| Previous changeset 19:9da02be9c6cc (2019-05-10) Next changeset 21:e7b2202befea (2019-05-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 89976e27bd11f1da3c95a5df6b67297496a8a89b |
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modified:
rgFastQC.xml test-data/fastqc_contaminants.txt test-data/fastqc_customlimits.txt test-data/fastqc_data.txt test-data/fastqc_data_hisat.txt test-data/fastqc_report.html test-data/fastqc_report_hisat.html |
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added:
test-data/1000trimmed.fastq test-data/1000trimmed.fastq.bz2 test-data/1000trimmed.fastq.gz test-data/fastqc_adapters.txt test-data/fastqc_data_adapters.txt test-data/fastqc_data_contaminants.txt test-data/fastqc_data_customlimits.txt test-data/fastqc_data_kmer.txt test-data/fastqc_data_min_length.txt test-data/fastqc_data_nogroup.txt test-data/fastqc_report_adapters.html test-data/fastqc_report_contaminants.html test-data/fastqc_report_customlimits.html test-data/fastqc_report_kmer.html test-data/fastqc_report_min_length.html test-data/fastqc_report_nogroup.html |
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removed:
test-data/1000gsample.fastq test-data/1000gsample.fastq.bz2 test-data/1000gsample.fastq.gz test-data/fastqc_data2.txt test-data/fastqc_report2.html |
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| diff -r 9da02be9c6cc -r ddf5c37952ac rgFastQC.xml --- a/rgFastQC.xml Fri May 10 14:23:53 2019 -0400 +++ b/rgFastQC.xml Thu May 16 07:45:56 2019 -0400 |
| [ |
| b'@@ -1,9 +1,17 @@\n-<tool id="fastqc" name="FastQC" version="0.72">\n+<tool id="fastqc" name="FastQC" version="0.72+galaxy1">\n <description>Read Quality reports</description>\n <requirements>\n- <requirement type="package" version="0.11.7">fastqc</requirement>\n+ <requirement type="package" version="0.11.8">fastqc</requirement>\n </requirements>\n- <command detect_errors="exit_code"><![CDATA[\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="FastQC returned non zero exit code" />\n+ <exit_code range=":-1" level="fatal" description="FastQC returned non zero exit code" />\n+ <regex match="There is insufficient memory for the Java Runtime Environment"\n+ source="stdout"\n+ level="fatal_oom"\n+ description="Out of memory error occurred" />\n+ </stdio>\n+ <command><![CDATA[\n #import re\n #set input_name = re.sub(\'[^\\w\\-\\s]\', \'_\', str($input_file.element_identifier))\n \n@@ -27,17 +35,25 @@\n mkdir -p \'${html_file.files_path}\' &&\n fastqc\n --outdir \'${html_file.files_path}\'\n-\n #if $contaminants.dataset and str($contaminants) > \'\'\n --contaminants \'${contaminants}\'\n #end if\n \n+ #if $adapters.dataset and str($adapters) > \'\'\n+ --adapters \'${adapters}\'\n+ #end if\n+\n #if $limits.dataset and str($limits) > \'\'\n --limits \'${limits}\'\n #end if\n \n --quiet\n --extract\n+ #if $min_length:\n+ --min_length $min_length\n+ #end if\n+ $nogroup\n+ --kmers $kmers\n -f \'${format}\'\n \'${input_file_sl}\'\n \n@@ -50,8 +66,17 @@\n label="Short read data from your current history" />\n <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"\n help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA" />\n+ <param argument="--adapters" type="data" format="tabular" optional="true" label="Adapter list"\n+ help="list of adapters adapter sequences which will be explicity searched against the library. tab delimited file with 2 columns: name and sequence." />\n <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"\n help="a file that specifies which submodules are to be executed (default=all) and also specifies the thresholds for the each submodules warning parameter" />\n+ <param argument="--nogroup" type="boolean" truevalue="--nogroup" falsevalue="" checked="False"\n+ label="Disable grouping of bases for reads >50bp" help="Using this option will cause fastqc to crash and burn if you use it on really long reads, and your plots may end up a ridiculous size. You have been warned!"/>\n+ <param argument="--min_length" type="integer" value="" optional="true"\n+ label="Lower limit on the length of the sequence to be shown in the report"\n+ help=" As long as you set this to a value greater or equal to your longest read length then this will be the sequence length used to create your read groups. This can be useful for making directly comaparable statistics from datasets with somewhat variable read lengths."/>\n+ <param argument="--kmers" type="integer" value="7" min="2" max="10"\n+ label="length of Kmer to look for" help="note: the Kmer test is disabled and needs to be enabled using a custom Submodule and limits file"/>\n </inputs>\n <outputs>\n <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Webpage" />\n@@ -59,43 +84,67 @@\n </outputs>\n <tests>\n <test>\n- <param name="input_file" value="1000gsample.fastq" />\n+ <param name="input_file" value="10'..b'output name="text_file" file="fastqc_data_adapters.txt" ftype="txt"/>\n+ </test>\n+ <test>\n+ <param name="input_file" value="1000trimmed.fastq" />\n+ <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />\n+ <output name="html_file" file="fastqc_report_customlimits.html" ftype="html" lines_diff="100"/>\n+ <output name="text_file" file="fastqc_data_customlimits.txt" ftype="txt"/>\n </test>\n <test>\n- <param name="input_file" value="1000gsample.fastq" />\n+ <param name="input_file" value="1000trimmed.fastq" ftype="fastq" />\n+ <param name="kmers" value="3" />\n <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />\n- <output name="html_file" file="fastqc_report2.html" ftype="html" lines_diff="100"/>\n- <output name="text_file" file="fastqc_data2.txt" ftype="txt" lines_diff="4"/>\n+ <output name="html_file" file="fastqc_report_kmer.html" ftype="html" lines_diff="100"/>\n+ <output name="text_file" file="fastqc_data_kmer.txt" ftype="txt"/>\n+ <assert_command>\n+ <has_text text="--kmers 3"/>\n+ </assert_command>\n </test>\n <test>\n- <param name="input_file" value="1000gsample.fastq.gz" ftype="fastq.gz" />\n- <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />\n- <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>\n- <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/>\n+ <param name="input_file" value="1000trimmed.fastq" />\n+ <param name="min_length" value="108" />\n+ <output name="html_file" file="fastqc_report_min_length.html" ftype="html" lines_diff="100"/>\n+ <output name="text_file" file="fastqc_data_min_length.txt" ftype="txt"/>\n </test>\n <test>\n- <param name="input_file" value="1000gsample.fastq.bz2" ftype="fastq.bz2" />\n- <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />\n- <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>\n- <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/>\n+ <param name="input_file" value="1000trimmed.fastq" ftype="fastq" />\n+ <param name="nogroup" value="--nogroup" />\n+ <output name="html_file" file="fastqc_report_nogroup.html" ftype="html" lines_diff="100"/>\n+ <output name="text_file" file="fastqc_data_nogroup.txt" ftype="txt"/>\n+ <assert_command>\n+ <has_text text="--nogroup"/>\n+ </assert_command>\n </test>\n <test>\n <param name="input_file" value="hisat_output_1.bam" ftype="bam" />\n <output name="html_file" file="fastqc_report_hisat.html" ftype="html" lines_diff="100"/>\n- <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt" lines_diff="4"/>\n+ <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt"/>\n </test>\n </tests>\n- <help>\n+ <help><![CDATA[\n .. class:: infomark\n \n **Purpose**\n \n FastQC aims to provide a simple way to do some quality control checks on raw\n sequence data coming from high throughput sequencing pipelines.\n-It provides a modular set of analyses which you can use to give a quick\n+It provides a set of analyses which you can use to get a quick\n impression of whether your data has any problems of\n which you should be aware before doing any further analysis.\n \n@@ -153,7 +202,7 @@\n All except Basic Statistics and Overrepresented sequences are plots.\n .. _FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/\n .. _Picard-tools: https://broadinstitute.github.io/picard/\n- </help>\n+ ]]></help>\n <citations>\n <citation type="bibtex">\n @unpublished{andrews_s,\n' |
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/1000gsample.fastq --- a/test-data/1000gsample.fastq Fri May 10 14:23:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,20000 +0,0 @@\n-@ERR005448.1 IL40_2446:5:1:0:964/2\n-GTCTCAGCTGCTTAGTCCAATGGCTCCCACACACACAGAAGCATGGCCAGCTCT\n-+\n-40539<=3<.<@@697;A=;79:9<9974.;9:8@=551%0)5+.2%*,02*0)\n-@ERR005448.2 IL40_2446:5:1:0:451/2\n-ATAAAGACCAGCCTGGCCAATGTGGTGAAACCCTGTCTCTACTAAAAGTACAAA\n-+\n->?A?<8=AB?:<B<:9;ABB=<78458:?@<@@<68@@BA><>@@>8/3>9=;?\n-@ERR005448.3 IL40_2446:5:1:0:1205/2\n-ATTCTACTCCAACTGATTCCATTCCATTCTATTCCTTTCTATTCCATTTCATTC\n-+\n-?:B7C;6<<;B6/7.09=05973.7864./288235A3&&/244,.056.322.\n-@ERR005448.4 IL40_2446:5:1:0:17/2\n-CACTTCCAGATACTCCAAAAAGAGTGTTTCCAACCTGCTCTAGTAATGGGAATG\n-+\n-BBBA=<=B6ABA<BB8>>@7=?>44>8;88=@=6B9??;B=6;8<:BB?@9=<A\n-@ERR005448.5 IL40_2446:5:1:0:719/2\n-ATTCCATCCTTGCAGGTGCACAGCTTTTGTTGCTTCTGCCCTTCCTCTCGCCCT\n-+\n-@>@>AA99975,382146;94:2009>5&.8-54;63-005896:3040+3343\n-@ERR005448.6 IL40_2446:5:1:0:156/2\n-CAGGAAAGGGCCTGGTGGGAGGTAATTGGATCATGGGGGTGGTTTCCTCCATGC\n-+\n-<:<=;A=4=A?@?4>>?0=84=?AAA>@:8BB<;=09;?'?;4??:A@>@?A>;\n-@ERR005448.8 IL40_2446:5:1:0:1162/2\n-GCTTATCAACAGAAAGCAAGGGTTAGCTATACTGACTTTAGACAGAATAGATTT\n-+\n-0=;=;8*<;7;=8A804848)15?:59?=090945?<?<789,+;<5'6)8595\n-@ERR005448.9 IL40_2446:5:1:0:257/2\n-ATGGAATCAACATCAAACGGAATAAAACGGAACTATCGAATGGAATCGAAGAGA\n-+\n-@-+6:7<::9<>?;7:;>=59:>78:<:<4@9*?@=:>8@A8894=7;3.3618\n-@ERR005448.10 IL40_2446:5:1:0:842/2\n-TGGATTCCACTCCATTCCATTGCACTCGCGTTGATTCCATTCCATTCCACTCCC\n-+\n->81>?>5>?=@?>@>?>=9;>79=6122,/&6'+,0'50)6&606-)5%%5)'+\n-@ERR005448.11 IL40_2446:5:1:0:947/2\n-AAAAAAAAAAAGCTGGGAGTGGGGTGTGGTGATGAGCGCCTGTAGTCCTAGCTA\n-+\n-AAAAAAAA?=>:8?:;539)=5><6511)347;674040443642-)8/6348:\n-@ERR005448.12 IL40_2446:5:1:0:389/2\n-CAGAGATGTTTAATATGAGCCAGGAATTCTGCTAGGCACTTTGTGTATGTTTTA\n-+\n-@?559>@76>CCC@CC;A80=B>7?B?=<;><B?66;A=BC>>;>6A><;?B>>\n-@ERR005448.13 IL40_2446:5:1:0:435/2\n-ACTGAATTTGGAAAGGGTCACTAGTGAACTTTTTTTTGGTGATACTAAGTAATT\n-+\n-89=7)?>C;8997/456>ABA8=588=4858@@>B>?0(6<9<?;<BB77;68<\n-@ERR005448.14 IL40_2446:5:1:0:552/2\n-CTTTGAGGGTGGGAAGGAATCCTGCCTCTAATTGCAGCTGTCACACCCCATCAG\n-+\n-AA?/*<9=<'99=9<=7@A===2'2=8==449?;;9(0*23>7,34%586:;==\n-@ERR005448.15 IL40_2446:5:1:0:770/2\n-AAAAAAGTGCTGTTGGACAACAGTAAAAATTGAGTCTGTGTATATTGAGCTGAA\n-+\n->>>60298:,:35?5,399;-9-19:4)8728460%2;5./.35)8332&5125\n-@ERR005448.16 IL40_2446:5:1:0:788/2\n-AATGGCTTTGACCAAAATGCTGATAGTAATATGGACAATGATGTCGAGGCTGAG\n-+\n->>>6;:AB8)6;=?=??=8<@=9;9;8:=9;854;9?;9748488752755707\n-@ERR005448.17 IL40_2446:5:1:0:813/2\n-CGGAGTTTGAAAACACTTGAACTGATCTATACTCAATGAGAGGAGGTCATTGAT\n-+\n-<;3'6<BA=A=A@@ABBA>BBB?=<B>C=@BA>>C@>B=<@A<>:;,7/.>710\n-@ERR005448.18 IL40_2446:5:1:0:1012/2\n-TGCCTACAATAGCAAATTTTGAAAAACATAGAGACCAAAATAAACCATAGTTAA\n-+\n->;4?4=??@B7'8>AA>?@;8=C?C;;:>=,=559*<D=9<>E<9<?8B4>;85\n-@ERR005448.19 IL40_2446:5:1:0:1150/2\n-TTATATGCAAGCGAAGAAGGTAAGTAGGTTACTGGATTTATGAGCCTGAGGTCA\n-+\n->=?AB8<:8438><=48;921<<00:3:69798)879:;;37<8639594/,0,\n-@ERR005448.20 IL40_2446:5:1:0:1254/2\n-TGTCTCTTCTCTCTTGAATTCCTGATCTGGCCTAAATTCGCACATACATTCTTT\n-+\n-95<AC=BB@C@AAC??<AAA:==8;?@:.,8??:=86:85-:6>?<<@C?;A8;\n-@ERR005448.21 IL40_2446:5:1:0:1669/2\n-CAGCACCTGCTTTGTTGGCCTGGGGATGTTTCCTAGGTGGTTTATAGGTGGTTT\n-+\n-8>3<A?36,8>@616<3199:6:730:4%6@9964,.&20'@52@6,16)/'.3\n-@ERR005448.22 IL40_2446:5:1:0:178/2\n-TCAGAGAGCCTTGGGCCAGAGTTCCAGGGTCTCTGGCAGTGGCTGCCAGGTGAG\n-+\n-)<806'29<<A770.<@?<?80A6A858.'9?7:4,'0'.1>.6?2%%+121''\n-@ERR005448.23 IL40_2446:5:1:0:57/2\n-ATGATGGTAGAGAGGACATTGTCAAAGATGCCAAAATTTTAGACTCATTGGGAG\n-+\n-A:3??AA9>>>B99;>ABCC>>C?B=0:BA=:ABB>@99?B;39B?79;06926\n-@ERR005448.24 IL40_2446:5:1:0:971/2\n-AAAATAATTCCCATTGCTATTTCTCGTGGATAGCATTAGAGCATCTGAATTTGG\n-+\n-AAB@>ACCCA>@B=<1:C>;=?>@=>6-18<4.287:6.0/4<:65-.::=6+1\n-@ERR005448.25 IL40_2446:5:1:0:685/2\n-TTCCATTCCACACGGGTTGGTTCCCTTGCATCCCTTTCCATTCCATTCTATTGC\n-+\n-:?A@@AAA?@@@95<:79393=:6<==4;<?7>0;9>973;4<352638%8724\n-@ERR005448.26 IL40_2446:5:1:0:311/2\n-GCTGACTGATAGGCCCCACTCGCGGTAGGGTGCTTCTAGCCCTTCCTACTGATA\n-+\n-=?99?=<><?>33==?=A@=<6@74752277=4=<3<:(7977<7<78582:97\n-@ERR005448.27 IL40_2446:5:1:0:528/2\n-AGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCAT\n-+\n-BACB<.;;?C@:=ABC@891:6<AAAB=3>@?8;<79=9>=<??<@9-7-6<;;\n-@ERR005448.28 IL40_2446:5:1:0:"..b"3&/-'+++/6/',1.,\n-@ERR005448.1075769 IL40_2446:5:10:1190:4/1\n-GCCGCAGCTCACATTTTGATATGGCTCAGGAAAGAGAAGCCTTGCTAAAGAAGC\n-+\n-@@>A?9>A?=0=2?AAA=8<<;??@=8(:85/,659513;705795&-)5-3/4\n-@ERR005448.1076602 IL40_2446:5:10:1203:4/1\n-TGTTTATAGCAGTACAATTCATGATTGCAAAGATATGGAACAAACCTAATTGCC\n-+\n-AC@C?:=B?>8<)9=?CA8;1<?;=9@@;8@=:<:)2;,<><21947239/95A\n-@ERR005448.1077152 IL40_2446:5:10:1211:6/1\n-GAACTCTACGGGAACTATGGCTTCCACCTGCATGGTATCTCTTAGGTACAGATC\n-+\n-9099?A@A82<?9956:7776:422*/7,&,200/+.33531.&,6-/.51+&-\n-@ERR005448.1077221 IL40_2446:5:10:1212:900/1\n-AGAGGTGATGAAGTCAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n-+\n-<>.8><2'72:@?-@><7<>:><?@@B@@AA>@BBA@ABB?@>@A@?@=<?@;B\n-@ERR005448.1077313 IL40_2446:5:10:1213:6/1\n-CATCTCGTAAGTTTCTCTTCCCCTGTGATGCCCATTTTTCTTGTTTTTTTTTTT\n-+\n-?BAB?@A9>9A9CCCC@CCCCBCAA>B>@C@<<0=A?A?@A@A;BCACACA@=<\n-@ERR005448.1077487 IL40_2446:5:10:1216:5/1\n-GCAATGGAATGGTGAAAAGAAATGTCAGCTGCGACTGGGCCACTGCACTCCAGC\n-+\n-B=1@A?;07@BA;A85::<?=?<@=84@787&56533)71335254.,0/2&..\n-@ERR005448.1077616 IL40_2446:5:10:1218:2/1\n-TTTGACATGGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGTAGTGGTACAATCTC\n-+\n-@@BB@?1>BB<?@AABB@>BB@@BBB@A=BB=BB;=>7>==:4=A885=<>859\n-@ERR005448.1078324 IL40_2446:5:10:1230:4/1\n-CAAATCCAAGTGAGAACTGCCTTGTTAGAGGAAAGGCTGTTTTCTACCTATGGA\n-+\n-@:40?BB=<A?A=@<8=:>@>A?B<?=>7>?709>>;8;-.584.&/4,)023&\n-@ERR005448.1078507 IL40_2446:5:10:1233:2/1\n-GATTCAATCACCTCCCACTAGGCCCCTCCTCCAGCACTGGGGATTACAATTCAG\n-+\n-?77.=:5;</;?AA?;::5597/:??=;7->4&775711/71*.30233656-)\n-@ERR005448.1078651 IL40_2446:5:10:1235:1070/1\n-TAAACAAAAGGCATGAAGCTCTAAGCCAGTGGGCTTGAATTTTCTCCACCATAA\n-+\n-?8>AB?<84?CAB@;;9AA;AA;?9?@@B7><>>AC@;1==B>@A?A=@<47(2\n-@ERR005448.1078696 IL40_2446:5:10:1236:6/1\n-CTGAGCTGGAGTTCTACGAATCATGGTCTGGAGATGAAAACTGGGAAGACAAAG\n-+\n-AB>;@A?@?7>?BB>9<>:8>@<=?@:AB@>4=::@52/56<><;0+8/46),7\n-@ERR005448.1078883 IL40_2446:5:10:1239:6/1\n-GCTTCAGTCTCCCTTGAAATGTAAATATGCAGGAAGATAGCCTTTCGGTTTTCC\n-+\n-BA:>AB:@B@@B@?;;;7;:@>:899<B>>A95,-777,25;,05-;,&58:57\n-@ERR005448.1079004 IL40_2446:5:10:1241:4/1\n-GTGCTTATCATCTTAGAGAACACGTGTATCATTATGAACAGAATGATGCTAGAA\n-+\n-C9CCA8'9@??ACA=A9A>;?=>C;@@BC>=@@@@@7@86=<=;C?=A=;5?1<\n-@ERR005448.1079882 IL40_2446:5:10:1255:5/1\n-AATGGAATGGAATGGAATGGAATCACCTCTATTGCAATCGAATGGAATGGAATG\n-+\n-9;AB?87@B;AACAA>?BCB>9?C=?ABBB>C@CA?>CB9(4?A>><@@:;;;@\n-@ERR005448.1080580 IL40_2446:5:10:1267:4/1\n-GATTAACTATGATGACTGTTTTGTTCACAAGGTGGACATTTTTAACTGTGAAAA\n-+\n-@:=A<9=?7?>3:A9=C@;=?B@::@?=7/<<6=;807296>:3158=4>57.,\n-@ERR005448.1080835 IL40_2446:5:10:1271:3/1\n-CACGTTTATTGCGGCACTATTCACAATAGCAAAGACTTGGCACCAACCCAAACG\n-+\n-?37A;?>A7;9;-A=1;=;;5@@>@B=1;/979>6>69:8(:>932A@>7/)&3\n-@ERR005448.1081009 IL40_2446:5:10:1273:4/1\n-TGAAGAATGTCAATGGTAGTTTGATGGGAATAGCATTGAATCTATGAATTTCTT\n-+\n-CC=+A5=?B6@A8CBC7<;2>>B4@B@;<6:7@94:8=337:;1<7756::77B\n-@ERR005448.1081178 IL40_2446:5:10:1276:6/1\n-TAGGGTCATTATAGATATAGTTAGATAAGATGAGGTCATATTGAAGCAGGATGG\n-+\n-<+;BC7A:@??=><5A=ACB7B>CB<@CCAAC2C?.:B>9;A<-8;372=0458\n-@ERR005448.1081342 IL40_2446:5:10:1279:4/1\n-AGGGGAGTAGGCTTACTTTGTATCTGACCCACGTTTCCTCGAGACAAAACACCC\n-+\n->=BA==='<<ABA?<@AAA@@98B=<@<@:6=@54?B?1??/=,176699650(\n-@ERR005448.1081475 IL40_2446:5:10:1281:6/1\n-CATTCCGGGTCACTTTTTCCTGTCCTTTTGAGGCCAGAAATGCATATTGTAATG\n-+\n->6>@BBBBB7BB<=ABBBB@@B(278B7@@9<4;A>@448-@A(=(7@88;78;\n-@ERR005448.1081577 IL40_2446:5:10:1282:3/1\n-AGGGAGCCTCTCATGAGAGAAACACAGGGAAGGTGGGAAGGGAGATCCTGGGCT\n-+\n-;5@BBBAB@<:<=:7:6@A@0@@A=7>9?<<03.<>5-(;<?3570'2,@><76\n-@ERR005448.1081665 IL40_2446:5:10:1284:5/1\n-GACCAATAAGGAAGAAAAGAGAGAAGAATCAAATAGACGCATTAAAAAATGATA\n-+\n-.=@/<;?59>=66?739=?;:/=79?<4,994<94@878/96111.32711175\n-@ERR005448.1081931 IL40_2446:5:10:1288:2/1\n-AGTGATGAACGGATAAGCGAAGTGTGCTACATATAACAATGGAATATTATCCAA\n-+\n-@CC><635>94::=>5AB<19B>AC<);B::>BB@C<C?=B96.;:?4:6)'&5\n-@ERR005448.1081992 IL40_2446:5:10:1289:600/2\n-TGCTCTTCTGTTTGCTCTTCTGTTTACCATTCTCTTCTTCTGGGATTTCTACTG\n-+\n-BACC@ABBA?@CC?CCACBCCC@BCBABABABA?ACA?CBCA@?AA@CBBA@@:\n-@ERR005448.1082627 IL40_2446:5:10:1299:6/1\n-CTTAGGCATTTTGAAGTTCTTGTGTGCCAGAGCTGTGGCTGGGGGTTTGTCTCA\n-+\n->@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A,32;:(6-3/\n" |
