@FFFFFHHHHHJJJJJJIJJJJIJJJJIJJJJJJ#1C#####00?FIJJJJJJ#######--##,5?DDEEEFCFFEDD################### +@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 1:N:0: +GTCCAACGTTGGAGGAGGAGCCGCCATGAATGCCCTGCGNNNNTTCTACCTGGAGANNNCGGTGGTCACACGAGCCTACACCACGGTCNNCGTGCTNNNN ++ +CCCFFFFFHHHHGJJGHJGHIJJJJJJJJJJJJJJJJJJ####.-;DHIJJHHHHH###,,=?BDBDDDDDDDDDDDDDDDDDDDDDD##+28@DD#### +@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 1:N:0: +CATATATGGACTCAAGACCTAATTGCATTAACCGTCTGTNNNNTACGTAGCGTATGNNATTGCGCACTTCTTCTGCGGATAGTCCTTCNNCATCTCNNNN ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJIJ####20?GHIJJJIJIJ##-5CEFHFFDDEEDDDDDDDDDDDDDEDDDD##+2?BDD#### +@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 1:N:0: +TACTTATACATATACTTATAGGCATACTTATACGACTTCNNNNCCCGGTTAATATGNNGTGGCCCGTATAAGTTAATGGGCACAACCGNNTGGGACNNNN ++ +CCCFFFFFHHHHHIJJJJJJJJJJJIJJJJJJJJJJJJJ####00BFHGIIJJJJJ##--BEHJJHDFFEDEEFEEEDDDDDDDDDDD##+2<B@B#### +@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150 1:N:0: +CACCATTCCACTCGCATGTGTATCTAATGAATGCCTCAANACGCTCCTGAACGCAANCAGGTATGTGTGGTAGACCAAAAAAAAAAAANCGGCAGGTANN ++ +CCCFFFFFHHHHHJJJJJJJHIJJJJJJJJJJJJJJJJJ#2?FHIJJJJHIJJJJJ#.;DHCHHHHHHHFDFFEEEEDDDDDDDDDDD############ +@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151 1:N:0: +AAGCATAACTTAAGGCTGAAAATTATTTATTTGACTTGTGTCAAATATAAAAATGTNTTGTGTAGAAACGGTAATGTGAAATTAATGTNAAATATTCTNN ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJIIIJJJJHIJJJJIJIJJJIJIJJI#0?FGIIJJJJJJIIEIJJHHHGHHHFFFFFF#,;ABDEDEE## +@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159 1:N:0: +GTACTGTGCAATGCAAGTGGATTAGAGGATTGCAGCTGGAGGGGTAACAGCAGTGCNTTCGAAATATGTATCTTACAGCATTTCTGGGNTCCTCGTCCGN ++ +CCCFFFFFHHHHHJJJJHIIIIJIJIJJJJJJJJJJJJJFHJJJ?FHCFFHGIGHC#-5;DHHFHHHFCDFFFFFEEEECEDCDCCDC#,8<BBDABB## +@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170 1:N:0: +CTCCACCTCTTGGGTGTATTGGTTGGCCGTTTTACTCTTTTGTTGGAGACTGAGAANCTTAGCTGATATAACTTCTACCGATTCTCCTTTAACTGCACTT ++ +?@@FFDFFHFHHHI?FEEEHHIHHGIEGHHIJJHIIGIIIJFGIJJHIIIEHIIHG#-;CEHHHHDFFFFFDEEC@CECDD?@CDD@CACDCDDDDCDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174 1:N:0: +CATACGAAATGACCAAATCCTAGGTGTTTGAGCGCGGACTGGAGGCGATTCCGCTGTCCGTGGATCTGTGGATCCACTACCTAATGCACGTTAAGTCCAA ++ +@@@DADDDHHAHHGGB@BHIIIFE<AHHI;4?9DHGE@A;AHGEHEE>AC@@CB@BBA@?BBBBA@CCDCCCCC<493?CCCCCC>:>A<8???AC#### +@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176 1:N:0: +GTCTCAGGAAGAGAAAAAAATATAAAGTGTCAAGGGGCGTGTGCAGCGACACTTCGCCGACCCCTCCCCACATTATTTTTTTGCCGCCCGCTGGTAGCAG ++ +;@@BDDDA:DBFDF;A<A@EGGB@:?D1:D?9:BGIDGE4@########################################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187 1:N:0: +ATATAAAAATAATCAAACTACATCGACAAAATGTCAATATCATGCAGCTGCTTCAAAACCAAAATGATGATTTTTTGAGAAGTGATTATTTAAATGTCGT ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJIJJIJJJJJJJJJJJJJJJJJJJJJJJJJJIJIJJJJJJJJJJHHFFDDDEDCDDFEEDFEEEDEEFEDD |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/illu_file_2_index.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illu_file_2_index.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,100 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097 3:N:0: +NNNNCNNN ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140 3:N:0: +CTCTCTAT ++ +CCCFFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170 3:N:0: +CTCTCTAT ++ +CCCFFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179 3:N:0: +TAGATCGC ++ +CCCFFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184 3:N:0: +CTCTCTAT ++ +@C@FFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193 3:N:0: +TAGATCGC ++ +CBCFFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204 3:N:0: +CTCTCTAT ++ +CCCFFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207 3:N:0: +CTCTCTAT ++ +BCCFDFEF +@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 3:N:0: +TAGATCGC ++ +B@@FFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222 3:N:0: +CTCTCTAT ++ +CCCFFFDF +@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233 3:N:0: +CTCTCTAT ++ +?@@DDDDF +@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240 3:N:0: +TAGATCGC ++ +C@CFFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245 3:N:0: +TAGATCGC ++ +@@@DFD=B +@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 3:N:0: +NNNNCNNN ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 3:N:0: +NNNNCNNN ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 3:N:0: +NNCTCTNN ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 3:N:0: +NNCTCTNT ++ +######## +@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 3:N:0: +NNCTCTAT ++ +##0<@@?@ +@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150 3:N:0: +TAGATCGC ++ +CCCFFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151 3:N:0: +CTCTCTAT ++ +CCCFFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159 3:N:0: +TAGATCGC ++ +CCCFFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170 3:N:0: +TAGATCGC ++ +CCCFFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174 3:N:0: +CTCTCTAT ++ +CCCFFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176 3:N:0: +TAGATCGC ++ +CCCFFFFF +@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187 3:N:0: +CTCTCTAT ++ +CCCFFFFF |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/illu_file_2_sequence.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illu_file_2_sequence.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,100 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097 4:N:0: +NNNNNGAGAATGGTGNNNNTGTNNNNNTCCTAATATTCCATTTATGCTATATCCAGTCGTTCTNNNNNNNNNNNNNNNNNNNNNNNNNGTGGTTTCATNN ++ +#####22@>@@@@@@####43@#####11=?????????>?????????????????????@?##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140 4:N:0: +NNNNNATTATATGAAAGNAATATAAAATTTATATATAAATTTGGAAGAATTATCATGTGCGCTCNNNNNNNNNTTANANATNNNNNNAGAGTTATATGAN ++ +#####22@@@@@@@?@@#3=>?@@?@@@?@?@>?????>????????????>??????@?????