| Previous changeset 1:17ad142b56e6 (2021-10-05) Next changeset 3:8157a81f511c (2022-02-01) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad" |
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modified:
bbmap.xml macros.xml |
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added:
test-data/adapters.fa.gz test-data/bduk_output_dump1.fasta test-data/bduk_output_quhist1.tabular test-data/bduk_outputu1.fastqsanger test-data/bduk_outputu2.fastqsanger |
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| diff -r 17ad142b56e6 -r e0ca2ec4f5d9 bbmap.xml --- a/bbmap.xml Tue Oct 05 20:06:15 2021 +0000 +++ b/bbmap.xml Thu Nov 11 16:38:09 2021 +0000 |
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| @@ -61,23 +61,7 @@ #end if ]]></command> <inputs> - <conditional name="input_type_cond"> - <param name="input_type" type="select" label="Choose the category of the files to be analyzed"> - <option value="single" selected="true">Single dataset</option> - <option value="pair">Dataset pair</option> - <option value="paired">List of dataset pairs</option> - </param> - <when value="single"> - <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> - </when> - <when value="pair"> - <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> - <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/> - </when> - <when value="paired"> - <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/> - </when> - </conditional> + <expand macro="input_type_cond"/> <expand macro="reference_source_cond"/> <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can significantly extend the run time of the tool (it runs using a single thread)."> <option value="coordinate" selected="True">Sort by chromosomal coordinates</option> |
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| diff -r 17ad142b56e6 -r e0ca2ec4f5d9 macros.xml --- a/macros.xml Tue Oct 05 20:06:15 2021 +0000 +++ b/macros.xml Thu Nov 11 16:38:09 2021 +0000 |
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| @@ -31,6 +31,25 @@ </conditional> </actions> </macro> + <macro name="input_type_cond"> + <conditional name="input_type_cond"> + <param name="input_type" type="select" label="Choose the category of the files to be analyzed"> + <option value="single" selected="true">Single dataset</option> + <option value="pair">Dataset pair</option> + <option value="paired">List of dataset pairs</option> + </param> + <when value="single"> + <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> + </when> + <when value="pair"> + <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> + <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/> + </when> + <when value="paired"> + <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/> + </when> + </conditional> + </macro> <macro name="reference_source_cond"> <conditional name="ref_source_cond"> <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history"> @@ -46,10 +65,24 @@ </param> </when> <when value="history"> - <param name="reference" type="data" format="fasta" label="Using reference genome"> - <validator type="no_options" message="The current history does not include a fasta dataset"/> + <param name="reference" type="data" format="fasta" label="Using reference genome"/> + </when> + </conditional> + </macro> + <macro name="ktrim_cond"> + <conditional name="ktrim_cond"> + <param name="ktrim_select" type="select" label="Trim reads to remove bases matching reference kmers?