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| Binary file test-data/1000gsample.fastq.bz2 has changed |
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| Binary file test-data/1000gsample.fastq.gz has changed |
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| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/1000trimmed.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1000trimmed.fastq Thu May 16 07:45:56 2019 -0400 |
| b |
| b"@@ -0,0 +1,19620 @@\n+@ERR005448.2 IL40_2446:5:1:0:451/2\n+ACACTCTTTCCCTACACGACGCTGTTCCATCTACACTCTTTCCCTACACGACGCTGTTCCATCT\n++\n+>?A?<8=AB?:<B<:9;ABB=<78458:?@<@>?A?<8=AB?:<B<:9;ABB=<78458:?@<@\n+@ERR005448.2 IL40_2446:5:1:0:451/2\n+ATAAAGACCAGCCTGGCCAATGTGGTGAAACCCTGTCTCTACTAAAAGTACAAAATAAAGACCAGCCTGGCCAATGTGGTGAAACCCTGTCTCTACTAAAAGTACAAA\n++\n+>?A?<8=AB?:<B<:9;ABB=<78458:?@<@@<68@@BA><>@@>8/3>9=;?>?A?<8=AB?:<B<:9;ABB=<78458:?@<@@<68@@BA><>@@>8/3>9=;?\n+@ERR005448.3 IL40_2446:5:1:0:1205/2\n+ATTCTACTCCAACT\n++\n+?:B7C;6<<;B6/7\n+@ERR005448.4 IL40_2446:5:1:0:17/2\n+CACTTCCAGATACTCCAAAAAGAGTGTTTCCAACCTGCTCTAGTAATGGGAATGCACTTCCAGATACTCCAAAAAGAGTGTTTCCAACCTGCTCTAGTAATGGGAATG\n++\n+BBBA=<=B6ABA<BB8>>@7=?>44>8;88=@=6B9??;B=6;8<:BB?@9=<ABBBA=<=B6ABA<BB8>>@7=?>44>8;88=@=6B9??;B=6;8<:BB?@9=<A\n+@ERR005448.5 IL40_2446:5:1:0:719/2\n+ATTCCATCCTT\n++\n+@>@>AA99975\n+@ERR005448.6 IL40_2446:5:1:0:156/2\n+CAGGAAAGGGCCTGGTGGGAGGTAATTGGATCATGGGGGTGGTTTCCTCCATGCCAGGAAAGGGCCTGGTGGGAGGTAATTGGATCATGGGGGTGGTTTCCTCCATGC\n++\n+<:<=;A=4=A?@?4>>?0=84=?AAA>@:8BB<;=09;?'?;4??:A@>@?A>;<:<=;A=4=A?@?4>>?0=84=?AAA>@:8BB<;=09;?'?;4??:A@>@?A>;\n+@ERR005448.8 IL40_2446:5:1:0:1162/2\n+GCTTATCAACAGAAAGCA\n++\n+0=;=;8*<;7;=8A8048\n+@ERR005448.10 IL40_2446:5:1:0:842/2\n+TGGATTCCACTCCATTCCATTGCAC\n++\n+>81>?>5>?=@?>@>?>=9;>79=6\n+@ERR005448.11 IL40_2446:5:1:0:947/2\n+AAAAAAAAAAAGCTGGGAG\n++\n+AAAAAAAA?=>:8?:;539\n+@ERR005448.12 IL40_2446:5:1:0:389/2\n+CAGAGATGTTTAATATGAGCCAGGAATTCTGCTAGGCACTTTGTGTATGTTTTACAGAGATGTTTAATATGAGCCAGGAATTCTGCTAGGCACTTTGTGTATGTTTTA\n++\n+@?559>@76>CCC@CC;A80=B>7?B?=<;><B?66;A=BC>>;>6A><;?B>>@?559>@76>CCC@CC;A80=B>7?B?=<;><B?66;A=BC>>;>6A><;?B>>\n+@ERR005448.13 IL40_2446:5:1:0:435/2\n+ACTGAATTTGGAA\n++\n+89=7)?>C;8997\n+@ERR005448.14 IL40_2446:5:1:0:552/2\n+CTTTGA\n++\n+AA?/*<\n+@ERR005448.15 IL40_2446:5:1:0:770/2\n+AAAA\n++\n+>>>6\n+@ERR005448.16 IL40_2446:5:1:0:788/2\n+AATGGCTTTGA\n++\n+>>>6;:AB8)6\n+@ERR005448.18 IL40_2446:5:1:0:1012/2\n+TGCCTACAATAGCAAATTTTGAAAAACATAGAG\n++\n+>;4?4=??@B7'8>AA>?@;8=C?C;;:>=,=5\n+@ERR005448.19 IL40_2446:5:1:0:1150/2\n+TTATATGCAAGCGAAGAAGGTAAGTA\n++\n+>=?AB8<:8438><=48;921<<00:\n+@ERR005448.20 IL40_2446:5:1:0:1254/2\n+TGTCTCTTCTCTCTTGAATTCCTGATCT\n++\n+95<AC=BB@C@AAC??<AAA:==8;?@:\n+@ERR005448.21 IL40_2446:5:1:0:1669/2\n+CAGCACCT\n++\n+8>3<A?36\n+@ERR005448.23 IL40_2446:5:1:0:57/2\n+ATGATGGTAGAGAGGACATTGTCAAAGATGCCAAAATTTTAGACTCATTGGG\n++\n+A:3??AA9>>>B99;>ABCC>>C?B=0:BA=:ABB>@99?B;39B?79;069\n+@ERR005448.24 IL40_2446:5:1:0:971/2\n+AAAATAATTCCCATTGCTATTTCTCGT\n++\n+AAB@>ACCCA>@B=<1:C>;=?>@=>6\n+@ERR005448.25 IL40_2446:5:1:0:685/2\n+TTCCATTCCACACGGGTTGGTTCCCTTGCATCCCTTTCCATTCCA\n++\n+:?A@@AAA?@@@95<:79393=:6<==4;<?7>0;9>973;4<35\n+@ERR005448.26 IL40_2446:5:1:0:311/2\n+GCTGACTGATAGGCCCCACTCGCGGTA\n++\n+=?99?=<><?>33==?=A@=<6@7475\n+@ERR005448.27 IL40_2446:5:1:0:528/2\n+AGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCA\n++\n+BACB<.;;?C@:=ABC@891:6<AAAB=3>@?8;<79=9>=<??<@9-7\n+@ERR005448.28 IL40_2446:5:1:0:315/2\n+AACTTTTACTATCTGTACCATTCCTGTACTCTGACATTACCTGGTTATGTCTGAAACTTTTACTATCTGTACCATTCCTGTACTCTGACATTACCTGGTTATGTCTG\n++\n+AAC?CA@?=ABB=A;>@><?B?;7;78C??C:6<A@B@;:@B>;6>>;53=854AAC?CA@?=ABB=A;>@><?B?;7;78C??C:6<A@B@;:@B>;6>>;53=85\n+@ERR005448.29 IL40_2446:5:1:0:1616/2\n+TATAATCTTAATGGGATCCATCATTGACCAAAATGCAGCCCATCATTGACCAAATATAATCTTAATGGGATCCATCATTGACCAAAATGCAGCCCATCATTGACCAAA\n++\n+C>:@ACCBCCC=8677B>?C?6>:@:@=;=@CC=6:>863:@<<=<609<;?;BC>:@ACCBCCC=8677B>?C?6>:@:@=;=@CC=6:>863:@<<=<609<;?;B\n+@ERR005448.30 IL40_2446:5:1:0:852/2\n+TGATGTGTG\n++\n+?6<?:9/75\n+@ERR005448.31 IL40_2446:5:1:0:1684/2\n+AGAAGGATACCGACTGGA\n++\n+=/;>85:A>;:4=<<446\n+@ERR005448.32 IL40_2446:5:1:1:881/2\n+GTCTAGGAATTTATTTATTTTCCCTATATTTTTCAGTTCACTAGCATATAGTTGGTCTAGGAATTTATTTATTTTCCCTATATTTTTCAGTTCACTAGCATATAGTTG\n++\n+C7?6>B@==8>>8@CCA@A=@<>>@@ACCACB:::;3A5=4?>3><8=CA=826C7?6>B@==8>>8@CCA@A=@<>>@@ACCACB:::;3A5=4?>3><8=CA=826\n+@ERR005448.33 IL40_2446:5:1:1:412/2\n+GTCCCAGGGCCCAGAAGAGCTTGTGGCCTCCTTGCAGACATCAGTAGTGGCCCCGTCCCAGGGCCCAGAAGAGCTTGTGGCCTCCTTGCAGACATCAGTAGTGGCCCC\n++\n+<8>A?=5929@@><=?7?9@A<4:49>A?>AA;289<?>:;9<:3?6969<<8<<8>A?=5929@@><=?7?9"..b"=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n" 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| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/1000trimmed.fastq.bz2 |
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| Binary file test-data/1000trimmed.fastq.bz2 has changed |
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| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/1000trimmed.fastq.gz |
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| Binary file test-data/1000trimmed.fastq.gz has changed |
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| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_adapters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_adapters.txt Thu May 16 07:45:56 2019 -0400 |
| [ |
| b"@@ -0,0 +1,170 @@\n+# This file contains a list of potential contaminants which are\n+# frequently found in high throughput sequencing reactions. These\n+# are mostly sequences of adapters / primers used in the various\n+# sequencing chemistries.\n+# \n+# Please DO NOT rely on these sequences to design your own oligos, some\n+# of them are truncated at ambiguous positions, and none of them are\n+# definitive sequences from the manufacturers so don't blame us if you\n+# try to use them and they don't work.\n+#\n+# You can add more sequences to the file by putting one line per entry\n+# and specifying a name[tab]sequence. If the contaminant you add is \n+# likely to be of use to others please consider sending it to the FastQ\n+# authors, either via a bug report at www.bioinformatics.bbsrc.ac.uk/bugzilla/\n+# or by directly emailing simon.andrews@bbsrc.ac.uk so other users of\n+# the program can benefit.\n+\n+Illumina Single End Apapter 1\t\t\t\t\tACACTCTTTCCCTACACGACGCTGTTCCATCT\n+Illumina Single End Apapter 2\t\t\t\t\tCAAGCAGAAGACGGCATACGAGCTCTTCCGATCT\n+Illumina Single End PCR Primer 1\t\t\t\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Single End PCR Primer 2\t\t\t\tCAAGCAGAAGACGGCATACGAGCTCTTCCGATCT\n+Illumina Single End Sequencing Primer\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+\n+Illumina Paired End Adapter 1\t\t\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Paired End Adapter 2\t\t\t\t\tCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\n+Illumina Paried End PCR Primer 1\t\t\t\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Paired End PCR Primer 2\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\n+Illumina Paried End Sequencing Primer 1\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Paired End Sequencing Primer 2\t\t\tCGGTCTCGGCATTCCTACTGAACCGCTCTTCCGATCT\n+\n+Illumina DpnII expression Adapter 1\t\t\t\tACAGGTTCAGAGTTCTACAGTCCGAC\n+Illumina DpnII expression Adapter 2\t\t\t\tCAAGCAGAAGACGGCATACGA\n+Illumina DpnII expression PCR Primer 1\t\t\tCAAGCAGAAGACGGCATACGA\n+Illumina DpnII expression PCR Primer 2\t\t\tAATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA\n+Illumina DpnII expression Sequencing Primer\t\tCGACAGGTTCAGAGTTCTACAGTCCGACGATC\n+\n+Illumina NlaIII expression Adapter 1\t\t\tACAGGTTCAGAGTTCTACAGTCCGACATG\n+Illumina NlaIII expression Adapter 2\t\t\tCAAGCAGAAGACGGCATACGA\n+Illumina NlaIII expression PCR Primer 1\t\t\tCAAGCAGAAGACGGCATACGA\n+Illumina NlaIII expression PCR Primer 2\t\t\tAATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA\n+Illumina NlaIII expression Sequencing Primer\tCCGACAGGTTCAGAGTTCTACAGTCCGACATG\n+\n+Illumina Small RNA Adapter 1\t\t\t\t\tGTTCAGAGTTCTACAGTCCGACGATC\n+Illumina Small RNA Adapter 2\t\t\t\t\tTCGTATGCCGTCTTCTGCTTGT\n+Illumina Small RNA RT Primer\t\t\t\t\tCAAGCAGAAGACGGCATACGA\n+Illumina Small RNA PCR Primer 1\t\t\t\t\tCAAGCAGAAGACGGCATACGA\n+Illumina Small RNA PCR Primer 2\t\t\t\t\tAATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA\n+Illumina Small RNA Sequencing Primer\t\t\tCGACAGGTTCAGAGTTCTACAGTCCGACGATC\n+\n+Illumina Multiplexing Adapter 1\t\t\t\t\tGATCGGAAGAGCACACGTCT\n+Illumina Multiplexing Adapter 2\t\t\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Multiplexing PCR Primer 1.01\t\t\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Multiplexing PCR Primer 2.01\t\t\tGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\n+Illumina Multiplexing Read1 Sequencing Primer\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Multiplexing Index Sequencing Primer\tGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\n+Illumina Multiplexing Read2 Sequencing Primer\tGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\n+\n+Illumina PCR Primer Index 1\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTC\n+Illumina PCR Primer Index 2\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTC\n+Illumina PCR Primer Index 3\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTC\n+Illumina PCR Primer Index 4\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTC\n+Illumina PCR Primer Index 5\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTC\n+Illumina PCR Primer Index 6\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTC\n+Illumina PCR Primer Index 7\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTC\n+Illum"..b"AAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 13\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTTGACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 14\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGGAACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 15\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGACATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 16\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGGACGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 17\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCTCTACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 18\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 19\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTTTCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 20\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGGCCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 21\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGAAACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 22\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGTACGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 23\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCCACTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 24\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCTACCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 25\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATCAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 26\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCTCATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 27\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 28\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCTTTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 29\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTAGTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 30\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCCGGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 31\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATCGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 32\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGAGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 33\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGCCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 34\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCCATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 35\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATAAAATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 36\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGTTGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 37\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATTCCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 38\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATAGCTAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 39\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGTATAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 40\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTCTGAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 41\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGTCGTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 42\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGATTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 43\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCTGTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 44\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATTATAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 45\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGAATGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 46\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTCGGGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 47\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 48\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGCCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+\n+ABI Dynabead EcoP Oligo\t\t\t\t\t\t\tCTGATCTAGAGGTACCGGATCCCAGCAGT\n+ABI Solid3 Adapter A\t\t\t\t\t\t\tCTGCCCCGGGTTCCTCATTCTCTCAGCAGCATG\n+ABI Solid3 Adapter B\t\t\t\t\t\t\tCCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT\n+ABI Solid3 5' AMP Primer\t\t\t\t\t\tCCACTACGCCTCCGCTTTCCTCTCTATG\n+ABI Solid3 3' AMP Primer\t\t\t\t\t\tCTGCCCCGGGTTCCTCATTCT\n+ABI Solid3 EF1 alpha Sense Primer\t\t\t\tCATGTGTGTTGAGAGCTTC\n+ABI Solid3 EF1 alpha Antisense Primer\t\t\tGAAAACCAAAGTGGTCCAC\n+ABI Solid3 GAPDH Forward Primer\t\t\t\t\tTTAGCACCCCTGGCCAAGG\n+ABI Solid3 GAPDH Reverse Primer\t\t\t\t\tCTTACTCCTTGGAGGCCATG\n" |
