| Next changeset 1:a12ce5668966 (2015-06-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f |
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added:
art_454.xml art_illumina.xml art_solid.xml macros.xml test-data/art.454.01.fq test-data/art.454.01.sam test-data/art.454.01.stat test-data/art.454.02.fq test-data/art.454.02.sam test-data/art.454.02.stat test-data/art.454.021.fq test-data/art.454.022.fq test-data/art.illumina.01.aln test-data/art.illumina.01.fq test-data/art.illumina.01.sam test-data/art.illumina.02.sam test-data/art.illumina.021.aln test-data/art.illumina.021.fq test-data/art.illumina.022.aln test-data/art.illumina.022.fq test-data/art.illumina.03.sam test-data/art.illumina.031.aln test-data/art.illumina.031.fq test-data/art.illumina.032.aln test-data/art.illumina.032.fq test-data/art.solid.01.fq test-data/art.solid.01.map test-data/art.solid.01.sam test-data/art.solid.02.sam test-data/art.solid.02_F3.fq test-data/art.solid.02_F3.map test-data/art.solid.02_F5.fq test-data/art.solid.02_F5.map test-data/input.fa tool_dependencies.xml |
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| diff -r 000000000000 -r b98d6fffd00b art_454.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/art_454.xml Thu Jun 11 11:51:06 2015 -0400 |
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| @@ -0,0 +1,155 @@ +<tool id="art_454" name="ART 454" version="2014.11.03.0"> + <description>simulates pyrosequencing data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <command><![CDATA[ +art_454 $t + +$aln +$sam + +#if $rndSeed and $rndSeed > -1: +-r $rndSeed +#end if + +#if $c +-c $c +#end if + +#if $generate.amplicon.use_amplicon == "amplicon_true": + #if $generate.choice == "single_end": + -A + #else: + -B + #end if +#end if + +$input_seq_file +output + +#if $generate.choice == "single_end": + $fold_coverage +#else: + $fold_coverage + $generate.fragment_size + $generate.fragment_sd +#end if + +#if $generate.amplicon.use_amplicon == "amplicon_true": + #if $generate.choice == "single_end": + $generate.amplicon.reads_per_amplicon + #else: + $generate.amplicon.read_pairs_per_amplicon + #end if +#end if +; +]]></command> + <inputs> + <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/> + <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/> + + <conditional name="generate"> + <param name="choice" type="select" label="Type of data to generate"> + <option value="single_end">Single-End</option> + <option value="paired_end">Paired-End</option> + </param> + <when value="single_end"> + <expand macro="amplicon" /> + </when> + <when value="paired_end"> + <expand macro="frag_len_sd" /> + <expand macro="amplicon_pair" /> + </when> + </conditional> + + + <expand macro="sam" /> + <expand macro="aln" /> + + <param type="boolean" label="indicate to simulate reads from the built-in GS FLX Titanium profile (-t)" name="t" truevalue="-t" falsevalue="" optional="true" /> + <param label="specify the number of flow cycles by the sequencer [100 for GS-FLX, 200 for GS-FLX Titanium] (-c)" name="c" type="integer" value="100" optional="true" /> + + <expand macro="rndSeed" /> + </inputs> + <outputs> + <!-- Single End --> + <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of 454 sequencing of $input_seq_file.name"> + <filter>generate['choice'] == "single_end"</filter> + </data> + + <!-- Paired End --> + <data format="fastq" name="output_fq1_paired" from_work_dir="output1.fq" label="Simulated of 454 sequencing of $input_seq_file.name (Forward)"> + <filter>generate['choice'] != "single_end"</filter> + </data> + <data format="fastq" name="output_fq2_paired" from_work_dir="output2.fq" label="Simulated of 454 sequencing of $input_seq_file.name (Reverse)"> + <filter>generate['choice'] != "single_end"</filter> + </data> + <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated 454 data to $input_seq_file.name"> + <filter>sam</filter> + </data> + + <!-- Single End --> + <data format="aln" name="output_aln1_single" from_work_dir="output.aln" label="Alignment of Simulated 454 data to $input_seq_file.name"> + <filter>aln and generate['choice'] == "single_end"</filter> + </data> + <!-- Paired End --> + <data format="aln" name="output_aln1_paired" from_work_dir="output1.aln" label="Alignment of Simulated 454 data to $input_seq_file.name"> + <filter>aln and generate['choice'] != "single_end"</filter> + </data> + <data format="aln" name="output_aln2_paired" from_work_dir="output2.aln" label="Alignment of Simulated 454 data to $input_seq_file.name"> + <filter>generate['choice'] != "single_end" and generate['amplicon']['use_amplicon'] == "amplicon_true"</filter> + </data> + </outputs> + <tests> + <!-- Single End tests --> + <test> + <param name="rndSeed" value="42" /> + <param name="input_seq_file" value="input.fa" /> + <param name="fold_coverage" value="20" /> + <param name="choice" value="single_end" /> + <output name="output_fq1_single" file="art.454.01.fq" /> + </test> + <test> + <param name="rndSeed" value="42" /> + <param name="input_seq_file" value="input.fa" /> + <param name="fold_coverage" value="20" /> + <param name="choice" value="single_end" /> + <param name="sam" value="True" /> + <output name="output_fq1_single" file="art.454.01.fq" /> + <output name="output_sam" file="art.454.01.sam" lines_diff="2"/> + </test> + <!-- Paired End tests --> + <test> + <param name="rndSeed" value="42" /> + <param name="input_seq_file" value="input.fa" /> + <param name="fold_coverage" value="20" /> + <param name="choice" value="paired_end" /> + <param name="fragment_size" value="105" /> + <param name="fragment_sd" value="5" /> + <param name="sam" value="True" /> + <output name="output_fq1_paired" file="art.454.021.fq" /> + <output name="output_fq2_paired" file="art.454.022.fq" /> + <output name="output_sam" file="art.454.02.sam" lines_diff="2"/> + </test> + </tests> + <help><![CDATA[ +Art 454 Pyrosequencing Simulator +================================ + +ART_454 is a simulation program to generate sequence read data of Roche 454 +Pyrosequencing sequencers. ART generates reads according to the empirical read +quality profile and the calibrated error profile of uncall/overcall +homopolymers from real 454 read data. ART has been using for testing or +benchmarking a variety of method or tools for next-generation sequencing data +analysis, including read alignment, de novo assembly, detection of SNP, CNV, or +other structure variation. + +art_454 can generate both single-end and paired-end of 454 sequencing platform. +Besides for regular genome DNA and cDNA sequencing simulation, art_454 also +supports amplicon sequencing. The reference sequences can be either DNA or RNA. + ]]></help> + <expand macro="citation" /> +</tool> + |
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| diff -r 000000000000 -r b98d6fffd00b art_illumina.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/art_illumina.xml Thu Jun 11 11:51:06 2015 -0400 |
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| @@ -0,0 +1,158 @@ +<tool id="art_illumina" name="ART Illumina" version="2014.11.03.0"> + <description>simulates sequencing data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <command><![CDATA[ +art_illumina + +#if str($sam) == "-s": + --samout +#end if + +#if not str($aln) == "-a": + --noALN +#end if + +#if str($generate.choice) == "paired_end": + --paired + --mflen $generate.fragment_size + --sdev $generate.fragment_sd +#else if str($generate.choice) == "mate_pair": + --matepair + --mflen $generate.fragment_size + --sdev $generate.fragment_sd +#end if + +--in $input_seq_file +--len $read_length +--fcov $fold_coverage + +$amplicon + +--insRate $insRate +--insRate2 $insRate2 +--delRate $delRate +--delRate2 $delRate2 + +#if $rndSeed and $rndSeed > -1: + --rndSeed $rndSeed +#end if + +--out output; +]]></command> + <inputs> + <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/> + <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/> + <param label="length of reads to be simulated" name="read_length" type="integer" value="100"/> + <param label="amplicon sequencing simulation" name="amplicon" type="boolean" truevalue="--amplicon" falsevalue="" /> + + <conditional name="generate"> + <param name="choice" type="select" label="Type of data to generate"> + <option value="single_end">Single-End</option> + <option value="paired_end">Paired-End</option> + <option value="mate_pair">Mate-Pair</option> + </param> + <when value="single_end"> + </when> + <when value="paired_end"> + <expand macro="frag_len_sd" /> + </when> + <when value="mate_pair"> + <expand macro="frag_len_sd" /> + </when> + </conditional> + + <expand macro="aln" /> + <expand macro="sam" /> + + <param label="the first-read insertion rate" help="(--insRate)" name="insRate" type="float" value="0.00009" /> + <param label="the second-read insertion rate" help="(--insRate2)" name="insRate2" type="float" value="0.00015" /> + <param label="the first-read deletion rate" help="(--delRate)" name="delRate" type="float" value="0.00011" /> + <param label="the second-read deletion rate" help="(--delRate2)" name="delRate2" type="float" value="0.00023" /> + + <expand macro="rndSeed" /> + <!-- todo: id, errfree, masN, qShift(2), sepProf --> + </inputs> + <outputs> + <!-- Single End --> + <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of Illumina sequencing of $input_seq_file.name"> + <filter>generate['choice'] == "single_end"</filter> + </data> + + <!-- Paired End --> + <data format="fastq" name="output_fq1_paired" from_work_dir="output1.fq" label="Simulated of Illumina sequencing of $input_seq_file.name (Forward)"> + <filter>generate['choice'] != "single_end"</filter> + </data> + <data format="fastq" name="output_fq2_paired" from_work_dir="output2.fq" label="Simulated of Illumina sequencing of $input_seq_file.name (Reverse)"> + <filter>generate['choice'] != "single_end"</filter> + </data> + <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated Illumina data to $input_seq_file.name"> + <filter>sam</filter> + </data> + + <!-- Single End --> + <data format="aln" name="output_aln1_single" from_work_dir="output.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name"> + <filter>aln and generate['choice'] == "single_end"</filter> + </data> + + <!-- paired end --> + <data format="aln" name="output_aln1_paired" from_work_dir="output1.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name"> + <filter>aln and generate['choice'] != "single_end"</filter> + </data> + <data format="aln" name="output_aln2_paired" from_work_dir="output2.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name"> + <filter>aln and generate['choice'] != "single_end"</filter> + </data> + </outputs> + <tests> + <test> + <param name="rndSeed" value="42" /> + <param name="input_seq_file" value="input.fa" /> + <param name="fold_coverage" value="20" /> + <param name="read_length" value="200" /> + <param name="choice" value="single_end" /> + <param name="aln" value="True" /> + <param name="sam" value="True" /> + + <output name="output_fq1_single" file="art.illumina.01.fq" /> + <output name="output_aln1_single" file="art.illumina.01.aln" lines_diff="2"/> + <output name="output_sam" file="art.illumina.01.sam" lines_diff="2"/> + </test> + <test> + <param name="rndSeed" value="42" /> + <param name="input_seq_file" value="input.fa" /> + <param name="fold_coverage" value="20" /> + <param name="read_length" value="200" /> + <param name="choice" value="paired_end" /> + <param name="fragment_size" value="300" /> + <param name="fragment_sd" value="10" /> + <param name="aln" value="True" /> + <param name="sam" value="True" /> + + <output name="output_fq1_paired" file="art.illumina.021.fq" /> + <output name="output_fq2_paired" file="art.illumina.022.fq" /> + <output name="output_aln1_paired" file="art.illumina.021.aln" lines_diff="2"/> + <output name="output_aln2_paired" file="art.illumina.022.aln" lines_diff="2"/> + <output name="output_sam" file="art.illumina.02.sam" lines_diff="2"/> + </test> + </tests> + <help><![CDATA[ +Art Illumina Simulator +====================== + +ART (art_Illumina Q version) is a simulation program to generate sequence read +data of Illumina sequencers. ART generates reads according to the empirical +read quality profile summarized from large real read data. ART has been using +for testing or benchmarking a variety of methods or tools for next-generation +sequencing data analysis, including read alignment, de novo assembly, detection +of SNP, CNV, or other structure variation. + +art_Illumina can generate single-end, paired-end, mate-pair reads, and +amplicon sequencing simulation of Illumina sequencing platform. Its outputs +include FASTQ read, ALN and/or SAM alignment files. + + ]]></help> + <expand macro="citation" /> +</tool> + |
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| diff -r 000000000000 -r b98d6fffd00b art_solid.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/art_solid.xml Thu Jun 11 11:51:06 2015 -0400 |