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="ktrim" type="select" label="Select trimming position"> + <option value="r">Trim to the right</option> + <option value="l">Trim to the left</option> </param> - </when> + <param argument="minlength" type="integer" value="10" label="Minimum read length" help="Trimmed reads shorter than this will be discarded, pairs will be discarded if both are shorter."/> + </when> </conditional> </macro> <xml name="citations"> |
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| diff -r 17ad142b56e6 -r e0ca2ec4f5d9 test-data/adapters.fa.gz |
| b |
| Binary file test-data/adapters.fa.gz has changed |
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| diff -r 17ad142b56e6 -r e0ca2ec4f5d9 test-data/bduk_output_dump1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bduk_output_dump1.fasta Thu Nov 11 16:38:09 2021 +0000 |
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| @@ -0,0 +1,100 @@ +>116 +GAGATGGAACTGTAACTGGAGTTCCTT +>7 +TGCCTAAGTGACTAGAGTTCAGACGTG +>28 +TGAACTCCAGTCAAATTCCTTTATCTC +>141 +GCATACGAGATGTATAGGTGACTGGAG +>3 +GTTCAGCAGGAATACCGAGACCGATCT +>126 +GGTAGCATCTCGTATGCCGTCTTCTGC +>123 +GCCAAGGAACTCCAGTCACGTTTCGAT +>126 +ATACGAGATGCTAACGTGACTGGAGTT +>18 +CCGTATCTCGTATACCGTCTTCTGCTT +>26 +TCTGAACTCCAGTAACGAGTGGATATC +>17 +GAAGACGGCATACAAGATTGTTGACTG +>22 +TGAACTCCAGTCAAGTGAAACGATCTC +>50 +ACGCTACGCTATCACGTATGCCGTCTT +>103 +TCGGGTGCCAAGGAACTCCAGTCACAT +>141 +ATACATCTCGTATACCGTCTTCTGCTT +>113 +TCGGGTGCCAAGGAACTCCAGTCACGG +>84 +GAGATTACTACGCATCTCGTGGGCTCG +>122 +CGTGGCCATCTCGAATGCCGTCTTCTG +>139 +TCCAGTCACCGGAATATCTCGTATGCC +>42 +CAGAAGACGGCATACGAGATTCGCCTT +>107 +TGTGTGACTGGAGATCCTTGGCACCCG +>140 +CATACGAGATAGCAAGGTGACTGGAGT +>6 +GGTGACTGGAGTTAAGACGTGTGCTCT +>30 +TCTCTTATACACAACTCCGAGCCCACG +>122 +CAGTCACGTGGCCATCTCGTATGCCGT +>19 +GTCACATGTCAGAATCTCGTATGCCGT +>41 +GCGTGTAGATCTCAGTGGTCGCCGTAT +>1 +GTGACTGGAGTTCAGACGTGTGCTCTT +>15 +GTCTGAACTCCAGACACGGCTACATCT +>4 +TCCGATCTCAAGCAGAAGACGGCATAC +>119 +GAAGACGGCATACAAGATCTCTACGTG +>129 +GTCACATTCCTATATCGTATGCCGTCT +>107 +GATCACTGTGTGAATGGAGTTCCTTGG +>9 +ATACGAGATCACTATGTGACTGGAGTT +>24 +CTGAACTCCAGTCACGTTTCGGAATCT +>116 +TGGAACTGTGACTAGAGTTCCTTGGCA +>13 +GAAGACGGCATACAAGATCTGATCGTG +>30 +TCTTATACACATCACCGAGCCCACGAG +>49 +CAGAGAGGATCTCATATGCCGTCTTCT +>133 +TCGTGGTGACTGGAGTTCCTTGGCACC +>8 +CAGTCACTGACCAATCTCGTATGCCGT +>33 +TCTAGTGTAGATCACGGTGGTCGCCGT +>21 +TGCGGACGTGACTAGAGTTCAGACGTG +>37 +GACGACTCCTTACATGTAGATCTCGGT +>124 +GTACGGTGACTGGAGTTCCTTGGCACC +>69 +TACACTTATGCGAACGTCGGCAGCGTC +>149 +GCATACGAGATCTACGAGTGACTGGAG +>124 +GAGATCGTACGGTAACTGGAGTTCCTT +>105 +GCCAAGGAACTCCAGTCACTTAGGCAT +>150 +CAGTCACTCGGCAATCTCGTATGCCGT |
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| diff -r 17ad142b56e6 -r e0ca2ec4f5d9 test-data/bduk_output_quhist1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bduk_output_quhist1.tabular Thu Nov 11 16:38:09 2021 +0000 |
| b |