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_contaminants.txt --- a/test-data/fastqc_contaminants.txt Fri May 10 14:23:53 2019 -0400 +++ b/test-data/fastqc_contaminants.txt Thu May 16 07:45:56 2019 -0400 |
| b |
| b'@@ -14,157 +14,4 @@\n # authors, either via a bug report at www.bioinformatics.bbsrc.ac.uk/bugzilla/\n # or by directly emailing simon.andrews@bbsrc.ac.uk so other users of\n # the program can benefit.\n-\n-Illumina Single End Apapter 1\t\t\t\t\tACACTCTTTCCCTACACGACGCTGTTCCATCT\n-Illumina Single End Apapter 2\t\t\t\t\tCAAGCAGAAGACGGCATACGAGCTCTTCCGATCT\n-Illumina Single End PCR Primer 1\t\t\t\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n-Illumina Single End PCR Primer 2\t\t\t\tCAAGCAGAAGACGGCATACGAGCTCTTCCGATCT\n-Illumina Single End Sequencing Primer\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n-\n-Illumina Paired End Adapter 1\t\t\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n-Illumina Paired End Adapter 2\t\t\t\t\tCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\n-Illumina Paried End PCR Primer 1\t\t\t\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n-Illumina Paired End PCR Primer 2\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\n-Illumina Paried End Sequencing Primer 1\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n-Illumina Paired End Sequencing Primer 2\t\t\tCGGTCTCGGCATTCCTACTGAACCGCTCTTCCGATCT\n-\n-Illumina DpnII expression Adapter 1\t\t\t\tACAGGTTCAGAGTTCTACAGTCCGAC\n-Illumina DpnII expression Adapter 2\t\t\t\tCAAGCAGAAGACGGCATACGA\n-Illumina DpnII expression PCR Primer 1\t\t\tCAAGCAGAAGACGGCATACGA\n-Illumina DpnII expression PCR Primer 2\t\t\tAATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA\n-Illumina DpnII expression Sequencing Primer\t\tCGACAGGTTCAGAGTTCTACAGTCCGACGATC\n-\n-Illumina NlaIII expression Adapter 1\t\t\tACAGGTTCAGAGTTCTACAGTCCGACATG\n-Illumina NlaIII expression Adapter 2\t\t\tCAAGCAGAAGACGGCATACGA\n-Illumina NlaIII expression PCR Primer 1\t\t\tCAAGCAGAAGACGGCATACGA\n-Illumina NlaIII expression PCR Primer 2\t\t\tAATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA\n-Illumina NlaIII expression Sequencing Primer\tCCGACAGGTTCAGAGTTCTACAGTCCGACATG\n-\n-Illumina Small RNA Adapter 1\t\t\t\t\tGTTCAGAGTTCTACAGTCCGACGATC\n-Illumina Small RNA Adapter 2\t\t\t\t\tTCGTATGCCGTCTTCTGCTTGT\n-Illumina Small RNA RT Primer\t\t\t\t\tCAAGCAGAAGACGGCATACGA\n-Illumina Small RNA PCR Primer 1\t\t\t\t\tCAAGCAGAAGACGGCATACGA\n-Illumina Small RNA PCR Primer 2\t\t\t\t\tAATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA\n-Illumina Small RNA Sequencing Primer\t\t\tCGACAGGTTCAGAGTTCTACAGTCCGACGATC\n-\n-Illumina Multiplexing Adapter 1\t\t\t\t\tGATCGGAAGAGCACACGTCT\n-Illumina Multiplexing Adapter 2\t\t\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n-Illumina Multiplexing PCR Primer 1.01\t\t\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n-Illumina Multiplexing PCR Primer 2.01\t\t\tGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\n-Illumina Multiplexing Read1 Sequencing Primer\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n-Illumina Multiplexing Index Sequencing Primer\tGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\n-Illumina Multiplexing Read2 Sequencing Primer\tGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\n-\n-Illumina PCR Primer Index 1\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTC\n-Illumina PCR Primer Index 2\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTC\n-Illumina PCR Primer Index 3\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTC\n-Illumina PCR Primer Index 4\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTC\n-Illumina PCR Primer Index 5\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTC\n-Illumina PCR Primer Index 6\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTC\n-Illumina PCR Primer Index 7\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTC\n-Illumina PCR Primer Index 8\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTC\n-Illumina PCR Primer Index 9\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTC\n-Illumina PCR Primer Index 10\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTC\n-Illumina PCR Primer Index 11\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTC\n-Illumina PCR Primer Index 12\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTC\n-\n-Illumina DpnII Gex Adapter 1\t\t\t\t\tGATCGTCGGACTGTAGAACTCTGAAC\n-Illumina DpnII Gex Adapter 1.01\t\t\t\t\tACAGGTTCAGAGTTCTACAGTCCGAC\n-Illumina DpnII Gex Adapter 2\t\t\t\t\tCAAGCAGAAGACGGCATACGA\n-Illumina DpnII Gex Adapter 2.01\t\t\t\t\tTCGTATGCCGTCTTCTGCTTG\n-Illumina DpnII Gex PCR Primer 1\t\t\t\t\tCAAGCAGAAGACGGCATACGA\n-Illumina DpnII G'..b"PCR Primer, Index 13\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTTGACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 14\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGGAACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 15\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGACATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 16\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGGACGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 17\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCTCTACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 18\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 19\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTTTCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 20\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGGCCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 21\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGAAACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 22\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGTACGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 23\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCCACTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 24\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCTACCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 25\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATCAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 26\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCTCATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 27\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 28\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCTTTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 29\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTAGTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 30\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCCGGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 31\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATCGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 32\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGAGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 33\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGCCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 34\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCCATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 35\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATAAAATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 36\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGTTGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 37\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATTCCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 38\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATAGCTAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 39\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGTATAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 40\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTCTGAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 41\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGTCGTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 42\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGATTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 43\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCTGTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 44\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATTATAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 45\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGAATGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 46\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTCGGGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 47\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-RNA PCR Primer, Index 48\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGCCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n-\n-ABI Dynabead EcoP Oligo\t\t\t\t\t\t\tCTGATCTAGAGGTACCGGATCCCAGCAGT\n-ABI Solid3 Adapter A\t\t\t\t\t\t\tCTGCCCCGGGTTCCTCATTCTCTCAGCAGCATG\n-ABI Solid3 Adapter B\t\t\t\t\t\t\tCCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT\n-ABI Solid3 5' AMP Primer\t\t\t\t\t\tCCACTACGCCTCCGCTTTCCTCTCTATG\n-ABI Solid3 3' AMP Primer\t\t\t\t\t\tCTGCCCCGGGTTCCTCATTCT\n-ABI Solid3 EF1 alpha Sense Primer\t\t\t\tCATGTGTGTTGAGAGCTTC\n-ABI Solid3 EF1 alpha Antisense Primer\t\t\tGAAAACCAAAGTGGTCCAC\n-ABI Solid3 GAPDH Forward Primer\t\t\t\t\tTTAGCACCCCTGGCCAAGG\n-ABI Solid3 GAPDH Reverse Primer\t\t\t\t\tCTTACTCCTTGGAGGCCATG\n+TestContaminant\tATGCATGCATGCATGCATGCATGC\n" |
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_customlimits.txt --- a/test-data/fastqc_customlimits.txt Fri May 10 14:23:53 2019 -0400 +++ b/test-data/fastqc_customlimits.txt Thu May 16 07:45:56 2019 -0400 |
| b |
| @@ -1,15 +1,15 @@ # For each of the modules you can choose to not run that # module at all by setting the value below to 1 for the # modules you want to remove. -duplication ignore 1 +duplication ignore 0 kmer ignore 0 n_content ignore 0 overrepresented ignore 0 quality_base ignore 0 sequence ignore 0 gc_sequence ignore 0 -quality_sequence ignore 1 -tile ignore 1 +quality_sequence ignore 0 +tile ignore 0 sequence_length ignore 0 adapter ignore 0 @@ -34,7 +34,7 @@ # threshold for the overrepresented sequences to be reported # at all as the proportion of the library which must be seen # as a single sequence -overrepresented warn 0.001 +overrepresented warn 0.1 overrepresented error 1 # The per base quality filter uses two values, one for the value @@ -42,13 +42,13 @@ # median quality. Failing either of these will trigger the alert quality_base_lower warn 10 quality_base_lower error 5 -quality_base_median warn 50 +quality_base_median warn 25 quality_base_median error 20 # The per base sequence content module tests the maximum deviation # between A and T or C and G -sequence warn 2 -sequence error 5 +sequence warn 10 +sequence error 20 # The per sequence GC content tests the maximum deviation between # the theoretical distribution and the real distribution @@ -81,4 +81,4 @@ adapter error 10 - \ No newline at end of file + |
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_data.txt --- a/test-data/fastqc_data.txt Fri May 10 14:23:53 2019 -0400 +++ b/test-data/fastqc_data.txt Thu May 16 07:45:56 2019 -0400 |
| b |
| b'@@ -1,803 +1,259 @@\n-##FastQC\t0.11.6\n+##FastQC\t0.11.8\n >>Basic Statistics\tpass\n #Measure\tValue\n-Filename\t1000gsample_fastq_bz2.bz2\n+Filename\t1000trimmed_fastq\n File type\tConventional base calls\n Encoding\tSanger / Illumina 1.9\n-Total Sequences\t5000\n+Total Sequences\t4905\n Sequences flagged as poor quality\t0\n-Sequence length\t54\n-%GC\t43\n->>END_MODULE\n->>Per base sequence quality\twarn\n-#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n-1\t28.9946\t31.0\t27.0\t33.0\t22.0\t34.0\n-2\t28.486\t30.0\t26.0\t32.0\t21.0\t33.0\n-3\t28.5272\t30.0\t26.0\t32.0\t21.0\t34.0\n-4\t28.6252\t30.0\t26.0\t32.0\t22.0\t33.0\n-5\t28.4804\t30.0\t26.0\t32.0\t21.0\t33.0\n-6\t28.5128\t30.0\t26.0\t32.0\t22.0\t33.0\n-7\t28.4102\t30.0\t26.0\t32.0\t21.0\t33.0\n-8\t28.4674\t30.0\t26.0\t32.0\t22.0\t33.0\n-9\t28.182\t30.0\t26.0\t32.0\t21.0\t33.0\n-10\t28.0908\t30.0\t26.0\t32.0\t21.0\t33.0\n-11\t28.1876\t30.0\t26.0\t32.0\t21.0\t33.0\n-12\t28.1742\t30.0\t26.0\t32.0\t21.0\t33.0\n-13\t27.923\t30.0\t25.0\t32.0\t20.0\t33.0\n-14\t27.8984\t29.0\t25.0\t32.0\t21.0\t33.0\n-15\t27.6112\t29.0\t25.0\t32.0\t20.0\t33.0\n-16\t27.6638\t29.0\t25.0\t32.0\t20.0\t33.0\n-17\t27.5734\t29.0\t25.0\t32.0\t20.0\t33.0\n-18\t27.6348\t29.0\t25.0\t32.0\t20.0\t33.0\n-19\t27.6526\t29.0\t25.0\t32.0\t20.0\t33.0\n-20\t27.2716\t29.0\t24.0\t32.0\t19.0\t33.0\n-21\t27.2642\t29.0\t25.0\t31.0\t19.0\t33.0\n-22\t26.881\t28.0\t24.0\t31.0\t19.0\t33.0\n-23\t26.8124\t28.0\t24.0\t31.0\t19.0\t33.0\n-24\t26.8204\t28.0\t24.0\t31.0\t19.0\t33.0\n-25\t26.6606\t28.0\t24.0\t31.0\t18.0\t33.0\n-26\t26.3806\t28.0\t23.0\t31.0\t18.0\t33.0\n-27\t25.947\t28.0\t23.0\t31.0\t17.0\t33.0\n-28\t25.7446\t27.0\t22.0\t31.0\t16.0\t33.0\n-29\t25.6856\t27.0\t22.0\t31.0\t16.0\t33.0\n-30\t25.5228\t27.0\t22.0\t31.0\t16.0\t33.0\n-31\t25.354\t27.0\t22.0\t30.0\t16.0\t32.0\n-32\t25.1656\t27.0\t22.0\t30.0\t16.0\t32.0\n-33\t25.0164\t26.0\t21.0\t30.0\t15.0\t32.0\n-34\t24.75\t26.0\t21.0\t30.0\t15.0\t32.0\n-35\t24.3926\t26.0\t21.0\t30.0\t15.0\t32.0\n-36\t24.1122\t25.0\t20.0\t30.0\t14.0\t32.0\n-37\t23.8612\t25.0\t20.0\t29.0\t13.0\t32.0\n-38\t23.7544\t25.0\t20.0\t29.0\t13.0\t32.0\n-39\t23.485\t25.0\t19.0\t29.0\t13.0\t32.0\n-40\t23.1984\t24.0\t19.0\t29.0\t13.0\t32.0\n-41\t23.0976\t24.0\t19.0\t29.0\t13.0\t32.0\n-42\t22.9212\t24.0\t19.0\t28.0\t13.0\t31.0\n-43\t22.5172\t24.0\t18.0\t28.0\t12.0\t31.0\n-44\t22.3234\t23.0\t18.0\t28.0\t12.0\t31.0\n-45\t22.1372\t23.0\t18.0\t28.0\t11.0\t31.0\n-46\t22.2166\t23.0\t18.0\t28.0\t11.0\t31.0\n-47\t22.075\t23.0\t18.0\t28.0\t11.0\t31.0\n-48\t21.4592\t22.0\t17.0\t27.0\t11.0\t31.0\n-49\t21.0954\t22.0\t16.0\t27.0\t10.0\t30.0\n-50\t20.9356\t22.0\t16.0\t27.0\t10.0\t30.0\n-51\t20.6152\t21.0\t15.0\t27.0\t9.0\t30.0\n-52\t20.6588\t21.0\t16.0\t27.0\t9.0\t30.0\n-53\t19.5852\t20.0\t14.0\t25.0\t9.0\t29.0\n-54\t19.9424\t21.0\t14.0\t26.0\t7.0\t30.0\n+Sequence length\t1-108\n+%GC\t40\n >>END_MODULE\n->>Per tile sequence