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| @@ -0,0 +1,161 @@ +<tool id="art_solid" name="ART SOLiD" version="2014.11.03.0"> + <description>simulates SOLiD data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <command><![CDATA[ +art_SOLiD + +$sam + +#if $rndSeed and $rndSeed > -1: + -r $rndSeed +#end if + +#if $generate.amplicon.use_amplicon == "amplicon_true": + -A + + #if $generate.choice == "single_end": + s + #else if $generate.choice == "paired_end": + p + #else: + m + #end if + +#end if + +$input_seq_file +output + +#if $generate.choice == "single_end": + $generate.LEN_READ + $fold_coverage +#else if $generate.choice == "paired_end": + $generate.LEN_READ_F3 + $generate.LEN_READ_F5 + $fold_coverage + $generate.fragment_size + $generate.fragment_sd +#else: + $generate.LEN_READ + $fold_coverage + $generate.fragment_size + $generate.fragment_sd +#end if + +#if $generate.amplicon.use_amplicon == "amplicon_true": + #if $generate.choice == "single_end": + $generate.amplicon.reads_per_amplicon + #else: + $generate.amplicon.read_pairs_per_amplicon + #end if +#end if +]]></command> + <inputs> + <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/> + <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/> + + <conditional name="generate"> + <param name="choice" type="select" label="Type of data to generate"> + <option value="single_end">Single-End</option> + <option value="paired_end">Paired-End</option> + <option value="paired_end">Mate Pair</option> + </param> + <when value="single_end"> + <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" /> + <expand macro="amplicon" /> + </when> + <when value="paired_end"> + <param name="LEN_READ_F3" type="integer" label="Length of F3 reads" value="100" /> + <param name="LEN_READ_F5" type="integer" label="Length of F5 reads" value="100" /> + <expand macro="frag_len_sd" /> + <expand macro="amplicon_pair" /> + </when> + <when value="mate_pair"> + <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" /> + <expand macro="frag_len_sd" /> + <expand macro="amplicon_pair" /> + </when> + </conditional> + + <expand macro="sam" /> + <expand macro="rndSeed" /> + + </inputs> + <outputs> + + <!-- Single End --> + <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name"> + <filter>generate['choice'] == "single_end"</filter> + </data> + + <!-- Paired End --> + <data format="fastq" name="output_fq1_paired" from_work_dir="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F3)"> + <filter>generate['choice'] == "paired_end"</filter> + </data> + <data format="fastq" name="output_fq2_paired" from_work_dir="output_F5.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F5)"> + <filter>generate['choice'] == "paired_end"</filter> + </data> + + <!-- Mate Pair --> + <data format="fastq" name="output_fq1_mate" from_work_dir="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Forward)"> + <filter>generate['choice'] == "mate_pair"</filter> + </data> + <data format="fastq" name="output_fq2_mate" from_work_dir="output_R3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Reverse)"> + <filter>generate['choice'] == "mate_pair"</filter> + </data> + + <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated SOLiD data to $input_seq_file.name"> + <filter>sam</filter> + </data> + <!-- todo? map file --> + </outputs> + <tests> + <!-- Single End tests --> + <test> + <param name="rndSeed" value="42" /> + <param name="input_seq_file" value="input.fa" /> + <param name="LEN_READ" value="25" /> + <param name="fold_coverage" value="10" /> + <param name="choice" value="single_end" /> + <param name="sam" value="False" /> + + <output name="output_fq1_single" file="art.solid.01.fq" /> + </test> + <test> + <param name="rndSeed" value="42" /> + <param name="input_seq_file" value="input.fa" /> + <param name="fold_coverage" value="20" /> + <param name="choice" value="paired_end" /> + <param name="LEN_READ_F3" value="50" /> + <param name="LEN_READ_F5" value="50" /> + <param name="fragment_size" value="75" /> + <param name="fragment_sd" value="10" /> + <param name="sam" value="True" /> + + <output name="output_fq1_paired" file="art.solid.02_F3.fq" /> + <output name="output_fq2_paired" file="art.solid.02_F5.fq" /> + <output name="output_sam" file="art.solid.02.sam" lines_diff="2"/> + </test> + </tests> + <help><![CDATA[ +Art SOLiD Simulator +=================== + +ART_SOLiD is a simulation program to generate sequence read data of SOLiD +sequencing reads. ART generates reads according to a SOLiD read error profile. +The built-in error profile is an empiricial error profile summarized from large +SOLiD sequencing data. ART has been using for testing or benchmarking a variety +of method or tools for next-generation sequencing data analysis, including read +alignment, de novo assembly, detection of SNP, CNV, or other structure +variation. + +art_SOLiD can generate both single-end, matepair, and paired-end of SOLiD +sequencing platform. art_SOLiD also support amplicon sequencing simulation with +RNA references. + ]]></help> + <expand macro="citation" /> +</tool> + |
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| diff -r 000000000000 -r b98d6fffd00b macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jun 11 11:51:06 2015 -0400 |
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| @@ -0,0 +1,62 @@ +<macros> + <token name="@WRAPPER_VERSION@">2014.11.03.0</token> + <xml name="stdio"> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + </xml> + <xml name="aln"> + <param type="boolean" label="output ALN alignment file (-a)" name="aln" + truevalue="-a" falsevalue="" /> + </xml> + <xml name="sam"> + <param type="boolean" label="output SAM alignment file (-s)" name="sam" + truevalue="-s" falsevalue="" /> + </xml> + + <xml name="rndSeed"> + <param label="specify a fixed, random seed for the simulation" + help="Use -1 to request a random seed (-r)" name="rndSeed" + type="integer" value="-1" optional="true" /> + </xml> + + <xml name="citation"> + <citations> + <citation type="doi">10.1093/bioinformatics/btr708</citation> + </citations> + </xml> + + <xml name="amplicon"> + <conditional name="amplicon"> + <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" /> + <when value="amplicon_true"> + <param label="number of reads per amplicon (for 5'end amplicon sequencing)" name="reads_per_amplicon" type="integer" value="0"/> + </when> + <when value="amplicon_false"> + </when> + </conditional> + </xml> + + <xml name="amplicon_pair"> + <conditional name="amplicon"> + <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" /> + <when value="amplicon_true"> + <param label="number of read pairs per amplicon (for two-end amplicon sequencing)" name="read_pairs_per_amplicon" type="integer" value="0"/> + </when> + <when value="amplicon_false"> + </when> + </conditional> + </xml> + + <xml name="frag_len_sd"> + <param label="the average DNA fragment size" + name="fragment_size" type="integer" value="200" minimum="101" /> + <param label="the standard deviation of the DNA fragment size" + name="fragment_sd" type="integer" value="0"/> + </xml> +</macros> |
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| diff -r 000000000000 -r b98d6fffd00b test-data/art.454.01.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.454.01.fq Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,488 @@\n+@chr1-515-1\n+TATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTG\n++\n+AD/<;FC99CD=I:C;;@IIIA9FCCC@@II;DC==?IHH7>>FFID8DDCCDDC..777BA3\n+@chr1-1111-1\n+CGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAAAATAAAAATTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATtCTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAAC\n++\n+HA5DBBEG=AFH5I5555<<B,FFFIFFBDDFC?<<6=<332I<00ID3D:----------D55557//442=:F9,,CCC@II=CCC??99AA,@@@<AABCCI:D)E,,;;EE:FFDDD.DEE:::,AD,,>?==DDAGDDE6EEF-CC7@?EAIFF:1--6HGBBB6611F14///3EEF@DDDBCDEEIH..I\n+@chr1-1115-1\n+CTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCaGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACT\n++\n+C***C33FAA;;;FFCI---55FDD<<II>2DDD;;*AA?BBBHIC55FG...F/D8922,1CEAAD::::<,,,,,,>////////A5AGI33AFD::?-@IICFAII?CC1HHF5D--8888FF5E;;<111IF=6I0EEII<A--2AEFFFFCCFF9:::FF000AA,=FFF=@CGG<<--B,4@<>>?CCH,,,AACII62???ICA@@H>GFIIA<<F3ADIDDD5C?CCCCCI;;I@DDF06666CCCCCE..------=?IIF@@-EI693<@\n+@chr1-795-1\n+CAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATG\n++\n+HDD**)B@CCAAAF?I;40FE=DD<HFHHHII8:<2?,,,ECC<:::ADF322>BAA@::@@@/E??<<<4@=@=F7777>;7GIHHHFFF?F3=6660II4B?,,,--GG;F.HHHAF8FFEIEFEF=?;9=:;????7AD5--<4AA@>>>4D>CC69C00@@@ICI6=@DD?DFB=7FFFFG4EFF,,,,,,,,,,D48877/////FII0I33:C;==AB0=FFFIICFA\n+@chr1-265-1\n+CCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGT\n++\n+AA==7IFDE>>CAADFCC3.F>>06;;D18FDDFFFCHHI??FFFFII5IFFF>@=DDIIFFFEFFD==<==IAABFA<IICCGGGDG210G?CCC60:E:==ADAAI6FFF8DDDDD4FF:6;,,,DDF8FFFFFHCC<<;;C9I7IIIDA?ABBBCFEFFFFDDDAIEEE;;IIEC>>522222222220///////..AC3CDAADFCHHD?D..I7@::5AAI..IB@AA;;;;:BEACC=,,,E6CF<I>>II::I\n+@chr1-1112-1\n+CGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTT\n++\n+6<IIAAADCCFII777II0ADDD.1FFFFFAAIII?4AAA55G=::7/I<<??FFFIFACCEFEEEI??;34611---,,1>>AAAA99IDIFIAA?CI<=H-C<<7AFIIC<<=D??3CIII//55DI6FCCF<<>FHICBD??IIE7---944E:F:7FFI,0@C@,,,>>CF?????F88FF56E1D?H?<IFF=00,8:F55,,;;;;F4CCFIFHHC=DDF<FAI>88EE<7777GAFF32IID87777;??==\n+@chr1-722-1\n+GGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTGTCTAACTTTATCGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTC\n++\n+FFDDFCA3EEGHHBIC.:??AFFFF;83D>>>>4::GBG222,,AE000IIC,,HH<<.0C;?CC.==7EEEAAI7=CC///F17B@I@B@CC6:?FFF>>IG555;;/FF33;;CHFDGAAE,,C;;:B?5EECD--->IDCC3AAA:FFC?D?@;?DD(333I2DFDD.1317BDD55,???@FEF>ICC???IDI?FFCCCC:III===CEI::II50IIH?FFC522/7::2333?CDACCACC;CII;F5559CEE7FCCC?IIADGGG33IC>88==FE7FD1.:A<B---GCE@@11000;FDFFD55F::?AF\n+@chr1-1282-1\n+TCGgAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTATCGACAACAAGAAGCAGCCTTATGGCCGTCAACATACATATC\n++\n+I<H,FFF0FFEFFF@FDECFEE887HH5550F>?...AI=;;5EEFAAIIDHHHFF..6GD00-FFF?FFCDFC:====;;F;6555@5DDFFFAEF67@....,4FE1...=66=HIICCCC>73C7000AD11;I>CCCAA<?GI87A6H44C3IFBBBBBD9CAFFEEIIFF<<@BBFFI4D==<BB<IID:F))F7FCIAI?66FI@F2++++++++E/////---//:;;F9FFAF,,..FFB;;6-?@F>IIHII?CFIAF7B@@7??AAA5>F6A'..b'GTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAnTTAGACAAAACCAGCGAtAAAGTTAGACAAAACCaGCGTTATAACGCCAGCAGTCCA\n++\n+FF<F:DDD633FF=FBBFDFFC9AA-;3A.FBB5.FFCHFABBIGEE<??///E66DCCC=CH;==,,CCFEE...6DBBDDDA<<II8II6FF=39669EEDDFFICDED??D33FA<0ICCCCCCF;;CCCF000III=EBIIABBBB7D>9<CCCFCC58=I1111FF/DDDFADDFIII8IIIEE4BE5::0I52,,,0II@AA=3344FFFC@EF)C??;55I9A7FFFFII,@A;FFIADDDCBBCFCC@@III\n+@chr1-1233-1\n+GGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGtTTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAATTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCT\n++\n+IICCCF?I<<EBBB33IAAA=DCCFC69ECAI5AEE=CFFF>@AABE@66H9E<<<.>?4EEADAD?FFIIAA>FF444,B55<<<7I3<<<DDD66=F!---22::FCF==;><<IFFG5G?5CCDDEEI44===IF7766675@DDD;===D4?D;>>>FFBA278855AAD5;,..IIHH6E8BBB;D3AA>A6=I:CC7FF4EEEEC@AF33I7::DD..@HIFFIE?==IDDCHHDI=\n+@chr1-930-1\n+CGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGC\n++\n+D3:::7EC6602?=HHI?HHCIFFFF446668F<7D77ADDD0F=1>6622>II?BF<<<AAFFIIIEE?FF;;DDD6GDDII:FFIDDDDFD::HHFFC,5AAA6FFADDC??225EE:>111FFC0099??D@DI4DDIEEG886,@IIIIICCCIED--.A??==ICG.BB5>::IIHH;6DC>>>DII:87,,,IIII<<:30>CC::AA?><9DEEFII@GGG<CFIIDD776?BHFF--CCAA,,?111111666114,,,,,,,,>I,BH,09I5D?;7A88HFFFFADDDAAD>IHHFFFFD8@F??@AAAF?B4<\n+@chr1-1103-1\n+CTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAtAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAaCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACC\n++\n+AF88FFC6?4F3BBE9??:FF:11..;<1D?GCFGGADDI<=II<6IFF;<ICC4H34655511111DEEEEE8::::?FGIDIICC?>FIFCCCIIFFCB3<<<@DD?@@>7D8;DDGIIIF>>@@@A5:6===E=C223888AAFI??5AIII3??:3:FDA65E@FF?F;FFFAAFF.F6FFF@88:DD1EA>?II>>CCFFF666F7AAEEE4?F33555G,,A<1111>>AADFDAA?DFF7FF7D:IC4466AAF>>DDDEIFF:88FII22-----5I=AF888<D?F;><;;=744E7E68;II\n+@chr1-669-1\n+CATTTAGAATCAACAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTT\n++\n+=H888I3FBI0II@EB?HH?CFFFFFD1F5550--4IC=FFGG..?DFDA1===2116A7I=?<6CCF<E6::?C??II33<AE3IGFF=HCCHD;55E==77I;5CCC3FF8CCI75>A22DDFG<IIAAAFI::CCCI65::IDDB@IE?6===66???.CHHHIIIFII2AFF>;;IIHHICCFFFA:,,888CF/15IGGGG=I6FIAAAGFFDEII++++EEI6ACCCFFBBA1A00.E;I0G?FG<@ACC5>A7DC\n+@chr1-470-1\n+ACAAGCCGATACTTGGAACAATTTCTGGAAAGaCGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAAcAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCG\n++\n+AIFFFFF<A568II..EEE77000I05:6665!8FFCCCC--II;;F>AA<FA?:.C<4I??5;>BAAC---@@==FF2:::C--4@=G9IFF77II77IEEDDD3IDD===H@ICCDAADCC<F?IIIAA,0D7F666CFFIAAIICFAEE:<AA6EE00/F>--<<<ICI==9FFFFHHCIAHHHIDDCA=9???=BAC=??IDFF9;HH!BCC;;<IEFFFD@F<FFFA??C<HCEFFFBB6<DC?FAAA=::FI7F3333HH=;3C.-<=CC>C00I,@CCFEE.IAA0IA@DDFDAA:;:CFFI::I22F\n+@chr1-588-2\n+AACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGA\n++\n+AAFIID?1224A>==D6GEEE1==H<<F7FHFA>IIDDA??466C<55FFF7;DIIBDDDD?CEDC---D??@CFA----66>///;DIIFBII7=DDEECCCIII1I5A,,,?CCA<FGCCCCAAI6F.6.???:77ECEC;;;::=8IBIFFI3CC:?<<IFFAFF::=-??,D@???IIDDI::A<<IFFCFFD>:AD88FF25FHFCCCCF66DDEE5?66FIIC:7A97\n' |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.454.01.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.454.01.sam Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,125 @@\n+@HD\tVN:1.4\tSQ:unsorted\n+@SQ\tSN:chr1\tLN:1626\n+@PG\tID:02\tPN:ART_454\tCL:art_454 -a -s -r 42 test-data/input.fa test-data/art.454.01 20 \n+chr1-515-1\t16\tchr1\t1049\t99\t63=\t*\t0\t0\tCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATA\t3AB777..CDDCCDD8DIFF>>7HHI?==CD;II@@CCCF9AIII@;;C:I=DC99CF;</DA\n+chr1-1111-1\t16\tchr1\t320\t99\t89=1X36=1D10=2I59=\t*\t0\t0\tGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGNATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAATTTTTATTTTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCG\tI..HIEEDCBDDD@FEE3///41F1166BBBGH6--1:FFIAE?@7CC-FEE6EDDGADD==?>,,DA,:::EED.DDDFF:EE;;,,E)D:ICCBAA<@@@,AA99??CCC=II@CCC,,9F:=244//75555D----------:D3DI00<I233<=6<<?CFDDBFFIFFF,B<<5555I5HFA=GEBBD5AH\n+chr1-1115-1\t0\tchr1\t1116\t99\t77=1I92=1X109=\t*\t0\t0\tCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCaGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACT\tC***C33FAA;;;FFCI---55FDD<<II>2DDD;;*AA?BBBHIC55FG...F/D8922,1CEAAD::::<,,,,,,>////////A5AGI33AFD::?-@IICFAII?CC1HHF5D--8888FF5E;;<111IF=6I0EEII<A--2AEFFFFCCFF9:::FF000AA,=FFF=@CGG<<--B,4@<>>?CCH,,,AACII62???ICA@@H>GFIIA<<F3ADIDDD5C?CCCCCI;;I@DDF06666CCCCCE..------=?IIF@@-EI693<@\n+chr1-795-1\t16\tchr1\t600\t99\t35=2I197=\t*\t0\t0\tCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTG\tAFCIIFFF=0BA==;C:33I0IIF/////77884D,,,,,,,,,,FFE4GFFFF7=BFD?DD@=6ICI@@@00C96CC>D4>>>@AA4<--5DA7????;:=9;?=FEFEIEFF8FAHHH.F;GG--,,,?B4II0666=3F?FFFHHHIG7;>7777F=@=@4<<<??E/@@@::@AAB>223FDA:::<CCE,,,?2<:8IIHHHFH<DD=EF04;I?FAAACC@B)**DDH\n+chr1-265-1\t0\tchr1\t266\t99\t45=1I154=1I60=\t*\t0\t0\tCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGT\tAA==7IFDE>>CAADFCC3.F>>06;;D18FDDFFFCHHI??FFFFII5IFFF>@=DDIIFFFEFFD==<==IAABFA<IICCGGGDG210G?CCC60:E:==ADAAI6FFF8DDDDD4FF:6;,,,DDF8FFFFFHCC<<;;C9I7IIIDA?ABBBCFEFFFFDDDAIEEE;;IIEC>>522222222220///////..AC3CDAADFCHHD?D..I7@::5AAI..IB@AA;;;;:BEACC=,,,E6CF<I>>II::I\n+chr1-1112-1\t0\tchr1\t1113\t99\t114=1I144=\t*\t0\t0\tCGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTT\t6<IIAAADCCFII777II0ADDD.1FFFFFAAIII?4AAA55G=::7/I<<??FFFIFACCEFEEEI??;34611---,,1>>AAAA99IDIFIAA?CI<=H-C<<7AFIIC<<=D??3CIII//55DI6FCCF<<>FHICBD??IIE7---944E:F:7FFI,0@C@,,,>>CF?????F88FF56E1D?H?<IFF=00,8:F55,,;;;;F4CCFIFHHC=DDF<FAI>88EE<7777GAFF32IID87777;??==\n+chr1-722-1\t0\tchr1\t723\t99\t195=1D126=\t*\t0\t0\tGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTGTCTAACTTTATCGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTC\tFFDDFCA3EEGHHBIC.:??AFFFF;83D>>>>4::GBG222,,AE000IIC,,HH<<.0C;?CC.==7EEEAAI7=CC///F17B@I@B@CC6:?FFF>>IG555;;/FF33;;CHFDGAAE,,C;;:B?5EECD--->IDCC3AAA:FFC?D?@;?DD(333I2DFDD.1317BDD55,???@FEF>ICC???IDI?FFCCCC:III===CEI::II50IIH?FFC522/7::2333?CDACCACC;CII;F5559CEE7FCCC?IIADGGG33IC>88==FE7FD1.:A<B---GCE@@11000;FDFFD55F::?AF\n+chr1-1282-1\t16\tchr1\t39\t99\t302=1X3=\t*\t0\t0\tGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGT'..b'AATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTT\tIII@@CCFCBBCDDDAIFF;A@,IIFFFF7A9I55;??C)FE@CFFF4433=AA@II0,,,25I0::5EB4EEIII8IIIFDDAFDDD/FF1111I=85CCFCCC<9>D7BBBBAIIBE=III000FCCC;;FCCCCCCI0<AF33D??DEDCIFFDDEE96693=FF6II8II<<ADDDBBD6...EEFCC,,==;HC=CCCD66E///??