#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170 4:N:0: +NTATTAGCTATTGGATTATTAGGATTTATTGTATGAGCTCATCATATATTTACCGTTGGAATAGATNTAGATACTCGAGCTTATTTTACCTCAGCTACTA ++ +#4=DFFFFHHHHHJEHIHHJIJJHIJJIJJJIJJJIJJJJIJJJJIJIIJIGJJJJJJJJJJJJJJ#-;CFHIJJJHHHFFFFFEEEEEEEDDDDDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179 4:N:0: +CTTCTCAGAGATCTGCATCTAATCTAGCTGCTCCCATGCTACCCCTGAATACCCTACACGGCCTGAACAGTCGCCCCACAAGTCTGGCGTGGGGCTGTCT ++ +@@CDFFDFHF?HHGBHHIJJIGIIIJGIJBEHIGID<9EHIIJJI@;?BGGHIIIIIIIIIIIAGE@HHH?EDFDDB?B?9?:ACCC(85>>B>>@BBD@ +@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184 4:N:0: +CTTTTCCATTCTGTATGCCCTTCCCTCTCGCACACTCGACCCAATGACCCGCTTTGCTCTGTTTACCTCTCCGCTCTGTTTTTGCACTTGGAAATTGCTA ++ +B@CFFFFFHGDHHGGIJJIJJJGHIIIGFHHIIGIIIJIJJEHGEGGIJJIIIIGGGHGGFHHFEC@BCEDECDDDDDDDDDD?AC>ACCCCACADCCDD +@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193 4:N:0: +GCTGTTTGAAAGCAAGGAGCGCAAGAAATCGTATGCCCATGTTGACCAGTTTGAATATGAGATAATCGTGCAAACACTCCCAAGGAACTGTCTCTTATAC ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJHJJJJJGHIIIIIJJIJIJEEEEHHFFFEEEEDED3=CDDDDDDDDCDDDDDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204 4:N:0: +TTAATATTCTTCGACTTCCAAGACGTTCATAAGATACATTAGCTAAACAAAATAACCCAGAAGAACATAAACCATGAGCAATTATTAATGTATAAGAACC ++ +CCCFFFFFHHHFHIJJJJJJJJJJIIGIIIJJIIGHJJJJIJJIIJIJJJIJJIJJJJJJJJIGIJIIJJHHFHHFFFFFEDEEEFFFEDDDEFEDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207 4:N:0: +CATTATTATATTTATTGGAGTTAATTTAACATTTTTTCCTCAACATTTTTTAGGATTGGCTGGAATACCTCGACGTTATTCAGATTACCCAGATGCTTAC ++ +@?@DDDFDHDHHHIJJJJEHHHIIIIJIJHIHIJJJJIGHEIIIJJIJJJHHGIIIJIJIJIJEHGHGFHFH8?ABC?BC>>AADDCACDDDDD<@CD>> +@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 4:N:0: +CNATTGGGCATAGCCATCGAGGTGTGTCCGGTGTCAAATCAAGTGCTGCAACTGGGCGTGGACTATCGGAATCATCCGGCGGCACTGCTGTTGGCCGCCA ++ +C#1ADDFFHHHHGJJJJJJIJJAGHHGIHHIDFGHIJJJGIJJGIJJIIJIJJIJJJJHHFEFEECACDDBB@CCD@?BDDDDDDDDDDDDCDB:@>BBD +@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222 4:N:0: +GTCCATGACCATTAACAGGAGCTATCGGAGCTATAACAACTGTATCAGGTATAGTAAAATGATTTCATCAATATGATATTTCATTATTTGTATTAGGTAA ++ +@BCFFFFFHHFHGJJJJJJIIJJGJIIJGHGHIIIJIJJIGIHIIGIIJBFDIIGHJJIJJGIEIEGHIJCH@EHFHGHHHGFFFFFFFFFDDEEDCAC@ +@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233 4:N:0: +GAAATAAACCAAGATACCTTGTGTTTCTTGGCAAGAAAGCAAAACATTGATGCAATTATTGGTATAATAACTTGTAAGATTGGTAATTGCATTAAATTGT ++ +@@<DDAD4DB?:3E3+2AEAHHFIIIIIIIE9?9?3DGFF>;;F;D9BD9?@DCFFICFGF@FCF@@F@C@DF<7C@E3?ECC>7@DDBAADA;;;>A:A +@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240 4:N:0: +CATATGCAGCAATCGCAGCAACAACTAAATGGAAACCAACAGCATCTGCCCATCAATCGTCAACCGGCGCCACAGCAATCACACTTCCTGGACAATTCAA ++ +@@?DFFFDHDHHHIGJIJJJJJJJIJJIJJJJJIJJJIIJJJJJJIIJJJHHGGGEGIJEHIJGHFFDDDDD@BBDCDDDDDDDDDDDDDDBDDBDDDDE +@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245 4:N:0: +AATTTCTTTATTAAATAGAATTGTTTCTTGATCTTGAATTTCTATAATTTTATTATCTTTTTTATCTTTTTTTAGAGCTGCTTATACTTTATATTTATAT ++ +?@@DFBEDHFHHGJIIHIEEHIIIIJIJJJ?FFHGHFGHIJHGGIGDFFIG9EHGHEHIJJJJGIFHIGIJJA=;?>CEBBEECCC;>CDCA;BDD>@;C +@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 4:N:0: +NNNNNATAATTTGTTNNNNNNNNNNNNTTCACAATTTGGTCAATAGCTTGCATAGAAAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNTAATCCAGCNN ++ +#####42@>@@@@@@############11=???????????????????????>????@@@@@##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 4:N:0: +NNNNNGTTCTATCAGNNNNTTTNNNNNTAACTTATTGAGGTTTATGTGGTTCTTATACATTAANNNNNNNNNNNNNNNNNNNNNNNNNTGGGTTATTTNN ++ +#####42@@@?@@@@####43@#####11=???????8??>??>??????????????@@@@@##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 4:N:0: +NNNNNAAAGTTGGCANNNNATATNNNCGAAGATAATACACGTACACGTCATCCGCGATTTAGAANNNNNNNNNNNNNNNNNNNNNNNNCGCCAAGGTGNN ++ +#####22@@@@@@@?####33@@###14=???????????????????????????????????#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 4:N:0: +NNNNNGCACACCAATNNNATTATNATGTTATTTAATACATTTATTAAAGAGAATAATGAAATTTNNNNNNNNNANNNNNNNNNNNNNNTATATTCTGCNN ++ +#####22@@@@@@@?###34@@@#1@????????????????????????????????@@@@@@#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 4:N:0: +NNNNNTAAGAGAGTANNNATAAGATACTCCAAGCAAAAGCAGAGTATCTGTAAACACTTCGCTCNNNNNNNNNGNNNNNNNNNNNNNCCGTGCAAGTCNN ++ +#####22@??@?@??###44@@@@?@?@@@????????????>?<?????????????@@???@#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150 4:N:0: +NNNGNCAAGACAGTGACAATTCAAATTACACATGCGCGTTGCGCACTCACAGATACAAAGATACANNNANNNNCGGGCATACNTNNNAACAGAGCGACTG ++ +###2#4<@@@@@??@@@@?@@@@@@@@@@@@@@@???????????????????????????????################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151 4:N:0: +NNNGNGACATACTCAATATGTTTTACATATTTATGACAGACCTTCTCAAACAGAATATTTTACATNNNTTNNNCATTACCGTTTNNNCACAACACATTTT ++ +###2#2:@?@?@@@?????@@@@@@?@??@@@???@@?????????????????????@@@@@@@###-8###--=?????==?################ +@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159 4:N:0: +NNNCNCGGCATACCTGCTGCCATTGGTCACACTGGCAGATTACGCGATTATTTTTTTTACGGAAANNNTGNNNTTTCCCTTCCGGNNTGAATTGCCTGGA ++ +###2#2:@@?@@@@@@@@@?@?@??@??@@@@??????<????????<?????????=<?######################################## +@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170 4:N:0: +NATAAAGACCTACTAAACCTAACAATTCCAGCTATATTAACATTAGCTGAAGACACTAATCAGGAANAATTTAAAACAGAAAACATAATGGCACAGTCCA ++ +#4=AAAAACCCCCCBCCCBBB7CCCCCCBCCBBAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB#.;AAABBAAAAA@AA@@@@@@B>==?AA????A +@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174 4:N:0: +NCGTGGAAGTCTTTGCGCAGACGGATCACCTCCTCGTTTGCAAGTGTGATAGGTACATCATGCTTTNTGTTCAAATCTTGGAAAATGAAATGTGCATGTA ++ +#+1=BBBB?FCBFG4?@@1<?A:6EF:?9)?00??:BDD1<B########################################################## +@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176 4:N:0: +GATATAGACCGTTAGTCGGCGGGCGGTACCTGGTACCAGCGGGCGGCAAAAAAATAATGTGGGGAGGGGTCGGCGAAGTGTCGCTGAAAACGCCCCTTGC ++ +???DDDDDDD:@AE@AED@E?############################################################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187 4:N:0: +ATTTATGGATCAACATTTTTTATAGCAACAGGATTTCACGGAATTCATGTATTAATCGGAACAACTTTTTTATTAGTATGTTTACTACGACATTTAAATA ++ +BBCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJJJIJJJJJJJIHGIGIIJJJIJJJJHHHHHHDDEEEEDEFEFEEDDDEDDDDDDDEEEDEE |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/illu_summary_PE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illu_summary_PE.