quality\tpass\n-#Tile\tBase\tMean\n-1\t1\t0.4542485249902164\n-1\t2\t0.02493171505959424\n-1\t3\t0.004493134032774293\n-1\t4\t0.6119404948560927\n-1\t5\t0.5283275008594686\n-1\t6\t0.3741933003058371\n-1\t7\t-0.2985554485298749\n-1\t8\t0.6040181642739206\n-1\t9\t0.43795745033596845\n-1\t10\t0.05327706110314523\n-1\t11\t0.8097461135057031\n-1\t12\t0.9171964750225641\n-1\t13\t1.0716973449965757\n-1\t14\t0.562649938864773\n-1\t15\t0.5112535943737946\n-1\t16\t0.7098461441939676\n-1\t17\t0.3989886413671577\n-1\t18\t0.2351551176870892\n-1\t19\t0.002716666680861124\n-1\t20\t-0.5270840838615776\n-1\t21\t0.08959510509382795\n-1\t22\t-0.6322238602545553\n-1\t23\t-0.8566085860715056\n-1\t24\t-0.8167218970288026\n-1\t25\t0.7728199138173544\n-1\t26\t-0.26898877195552373\n-1\t27\t-0.7734079986509634\n-1\t28\t0.46313879073469266\n-1\t29\t-1.0803714983510417\n-1\t30\t-0.9107347156963463\n-1\t31\t-1.1279249650605188\n-1\t32\t0.03588141895047414\n-1\t33\t-0.3276409211703317\n-1\t34\t0.07833890179158587\n-1\t35\t-0.8393131051954583\n-1\t36\t-1.024889600311596\n-1\t37\t-1.4177418858492992\n-1\t38\t-1.912918888443187\n-1\t39\t-1.880569234686881\n-1\t40\t-0.9901560786471286\n-1\t41\t-1.9499635516515283\n-1\t42\t-2.3754765893384793\n-1\t43\t-1.6682056704307335\n-1\t44\t-2.2432919652101226\n-1\t45\t-2.1214550638335794\n-1\t46\t-1.6941624871292404\n-1\t47\t-2.261740586778952\n-1\t48\t-0.47246064535067234\n-1\t49\t-1.345180096970381\n-1\t50\t-1.3012642855865373\n-1\t51\t-1.6748103331735038\n-1\t52\t-1.4936238782530324\n-1\t53\t-0.9900326328970834\n-1\t54\t-0.9042724595665739\n-2\t1\t0.27305194379363584\n-2\t2\t-0.40803531790744074\n-2\t3\t-1.054114924575284\n-2\t4\t0.024'..b"0.47491224447656405\t0.9378185524974516\n+3\t0.041296716911005574\t0.12232415902140673\n+4\t0.020648358455502787\t0.08154943934760449\n+5\t0.0\t0.0\n 6\t0.0\t0.0\n-7\t0.04019292604501608\t0.27999999999999997\n+7\t0.0\t0.0\n 8\t0.0\t0.0\n 9\t0.0\t0.0\n->10\t0.0\t0.0\n+>10\t0.020648358455502787\t0.672782874617737\n >50\t0.0\t0.0\n >100\t0.0\t0.0\n >500\t0.0\t0.0\n@@ -882,52 +364,61 @@\n >>END_MODULE\n >>Overrepresented sequences\twarn\n #Sequence\tCount\tPercentage\tPossible Source\n-CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAAT\t7\t0.13999999999999999\tIllumina Paired End PCR Primer 2 (96% over 33bp)\n-CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGAC\t7\t0.13999999999999999\tIllumina Paired End PCR Primer 2 (100% over 35bp)\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\t33\t0.672782874617737\tNo Hit\n >>END_MODULE\n >>Adapter Content\tpass\n #Position\tIllumina Universal Adapter\tIllumina Small RNA 3' Adapter\tIllumina Small RNA 5' Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n 1\t0.0\t0.0\t0.0\t0.0\t0.0\n-2\t0.02\t0.0\t0.0\t0.0\t0.0\n-3\t0.02\t0.0\t0.0\t0.0\t0.0\n-4\t0.02\t0.0\t0.0\t0.0\t0.0\n-5\t0.02\t0.0\t0.0\t0.0\t0.0\n-6\t0.02\t0.0\t0.0\t0.0\t0.0\n-7\t0.02\t0.0\t0.0\t0.0\t0.0\n-8\t0.02\t0.0\t0.0\t0.0\t0.0\n-9\t0.02\t0.0\t0.0\t0.0\t0.0\n-10\t0.02\t0.0\t0.0\t0.0\t0.0\n-11\t0.02\t0.0\t0.0\t0.0\t0.0\n-12\t0.02\t0.0\t0.0\t0.0\t0.0\n-13\t0.02\t0.0\t0.0\t0.0\t0.0\n-14\t0.02\t0.0\t0.0\t0.0\t0.0\n-15\t0.02\t0.0\t0.0\t0.0\t0.0\n-16\t0.02\t0.0\t0.0\t0.0\t0.0\n-17\t0.02\t0.0\t0.0\t0.0\t0.0\n-18\t0.02\t0.0\t0.0\t0.0\t0.0\n-19\t0.06\t0.0\t0.0\t0.0\t0.0\n-20\t0.36\t0.0\t0.0\t0.0\t0.0\n-21\t0.36\t0.0\t0.0\t0.0\t0.0\n-22\t0.36\t0.0\t0.0\t0.0\t0.0\n-23\t0.36\t0.0\t0.0\t0.0\t0.0\n-24\t0.36\t0.0\t0.0\t0.0\t0.0\n-25\t0.4\t0.0\t0.0\t0.0\t0.0\n-26\t0.4\t0.0\t0.0\t0.0\t0.0\n-27\t0.42\t0.0\t0.0\t0.0\t0.0\n-28\t0.62\t0.0\t0.0\t0.0\t0.0\n-29\t0.66\t0.0\t0.0\t0.0\t0.0\n-30\t0.68\t0.0\t0.0\t0.0\t0.0\n-31\t0.68\t0.0\t0.0\t0.0\t0.0\n-32\t0.68\t0.0\t0.0\t0.0\t0.0\n-33\t0.68\t0.0\t0.0\t0.0\t0.0\n-34\t0.7\t0.0\t0.0\t0.0\t0.0\n-35\t0.76\t0.0\t0.0\t0.0\t0.0\n-36\t0.8\t0.0\t0.0\t0.0\t0.0\n-37\t0.88\t0.0\t0.0\t0.0\t0.0\n-38\t1.0\t0.0\t0.0\t0.0\t0.0\n-39\t1.12\t0.0\t0.0\t0.0\t0.0\n-40\t1.22\t0.0\t0.0\t0.0\t0.0\n-41\t1.38\t0.0\t0.0\t0.0\t0.0\n-42\t1.48\t0.0\t0.0\t0.0\t0.0\n-43\t1.68\t0.0\t0.0\t0.0\t0.0\n+2\t0.0\t0.0\t0.0\t0.0\t0.0\n+3\t0.0\t0.0\t0.0\t0.0\t0.0\n+4\t0.0\t0.0\t0.0\t0.0\t0.0\n+5\t0.0\t0.0\t0.0\t0.0\t0.0\n+6\t0.0\t0.0\t0.0\t0.0\t0.0\n+7\t0.0\t0.0\t0.0\t0.0\t0.0\n+8\t0.0\t0.0\t0.0\t0.0\t0.0\n+9\t0.0\t0.0\t0.0\t0.0\t0.0\n+10-11\t0.0\t0.0\t0.0\t0.0\t0.0\n+12-13\t0.0\t0.0\t0.0\t0.0\t0.0\n+14-15\t0.0\t0.0\t0.0\t0.0\t0.0\n+16-17\t0.0\t0.0\t0.0\t0.0\t0.0\n+18-19\t0.0\t0.0\t0.0\t0.0\t0.0\n+20-21\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+22-23\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+24-25\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+26-27\t0.1325178389398573\t0.0\t0.0\t0.0\t0.0\n+28-29\t0.2038735983690112\t0.0\t0.0\t0.0\t0.0\n+30-31\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+32-33\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+34-35\t0.24464831804281345\t0.0\t0.0\t0.0\t0.0\n+36-37\t0.3058103975535168\t0.0\t0.0\t0.0\t0.0\n+38-39\t0.4383282364933741\t0.0\t0.0\t0.0\t0.0\n+40-41\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+42-43\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+44-45\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+46-47\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+48-49\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+50-51\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+52-53\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+54-55\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+56-57\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+58-59\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+60-61\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+62-63\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+64-65\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+66-67\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+68-69\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+70-71\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+72-73\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+74-75\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+76-77\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+78-79\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+80-81\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+82-83\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+84-85\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+86-87\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+88-89\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+90-91\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+92-93\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+94-95\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+96-97\t0.47910295616717635\t0.0\t0.0\t0.0\t0.0\n >>END_MODULE\n" |
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_data2.txt --- a/test-data/fastqc_data2.txt Fri May 10 14:23:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5317 +0,0 @@\n-##FastQC\t0.11.6\n->>Basic Statistics\tpass\n-#Measure\tValue\n-Filename\t1000gsample_fastq\n-File type\tConventional base calls\n-Encoding\tSanger / Illumina 1.9\n-Total Sequences\t5000\n-Sequences flagged as poor quality\t0\n-Sequence length\t54\n-%GC\t43\n->>END_MODULE\n->>Per base sequence quality\twarn\n-#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n-1\t28.9946\t31.0\t27.0\t33.0\t22.0\t34.0\n-2\t28.486\t30.0\t26.0\t32.0\t21.0\t33.0\n-3\t28.5272\t30.0\t26.0\t32.0\t21.0\t34.0\n-4\t28.6252\t30.0\t26.0\t32.0\t22.0\t33.0\n-5\t28.4804\t30.0\t26.0\t32.0\t21.0\t33.0\n-6\t28.5128\t30.0\t26.0\t32.0\t22.0\t33.0\n-7\t28.4102\t30.0\t26.0\t32.0\t21.0\t33.0\n-8\t28.4674\t30.0\t26.0\t32.0\t22.0\t33.0\n-9\t28.182\t30.0\t26.0\t32.0\t21.0\t33.0\n-10\t28.0908\t30.0\t26.0\t32.0\t21.0\t33.0\n-11\t28.1876\t30.0\t26.0\t32.0\t21.0\t33.0\n-12\t28.1742\t30.0\t26.0\t32.0\t21.0\t33.0\n-13\t27.923\t30.0\t25.0\t32.0\t20.0\t33.0\n-14\t27.8984\t29.0\t25.0\t32.0\t21.0\t33.0\n-15\t27.6112\t29.0\t25.0\t32.0\t20.0\t33.0\n-16\t27.6638\t29.0\t25.0\t32.0\t20.0\t33.0\n-17\t27.5734\t29.0\t25.0\t32.0\t20.0\t33.0\n-18\t27.6348\t29.0\t25.0\t32.0\t20.0\t33.0\n-19\t27.6526\t29.0\t25.0\t32.0\t20.0\t33.0\n-20\t27.2716\t29.0\t24.0\t32.0\t19.0\t33.0\n-21\t27.2642\t29.0\t25.0\t31.0\t19.0\t33.0\n-22\t26.881\t28.0\t24.0\t31.0\t19.0\t33.0\n-23\t26.8124\t28.0\t24.0\t31.0\t19.0\t33.0\n-24\t26.8204\t28.0\t24.0\t31.0\t19.0\t33.0\n-25\t26.6606\t28.0\t24.0\t31.0\t18.0\t33.0\n-26\t26.3806\t28.0\t23.0\t31.0\t18.0\t33.0\n-27\t25.947\t28.0\t23.0\t31.0\t17.0\t33.0\n-28\t25.7446\t27.0\t22.0\t31.0\t16.0\t33.0\n-29\t25.6856\t27.0\t22.0\t31.0\t16.0\t33.0\n-30\t25.5228\t27.0\t22.0\t31.0\t16.0\t33.0\n-31\t25.354\t27.0\t22.0\t30.0\t16.0\t32.0\n-32\t25.1656\t27.0\t22.0\t30.0\t16.0\t32.0\n-33\t25.0164\t26.0\t21.0\t30.0\t15.0\t32.0\n-34\t24.75\t26.0\t21.0\t30.0\t15.0\t32.0\n-35\t24.3926\t26.0\t21.0\t30.0\t15.0\t32.0\n-36\t24.1122\t25.0\t20.0\t30.0\t14.0\t32.0\n-37\t23.8612\t25.0\t20.0\t29.0\t13.0\t32.0\n-38\t23.7544\t25.0\t20.0\t29.0\t13.0\t32.0\n-39\t23.485\t25.0\t19.0\t29.0\t13.0\t32.0\n-40\t23.1984\t24.0\t19.0\t29.0\t13.0\t32.0\n-41\t23.0976\t24.0\t19.0\t29.0\t13.0\t32.0\n-42\t22.9212\t24.0\t19.0\t28.0\t13.0\t31.0\n-43\t22.5172\t24.0\t18.0\t28.0\t12.0\t31.0\n-44\t22.3234\t23.0\t18.0\t28.0\t12.0\t31.0\n-45\t22.1372\t23.0\t18.0\t28.0\t11.0\t31.0\n-46\t22.2166\t23.0\t18.0\t28.0\t11.0\t31.0\n-47\t22.075\t23.0\t18.0\t28.0\t11.0\t31.0\n-48\t21.4592\t22.0\t17.0\t27.0\t11.0\t31.0\n-49\t21.0954\t22.0\t16.0\t27.0\t10.0\t30.0\n-50\t20.9356\t22.0\t16.0\t27.0\t10.0\t30.0\n-51\t20.6152\t21.0\t15.0\t27.0\t9.0\t30.0\n-52\t20.6588\t21.0\t16.0\t27.0\t9.0\t30.0\n-53\t19.5852\t20.0\t14.0\t25.0\t9.0\t29.0\n-54\t19.9424\t21.0\t14.0\t26.0\t7.0\t30.0\n->>END_MODULE\n->>Per base sequence content\tfail\n-#Base\tG\tA\tT\tC\n-1\t21.5\t32.64\t25.919999999999998\t19.939999999999998\n-2\t24.04\t31.72\t26.540000000000003\t17.7\n-3\t21.58\t28.860000000000003\t29.42\t20.14\n-4\t21.58\t28.28\t28.9\t21.240000000000002\n-5\t21.16\t29.720000000000002\t28.32\t20.8\n-6\t22.38\t29.24\t25.72\t22.66\n-7\t21.34\t30.320000000000004\t28.24\t20.1\n-8\t21.58\t29.060000000000002\t27.939999999999998\t21.42\n-9\t20.3\t28.48\t28.58\t22.64\n-10\t21.2\t30.84\t26.56\t21.4\n-11\t21.14\t28.64\t27.279999999999998\t22.939999999999998\n-12\t21.32\t28.88\t28.999999999999996\t20.8\n-13\t20.36\t29.220000000000002\t28.939999999999998\t21.48\n-14\t20.02\t29.2\t29.220000000000002\t21.560000000000002\n-15\t20.200000000000003\t29.220000000000002\t28.38\t22.2\n-16\t20.34\t29.38\t29.299999999999997\t20.979999999999997\n-17\t20.599999999999998\t29.14\t28.499999999999996\t21.759999999999998\n-18\t20.599999999999998\t27.92\t29.4\t22.08\n-19\t21.66\t28.46\t28.58\t21.3\n-20\t20.0\t29.24\t28.96\t21.8\n-21\t21.72\t28.499999999999996\t28.18\t21.6\n-22\t20.52\t30.880000000000003\t27.3\t21.3\n-23\t20.72\t28.9\t29.720000000000002\t20.66\n-24\t21.12\t28.62\t27.58\t22.68\n-25\t21.099999999999998\t29.060000000000002\t29.160000000000004\t20.68\n-26\t22.18887555022009\t28.391356542617046\t28.131252501000397\t21.288515406162464\n-27\t21.344268853770753\t28.525705141028208\t28.765753150630125\t21.364272854570913\n-28\t19.34\t30.54\t27.46\t22.66\n-29\t20.90418083616723\t29.12582516503301\t29.045809161832363\t20.924184836967395\n-30\t21.099999999999998\t29.4\t27.439999999999998\t22.06\n-31\t20.84\t28.04\t28.660000000000004\t22.46\n-32\t19.847939175670266\t28.371348539415763\t28.7515006002401\t23.02921168467387\n-33\t22.084416883376676\t28.62572514502901\t27.265453090618124\t22.024404880976'..b" Paired End PCR Primer 2 (98% over 53bp)\n-TCACGTGTCAATCATGCCCTGGTCATTTCGATCAGCTGTGACACCTGTTGATTA\t1\t0.02\tNo Hit\n-AACACTATTAGAAACTGTCAGGCCCAAGAGACACATATGGGAAATTTGCTGGAC\t1\t0.02\tNo Hit\n-GTCCAAGTGTTCTATTTTGTTCAATGCTCACCTATAAGTGAGAACATGCAGTGT\t1\t0.02\tNo Hit\n-GTGGGGAACCCTATATCTCCCCCACCCTGTTTTCACTGTTTTCCTTCCCCTTGC\t1\t0.02\tNo Hit\n-AACTCCACAAAAAGAGTGTTTCAAATCTGCTCTTTCTGAAGGAAGGGTCAACTC\t1\t0.02\tNo Hit\n-GTGGACATTGATCTTATTTTTATTTGTAAGAATGCATCAAGCTTTTTCCTGTTC\t1\t0.02\tNo Hit\n-AGAAAGGGGGATGCTGTGGCCTGCTGGGACACTGATGCAGGCTTCCTATTCCCT\t1\t0.02\tNo Hit\n-TAGGGGAATGGGGTTATCATTATTATCATTATCATTATTTAGTTCCCCAACCCA\t1\t0.02\tNo Hit\n-CTTTCTTACTTTCATGTTTTTGTTCATCTTGTCGAGGCAGCAAGTTTATTATCA\t1\t0.02\tNo Hit\n-GAACTCGGTGTGTGTTAAATTTAGGGGAGTCTGGTGGTAAGATTATTATGGAAA\t1\t0.02\tNo Hit\n-CCAGATGGTTAGTGCTCTGAGCTACTAGAGACCCCATTTGATGCCCCAGTTACC\t1\t0.02\tNo Hit\n-ATGGGTCCTGCAGCTGTGCATGGGCACCCATCATCAGACACAGCCTTCTGATCA\t1\t0.02\tNo Hit\n-GGAACATATTTTGTCACAGGTAAGAACCATGCCATAGAAGTTAGTCAGGCAGTT\t1\t0.02\tNo Hit\n-TCTCTTTCTTTCTCTTTCTCCTTCCTTCCTTCCTTCTTTCTTTCTTTCTTTTTC\t1\t0.02\tNo Hit\n-CACCGGGGGTTCAAGGGTACAGGGGAGTCCGACATAGACAGGAAATAACATGAA\t1\t0.02\tNo Hit\n-CACTCTGTCACCCAGGCTGGAGGGCAGTGGTACAATCTCGGCTCACTGCAGCCT\t1\t0.02\tNo Hit\n-ATGAAGACACCTAAAGAAAACCAGAATAAGGCCAGGCATGGAGGTGGCTGCATC\t1\t0.02\tNo Hit\n-TGGAATCATTGAACGGAATTGAATGGAACCGTCATCGAATGAATTGAATGCAAT\t1\t0.02\tNo Hit\n-AAAAAAGATCCACCACCGTACCTACACCAATCATGTAAATTATTCATAGTATAT\t1\t0.02\tNo Hit\n-TTAGCTAAAATTTTAAAGGCCAAGCGTGGGGCTGCCACTTTAGAGCAACAAGAA\t1\t0.02\tNo Hit\n-ATTATATTATCATTCTTAAGATAAATGGGTCAGTCGTTCCATTAGGACACTTAT\t1\t0.02\tNo Hit\n-AGAAAGGGCATCCAGATTGAAAAAGAGGAAGTCAAACTCTATTTGCTGATAATA\t1\t0.02\tNo Hit\n-AAGAAAATTCGGAATGAAGGCACTGGAAATGCAGATACATCCATGAAAGAATGT\t1\t0.02\tNo Hit\n-TTATACATGTCCACAAAGAATTTATATGCAAGTGTTTTCATTTCAAAGTGCTGC\t1\t0.02\tNo Hit\n-CACTCAGTTCTGTGTTTGCACAACTCTGTGCAGTTGTTAAATGCCTACAAAAAG\t1\t0.02\tNo Hit\n-TTATGCTCTGCTTCCTCTTGAACACTTTGCCACTTAGAAATTTCTTCCTCCAGA\t1\t0.02\tNo Hit\n-AGACATAAAATCCCTGTAGCCAAGGCAGTAAAACATAGAGGGGTATATGAGAGT\t1\t0.02\tNo Hit\n-TGGAAACGGGCTTTCTTCATATTATGCTATACAGAAGAATTCTCCGAACTTTCC\t1\t0.02\tNo Hit\n-CTGCCACTCTGCCTCCTCCCCTCAGCCCTGTCCCTCAGTAGGTATCTTCCAAAG\t1\t0.02\tNo Hit\n-AAAGTATATTGTTCTATTGAGATAGTCATGGACCAGGCTTATGTGGAATCAATA\t1\t0.02\tNo Hit\n-CTGCTCTGAGCACTTAGCACGCTCTAGTTCATGCAGCGATCCTCACGACCACCC\t1\t0.02\tNo Hit\n-GGCGACACATGGAGCTGGCCCAGCAAGAGGTTCTAACATCAGTGACAGATAGGA\t1\t0.02\tNo Hit\n-ATAAAATGTTCCAAAATCTATGAAATATTAAATATTATACTTCAAAATAAAGTA\t1\t0.02\tNo Hit\n-AGATTGGAATTGAATCAAGGCAGCCTAGTTTCAGAGTACATACTCTGTGTTTTC\t1\t0.02\tNo Hit\n-TAACTCTTTATAAAGCATATATAGCATCTGAACAAGAAATATGACACTAAGTCT\t1\t0.02\tNo Hit\n-GTGAATGATGTCACAGATGCTGAACAAATGCCAATTGTGAGCCAGGTATGGAGC\t1\t0.02\tNo Hit\n-AAGAATGTGGAAGTTAAGGGAGAAGAAATGTCAGTGTCATTCCTAAAGATAGTG\t1\t0.02\tNo Hit\n-TGTTATCTTCATTTGCTAGGTTATTCCACAAGCCAAGCATCCATTTCTGTGAAG\t1\t0.02\tNo Hit\n->>END_MODULE\n->>Adapter Content\tpass\n-#Position\tIllumina Universal Adapter\tIllumina Small RNA 3' Adapter\tIllumina Small RNA 5' Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n-1\t0.0\t0.0\t0.0\t0.0\t0.0\n-2\t0.02\t0.0\t0.0\t0.0\t0.0\n-3\t0.02\t0.0\t0.0\t0.0\t0.0\n-4\t0.02\t0.0\t0.0\t0.0\t0.0\n-5\t0.02\t0.0\t0.0\t0.0\t0.0\n-6\t0.02\t0.0\t0.0\t0.0\t0.0\n-7\t0.02\t0.0\t0.0\t0.0\t0.0\n-8\t0.02\t0.0\t0.0\t0.0\t0.0\n-9\t0.02\t0.0\t0.0\t0.0\t0.0\n-10\t0.02\t0.0\t0.0\t0.0\t0.0\n-11\t0.02\t0.0\t0.0\t0.0\t0.0\n-12\t0.02\t0.0\t0.0\t0.0\t0.0\n-13\t0.02\t0.0\t0.0\t0.0\t0.0\n-14\t0.02\t0.0\t0.0\t0.0\t0.0\n-15\t0.02\t0.0\t0.0\t0.0\t0.0\n-16\t0.02\t0.0\t0.0\t0.0\t0.0\n-17\t0.02\t0.0\t0.0\t0.0\t0.0\n-18\t0.02\t0.0\t0.0\t0.0\t0.0\n-19\t0.06\t0.0\t0.0\t0.0\t0.0\n-20\t0.36\t0.0\t0.0\t0.0\t0.0\n-21\t0.36\t0.0\t0.0\t0.0\t0.0\n-22\t0.36\t0.0\t0.0\t0.0\t0.0\n-23\t0.36\t0.0\t0.0\t0.0\t0.0\n-24\t0.36\t0.0\t0.0\t0.0\t0.0\n-25\t0.4\t0.0\t0.0\t0.0\t0.0\n-26\t0.4\t0.0\t0.0\t0.0\t0.0\n-27\t0.42\t0.0\t0.0\t0.0\t0.0\n-28\t0.62\t0.0\t0.0\t0.0\t0.0\n-29\t0.66\t0.0\t0.0\t0.0\t0.0\n-30\t0.68\t0.0\t0.0\t0.0\t0.0\n-31\t0.68\t0.0\t0.0\t0.0\t0.0\n-32\t0.68\t0.0\t0.0\t0.0\t0.0\n-33\t0.68\t0.0\t0.0\t0.0\t0.0\n-34\t0.7\t0.0\t0.0\t0.0\t0.0\n-35\t0.76\t0.0\t0.0\t0.0\t0.0\n-36\t0.8\t0.0\t0.0\t0.0\t0.0\n-37\t0.88\t0.0\t0.0\t0.0\t0.0\n-38\t1.0\t0.0\t0.0\t0.0\t0.0\n-39\t1.12\t0.0\t0.0\t0.0\t0.0\n-40\t1.22\t0.0\t0.0\t0.0\t0.0\n-41\t1.38\t0.0\t0.0\t0.0\t0.0\n-42\t1.48\t0.0\t0.0\t0.0\t0.0\n-43\t1.68\t0.0\t0.0\t0.0\t0.0\n->>END_MODULE\n->>Kmer Content\tpass\n->>END_MODULE\n" |