<EEGIBBAFHCFF.5BBF.A3;-AA9CFFDFBBF=FF336DDD:F<FF\n+chr1-1233-1\t16\tchr1\t149\t99\t33=1D49=1D61=1X99=\t*\t0\t0\tAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAATTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAANCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCC\t=IDHHCDDI==?EIFFIH@..DD::7I33FA@CEEEE4FF7CC:I=6A>AA3D;BBB8E6HHII..,;5DAA558872ABFF>>>;D?4D===;DDD@5766677FI===44IEEDDCC5?G5GFFI<<>;==FCF::22---!F=66DDD<<<3I7<<<55B,444FF>AAIIFF?DADAEE4?>.<<<E9H66@EBAA@>FFFC=EEA5IACE96CFCCD=AAAI33BBBE<<I?FCCCII\n+chr1-930-1\t0\tchr1\t931\t99\t257=1I66=\t*\t0\t0\tCGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGC\tD3:::7EC6602?=HHI?HHCIFFFF446668F<7D77ADDD0F=1>6622>II?BF<<<AAFFIIIEE?FF;;DDD6GDDII:FFIDDDDFD::HHFFC,5AAA6FFADDC??225EE:>111FFC0099??D@DI4DDIEEG886,@IIIIICCCIED--.A??==ICG.BB5>::IIHH;6DC>>>DII:87,,,IIII<<:30>CC::AA?><9DEEFII@GGG<CFIIDD776?BHFF--CCAA,,?111111666114,,,,,,,,>I,BH,09I5D?;7A88HFFFFADDDAAD>IHHFFFFD8@F??@AAAF?B4<\n+chr1-1103-1\t16\tchr1\t212\t99\t122=1X152=1X36=\t*\t0\t0\tGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGNTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTNTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAG\tII;86E7E447=;;<>;F?D<888FA=I5-----22IIF88:FFIEDDD>>FAA6644CI:D7FF7FFD?AADFDAA>>1111<A,,G55533F?4EEEAA7F666FFFCC>>II?>AE1DD:88@FFF6F.FFAAFFF;F?FF@E56ADF:3:??3IIIA5??IFAA888322C=E===6:5A@@@>>FIIIGDD;8D7>@@?DD@<<<3BCFFIICCCFIF>?CCIIDIGF?::::8EEEEED11111555643H4CCI<;FFI6<II=<IDDAGGFCG?D1<;..11:FF:??9EBB3F4?6CFF88FA\n+chr1-669-1\t16\tchr1\t696\t99\t262=\t*\t0\t0\tAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCGCCCTGTGGCCTGTTGATTCTAAATG\tCD7A>5CCA@<GF?G0I;E.00A1ABBFFCCCA6IEE++++IIEDFFGAAAIF6I=GGGGI51/FC888,,:AFFFCCIHHII;;>FFA2IIFIIIHHHC.???66===6?EI@BDDI::56ICCC::IFAAAII<GFDD22A>57ICC8FF3CCC5;I77==E55;DHCCH=FFGI3EA<33II??C?::6E<FCC6<?=I7A6112===1ADFD?..GGFF=CI4--0555F1DFFFFFC?HH?BE@II0IBF3I888H=\n+chr1-470-1\t16\tchr1\t842\t99\t102=1X179=1X32=\t*\t0\t0\tCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCGCCCTGTGGCCTNTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGNCTTTCCAGAAATTGTTCCAAGTATCGGCTTGT\tF22I::IFFC:;:AADFDD@AI0AAI.EEFCC@,I00C>CC=<-.C3;=HH3333F7IF::=AAAF?CD<6BBFFFECH<C??AFFF<F@DFFFEI<;;CCB!HH;9FFDI??=CAB=???9=ACDDIHHHAICHHFFFF9==ICI<<<-->F/00EE6AA<:EEAFCIIAAIFFC666F7D0,AAIII?F<CCDAADCCI@H===DDI3DDDEEI77II77FFI9G=@4--C:::2FF==@@---CAAB>;5??I4<C.:?AF<AA>F;;II--CCCCFF8!5666:50I00077EEE..II865A<FFFFFIA\n+chr1-588-2\t16\tchr1\t805\t99\t234=\t*\t0\t0\tTCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTT\t79A7:CIIF66?5EEDD66FCCCCFHF52FF88DA:>DFFCFFI<<A::IDDII???@D,??-=::FFAFFI<<?:CC3IFFIBI8=::;;;CECE77:???.6.F6IAACCCCGF<ACC?,,,A5I1IIICCCEEDD=7IIBFIID;///>66----AFC@??D---CDEC?DDDDBIID;7FFF55<C664??ADDII>AFHF7F<<H==1EEEG6D==>A4221?DIIFAA\n' |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.454.01.stat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.454.01.stat Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,1626 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3\n+1598\t0\t3\n+1599\t0\t3\n+1600\t0\t3\n+1601\t0\t3\n+1602\t0\t3\n+1603\t0\t3\n+1604\t0\t3\n+1605\t0\t3\n+1606\t0\t3\n+1607\t0\t3\n+1608\t0\t3\n+1609\t0\t3\n+1610\t0\t3\n+1611\t0\t3\n+1612\t0\t3\n+1613\t0\t3\n+1614\t0\t3\n+1615\t0\t3\n+1616\t0\t3\n+1617\t0\t2\n+1618\t0\t2\n+1619\t0\t1\n+1620\t0\t1\n+1621\t0\t1\n+1622\t0\t0\n+1623\t0\t0\n+1624\t0\t0\n+1625\t0\t0\n' |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.454.02.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.454.02.fq Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,488 @@\n+@chr1-515-1\n+TATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTG\n++\n+AD/<;FC99CD=I:C;;@IIIA9FCCC@@II;DC==?IHH7>>FFID8DDCCDDC..777BA3\n+@chr1-1111-1\n+CGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAAAATAAAAATTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATtCTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAAC\n++\n+HA5DBBEG=AFH5I5555<<B,FFFIFFBDDFC?<<6=<332I<00ID3D:----------D55557//442=:F9,,CCC@II=CCC??99AA,@@@<AABCCI:D)E,,;;EE:FFDDD.DEE:::,AD,,>?==DDAGDDE6EEF-CC7@?EAIFF:1--6HGBBB6611F14///3EEF@DDDBCDEEIH..I\n+@chr1-1115-1\n+CTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCaGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACT\n++\n+C***C33FAA;;;FFCI---55FDD<<II>2DDD;;*AA?BBBHIC55FG...F/D8922,1CEAAD::::<,,,,,,>////////A5AGI33AFD::?-@IICFAII?CC1HHF5D--8888FF5E;;<111IF=6I0EEII<A--2AEFFFFCCFF9:::FF000AA,=FFF=@CGG<<--B,4@<>>?CCH,,,AACII62???ICA@@H>GFIIA<<F3ADIDDD5C?CCCCCI;;I@DDF06666CCCCCE..------=?IIF@@-EI693<@\n+@chr1-795-1\n+CAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATG\n++\n+HDD**)B@CCAAAF?I;40FE=DD<HFHHHII8:<2?,,,ECC<:::ADF322>BAA@::@@@/E??<<<4@=@=F7777>;7GIHHHFFF?F3=6660II4B?,,,--GG;F.HHHAF8FFEIEFEF=?;9=:;????7AD5--<4AA@>>>4D>CC69C00@@@ICI6=@DD?DFB=7FFFFG4EFF,,,,,,,,,,D48877/////FII0I33:C;==AB0=FFFIICFA\n+@chr1-265-1\n+CCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGT\n++\n+AA==7IFDE>>CAADFCC3.F>>06;;D18FDDFFFCHHI??FFFFII5IFFF>@=DDIIFFFEFFD==<==IAABFA<IICCGGGDG210G?CCC60:E:==ADAAI6FFF8DDDDD4FF:6;,,,DDF8FFFFFHCC<<;;C9I7IIIDA?ABBBCFEFFFFDDDAIEEE;;IIEC>>522222222220///////..AC3CDAADFCHHD?D..I7@::5AAI..IB@AA;;;;:BEACC=,,,E6CF<I>>II::I\n+@chr1-1112-1\n+CGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTT\n++\n+6<IIAAADCCFII777II0ADDD.1FFFFFAAIII?4AAA55G=::7/I<<??FFFIFACCEFEEEI??;34611---,,1>>AAAA99IDIFIAA?CI<=H-C<<7AFIIC<<=D??3CIII//55DI6FCCF<<>FHICBD??IIE7---944E:F:7FFI,0@C@,,,>>CF?????F88FF56E1D?H?<IFF=00,8:F55,,;;;;F4CCFIFHHC=DDF<FAI>88EE<7777GAFF32IID87777;??==\n+@chr1-722-1\n+GGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTGTCTAACTTTATCGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTC\n++\n+FFDDFCA3EEGHHBIC.:??AFFFF;83D>>>>4::GBG222,,AE000IIC,,HH<<.0C;?CC.==7EEEAAI7=CC///F17B@I@B@CC6:?FFF>>IG555;;/FF33;;CHFDGAAE,,C;;:B?5EECD--->IDCC3AAA:FFC?D?@;?DD(333I2DFDD.1317BDD55,???@FEF>ICC???IDI?FFCCCC:III===CEI::II50IIH?FFC522/7::2333?CDACCACC;CII;F5559CEE7FCCC?IIADGGG33IC>88==FE7FD1.:A<B---GCE@@11000;FDFFD55F::?AF\n+@chr1-1282-1\n+TCGgAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTATCGACAACAAGAAGCAGCCTTATGGCCGTCAACATACATATC\n++\n+I<H,FFF0FFEFFF@FDECFEE887HH5550F>?...AI=;;5EEFAAIIDHHHFF..6GD00-FFF?FFCDFC:====;;F;6555@5DDFFFAEF67@....,4FE1...=66=HIICCCC>73C7000AD11;I>CCCAA<?GI87A6H44C3IFBBBBBD9CAFFEEIIFF<<@BBFFI4D==<BB<IID:F))F7FCIAI?66FI@F2++++++++E/////---//:;;F9FFAF,,..FFB;;6-?@F>IIHII?CFIAF7B@@7??AAA5>F6A'..b'GTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAnTTAGACAAAACCAGCGAtAAAGTTAGACAAAACCaGCGTTATAACGCCAGCAGTCCA\n++\n+FF<F:DDD633FF=FBBFDFFC9AA-;3A.FBB5.FFCHFABBIGEE<??///E66DCCC=CH;==,,CCFEE...6DBBDDDA<<II8II6FF=39669EEDDFFICDED??D33FA<0ICCCCCCF;;CCCF000III=EBIIABBBB7D>9<CCCFCC58=I1111FF/DDDFADDFIII8IIIEE4BE5::0I52,,,0II@AA=3344FFFC@EF)C??;55I9A7FFFFII,@A;FFIADDDCBBCFCC@@III\n+@chr1-1233-1\n+GGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGtTTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAATTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCT\n++\n+IICCCF?I<<EBBB33IAAA=DCCFC69ECAI5AEE=CFFF>@AABE@66H9E<<<.>?4EEADAD?FFIIAA>FF444,B55<<<7I3<<<DDD66=F!---22::FCF==;><<IFFG5G?5CCDDEEI44===IF7766675@DDD;===D4?D;>>>FFBA278855AAD5;,..IIHH6E8BBB;D3AA>A6=I:CC7FF4EEEEC@AF33I7::DD..@HIFFIE?==IDDCHHDI=\n+@chr1-930-1\n+CGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGC\n++\n+D3:::7EC6602?=HHI?HHCIFFFF446668F<7D77ADDD0F=1>6622>II?BF<<<AAFFIIIEE?FF;;DDD6GDDII:FFIDDDDFD::HHFFC,5AAA6FFADDC??225EE:>111FFC0099??D@DI4DDIEEG886,@IIIIICCCIED--.A??==ICG.BB5>::IIHH;6DC>>>DII:87,,,IIII<<:30>CC::AA?><9DEEFII@GGG<CFIIDD776?BHFF--CCAA,,?111111666114,,,,,,,,>I,BH,09I5D?;7A88HFFFFADDDAAD>IHHFFFFD8@F??@AAAF?B4<\n+@chr1-1103-1\n+CTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAtAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAaCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACC\n++\n+AF88FFC6?4F3BBE9??:FF:11..;<1D?GCFGGADDI<=II<6IFF;<ICC4H34655511111DEEEEE8::::?FGIDIICC?>FIFCCCIIFFCB3<<<@DD?@@>7D8;DDGIIIF>>@@@A5:6===E=C223888AAFI??5AIII3??:3:FDA65E@FF?F;FFFAAFF.F6FFF@88:DD1EA>?II>>CCFFF666F7AAEEE4?F33555G,,A<1111>>AADFDAA?DFF7FF7D:IC4466AAF>>DDDEIFF:88FII22-----5I=AF888<D?F;><;;=744E7E68;II\n+@chr1-669-1\n+CATTTAGAATCAACAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTT\n++\n+=H888I3FBI0II@EB?HH?CFFFFFD1F5550--4IC=FFGG..?DFDA1===2116A7I=?<6CCF<E6::?C??II33<AE3IGFF=HCCHD;55E==77I;5CCC3FF8CCI75>A22DDFG<IIAAAFI::CCCI65::IDDB@IE?6===66???.CHHHIIIFII2AFF>;;IIHHICCFFFA:,,888CF/15IGGGG=I6FIAAAGFFDEII++++EEI6ACCCFFBBA1A00.E;I0G?FG<@ACC5>A7DC\n+@chr1-470-1\n+ACAAGCCGATACTTGGAACAATTTCTGGAAAGaCGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAAcAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCG\n++\n+AIFFFFF<A568II..EEE77000I05:6665!8FFCCCC--II;;F>AA<FA?:.C<4I??5;>BAAC---@@==FF2:::C--4@=G9IFF77II77IEEDDD3IDD===H@ICCDAADCC<F?IIIAA,0D7F666CFFIAAIICFAEE:<AA6EE00/F>--<<<ICI==9FFFFHHCIAHHHIDDCA=9???=BAC=??IDFF9;HH!BCC;;<IEFFFD@F<FFFA??C<HCEFFFBB6<DC?FAAA=::FI7F3333HH=;3C.-<=CC>C00I,@CCFEE.IAA0IA@DDFDAA:;:CFFI::I22F\n+@chr1-588-2\n+AACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGA\n++\n+AAFIID?1224A>==D6GEEE1==H<<F7FHFA>IIDDA??466C<55FFF7;DIIBDDDD?CEDC---D??@CFA----66>///;DIIFBII7=DDEECCCIII1I5A,,,?CCA<FGCCCCAAI6F.6.???:77ECEC;;;::=8IBIFFI3CC:?<<IFFAFF::=-??,D@???IIDDI::A<<IFFCFFD>:AD88FF25FHFCCCCF66DDEE5?66FIIC:7A97\n' |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.454.02.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.454.02.sam Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,929 @@\n+@HD\tVN:1.4\tSQ:unsorted\n+@SQ\tSN:chr1\tLN:1626\n+@PG\tID:02\tPN:ART_454\tCL:art_454 -s -r 42 test-data/input.fa test-data/art.454.02 20 105 5 \n+chr1_1\t99\tchr1\t1047\t99\t27=\t=\t1122\t111\tTCCAGAAATTGTTCCAAGTATCGGCTT\t:GC?7...IICEECCII6I?BC<<F<@\n+chr1_1\t147\tchr1\t1122\t99\t36=\t=\t1047\t-111\tCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTT\t<?CIAAADD7?HHHFFF>>55HHICF;;II488I44\n+chr1_2\t99\tchr1\t532\t99\t43=\t=\t597\t99\tCGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTT\tFA3BB737G?FFFFDD69CCCAB,FFFFIIGBDFC>>>44=:8\n+chr1_2\t147\tchr1\t597\t99\t4=1X29=\t=\t532\t-99\tCTTCNTGTGCCTGTAAAACGAAGCGGTAAAAATT\tC,,17I3AIEEHCI0002:D00DI00<---,,33\n+chr1_3\t99\tchr1\t1423\t99\t35=\t=\t1499\t97\tGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATG\tI<<EEFF///--FF;F::IIFD3E,<F:FDDD.DF\n+chr1_3\t147\tchr1\t1499\t99\t21=\t=\t1423\t-97\tTTTCCAGAAATTGTTCCAAGT\tDDDA>I;///55@CC???DAA\n+chr1_4\t83\tchr1\t102\t99\t7=1X25=\t=\t33\t-102\tAACGAAGNGGTAAAAATTTTTATTTTTTTTCTC\t00BD@AA!DD=13336:@@@@7//000000FAF\n+chr1_4\t163\tchr1\t33\t99\t18=1X2=\t=\t102\t102\tCATCGTGATATGTATGTTtAC\tDF3FFADDBCDFI0ICBB,C5\n+chr1_5\t99\tchr1\t998\t99\t40=\t=\t1051\t103\tTTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGT\tAAAIIAAACFDB?ABBIIIBDDDGBI<<EE555CD755IB\n+chr1_5\t147\tchr1\t1051\t99\t50=\t=\t998\t-103\tGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTG\tA...77?GGDF<<AIA5F=<>44AFFFAC><<AA26:?DD??I;,,FCFA\n+chr1_6\t99\tchr1\t920\t99\t22=\t=\t992\t103\tTCTAACTTTATCGCCCTGTGGC\tB<6AADCCCB?7?FFFCAB5:8\n+chr1_6\t147\tchr1\t992\t99\t31=\t=\t920\t-103\tCAGAAATTGTTCCAAGTATCGGCTTGTTTAC\t?:E??@99C22FF::67B?:EE>FF2110ID\n+chr1_7\t83\tchr1\t1406\t99\t20=\t=\t1330\t-96\tGGCACAAGTACCAACCAGAA\t==D7F=<=F8;;::II6H<<\n+chr1_7\t163\tchr1\t1330\t99\t31=\t=\t1406\t96\tAGAACTTCATGTGCCTGTAAAACGAAGCGGT\t<IAB066IG3I7IBBAAH333.-AAAFA.-4\n+chr1_8\t83\tchr1\t586\t99\t29=\t=\t505\t-110\tTCGAAGTAGAACTTCATGTGCCTGTAAAA\t:IDFF:FIDDD7DDFI=D3B33IGF==<<\n+chr1_8\t163\tchr1\t505\t99\t28=1X46=\t=\t586\t110\tTAACTTTATCGCTGGTTAGTTTCTTCACaCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGA\t3DA>CCCFIF?>BCC88C:FFFD>>F0C5--+ICC9C<688HHIIHEE--=55HHFF?;6.IFF>II:BBBCFII\n+chr1_9\t99\tchr1\t1380\t99\t22=\t=\t1425\t108\tCTCACTTCTGTTACTCCAGCTT\t1;G:6AAB;DEE6AGDD7DF??\n+chr1_9\t147\tchr1\t1425\t99\t63=\t=\t1380\t-108\tACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCG\tD=68C::::43>B@11C;ECFII?F<I???6FFIIDDFFFF8FAA4655@IDF?70000AB,A\n+chr1_10\t99\tchr1\t236\t99\t50=\t=\t310\t97\tATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTAC\t?EFAF2222E=;DFC111AADI63:77>AA--,,IA3I=::DBB<?:>I?\n+chr1_10\t147\tchr1\t310\t99\t23=\t=\t236\t-97\tTCCAGAAATTGTTCCAAGTATCG\t;77EF@@@IIIFFFF<<0BID@A\n+chr1_11\t83\tchr1\t661\t99\t46=\t=\t599\t-108\tGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGC\tD5IIFIII22IIFB=?IHBBFFFFEF561?6C55555@/B<11@DB\n+chr1_11\t163\tchr1\t599\t99\t29=\t=\t661\t108\tTCATGTGCCTGTAAAACGAAGCGGTAAAA\tD?;?73FFF<CDBBBBA<IICI66C9975\n+chr1_12\t99\tchr1\t65\t99\t57=\t=\t139\t101\tTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTT\t?CC44077E88?ADAI6FF6:DEE<F?=BF::CB8>@@@EHII:;III22255////\n+chr1_12\t147\tchr1\t139\t99\t27=\t=\t65\t-101\tCTGTTACTCCAGCTTCTTCGGCACAAG\t9DBBC?DFGG;F?FFFFFEEEC1FAAI\n+chr1_13\t83\tchr1\t298\t99\t23=\t=\t218\t-103\tAGTTACCGTCTTTCCAGAAATTG\tE7DDFIIFI:>>>11CA448FF6\n+chr1_13\t163\tchr1\t218\t99\t41=\t=\t298\t103\tATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGA\tF<II55..<5BI..I=;;EF:AC,,//CDDCDE000<<CAC\n+chr1_14\t83\tchr1\t171\t99\t65=\t=\t128\t-108\tACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTT\tFII8F::A<G@EEFFF/77DHH6@?;IIG3>F4..,5=I03FFCCC-/EII====I<6AII:@BB\n+chr1_14\t163\tchr1\t128\t99\t40=\t=\t171\t108\tTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTA\t4444C?=2B0.FA85:CF;4=<8:77I778FFDAAII=FE\n+chr1_15\t83\tchr1\t1295\t99\t21=\t=\t1213\t-103\tCCAAGTATCGGCTTGTTTACG\t99::FE=D7FFC??AB>>3AD\n+chr1_15\t163\tchr1\t1213\t99\t22=\t=\t1295\t103\tTACTCCAGCTTCTTCGGCATGG\t6>=IDD:DC44C<<944E:F88\n+chr1_16\t99\tchr1\t23\t99\t23=\t=\t91\t99\tAGTGGTTGAACATCGTGATATGT\tII>DDCCFCCI@AF:F7E1D?HA\n+chr1_16\t147\tchr1\t91\t99\t31=\t=\t23\t-99\tTGTGCCTGTAAAACGAAGCGGTAAAAATTTT\t,BI?CCDDA1111I?.4>A22C-----FFFF\n+chr1_17\t83\tchr1\t318\t99\t28=\t=\t255\t-91\tTTGTTCCAAGTATCGGCTTGTTTACGAA\t<<CDD11@@GIFFE@@A::E@@@G<I11\n+chr1_17\t163\tchr1\t255\t99\t43=\t=\t318\t91\tCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGA\t7DA=@@--ABB8>EE-8F:D69DDD?885=A;@@12555BGAF\n+chr1_18\t99\tchr1\t501\t99\t26=\t=\t575\t100\tTGTCTAA'..b'IGGF!CF66--;;?F95IHBFCC74I3A:DDC@::FDIIH>H\n+chr1_446\t163\tchr1\t271\t99\t33=\t=\t337\t108\tTATCGGCTTGTTTACGAATTAAATCGAAGTTAC\tIIIDFFDBB6IIIIIFFF>=000CACDDDBB>1\n+chr1_447\t83\tchr1\t836\t99\t49=\t=\t790\t-95\tAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTAT\tAA6/=IFDG:;;28884F>88IIFFFF>>;;?A33<<FE@AFHD2DDD=\n+chr1_447\t163\tchr1\t790\t99\t29=\t=\t836\t95\tTGTTTACGAATTAAATCGAAGTTACCGTC\t76FFFFCCGGHHIIIG>1IIF;;FDDDC.