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,11 @@ +## +## +Processed Reads (pairs) 25 +Assigned Reads (pairs) 10 +Unassigned Reads (pairs) 15 +# Individual sample read (pair) counts : +emb681m1 2 +emb681m4 2 +emb681m5 2 +emb6801m2 2 +emb6801m1 2 |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/illu_unassigned_1_PE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illu_unassigned_1_PE.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,60 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097 1:N:0: +GTCATATCAATGCCAATAGCAATGAAACCACCCATANAANNNNNACGGCTGAACANNNNNNNACNNGATATAGCATAAATGNANNNTNNNNANTNNNNNN ++ +CCCFFFFFHHHHHJJJJJJJJJJJIJJJIJJJJJJI#1?#####00?FHIJJJJI#######--##,,=A=CDDDDDDDEE################### +@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140 1:N:0: +ATTTAAAATTTATCTCTTTTCATATAACTCTCTGGTAATNNNNAACATAAAACCGANCGCACATGATAATTCTTCCAAATTTATATATNAATTTTATANN ++ +BBCFFFDFHHHGHHIJJJJJJIJIJIGHHHIJJJJGGIJ####11?DHHIIIIGHI#-<FEHGIJIJHGHFHHHHHFFFFFFEFEEEE#,;?BDDFDE## +@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170 1:N:0: +GTTCCATGTAAAGTAGCTAATCAACTAAAAATTTTAATTCCAGTAGGAACTGCAATNATTATAGTAGCTGAGGTAAAATAAGCTCGAGTATCTACATCTA ++ +CCCFFFFFHHHHHIJJJJJJJJJJJJIJJJJJJJJJJJJIJJJIIJJJJJJJJJJI#0?FHIJJJJJJJJGIJHIIJJJHHHHHHFFD@CEEEFDDDDDC +@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 1:N:0: +ATTCAAAGTAAATTAAATGCGAAAATAAAAGGCAGCATGAGNTANTTACTNAAANGGGGTCATNAACAGTACTTGTGCTCCNCCANGTCGNCGNTNCNCT ++ +@@CFFFFFFHHHHJJJIJJJJJJJIJIJJJJJJJJJJJJJJ#0?#0?DHI#-;F#-;DH?EFH#,;BCDEEEEEDDCCCDD#,8?#,5?B########## +@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 1:N:0: +CTATAAAAGTTTATAAATGGCAACCTTAAGTGTAANNNANNNNNTATGCACAGNANNNNNNNNANNNATGCAAAACGACTCNNNNNNNNNNNNCNNNNNN ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJIIHIJ###1#####20?FHJJJJ#.########-###--;BDFEEECDDDD################### +@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 1:N:0: +TCCAAGACGTTCATAAGATACATTAGCTAAACAAAANAANNNNNAAGAACATAAANNNNNNNCANNTATTAATGTATAAGANCNNNANNNNCNTNNNNNN ++ +CC@FFFFFHHHHHJJJJJJIJJJJIJJJJIJJJJJJ#1C#####00?FIJJJJJJ#######--##,5?DDEEEFCFFEDD################### +@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 1:N:0: +GTCCAACGTTGGAGGAGGAGCCGCCATGAATGCCCTGCGNNNNTTCTACCTGGAGANNNCGGTGGTCACACGAGCCTACACCACGGTCNNCGTGCTNNNN ++ +CCCFFFFFHHHHGJJGHJGHIJJJJJJJJJJJJJJJJJJ####.-;DHIJJHHHHH###,,=?BDBDDDDDDDDDDDDDDDDDDDDDD##+28@DD#### +@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 1:N:0: +CATATATGGACTCAAGACCTAATTGCATTAACCGTCTGTNNNNTACGTAGCGTATGNNATTGCGCACTTCTTCTGCGGATAGTCCTTCNNCATCTCNNNN ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJIJ####20?GHIJJJIJIJ##-5CEFHFFDDEEDDDDDDDDDDDDDEDDDD##+2?BDD#### +@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 1:N:0: +TACTTATACATATACTTATAGGCATACTTATACGACTTCNNNNCCCGGTTAATATGNNGTGGCCCGTATAAGTTAATGGGCACAACCGNNTGGGACNNNN ++ +CCCFFFFFHHHHHIJJJJJJJJJJJIJJJJJJJJJJJJJ####00BFHGIIJJJJJ##--BEHJJHDFFEDEEFEEEDDDDDDDDDDD##+2<B@B#### +@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150 1:N:0: +CACCATTCCACTCGCATGTGTATCTAATGAATGCCTCAANACGCTCCTGAACGCAANCAGGTATGTGTGGTAGACCAAAAAAAAAAAANCGGCAGGTANN ++ +CCCFFFFFHHHHHJJJJJJJHIJJJJJJJJJJJJJJJJJ#2?FHIJJJJHIJJJJJ#.;DHCHHHHHHHFDFFEEEEDDDDDDDDDDD############ +@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151 1:N:0: +AAGCATAACTTAAGGCTGAAAATTATTTATTTGACTTGTGTCAAATATAAAAATGTNTTGTGTAGAAACGGTAATGTGAAATTAATGTNAAATATTCTNN ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJIIIJJJJHIJJJJIJIJJJIJIJJI#0?FGIIJJJJJJIIEIJJHHHGHHHFFFFFF#,;ABDEDEE## +@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159 1:N:0: +GTACTGTGCAATGCAAGTGGATTAGAGGATTGCAGCTGGAGGGGTAACAGCAGTGCNTTCGAAATATGTATCTTACAGCATTTCTGGGNTCCTCGTCCGN ++ +CCCFFFFFHHHHHJJJJHIIIIJIJIJJJJJJJJJJJJJFHJJJ?FHCFFHGIGHC#-5;DHHFHHHFCDFFFFFEEEECEDCDCCDC#,8<BBDABB## +@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170 1:N:0: +CTCCACCTCTTGGGTGTATTGGTTGGCCGTTTTACTCTTTTGTTGGAGACTGAGAANCTTAGCTGATATAACTTCTACCGATTCTCCTTTAACTGCACTT ++ +?@@FFDFFHFHHHI?FEEEHHIHHGIEGHHIJJHIIGIIIJFGIJJHIIIEHIIHG#-;CEHHHHDFFFFFDEEC@CECDD?@CDD@CACDCDDDDCDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174 1:N:0: +CATACGAAATGACCAAATCCTAGGTGTTTGAGCGCGGACTGGAGGCGATTCCGCTGTCCGTGGATCTGTGGATCCACTACCTAATGCACGTTAAGTCCAA ++ +@@@DADDDHHAHHGGB@BHIIIFE<AHHI;4?9DHGE@A;AHGEHEE>AC@@CB@BBA@?BBBBA@CCDCCCCC<493?CCCCCC>:>A<8???AC#### +@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176 1:N:0: +GTCTCAGGAAGAGAAAAAAATATAAAGTGTCAAGGGGCGTGTGCAGCGACACTTCGCCGACCCCTCCCCACATTATTTTTTTGCCGCCCGCTGGTAGCAG ++ +;@@BDDDA:DBFDF;A<A@EGGB@:?D1:D?9:BGIDGE4@########################################################### |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/illu_unassigned_2_PE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illu_unassigned_2_PE.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,60 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097 4:N:0: +NNNNNGAGAATGGTGNNNNTGTNNNNNTCCTAATATTCCATTTATGCTATATCCAGTCGTTCTNNNNNNNNNNNNNNNNNNNNNNNNNGTGGTTTCATNN ++ +#####22@>@@@@@@####43@#####11=?????????>?????????????????????@?##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140 4:N:0: +NNNNNATTATATGAAAGNAATATAAAATTTATATATAAATTTGGAAGAATTATCATGTGCGCTCNNNNNNNNNTTANANATNNNNNNAGAGTTATATGAN ++ +#####22@@@@@@@?@@#3=>?@@?@@@?@?@>?????>????????????>??????@?????#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170 4:N:0: +NTATTAGCTATTGGATTATTAGGATTTATTGTATGAGCTCATCATATATTTACCGTTGGAATAGATNTAGATACTCGAGCTTATTTTACCTCAGCTACTA ++ +#4=DFFFFHHHHHJEHIHHJIJJHIJJIJJJIJJJIJJJJIJJJJIJIIJIGJJJJJJJJJJJJJJ#-;CFHIJJJHHHFFFFFEEEEEEEDDDDDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 4:N:0: +CNATTGGGCATAGCCATCGAGGTGTGTCCGGTGTCAAATCAAGTGCTGCAACTGGGCGTGGACTATCGGAATCATCCGGCGGCACTGCTGTTGGCCGCCA ++ +C#1ADDFFHHHHGJJJJJJIJJAGHHGIHHIDFGHIJJJGIJJGIJJIIJIJJIJJJJHHFEFEECACDDBB@CCD@?BDDDDDDDDDDDDCDB:@>BBD +@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 4:N:0: +NNNNNATAATTTGTTNNNNNNNNNNNNTTCACAATTTGGTCAATAGCTTGCATAGAAAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNTAATCCAGCNN ++ +#####42@>@@@@@@############11=???????????????????????