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_data_adapters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_data_adapters.txt Thu May 16 07:45:56 2019 -0400 |
| b |
| b'@@ -0,0 +1,417 @@\n+##FastQC\t0.11.8\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\t1000trimmed_fastq\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t4905\n+Sequences flagged as poor quality\t0\n+Sequence length\t1-108\n+%GC\t40\n+>>END_MODULE\n+>>Per base sequence quality\tpass\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th 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sequence quality scores\twarn\n+#Quality\tCount\n+20\t7.0\n+21\t24.0\n+22\t47.0\n+23\t78.0\n+24\t226.0\n+25\t513.0\n+26\t830.0\n+27\t1017.0\n+28\t947.0\n+29\t645.0\n+30\t352.0\n+31\t157.0\n+32\t55.0\n+33\t6.0\n+34\t1.0\n+>>END_MODULE\n+>>Per base sequence content\tpass\n+#Base\tG\tA\tT\tC\n+1\t21.223241590214066\t33.00713557594291\t25.97349643221203\t19.79612640163099\n+2\t23.76580987352101\t31.415748674010608\t27.315381476948186\t17.503059975520195\n+3\t21.876916785933346\t28.70578613780413\t29.46227765283173\t19.95501942343079\n+4\t21.55048324079786\t28.295290972650626\t28.850503804236066\t21.303721982315444\n+5\t21.219055543998337\t30.205949656750576\t28.271271063033076\t20.3037237362'..b'6901122\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+41\t0.040774719673802244\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.020387359836901122\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.020387359836901122\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+42\t0.040774719673802244\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.020387359836901122\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.020387359836901122\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+43\t0.040774719673802244\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.020387359836901122\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.020387359836901122\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+44\t0.040774719673802244\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.020387359836901122\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.020387359836901122\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+45\t0.040774719673802244\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.020387359836901122\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.020387359836901122\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+46\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.040774719673802244\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.040774719673802244\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.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|
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_data_contaminants.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_data_contaminants.txt Thu May 16 07:45:56 2019 -0400 |
| b |
| b'@@ -0,0 +1,424 @@\n+##FastQC\t0.11.8\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\t1000trimmed_fastq\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t4905\n+Sequences flagged as poor quality\t0\n+Sequence length\t1-108\n+%GC\t40\n+>>END_MODULE\n+>>Per base sequence quality\tpass\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t29.282772680937818\t31.0\t27.0\t33.0\t23.0\t34.0\n+2\t28.832925336597306\t30.0\t27.0\t32.0\t22.0\t33.0\n+3\t28.896953588223266\t30.0\t27.0\t32.0\t23.0\t34.0\n+4\t29.006785934608267\t30.0\t27.0\t32.0\t23.0\t34.0\n+5\t28.9377990430622\t30.0\t27.0\t32.0\t22.0\t34.0\n+6\t29.002938706968934\t30.0\t27.0\t32.0\t23.0\t34.0\n+7\t28.899830220713074\t30.0\t27.0\t32.0\t22.0\t34.0\n+8\t28.900706184463942\t30.0\t27.0\t32.0\t22.0\t33.0\n+9\t28.754602555772145\t30.0\t27.0\t32.0\t22.0\t34.0\n+10-11\t28.822083022456294\t30.0\t27.0\t32.0\t22.5\t33.0\n+12-13\t28.74898578710789\t30.0\t26.5\t32.0\t22.0\t33.0\n+14-15\t28.53370750727077\t30.0\t26.0\t32.0\t22.0\t33.5\n+16-17\t28.52661127583153\t30.0\t26.0\t32.0\t22.0\t33.0\n+18-19\t28.68343192244741\t30.0\t26.0\t32.0\t22.5\t33.0\n+20-21\t28.370130166336985\t29.5\t26.0\t32.0\t22.0\t33.0\n+22-23\t28.185946266098476\t29.0\t26.0\t32.0\t22.0\t33.0\n+24-25\t28.13009469533431\t29.0\t26.0\t32.0\t21.5\t33.0\n+26-27\t28.075768267577\t29.0\t26.0\t32.0\t21.5\t33.0\n+28-29\t27.828024188665616\t29.0\t25.0\t32.0\t21.0\t33.0\n+30-31\t27.792826876513317\t29.0\t25.0\t31.5\t21.0\t33.0\n+32-33\t27.490989073616355\t28.0\t25.0\t31.0\t21.0\t33.0\n+34-35\t27.357199679261562\t28.0\t24.5\t31.0\t21.0\t33.0\n+36-37\t27.062158129410527\t28.0\t24.0\t31.0\t20.5\t33.0\n+38-39\t27.238022216783758\t28.0\t24.0\t31.0\t21.0\t33.0\n+40-41\t27.028963434226593\t28.0\t24.0\t31.0\t20.5\t33.0\n+42-43\t26.90862078496675\t27.0\t24.0\t31.0\t20.5\t33.0\n+44-45\t26.632003369751054\t27.0\t24.0\t30.0\t20.0\t32.0\n+46-47\t26.83042786373109\t27.5\t24.0\t31.0\t20.5\t32.0\n+48-49\t26.431681832255798\t27.0\t23.5\t30.0\t20.0\t32.0\n+50-51\t26.219000735104444\t27.0\t23.0\t30.0\t20.0\t32.0\n+52-53\t25.925690423864786\t26.5\t22.5\t29.5\t19.5\t31.5\n+54-55\t27.995241016389798\t29.5\t25.5\t31.5\t20.5\t33.0\n+56-57\t30.410857897242785\t31.5\t28.5\t33.0\t25.5\t34.0\n+58-59\t30.4083885209713\t31.5\t28.5\t33.0\t25.5\t34.0\n+60-61\t30.444812362030905\t31.5\t29.0\t33.0\t26.0\t34.0\n+62-63\t30.44039735099338\t31.5\t29.0\t33.0\t25.5\t34.0\n+64-65\t30.441712697003883\t31.5\t29.0\t33.0\t25.5\t34.0\n+66-67\t30.51141384388807\t32.0\t29.0\t33.0\t25.5\t34.0\n+68-69\t30.05117820324006\t31.0\t28.0\t33.0\t24.5\t34.0\n+70-71\t30.276141384388808\t31.0\t29.0\t33.0\t25.0\t34.0\n+72-73\t30.385493372606774\t31.5\t29.0\t33.0\t25.5\t34.0\n+74-75\t30.213549337260677\t31.0\t28.5\t33.0\t25.5\t34.0\n+76-77\t29.678939617083948\t31.0\t28.0\t33.0\t24.5\t34.0\n+78-79\t30.019145802650957\t31.0\t28.0\t33.0\t24.5\t34.0\n+80-81\t29.664212076583212\t31.0\t27.5\t33.0\t24.0\t34.0\n+82-83\t29.653534609720175\t31.0\t28.0\t32.5\t24.5\t34.0\n+84-85\t29.425625920471283\t30.5\t27.0\t32.0\t24.0\t34.0\n+86-87\t29.34057437407953\t30.0\t27.0\t32.5\t24.0\t34.0\n+88-89\t28.785714285714285\t30.0\t27.0\t32.0\t22.5\t33.5\n+90-91\t28.667525773195877\t29.5\t26.0\t32.0\t23.0\t33.0\n+92-93\t28.565905743740796\t29.0\t26.0\t32.0\t23.0\t33.0\n+94-95\t28.271723122238583\t29.0\t26.0\t32.0\t22.5\t33.0\n+96-97\t27.94955817378498\t29.0\t25.5\t31.0\t22.0\t33.0\n+98-99\t27.641132075471695\t28.0\t25.0\t31.0\t21.5\t33.0\n+100-101\t27.614716981132077\t28.0\t25.0\t31.0\t21.5\t33.0\n+102-103\t27.196226415094337\t28.0\t24.5\t31.0\t21.0\t32.5\n+104-105\t26.870943396226416\t27.5\t24.0\t31.0\t20.0\t32.5\n+106-107\t26.367593937711003\t27.0\t23.5\t30.0\t20.5\t32.0\n+108\t27.5650623885918\t28.0\t24.0\t31.0\t22.0\t33.0\n+>>END_MODULE\n+>>Per sequence quality scores\twarn\n+#Quality\tCount\n+20\t7.0\n+21\t24.0\n+22\t47.0\n+23\t78.0\n+24\t226.0\n+25\t513.0\n+26\t830.0\n+27\t1017.0\n+28\t947.0\n+29\t645.0\n+30\t352.0\n+31\t157.0\n+32\t55.0\n+33\t6.0\n+34\t1.0\n+>>END_MODULE\n+>>Per base sequence content\tpass\n+#Base\tG\tA\tT\tC\n+1\t21.223241590214066\t33.00713557594291\t25.97349643221203\t19.79612640163099\n+2\t23.76580987352101\t31.415748674010608\t27.315381476948186\t17.503059975520195\n+3\t21.876916785933346\t28.70578613780413\t29.46227765283173\t19.95501942343079\n+4\t21.55048324079786\t28.295290972650626\t28.850503804236066\t21.303721982315444\n+5\t21.219055543998337\t30.205949656750576\t28.271271063033076\t20.3037237362'..b"17.0\n+92\t15.5\n+93\t14.5\n+94\t13.5\n+95\t13.5\n+96\t15.0\n+97\t15.5\n+98\t17.0\n+99\t16.0\n+100\t13.5\n+>>END_MODULE\n+>>Per base N content\tpass\n+#Base\tN-Count\n+1\t0.0\n+2\t0.0\n+3\t0.0\n+4\t0.0\n+5\t0.0\n+6\t0.0\n+7\t0.0\n+8\t0.0\n+9\t0.0\n+10-11\t0.0\n+12-13\t0.0\n+14-15\t0.0\n+16-17\t0.0\n+18-19\t0.0\n+20-21\t0.0\n+22-23\t0.0\n+24-25\t0.0\n+26-27\t0.0\n+28-29\t0.0\n+30-31\t0.0\n+32-33\t0.0\n+34-35\t0.0\n+36-37\t0.0\n+38-39\t0.0\n+40-41\t0.0\n+42-43\t0.0\n+44-45\t0.0\n+46-47\t0.0\n+48-49\t0.0\n+50-51\t0.0\n+52-53\t0.0\n+54-55\t0.0\n+56-57\t0.0\n+58-59\t0.0\n+60-61\t0.0\n+62-63\t0.0\n+64-65\t0.0\n+66-67\t0.0\n+68-69\t0.0\n+70-71\t0.0\n+72-73\t0.0\n+74-75\t0.0\n+76-77\t0.0\n+78-79\t0.0\n+80-81\t0.0\n+82-83\t0.0\n+84-85\t0.0\n+86-87\t0.0\n+88-89\t0.0\n+90-91\t0.0\n+92-93\t0.0\n+94-95\t0.0\n+96-97\t0.0\n+98-99\t0.0\n+100-101\t0.0\n+102-103\t0.0\n+104-105\t0.0\n+106-107\t0.0\n+108\t0.0\n+>>END_MODULE\n+>>Sequence Length Distribution\twarn\n+#Length\tCount\n+0-4\t98.0\n+5-9\t250.0\n+10-14\t257.0\n+15-19\t279.0\n+20-24\t321.0\n+25-29\t396.0\n+30-34\t401.0\n+35-39\t433.0\n+40-44\t401.0\n+45-49\t385.0\n+50-54\t320.0\n+55-59\t5.0\n+60-64\t1.0\n+65-69\t0.0\n+70-74\t0.0\n+75-79\t0.0\n+80-84\t0.0\n+85-89\t0.0\n+90-94\t0.0\n+95-99\t33.0\n+100-104\t0.0\n+105-109\t1325.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\tpass\n+#Total Deduplicated Percentage\t98.73598369011212\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t99.44249432170142\t98.1855249745158\n+2\t0.47491224447656405\t0.9378185524974516\n+3\t0.041296716911005574\t0.12232415902140673\n+4\t0.020648358455502787\t0.08154943934760449\n+5\t0.0\t0.0\n+6\t0.0\t0.0\n+7\t0.0\t0.0\n+8\t0.0\t0.0\n+9\t0.0\t0.0\n+>10\t0.020648358455502787\t0.672782874617737\n+>50\t0.0\t0.0\n+>100\t0.0\t0.0\n+>500\t0.0\t0.0\n+>1k\t0.0\t0.0\n+>5k\t0.0\t0.0\n+>10k+\t0.0\t0.0\n+>>END_MODULE\n+>>Overrepresented sequences\twarn\n+#Sequence\tCount\tPercentage\tPossible Source\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\t33\t0.672782874617737\tTestContaminant (100% over 24bp)\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA 3' Adapter\tIllumina Small RNA 5' Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0.0\t0.0\t0.0\t0.0\t0.0\n+2\t0.0\t0.0\t0.0\t0.0\t0.0\n+3\t0.0\t0.0\t0.0\t0.0\t0.0\n+4\t0.0\t0.0\t0.0\t0.0\t0.0\n+5\t0.0\t0.0\t0.0\t0.0\t0.0\n+6\t0.0\t0.0\t0.0\t0.0\t0.0\n+7\t0.0\t0.0\t0.0\t0.0\t0.0\n+8\t0.0\t0.0\t0.0\t0.0\t0.0\n+9\t0.0\t0.0\t0.0\t0.0\t0.0\n+10-11\t0.0\t0.0\t0.0\t0.0\t0.0\n+12-13\t0.0\t0.0\t0.0\t0.0\t0.0\n+14-15\t0.0\t0.0\t0.0\t0.0\t0.0\n+16-17\t0.0\t0.0\t0.0\t0.0\t0.0\n+18-19\t0.0\t0.0\t0.0\t0.0\t0.0\n+20-21\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+22-23\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+24-25\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+26-27\t0.1325178389398573\t0.0\t0.0\t0.0\t0.0\n+28-29\t0.2038735983690112\t0.0\t0.0\t0.0\t0.0\n+30-31\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+32-33\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+34-35\t0.24464831804281345\t0.0\t0.0\t0.0\t0.0\n+36-37\t0.3058103975535168\t0.0\t0.0\t0.0\t0.0\n+38-39\t0.4383282364933741\t0.0\t0.0\t0.0\t0.0\n+40-41\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+42-43\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+44-45\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+46-47\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+48-49\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+50-51\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+52-53\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+54-55\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+56-57\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+58-59\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+60-61\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+62-63\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+64-65\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+66-67\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+68-69\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+70-71\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+72-73\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+74-75\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+76-77\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+78-79\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+80-81\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+82-83\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+84-85\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+86-87\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+88-89\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+90-91\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+92-93\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+94-95\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+96-97\t0.47910295616717635\t0.0\t0.0\t0.0\t0.0\n+>>END_MODULE\n" |
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_data_customlimits.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_data_customlimits.txt Thu May 16 07:45:56 2019 -0400 |
| b |
| b'@@ -0,0 +1,426 @@\n+##FastQC\t0.11.8\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\t1000trimmed_fastq\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t4905\n+Sequences flagged as poor quality\t0\n+Sequence length\t1-108\n+%GC\t40\n+>>END_MODULE\n+>>Per base sequence quality\tpass\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t29.282772680937818\t31.0\t27.0\t33.0\t23.0\t34.0\n+2\t28.832925336597306\t30.0\t27.0\t32.0\t22.0\t33.0\n+3\t28.896953588223266\t30.0\t27.0\t32.0\t23.0\t34.0\n+4\t29.006785934608267\t30.0\t27.0\t32.0\t23.0\t34.0\n+5\t28.9377990430622\t30.0\t27.0\t32.0\t22.0\t34.0\n+6\t29.002938706968934\t30.0\t27.0\t32.0\t23.0\t34.0\n+7\t28.899830220713074\t30.0\t27.0\t32.0\t22.0\t34.0\n+8\t28.900706184463942\t30.0\t27.0\t32.0\t22.0\t33.0\n+9\t28.754602555772145\t30.0\t27.0\t32.0\t22.0\t34.0\n+10-11\t28.822083022456294\t30.0\t27.0\t32.0\t22.5\t33.0\n+12-13\t28.74898578710789\t30.0\t26.5\t32.0\t22.0\t33.0\n+14-15\t28.53370750727077\t30.0\t26.0\t32.0\t22.0\t33.5\n+16-17\t28.52661127583153\t30.0\t26.0\t32.0\t22.0\t33.0\n+18-19\t28.68343192244741\t30.0\t26.0\t32.0\t22.5\t33.0\n+20-21\t28.370130166336985\t29.5\t26.0\t32.0\t22.0\t33.0\n+22-23\t28.185946266098476\t29.0\t26.0\t32.0\t22.0\t33.0\n+24-25\t28.13009469533431\t29.0\t26.0\t32.0\t21.5\t33.0\n+26-27\t28.075768267577\t29.0\t26.0\t32.0\t21.5\t33.0\n+28-29\t27.828024188665616\t29.0\t25.0\t32.0\t21.0\t33.0\n+30-31\t27.792826876513317\t29.0\t25.0\t31.5\t21.0\t33.0\n+32-33\t27.490989073616355\t28.0\t25.0\t31.0\t21.0\t33.0\n+34-35\t27.357199679261562\t28.0\t24.5\t31.0\t21.0\t33.0\n+36-37\t27.062158129410527\t28.0\t24.0\t31.0\t20.5\t33.0\n+38-39\t27.238022216783758\t28.0\t24.0\t31.0\t21.0\t33.0\n+40-41\t27.028963434226593\t28.0\t24.0\t31.0\t20.5\t33.0\n+42-43\t26.90862078496675\t27.0\t24.0\t31.0\t20.5\t33.0\n+44-45\t26.632003369751054\t27.0\t24.0\t30.0\t20.0\t32.0\n+46-47\t26.83042786373109\t27.5\t24.0\t31.0\t20.5\t32.0\n+48-49\t26.431681832255798\t27.0\t23.5\t30.0\t20.0\t32.0\n+50-51\t26.219000735104444\t27.0\t23.0\t30.0\t20.0\t32.0\n+52-53\t25.925690423864786\t26.5\t22.5\t29.5\t19.5\t31.5\n+54-55\t27.995241016389798\t29.5\t25.5\t31.5\t20.5\t33.0\n+56-57\t30.410857897242785\t31.5\t28.5\t33.0\t25.5\t34.0\n+58-59\t30.4083885209713\t31.5\t28.5\t33.0\t25.5\t34.0\n+60-61\t30.444812362030905\t31.5\t29.0\t33.0\t26.0\t34.0\n+62-63\t30.44039735099338\t31.5\t29.0\t33.0\t25.5\t34.0\n+64-65\t30.441712697003883\t31.5\t29.0\t33.0\t25.5\t34.0\n+66-67\t30.51141384388807\t32.0\t29.0\t33.0\t25.5\t34.0\n+68-69\t30.05117820324006\t31.0\t28.0\t33.0\t24.5\t34.0\n+70-71\t30.276141384388808\t31.0\t29.0\t33.0\t25.0\t34.0\n+72-73\t30.385493372606774\t31.5\t29.0\t33.0\t25.5\t34.0\n+74-75\t30.213549337260677\t31.0\t28.5\t33.0\t25.5\t34.0\n+76-77\t29.678939617083948\t31.0\t28.0\t33.0\t24.5\t34.0\n+78-79\t30.019145802650957\t31.0\t28.0\t33.0\t24.5\t34.0\n+80-81\t29.664212076583212\t31.0\t27.5\t33.0\t24.0\t34.0\n+82-83\t29.653534609720175\t31.0\t28.0\t32.5\t24.5\t34.0\n+84-85\t29.425625920471283\t30.5\t27.0\t32.0\t24.0\t34.0\n+86-87\t29.34057437407953\t30.0\t27.0\t32.5\t24.0\t34.0\n+88-89\t28.785714285714285\t30.0\t27.0\t32.0\t22.5\t33.5\n+90-91\t28.667525773195877\t29.5\t26.0\t32.0\t23.0\t33.0\n+92-93\t28.565905743740796\t29.0\t26.0\t32.0\t23.0\t33.0\n+94-95\t28.271723122238583\t29.0\t26.0\t32.0\t22.5\t33.0\n+96-97\t27.94955817378498\t29.0\t25.5\t31.0\t22.0\t33.0\n+98-99\t27.641132075471695\t28.0\t25.0\t31.0\t21.5\t33.0\n+100-101\t27.614716981132077\t28.0\t25.0\t31.0\t21.5\t33.0\n+102-103\t27.196226415094337\t28.0\t24.5\t31.0\t21.0\t32.5\n+104-105\t26.870943396226416\t27.5\t24.0\t31.0\t20.0\t32.5\n+106-107\t26.367593937711003\t27.0\t23.5\t30.0\t20.5\t32.0\n+108\t27.5650623885918\t28.0\t24.0\t31.0\t22.0\t33.0\n+>>END_MODULE\n+>>Per