\n+chr1_448\t99\tchr1\t435\t99\t22=\t=\t505\t95\tAAGGAAGCGGTAAAAATTTTTA\tGGIIC@FCGG@@@@@@35776F\n+chr1_448\t147\tchr1\t505\t99\t25=\t=\t435\t-95\tTAACTTTATCGCTGGTTAGTTTCTT\t4II<???7C?;BD66DDFAAAA755\n+chr1_449\t99\tchr1\t1235\t99\t33=\t=\t1316\t105\tTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTC\t@@==I?DCDB???F<EDAFAIICCIA;;;IBDI\n+chr1_449\t147\tchr1\t1316\t99\t24=\t=\t1235\t-105\tAATTAAATCGAAGTAGAACTTCAT\tFF>>///FF:DD35FB..DDD7:F\n+chr1_450\t83\tchr1\t611\t99\t18=1D19=\t=\t543\t-105\tAAAACGAAGCGGTAAAAATTTTATTTTTTTTCTCACT\t====IIBBEF42F:::::----9///////-AFF/C9\n+chr1_450\t163\tchr1\t543\t99\t35=\t=\t611\t105\tTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTAC\t;;;2.IFBAAEEDAA44FF06.FB33.44A@@@FI\n+chr1_451\t83\tchr1\t1069\t99\t35=\t=\t1006\t-98\tGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTG\tAAI22DEDDFEDEE77@@@2=:II63IICDF?FI6\n+chr1_451\t163\tchr1\t1006\t99\t29=\t=\t1069\t98\tAGTATCGGCTTGTTTACGAATTAAATCGA\tEA3FC?<<CGGF555?A9FF1199;IEIH\n+chr1_452\t83\tchr1\t158\t99\t20=\t=\t82\t-96\tGGCACAAGTACCAACCAGAA\t826I<<=?E6<<DD>@CDII\n+chr1_452\t163\tchr1\t82\t99\t21=\t=\t158\t96\tAGAACTTCATGTGCCTGTAAA\t8->>E88@CFEGFIIF50777\n+chr1_453\t99\tchr1\t586\t99\t32=\t=\t670\t105\tTCGAAGTAGAACTTCATGTGCCTGTAAAACGA\tE3F66<F6C;;=DDC3;A=6::<II1111CIC\n+chr1_453\t147\tchr1\t670\t99\t21=\t=\t586\t-105\tGCACAAGTACCAACCAGAACG\tIC3C<<>AHDDFFGGCICCBI\n+chr1_454\t99\tchr1\t316\t99\t70=\t=\t392\t100\tAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACC\tAA=<F887733D,CDI>>AFF8FFFGHA/-II777GFI770I<<?>DA4ICEF6@@5FIIHA?????7:9\n+chr1_454\t147\tchr1\t392\t99\t24=\t=\t316\t-100\tCCAGAAATTGTTCCAAGTATCGGC\t66?I:::II700<<FF;F?BCFFE\n+chr1_455\t83\tchr1\t554\t99\t34=1X25=\t=\t509\t-105\tTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCNAAGTAGAACTTCATGTGCCTGTAAA\tC?II87CC.AFAF44;II4@@@DE=DDDDFFFC;3CAI@>D44><<;04BFD;;7<@122\n+chr1_455\t163\tchr1\t509\t99\t23=\t=\t554\t105\tTTTATCGCTGGTTAGTTTCTTCA\tDDDB;DE=AAAFF?3>>>:HHCG\n+chr1_456\t83\tchr1\t519\t99\t39=\t=\t452\t-106\tGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTT\tI<:FIAA?G96A;FFBFF/AAGF0:::42<D...AB-II\n+chr1_456\t163\tchr1\t452\t99\t3=1D30=\t=\t519\t106\tTTTATTTTTTTTCTCACTTCTGTTACTCCAGCT\tC?@<555555//IF0ICCCB<DAA;IA44G@I)\n+chr1_457\t99\tchr1\t927\t99\t28=\t=\t970\t114\tTTATCGCCCTGTGGCCTGTTGATTCTAA\t666DFA555=<ACCFFHC<<EIEE@;66\n+chr1_457\t147\tchr1\t970\t99\t71=\t=\t927\t-114\tTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTAC\tDDDAIE<F>>>>F==33DHHH--9F;;;<<IDDAAFFIG?-?79<CC:FFF3B?AD73,,,9AHFFC66DD\n+chr1_458\t83\tchr1\t337\t99\t47=\t=\t280\t-104\tGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTA\tAFFF3C<??FFCCD:AFFFC=HHC8:A8@DI,F886D0,EA;;FFF;\n+chr1_458\t163\tchr1\t280\t99\t40=\t=\t337\t104\tGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATT\tBHEEAI3IIAAAAA<I4AAGFFFFF>I7FFHII@;,,,DD\n+chr1_459\t83\tchr1\t1199\t99\t20=\t=\t1116\t-103\tTTTCTCACTTCTGTTACTCC\t>??B<7FGFFH>I--HI3II\n+chr1_459\t163\tchr1\t1116\t99\t48=\t=\t1199\t103\tCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAA\tDFFF@880FD623??76:::FFF<<AA33F:?AFCCDCC@DDDCF5CC\n+chr1_460\t83\tchr1\t1521\t99\t26=\t=\t1443\t-104\tTCGGCTTGTTTACGAATTAAATCGAA\t7F@?IIIDFFFAGA=?>>BBB4>DAA\n+chr1_460\t163\tchr1\t1443\t99\t25=\t=\t1521\t104\tCGTGTAGCGTTTATGTTGGTTTCAT\tDAHF<5ICAFFFIA=.2<<:::E:A\n+chr1_461\t83\tchr1\t278\t99\t49=\t=\t219\t-108\tTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAA\t@@6?AAF6DCCCC@@?8DAFFEAA6IIF:<111DD4;336??:AAFF??\n+chr1_461\t163\tchr1\t219\t99\t49=\t=\t278\t108\tTGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCC\tIEE2222:I<=GGIGGHFBFIH....D9<:8FDDDII=AA9900<==>>\n+chr1_462\t99\tchr1\t96\t99\t22=\t=\t153\t98\tCTGTAAAACGAAGCGGTAAAAA\tA:=CDDDDI<11DDAA?37733\n+chr1_462\t147\tchr1\t153\t99\t41=\t=\t96\t-98\tTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCT\tI?HH4DD,CD<:4<B==33AA??AAIFII/////?FAI77D\n+chr1_463\t99\tchr1\t317\t99\t23=1D\t=\t370\t104\tATTGTTCCAAGTATCGGCTTGTT\t2@@HDGIIAA5IACD;61DDEBB\n+chr1_463\t147\tchr1\t370\t99\t51=\t=\t317\t-104\tTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTT\tAA?IDDC@;;CBB?II8A<11188I<>>>AAHDDAA33I>DIIDD2BB333\n' |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.454.02.stat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.454.02.stat Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,1626 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599\t0\t0\n+1600\t0\t0\n+1601\t0\t0\n+1602\t0\t0\n+1603\t0\t0\n+1604\t0\t0\n+1605\t0\t0\n+1606\t0\t0\n+1607\t0\t0\n+1608\t0\t0\n+1609\t0\t0\n+1610\t0\t0\n+1611\t0\t0\n+1612\t0\t0\n+1613\t0\t0\n+1614\t0\t0\n+1615\t0\t0\n+1616\t0\t0\n+1617\t0\t0\n+1618\t0\t0\n+1619\t0\t0\n+1620\t0\t0\n+1621\t0\t0\n+1622\t0\t0\n+1623\t0\t0\n+1624\t0\t0\n+1625\t0\t0\n' |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.454.021.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.454.021.fq Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,1852 @@\n+@chr1_1-1\n+TCCAGAAATTGTTCCAAGTATCGGCTT\n++\n+:GC?7...IICEECCII6I?BC<<F<@\n+@chr1_2-1\n+CGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTT\n++\n+FA3BB737G?FFFFDD69CCCAB,FFFFIIGBDFC>>>44=:8\n+@chr1_3-1\n+GAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATG\n++\n+I<<EEFF///--FF;F::IIFD3E,<F:FDDD.DF\n+@chr1_4-1\n+GAGAAAAAAAATAAAAATTTTTACCtCTTCGTT\n++\n+FAF000000//7@@@@:63331=DD!AA@DB00\n+@chr1_5-1\n+TTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGT\n++\n+AAAIIAAACFDB?ABBIIIBDDDGBI<<EE555CD755IB\n+@chr1_6-1\n+TCTAACTTTATCGCCCTGTGGC\n++\n+B<6AADCCCB?7?FFFCAB5:8\n+@chr1_7-1\n+TTCTGGTTGGTACTTGTGCC\n++\n+<<H6II::;;8F=<=F7D==\n+@chr1_8-1\n+TTTTACAGGCACATGAAGTTCTACTTCGA\n++\n+<<==FGI33B3D=IFDD7DDDIF:FFDI:\n+@chr1_9-1\n+CTCACTTCTGTTACTCCAGCTT\n++\n+1;G:6AAB;DEE6AGDD7DF??\n+@chr1_10-1\n+ATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTAC\n++\n+?EFAF2222E=;DFC111AADI63:77>AA--,,IA3I=::DBB<?:>I?\n+@chr1_11-1\n+GCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGC\n++\n+BD@11<B/@55555C6?165FEFFFFBBHI?=BFII22IIIFII5D\n+@chr1_12-1\n+TGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTT\n++\n+?CC44077E88?ADAI6FF6:DEE<F?=BF::CB8>@@@EHII:;III22255////\n+@chr1_13-1\n+CAATTTCTGGAAAGACGGTAACT\n++\n+6FF844AC11>>>:IFIIFDD7E\n+@chr1_14-1\n+AAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGT\n++\n+BB@:IIA6<I====IIE/-CCCFF30I=5,..4F>3GII;?@6HHD77/FFFEE@G<A::F8IIF\n+@chr1_15-1\n+CGTAAACAAGCCGATACTTGG\n++\n+DA3>>BA??CFF7D=EF::99\n+@chr1_16-1\n+AGTGGTTGAACATCGTGATATGT\n++\n+II>DDCCFCCI@AF:F7E1D?HA\n+@chr1_17-1\n+TTCGTAAACAAGCCGATACTTGGAACAA\n++\n+11I<G@@@E::A@@EFFIG@@11DDC<<\n+@chr1_18-1\n+TGTCTAACTTTATCGCTGGTTAGTTT\n++\n+9FDIC,,H662C6=5FD88884A;;;\n+@chr1_19-1\n+CTTGGAACAATTTCTGGAAAGACGGTAAA\n++\n+0BBBB==ICCFFF=H==99;A6<884CCE\n+@chr1_20-1\n+AAGAAGCTGGAGTAACAGAAGTGAtAAAAAAAAATAAAAATTTTTAC\n++\n+BBI44A4455;:<IID>A@@F8IG.777333333C1111199999IC\n+@chr1_21-1\n+AATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTT\n++\n+CCFG///DA9<BCF51FCD.BADDDCAAB5DD8H==333\n+@chr1_22-1\n+CGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACG\n++\n+?=CA;>>CFF:000FFD..FF>?3D?CECDG??AGGGIDI\n+@chr1_23-1\n+TTCTTCGGCATGGTTTTGTCTAACTTTATCGCT\n++\n+33.DD5??1IADDAAAAI7C,11FC>;HE=8=H\n+@chr1_24-1\n+CAGAAGTGAGAAAAAAAATAAA\n++\n+7CFII<FDED////////?AAA\n+@chr1_25-1\n+CTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACG\n++\n+IFFFFFFFIEC:FBBBB@6=>4C777<<IHHHH==AAAFF99I>=76AAIFFF2268BF\n+@chr1_26-1\n+CCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAA\n++\n+IIF6=;;C@@GCCDF>EE?AIFFIIGG=F@@FF.D---\n+@chr1_27-1\n+TTCTGTTACTCCAGCTTCTTCGGCACAAG\n++\n+==85I==F:ECCCF711?>;FIIBIDEEI\n+@chr1_28-1\n+GAAGTGGACTGCTGGCGTTATAACGCCTTTACCGT\n++\n+DII6F00EFIEFFED<EDDCCEIFI<<HHFF@>5D\n+@chr1_29-1\n+TCTGGAAAGACGGTAAAAGCGATAAAGTTAGA\n++\n+FD.IIHHHEE?II<IGGG9EI6:BBB;ECEFI\n+@chr1_30-1\n+CTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTG\n++\n+?DC:I36ICDDE3??EAFF>>>IAA6FF448FFFDAAAII>\n+@chr1_31-1\n+GGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGA\n++\n+DDBAA?F6DDFIIE=IDFDDI===IICCGGFA:FE\n+@chr1_32-1\n+CAAGCCGATACTTGGAACAATTT\n++\n+I,,877C?CD.313356IFF?FF\n+@chr1_33-1\n+TCGCTTTTACCGTCTTTCCAG\n++\n+A?DC2222FIICBDHHH:9GD\n+@chr1_34-1\n+AAGTGAGAAAAAAAAATAAAAATTT\n++\n+006AHFC118888881DGGGGG>>>\n+@chr1_35-1\n+CTACAtGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAA\n++\n+AEIIF4=HA>DFBA@-----C@DIIIDIFF88FF-D611@D?31ADD\n+@chr1_36-1\n+CCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGC\n++\n+EEAAFFHF@HHFFF6FFF9IFCCIGFFFEHF55>:IICA=H=\n+@chr1_37-1\n+CGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCT\n++\n+DCFFFF111@I700IC//GEGI:D>>8;66<B::C:D<II.///F?EHII?666/<:I=I\n+@chr1_38-1\n+ATTGTTCCAAGTATCGGCTTGTTTACGAA\n++\n+F==3EEII??AAFG4@?977FBBG6B=44\n+@chr1_39-1\n+CAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACG\n++\n+C=FFCCDA88FFF>48AA?....I5I7E777D=6IFFICCDD66;A9444FF<<IADEEBD@\n+@chr1_40-1\n+AGTGAGAAAAAAAAATAAAAATTTTTA\n++\n+D9<IDC,,,,,,,--H,,,,,FFFFFF\n+@chr1_41-1\n+ACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAA\n++\n+DDDF<:@DDFFF>IBDAEI3344??GDF?AAIA885=33A3DGCI69F<<<D=F4./<<77?6@CCC4??\n+@chr1_42-1\n+TCTGGTTGGTACTTGTGCCGAAGAA\n++\n+DDF>>21AA>FAAA?7AII===FEE\n+@chr1_43-1\n+GAGTAACAGAAGTGAGAAAAAA\n++\n+FCE3?@GI=CCDCBEF,,,,,,\n+@chr1_44-1\n+AGTCCACTTCGATTTAATTCGTAAACAAGC\n++\n+2IFAAAAAAFIIFFFFFDB4CI;::AA??;\n+@chr1_45'..b'+GTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGG\n++\n+8<<AB;A/220BBBA?<<<HH,,?<:DDDCFCEDDI;A:A..IAE<55555F?FCDD,<??FFII\n+@chr1_421-1\n+TTTGTCTAACTTTATCGCTGGTTAG\n++\n+=113D,H@@I...:IDE=>65CCDD\n+@chr1_422-1\n+GGTAAAAATTTTTTATTTTTTTTTCTC\n++\n+<<A/////::>>;;I.........@ED\n+@chr1_423-1\n+GATTTAATTCGTAAACAAGCCGATAC\n++\n+IFEEGEEIID@I<;;D>>DDD@@,@?\n+@chr1_424-1\n+CGGTAAGCGTGAAGAAACTAACCAGCGATAA\n++\n+IDD8::0E::I..I<<<ADEE??DFFFE7<>\n+@chr1_425-1\n+ACcAATTAAATCGAAGTGGACTGCTGGCGT\n++\n+0=/FFCC;;;DF7GGDDDDA-AD<C33ECA\n+@chr1_426-1\n+AGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAA\n++\n+I?D;DACC<II-...:F1ED66DDBEFDAAECC<?=977745AIC13DFA3444DHFF==CC<33\n+@chr1_427-1\n+GTCCACTTCGATTTAATTCG\n++\n+@4IIEE9;HAA;66HHIGID\n+@chr1_428-1\n+GATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAG\n++\n+1IFFFFF..?:AFFFFAAFCC?@FI@9=..HHFAAHHHA7//;;;I\n+@chr1_429-1\n+ACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTA\n++\n+A==CF6HHHCCA>,,,,,I8888IIF=F35CC@FFI666I\n+@chr1_430-1\n+TTGTTTACGAATTAAATCGAAGTG\n++\n+III@@A?EIDD<<FFFAFA..@40\n+@chr1_431-1\n+CCAAGTATCGGCTTGTTTACG\n++\n+BB118FBFD55III2BBC5I@\n+@chr1_432-1\n+ATACTTGGAACAATTTCTGGAAAGACGGT\n++\n+FH0DB===95EDBAAAFDDD666?AA55A\n+@chr1_433-1\n+TTATTTTTTTTTCTCACTTCTGTTACTCCAGCTT\n++\n+BBA//////111:CII>IICDA74?43<<FF<77\n+@chr1_434-1\n+TTCCAAGTATCGGCTTGTTTcCGAATTAAATCGAAGTGGACTGCTGGCG\n++\n+IIIIIIDFIGB99=EEDCCC@CBDDFFFFFDC3DDD:DD?6ICI3II:C\n+@chr1_435-1\n+AGAAGCTGGAGTAACAGAAGTGAGAAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACA\n++\n+F3IIFDDBE?,6IIC8F//>FFEF777555555F2////66666I:<B<66FC::::A:I\n+@chr1_436-1\n+TTTCTGGAAAGACGGTAAGCGTGAAtAAACTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAA\n++\n+EEEAAB96667C4FF1CC2AI=IAA!GGHI?IIEE=D5595-,,<77I:FIGGGGAA./FFF?CCEDDI<DFF>.D?A\n+@chr1_437-1\n+AGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATT\n++\n+3?+++*****C.....233335==IACCIIHHCHFAA\n+@chr1_438-1\n+TGGCGTTATAACGCCTTTACCGTCT\n++\n+EFFICFFC=9936;;CCC,CC?I:A\n+@chr1_439-1\n+GTAAGCGTGAAGAAACTAACCAGCG\n++\n+=BGGIFD6I88:2,,IFFFAD6;7?\n+@chr1_440-1\n+CTGGAAAGACGGTAACTTCGATTTA\n++\n+6B2.HHH<IA@@4A?D44:9D/33?\n+@chr1_441-1\n+TACCGTCTTTCCAGAAATTGT\n++\n+IFII7?GCCCII>A:::GDD.\n+@chr1_442-1\n+CCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAA\n++\n+88IF@///??FD===AAH??AAFF>FB3CAACBF???@D@HII\n+@chr1_443-1\n+AACTAACCAGCGATAAAGTTAGA\n++\n+II<?II::A4AIII<<8FFF1CD\n+@chr1_444-1\n+CGATAAAGTTAGACAAAACC\n++\n+HFI5FFFDDDIF0I=???,,\n+@chr1_445-1\n+CAAGCCGATACTTGGAACAATTT\n++\n+@11BAAD0D3>==44=>7AAHDD\n+@chr1_446-1\n+GCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGaAAAC\n++\n+H>HIIDF::@CDD:A3I47CCFBHI59F?;;--66FC!FGGI\n+@chr1_447-1\n+ATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTT\n++\n+=DDD2DHFA@EF<<33A?;;>>FFFFII88>F48882;;:GDFI=/6AA\n+@chr1_448-1\n+AAGGAAGCGGTAAAAATTTTTA\n++\n+GGIIC@FCGG@@@@@@35776F\n+@chr1_449-1\n+TTTTGTCTAACTTTATCGCTGGTTAGTTTCTTC\n++\n+@@==I?DCDB???F<EDAFAIICCIA;;;IBDI\n+@chr1_450-1\n+AGTGAGAAAAAAAATAAAATTTTTACCGCTTCGTTTT\n++\n+9C/FFA-///////9----:::::F24FEBBII====\n+@chr1_451-1\n+CAGCAGTCCACTTCGATTTAATTCGTAAACAAGCC\n++\n+6IF?FDCII36II:=2@@@77EEDEFDDED22IAA\n+@chr1_452-1\n+TTCTGGTTGGTACTTGTGCC\n++\n+IIDC@>DD<<6E?=<<I628\n+@chr1_453-1\n+TCGAAGTAGAACTTCATGTGCCTGTAAAACGA\n++\n+E3F66<F6C;;=DDC3;A=6::<II1111CIC\n+@chr1_454-1\n+AATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACC\n++\n+AA=<F887733D,CDI>>AFF8FFFGHA/-II777GFI770I<<?>DA4ICEF6@@5FIIHA?????7:9\n+@chr1_455-1\n+TTTACAGGCACATGAAGTTCTACTTnGATTTAATTCGTAAACAAGCCGATACTTGGAACA\n++\n+221@<7;;DFB40;<<>44D>@IAC3;CFFFDDDD=ED@@@4II;44FAFA.CC78II?C\n+@chr1_456-1\n+AACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAAC\n++\n+II-BA...D<24:::0FGAA/FFBFF;A69G?AAIF:<I\n+@chr1_457-1\n+TTATCGCCCTGTGGCCTGTTGATTCTAA\n++\n+666DFA555=<ACCFFHC<<EIEE@;66\n+@chr1_458-1\n+TAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAAC\n++\n+;FFF;;AE,0D688F,ID@8A:8CHH=CFFFA:DCCFF??<C3FFFA\n+@chr1_459-1\n+GGAGTAACAGAAGTGAGAAA\n++\n+II3IH--I>HFFGF7<B??>\n+@chr1_460-1\n+TTCGATTTAATTCGTAAACAAGCCGA\n++\n+AAD>4BBB>>?=AGAFFFDIII?@F7\n+@chr1_461-1\n+TTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAA\n++\n+??FFAA:??633;4DD111<:FII6AAEFFAD8?@@CCCCD6FAA?6@@\n+@chr1_462-1\n+CTGTAAAACGAAGCGGTAAAAA\n++\n+A:=CDDDDI<11DDAA?37733\n+@chr1_463-1\n+ATTGTTCCAAGTATCGGCTTGTT\n++\n+2@@HDGIIAA5IACD;61DDEBB\n' |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.454.022.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.454.022.fq Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,1852 @@\n+@chr1_1-2\n+AACAAGCCGATACTTGGAACAATTTCTGGAAAGACG\n++\n+44I884II;;FCIHH55>>FFFHHH?7DDAAAIC?<\n+@chr1_2-2\n+AATTTTTACCGCTTCGTTTTACAGGCACAcGAAG\n++\n+33,,---<00ID00D:2000ICHEEIA3I71,,C\n+@chr1_3-2\n+ACTTGGAACAATTTCTGGAAA\n++\n+AAD???CC@55///;I>ADDD\n+@chr1_4-2\n+CATCGTGATATGTATGTTtAC\n++\n+DF3FFADDBCDFI0ICBB,C5\n+@chr1_5-2\n+CAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTC\n++\n+AFCF,,;I??DD?:62AA<<>CAFFFA44><=F5AIA<<FDGG?77...A\n+@chr1_6-2\n+GTAAACAAGCCGATACTTGGAACAATTTCTG\n++\n+DI0112FF>EE:?B76::FF22C99@??E:?\n+@chr1_7-2\n+AGAACTTCATGTGCCTGTAAAACGAAGCGGT\n++\n+<IAB066IG3I7IBBAAH333.-AAAFA.-4\n+@chr1_8-2\n+TAACTTTATCGCTGGTTAGTTTCTTCACaCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGA\n++\n+3DA>CCCFIF?>BCC88C:FFFD>>F0C5--+ICC9C<688HHIIHEE--=55HHFF?;6.IFF>II:BBBCFII\n+@chr1_9-2\n+CGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGT\n++\n+A,BA00007?FDI@5564AAF8FFFFDDIIFF6???I<F?IIFCE;C11@B>34::::C86=D\n+@chr1_10-2\n+CGATACTTGGAACAATTTCTGGA\n++\n+A@DIB0<<FFFFIII@@@FE77;\n+@chr1_11-2\n+TCATGTGCCTGTAAAACGAAGCGGTAAAA\n++\n+D?;?73FFF<CDBBBBA<IICI66C9975\n+@chr1_12-2\n+CTTGTGCCGAAGAAGCTGGAGTAACAG\n++\n+IAAF1CEEEFFFFF?F;GGFD?CBBD9\n+@chr1_13-2\n+ATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGA\n++\n+F<II55..