>????@@@@@##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 4:N:0: +NNNNNGTTCTATCAGNNNNTTTNNNNNTAACTTATTGAGGTTTATGTGGTTCTTATACATTAANNNNNNNNNNNNNNNNNNNNNNNNNTGGGTTATTTNN ++ +#####42@@@?@@@@####43@#####11=???????8??>??>??????????????@@@@@##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 4:N:0: +NNNNNAAAGTTGGCANNNNATATNNNCGAAGATAATACACGTACACGTCATCCGCGATTTAGAANNNNNNNNNNNNNNNNNNNNNNNNCGCCAAGGTGNN ++ +#####22@@@@@@@?####33@@###14=???????????????????????????????????#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 4:N:0: +NNNNNGCACACCAATNNNATTATNATGTTATTTAATACATTTATTAAAGAGAATAATGAAATTTNNNNNNNNNANNNNNNNNNNNNNNTATATTCTGCNN ++ +#####22@@@@@@@?###34@@@#1@????????????????????????????????@@@@@@#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 4:N:0: +NNNNNTAAGAGAGTANNNATAAGATACTCCAAGCAAAAGCAGAGTATCTGTAAACACTTCGCTCNNNNNNNNNGNNNNNNNNNNNNNCCGTGCAAGTCNN ++ +#####22@??@?@??###44@@@@?@?@@@????????????>?<?????????????@@???@#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150 4:N:0: +NNNGNCAAGACAGTGACAATTCAAATTACACATGCGCGTTGCGCACTCACAGATACAAAGATACANNNANNNNCGGGCATACNTNNNAACAGAGCGACTG ++ +###2#4<@@@@@??@@@@?@@@@@@@@@@@@@@@???????????????????????????????################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151 4:N:0: +NNNGNGACATACTCAATATGTTTTACATATTTATGACAGACCTTCTCAAACAGAATATTTTACATNNNTTNNNCATTACCGTTTNNNCACAACACATTTT ++ +###2#2:@?@?@@@?????@@@@@@?@??@@@???@@?????????????????????@@@@@@@###-8###--=?????==?################ +@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159 4:N:0: +NNNCNCGGCATACCTGCTGCCATTGGTCACACTGGCAGATTACGCGATTATTTTTTTTACGGAAANNNTGNNNTTTCCCTTCCGGNNTGAATTGCCTGGA ++ +###2#2:@@?@@@@@@@@@?@?@??@??@@@@??????<????????<?????????=<?######################################## +@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170 4:N:0: +NATAAAGACCTACTAAACCTAACAATTCCAGCTATATTAACATTAGCTGAAGACACTAATCAGGAANAATTTAAAACAGAAAACATAATGGCACAGTCCA ++ +#4=AAAAACCCCCCBCCCBBB7CCCCCCBCCBBAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB#.;AAABBAAAAA@AA@@@@@@B>==?AA????A +@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174 4:N:0: +NCGTGGAAGTCTTTGCGCAGACGGATCACCTCCTCGTTTGCAAGTGTGATAGGTACATCATGCTTTNTGTTCAAATCTTGGAAAATGAAATGTGCATGTA ++ +#+1=BBBB?FCBFG4?@@1<?A:6EF:?9)?00??:BDD1<B########################################################## +@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176 4:N:0: +GATATAGACCGTTAGTCGGCGGGCGGTACCTGGTACCAGCGGGCGGCAAAAAAATAATGTGGGGAGGGGTCGGCGAAGTGTCGCTGAAAACGCCCCTTGC ++ +???DDDDDDD:@AE@AED@E?############################################################################### |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/markdupes_DNase_sorted.bam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/markdupes_DNase_sorted.bam Wed Nov 25 12:37:01 2015 -0500 |
| b |
| b'@@ -0,0 +1,1755 @@\n+@HD\tVN:1.4\tSO:coordinate\n+@SQ\tSN:chr2L\tLN:23011544\n+@SQ\tSN:chr2LHet\tLN:368872\n+@SQ\tSN:chr2R\tLN:21146708\n+@SQ\tSN:chr2RHet\tLN:3288761\n+@SQ\tSN:chr3L\tLN:24543557\n+@SQ\tSN:chr3LHet\tLN:2555491\n+@SQ\tSN:chr3R\tLN:27905053\n+@SQ\tSN:chr3RHet\tLN:2517507\n+@SQ\tSN:chr4\tLN:1351857\n+@SQ\tSN:chrM\tLN:19517\n+@SQ\tSN:chrX\tLN:22422827\n+@SQ\tSN:chrXHet\tLN:204112\n+@SQ\tSN:chrYHet\tLN:347038\n+@PG\tID:bowtie2\tPN:bowtie2\tVN:2.2.4\tCL:"/g/funcgen/galaxy-dist/dependencies/bowtie2/2.2.4/devteam/package_bowtie_2_2_4/172979b6bf77/bowtie2-align-s --wrapper basic-0 -p 16 -x /g/funcgen/indices/bowtie2_v2_0_0/d.melanogaster/dm3/d_melanogaster_fb5_22 --fast -1 /tmp/28361.inpipe1 -2 /tmp/28361.inpipe2"\n+HISEQ:44:C6KC0ANXX:5:1206:2561:55252:TTGGTATG:TACGAACC:TCAGGACT\t177\tchr4\t492\t1\t116M\tchr3RHet\t1667730\t0\tAGATGTGGTGGATAAATGTGTGCGGGCACACTAATGGCCGCCATCGTAAGCCGCGAAAAGCTTAGCGTGCATTGTCGATCGAGAGTTTGGAGGGCAAACTGCGGTAAGATAAGATT\tFFFB/777///7////B7FF7/7/77/7/BFFF//F7///<<FBFFFFFF/FFBFFB/B<FF/</B/FB<</<B<</BFF<FBB/FFF<//</FFFF//<F<F/FB/<</<FBBFF\tAS:i:-3\tXS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:4T111\tYT:Z:UP\n+HISEQ:44:C6KC0ANXX:5:2316:7060:1967:TTGGTATG:NACGCCAT:AGTGCTGT\t133\tchr4\t909\t0\t*\t=\t909\t0\tTAAGATCNNNNNNNNNTNANNNNNNNANNCACGGAGNNNNNNCNNAGACTGCCTNNGTNNNNGCNNNNNNTCNNNNNNNNNNNNNNNTNNTNNNNNNNNNNNNGNNTTTNGNNNNN\tFFFFFFF#############################################################################################################\tYT:Z:UP\tYF:Z:NS\n+HISEQ:44:C6KC0ANXX:5:2316:7060:1967:TTGGTATG:NACGCCAT:AGTGCTGT\t89\tchr4\t909\t0\t116M\t=\t909\t0\tNCAGATGGGTTTGGGCCCAACTAGTGGGTTCTCTGCCCCTTTCCTGGCTAGGNNGTCCGCTAGCTCATTTNCCGGGATGTTGTTGTGTCCCGGGACCCACCTTATTGTGAGTTTGT\t#BFFF<FFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFBFFBFFFFFFB/F</##FFFFFFFFFFFFFF<<#FFBFBFFFFFFFF/FFFFFBFFFFFFFF<FFFFFFFFFFFFFFFF\tAS:i:-28\tXS:i:-28\tXN:i:0\tXM:i:9\tXO:i:0\tXG:i:0\tNM:i:9\tMD:Z:0A4A0T4C8T3A27T0T16C45\tYT:Z:UP\n+HISEQ:44:C6KC0ANXX:5:1114:20011:54595:TTGGTATG:GTTCTGCT:GAGAAGAG\t133\tchr4\t928\t0\t*\t=\t928\t0\tCCTCTATCAACTTTAGTAATCCCAGTACTCTGTGGTGACCAACACCACAGAATGGTTCGGGCCCAATTAGAGGGTTCTCTTTCTTCTCTCTCTTTCCTGGCTAGGTTTTCCGCTAG\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFF\tYT:Z:UP\n+HISEQ:44:C6KC0ANXX:5:1114:20011:54595:TTGGTATG:GTTCTGCT:GAGAAGAG\t89\tchr4\t928\t0\t16M7I93M\t=\t928\t0\tATTAGAGGGTTCTCTTTCTTCTCTCTCTTTCCTGGCTAGGTTTTCCGCTAGCTCATTTCCCGGGATGTTGTTGTGTCCCGGGACCCACCCTATTATGAGTTTGTTAATAGCTCCTA\tBFFFFFFFFFFFFFF/FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tAS:i:-69\tXN:i:0\tXM:i:9\tXO:i:1\tXG:i:7\tNM:i:16\tMD:Z:15G0C1C16G46T4G10G1C6A1\tYT:Z:UP\n+HISEQ:44:C6KC0ANXX:5:1206:3433:8421:TTGGTATG:GACATGAG:CTGATGTG\t163\tchr4\t1061\t1\t116M\t=\t1067\t122\tCATTTACTAGCTTAGATGTTATCTTAGTTTTGCTGAGCGCCTTCATGGCTGCTTGACTATCAGACAGTATAGCAATGTCCTTGCCATGATAGTTCCTTTTCAGATTAAACTCTGCA\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFF/FFFFFF#\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:116\tYS:i:0\tYT:Z:CP\n+HISEQ:44:C6KC0ANXX:5:1206:3433:8421:TTGGTATG:GACATGAG:CTGATGTG\t83\tchr4\t1067\t1\t116M\t=\t1061\t-122\tCTAGCTTAGATGTTATCTTAGTTTTGCTGAGCGCCTTCATGGCTGCTTGACTATCAGACAGTATAGCAATGTCCTTGCCATGATAGTTCCTTTTCAGATTAAACTCTGCACAGCGT\