sequence quality scores\twarn\n+#Quality\tCount\n+20\t7.0\n+21\t24.0\n+22\t47.0\n+23\t78.0\n+24\t226.0\n+25\t513.0\n+26\t830.0\n+27\t1017.0\n+28\t947.0\n+29\t645.0\n+30\t352.0\n+31\t157.0\n+32\t55.0\n+33\t6.0\n+34\t1.0\n+>>END_MODULE\n+>>Per base sequence content\tpass\n+#Base\tG\tA\tT\tC\n+1\t21.223241590214066\t33.00713557594291\t25.97349643221203\t19.79612640163099\n+2\t23.76580987352101\t31.415748674010608\t27.315381476948186\t17.503059975520195\n+3\t21.876916785933346\t28.70578613780413\t29.46227765283173\t19.95501942343079\n+4\t21.55048324079786\t28.295290972650626\t28.850503804236066\t21.303721982315444\n+5\t21.219055543998337\t30.205949656750576\t28.271271063033076\t20.3037237362'..b"15.5\n+93\t14.5\n+94\t13.5\n+95\t13.5\n+96\t15.0\n+97\t15.5\n+98\t17.0\n+99\t16.0\n+100\t13.5\n+>>END_MODULE\n+>>Per base N content\tpass\n+#Base\tN-Count\n+1\t0.0\n+2\t0.0\n+3\t0.0\n+4\t0.0\n+5\t0.0\n+6\t0.0\n+7\t0.0\n+8\t0.0\n+9\t0.0\n+10-11\t0.0\n+12-13\t0.0\n+14-15\t0.0\n+16-17\t0.0\n+18-19\t0.0\n+20-21\t0.0\n+22-23\t0.0\n+24-25\t0.0\n+26-27\t0.0\n+28-29\t0.0\n+30-31\t0.0\n+32-33\t0.0\n+34-35\t0.0\n+36-37\t0.0\n+38-39\t0.0\n+40-41\t0.0\n+42-43\t0.0\n+44-45\t0.0\n+46-47\t0.0\n+48-49\t0.0\n+50-51\t0.0\n+52-53\t0.0\n+54-55\t0.0\n+56-57\t0.0\n+58-59\t0.0\n+60-61\t0.0\n+62-63\t0.0\n+64-65\t0.0\n+66-67\t0.0\n+68-69\t0.0\n+70-71\t0.0\n+72-73\t0.0\n+74-75\t0.0\n+76-77\t0.0\n+78-79\t0.0\n+80-81\t0.0\n+82-83\t0.0\n+84-85\t0.0\n+86-87\t0.0\n+88-89\t0.0\n+90-91\t0.0\n+92-93\t0.0\n+94-95\t0.0\n+96-97\t0.0\n+98-99\t0.0\n+100-101\t0.0\n+102-103\t0.0\n+104-105\t0.0\n+106-107\t0.0\n+108\t0.0\n+>>END_MODULE\n+>>Sequence Length Distribution\twarn\n+#Length\tCount\n+0-4\t98.0\n+5-9\t250.0\n+10-14\t257.0\n+15-19\t279.0\n+20-24\t321.0\n+25-29\t396.0\n+30-34\t401.0\n+35-39\t433.0\n+40-44\t401.0\n+45-49\t385.0\n+50-54\t320.0\n+55-59\t5.0\n+60-64\t1.0\n+65-69\t0.0\n+70-74\t0.0\n+75-79\t0.0\n+80-84\t0.0\n+85-89\t0.0\n+90-94\t0.0\n+95-99\t33.0\n+100-104\t0.0\n+105-109\t1325.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\tpass\n+#Total Deduplicated Percentage\t98.73598369011212\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t99.44249432170142\t98.1855249745158\n+2\t0.47491224447656405\t0.9378185524974516\n+3\t0.041296716911005574\t0.12232415902140673\n+4\t0.020648358455502787\t0.08154943934760449\n+5\t0.0\t0.0\n+6\t0.0\t0.0\n+7\t0.0\t0.0\n+8\t0.0\t0.0\n+9\t0.0\t0.0\n+>10\t0.020648358455502787\t0.672782874617737\n+>50\t0.0\t0.0\n+>100\t0.0\t0.0\n+>500\t0.0\t0.0\n+>1k\t0.0\t0.0\n+>5k\t0.0\t0.0\n+>10k+\t0.0\t0.0\n+>>END_MODULE\n+>>Overrepresented sequences\twarn\n+#Sequence\tCount\tPercentage\tPossible Source\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\t33\t0.672782874617737\tNo Hit\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA 3' Adapter\tIllumina Small RNA 5' Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0.0\t0.0\t0.0\t0.0\t0.0\n+2\t0.0\t0.0\t0.0\t0.0\t0.0\n+3\t0.0\t0.0\t0.0\t0.0\t0.0\n+4\t0.0\t0.0\t0.0\t0.0\t0.0\n+5\t0.0\t0.0\t0.0\t0.0\t0.0\n+6\t0.0\t0.0\t0.0\t0.0\t0.0\n+7\t0.0\t0.0\t0.0\t0.0\t0.0\n+8\t0.0\t0.0\t0.0\t0.0\t0.0\n+9\t0.0\t0.0\t0.0\t0.0\t0.0\n+10-11\t0.0\t0.0\t0.0\t0.0\t0.0\n+12-13\t0.0\t0.0\t0.0\t0.0\t0.0\n+14-15\t0.0\t0.0\t0.0\t0.0\t0.0\n+16-17\t0.0\t0.0\t0.0\t0.0\t0.0\n+18-19\t0.0\t0.0\t0.0\t0.0\t0.0\n+20-21\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+22-23\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+24-25\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+26-27\t0.1325178389398573\t0.0\t0.0\t0.0\t0.0\n+28-29\t0.2038735983690112\t0.0\t0.0\t0.0\t0.0\n+30-31\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+32-33\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+34-35\t0.24464831804281345\t0.0\t0.0\t0.0\t0.0\n+36-37\t0.3058103975535168\t0.0\t0.0\t0.0\t0.0\n+38-39\t0.4383282364933741\t0.0\t0.0\t0.0\t0.0\n+40-41\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+42-43\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+44-45\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+46-47\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+48-49\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+50-51\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+52-53\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+54-55\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+56-57\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+58-59\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+60-61\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+62-63\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+64-65\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+66-67\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+68-69\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+70-71\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+72-73\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+74-75\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+76-77\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+78-79\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+80-81\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+82-83\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+84-85\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+86-87\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+88-89\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+90-91\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+92-93\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+94-95\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+96-97\t0.47910295616717635\t0.0\t0.0\t0.0\t0.0\n+>>END_MODULE\n+>>Kmer Content\tpass\n+>>END_MODULE\n" |
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_data_hisat.txt --- a/test-data/fastqc_data_hisat.txt Fri May 10 14:23:53 2019 -0400 +++ b/test-data/fastqc_data_hisat.txt Thu May 16 07:45:56 2019 -0400 |
| b |
| @@ -1,4 +1,4 @@ -##FastQC 0.11.5 +##FastQC 0.11.8 >>Basic Statistics pass #Measure Value Filename hisat_output_1_bam @@ -444,5 +444,3 @@ 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 >>END_MODULE ->>Kmer Content pass ->>END_MODULE |
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_data_kmer.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_data_kmer.txt Thu May 16 07:45:56 2019 -0400 |
| b |
| b'@@ -0,0 +1,429 @@\n+##FastQC\t0.11.8\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\t1000trimmed_fastq\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t4905\n+Sequences flagged as poor quality\t0\n+Sequence length\t1-108\n+%GC\t40\n+>>END_MODULE\n+>>Per base sequence quality\tpass\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t29.282772680937818\t31.0\t27.0\t33.0\t23.0\t34.0\n+2\t28.832925336597306\t30.0\t27.0\t32.0\t22.0\t33.0\n+3\t28.896953588223266\t30.0\t27.0\t32.0\t23.0\t34.0\n+4\t29.006785934608267\t30.0\t27.0\t32.0\t23.0\t34.0\n+5\t28.9377990430622\t30.0\t27.0\t32.0\t22.0\t34.0\n+6\t29.002938706968934\t30.0\t27.0\t32.0\t23.0\t34.0\n+7\t28.899830220713074\t30.0\t27.0\t32.0\t22.0\t34.0\n+8\t28.900706184463942\t30.0\t27.0\t32.0\t22.0\t33.0\n+9\t28.754602555772145\t30.0\t27.0\t32.0\t22.0\t34.0\n+10-11\t28.822083022456294\t30.0\t27.0\t32.0\t22.5\t33.0\n+12-13\t28.74898578710789\t30.0\t26.5\t32.0\t22.0\t33.0\n+14-15\t28.53370750727077\t30.0\t26.0\t32.0\t22.0\t33.5\n+16-17\t28.52661127583153\t30.0\t26.0\t32.0\t22.0\t33.0\n+18-19\t28.68343192244741\t30.0\t26.0\t32.0\t22.5\t33.0\n+20-21\t28.370130166336985\t29.5\t26.0\t32.0\t22.0\t33.0\n+22-23\t28.185946266098476\t29.0\t26.0\t32.0\t22.0\t33.0\n+24-25\t28.13009469533431\t29.0\t26.0\t32.0\t21.5\t33.0\n+26-27\t28.075768267577\t29.0\t26.0\t32.0\t21.5\t33.0\n+28-29\t27.828024188665616\t29.0\t25.0\t32.0\t21.0\t33.0\n+30-31\t27.792826876513317\t29.0\t25.0\t31.5\t21.0\t33.0\n+32-33\t27.490989073616355\t28.0\t25.0\t31.0\t21.0\t33.0\n+34-35\t27.357199679261562\t28.0\t24.5\t31.0\t21.0\t33.0\n+36-37\t27.062158129410527\t28.0\t24.0\t31.0\t20.5\t33.0\n+38-39\t27.238022216783758\t28.0\t24.0\t31.0\t21.0\t33.0\n+40-41\t27.028963434226593\t28.0\t24.0\t31.0\t20.5\t33.0\n+42-43\t26.90862078496675\t27.0\t24.0\t31.0\t20.5\t33.0\n+44-45\t26.632003369751054\t27.0\t24.0\t30.0\t20.0\t32.0\n+46-47\t26.83042786373109\t27.5\t24.0\t31.0\t20.5\t32.0\n+48-49\t26.431681832255798\t27.0\t23.5\t30.0\t20.0\t32.0\n+50-51\t26.219000735104444\t27.0\t23.0\t30.0\t20.0\t32.0\n+52-53\t25.925690423864786\t26.5\t22.5\t29.5\t19.5\t31.5\n+54-55\t27.995241016389798\t29.5\t25.5\t31.5\t20.5\t33.0\n+56-57\t30.410857897242785\t31.5\t28.5\t33.0\t25.5\t34.0\n+58-59\t30.4083885209713\t31.5\t28.5\t33.0\t25.5\t34.0\n+60-61\t30.444812362030905\t31.5\t29.0\t33.0\t26.0\t34.0\n+62-63\t30.44039735099338\t31.5\t29.0\t33.0\t25.5\t34.0\n+64-65\t30.441712697003883\t31.5\t29.0\t33.0\t25.5\t34.0\n+66-67\t30.51141384388807\t32.0\t29.0\t33.0\t25.5\t34.0\n+68-69\t30.05117820324006\t31.0\t28.0\t33.0\t24.5\t34.0\n+70-71\t30.276141384388808\t31.0\t29.0\t33.0\t25.0\t34.0\n+72-73\t30.385493372606774\t31.5\t29.0\t33.0\t25.5\t34.0\n+74-75\t30.213549337260677\t31.0\t28.5\t33.0\t25.5\t34.0\n+76-77\t29.678939617083948\t31.0\t28.0\t33.0\t24.5\t34.0\n+78-79\t30.019145802650957\t31.0\t28.0\t33.0\t24.5\t34.0\n+80-81\t29.664212076583212\t31.0\t27.5\t33.0\t24.0\t34.0\n+82-83\t29.653534609720175\t31.0\t28.0\t32.5\t24.5\t34.0\n+84-85\t29.425625920471283\t30.5\t27.0\t32.0\t24.0\t34.0\n+86-87\t29.34057437407953\t30.0\t27.0\t32.5\t24.0\t34.0\n+88-89\t28.785714285714285\t30.0\t27.0\t32.0\t22.5\t33.5\n+90-91\t28.667525773195877\t29.5\t26.0\t32.0\t23.0\t33.0\n+92-93\t28.565905743740796\t29.0\t26.0\t32.0\t23.0\t33.0\n+94-95\t28.271723122238583\t29.0\t26.0\t32.0\t22.5\t33.0\n+96-97\t27.94955817378498\t29.0\t25.5\t31.0\t22.0\t33.0\n+98-99\t27.641132075471695\t28.0\t25.0\t31.0\t21.5\t33.0\n+100-101\t27.614716981132077\t28.0\t25.0\t31.0\t21.5\t33.0\n+102-103\t27.196226415094337\t28.0\t24.5\t31.0\t21.0\t32.5\n+104-105\t26.870943396226416\t27.5\t24.0\t31.0\t20.0\t32.5\n+106-107\t26.367593937711003\t27.0\t23.5\t30.0\t20.5\t32.0\n+108\t27.5650623885918\t28.0\t24.0\t31.0\t22.0\t33.0\n+>>END_MODULE\n+>>Per sequence quality scores\twarn\n+#Quality\tCount\n+20\t7.0\n+21\t24.0\n+22\t47.0\n+23\t78.0\n+24\t226.0\n+25\t513.0\n+26\t830.0\n+27\t1017.0\n+28\t947.0\n+29\t645.0\n+30\t352.0\n+31\t157.0\n+32\t55.0\n+33\t6.0\n+34\t1.0\n+>>END_MODULE\n+>>Per base sequence content\tpass\n+#Base\tG\tA\tT\tC\n+1\t21.223241590214066\t33.00713557594291\t25.97349643221203\t19.79612640163099\n+2\t23.76580987352101\t31.415748674010608\t27.315381476948186\t17.503059975520195\n+3\t21.876916785933346\t28.70578613780413\t29.46227765283173\t19.95501942343079\n+4\t21.55048324079786\t28.295290972650626\t28.850503804236066\t21.303721982315444\n+5\t21.219055543998337\t30.205949656750576\t28.271271063033076\t20.3037237362'..b"\n+1\t0.0\n+2\t0.0\n+3\t0.0\n+4\t0.0\n+5\t0.0\n+6\t0.0\n+7\t0.0\n+8\t0.0\n+9\t0.0\n+10-11\t0.0\n+12-13\t0.0\n+14-15\t0.0\n+16-17\t0.0\n+18-19\t0.0\n+20-21\t0.0\n+22-23\t0.0\n+24-25\t0.0\n+26-27\t0.0\n+28-29\t0.0\n+30-31\t0.0\n+32-33\t0.0\n+34-35\t0.0\n+36-37\t0.0\n+38-39\t0.0\n+40-41\t0.0\n+42-43\t0.0\n+44-45\t0.0\n+46-47\t0.0\n+48-49\t0.0\n+50-51\t0.0\n+52-53\t0.0\n+54-55\t0.0\n+56-57\t0.0\n+58-59\t0.0\n+60-61\t0.0\n+62-63\t0.0\n+64-65\t0.0\n+66-67\t0.0\n+68-69\t0.0\n+70-71\t0.0\n+72-73\t0.0\n+74-75\t0.0\n+76-77\t0.0\n+78-79\t0.0\n+80-81\t0.0\n+82-83\t0.0\n+84-85\t0.0\n+86-87\t0.0\n+88-89\t0.0\n+90-91\t0.0\n+92-93\t0.0\n+94-95\t0.0\n+96-97\t0.0\n+98-99\t0.0\n+100-101\t0.0\n+102-103\t0.0\n+104-105\t0.0\n+106-107\t0.0\n+108\t0.0\n+>>END_MODULE\n+>>Sequence Length Distribution\twarn\n+#Length\tCount\n+0-4\t98.0\n+5-9\t250.0\n+10-14\t257.0\n+15-19\t279.0\n+20-24\t321.0\n+25-29\t396.0\n+30-34\t401.0\n+35-39\t433.0\n+40-44\t401.0\n+45-49\t385.0\n+50-54\t320.0\n+55-59\t5.0\n+60-64\t1.0\n+65-69\t0.0\n+70-74\t0.0\n+75-79\t0.0\n+80-84\t0.0\n+85-89\t0.0\n+90-94\t0.0\n+95-99\t33.0\n+100-104\t0.0\n+105-109\t1325.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\tpass\n+#Total Deduplicated Percentage\t98.73598369011212\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t99.44249432170142\t98.1855249745158\n+2\t0.47491224447656405\t0.9378185524974516\n+3\t0.041296716911005574\t0.12232415902140673\n+4\t0.020648358455502787\t0.08154943934760449\n+5\t0.0\t0.0\n+6\t0.0\t0.0\n+7\t0.0\t0.0\n+8\t0.0\t0.0\n+9\t0.0\t0.0\n+>10\t0.020648358455502787\t0.672782874617737\n+>50\t0.0\t0.0\n+>100\t0.0\t0.0\n+>500\t0.0\t0.0\n+>1k\t0.0\t0.0\n+>5k\t0.0\t0.0\n+>10k+\t0.0\t0.0\n+>>END_MODULE\n+>>Overrepresented sequences\twarn\n+#Sequence\tCount\tPercentage\tPossible Source\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\t33\t0.672782874617737\tNo Hit\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA 3' Adapter\tIllumina Small RNA 5' Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0.0\t0.0\t0.0\t0.0\t0.0\n+2\t0.0\t0.0\t0.0\t0.0\t0.0\n+3\t0.0\t0.0\t0.0\t0.0\t0.0\n+4\t0.0\t0.0\t0.0\t0.0\t0.0\n+5\t0.0\t0.0\t0.0\t0.0\t0.0\n+6\t0.0\t0.0\t0.0\t0.0\t0.0\n+7\t0.0\t0.0\t0.0\t0.0\t0.0\n+8\t0.0\t0.0\t0.0\t0.0\t0.0\n+9\t0.0\t0.0\t0.0\t0.0\t0.0\n+10-11\t0.0\t0.0\t0.0\t0.0\t0.0\n+12-13\t0.0\t0.0\t0.0\t0.0\t0.0\n+14-15\t0.0\t0.0\t0.0\t0.0\t0.0\n+16-17\t0.0\t0.0\t0.0\t0.0\t0.0\n+18-19\t0.0\t0.0\t0.0\t0.0\t0.0\n+20-21\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+22-23\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+24-25\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+26-27\t0.1325178389398573\t0.0\t0.0\t0.0\t0.0\n+28-29\t0.2038735983690112\t0.0\t0.0\t0.0\t0.0\n+30-31\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+32-33\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+34-35\t0.24464831804281345\t0.0\t0.0\t0.0\t0.0\n+36-37\t0.3058103975535168\t0.0\t0.0\t0.0\t0.0\n+38-39\t0.4383282364933741\t0.0\t0.0\t0.0\t0.0\n+40-41\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+42-43\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+44-45\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+46-47\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+48-49\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+50-51\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+52-53\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+54-55\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+56-57\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+58-59\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+60-61\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+62-63\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+64-65\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+66-67\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+68-69\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+70-71\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+72-73\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+74-75\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+76-77\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+78-79\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+80-81\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+82-83\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+84-85\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+86-87\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+88-89\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+90-91\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+92-93\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+94-95\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+96-97\t0.47910295616717635\t0.0\t0.0\t0.0\t0.0\n+>>END_MODULE\n+>>Kmer Content\twarn\n+#Sequence\tCount\tPValue\tObs/Exp Max\tMax Obs/Exp Position\n+ACG\t80\t0.0068203025\t21.952587\t94-95\n+TAT\t565\t1.3306382E-4\t9.658028\t104-105\n+>>END_MODULE\n" |