<5BI..I=;;EF:AC,,//CDDCDE000<<CAC\n+@chr1_14-2\n+TTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTA\n++\n+4444C?=2B0.FA85:CF;4=<8:77I778FFDAAII=FE\n+@chr1_15-2\n+TACTCCAGCTTCTTCGGCATGG\n++\n+6>=IDD:DC44C<<944E:F88\n+@chr1_16-2\n+AAAATTTTTACCGCTTCGTTTTACAGGCACA\n++\n+FFFF-----C22A>4.?I1111ADDCC?IB,\n+@chr1_17-2\n+CAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGA\n++\n+7DA=@@--ABB8>EE-8F:D69DDD?885=A;@@12555BGAF\n+@chr1_18-2\n+GAAGTTCTACTTCGATTTAATTCGTA\n++\n+F22:IIDF17B@IA@@@?EE>>:;?I\n+@chr1_19-2\n+CTTTCCAGAAATTGTTCCAAGTATCGGCTTG\n++\n+2DDDIIDC---<<CDD<<FF5-D:<DD8><7\n+@chr1_20-2\n+AGAAATTGTTCCAAGTATCGGCTT\n++\n+F@???<=E?@//:67EAHA22I:5\n+@chr1_21-2\n+CGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAAT\n++\n+C1C,,33FFIF7855FFGG@@B5557??F44IF8C.;<A?AAC..F\n+@chr1_22-2\n+AAAAATAAAAATTTTTACCGCTTCGTTT\n++\n+444..F88666333--9DDFIDDA=CCC\n+@chr1_23-2\n+TTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGA\n++\n+HHIFABCCIF6>BA776;I@I<<<ACC/=?CEDII=<FF--@::111B530I\n+@chr1_24-2\n+ATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGT\n++\n+C<IID:FF(((F55AI9...DDFI113FF20000AAE?\n+@chr1_25-2\n+TAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGAT\n++\n+I,,,?II4..:?FDBAAIIAAFEEGHHA=GG888D@7,,IIIAEDDIFD\n+@chr1_26-2\n+GGTAAAAGCGATAAAGTTAGA\n++\n+FFDEEEEIC6H6:::4CCFIG\n+@chr1_27-2\n+GATAAAGTTAGcCAAAACCATGA\n++\n+3=9444?FFF?3F??@@CCFAII\n+@chr1_28-2\n+TAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAcC\n++\n+9DDDD:55511FFFEF44A???<=I;;<..EEAC1;;;.DD5D\n+@chr1_29-2\n+TCCAGCTTCTTCGGCACAAgTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGT\n++\n+DCCDHCFD@@<C@@DI@AA!<D22DE00DD..CCF413333ECI?IIIAD><F:\n+@chr1_30-2\n+AATAAAAATTTTTACCGCTTCCTTCGATTTAATTCG\n++\n+=AC00006.....C66FG..,,FFHH=HHHDDAA=?\n+@chr1_31-2\n+GGAAGCGGTAAAAATTTTTATTTTTTTTCTC\n++\n+77CC89DDA==>>?FFF>>@004444--?,>\n+@chr1_32-2\n+TCGCTTTTACCGTCTTTCCAnAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTT\n++\n+9E??8888700CII..*IG-F@@@CCADDCCFFCF<<F33-<:CDDDFCF,,FFHHHFD4<<5DF@??:75888\n+@chr1_33-2\n+AACAAGCCGATACTTGGAACAATTTCT\n++\n+GFDDD9DD=;CDD3199==EDD;;;@I\n+@chr1_34-2\n+CTGCTGGCGTTATAACGCCTTT\n++\n+FI?4F44FF<<FI@@DI75FFF\n+@chr1_35-2\n+CATGTGCCTGTAAAACGAAGCG\n++\n+DEF:@6HH69;9999IIII=?E\n+@chr1_36-2\n+AGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTAT\n++\n+F7@@3FEI3311DDB3FF1:FFE3FFBI2F????FF:D=1<</F\n+@chr1_37-2\n+TTTAGAATCAACAGGCCACAGGGCGATA\n++\n+FFF>CB@CF--I<9911I4CAAAEEDI7\n+@chr1_38-2\n+CCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGG\n++\n+8>DFIF??@@<E@@AA7CCCFF47CFBHHH9HICIIFGA:EDDIIFFF==FFEAF--\n+@chr1_39-2\n+CACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAG\n++\n+CECFFF7FCCCC..ECHHCF3AFFFFFCDI;FFHDIFIFFDF\n+@chr1_40-2\n+TTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTG\n++\n+AAFD:<3B22HHH<22C<I22233D?,,,DDDDD=<AA7<G9;BBIFF0\n+@chr1_41-2\n+GAAGTTACCGTCTTTCCAGAAATTGTTCCAAGT\n++\n+>33ACCI22B9B///DDF9EEEEEDDDCGBAGB\n+@chr1_42-2\n+AACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTT\n++\n+II5GGFADG@EII64I7775A;<>FIGGF::::9-----I//////\n+@chr1_43-2\n+TATCGGCTTGTTTACtAATTAAATCGAAGTAGAACTTCAT\n++\n+;B3D8'..b"A?\n+@chr1_421-2\n+GGCACATGAAGTTCTACTTCATTTAATTCGTAAACAAGCCGATACTTGGAA\n++\n+//DD>8?DEG;GGIAFIAAG;338DDCCIFE220FCC7IID87IDFFFFGG\n+@chr1_422-2\n+AACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAA\n++\n+;:F6DCCCFF6FAEAD9HF22BFED;;;96F,II7669DD,,?@AFCCCDEEII>663::\n+@chr1_423-2\n+TCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCT\n++\n+FBB:DI339IIF59EAIAA,,,,;IFIAAFCCC=7I::I\n+@chr1_424-2\n+TCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTTCTtACTTgTGTTACTCCAGCTTCTTCGGCATGGTTTT\n++\n+@FD<<33FE:5HH>//////////I.........H;!HAFC/A:::E7FEE6IIDD:CCF::FFDGG....\n+@chr1_425-2\n+GCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAG\n++\n+7=EECCCC>F9BBBEEGG7GAHHHAAA;AA;5;3AAAFFHH:66===.<<<EEED\n+@chr1_426-2\n+AAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAAAT\n++\n+55=CIDD?CFFFAC18895D?A********EDDDDDDC\n+@chr1_427-2\n+AGAAATTGTTCCAAGTATCGG\n++\n+?C;4522D15IIIIGCGAFEE\n+@chr1_428-2\n+ACTTTATCGCCCTGTGGCCTG\n++\n+F:661@38I..03CHFF>>FF\n+@chr1_429-2\n+AAGCTGGAGTAACAGAAGTGAGAAAAAA\n++\n+;;05:FF7IG62EI?FF<IF?<444444\n+@chr1_430-2\n+GAATCAACAGGCCACAGGGCG\n++\n+DIIHDAA7ACCAAC5DCCCCI\n+@chr1_431-2\n+ACAGGCCACAGGGCGATAAAGTTAGACAAAACC\n++\n+7FIFFFFFA?BAA,7IIDDDA44FB672222AA\n+@chr1_432-2\n+TGTCTAACTTTATCGCTTTTACCGT\n++\n+A:HCHEEI6663CI7.<DDD=II0E\n+@chr1_433-2\n+TGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCC\n++\n+=IHHH//44A:.666I@.I07CFF5C=9ICAE22213?F3IIIF;FFFFHHH<IIIE48II\n+@chr1_434-2\n+AGGCCACAGGGCGATAAAGTTAGACAAAAC\n++\n+I7.FFIIC76:=B1I113=33AF3?CCC;F\n+@chr1_435-2\n+GGCTTGTTTACGAATTAAATCGAAGTAGAACTTCAaGTGC\n++\n+@@FCCI1..?3BDDD=//1CII88CD6FAACAAIB8C:>6\n+@chr1_436-2\n+GCGGTAAAAATTTTTATTTTTTTTTCTCACTT\n++\n+IAIIC2225;;;@==D'********C7==DII\n+@chr1_437-2\n+TTATAACGCCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACG\n++\n+@@FI22F3DDGGF::ECA???DD=A;;;AAFIIII..IDI?F..CDD?<<;IDC\n+@chr1_438-2\n+TGAGAAAAAAAAATAAAAATTTTTTACCGCTTCCTTCGATTT\n++\n+BDHC.........H33332BBGGGE9CC>BEEIIIIHIH444\n+@chr1_439-2\n+TTAAATCGAAGGAAGCGGTAAAA\n++\n+B?DBB6IE77<<B@D(B@<....\n+@chr1_440-2\n+GGTTTCATGGTTTTGTCTAACTTTATCG\n++\n+FFFFF,FA@@....9II2?:F666E7:?\n+@chr1_441-2\n+AGCTGGAGTAACAGAAGTGAGAAAAAAAAT\n++\n+6I:8AAI=AAAD7BCCA5BFE77777777<\n+@chr1_442-2\n+AGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATT\n++\n+CIB,>=IF?@GG?FEEA19I6//////--C::>>>111//:AAIC2;66FF<FDDD\n+@chr1_443-2\n+AATTAAATCGAAGGAAGCGGTAAAAATTTTTAT\n++\n+..,0,,1AHDAAAA,,DDDDD8::7766655?G\n+@chr1_444-2\n+CAAGTATCGGCTTGTTTACGAAT\n++\n+D57ID:?<IIA>=DHHHC7?DDI\n+@chr1_445-2\n+TTCTCACTTCTGTTACTCCAGCTTCTTCGGC\n++\n+BB8:CGI<<AIIDDIDD@@DB=,,:AAC55D\n+@chr1_446-2\n+TATCGGCTTGTTTACGAATTAAATCGAAGTTAC\n++\n+IIIDFFDBB6IIIIIFFF>=000CACDDDBB>1\n+@chr1_447-2\n+TGTTTACGAATTAAATCGAAGTTACCGTC\n++\n+76FFFFCCGGHHIIIG>1IIF;;FDDDC.\n+@chr1_448-2\n+AAGAAACTAACCAGCGATAAAGTTA\n++\n+557AAAAFDD66DB;?C7???<II4\n+@chr1_449-2\n+ATGAAGTTCTACTTCGATTTAATT\n++\n+F:7DDD..BF53DD:FF///>>FF\n+@chr1_450-2\n+TTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTAC\n++\n+;;;2.IFBAAEEDAA44FF06.FB33.44A@@@FI\n+@chr1_451-2\n+AGTATCGGCTTGTTTACGAATTAAATCGA\n++\n+EA3FC?<<CGGF555?A9FF1199;IEIH\n+@chr1_452-2\n+AGAACTTCATGTGCCTGTAAA\n++\n+8->>E88@CFEGFIIF50777\n+@chr1_453-2\n+CGTTCTGGTTGGTACTTGTGC\n++\n+IBCCICGGFFDDHA><<C3CI\n+@chr1_454-2\n+GCCGATACTTGGAACAATTTCTGG\n++\n+EFFCB?F;FF<<007II:::I?66\n+@chr1_455-2\n+TTTATCGCTGGTTAGTTTCTTCA\n++\n+DDDB;DE=AAAFF?3>>>:HHCG\n+@chr1_456-2\n+TTTATTTTTTTTCTCACTTCTGTTACTCCAGCT\n++\n+C?@<555555//IF0ICCCB<DAA;IA44G@I)\n+@chr1_457-2\n+GTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAA\n++\n+DD66CFFHA9,,,37DA?B3FFF:CC<97?-?GIFFAADDI<<;;;F9--HHHD33==F>>>>F<EIADDD\n+@chr1_458-2\n+GTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATT\n++\n+BHEEAI3IIAAAAA<I4AAGFFFFF>I7FFHII@;,,,DD\n+@chr1_459-2\n+CTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAA\n++\n+DFFF@880FD623??76:::FFF<<AA33F:?AFCCDCC@DDDCF5CC\n+@chr1_460-2\n+CGTGTAGCGTTTATGTTGGTTTCAT\n++\n+DAHF<5ICAFFFIA=.2<<:::E:A\n+@chr1_461-2\n+TGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCC\n++\n+IEE2222:I<=GGIGGHFBFIH....D9<:8FDDDII=AA9900<==>>\n+@chr1_462-2\n+AGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGA\n++\n+D77IAF?/////IIFIAA??AA33==B<4:<DC,DD4HH?I\n+@chr1_463-2\n+AACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAA\n++\n+333BB2DDIID>I33AADDHAA>>><I88111<A8II?BBC;;@CDDI?AA\n" |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.illumina.01.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.illumina.01.aln Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,484 @@\n+##ART_Illumina\tread_length\t200\n+@CM\tart_illumina -i test-data/input.fa -l 200 -f 20 -o test-data/art.illumina.01 -m 200 -rs 42 --insRate 0.00009 --insRate2 0.00015 --delRate 0.00011 --delRate2 0.00023 --samout \n+@SQ\tchr1\t1626\n+##Header End\n+>chr1\tchr1-160\t47\t+\n+GTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACC\n+GTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTATCTTTATCGCTTTTACC\n+>chr1\tchr1-159\t568\t+\n+CTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAG\n+CTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCCTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAG\n+>chr1\tchr1-158\t955\t-\n+GCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAG\n+GCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTACCCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAG\n+>chr1\tchr1-157\t479\t+\n+CCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTAC\n+CCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTAC\n+>chr1\tchr1-156\t491\t+\n+GCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGT\n+GCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGT\n+>chr1\tchr1-155\t459\t+\n+TTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCC\n+TTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCC\n+>chr1\tchr1-154\t443\t-\n+TACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACG\n+TACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACG\n+>chr1\tchr1-153\t130\t-\n+CGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTT\n+CGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCCATTTAATTCGTAAACAAGCCGATACTT\n+>chr1\tchr1-152\t23\t+\n+GTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTT\n+GTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTC'..b'AGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTTTCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTAC\n+>chr1\tchr1-9\t1225\t+\n+TCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAA\n+TCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAGCCAGAA\n+>chr1\tchr1-8\t395\t+\n+AAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGA\n+AAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCAAGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGA\n+>chr1\tchr1-7\t1130\t+\n+AGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTA\n+AGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTA\n+>chr1\tchr1-6\t970\t+\n+TTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATC\n+TTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGCAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATC\n+>chr1\tchr1-5\t931\t-\n+TTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACC\n+TTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACC\n+>chr1\tchr1-4\t847\t-\n+TGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAAT\n+TGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAAT\n+>chr1\tchr1-3\t1410\t-\n+AAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTATCGACAACAAGAAGCAGCCTTATGGCCGTCAACATACATATCACGATGTTCAACCACTAATAGG\n+AAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTATCGACAACAAGAAGCAGCCTTATGGCCGTCAACATACATATCACGATGTTCAACCACTAATAGG\n+>chr1\tchr1-2\t769\t-\n+ATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGG\n+ATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTTTGCCGAAGAAGCTGG\n+>chr1\tchr1-1\t376\t-\n+ATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTC\n+ATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTC\n' |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.illumina.01.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.illumina.01.fq Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b"@@ -0,0 +1,640 @@\n+@chr1-160\n+GTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTATCTTTATCGCTTTTACC\n++\n+?A?9?BB?@D@DDDEBFGGGGGIHHIIIFEFIIHIHHGHHIHIHHIIIHHHFIDIFIHFFIHCIIIDFFHHFFHIHHHFIIHCIHIEHHHIGIIBHIEIDHHGIDDGHHHHHEHGHGGG3HFFHEFFCGFEE;GEDGGGFFE9G?FGGBCG?FGGGEEGGGDEGGG<GFG?GEBGFGE?GEGG(GGG=AG:GGEGG?GEG\n+@chr1-159\n+CTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCCTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAG\n++\n+?????B?BDDBDBEDDFGGGGFHEHIIIHIHI9IIHICFHIHIIHIIIHIH>CIEHIIFFHH?HH5EFDGHIIHI)DHIHHEHHBHIIHC=?HCH+DHFF?HBHFIHFHGHIHFGHHFGFFGG+GB,GHEHH82GEIEGFGEFEG)<GEGCG?GGGGGEG;EG?EEEEG6GFFEGDE6GGG?GGGEEGEGEEEGFGEG?0\n+@chr1-158\n+GCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTACCCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAG\n++\n+A?AA?BBBDABDDD?<FGGFFGIIFHFHIHAIHIHEHIEIIGHIIHICEHHHHFFIHHFFIFIFFGGI=HIIIDIHHHHI-BEHGGGIHHDHHIHIFIHFGHD5HHHCF+HF@HHFEDEHGFEFEGEGGHHHF1H2GEBAEGEFGEG;ECG0FBEGGGEFGEE4EE;CGCEEAGG+*G:EG*EEAGE6EGF06.:EE?FE\n+@chr1-157\n+CCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTAC\n++\n+=??9?BB=DD@DDDDEFGFFEGFHHHIII>HII=IHIIHHIHCAIH@HGFIHI>IFHHDHHHGEHFHFE?IIHIIHDIIHFII=IHFHEHIHIAIGGHHHHFF*IEHBDGGFDFFH7HED,HHH<GEFHGGE,=EIEG:EEFGEGCEGGFAGFGGGFGGFGGGGGEG?BGFFEEGCFCAEGE?ECGGGGGCEG??FEGGF\n+@chr1-156\n+GCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGT\n++\n+A???<BBBDDDDDBDDGCFCFGHHII>FBHI9HDIHIHHHBDIHHHI@HHFIDIFIIFFIHIIEIHIIIHFIHFHIHHIII*IIIIIHECFIIIIIHHHG6IFHCHFHICHHCFHHEHFFHGCGF;GHGEEGEGEEDFHCGG*GGGGCFGFEEGGGGGGFG;EAGFFG*F6G?:E:G0CEGGFEEFDC>:G*?GAGEGGE\n+@chr1-155\n+TTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCC\n++\n+A??AABBBDDDDDDDBCFGGGGH>FIIICEHCH7IGIIDHHHFGIIH>EDIIIHIDHI=HIHHFHHHFGHHI=IEIHH-HIIGHH5HIHHGHDIHHFDHHHFHHIHHFCHHHHEF?EHHHHDFH3BFEECHHEEGEGEGGHFGGG0GH*GGGGEFGEG?G0GGEECG=FE/EGG:GGGGGEGE9GGGEGG9GGGECG8EE\n+@chr1-154\n+TACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACG\n++\n+A????B?BDDDDDBDBFCGGAFIHF>FEHIIHIFICIFIFIEFHGIHHI0F0HIHHIHHGHGH5HHCHIIHHIIIFHHIHHDHIAIF?HIHIEIIHHI<GHHIHFH;HEHGH4HFAHGDEFGCFG*D?HDFGGEFBAG*EFEGFEEGCGGF=EGFGGGGFGEEGGGGGFG6)EGFGCCGGGC4EGG8EEGGCCEGGAGFG\n+@chr1-153\n+CGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCCATTTAATTCGTAAACAAGCCGATACTT\n++\n+A???A?BBD<DDBDDDGCGGGFHIHHIHIIEIHFHHHF.IGIHHIIIHIIGIFIIHGHF9HGI=HCHIGHIHHDIIIIHIHIHIHGHIIHIG-HHHHIHIHDHHFGHECF@HBHGHH=GHHFDHHGEGFGGGG:G?EEEFFECG:GE3GGGG?:E*GGG:ECGCEFEGGGAE'E68?E;G@GFC1GCGFGGG8G>E?EGG\n+@chr1-152\n+GTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTT\n++\n+??A?ABBBADBEDDDD/FCGFGFIFFIIIEHFIFIIIHCIAFIHHH.HID@EIGIIHHIFIEHHHGBFIEFIHFHIIHGHHHIFHHFDEIHIDIFHDGHIHIHHDDHIHHH1FFFHHG*=FFHGDC5EFGEHG7GGDEGGEEGFG:EGFEGGGGFHGFECEFAGGGGGDGFF.E8GEEEGG8GGGEGEGGFEFGC?F:GG\n+@chr1-151\n+CCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAGCCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGG\n++\n+?5"..b"TCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTAC\n++\n+????A<BBDB@DDDBDFGCGCFIIFFHE0HHHHHHHHFIGHIIIIEH=IHIICHIHI=HIGIDIHHGIIFFHEFEIHHIFGHFHFIIIIFHG5IEHHHHGHHHHHHHFHHGHEHDFHHFG<*H?H=FEGHGDFFHEEGGGC@FEGGGFF;0G;GGGGAEF.GGFEGGGEGEFGGGFGGG?GGGGGEGGEGEFG:8EG*G;\n+@chr1-9\n+TCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAGCCAGAA\n++\n+A????,?