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:116\tYS:i:0\tYT:Z:CP\n+HISEQ:44:C6KC0ANXX:5:1106:10689:34373:TTGGTATG:CACACACA:TTCGTTCG\t163\tchr4\t1152\t1\t116M\t=\t1314\t278\tGTTCCTTTTCAGATTAAACTCTGCACAGCGTCCAATAGCACAGACTTCAGCTTGAATGCTGGTGTATCTGCCCATTGATTCGTGGTATTTCAACCTGGGGCCCACTTCCCTCGTCG\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFBFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFBFFF\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:116\tYS:i:0\tYT:Z:CP\n+HISEQ:44:C6KC0ANXX:5:2202:16753:37705:TTGGTATG:CACACACA:TTCGTTCG\t163\tchr4\t1152\t1\t116M\t=\t1314\t278\tGTTCCTTTTCAGATTAAACTCTGCACAGCGTCCAATAGCACAGACTTCAGCTTGAATGCTGGTGTATCTGCCCATTGATTCGTGGTATTTCAACCTGG'..b'TATCACTCCTCTGTATGCGAGAACGCTGGCAGAGGCTTTGCTCTCCCCCTGTTGGGTCCTTCGTATCTTTTTGACCTGTTTGCCAAAGTCGCTAAGATTGGGATCGGCCTTCAG\tFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:116\tYS:i:0\tYT:Z:CP\n+HISEQ:44:C6KC0ANXX:5:2315:14717:78128:TTGGTATG:CTGAGTGT:GGCCTAAT\t83\tchr4\t16664\t1\t116M\t=\t16587\t-193\tTCTATCACTCCTCTGTATGCGAGAACGCTGGCAGAGGCTTTGCTCTCCCCCTGTTGGGTCCTTCGTATCTTTTTGACCTGTTTGCCAAAGTCGCTAAGATTGGGATCGGCCTTCAG\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:116\tYS:i:0\tYT:Z:CP\n+HISEQ:44:C6KC0ANXX:5:2315:16735:71410:TTGGTATG:CTGAGTGT:GGCCTAAT\t83\tchr4\t16664\t1\t116M\t=\t16587\t-193\tTCTATCACTCCTCTGTATGCGAGAACGCTGGCAGAGGCTTTGCTCTCCCCCTGTTGGGTCCTTCGTATCTTTTTGACCTGTTTGCCAAAGTCGCTAAGATTGGGATCGGCCTTCAG\tFFFFFFFFFFFBFFF<FFFFFFFFBFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB/FFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFF\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:116\tYS:i:0\tYT:Z:CP\n+HISEQ:44:C6KC0ANXX:5:2315:19710:12913:TTGGTATG:CTGAGTGT:GGCCTAAT\t83\tchr4\t16664\t1\t116M\t=\t16587\t-193\tTCTATCACTCCTCTGTATGCGAGAACGCTGGCAGAGGCTTTGCTCTCCCCCTGTTGGGTCCTTCGTATCTTTTTGACCTGTTTGCCAAAGTCGCTAAGATTGGGATCGGCCTTCAG\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:116\tYS:i:0\tYT:Z:CP\n+HISEQ:44:C6KC0ANXX:5:2316:4794:29646:TTGGTATG:AGCTACCA:AGCTCTAG\t99\tchr4\t16746\t1\t116M\t=\t17010\t380\tTGCCAAAGTCGCTAAGATTGGGATCGGCCTTCAGCGTACGGAGCATGTCGGCGTACGAAGCTTCACCGGTCTTTATGAGGATAATACCCTTCTTACGCAAGCGCTTCGGCATTACT\tFFFFFFFFFFFFFFBFBFFFFFFFFFBFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFBBBFFFFFFFFFFFFFFFFFFF<FFBBFFFFFFFFFFFFFFFFFFBFFFFBFFFFFFF\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:116\tYS:i:0\tYT:Z:CP\n+HISEQ:44:C6KC0ANXX:5:2313:5718:90043:TTGGTATG:CAACTGGT:CAACTGGT\t163\tchr4\t16912\t1\t116M\t=\t16979\t183\tGACCGGTTTTGGCTCCTTTCGCTTAGAATTAGTCGTTTTGGTAGGCTTGGTTGGCAACTCTGAATGTGGCTTCACTGGGACGATTTTTGGCGCCACTGCTATACGGTCCTTCGTCT\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tAS:i:-25\tXS:i:-25\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:21T10C24G42G1G13\tYS:i:-20\tYT:Z:CP\n+HISEQ:44:C6KC0ANXX:5:2313:5718:90043:TTGGTATG:CAACTGGT:CAACTGGT\t83\tchr4\t16979\t1\t116M\t=\t16912\t-183\tGGCTTCACTGGGACGATTTTTGGCGCCACTGCTATACGGTCCTTCGTCTGCAGAGTCTCCGTCTGGGTGGCGTTATCCCGGGAAGAAGCATCTTTACCAGCACCCTCTTGTACCTG\tFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tAS:i:-20\tXS:i:-20\tXN:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tNM:i:4\tMD:Z:33G1G19C16G43\tYS:i:-25\tYT:Z:CP\n+HISEQ:44:C6KC0ANXX:5:2316:4794:29646:TTGGTATG:AGCTACCA:AGCTCTAG\t147\tchr4\t17010\t1\t116M\t=\t16746\t-380\tCTGTGCGGTCCTTCGTCTGCAGAGCCTCCGTCTGGGTGGCGGTATCCCGGGAAGAAGCATCTTTACCAGCACCCTCTTGTACCTGAATCGCTCTAGAGTTGAGTGCAGCCAGGTCA\tBFFBFBBF<FF<FFFFFFFFFFFFBBBBFFFF<FFFBFFFBFFF<FFFFFFFFBFFF<FFFFFFFFFFFFFFFFFFBFFBFFFFFFFBFFFFFBFFFFFFFFFFFFFFFBFFF<FF\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:116\tYS:i:0\tYT:Z:CP\n+HISEQ:44:C6KC0ANXX:5:2102:13765:43133:TTGGTATG:ACACTCAG:ATCGCGTA\t163\tchr4\t17809\t1\t116M\t=\t17870\t177\tCCTCCGCGTGCTCTTCAGTCCTTGCTAGCTAGTCCTTGCTAGGGACTGTCAGTCAAGGTATGACTTTGGTGAGCAGGATGTGAGGCCAAGTCACACCCAATCCTTCATTGTAGTCC\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:116\tYS:i:0\tYT:Z:CP\n+HISEQ:44:C6KC0ANXX:5:2102:13765:43133:TTGGTATG:ACACTCAG:ATCGCGTA\t83\tchr4\t17870\t1\t116M\t=\t17809\t-177\tGACTTTGGTGAGCAGGATGTGAGGCCAAGTCACACCCAATCCTTCATTGTAGTCCATGAGGGCTCCTCCTTTCACCCTATAGTCGACTTTTACGACAAGCCGGGAACGCTGAGGTA\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:116\tYS:i:0\tYT:Z:CP\n' |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/markdupes_DNase_sorted_marked.bam |
| b |
| Binary file test-data/markdupes_DNase_sorted_marked.bam has changed |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/markdupes_metrics.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/markdupes_metrics.txt Wed Nov 25 12:37:01 2015 -0500 |
| [ |
| @@ -0,0 +1,112 @@ +## htsjdk.samtools.metrics.StringHeader +# org.embl.gbcs.je.jeduplicates.MarkDuplicatesWithMolecularCode MISMATCHES=2 MAX_NUMBER_OF_N=1 BARCODE_FILE=/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_5.dat SLOTS=[-1, -2] INPUT=[/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_4.dat] OUTPUT=/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_6.dat METRICS_FILE=/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_7.dat COMMENT=[test-run] REMOVE_DUPLICATES=true ASSUME_SORTED=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT SPLIT_CHAR=: TRIM_HEADERS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMolecularCode COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Tue Nov 10 17:01:18 CET 2015 + +## METRICS CLASS picard.sam.DuplicationMetrics +LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE +Unknown Library 196 674 196 186 467 0 0.725389 216 + +## HISTOGRAM java.lang.Double +BIN VALUE +1.0 0.997418 +2.0 1.041445 +3.0 1.043389 +4.0 1.043474 +5.0 1.043478 +6.0 1.043478 +7.0 1.043478 +8.0 1.043478 +9.0 1.043478 +10.0 1.043478 +11.0 1.043478 +12.0 1.043478 +13.0 1.043478 +14.0 1.043478 +15.0 1.043478 +16.0 1.043478 +17.0 1.043478 +18.0 1.043478 +19.0 1.043478 +20.0 1.043478 +21.0 1.043478 +22.0 1.043478 +23.0 1.043478 +24.0 1.043478 +25.0 1.043478 +26.0 1.043478 +27.0 1.043478 +28.0 1.043478 +29.0 1.043478 +30.0 1.043478 +31.0 1.043478 +32.0 1.043478 +33.0 1.043478 +34.0 1.043478 +35.0 1.043478 +36.0 1.043478 +37.0 1.043478 +38.0 1.043478 +39.0 1.043478 +40.0 1.043478 +41.0 1.043478 +42.0 1.043478 +43.0 1.043478 +44.0 1.043478 +45.0 1.043478 +46.0 1.043478 +47.0 1.043478 +48.0 1.043478 +49.0 1.043478 +50.0 1.043478 +51.0 1.043478 +52.0 1.043478 +53.0 1.043478 +54.0 1.043478 +55.0 1.043478 +56.0 1.043478 +57.0 1.043478 +58.0 1.043478 +59.0 1.043478 +60.0 1.043478 +61.0 1.043478 +62.0 1.043478 +63.0 1.043478 +64.0 1.043478 +65.0 1.043478 +66.0 1.043478 +67.0 1.043478 +68.0 1.043478 +69.0 1.043478 +70.0 1.043478 +71.0 1.043478 +72.0 1.043478 +73.0 1.043478 +74.0 1.043478 +75.0 1.043478 +76.0 1.043478 +77.0 1.043478 +78.0 1.043478 +79.0 1.043478 +80.0 1.043478 +81.0 1.043478 +82.0 1.043478 +83.0 1.043478 +84.0 1.043478 +85.0 1.043478 +86.0 1.043478 +87.0 1.043478 +88.0 1.043478 +89.0 1.043478 +90.0 1.043478 +91.0 1.043478 +92.0 1.043478 +93.0 1.043478 +94.0 1.043478 +95.0 1.043478 +96.0 1.043478 +97.0 1.043478 +98.0 1.043478 +99.0 1.043478 +100.0 1.043478 + |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/markdupes_umis.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/markdupes_umis.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,96 @@ +AACGCCAT +CAACTGGT +GCCGATTA +AAGGTACG +CAAGTCGT +GCGGTATT +AATTCCGG +CACACACA +GGAATTGG +ACACAGAG +CAGTACTG +GGATAACG +ACACTCAG +CATCAGCA +GGCCTAAT +ACACTGTG +CATCGTTC +GGCGTATT +ACAGGACA +CCAAGGTT +GTCTTGTC +ACCTGTAG +CCTAGCTT +GTGATGAG +ACGAAGGT +CGATTACG +GTGATGTC +ACGACTTG +CGCCTATT +GTGTACTG +ACGTCAAC +CGTTCCAT +GTGTAGTC +ACGTCATG +CGTTGGAT +GTTCACCT +ACTGTCAG +CTACGTTC +GTTCTGCT +ACTGTGAC +CTACTCGT +GTTGTCGA +AGACACTC +CTAGAGGA +TACGAACC +AGAGGAGA +CTAGGAAG +TAGCAAGG +AGCATCGT +CTAGGTAC +TAGCTAGC +AGCATGGA +CTCAGTCT +TAGGTTCG +AGCTACCA +CTGACTGA +TATAGCGC +AGCTCTAG +CTGAGTGT +TCAGGACT +AGGACAAC +CTGATGTG +TCCACATC +AGGACATG +CTGTTCAC +TCGACTTC +AGGTTGCT +CTTCGTTG +TCGTAGGT +AGTCGAGA +GAACAGGT +TCGTCATC +AGTGCTGT +GAAGACCA +TGAGACTC +ATAAGCGG +GAAGTGCA +TGAGAGTG +ATCCATGG +GACATGAG +TGAGTGAG +ATCGAACC +GAGAAGAG +TGCTTGGA +ATCGCGTA +GAGAAGTC +TGGAGTAG +ATCGTTGG +GATCCTAG +TGTGTGTG +CAACGATC +GATGTCGT +TTCGCCTA +CAACGTTG +GCCGATAT +TTCGTTCG \ No newline at end of file |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/picard_MarkDuplicates.bam |
| b |
| Binary file test-data/picard_MarkDuplicates.bam has changed |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/picard_MarkDuplicates_test1.bam |
| b |
| Binary file test-data/picard_MarkDuplicates_test1.bam has changed |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/sample1_CACTGTGTATAG_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1_CACTGTGTATAG_1.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,24 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097:1:N:0:CACTGT +TCAATGCCAATAGCAATGAAACCACCCATANAANNNNNACGGCTGAACANNNNNNNACNNGATATAGCATAAATGNANNNTNNNNANTNNNNNN ++ +FFHHHHHJJJJJJJJJJJIJJJIJJJJJJI#1?#####00?FHIJJJJI#######--##,,=A=CDDDDDDDEE################### +@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140:1:N:0:CACTGT +AATTTATCTCTTTTCATATAACTCTCTGGTAATNNNNAACATAAAACCGANCGCACATGATAATTCTTCCAAATTTATATATNAATTTTATANN ++ +DFHHHGHHIJJJJJJIJIJIGHHHIJJJJGGIJ####11?DHHIIIIGHI#-<FEHGIJIJHGHFHHHHHFFFFFFEFEEEE#,;?BDDFDE## +@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170:1:N:0:CACTGT +TGTAAAGTAGCTAATCAACTAAAAATTTTAATTCCAGTAGGAACTGCAATNATTATAGTAGCTGAGGTAAAATAAGCTCGAGTATCTACATCTA ++ +FFHHHHHIJJJJJJJJJJJJIJJJJJJJJJJJJIJJJIIJJJJJJJJJJI#0?FHIJJJJJJJJGIJHIIJJJHHHHHHFFD@CEEEFDDDDDC +@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179:1:N:0:CACTGT +ACCAGACTTGTGGGGCGACTGTTCAGGCCGTGTAGGGCATTCAGGGGTAGCATGGGAGCAGCTAGATTAGATGCAGATCTCTGAGAAGCTGTCT ++ +BDDBFDFIIEF??8@EFGFHFGAFFGGIHH;5.=CEE),7.;(;ACB9>?CAAC??9?B@9??C:(:@A::@CC:4+:>@C@AAC(>9?CCCC@ +@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184:1:N:0:CACTGT +GTGGGAAAGGGAAGGGCAAGGGGGAGGGGAAGAATTTAACCGGGCGGGAGGAGAATCGGGCAGGGAAGAATGGTTGGTTGGTGGAACAACTGAA ++ +EDHHHDHJJGIGIJCBDHEHGJJJBGEHIBGGHFGFFGGHFFDD>?BDBBDDDDDD@ADD;>@D98AB?CCDD:CBB<ADD8<?<@?B?ACDCA +@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193:1:N:0:CACTGT +GCGAGTGTTTGCACGATTATCTCATATTCAAACTGGTCAACATGGGCATACGATTTCTTGCGCTCCTTGCTTTCAAACAGCCTGTCTCTTATAC ++ +F+CFHFHIIJJJJJJIJJIJJJJJJJJJJIJJJJJJBGIJJJJJJJJJJJJJJJJIJJJJHHFFFDEEEDDDDDDDDDDDBBDDDDDDDDDDDD |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/sample1_CACTGTGTATAG_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1_CACTGTGTATAG_2.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,24 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097:4:N:0:GTATAG +AGAATGGTGNNNNTGTNNNNNTCCTAATATTCCATTTATGCTATATCCAGTCGTTCTNNNNNNNNNNNNNNNNNNNNNNNNNGTGGTTTCATNN ++ +2@>@@@@@@####43@#####11=?????????>?????????????????????@?##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140:4:N:0:GTATAG +TTATATGAAAGNAATATAAAATTTATATATAAATTTGGAAGAATTATCATGTGCGCTCNNNNNNNNNTTANANATNNNNNNAGAGTTATATGAN ++ +2@@@@@@@?@@#3=>?@@?@@@?@?@>?????>????????????>??????@?????#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170:4:N:0:GTATAG +GCTATTGGATTATTAGGATTTATTGTATGAGCTCATCATATATTTACCGTTGGAATAGATNTAGATACTCGAGCTTATTTTACCTCAGCTACTA ++ +FFHHHHHJEHIHHJIJJHIJJIJJJIJJJIJJJJIJJJJIJIIJIGJJJJJJJJJJJJJJ#-;CFHIJJJHHHFFFFFEEEEEEEDDDDDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179:4:N:0:GTATAG +AGAGATCTGCATCTAATCTAGCTGCTCCCATGCTACCCCTGAATACCCTACACGGCCTGAACAGTCGCCCCACAAGTCTGGCGTGGGGCTGTCT ++ +DFHF?HHGBHHIJJIGIIIJGIJBEHIGID<9EHIIJJI@;?BGGHIIIIIIIIIIIAGE@HHH?EDFDDB?B?9?:ACCC(85>>B>>@BBD@ +@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184:4:N:0:GTATAG +CATTCTGTATGCCCTTCCCTCTCGCACACTCGACCCAATGACCCGCTTTGCTCTGTTTACCTCTCCGCTCTGTTTTTGCACTTGGAAATTGCTA ++ +FFHGDHHGGIJJIJJJGHIIIGFHHIIGIIIJIJJEHGEGGIJJIIIIGGGHGGFHHFEC@BCEDECDDDDDDDDDD?AC>ACCCCACADCCDD +@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193:4:N:0:GTATAG +TGAAAGCAAGGAGCGCAAGAAATCGTATGCCCATGTTGACCAGTTTGAATATGAGATAATCGTGCAAACACTCCCAAGGAACTGTCTCTTATAC ++ +FFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJHJJJJJGHIIIIIJJIJIJEEEEHHFFFEEEEDED3=CDDDDDDDDCDDDDDDDDD |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/sample2_ATTCCGTCCGTC_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample2_ATTCCGTCCGTC_1.