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_data_min_length.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_data_min_length.txt Thu May 16 07:45:56 2019 -0400 |
| b |
| b'@@ -0,0 +1,430 @@\n+##FastQC\t0.11.8\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\t1000trimmed_fastq\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t4905\n+Sequences flagged as poor quality\t0\n+Sequence length\t1-108\n+%GC\t40\n+>>END_MODULE\n+>>Per base sequence quality\tpass\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t29.282772680937818\t31.0\t27.0\t33.0\t23.0\t34.0\n+2\t28.832925336597306\t30.0\t27.0\t32.0\t22.0\t33.0\n+3\t28.896953588223266\t30.0\t27.0\t32.0\t23.0\t34.0\n+4\t29.006785934608267\t30.0\t27.0\t32.0\t23.0\t34.0\n+5\t28.9377990430622\t30.0\t27.0\t32.0\t22.0\t34.0\n+6\t29.002938706968934\t30.0\t27.0\t32.0\t23.0\t34.0\n+7\t28.899830220713074\t30.0\t27.0\t32.0\t22.0\t34.0\n+8\t28.900706184463942\t30.0\t27.0\t32.0\t22.0\t33.0\n+9\t28.754602555772145\t30.0\t27.0\t32.0\t22.0\t34.0\n+10-11\t28.822083022456294\t30.0\t27.0\t32.0\t22.5\t33.0\n+12-13\t28.74898578710789\t30.0\t26.5\t32.0\t22.0\t33.0\n+14-15\t28.53370750727077\t30.0\t26.0\t32.0\t22.0\t33.5\n+16-17\t28.52661127583153\t30.0\t26.0\t32.0\t22.0\t33.0\n+18-19\t28.68343192244741\t30.0\t26.0\t32.0\t22.5\t33.0\n+20-21\t28.370130166336985\t29.5\t26.0\t32.0\t22.0\t33.0\n+22-23\t28.185946266098476\t29.0\t26.0\t32.0\t22.0\t33.0\n+24-25\t28.13009469533431\t29.0\t26.0\t32.0\t21.5\t33.0\n+26-27\t28.075768267577\t29.0\t26.0\t32.0\t21.5\t33.0\n+28-29\t27.828024188665616\t29.0\t25.0\t32.0\t21.0\t33.0\n+30-31\t27.792826876513317\t29.0\t25.0\t31.5\t21.0\t33.0\n+32-33\t27.490989073616355\t28.0\t25.0\t31.0\t21.0\t33.0\n+34-35\t27.357199679261562\t28.0\t24.5\t31.0\t21.0\t33.0\n+36-37\t27.062158129410527\t28.0\t24.0\t31.0\t20.5\t33.0\n+38-39\t27.238022216783758\t28.0\t24.0\t31.0\t21.0\t33.0\n+40-41\t27.028963434226593\t28.0\t24.0\t31.0\t20.5\t33.0\n+42-43\t26.90862078496675\t27.0\t24.0\t31.0\t20.5\t33.0\n+44-45\t26.632003369751054\t27.0\t24.0\t30.0\t20.0\t32.0\n+46-47\t26.83042786373109\t27.5\t24.0\t31.0\t20.5\t32.0\n+48-49\t26.431681832255798\t27.0\t23.5\t30.0\t20.0\t32.0\n+50-51\t26.219000735104444\t27.0\t23.0\t30.0\t20.0\t32.0\n+52-53\t25.925690423864786\t26.5\t22.5\t29.5\t19.5\t31.5\n+54-55\t27.995241016389798\t29.5\t25.5\t31.5\t20.5\t33.0\n+56-57\t30.410857897242785\t31.5\t28.5\t33.0\t25.5\t34.0\n+58-59\t30.4083885209713\t31.5\t28.5\t33.0\t25.5\t34.0\n+60-61\t30.444812362030905\t31.5\t29.0\t33.0\t26.0\t34.0\n+62-63\t30.44039735099338\t31.5\t29.0\t33.0\t25.5\t34.0\n+64-65\t30.441712697003883\t31.5\t29.0\t33.0\t25.5\t34.0\n+66-67\t30.51141384388807\t32.0\t29.0\t33.0\t25.5\t34.0\n+68-69\t30.05117820324006\t31.0\t28.0\t33.0\t24.5\t34.0\n+70-71\t30.276141384388808\t31.0\t29.0\t33.0\t25.0\t34.0\n+72-73\t30.385493372606774\t31.5\t29.0\t33.0\t25.5\t34.0\n+74-75\t30.213549337260677\t31.0\t28.5\t33.0\t25.5\t34.0\n+76-77\t29.678939617083948\t31.0\t28.0\t33.0\t24.5\t34.0\n+78-79\t30.019145802650957\t31.0\t28.0\t33.0\t24.5\t34.0\n+80-81\t29.664212076583212\t31.0\t27.5\t33.0\t24.0\t34.0\n+82-83\t29.653534609720175\t31.0\t28.0\t32.5\t24.5\t34.0\n+84-85\t29.425625920471283\t30.5\t27.0\t32.0\t24.0\t34.0\n+86-87\t29.34057437407953\t30.0\t27.0\t32.5\t24.0\t34.0\n+88-89\t28.785714285714285\t30.0\t27.0\t32.0\t22.5\t33.5\n+90-91\t28.667525773195877\t29.5\t26.0\t32.0\t23.0\t33.0\n+92-93\t28.565905743740796\t29.0\t26.0\t32.0\t23.0\t33.0\n+94-95\t28.271723122238583\t29.0\t26.0\t32.0\t22.5\t33.0\n+96-97\t27.94955817378498\t29.0\t25.5\t31.0\t22.0\t33.0\n+98-99\t27.641132075471695\t28.0\t25.0\t31.0\t21.5\t33.0\n+100-101\t27.614716981132077\t28.0\t25.0\t31.0\t21.5\t33.0\n+102-103\t27.196226415094337\t28.0\t24.5\t31.0\t21.0\t32.5\n+104-105\t26.870943396226416\t27.5\t24.0\t31.0\t20.0\t32.5\n+106-107\t26.367593937711003\t27.0\t23.5\t30.0\t20.5\t32.0\n+108\t27.5650623885918\t28.0\t24.0\t31.0\t22.0\t33.0\n+>>END_MODULE\n+>>Per sequence quality scores\twarn\n+#Quality\tCount\n+20\t7.0\n+21\t24.0\n+22\t47.0\n+23\t78.0\n+24\t226.0\n+25\t513.0\n+26\t830.0\n+27\t1017.0\n+28\t947.0\n+29\t645.0\n+30\t352.0\n+31\t157.0\n+32\t55.0\n+33\t6.0\n+34\t1.0\n+>>END_MODULE\n+>>Per base sequence content\tpass\n+#Base\tG\tA\tT\tC\n+1\t21.223241590214066\t33.00713557594291\t25.97349643221203\t19.79612640163099\n+2\t23.76580987352101\t31.415748674010608\t27.315381476948186\t17.503059975520195\n+3\t21.876916785933346\t28.70578613780413\t29.46227765283173\t19.95501942343079\n+4\t21.55048324079786\t28.295290972650626\t28.850503804236066\t21.303721982315444\n+5\t21.219055543998337\t30.205949656750576\t28.271271063033076\t20.3037237362'..b"\n+1\t0.0\n+2\t0.0\n+3\t0.0\n+4\t0.0\n+5\t0.0\n+6\t0.0\n+7\t0.0\n+8\t0.0\n+9\t0.0\n+10-11\t0.0\n+12-13\t0.0\n+14-15\t0.0\n+16-17\t0.0\n+18-19\t0.0\n+20-21\t0.0\n+22-23\t0.0\n+24-25\t0.0\n+26-27\t0.0\n+28-29\t0.0\n+30-31\t0.0\n+32-33\t0.0\n+34-35\t0.0\n+36-37\t0.0\n+38-39\t0.0\n+40-41\t0.0\n+42-43\t0.0\n+44-45\t0.0\n+46-47\t0.0\n+48-49\t0.0\n+50-51\t0.0\n+52-53\t0.0\n+54-55\t0.0\n+56-57\t0.0\n+58-59\t0.0\n+60-61\t0.0\n+62-63\t0.0\n+64-65\t0.0\n+66-67\t0.0\n+68-69\t0.0\n+70-71\t0.0\n+72-73\t0.0\n+74-75\t0.0\n+76-77\t0.0\n+78-79\t0.0\n+80-81\t0.0\n+82-83\t0.0\n+84-85\t0.0\n+86-87\t0.0\n+88-89\t0.0\n+90-91\t0.0\n+92-93\t0.0\n+94-95\t0.0\n+96-97\t0.0\n+98-99\t0.0\n+100-101\t0.0\n+102-103\t0.0\n+104-105\t0.0\n+106-107\t0.0\n+108\t0.0\n+>>END_MODULE\n+>>Sequence Length Distribution\twarn\n+#Length\tCount\n+0-4\t98.0\n+5-9\t250.0\n+10-14\t257.0\n+15-19\t279.0\n+20-24\t321.0\n+25-29\t396.0\n+30-34\t401.0\n+35-39\t433.0\n+40-44\t401.0\n+45-49\t385.0\n+50-54\t320.0\n+55-59\t5.0\n+60-64\t1.0\n+65-69\t0.0\n+70-74\t0.0\n+75-79\t0.0\n+80-84\t0.0\n+85-89\t0.0\n+90-94\t0.0\n+95-99\t33.0\n+100-104\t0.0\n+105-109\t1325.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\tpass\n+#Total Deduplicated Percentage\t98.73598369011212\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t99.44249432170142\t98.1855249745158\n+2\t0.47491224447656405\t0.9378185524974516\n+3\t0.041296716911005574\t0.12232415902140673\n+4\t0.020648358455502787\t0.08154943934760449\n+5\t0.0\t0.0\n+6\t0.0\t0.0\n+7\t0.0\t0.0\n+8\t0.0\t0.0\n+9\t0.0\t0.0\n+>10\t0.020648358455502787\t0.672782874617737\n+>50\t0.0\t0.0\n+>100\t0.0\t0.0\n+>500\t0.0\t0.0\n+>1k\t0.0\t0.0\n+>5k\t0.0\t0.0\n+>10k+\t0.0\t0.0\n+>>END_MODULE\n+>>Overrepresented sequences\twarn\n+#Sequence\tCount\tPercentage\tPossible Source\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\t33\t0.672782874617737\tNo Hit\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA 3' Adapter\tIllumina Small RNA 5' Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0.0\t0.0\t0.0\t0.0\t0.0\n+2\t0.0\t0.0\t0.0\t0.0\t0.0\n+3\t0.0\t0.0\t0.0\t0.0\t0.0\n+4\t0.0\t0.0\t0.0\t0.0\t0.0\n+5\t0.0\t0.0\t0.0\t0.0\t0.0\n+6\t0.0\t0.0\t0.0\t0.0\t0.0\n+7\t0.0\t0.0\t0.0\t0.0\t0.0\n+8\t0.0\t0.0\t0.0\t0.0\t0.0\n+9\t0.0\t0.0\t0.0\t0.0\t0.0\n+10-11\t0.0\t0.0\t0.0\t0.0\t0.0\n+12-13\t0.0\t0.0\t0.0\t0.0\t0.0\n+14-15\t0.0\t0.0\t0.0\t0.0\t0.0\n+16-17\t0.0\t0.0\t0.0\t0.0\t0.0\n+18-19\t0.0\t0.0\t0.0\t0.0\t0.0\n+20-21\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+22-23\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+24-25\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+26-27\t0.1325178389398573\t0.0\t0.0\t0.0\t0.0\n+28-29\t0.2038735983690112\t0.0\t0.0\t0.0\t0.0\n+30-31\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+32-33\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+34-35\t0.24464831804281345\t0.0\t0.0\t0.0\t0.0\n+36-37\t0.3058103975535168\t0.0\t0.0\t0.0\t0.0\n+38-39\t0.4383282364933741\t0.0\t0.0\t0.0\t0.0\n+40-41\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+42-43\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+44-45\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+46-47\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+48-49\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+50-51\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+52-53\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+54-55\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+56-57\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+58-59\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+60-61\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+62-63\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+64-65\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+66-67\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+68-69\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+70-71\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+72-73\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+74-75\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+76-77\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+78-79\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+80-81\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+82-83\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+84-85\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+86-87\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+88-89\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+90-91\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+92-93\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+94-95\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+96-97\t0.47910295616717635\t0.0\t0.0\t0.0\t0.0\n+98-99\t0.0\t0.0\t0.0\t0.0\t0.0\n+100-101\t0.0\t0.0\t0.0\t0.0\t0.0\n+102-103\t0.0\t0.0\t0.0\t0.0\t0.0\n+104-105\t0.0\t0.0\t0.0\t0.0\t0.0\n+106-107\t0.0\t0.0\t0.0\t0.0\t0.0\n+108\t0.0\t0.0\t0.0\t0.0\t0.0\n+>>END_MODULE\n" |
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_data_nogroup.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_data_nogroup.txt Thu May 16 07:45:56 2019 -0400 |
| b |
| b'@@ -0,0 +1,701 @@\n+##FastQC\t0.11.8\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\t1000trimmed_fastq\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t4905\n+Sequences flagged as poor quality\t0\n+Sequence length\t1-108\n+%GC\t40\n+>>END_MODULE\n+>>Per base sequence quality\tpass\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t29.282772680937818\t31.0\t27.0\t33.0\t23.0\t34.0\n+2\t28.832925336597306\t30.0\t27.0\t32.0\t22.0\t33.0\n+3\t28.896953588223266\t30.0\t27.0\t32.0\t23.0\t34.0\n+4\t29.006785934608267\t30.0\t27.0\t32.0\t23.0\t34.0\n+5\t28.9377990430622\t30.0\t27.0\t32.0\t22.0\t34.0\n+6\t29.002938706968934\t30.0\t27.0\t32.0\t23.0\t34.0\n+7\t28.899830220713074\t30.0\t27.0\t32.0\t22.0\t34.0\n+8\t28.900706184463942\t30.0\t27.0\t32.0\t22.0\t33.0\n+9\t28.754602555772145\t30.0\t27.0\t32.0\t22.0\t34.0\n+10\t28.7412771560237\t30.0\t27.0\t32.0\t22.0\t33.0\n+11\t28.90288888888889\t30.0\t27.0\t32.0\t23.0\t33.0\n+12\t28.87929100291676\t30.0\t27.0\t32.0\t22.0\t33.0\n+13\t28.618680571299024\t30.0\t26.0\t32.0\t22.0\t33.0\n+14\t28.638112688960145\t30.0\t26.0\t32.0\t22.0\t34.0\n+15\t28.429302325581396\t30.0\t26.0\t32.0\t22.0\t33.0\n+16\t28.569205376090544\t30.0\t26.0\t32.0\t22.0\t33.0\n+17\t28.484017175572518\t30.0\t26.0\t32.0\t22.0\t33.0\n+18\t28.661082787084244\t30.0\t26.0\t32.0\t22.0\t33.0\n+19\t28.70578105781058\t30.0\t26.0\t32.0\t23.0\t33.0\n+20\t28.363591146480974\t30.0\t26.0\t32.0\t22.0\t33.0\n+21\t28.376669186192995\t29.0\t26.0\t32.0\t22.0\t33.0\n+22\t28.165041067761805\t29.0\t26.0\t32.0\t22.0\t33.0\n+23\t28.206851464435147\t29.0\t26.0\t32.0\t22.0\t33.0\n+24\t28.23748668796592\t29.0\t26.0\t32.0\t22.0\t33.0\n+25\t28.022702702702702\t29.0\t26.0\t32.0\t21.0\t33.0\n+26\t28.144438295517432\t29.0\t26.0\t32.0\t22.0\t33.0\n+27\t28.00709823963657\t29.0\t26.0\t32.0\t21.0\t33.0\n+28\t27.809689585146504\t29.0\t25.0\t32.0\t21.0\t33.0\n+29\t27.846358792184724\t29.0\t25.0\t32.0\t21.0\t33.0\n+30\t27.835653753026634\t29.0\t25.0\t32.0\t21.0\t33.0\n+31\t27.75\t29.0\t25.0\t31.0\t21.0\t33.0\n+32\t27.617984693877553\t28.0\t25.0\t31.0\t21.0\t33.0\n+33\t27.363993453355157\t28.0\t25.0\t31.0\t21.0\t33.0\n+34\t27.426421404682273\t28.0\t25.0\t31.0\t21.0\t33.0\n+35\t27.287977953840855\t28.0\t24.0\t31.0\t21.0\t33.0\n+36\t27.099041533546327\t28.0\t24.0\t31.0\t20.0\t33.0\n+37\t27.025274725274727\t28.0\t24.0\t31.0\t21.0\t33.0\n+38\t27.29315589353612\t28.0\t24.0\t31.0\t21.0\t33.0\n+39\t27.182888540031396\t28.0\t24.0\t31.0\t21.0\t33.0\n+40\t26.99109311740891\t28.0\t24.0\t31.0\t20.0\t33.0\n+41\t27.06683375104428\t28.0\t24.0\t31.0\t21.0\t33.0\n+42\t27.0341252699784\t27.0\t24.0\t31.0\t21.0\t33.0\n+43\t26.783116299955097\t27.0\t24.0\t31.0\t20.0\t33.0\n+44\t26.623600746268657\t27.0\t24.0\t30.0\t20.0\t32.0\n+45\t26.640405993233447\t27.0\t24.0\t30.0\t20.0\t32.0\n+46\t26.946867167919798\t28.0\t24.0\t31.0\t21.0\t32.0\n+47\t26.713988559542383\t27.0\t24.0\t31.0\t20.0\t32.0\n+48\t26.461663947797717\t27.0\t24.0\t30.0\t20.0\t32.0\n+49\t26.401699716713882\t27.0\t23.0\t30.0\t20.0\t32.0\n+50\t26.244655581947743\t27.0\t23.0\t30.0\t20.0\t32.0\n+51\t26.193345888261142\t27.0\t23.0\t30.0\t20.0\t32.0\n+52\t26.431592861863848\t27.0\t23.0\t30.0\t20.0\t32.0\n+53\t25.419787985865725\t26.0\t22.0\t29.0\t19.0\t31.0\n+54\t25.747813411078717\t27.0\t22.0\t30.0\t17.0\t32.0\n+55\t30.24266862170088\t32.0\t29.0\t33.0\t24.0\t34.0\n+56\t30.288235294117648\t31.0\t28.0\t33.0\t25.0\t34.0\n+57\t30.53348050036792\t32.0\t29.0\t33.0\t26.0\t34.0\n+58\t30.4878587196468\t32.0\t29.0\t33.0\t26.0\t34.0\n+59\t30.328918322295806\t31.0\t28.0\t33.0\t25.0\t34.0\n+60\t30.48933038999264\t32.0\t29.0\t33.0\t26.0\t34.0\n+61\t30.40029433406917\t31.0\t29.0\t33.0\t26.0\t34.0\n+62\t30.462104488594555\t31.0\t29.0\t33.0\t26.0\t34.0\n+63\t30.4186902133922\t32.0\t29.0\t33.0\t25.0\t34.0\n+64\t30.30831493745401\t31.0\t29.0\t33.0\t25.0\t34.0\n+65\t30.575110456553755\t32.0\t29.0\t33.0\t26.0\t34.0\n+66\t30.540500736377027\t32.0\t29.0\t33.0\t26.0\t34.0\n+67\t30.482326951399116\t32.0\t29.0\t33.0\t25.0\t34.0\n+68\t30.276141384388808\t31.0\t28.0\t33.0\t25.0\t34.0\n+69\t29.82621502209131\t31.0\t28.0\t33.0\t24.0\t34.0\n+70\t30.34462444771723\t31.0\t29.0\t33.0\t25.0\t34.0\n+71\t30.207658321060382\t31.0\t29.0\t33.0\t25.0\t34.0\n+72\t30.404270986745214\t32.0\t29.0\t33.0\t25.0\t34.0\n+73\t30.366715758468334\t31.0\t29.0\t33.0\t26.0\t34.0\n+74\t30.31222385861561\t31.0\t29.0\t33.0\t26.0\t34.0\n+75\t30.114874815905743\t31.0\t28.0\t33.0\t25.0\t34.0\n+76\t30.011045655375554\t31.0\t28.0\t33.0\t25.0\t34.0\n+77\t29.34'..b".020648358455502787\t0.672782874617737\n+>50\t0.0\t0.0\n+>100\t0.0\t0.0\n+>500\t0.0\t0.0\n+>1k\t0.0\t0.0\n+>5k\t0.0\t0.0\n+>10k+\t0.0\t0.0\n+>>END_MODULE\n+>>Overrepresented