<DDDDDDEDFCGGFFHIIHHIHIGHHIGIIHIIHIHIFGFHHFFIHIHDA7DHIHFCFHIEIHIEEFAHHGIIHIHIHD>HEEGIHH3HIHIHFHIH23HHFHGHG@HAEHHFH@EFGEEG@CEFHEG'EGFGCGFG,EGE,FGGGGECCGGEG=GGEFGG?EEEEGGE<GF?C::GGF8<?GEGG-GEFF0G\n+@chr1-8\n+AAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCAAGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGA\n++\n+9????BB8DBBED?DDAGFFFGIIIAHHIFIIHHHHFHHIHIIIIIHIH-GIIAHHCII+CHIH-HEFIIEFHA5HIHHHHIEHIHBIHIIHHI0HFEHBIIFH.F.HHGBHBEHHH7HD1GGGEGEGG=GG6HE;EEGCGGGGBGGGGE;GGGECEGGAGEGGECGGFGGEFGCGEGG+CGG=E?EGG6GEEGCGG4GE\n+@chr1-7\n+AGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTA\n++\n+???AA9BADDDBDDDBGF/FEGFIH>IHIHIIIHIHIIIHHHHIIFIIH,IIIFHHFHIIIIIGGIIIIHHFDI?-F>II?IHIIIDEHI.CHIHIHFIGHFHIFHHGHHFHFHGEHGFEGFEEDGEHHDDGFGGGEFCHAEGEEAGAGGEDEGFFEGEEGFGECG7F=CFCGCGGEE0GCECF6GGEEEGCGGF6EGGE\n+@chr1-6\n+TTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGCAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATC\n++\n+????ABB<:DDDDDDDFGGGFGHIFBHIICGHHIIHHGHHIHIHIAFEIFCFIHCIHHIHIFHFFFHHHEIGHIIHICHHFHIADI=HH+IDFHGHIIIHCIHHHH>FHHHHFHHGG,@H->:EGFGGFGHFFG>IEBDGG8G?GGFCGG?GGA?EFGGGEGEGGEGGGGGEGGEGFGGEGGEE(EGF;GEEFG2CCG?G\n+@chr1-5\n+TTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACC\n++\n+????ABBBDB@D@EEDF>F7FGEHCIHIHIHHHGIH>HEIIFHIFHHHHIHIHHGHHIHIHIGA;FHAIHIHIHGBFIHIHIHIHIHIHIHAHIDHCHHHFHFEFHFGEHEHGHHHG:G@HEDF@EHDHGHEDEFFGGG.E:GGGEGEEEFDGGGGGFGG?GAEAGGGEGGGGGFF:EGEGEGE6D>GG*GGG*C:F*0G\n+@chr1-4\n+TGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAAT\n++\n+?A??=B<B-DDDDDDBFGGGCGIIIHHFHIIHIIIIH/FHHIIEFGHIFIHFHF8HHHIICHHIHHHIHHFIHCIIHGHHFIIIIIHHEFGFIIIHFHFH+HHHHGDHHGGHFDHEHBH?FHECHEG1GGGGDCCGFEGCGH)'AGD8GG@?GEEGGGGEFE*GGBF?E:EC8ECBGECGEEGAG:GEGFGEGG:EGFGE\n+@chr1-3\n+AAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTATCGACAACAAGAAGCAGCCTTATGGCCGTCAACATACATATCACGATGTTCAACCACTAATAGG\n++\n+?9AA?BBBDDDDDDBDGFGGCGHFHHHHIFFIFEHHIIHHHHIIEBGDGIIHHEIAHFHHHHEHHHEHHHIF5IAEIHGFGAHIFGIHHHEIIGHHIHIHFHHFHHGHDHHGHGFHHEHEGHCFCG7ADHGFGEGFBB3EGGGGEHF8EEEG:EEC-EECEGG8EEFFFFGEEEGGEFGGG*FGEGGE?EGECEFFG*:C\n+@chr1-2\n+ATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTTTGCCGAAGAAGCTGG\n++\n+,?A??B?ABDD<B?DEFGGGGGHHFEHEIIIIAHHHFIHHIFHFGDFHDEGI0IDFIHHIF8IFHHHICDF>HIFHIHFIHHHHHIIGCEFGEEHHHDHHFHHHGIDFGGEHHHGEGEGGFHHGHFEGGGEGF=EG:F;EGDEG*G/F9G9EEG(EEE*G*EGEE*EEFEGEFD?G6A:<G?FA1FFEGFEGGGDE(FGE\n+@chr1-1\n+ATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTC\n++\n+A???A7?B<DDDDDDBGEFFFGFGHHHCIHIIICIICDHE/EIIIH>HHGHIFIIIHHIEHIIHIIGIII-IIIIIFIIICHHHHFDIHIIFHIHHH@HHIHHHFGHHFHEF?GHGHHDFH?GFHFHGFEDEGGB?EGGFBGGDEFGDEGGGGDEGFEEGGGEFEEGG<ECE?0FFFAGG+EGGFAG:F?6EGEG?GEGG\n" |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.illumina.01.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.illumina.01.sam Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b"@@ -0,0 +1,163 @@\n+@HD\tVN:1.4\tSQ:unsorted\n+@SQ\tSN:chr1\tLN:1626\n+@PG\tID:01\tPN:ART_Illumina\tCL:art_illumina -i test-data/input.fa -l 200 -f 20 -o test-data/art.illumina.01 -m 200 -rs 42 --insRate 0.00009 --insRate2 0.00015 --delRate 0.00011 --delRate2 0.00023 --samout \n+chr1-160\t0\tchr1\t48\t99\t183=1X16=\t*\t0\t0\tGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTATCTTTATCGCTTTTACC\t?A?9?BB?@D@DDDEBFGGGGGIHHIIIFEFIIHIHHGHHIHIHHIIIHHHFIDIFIHFFIHCIIIDFFHHFFHIHHHFIIHCIHIEHHHIGIIBHIEIDHHGIDDGHHHHHEHGHGGG3HFFHEFFCGFEE;GEDGGGFFE9G?FGGBCG?FGGGEEGGGDEGGG<GFG?GEBGFGE?GEGG(GGG=AG:GGEGG?GEG\n+chr1-159\t0\tchr1\t569\t99\t145=1X54=\t*\t0\t0\tCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCCTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAG\t?????B?BDDBDBEDDFGGGGFHEHIIIHIHI9IIHICFHIHIIHIIIHIH>CIEHIIFFHH?HH5EFDGHIIHI)DHIHHEHHBHIIHC=?HCH+DHFF?HBHFIHFHGHIHFGHHFGFFGG+GB,GHEHH82GEIEGFGEFEG)<GEGCG?GGGGGEG;EG?EEEEG6GFFEGDE6GGG?GGGEEGEGEEEGFGEG?0\n+chr1-158\t16\tchr1\t472\t99\t48=1X151=\t*\t0\t0\tCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGGTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGC\tEF?EE:.60FGE6EGAEE*GE:G*+GGAEECGC;EE4EEGFEGGGEBF0GCE;GEGFEGEABEG2H1FHHHGGEGEFEFGHEDEFHH@FH+FCHHH5DHGFHIFIHIHHDHHIGGGHEB-IHHHHIDIIIH=IGGFFIFIFFHHIFFHHHHECIHIIHGIIEIHEHIHIAHIHFHFIIGFFGGF<?DDDBADBBB?AA?A\n+chr1-157\t0\tchr1\t480\t99\t200=\t*\t0\t0\tCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTAC\t=??9?BB=DD@DDDDEFGFFEGFHHHIII>HII=IHIIHHIHCAIH@HGFIHI>IFHHDHHHGEHFHFE?IIHIIHDIIHFII=IHFHEHIHIAIGGHHHHFF*IEHBDGGFDFFH7HED,HHH<GEFHGGE,=EIEG:EEFGEGCEGGFAGFGGGFGGFGGGGGEG?BGFFEEGCFCAEGE?ECGGGGGCEG??FEGGF\n+chr1-156\t0\tchr1\t492\t99\t200=\t*\t0\t0\tGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGT\tA???<BBBDDDDDBDDGCFCFGHHII>FBHI9HDIHIHHHBDIHHHI@HHFIDIFIIFFIHIIEIHIIIHFIHFHIHHIII*IIIIIHECFIIIIIHHHG6IFHCHFHICHHCFHHEHFFHGCGF;GHGEEGEGEEDFHCGG*GGGGCFGFEEGGGGGGFG;EAGFFG*F6G?:E:G0CEGGFEEFDC>:G*?GAGEGGE\n+chr1-155\t0\tchr1\t460\t99\t200=\t*\t0\t0\tTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCC\tA??AABBBDDDDDDDBCFGGGGH>FIIICEHCH7IGIIDHHHFGIIH>EDIIIHIDHI=HIHHFHHHFGHHI=IEIHH-HIIGHH5HIHHGHDIHHFDHHHFHHIHHFCHHHHEF?EHHHHDFH3BFEECHHEEGEGEGGHFGGG0GH*GGGGEFGEG?G0GGEECG=FE/EGG:GGGGGEGE9GGGEGG9GGGECG8EE\n+chr1-154\t16\tchr1\t984\t99\t200=\t*\t0\t0\tCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTA\tGFGAGGECCGGEE8GGE4CGGGCCGFGE)6GFGGGGGEEGFGGGGFGE=FGGCGEEFGEFE*GABFEGGFDH?D*GFCGFEDGHAFH4HGHEH;HFHIHHG<IHHIIEIHIH?FIAIHDHHIHHFIIIHHIIHCHH5HGHGHHIHHIH0F0IHHIGHFEIFIFICIFIHIIHEF>FHIFAGGCFBDBDDDDDB?B????A\n+chr1-153\t16\tchr1\t1297\t99\t27=1X172=\t*\t0\t0\tAAGTATCGGCTTGTTTACGAATTAAATGGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCG\tGGE?E>G8GGGFGCG1CFG@G;E?86E'EAGGGEFECGCE:GGG*E:?GGGG3EG:GCEFFEEE?G:GGGGFGEGHHDFHHG=HHGHBH@FCEHGFHHDHIHIHHHH-GIHIIHGHIHIHIHIIIIDHHIHGIHCH=IGH9FHGHIIFIGIIHIIIHHIGI.FHHHFHIEIIHIHHIHFGGGCGDDDBDD<DBB?A???A\n+chr1-152\t0\tchr1\t24\t99\t200=\t*\t0\t0\tGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAG"..b"EGGGFF;0G;GGGGAEF.GGFEGGGEGEFGGGFGGG?GGGGGEGGEGEFG:8EG*G;\n+chr1-9\t0\tchr1\t1226\t99\t193=1X6=\t*\t0\t0\tTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAGCCAGAA\tA????,?<DDDDDDEDFCGGFFHIIHHIHIGHHIGIIHIIHIHIFGFHHFFIHIHDA7DHIHFCFHIEIHIEEFAHHGIIHIHIHD>HEEGIHH3HIHIHFHIH23HHFHGHG@HAEHHFH@EFGEEG@CEFHEG'EGFGCGFG,EGE,FGGGGECCGGEG=GGEFGG?EEEEGGE<GF?C::GGF8<?GEGG-GEFF0G\n+chr1-8\t0\tchr1\t396\t99\t99=1X100=\t*\t0\t0\tAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCAAGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGA\t9????BB8DBBED?DDAGFFFGIIIAHHIFIIHHHHFHHIHIIIIIHIH-GIIAHHCII+CHIH-HEFIIEFHA5HIHHHHIEHIHBIHIIHHI0HFEHBIIFH.F.HHGBHBEHHH7HD1GGGEGEGG=GG6HE;EEGCGGGGBGGGGE;GGGECEGGAGEGGECGGFGGEFGCGEGG+CGG=E?EGG6GEEGCGG4GE\n+chr1-7\t0\tchr1\t1131\t99\t200=\t*\t0\t0\tAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTA\t???AA9BADDDBDDDBGF/FEGFIH>IHIHIIIHIHIIIHHHHIIFIIH,IIIFHHFHIIIIIGGIIIIHHFDI?-F>II?IHIIIDEHI.CHIHIHFIGHFHIFHHGHHFHFHGEHGFEGFEEDGEHHDDGFGGGEFCHAEGEEAGAGGEDEGFFEGEEGFGECG7F=CFCGCGGEE0GCECF6GGEEEGCGGF6EGGE\n+chr1-6\t0\tchr1\t971\t99\t120=1X79=\t*\t0\t0\tTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGCAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATC\t????ABB<:DDDDDDDFGGGFGHIFBHIICGHHIIHHGHHIHIHIAFEIFCFIHCIHHIHIFHFFFHHHEIGHIIHICHHFHIADI=HH+IDFHGHIIIHCIHHHH>FHHHHFHHGG,@H->:EGFGGFGHFFG>IEBDGG8G?GGFCGG?GGA?EFGGGEGEGGEGGGGGEGGEGFGGEGGEE(EGF;GEEFG2CCG?G\n+chr1-5\t16\tchr1\t496\t99\t200=\t*\t0\t0\tGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAA\tG0*F:C*GGG*GG>D6EGEGEGE:FFGGGGGEGGGAEAG?GGFGGGGGDFEEEGEGGG:E.GGGFFEDEHGHDHE@FDEH@G:GHHHGHEHEGFHFEFHFHHHCHDIHAHIHIHIHIHIHIHIFBGHIHIHIAHF;AGIHIHIHHGHHIHIHHHHFIHFIIEH>HIGHHHIHIHICHEGF7F>FDEE@D@BDBBBA????\n+chr1-4\t16\tchr1\t580\t99\t200=\t*\t0\t0\tATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCA\tEGFGE:GGEGFGEG:GAGEEGCEGBCE8CE:E?FBGG*EFEGGGGEEG?@GG8DGA')HGCGEFGCCDGGGG1GEHCEHF?HBHEHDFHGGHHDGHHHH+HFHFHIIIFGFEHHIIIIIFHHGHIICHIFHHIHHHIHHCIIHHH8FHFHIFIHGFEIIHHF/HIIIIHIIHFHHIIIGCGGGFBDDDDDD-B<B=??A?\n+chr1-3\t16\tchr1\t17\t99\t200=\t*\t0\t0\tCCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTT\tC:*GFFECEGE?EGGEGF*GGGFEGGEEEGFFFFEE8GGECEE-CEE:GEEE8FHEGGGGE3BBFGEGFGHDA7GCFCHGEHEHHFGHGHHDHGHHFHHFHIHIHHGIIEHHHIGFIHAGFGHIEAI5FIHHHEHHHEHHHHFHAIEHHIIGDGBEIIHHHHIIHHEFIFFIHHHHFHGCGGFGDBDDDDDDBBB?AA9?\n+chr1-2\t16\tchr1\t658\t99\t15=1X184=\t*\t0\t0\tCCAGCTTCTTCGGCAAAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAAT\tEGF(EDGGGEFGEFF1AF?G<:A6G?DFEGEFEE*EEGE*G*EEE(GEE9G9F/G*GEDGE;F:GE=FGEGGGEFHGHHFGGEGEGHHHEGGFDIGHHHFHHDHHHEEGFECGIIHHHHHIFHIHFIH>FDCIHHHFI8FIHHIFDI0IGEDHFDGFHFIHHIFHHHAIIIIEHEFHHGGGGGFED?B<DDBA?B??A?,\n+chr1-1\t16\tchr1\t1051\t99\t200=\t*\t0\t0\tGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTAT\tGGEG?GEGE6?F:GAFGGE+GGAFFF0?ECE<GGEEFEGGGEEFGEDGGGGEDGFEDGGBFGGE?BGGEDEFGHFHFG?HFDHHGHG?FEHFHHGFHHHIHH@HHHIHFIIHIDFHHHHCIIIFIIIII-IIIGIIHIIHEIHHIIIFIHGHH>HIIIE/EHDCIICIIIHICHHHGFGFFFEGBDDDDDD<B?7A???A\n" |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.illumina.02.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.illumina.02.sam Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b"@@ -0,0 +1,163 @@\n+@HD\tVN:1.4\tSQ:unsorted\n+@SQ\tSN:chr1\tLN:1626\n+@PG\tID:01\tPN:ART_Illumina\tCL:art_illumina -i test-data/input.fa -l 200 -f 20 -o test-data/art.illumina.02 -m 200 -rs 42 --insRate 0.00009 --insRate2 0.00015 --delRate 0.00011 --delRate2 0.00023 --samout -p --mflen 300 --sdev 10 \n+chr1-160\t99\tchr1\t44\t99\t200=\t=\t156\t312\tGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTT\t?A?9?BB?@D@DDDEBFGGGGGIHHIIIFEFIIHIHHGHHIHIHHIIIHHHFIDIFIHFFIHCIIIDFFHHFFHIHHHFIIHCIHIEHHHIGIIBHIEIDHHGIDDGHHHHHEHGHGGG3HFFHEFFCGFEE;GEDGGGFFE9G?FGGBCG?FGGGEEGGGDEGGG<GFG?GEBGFGE?GEGG(GGG=AG:GGEGG?GEG\n+chr1-160\t147\tchr1\t156\t99\t18=1X16=1X6=1X71=1X85=\t=\t44\t-312\tTCGGCACAAGTACCAACCGGAACGTGAAAAAGCGTGCTGCGTATAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAATTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAA\tAE?#A4GAECEEGEEG(G0;F:?GGC:E8FEC?8:#ECF'E*#GEEFG=GGG=GEE@EGGEE@BFGDFGF'FEEDHEGHCH/EHG4HF+EFBHFHI*HH;BHFH(H-C)HH-FF'A.FIIF4DIFCFIHIHHHIHIHEFIFG-DDHBC-IHFH/HHHGDIFI5IFEHHIII0CF>8HEFFEFG@D<BD9BDDBB??????\n+chr1-158\t99\tchr1\t368\t99\t200=\t=\t476\t308\tCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCG\t????A?BBDDDEDABDGFA>FGIHHIIIFHFHIHAIHIHEHIEIIGHIIHICEHHHHFEIHHFFIFIFFGHI<HIIIDHHHHHH-BDHGGGIHHDGHIHIFHHFFHD5HHGCF+HF@HHFECEHGFEEEGEGGHGIF0H2GEBAFGEFGEG;ECG0FAEGGGEFGEE3EE:CGCEEAGG++G:EG*EEAGE6EGF06.:E\n+chr1-158\t147\tchr1\t476\t99\t44=1X4=1X25=1X2=1X27=1X93=\t=\t368\t-308\tTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGGTAGTATCTTCACGCTTACCGTCTTTCCAGAGATGGTTCCAAGTATCGGCTTGTTTACGAATAAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAA\tG6E/EE<CG(G(?G((G:;GG:GGGE?(G>EFEGG:G?EGFG#A(GG(B)'1AEEGE*D@FGGD:FFGFFHEH@F(FG#BHGFEHFGDEGFEHDHD.IIBHHIIHH)E*FHFH4HHCIIII@HFCIEICEEI'CIFHHHHHHH@IHHDIHFHIH9EHIHGF7IHHFH@I@IHHIHHIIGFGFFF?<DADDDDBBB???<?\n+chr1-156\t99\tchr1\t624\t99\t200=\t=\t739\t315\tAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCC\t???A?BB=DDEDDDDDFFGGCFEHIHHII;FCHI9HDIHIHHHADIHHHI@HHEIDIFIIFFIHIIEIHIIIHFIHFHIHHIII*HIIIIHDCEHIIIIHHHG5IFHCHFHICHHCFHHEHEFHFCGF;GHGEEGEFEEDFHCGG*GGGGCFGFEEGGGGGGFG;EAGFFG*F6G?8E:G0CEGGFEEFDC=:G*?GAGE\n+chr1-156\t147\tchr1\t739\t99\t200=\t=\t624\t-315\tCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCGCCCTGT\t(9FEFECE(G?EGGG).EG/(GG?G0CED;GEC8*.EECE)EEGFC=GE,AFGFG@F@GGGFEDFEG4EGHBGBFGG=GH=FHG+GFHF,FF=HHF+HCDIHH@FGIIIBIGHDDECFEIIHIHIHEHIGHIDBBHGHIHHHDC-HIDGH>EHCF>HIA=EHHHHFHIBCEGHHEIFEAC>GGFDDEDDDDDB@<?=???\n+chr1-154\t83\tchr1\t1087\t99\t200=\t=\t989\t-298\tATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAG\tGGEE8GGC1CGGGCCGFGE(6GFGGGGGEEGFGGGGFGE;EGGCGEEFGEFE*GABFEGGECI>C*FFBFEECFH@EH3GFHEH9HFHHHHF:IHHHIDHGHH?FIAHHDHHIHHFIIIHHIIHCHH5HHHHHHIHHIG/F/IHHIFHEEIFIFIBIFIHIIHEF?FHIHAHHEHEIEGGFGFGBDDDDDEDBBBA?A??\n+chr1-154\t163\tchr1\t989\t99\t31=1X111=1X18=1X6=1X1=1X28=\t=\t1087\t298\tTTCCAGAAATTGTTCCAAGTATCGGCTTGTTCACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAAAAATTGTTCCAAGTATCGCCTTGTTCAGGAATTAAATCGAAGGAAGCGGTAAAAAT\t???A?>BBDDDD-DBDGFFGFFIHHHIIIHI8IE5IGIG@H9IHH7EGGHEIFAHIHFHFCHGCIH,FFGH-HFHCFIHIH+I7BHIH+HCCHHFHBFIHHFHFHEHDED@+D.9FG/CGHEHE1BHCFGGEDEG3GEC=FE@(ECE;DFG@6FE<GEEECA(EGGGEA,G(E*(/CE?G:.(?FEEE:(8E?:;/*(GA\n+chr1-152\t83\tchr1\t635\t99\t62=1X137=\t=\t536\t-299\tTTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGA"..b"\t1256\t-298\tAAGCGGTAAAAATTTTTATTTTTTCTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATGGGCTTGTTTACGAATTAAATCGAAGTTACCG\tEA/E6FCEC:EGGGEEEACDEC8G(?E:GGFG:C;E??GECG8?7B?:GHBFDG8GCGE*GDFE1HGFG*E:GGHHECHAGEFFGEED)=ECDHHF:H=HEH?HFH;DHGH.ICDEFCIHIHFHH4FFFGHHEFHAAHHHHGHHHIEHFFF/IFGEHIHICDIBE-HH,AH0HIEEHICFF.FFDDDDDDD-BBB?,??A\n+chr1-8\t83\tchr1\t787\t99\t32=1X167=\t=\t692\t-295\tGCTTGTTTACGAATTAAATCGAAGTTACCGTCCTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGT\t6EGEEGCEGEGGDCGGE6FG+(E;EGGEEGGG/G<GGGFE:GGEGGEG0FEGGGEHEGFGGHG7IDFGGGFGHEHDGHEAHGHGHFGHHHIH3GHFGHF7IDIHHIIHIHHHIGDIHIH?HHHI=IIHIEDBHIICCFDHIDGIIFGHHEIIHHIIDIGIIFFHIHIHH9FIF9IHIFGGGF+GDEDDB@DBBBB?=A??\n+chr1-8\t163\tchr1\t692\t99\t115=1X33=1X50=\t=\t787\t295\tGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCCAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTACCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTG\t?????-BBDDBB@DD@CGFGGGIF-HHFHCGFHIHIIEFFIHH=AEEEDH=7HIFHH=ICEEHI=AIIFBDEIHF#=HEFFFFIEHHIIF-CHH@HH+H=CIF.HH.HFECHHGH+EDHDGHFEFF@DFHEGGGGFFGE'BGG*EF1GG#0EGE'E8<GG6;E*(EFECAEE1CFE*GBGGCEG(E>6G*GG>E(?(FGA\n+chr1-6\t99\tchr1\t790\t99\t200=\t=\t896\t306\tTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTT\t??A??BBBBDDDBBDBGGEEGFIHIHHFIEHIHGEHEIIHFHIHHHIHGIHIHFH@HDFHFHFHIGF?IFHFHAIIHHHIFIIHAGHHHIEHHGGHHHHHHHHFHHFFHH;>GHHG>ECGAEBGGF)EHFGGEG:C;EFGGFGEEGGEG*GGEGFGEF?EGG;EF?EGEGFEFEGG*GBGG*G*GEGEG*GGGG:EGF:E\n+chr1-6\t147\tchr1\t896\t99\t15=1X11=1X130=1X25=1X15=\t=\t790\t-306\tTGTCTAACTTTATCGATGGTTTTGTCTTACTTTATCGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAACTTGTTCCAAGTATCGGCTTGTTTACAAATTAAATCGAAGTG\tEEEG*CGGGA?E8/G#CE(G0*GE<EE*FCGEE?G0EEE?:=E;FCGEEG-EG?/;G:@*GEGEGEECEEFHFDC8HHF,?HEGEHHHCHEGHEHF+,HFHEHFGDHHHHHHGGHHHEGHIIHFEIHHAFHGIHHHFI;FBDHIHF@-GG7GHHHHHH+HHAHC?IH=IIHFHFHHIHGGGFGG--D--D-B-BB,,???\n+chr1-4\t99\tchr1\t709\t99\t200=\t=\t828\t319\tGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTAT\t????AB<B@DBBD@DEFGGGFFFHHIII;HCIIIHIHHHHFIIHIIHIIDIEHEHIIFIIHIIHHCHIHIHIHAGDII7III-FCH8?IH9HHH;5IHIGDG-HHFHG@HFHHFEHHEHHHHEFGEFFGFGGGGED',G;GG/EED4BEGGEGCGAFCFAGCGEGEFGEA(9:0EEDEEGCE6GFGGG(E?FG;GFEEFG\n+chr1-4\t147\tchr1\t828\t99\t67=1X104=1X27=\t=\t709\t-319\tATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTCTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTCTTCCAAGTATCGGCTTGTTTACGAATT\tCCCC'E:A:AGGG:?8/CCGGGFG:EA>AEG*EG:EEGEEEFEE.GGCEE(;FAEG;FDA;8GGDD;(DGHHFFHGE@EDHHHH3HGHFCFEHGHE'F.F8E<IDHF6DHHDHI@BEFHCFIHGHEDHFHEC=FHAFIGIIH=GHHH8IHHIEEDIIHFBHIHI+HHGIIIF,FIHIIF>FFFFBDDDDDDDB-??????