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,28 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204:1:N:0:ATTCCG +CATCTGTTGCTCATATAGGAATTGTTCTATCAGGACTTTTAACTATAACTTATTGAGGTTTATGTGGTTCTTATACATTAATAATTGCTCATGG ++ +DFHHHGHJJIJJJJJJJJJJJJJJJJJJIJJJJJJJIJJJIJJJJJJIJJJJJJIJJJHIJJJJHIIHHHHIJJJIJJHHHHHHFFFFEFCEEE +@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207:1:N:0:ATTCCG +GTCGTTGTGATACTAAACTTTCTCAAATAATAAAAAAAAAGAATAAAATTCCTAATAATGAAATAGTTGATCCAATAGTTGATACAATATTTCA ++ +FFHHHGHIIGIJJIIJJJJJJIIHIIJHGIHGJIJIJJJHGCCHIGGEHH>EEFFFFFFFACCEACEDCDCCCCCDCDEEDDDE(:ACCD:@D@ +@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211:1:N:0:ATTCCG +AGTAAATTAAATGCGAAAATAAAAGGCAGCATGAGNTANTTACTNAAANGGGGTCATNAACAGTACTTGTGCTCCNCCANGTCGNCGNTNCNCT ++ +FFFHHHHJJJIJJJJJJJIJIJJJJJJJJJJJJJJ#0?#0?DHI#-;F#-;DH?EFH#,;BCDEEEEEDDCCCDD#,8?#,5?B########## +@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222:1:N:0:ATTCCG +ATAGTAATAATATTACCTAATACAAATAATGAAATATCATATTGATGAAATCATTTTACTATACCTGATACAGTTGTTATAGCTCCGATAGCTC ++ +FDFHHHHJJIIJJJGJIIJJIIJHIJIJIJIIJJJJJJJIIJJIGGHIJJJIJGJJIIIHIIHJ>GHIIIIIIGGGIIJJJJIH)=ABDDDDEE +@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233:1:N:0:ATTCCG +AATTTAATGCAATTACCAATCTTACAAGTTATTATACCAATAATTGCATCTATGTTTTGCTTTCTTGACAAGAAACACAAGGTAACTTGGGTTA ++ +DD<DFDFB<?:EIBHHIIFF:AHI?HC<*:1:EF@G49D<B3?@F4?BDD*BG*?B??B<B8888@F)).@;@;@;=6?############### +@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240:1:N:0:ATTCCG +GGCATCGTTGCTGCTCTTAACGTCCAAATGGACGGGCGACTCCCCGAACATTGCCTCGAGTCGTGTCTCCACGGATTTCTGGACGTCCGAATCG ++ +FFHHHHHJJJIIIJIHGIJJIHHJJJHIJJJFHIJJBHGGHHHHFEDDDDDDDDDDDDDDCCBDDDDDDDDDDDDDDDDEDD@BDDDDBB@BBD +@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245:1:N:0:ATTCCG +AAATATAAAGTATAAGCAGCTCTAAAAAAAGATAAAAAAGATAATAAAATTATAGAAATTCAAGATCAAGAAACAATTCTATTTAATAAAGAAA ++ +FFFBDFHGIGHGJIJJJJJIIDHHIJJIGGHEEGGIIIIGGDHIGE@FHHIIJJFGGHGHCAHH@D;CD;CCCECDDCCDDDCD3>ACAA:@?C |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/sample2_ATTCCGTCCGTC_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample2_ATTCCGTCCGTC_2.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,28 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204:4:N:0:TCCGTC +TTCTTCGACTTCCAAGACGTTCATAAGATACATTAGCTAAACAAAATAACCCAGAAGAACATAAACCATGAGCAATTATTAATGTATAAGAACC ++ +FFHHHFHIJJJJJJJJJJIIGIIIJJIIGHJJJJIJJIIJIJJJIJJIJJJJJJJJIGIJIIJJHHFHHFFFFFEDEEEFFFEDDDEFEDDDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207:4:N:0:TCCGTC +TATATTTATTGGAGTTAATTTAACATTTTTTCCTCAACATTTTTTAGGATTGGCTGGAATACCTCGACGTTATTCAGATTACCCAGATGCTTAC ++ +FDHDHHHIJJJJEHHHIIIIJIJHIHIJJJJIGHEIIIJJIJJJHHGIIIJIJIJIJEHGHGFHFH8?ABC?BC>>AADDCACDDDDD<@CD>> +@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211:4:N:0:TCCGTC +GGCATAGCCATCGAGGTGTGTCCGGTGTCAAATCAAGTGCTGCAACTGGGCGTGGACTATCGGAATCATCCGGCGGCACTGCTGTTGGCCGCCA ++ +FFHHHHGJJJJJJIJJAGHHGIHHIDFGHIJJJGIJJGIJJIIJIJJIJJJJHHFEFEECACDDBB@CCD@?BDDDDDDDDDDDDCDB:@>BBD +@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222:4:N:0:TCCGTC +GACCATTAACAGGAGCTATCGGAGCTATAACAACTGTATCAGGTATAGTAAAATGATTTCATCAATATGATATTTCATTATTTGTATTAGGTAA ++ +FFHHFHGJJJJJJIIJJGJIIJGHGHIIIJIJJIGIHIIGIIJBFDIIGHJJIJJGIEIEGHIJCH@EHFHGHHHGFFFFFFFFFDDEEDCAC@ +@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233:4:N:0:TCCGTC +AACCAAGATACCTTGTGTTTCTTGGCAAGAAAGCAAAACATTGATGCAATTATTGGTATAATAACTTGTAAGATTGGTAATTGCATTAAATTGT ++ +D4DB?:3E3+2AEAHHFIIIIIIIE9?9?3DGFF>;;F;D9BD9?@DCFFICFGF@FCF@@F@C@DF<7C@E3?ECC>7@DDBAADA;;;>A:A +@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240:4:N:0:TCCGTC +CAGCAATCGCAGCAACAACTAAATGGAAACCAACAGCATCTGCCCATCAATCGTCAACCGGCGCCACAGCAATCACACTTCCTGGACAATTCAA ++ +FDHDHHHIGJIJJJJJJJIJJIJJJJJIJJJIIJJJJJJIIJJJHHGGGEGIJEHIJGHFFDDDDD@BBDCDDDDDDDDDDDDDDBDDBDDDDE +@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245:4:N:0:TCCGTC +TTTATTAAATAGAATTGTTTCTTGATCTTGAATTTCTATAATTTTATTATCTTTTTTATCTTTTTTTAGAGCTGCTTATACTTTATATTTATAT ++ +EDHFHHGJIIHIEEHIIIIJIJJJ?FFHGHFGHIJHGGIGDFFIG9EHGHEHIJJJJGIFHIGIJJA=;?>CEBBEECCC;>CDCA;BDD>@;C |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/sample3_GCTACCTGGTCA_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample3_GCTACCTGGTCA_1.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,24 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088:1:N:0:GCTACC +AAGTTTATAAATGGCAACCTTAAGTGTAANNNANNNNNTATGCACAGNANNNNNNNNANNNATGCAAAACGACTCNNNNNNNNNNNNCNNNNNN ++ +FFHHHHHJJJJJJJJJJJJJJJJJIIHIJ###1#####20?FHJJJJ#.########-###--;BDFEEECDDDD################### +@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095:1:N:0:GCTACC +ACGTTCATAAGATACATTAGCTAAACAAAANAANNNNNAAGAACATAAANNNNNNNCANNTATTAATGTATAAGANCNNNANNNNCNTNNNNNN ++ +FFHHHHHJJJJJJIJJJJIJJJJIJJJJJJ#1C#####00?FIJJJJJJ#######--##,5?DDEEEFCFFEDD################### +@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114:1:N:0:GCTACC +CGTTGGAGGAGGAGCCGCCATGAATGCCCTGCGNNNNTTCTACCTGGAGANNNCGGTGGTCACACGAGCCTACACCACGGTCNNCGTGCTNNNN ++ +FFHHHHGJJGHJGHIJJJJJJJJJJJJJJJJJJ####.-;DHIJJHHHHH###,,=?BDBDDDDDDDDDDDDDDDDDDDDDD##+28@DD#### +@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119:1:N:0:GCTACC +TGGACTCAAGACCTAATTGCATTAACCGTCTGTNNNNTACGTAGCGTATGNNATTGCGCACTTCTTCTGCGGATAGTCCTTCNNCATCTCNNNN ++ +FFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJIJ####20?GHIJJJIJIJ##-5CEFHFFDDEEDDDDDDDDDDDDDEDDDD##+2?BDD#### +@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124:1:N:0:GCTACC +TACATATACTTATAGGCATACTTATACGACTTCNNNNCCCGGTTAATATGNNGTGGCCCGTATAAGTTAATGGGCACAACCGNNTGGGACNNNN ++ +FFHHHHHIJJJJJJJJJJJIJJJJJJJJJJJJJ####00BFHGIIJJJJJ##--BEHJJHDFFEDEEFEEEDDDDDDDDDDD##+2<B@B#### +@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150:1:N:0:GCTACC +TCCACTCGCATGTGTATCTAATGAATGCCTCAANACGCTCCTGAACGCAANCAGGTATGTGTGGTAGACCAAAAAAAAAAAANCGGCAGGTANN ++ +FFHHHHHJJJJJJJHIJJJJJJJJJJJJJJJJJ#2?FHIJJJJHIJJJJJ#.;DHCHHHHHHHFDFFEEEEDDDDDDDDDDD############ |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/sample3_GCTACCTGGTCA_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample3_GCTACCTGGTCA_2.