sequences\twarn\n+#Sequence\tCount\tPercentage\tPossible Source\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\t33\t0.672782874617737\tNo Hit\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA 3' Adapter\tIllumina Small RNA 5' Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0.0\t0.0\t0.0\t0.0\t0.0\n+2\t0.0\t0.0\t0.0\t0.0\t0.0\n+3\t0.0\t0.0\t0.0\t0.0\t0.0\n+4\t0.0\t0.0\t0.0\t0.0\t0.0\n+5\t0.0\t0.0\t0.0\t0.0\t0.0\n+6\t0.0\t0.0\t0.0\t0.0\t0.0\n+7\t0.0\t0.0\t0.0\t0.0\t0.0\n+8\t0.0\t0.0\t0.0\t0.0\t0.0\n+9\t0.0\t0.0\t0.0\t0.0\t0.0\n+10\t0.0\t0.0\t0.0\t0.0\t0.0\n+11\t0.0\t0.0\t0.0\t0.0\t0.0\n+12\t0.0\t0.0\t0.0\t0.0\t0.0\n+13\t0.0\t0.0\t0.0\t0.0\t0.0\n+14\t0.0\t0.0\t0.0\t0.0\t0.0\n+15\t0.0\t0.0\t0.0\t0.0\t0.0\n+16\t0.0\t0.0\t0.0\t0.0\t0.0\n+17\t0.0\t0.0\t0.0\t0.0\t0.0\n+18\t0.0\t0.0\t0.0\t0.0\t0.0\n+19\t0.0\t0.0\t0.0\t0.0\t0.0\n+20\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+21\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+22\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+23\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+24\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+25\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+26\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n+27\t0.14271151885830785\t0.0\t0.0\t0.0\t0.0\n+28\t0.1834862385321101\t0.0\t0.0\t0.0\t0.0\n+29\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+30\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+31\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+32\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+33\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+34\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n+35\t0.2650356778797146\t0.0\t0.0\t0.0\t0.0\n+36\t0.2854230377166157\t0.0\t0.0\t0.0\t0.0\n+37\t0.32619775739041795\t0.0\t0.0\t0.0\t0.0\n+38\t0.4077471967380224\t0.0\t0.0\t0.0\t0.0\n+39\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+40\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+41\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+42\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+43\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+44\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+45\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+46\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+47\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+48\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+49\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+50\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+51\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+52\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+53\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+54\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+55\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+56\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+57\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+58\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+59\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+60\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+61\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+62\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+63\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+64\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+65\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+66\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+67\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+68\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+69\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+70\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+71\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+72\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+73\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+74\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+75\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+76\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+77\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+78\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+79\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+80\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+81\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+82\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+83\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+84\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+85\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+86\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+87\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+88\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+89\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+90\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+91\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+92\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+93\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+94\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+95\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+96\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n+97\t0.4892966360856269\t0.0\t0.0\t0.0\t0.0\n+>>END_MODULE\n" |
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_report.html --- a/test-data/fastqc_report.html Fri May 10 14:23:53 2019 -0400 +++ b/test-data/fastqc_report.html Thu May 16 07:45:56 2019 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<html><head><title>1000gsample_fastq_bz2.bz2 FastQC Report</title><style type="text/css">\r\n+<html><head><title>1000trimmed_fastq FastQC Report</title><style type="text/css">\r\n @media screen {\r\n div.summary {\r\n width: 18em;\r\n@@ -184,4 +184,4 @@\n padding-top: 0;\r\n margin-top: 0;\r\n }\r\n-</style></head><body><div class="header"><div id="header_title"><img src="data:image/png;base64,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" alt="FastQC"/>FastQC Report</div><div id="header_filename">Sa 23 Dez 2017<br/>1000gsample_fastq_bz2.bz2</div></div><div class="summary"><h2>Summary</h2><ul><li><img src="data:image/png;base64,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" alt="[PASS]"/><a href="#M0">Basic Statistics</a></li><li><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAYAAABzenr0AAAEpklEQVR42s1X'..b'8JLCaTyWQymQKr7CHCbq7AYjKZTCaTKbAEFpPJZDKZTIElsJhMJpPJZDIFlhuVyWQymUymwBJYTCaTyWQyBZbAYjKZTCaTyRRYDhQmk8lkMpkCS2AxmUwmk8kUWAKLyWQymUwmU2A5UJhMJpPJZAosgcVkMplMJlNgCSwmk8lkMpkCS2A5UJhMJpPJZAosNyqTyWQymUyBJbCYTCaTyWQKLIHFZDKZTCaTKbDcqEwmk8lkMgWWwGIymUwmkymwBBaTyWQymUymwHKgMJlMJpPJFFgCi8lkMplMpsASWEwmk8lkMpkCy4HCZDKZTCZTYAksJpPJZDKZAktgMZlMJpPJFFgCi8lkMplMJlNguVGZTCaTyWQKLIHFZDKZTCZTYAksJpPJZDKZTIHlRmUymUwmkymwBBaTyWQymUyBJbCYTCaTyWQyBZYDhclkMplMpsASWEwmk8lkMgWWwGIymUwmk8kUWA4UJpPJZDKZAktgMZlMJpPJFFgCi8lkMplMpsASWEwmk8lkMpkCy43KZDKZTCZTYAksJpPJZDKZAktgMZlMJpPJZAosBwqTyWQymcxjB9bwzhZrKfO3AovJZDKZTKbAyp3BSgVWaTYJLCaTyWQymQIrGUaT1wTLSWAxmUwmk8kUWJ0D687MzMzs0HMGi8lkMplMJtNDhA4UJpPJZDKZAktgMZlMJpPJFFjRwBr9FCGTyWQymUyBVRdYw8NNasnvwWIymUwmkymwKs9gdXMFFpPJZDKZTIElsJhMJpPJZAosgcVkMplMJpMpsNyoTCaTyWQyBZbAYjKZTCaTKbAEFpPJZDKZTKbAcqAwmUwmk8kUWAKLyWQymUymwBJYTCaTyWQymQLLgcJkMplMJlNgCSwmk8lkMpkCS2AxmUwmk8kUWALLgcJkMplMJlNguVGZTCaTyWQKLIHFZDKZTCZTYAksJpPJZDKZTIHlRmUymUwmkymwBBaTyWQymUyBJbCYTCaTyWQyBZYDhclkMplMpsASWEwmk8lkMgWWwGIymUwmk8kUWA4UJpPJZDKZAktgMZlMJpPJFFgCi8lkMplMpsASWEwmk8lkMpkCy43KZDKZTCZTYAksJpPJZDKZAktgMZlMJpPJZAosNyqTyWQymUyBJbCYTCaTyWQKLIHFZDKZTCaTKbAcKEwmk8lkMgWWwGIymUwmkymwBBaTyWQymUymwHKgMJlMJpPJFFgCi8lkMplMpsASWEwmk8lkMgWWwGIymUwmk8kUWG5UJpPJZDKZAktgMZlMJpPJFFgCi8lkMplMJlNgOVCYTCaTyWQePrCGkwksJvPWzTff/P43v/n9r33tjbu7N548+fcvfOG7n/rUtz/84e+8+OL3PvOZ05f/+tznJi8/+uQn3/zIR3700kuT10/e8P7luy++yGQymWcw33756WuvXSawSvNIYDGZvzR//vP/+/GP//db3/rZ17/+k1de+Z8nT/7z05++ijudH7700r35Hx//+A8/8YkffOxjb3zwg9974YVvv/vdz971rmfD4MWLFy9Hevnvz3/+3IE1SaLGxpq/+Z//6eOXf+8rCy+/+9eTl6cv/Mvrv/KNf3rfq9O/mr3t0/e9dcmn95dkMs9uPvrAlx/99l89+q0vPfrNx49+4+VHv/5o8vL0vf/81iXf+8r8r67mkvfX6/7a3V/H+2v6gS8/feFVtzuTybxS8+2Xv/izL113YN3N9sXfefLWe/PixYsXL168eLnQy19+6G/v+u0CgTXffTO+/Ptfibw8/bVXX3/PN+7/1yVdcs+XfPwHf/P4Q3/3+A///vEfffXxH//D4z/5x8nL0/f/6+u/+m/3/zv/K5d0SZd0SZc88yXffnn02bvrPoNlZmZmdrMTWGZmZmabBdbY9acIzczMzATWL7uq1+/BMjMzMxNYW76PkmiLR15pDq5ecni4LtdrmO2c1z1zmVWh5W338N5XL5kXFt+26AhJXTIi5N9749dR43sv/QJpue36fr2f4b2vfooix3zLUZe6fau/Zkv/yV191OXfe9FBm0G6v+0e3rv7uovf110ysJ5/0EWXWf28VOCrXyR1V6fo3qf9Gp1ekdLPauPnueIz3yKkvmAi73r1Oubv8qo/26vXcVXLf34qbvHUsZq6L468u4qvuPhRl3/b9vceOXjqjoGKdOvyqY7f1sEvt7qn5EaOtOAXXeOnYvH6xgu15ZPQKJy+bd1RV31fN1Y9TSjzcUbu6zKXKf0yD97vlX5dHyew2r+c8hfoFVh1n/HGL5KOiVOdfV0u0BhYXW6yyPHQcqezxR1u+9dRr6/B+Iddd2i1vG1KKD3qWt627np1rIqKQ6j9vrGxxc/z7WDTO8P2Tu1y1BXd13UJrOr7uu3+MdnrrrX1N67fQmDF/x0QPyE8Vp08F1h7CKzSO5HJvykrzhvvKrBKT7+33OgVh1b7vylTZy+q33vp2eXUwyWRf823PFiTun3j30gyD7XEk3rxva8+TBa8jMAquouoPl9eetTtM7CKjqjbCqxez4Iam097rp5a7PhPtPjj/fH33vJv04rnSAW/Q1d86dZ95vv+Kyd4hKQ+SxXfqlu+zeQf6qp472P5wxzV38bqnseTv4uPPCdj8btU3VFXnfUtT6ZZ/HPwSzL1XioerFn9c9HX9QXrqvEfJEXPZKq+r6vO+jH8LDFH3XECq2ON1T1Zqu85pIqv7fizQTv+m2w1CDY9gxV870XXfSx5QlLpV3jH52TEg6bjQ4QV773xX+GrR13w2Kv4eo9c9/zli4664PmwipCtuF8qve7jlg/WVLz3cZvHSbf4eg9+GoPvPXjURT7zqaOuy3MuF8Hgda/4YM7z3g8bWH0fTKz+iYBzPkg39nt2UZd76osE1tnee/znkrof0rt6DtZG7z3/Ge7yU7cVX+/xf0+3vPfMZ77ihwG3DqyKMugYWH3f+y3f1wUf5tv6h1pu8L7u+gKr8UGfFrz0p5yCl+x+65aek2t5aHmHP0W46R1i/JNW/VOuO/kpwro73MZTy71+UPeCz4Zpvw9p+dnV6vulome21T1YE3zvkWe/9Q2sw9/XtTyXKHj2q/GHT+t+dLTiNw8UfY9uf++7CKy6XwTV8bdGFX2FdP8tXBVPmql4ck/RZz74L5uW327SKETetuU8yuqX/Xa/mab9d8Nc5L2PzaeWS8/iNP4erEah7qgLHttb3GqOui3OSrbfz7ecLL+6o67uuuff9fnf+9jvP2bjN7abmZmZ9T675FNgZmZmJrDMzMzMBJaZmZmZwDIzMzMzgWVmZmYmsMzMzMwElpmZmZkJLDMzMzOBZWZmZiawzMyOc4eY/Y+W5C+TMXv9lzfMTGCZ2X4bouK/65cKkU3+E/SXy5G6/yrtnq+RmQksM7tAQzR+7z9YOggsMxNYZtY5sFJntuavfPvP88uvapM3zH+E8QtPPob8tci8fvG9BC+fdzSWmcAys1sMrHmjLDZT6g9xbfVsUOmF55WTvxaRj3M1sIqupsAyE1hmdvzAypxbyrRU5G+rX99+4fibbPQu6j4SMxNYZnaQwIq8fvHBr6sIrKKH8ASWmQksM7tMYGViYudnsBqrSGCZmcAys9bAOs9zsLYOrNUzbfEnTi2+l4rnYKkrM4FlZjcaWGP5TxHO/yr4U4TbBVbwWsR/+i9/vYKOwDITWGZmtpyedeXqN7mbCSwzM6uPMJ8EMxNYZmYCy8wElpmZmZnAMjMzM7vN/T8IyOYDRVp3cQAAAABJRU5ErkJg" alt="Adapter graph" width="800" height="600"/></p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.11.8)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_report2.html --- a/test-data/fastqc_report2.html Fri May 10 14:23:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
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alt="Adapter graph" width="800" height="600"/></p></div><div class="module"><h2 id="M11"><img 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alt="[OK]"/>Kmer Content</h2><p>No overrepresented Kmers</p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.11.6)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_report_adapters.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_report_adapters.html Thu May 16 07:45:56 2019 -0400 |
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alt="Adapter graph" width="800" height="600"/></p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.11.8)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_report_contaminants.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_report_contaminants.html Thu May 16 07:45:56 2019 -0400 |
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alt="Adapter graph" width="800" height="600"/></p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.11.8)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_report_customlimits.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_report_customlimits.html Thu May 16 07:45:56 2019 -0400 |
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alt="Adapter graph" width="800" height="600"/></p></div><div class="module"><h2 id="M11"><img src="data:image/png;base64,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" alt="[OK]"/>Kmer Content</h2><p>No overrepresented Kmers</p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.11.8)</div></body></html>\n\\ No newline at end of file\n' |
| b |
| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_report_hisat.html --- a/test-data/fastqc_report_hisat.html Fri May 10 14:23:53 2019 -0400 +++ b/test-data/fastqc_report_hisat.html Thu May 16 07:45:56 2019 -0400 |
| [ |
| b'@@ -184,4 +184,4 @@\n padding-top: 0;\r\n margin-top: 0;\r\n }\r\n-</style></head><body><div class="header"><div id="header_title"><img src="data:image/png;base64,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" alt="FastQC"/>FastQC Report</div><div id="header_filename">Thu 16 Nov 2017<br/>hisat_output_1_bam</div></div><div class="summary"><h2>Summary</h2><ul><li><img src="data:image/png;base64,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" alt="[PASS]"/><a href="#M0">Basic Statistics</a></li><li><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAYAAABzenr0AAAFlUlEQVR42s2XCUzTVxzHybIs0IgCLYqyQ9RtmhjCNKKbikajYVc22NThNjYjeC0yWBESxAV1Ckw8QEUF5ChnS4FyFETucwWU+7ClHKKiImLI4nCz9bv3/pS7ra1HtM1Lm/b/fp/ve+93PQMABq9y6D/Bz+ANNvethWxPw3Xs3wx/YAb9Tn6j/700AeZc1qccrhGPw2UNkk8Fx9voIceX9Tcz6Hf62/B/PPrsCxNgzjW043iyGjheRkOWQRzFt2IH/Nl4DDFyHj'..b'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" alt="Adapter graph" width="870" height="600"/></p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.11.8)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_report_kmer.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_report_kmer.html Thu May 16 07:45:56 2019 -0400 |
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alt="Kmer graph" width="870" height="600"/></p><table><thead><tr><th>Sequence</th><th>Count</th><th>PValue</th><th>Obs/Exp Max</th><th>Max Obs/Exp Position</th></tr></thead><tbody><tr><td>ACG</td><td>80</td><td>0.0068203025</td><td>21.952587</td><td>94-95</td></tr><tr><td>TAT</td><td>565</td><td>1.3306382E-4</td><td>9.658028</td><td>104-105</td></tr></tbody></table></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.11.8)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_report_min_length.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_report_min_length.html Thu May 16 07:45:56 2019 -0400 |
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alt="Adapter graph" width="885" height="600"/></p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.11.8)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 9da02be9c6cc -r ddf5c37952ac test-data/fastqc_report_nogroup.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_report_nogroup.html Thu May 16 07:45:56 2019 -0400 |
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alt="Adapter graph" width="1455" height="600"/></p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.11.8)</div></body></html>\n\\ No newline at end of file\n' |