\n+chr1-2\t83\tchr1\t482\t99\t200=\t=\t376\t-306\tAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCA\tCGGF:E?EFE*GCEEGGCDCEAEFAEEFFGGGGEEGGGEF?GFFFCFGG?GG)+=GGGGGGEDBGGEEGGHG?F,HFFHH@HHFEFIHHFHHHHHFHHFDHHHGIHIHFC/IHHHFHIGEHIIHIH5IIIHHHIHHHIHHHHHHAHIGFHH9FHHBIHFGAHIHHIIIG@EEHIHIHIGFC?GCDBDDDDBDBBB????=\n+chr1-2\t163\tchr1\t376\t99\t71=1X37=1X1=1X88=\t=\t482\t306\tCGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAGAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCATTTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTT\t???5,<?BDBDDD?DBF6FF8G0H;FHH?HIH@HHAIIHFFH.*HHFDHIHHIHEIBIHEFHIHFHHBHEH+IH,HCFHIFHHEF(EHIIIFHHIHHH+DHHDH9DDEH+D.GHEIHGFHFEC9D9HGFH+EEC@FEEG?E?B4;F27AF(G0?GCCG=(G?EEEF,/;(AF<EGC;GEEEEAEF?*0:?66EEE.CE:E\n" |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.illumina.021.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.illumina.021.aln Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,244 @@\n+##ART_Illumina\tread_length\t200\n+@CM\tart_illumina -i test-data/input.fa -l 200 -f 20 -o test-data/art.illumina.02 -m 200 -rs 42 --insRate 0.00009 --insRate2 0.00015 --delRate 0.00011 --delRate2 0.00023 --samout -p --mflen 300 --sdev 10 \n+@SQ\tchr1\t1626\n+##Header End\n+>chr1\tchr1-160/1-1\t43\t+\n+GTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTT\n+GTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTT\n+>chr1\tchr1-158/1-1\t367\t+\n+CGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCG\n+CGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCG\n+>chr1\tchr1-156/1-1\t623\t+\n+AAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCC\n+AAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCC\n+>chr1\tchr1-154/1-1\t340\t-\n+CTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGAT\n+CTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGAT\n+>chr1\tchr1-152/1-1\t792\t-\n+GAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAA\n+GAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCATTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAA\n+>chr1\tchr1-150/1-1\t1209\t-\n+AAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCAT\n+AAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCAT\n+>chr1\tchr1-148/1-1\t1170\t+\n+GAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTT\n+GAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTT\n+>chr1\tchr1-146/1-1\t1129\t-\n+CCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACT\n+CCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACCATTTATGGAAAGACGGTAACT\n+>chr1\tchr1-144/1-1\t73\t-\n+CGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTT\n+CGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAA'..b'TCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGATGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGC\n+>chr1\tchr1-18/1-1\t1168\t+\n+TCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTT\n+TCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTT\n+>chr1\tchr1-16/1-1\t468\t-\n+AAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAA\n+AAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAA\n+>chr1\tchr1-14/1-1\t1035\t+\n+GTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGT\n+GTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAGAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGAATGGT\n+>chr1\tchr1-12/1-1\t1141\t+\n+CAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGT\n+CAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACTATTTAAATCGAAGTAGAACTTCATGT\n+>chr1\tchr1-10/1-1\t1255\t+\n+GTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTA\n+GTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTA\n+>chr1\tchr1-8/1-1\t640\t-\n+ACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGC\n+ACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAGGACGGTAACTTCGATTTAATTCGTAAACAAGC\n+>chr1\tchr1-6/1-1\t789\t+\n+TGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTT\n+TGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTT\n+>chr1\tchr1-4/1-1\t708\t+\n+GTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTAT\n+GTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTAT\n+>chr1\tchr1-2/1-1\t945\t-\n+TGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCT\n+TGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCT\n' |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.illumina.021.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.illumina.021.fq Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b"@@ -0,0 +1,320 @@\n+@chr1-160/1\n+GTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTT\n++\n+?A?9?BB?@D@DDDEBFGGGGGIHHIIIFEFIIHIHHGHHIHIHHIIIHHHFIDIFIHFFIHCIIIDFFHHFFHIHHHFIIHCIHIEHHHIGIIBHIEIDHHGIDDGHHHHHEHGHGGG3HFFHEFFCGFEE;GEDGGGFFE9G?FGGBCG?FGGGEEGGGDEGGG<GFG?GEBGFGE?GEGG(GGG=AG:GGEGG?GEG\n+@chr1-158/1\n+CGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCG\n++\n+????A?BBDDDEDABDGFA>FGIHHIIIFHFHIHAIHIHEHIEIIGHIIHICEHHHHFEIHHFFIFIFFGHI<HIIIDHHHHHH-BDHGGGIHHDGHIHIFHHFFHD5HHGCF+HF@HHFECEHGFEEEGEGGHGIF0H2GEBAFGEFGEG;ECG0FAEGGGEFGEE3EE:CGCEEAGG++G:EG*EEAGE6EGF06.:E\n+@chr1-156/1\n+AAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCC\n++\n+???A?BB=DDEDDDDDFFGGCFEHIHHII;FCHI9HDIHIHHHADIHHHI@HHEIDIFIIFFIHIIEIHIIIHFIHFHIHHIII*HIIIIHDCEHIIIIHHHG5IFHCHFHICHHCFHHEHEFHFCGF;GHGEEGEFEEDFHCGG*GGGGCFGFEEGGGGGGFG;EAGFFG*F6G?8E:G0CEGGFEEFDC=:G*?GAGE\n+@chr1-154/1\n+CTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGAT\n++\n+??A?ABBBDEDDDDDBGFGFGGEIEHEHHAHIHF?FEHIIHIFIBIFIFIEEHFIHHI/F/GIHHIHHHHHH5HHCHIIHHIIIFHHIHHDHHAIF?HHGHDIHHHI:FHHHHFH9HEHFG3HE@HFCEEFBFF*C>ICEGGEFBAG*EFEGFEEGCGGE;EGFGGGGFGEEGGGGGFG6(EGFGCCGGGC1CGG8EEGG\n+@chr1-152/1\n+GAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCATTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAA\n++\n+?????5BBDDDDDDDDGGFCGCIHHHH/FCHHIFIFGIIIEHFIFIIIHBI?FIHHH-HIC@EIFIIHHIFIEHHHGBFIEFIHFHIIHGHHHHFHHEDDIGHDHFHDFHHGHHHDDGHGHG.EEEHHF);FEGGDB3EFGDGG8GGDEGGEEGFG8EGFEGGGGFGGFECEF@GGGGGDGFF.E8GEEEGG6GGGEGEG\n+@chr1-150/1\n+AAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCAT\n++\n+??A??=B?EDDDDDDDFEGFGGHHIHIFHHIIIIH=IDFIAHIIHDHIGHBGGHHIIHFEIDIH>HH5HIIHHIHIIIHFGHHHI=HIHHIGIIIIGHHHFHHHHHFHHHH.DEH=F=HHHH=FGHEHF@GGHBEFIG?GEGGF@EGEEEA>ACFGAGGGGEEGFGEFEFCGEGEFEGGGE)GECE@EAGG:?EGG'E?E\n+@chr1-148/1\n+GAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTT\n++\n+?AAA?BBBDDDDDDDDFCGFFFFIF@HIIIIFIIEFHHIIHHDHHIIIIHFIIHIIHGHHIHHHGHIHEHHHIHIHFHHIIHIH.HHHIEIIHHHI-EHEHCHHHHEHFHHFDHHDEGG>GFHEHEEGFHHE:G*GECFGGDGGGG;=EGB*A0EGEGGGGGAGEAEGEGE;6EGGC6)GGAGGAGGFFEE?AEGFG<D*\n+@chr1-146/1\n+CCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACCATTTATGGAAAGACGGTAACT\n++\n+?????BBBDDDD?BDDCFGGGGHIIFIFIEIFIHHIFIHIHAIHGHHHI58IIHHIIHIHHIIHEAFGIHFHIIIIHGHHGHGFIIIHGIIIHHEHHH8H?FIHEIHHEIDGFGH>FHGGGFF=@GGGHGFH7EGDEEGFE09GFGGGFEEGGG8GBGG<GH:GEGGGCGEGGEEEA1.GEEG*GGG>FECCEDGG:GFC\n+@chr1-144/1\n+CGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTT\n++\n+??A?AB>BDDDDDDDDFGGGGGIFEIHAFIIIFIFFHGIHIHIHGIHHIFGHIIIIHDIIIIHAHHFEIIHIHHHIHIHAFIHIHHIFHI@HIHHHCHHIHCHFHDBICH9FFHFHCEDHDEBHGGEGEHG5,FEGGEGGGG6CEE@FGEBGFEGEGG0CGGCGDFFGGCGGGG0CG?GFEGEG:GAGGC?GGEGCGC:G\n+@chr1-142/1\n+GAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTT"..b"TTTTTTCTCACTTCTGTTACTCCAGC\n++\n+A?A??AB<DDDBDEDDFFGGGGFHHCHIIIIIDIII>HIIIFBIFHEH5IFIHHEIHIIGHHIIGIGGD-FIFGIHIIIIHIHEHIEIHIF7GEHHI=I@@D:FHHHFHFEDEHFHGGGHEHHG7GE*GC=GE@HGGF:EGDG'GGGEEEEG=CEAGFAFGCCGECGCGGGF*DFGB>EFEGDEGFFG6GAGGEGCFEED\n+@chr1-18/1\n+TCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTT\n++\n+A??A?BBB:D@DDDEDFGF/FFIFAHHHEIHEHGDIGHHGHIIIFHFIHHIHIHII@GHF-7GHGHDHIIIHHHEHBGGHI@5HHIHHDIIDI?HDHHHHFHHHIIE*FGGHGGG5EHGFGFGFFHFHGCEHGBFF?GFEBGEGEGGGFEG*GEE6EGG9(DGGEFCECGGEG;08GGGC6GCG:GGFEGFEGF>C4EGC\n+@chr1-16/1\n+AAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAA\n++\n+=?A?ABBBD<DDDD@DGG8GGFHHHIHIHIIHHHAHHHDGHIIIHCIGIIFI+IGHHIHII=HFHHIIIIFHIFFFGIHEHIIHHF@I/HIIHE-=HHIHHEIFG@HHHIHFHHH?HHHHFHGHHGHFFG5HHHDEIGHGGGDEE?EEHEAEGG;GEGEGGEGGEGHEGGCCGEE9FGEF8EG6CGGGGEEEGA?:<?EG\n+@chr1-14/1\n+GTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAGAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGAATGGT\n++\n+5???=BBBBDDDDBDDFGBGGGEHIIHHIIIIHHHHHIIHHFHEHIIHIIEGIFHIEIFIICHHH,IIIIHHAIHHIH5HHEIHHHFHFHHCHDHDDHCCFHHFGFHCHHHFHFHFHBHHGFH=FFDGGEG<GEEDF?EEGGGGDG@GG*GEEGEGAFFGGE*GGEGAFCFE;E?EGCAFDGGGF?FGG*GECG*G:GGF\n+@chr1-12/1\n+CAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACTATTTAAATCGAAGTAGAACTTCATGT\n++\n+???A?BBB:E@DDBDDFEGGFFIIIIH;FIEHIIHFHDIHDCFHGCIIFIHHAHEIFIIHHI-HHHHFHHIIIADIEIIHHHIHI@GCICHFIHHH=FHHHHGHHHGHF@EHGCFEDHFHHHDGFHEF:C8GGFEFIGEEGF?AGFEGAGGGF.GGGGCG:DGGG.EGGGGEE(F+EGGGFGEGG4GGGGF/CCGGEEEG\n+@chr1-10/1\n+GTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTA\n++\n+?????BBBDDEDDDDB;CGGGFICIIFIIIIIIHIIH7IIIIFH@IIBIH=HIIHHIIEHH=HFHD?,EIIIHIFHIIHHFHIIHHFFEHIIHF/<H@=HHHFDHHHHGI7HGHGHFHAGEHEG?EGFFGHCFEEEGGGEGGGEGFDDEEGFA;?DEGGGFGG0GEEG=CGG4GCGEE:FGG'GG;0EGG?EE;EAEGGE\n+@chr1-8/1\n+ACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAGGACGGTAACTTCGATTTAATTCGTAAACAAGC\n++\n+??A=?BBBBD@BDDEDG+FGGGFIHI9FIF9HHIHIHFFIIGIDIIHHIIEHHGFIIGDIHDFCCIIHBDEIHII=IHHH?HIHIDGIHHHIHIIHHIDI7FHGFHG3HIHHHGFHGHGHAEHGDHEHGFGGGFDI7GHGGFGEHEGGGEF0GEGGEGG:EFGGG<G/GGGEEGGE;E(+GF6EGGCDGGEGECGEEGE6\n+@chr1-6/1\n+TGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTT\n++\n+??A??BBBBDDDBBDBGGEEGFIHIHHFIEHIHGEHEIIHFHIHHHIHGIHIHFH@HDFHFHFHIGF?IFHFHAIIHHHIFIIHAGHHHIEHHGGHHHHHHHHFHHFFHH;>GHHG>ECGAEBGGF)EHFGGEG:C;EFGGFGEEGGEG*GGEGFGEF?EGG;EF?EGEGFEFEGG*GBGG*G*GEGEG*GGGG:EGF:E\n+@chr1-4/1\n+GTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTAT\n++\n+????AB<B@DBBD@DEFGGGFFFHHIII;HCIIIHIHHHHFIIHIIHIIDIEHEHIIFIIHIIHHCHIHIHIHAGDII7III-FCH8?IH9HHH;5IHIGDG-HHFHG@HFHHFEHHEHHHHEFGEFFGFGGGGED',G;GG/EED4BEGGEGCGAFCFAGCGEGEFGEA(9:0EEDEEGCE6GFGGG(E?FG;GFEEFG\n+@chr1-2/1\n+TGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCT\n++\n+=????BBBDBDDDDBDCG?CFGIHIHIHEE@GIIIHHIHAGFHIBHHF9HHFGIHAHHHHHHIHHHIHHHIII5HIHIIHEGIHFHHHI/CFHIHIGHHHDFHHFHHHHHFHHIFEFHH@HHFFH,F?GHGGEEGGBDEGGGGGG=+)GG?GGFCFFFG?FEGGGEEGGGGFFEEAFEAECDCGGEECG*EFE?E:FGGC\n" |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.illumina.022.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.illumina.022.aln Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,244 @@\n+##ART_Illumina\tread_length\t200\n+@CM\tart_illumina -i test-data/input.fa -l 200 -f 20 -o test-data/art.illumina.02 -m 200 -rs 42 --insRate 0.00009 --insRate2 0.00015 --delRate 0.00011 --delRate2 0.00023 --samout -p --mflen 300 --sdev 10 \n+@SQ\tchr1\t1626\n+##Header End\n+>chr1\tchr1-160/2\t1271\t-\n+TTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGA\n+TTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATAATTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTATACGCAGCACGCTTTTTCACGTTCCGGTTGGTACTTGTGCCGA\n+>chr1\tchr1-158/2\t951\t-\n+TTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTA\n+TTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTTATTCGTAAACAAGCCGATACTTGGAACCATCTCTGGAAAGACGGTAAGCGTGAAGATACTACCCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTA\n+>chr1\tchr1-156/2\t688\t-\n+ACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAG\n+ACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAG\n+>chr1\tchr1-154/2\t988\t+\n+TTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAAT\n+TTCCAGAAATTGTTCCAAGTATCGGCTTGTTCACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAAAAATTGTTCCAAGTATCGCCTTGTTCAGGAATTAAATCGAAGGAAGCGGTAAAAAT\n+>chr1\tchr1-152/2\t535\t+\n+TACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTT\n+TACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTCGCGTTTATGTTGGTTTCATGGTTT\n+>chr1\tchr1-150/2\t121\t+\n+TATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGT\n+TATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGT\n+>chr1\tchr1-148/2\t167\t-\n+AACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAAC\n+AACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAGGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAAATTCTGGAAAGACGGTAAGCGTGAAGAAAC\n+>chr1\tchr1-146/2\t188\t+\n+GTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTC\n+GTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTGTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTC\n+>chr1\tchr1-144/2\t1249\t+\n+TCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAG\n+TCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTT'..b'CGCTACACGCAGGACGCTTTTTCAAGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAAC\n+>chr1\tchr1-18/2\t164\t-\n+ACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGA\n+ACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGA\n+>chr1\tchr1-16/2\t840\t+\n+TCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCGCCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTAC\n+TCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCACCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTATCCAGAAATTGCTCCGAGTATCGGCTTGTTTACGAATTAAATCGAAGTTAC\n+>chr1\tchr1-14/2\t301\t-\n+CGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAA\n+CGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTGTGGAAA\n+>chr1\tchr1-12/2\t186\t-\n+GGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAG\n+GGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGACACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAG\n+>chr1\tchr1-10/2\t73\t-\n+CGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTT\n+CGGTAACTTCGATTTAATTCGTAAACAAGCCCATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAGAAAAAATAAAAATTTTTACCGCTT\n+>chr1\tchr1-8/2\t691\t+\n+GAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTG\n+GAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCCAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTACCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTG\n+>chr1\tchr1-6/2\t531\t-\n+CACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACA\n+CACTTCGATTTAATTTGTAAACAAGCCGATACTTGGAACAAGTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAGTAAGACAAAACCATCGATAAAGTTAGACA\n+>chr1\tchr1-4/2\t599\t-\n+AATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAAT\n+AATTCGTAAACAAGCCGATACTTGGAAGAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAGAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAAT\n+>chr1\tchr1-2/2\t375\t+\n+CGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTT\n+CGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAGAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCATTTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTT\n' |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.illumina.022.