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,24 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088:4:N:0:TGGTCA +TAATTTGTTNNNNNNNNNNNNTTCACAATTTGGTCAATAGCTTGCATAGAAAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNTAATCCAGCNN ++ +2@>@@@@@@############11=???????????????????????>????@@@@@##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095:4:N:0:TGGTCA +TTCTATCAGNNNNTTTNNNNNTAACTTATTGAGGTTTATGTGGTTCTTATACATTAANNNNNNNNNNNNNNNNNNNNNNNNNTGGGTTATTTNN ++ +2@@@?@@@@####43@#####11=???????8??>??>??????????????@@@@@##################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114:4:N:0:TGGTCA +AAGTTGGCANNNNATATNNNCGAAGATAATACACGTACACGTCATCCGCGATTTAGAANNNNNNNNNNNNNNNNNNNNNNNNCGCCAAGGTGNN ++ +2@@@@@@@?####33@@###14=???????????????????????????????????#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119:4:N:0:TGGTCA +CACACCAATNNNATTATNATGTTATTTAATACATTTATTAAAGAGAATAATGAAATTTNNNNNNNNNANNNNNNNNNNNNNNTATATTCTGCNN ++ +2@@@@@@@?###34@@@#1@????????????????????????????????@@@@@@#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124:4:N:0:TGGTCA +AAGAGAGTANNNATAAGATACTCCAAGCAAAAGCAGAGTATCTGTAAACACTTCGCTCNNNNNNNNNGNNNNNNNNNNNNNCCGTGCAAGTCNN ++ +2@??@?@??###44@@@@?@?@@@????????????>?<?????????????@@???@#################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150:4:N:0:TGGTCA +AAGACAGTGACAATTCAAATTACACATGCGCGTTGCGCACTCACAGATACAAAGATACANNNANNNNCGGGCATACNTNNNAACAGAGCGACTG ++ +<@@@@@??@@@@?@@@@@@@@@@@@@@@???????????????????????????????################################### |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/sample4_CGAAACCACTGT_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample4_CGAAACCACTGT_1.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,24 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151:1:N:0:CGAAAC +AACTTAAGGCTGAAAATTATTTATTTGACTTGTGTCAAATATAAAAATGTNTTGTGTAGAAACGGTAATGTGAAATTAATGTNAAATATTCTNN ++ +FFHHHHHJJJJJJJJJJJJJJJJJJIIIJJJJHIJJJJIJIJJJIJIJJI#0?FGIIJJJJJJIIEIJJHHHGHHHFFFFFF#,;ABDEDEE## +@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159:1:N:0:CGAAAC +TGCAATGCAAGTGGATTAGAGGATTGCAGCTGGAGGGGTAACAGCAGTGCNTTCGAAATATGTATCTTACAGCATTTCTGGGNTCCTCGTCCGN ++ +FFHHHHHJJJJHIIIIJIJIJJJJJJJJJJJJJFHJJJ?FHCFFHGIGHC#-5;DHHFHHHFCDFFFFFEEEECEDCDCCDC#,8<BBDABB## +@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170:1:N:0:CGAAAC +CTCTTGGGTGTATTGGTTGGCCGTTTTACTCTTTTGTTGGAGACTGAGAANCTTAGCTGATATAACTTCTACCGATTCTCCTTTAACTGCACTT ++ +FFHFHHHI?FEEEHHIHHGIEGHHIJJHIIGIIIJFGIJJHIIIEHIIHG#-;CEHHHHDFFFFFDEEC@CECDD?@CDD@CACDCDDDDCDDD +@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174:1:N:0:CGAAAC +AAATGACCAAATCCTAGGTGTTTGAGCGCGGACTGGAGGCGATTCCGCTGTCCGTGGATCTGTGGATCCACTACCTAATGCACGTTAAGTCCAA ++ +DDHHAHHGGB@BHIIIFE<AHHI;4?9DHGE@A;AHGEHEE>AC@@CB@BBA@?BBBBA@CCDCCCCC<493?CCCCCC>:>A<8???AC#### +@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176:1:N:0:CGAAAC +GGAAGAGAAAAAAATATAAAGTGTCAAGGGGCGTGTGCAGCGACACTTCGCCGACCCCTCCCCACATTATTTTTTTGCCGCCCGCTGGTAGCAG ++ +DA:DBFDF;A<A@EGGB@:?D1:D?9:BGIDGE4@########################################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187:1:N:0:CGAAAC +AAATAATCAAACTACATCGACAAAATGTCAATATCATGCAGCTGCTTCAAAACCAAAATGATGATTTTTTGAGAAGTGATTATTTAAATGTCGT ++ +FFHHHHHJJJJJJJJJJJJJJJJJIJJIJJJJJJJJJJJJJJJJJJJJJJJJJJIJIJJJJJJJJJJHHFFDDDEDCDDFEEDFEEEDEEFEDD |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/sample4_CGAAACCACTGT_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample4_CGAAACCACTGT_2.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,24 @@ +@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151:4:N:0:CACTGT +ACATACTCAATATGTTTTACATATTTATGACAGACCTTCTCAAACAGAATATTTTACATNNNTTNNNCATTACCGTTTNNNCACAACACATTTT ++ +:@?@?@@@?????@@@@@@?@??@@@???@@?????????????????????@@@@@@@###-8###--=?????==?################ +@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159:4:N:0:CACTGT +GGCATACCTGCTGCCATTGGTCACACTGGCAGATTACGCGATTATTTTTTTTACGGAAANNNTGNNNTTTCCCTTCCGGNNTGAATTGCCTGGA ++ +:@@?@@@@@@@@@?@?@??@??@@@@??????<????????<?????????=<?######################################## +@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170:4:N:0:CACTGT +GACCTACTAAACCTAACAATTCCAGCTATATTAACATTAGCTGAAGACACTAATCAGGAANAATTTAAAACAGAAAACATAATGGCACAGTCCA ++ +AACCCCCCBCCCBBB7CCCCCCBCCBBAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB#.;AAABBAAAAA@AA@@@@@@B>==?AA????A +@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174:4:N:0:CACTGT +AAGTCTTTGCGCAGACGGATCACCTCCTCGTTTGCAAGTGTGATAGGTACATCATGCTTTNTGTTCAAATCTTGGAAAATGAAATGTGCATGTA ++ +BB?FCBFG4?@@1<?A:6EF:?9)?00??:BDD1<B########################################################## +@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176:4:N:0:CACTGT +GACCGTTAGTCGGCGGGCGGTACCTGGTACCAGCGGGCGGCAAAAAAATAATGTGGGGAGGGGTCGGCGAAGTGTCGCTGAAAACGCCCCTTGC ++ +DDDD:@AE@AED@E?############################################################################### +@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187:4:N:0:CACTGT +GGATCAACATTTTTTATAGCAACAGGATTTCACGGAATTCATGTATTAATCGGAACAACTTTTTTATTAGTATGTTTACTACGACATTTAAATA ++ +FFHHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJJJIJJJJJJJIHGIGIIJJJIJJJJHHHHHHDDEEEEDEFEFEEDDDEDDDDDDDEEEDEE |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/summary_PE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary_PE.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,10 @@ +## +## +Processed Reads (pairs) 25 +Assigned Reads (pairs) 25 +Unassigned Reads (pairs) 0 +# Individual sample read (pair) counts : +sample1 6 +sample4 6 +sample3 6 +sample2 7 |
| b |
| diff -r 000000000000 -r 101525093ba1 test-data/summary_SE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary_SE.txt Wed Nov 25 12:37:01 2015 -0500 |
| b |
| @@ -0,0 +1,10 @@ +## +## +Processed Reads (pairs) 25 +Assigned Reads (pairs) 25 +Unassigned Reads (pairs) 0 +# Individual sample read (pair) counts : +sample1 6 +sample4 6 +sample3 6 +sample2 7 |