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.illumina.022.fq Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b"@@ -0,0 +1,320 @@\n+@chr1-160/2\n+TTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATAATTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTATACGCAGCACGCTTTTTCACGTTCCGGTTGGTACTTGTGCCGA\n++\n+??????BBDDB9DB<D@GFEFFEH8>FC0IIIHHEFI5IFIDGHHH/HFHI-CBHDD-GFIFEHIHIHHHIHIFCFID4FIIF.A'FF-HH)C-H(HFHB;HH*IHFHBFE+FH4GHE/HCHGEHDEEF'FGFDGFB@EEGGE@EEG=GGG=GFEEG#*E'FCE#:8?CEF8E:CGG?:F;0G(GEEGEECEAG4A#?EA\n+@chr1-158/2\n+TTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTTATTCGTAAACAAGCCGATACTTGGAACCATCTCTGGAAAGACGGTAAGCGTGAAGATACTACCCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTA\n++\n+?<???BBBDDDDAD<?FFFGFGIIHHIHHI@I@HFHHI7FGHIHE9HIHFHIDHHI@HHHHHHHFIC'IEECIEICFH@IIIICHH4HFHF*E)HHIIHHBII.DHDHEFGEDGFHEFGHB#GF(F@HEHFFGFF:DGGF@D*EGEEA1')B(GG(A#GFGE?G:GGEFE>G(?EGGG:GG;:G((G?(G(GC<EE/E6G\n+@chr1-156/2\n+ACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAAAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAG\n++\n+???=?<@BDDDDDEDDFGG>CAEFIEHHGECBIHFHHHHE=AIH>FCHE>HGDIH-CDHHHIHGHBBDIHGIHEHIHIHIIEFCEDDHGIBIIIGF@HHIDCH+FHH=FF,FHFG+GHF=HG=GGFBGBHGE4GEFDEFGGG@F@GFGFA,EG=CFGEE)ECEE.*8CEG;DEC0G?GG(/GE.)GGGE?G(ECEFEF9(\n+@chr1-154/2\n+TTCCAGAAATTGTTCCAAGTATCGGCTTGTTCACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAAAAATTGTTCCAAGTATCGCCTTGTTCAGGAATTAAATCGAAGGAAGCGGTAAAAAT\n++\n+???A?>BBDDDD-DBDGFFGFFIHHHIIIHI8IE5IGIG@H9IHH7EGGHEIFAHIHFHFCHGCIH,FFGH-HFHCFIHIH+I7BHIH+HCCHHFHBFIHHFHFHEHDED@+D.9FG/CGHEHE1BHCFGGEDEG3GEC=FE@(ECE;DFG@6FE<GEEECA(EGGGEA,G(E*(/CE?G:.(?FEEE:(8E?:;/*(GA\n+@chr1-152/2\n+TACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTCGCGTTTATGTTGGTTTCATGGTTT\n++\n+A?????>B<DDDDBDDFFEGGCII;HHHBIHAHHHD.IIAIHIF-HEG@HF+HAIHHGFHGHIIHHCHGIHEHHHHCI?EGGEDHE6EHF<ED+DHHFF8F8F3H,HHIHBFEFH+HHEG?EHEE;=3FF?'FF0CFG;EFD)*GF,FEEAEG:HAA8CGFEGA6GEFGGAD1AE'*EEEGG0G/0.C?D?G*6>:0GGG\n+@chr1-150/2\n+TATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGT\n++\n+??==?BBBBDBDD?<DFEAF8;HEFHIF+5IIGI1IHHHIFIHIIHHGIH=5IIEDGBHHDFFHFFGIBIHGHFFH-+C-HE=HBFIHHHDHIHGD/I7DHHHHB.FD3HDHHEF;HFHEH,=HGF/GF=HEHF9=GEEG;FF6*A@GF*<F2CEGGEEEFEGF:0GGE?FGGDG(F8GC;(*?AE0A6EGG8GEA#D?E\n+@chr1-148/2\n+AACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAGGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAAATTCTGGAAAGACGGTAAGCGTGAAGAAAC\n++\n+A?<A59B??DDD<DDBFFGG6CAEHIIF-0FIHHIIHIBHI0HIHFAIIIII@9CH#IA-+HIH#IHHHHEHHIGFEHFCHFCHFFHFFHGFDGBDFHHBH=HE)DHEH5FFFHCH;HDFFGHG@+'FGGGEHEGIGEAEEG.GECGE1,1EGGC#(CEG<@<6GG/EAB*G/6FECE:EE?6C=EC?G#81=A?(?AEE\n+@chr1-146/2\n+GTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTGTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTC\n++\n+????=<BB@D-D@DD<FFCGGFBCH6.IIH9HHI5H9I.EH;HIHEIAHC=FHDHFEHACDDHHBHFDHFGFGEBDH@FCEGHIHDF-IGDBHIHHHC<FHHH3HHEFIHHEDCDHFG*E1DFGAEFHFGD@DHC@GEFGC@;EEEEG*EC8GGG(?EGG@?*E<AG*GEG;F*G6E?.EGCFE;EEE8EACGC*/EG8E\n+@chr1-144/2\n+TCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTTTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAATGTGAAAAAGCGTCCTGCGTGTAG\n++\n+?????BBADBDB<@@@?FC*FEIHHHIHHIFDHIH+HBFHGFHHGIHHEIHICFGHIFFHEHHIHFICGEHIHFG-ECHH<DGEH+=GFG-H5HHHCFHHHGHDH6EADHHF?DHHDHBGCCDD3GHDBG(HDF>?GED(E7EEE-CFGEC.GECGCB6E08ECGFEE:GEE-G8E(E6GGEGF*?EDEE/FGE6EAF6E\n+@chr1-142/2\n+CAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACTCTACACGCAGGACGCTTTATCACGTTCTGGTTGGTACTCGTGCAGAAAAAG"..b"TTCGTAAACAAGCCGATACTTGGAAC\n++\n+<,?=??>BBD5DBB?@GGGGF/HFHEH/HIFII@7EFEHHIIG9=HDIE;IH@F+HHGHFGIEG5FHFHGBFDHGFDHEHH@DIHDHFHAHE;8HAFGH+IHFBFHGHHH=FHEEFGHHE*GG;GEDBGGBGFFH'EEF;BGE@6GGGGF:GCG(8?AC/:EGG?GGGACGE8EG?EE(C?:?E(?G;E6AGF:E(*CGA\n+@chr1-18/2\n+ACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGA\n++\n+,????BBBBDDD?D?AFGGGFFHFIHHIIFDIIIIHGHII@HEEHFG+ED+IHGDF>IF.FH-EFHIHFIHHGIH*FE+HG-G5HHHHHIH.GHFHHDHI9EGHDEHGGHD4HH?BFGHDFFD+DGHHHFGHGEF.F;F@GGCEFEF:8EDF.FGCCE@?;6;*EG48GGCFEF:?:GCAAG(CEGGGC/0E;?EF*GG(\n+@chr1-16/2\n+TCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCACCCTGTGGCCTGTTGATTCTAAATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTATCCAGAAATTGCTCCGAGTATCGGCTTGTTTACGAATTAAATCGAAGTTAC\n++\n+5?A?5@BB??@@D-BDGCFGFGEE+FF@HHIHFHFG9A.DFDFIDHHAH=IEI?HIFI3IHIGIHHFHIFIDHE;HIHIHII5HIHHFGHF-HHIEHEIHHHHB3HHIHHHGHHEGF46HHFHFDHGHBGFGFE*FDHF(GDEE?GAF(CFGGEE0E?*G#EFE)F9CFGCE8G1CGC,GFFGEA:EGDEGDAC(A4:FG\n+@chr1-14/2\n+CGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAGACAAAACCATGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCCTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTGTGGAAA\n++\n+,?A=?/BBBDBDD5@9CFGGGFCIBCIE>IICFHF@HII.F+HI5HIDFH-5DC-FFHHHHFHIA+5IHIICIH-ID+AHHBH*FHFIH,FCG-@H2CHH-G+H+8HD<HHH<GHFDDEHEG*GG?EGEHFEEGDEG1GG*FG;?FFE')CCFC6EEE@GEGBGEEDCF:AGG6G(GEEGEG:C:?GFG6EA.#?FEF6A\n+@chr1-12/2\n+GGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAAAAAAAATAAAAATTTTTACCGCTTCGTTTTACAGGCACATGAAGTTCTACTTCGATTTAATTCGTAAACAAGCCGACACTTGGAACAATTTCTGGAAAGACGGTAAGCGTGAAGAAACTAACCAGCGATAAAGTTAG\n++\n+,????BBBDBD@+D@DGGFGGGICAI8FEHGFIHHFH9CFFHHFHH@HHGGHFGIGFIIHHFIG7HHHHI)-HHFCDHHI)DHFHHIBHHH+7HGBEDHICHIHFFIHHHHH(DDHH:HEHGEHEH6G1HGCGF0A/,G'GEGGG?EECEG=AC8F=?EA<:E(GE?GF6GEEGCC1G*DE+EFCGEE(GG<6E?(8E(G\n+@chr1-10/2\n+CGGTAACTTCGATTTAATTCGTAAACAAGCCCATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATGAAACCAACATAAACGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTACTTGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAGAAAAAATAAAAATTTTTACCGCTT\n++\n+A??,?BBB-DDDDDDDFF.FFCIHEEIH0HA,HH-EBIDCIHIHEGFI/FFFHEIHHHGHHHHAAHFEHHGFFF4HHFHIHICFEDCI.HGHD;HFH?HEH=H:FHHDCE=)DEEGFFEGAHCEHHGG:E*GFGH1EFDG*EGCG8GDFBHG:?B7?8GCEG??E;C:GFGG:E?(G8CEDCAEEEGGGE:CECF6E/AE\n+@chr1-8/2\n+GAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCCAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTACCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCTG\n++\n+?????-BBDDBB@DD@CGFGGGIF-HHFHCGFHIHIIEFFIHH=AEEEDH=7HIFHH=ICEEHI=AIIFBDEIHF#=HEFFFFIEHHIIF-CHH@HH+H=CIF.HH.HFECHHGH+EDHDGHFEFF@DFHEGGGGFFGE'BGG*EF1GG#0EGE'E8<GG6;E*(EFECAEE1CFE*GBGGCEG(E>6G*GG>E(?(FGA\n+@chr1-6/2\n+CACTTCGATTTAATTTGTAAACAAGCCGATACTTGGAACAAGTTCTGGAAAGACGGTAACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAGTAAGACAAAACCATCGATAAAGTTAGACA\n++\n+???,,BB-B-D--D--GGFGGGHIHHFHFHII=HI?CHAHH+HHHHHHG7GG-@FHIHDBF;IFHHHIGHFAHHIEFHIIHGEHHHGGHHHHHHDGFHEHFH,+FHEHGEHCHHHEGEH?,FHH8CDFHFEECEEGEGEG*@:G;/?GE-GEEGCF;E=:?EEE0G?EEGCF*EE<EG*0G(EC#G/8E?AGGGC*GEEE\n+@chr1-4/2\n+AATTCGTAAACAAGCCGATACTTGGAAGAATTTCTGGAAAGACGGTAAAAGCGATAAAGTTAGACAAAACCATTTAGAATCAACAGGCCACAGGGCGATAAAGTTAGACAAAACCAGCGATAAAGTTAGACAGAACCAGCGTTATAACGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCCGATACTTGGAACAAT\n++\n+??????-BDDDDDDDBFFFF>FIIHIF,FIIIGHH+IHIHBFHIIDEEIHHI8HHHG=HIIGIFAHF=CEHFHDEHGHIFCHFEB@IHDHHD6FHDI<E8F.F'EHGHEFCFHGH3HHHHDE@EGHFFHHGD(;DDGG8;ADF;GEAF;(EECGG.EEFEEEGEE:GE*GEA>AE:GFGGGCC/8?:GGGA:A:E'CCCC\n+@chr1-2/2\n+CGCCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAGAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCATTTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTT\n++\n+???5,<?BDBDDD?DBF6FF8G0H;FHH?HIH@HHAIIHFFH.*HHFDHIHHIHEIBIHEFHIHFHHBHEH+IH,HCFHIFHHEF(EHIIIFHHIHHH+DHHDH9DDEH+D.GHEIHGFHFEC9D9HGFH+EEC@FEEG?E?B4;F27AF(G0?GCCG=(G?EEEF,/;(AF<EGC;GEEEEAEF?*0:?66EEE.CE:E\n" |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.illumina.03.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.illumina.03.sam Thu Jun 11 11:51:06 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +@HD VN:1.4 SQ:unsorted +@SQ SN:chr1 LN:1626 +@PG ID:01 PN:ART_Illumina CL:art_illumina -i test-data/input.fa -l 200 -f 20 -o test-data/art.illumina.03 -m 200 -rs 42 --insRate 0.00009 --insRate2 0.00015 --delRate 0.00011 --delRate2 0.00023 --samout -mp --mflen 2001 --sdev 10 |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.illumina.031.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.illumina.031.aln Thu Jun 11 11:51:06 2015 -0400 |
| b |
| @@ -0,0 +1,4 @@ +##ART_Illumina read_length 200 +@CM art_illumina -i test-data/input.fa -l 200 -f 20 -o test-data/art.illumina.03 -m 200 -rs 42 --insRate 0.00009 --insRate2 0.00015 --delRate 0.00011 --delRate2 0.00023 --samout -mp --mflen 2001 --sdev 10 +@SQ chr1 1626 +##Header End |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.illumina.032.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.illumina.032.aln Thu Jun 11 11:51:06 2015 -0400 |
| b |
| @@ -0,0 +1,4 @@ +##ART_Illumina read_length 200 +@CM art_illumina -i test-data/input.fa -l 200 -f 20 -o test-data/art.illumina.03 -m 200 -rs 42 --insRate 0.00009 --insRate2 0.00015 --delRate 0.00011 --delRate2 0.00023 --samout -mp --mflen 2001 --sdev 10 +@SQ chr1 1626 +##Header End |
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.solid.01.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.solid.01.fq Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b"@@ -0,0 +1,2600 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| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.solid.01.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.solid.01.map Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,654 @@\n+##ART_SOLiD\tread_length\t25\n+@CM\tart_SOLiD -s -r 42 test-data/input.fa test-data/art.solid.01 25 10 \n+@SQ\tchr1\t1626\n+##Header 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|
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.solid.01.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.solid.01.sam Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b"@@ -0,0 +1,653 @@\n+@HD\tVN:1.4\tSQ:unsorted\n+@SQ\tSN:chr1\tLN:1626\n+@PG\tID:03\tPN:ART_SOLiD\tCL:art_SOLiD -s -r 42 test-data/input.fa test-data/art.solid.01 25 10 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|
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.solid.02.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.solid.02.sam Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b"@@ -0,0 +1,643 @@\n+@HD\tVN:1.4\tSQ:unsorted\n+@SQ\tSN:chr1\tLN:1626\n+@PG\tID:03\tPN:ART_SOLiD\tCL:art_SOLiD -s -r 42 test-data/input.fa test-data/art.solid.02 50 50 20 75 10 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|
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.solid.02_F3.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.solid.02_F3.fq Thu Jun 11 11:51:06 2015 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.solid.02_F3.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.solid.02_F3.map Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,324 @@\n+##ART_SOLiD\tread_length\t50\n+@CM\tart_SOLiD -s -r 42 test-data/input.fa test-data/art.solid.02 50 50 20 75 10 \n+@SQ\tchr1\t1626\n+##Header 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|
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.solid.02_F5.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.solid.02_F5.fq Thu Jun 11 11:51:06 2015 -0400 |
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| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/art.solid.02_F5.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/art.solid.02_F5.map Thu Jun 11 11:51:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,324 @@\n+##ART_SOLiD\tread_length\t50\n+@CM\tart_SOLiD -s -r 42 test-data/input.fa test-data/art.solid.02 50 50 20 75 10 \n+@SQ\tchr1\t1626\n+##Header 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|
| b |
| diff -r 000000000000 -r b98d6fffd00b test-data/input.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fa Thu Jun 11 11:51:06 2015 -0400 |
| b |
| @@ -0,0 +1,22 @@ +>chr1 +GACTCATGATTTCTTACCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGA +TAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGC +ACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGC +TTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTG +TTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTACCGTCTTTCCAGAAATT +GTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTC +CAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCTTTCCAGAAATTGTTCCA +AGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGTAAAAATTTTTATTTTTT +TTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATG +TTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAAT +TAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCG +TTATAACGCTGGTTTTGTCTAACTTTATCGCTGGTTTTGTCTAACTTTATCGCCCTGTGGCCTGTTGATTCTAAATGGTT +TTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTTAC +CGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGTTATAACGCCTTTA +CCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGGAAGCGGTAAAAATTTTTATTTTTTT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCATGGTTTTGTCTAACTTTATCGCTGGTTAGTTTCTTCACGCTTACCGTCT +TTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAGTAGAACTTCATGTGCCTGTAAAACGAAGCGGT +AAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACAAGTACCAACCAGAACGTGAAAAAGCGTCC +TGCGTGTAGCGTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATCGCTTTTACCGTCTTTCCAGAAATTGTTCCAAGTA +TCGGCTTGTTTACGAATTAAATCGAAGTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATC +GAAGTGGACTGCTGGCGTTATAACGC |
| b |
| diff -r 000000000000 -r b98d6fffd00b tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jun 11 11:51:06 2015 -0400 |
| b |
| @@ -0,0 +1,38 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="package_gsl_1_16" version="1.16"> + <repository changeset_revision="4391a79f86fa" name="package_gsl_1_16" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="art" version="2014_11_03"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://www.niehs.nih.gov/research/resources/assets/docs/artsrcvanillaicecream031114linuxtgz.tgz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="4391a79f86fa" name="package_gsl_1_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="gsl" version="1.16" /> + </repository> + </action> + <action type="autoconf" /> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable> + </action> + </actions> + </install> + <readme>ART is a set of simulation tools to generate synthetic next-generation +sequencing reads. ART simulates sequencing reads by mimicking real +sequencing process with empirical error models or quality profiles summarized +from large recalibrated sequencing data. ART can also simulate reads using user +own read error model or quality profiles. ART supports simulation of +single-end, paired-end/mate-pair reads of three major commercial +next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and +Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety +of method or tools for next-generation sequencing data analysis, including +read alignment, de novo assembly, SNP and structure variation discovery. +ART was used as a primary tool for the simulation study of the 1000 Genomes +Project . ART is implemented in C++ with optimized algorithms and is highly +efficient in read simulation. ART outputs reads in the FASTQ format, and +alignments in the ALN format. ART can also generate alignments in the SAM +alignment or UCSC BED file format. +</readme> + </package> +</tool_dependency> |