| @@ -0,0 +1,101 @@ +#BaseNum Read1_linear Read1_log Read2_linear Read2_log +1 16.400 4.332 32.940 32.694 +2 24.580 19.293 32.680 30.545 +3 29.880 28.913 32.720 32.218 +4 35.400 35.023 35.740 28.139 +5 35.610 35.076 35.980 34.688 +6 36.070 35.819 36.130 35.232 +7 36.030 35.134 35.750 28.304 +8 36.210 35.891 35.760 30.427 +9 37.770 36.724 37.550 36.174 +10 37.770 36.627 37.890 36.829 +11 38.130 34.528 37.720 35.825 +12 38.120 37.610 37.930 36.724 +13 37.600 29.816 37.860 33.975 +14 39.600 38.822 39.490 29.436 +15 39.240 37.118 39.430 34.527 +16 39.370 37.815 39.670 29.527 +17 39.230 35.062 39.310 34.199 +18 39.410 38.456 39.700 38.264 +19 39.470 38.621 38.680 28.791 +20 39.170 36.390 39.340 38.126 +21 39.340 38.280 39.320 37.141 +22 38.870 32.580 38.480 25.015 +23 39.370 37.125 38.850 32.436 +24 38.940 36.347 39.200 37.110 +25 38.560 36.248 39.000 28.586 +26 38.810 33.655 38.460 29.005 +27 38.930 35.395 38.560 25.539 +28 39.090 37.259 38.190 23.947 +29 38.610 25.879 38.730 30.749 +30 38.540 33.271 38.520 32.796 +31 38.840 33.517 38.040 30.447 +32 38.730 36.053 38.530 27.397 +33 38.340 34.385 38.880 35.605 +34 38.470 28.217 38.430 32.167 +35 37.350 30.035 38.560 26.684 +36 37.380 20.434 38.900 32.524 +37 37.810 32.591 38.450 34.632 +38 38.150 33.133 38.750 35.749 +39 37.660 31.924 38.420 26.003 +40 38.040 34.153 38.730 36.080 +41 37.970 35.596 39.020 37.708 +42 37.240 31.069 39.380 33.973 +43 37.740 29.175 38.840 35.607 +44 38.070 34.040 38.400 23.939 +45 37.690 30.131 38.160 26.507 +46 37.160 26.236 37.990 32.407 +47 37.820 35.168 37.330 29.388 +48 37.920 35.623 37.850 31.413 +49 38.150 34.322 37.830 27.255 +50 38.250 34.017 38.260 36.442 +51 38.060 36.455 36.270 30.125 +52 37.240 34.726 37.000 33.291 +53 37.700 32.804 37.210 34.667 +54 37.740 33.699 37.520 34.736 +55 37.780 33.713 37.880 35.604 +56 37.470 31.063 37.880 35.326 +57 36.680 26.593 36.810 22.646 +58 36.390 26.714 37.140 31.327 +59 35.960 29.732 36.900 20.404 +60 35.500 27.738 36.440 21.355 +61 35.800 28.761 36.200 20.579 +62 34.880 22.760 36.570 21.483 +63 35.560 30.716 36.180 21.372 +64 35.460 30.521 35.970 20.108 +65 35.090 25.249 35.450 20.127 +66 35.240 31.736 35.330 20.499 +67 35.230 25.003 35.410 21.618 +68 34.870 25.901 35.400 21.693 +69 34.560 24.095 35.200 21.684 +70 34.670 29.988 34.730 21.372 +71 35.010 32.741 34.710 21.582 +72 33.750 21.148 34.060 18.014 +73 34.130 29.634 34.040 18.342 +74 34.080 21.493 33.840 17.025 +75 33.590 20.367 33.380 16.366 +76 31.930 18.529 33.300 17.088 +77 32.400 18.486 32.360 15.307 +78 32.840 18.708 32.170 15.246 +79 33.190 18.732 32.130 15.504 +80 32.680 17.826 32.770 15.850 +81 32.690 17.578 32.640 15.552 +82 32.510 16.664 32.800 15.822 +83 31.640 15.134 32.350 15.209 +84 31.220 15.026 32.320 15.547 +85 31.270 14.413 32.170 15.387 +86 31.310 14.436 32.520 15.576 +87 32.130 14.923 32.070 15.354 +88 31.610 14.417 31.780 15.361 +89 31.240 14.665 32.290 15.854 +90 31.130 14.606 31.730 15.508 +91 31.350 14.867 32.120 14.926 +92 31.270 14.282 32.040 14.910 +93 31.790 14.879 31.770 14.676 +94 31.010 13.468 31.380 14.768 +95 30.280 12.737 31.220 14.847 +96 30.310 12.852 31.050 14.129 +97 30.390 12.411 31.160 13.935 +98 30.150 12.394 30.960 13.893 +99 30.300 11.964 30.610 13.166 +100 29.860 11.945 30.460 12.397 |
| b |
| diff -r 17ad142b56e6 -r e0ca2ec4f5d9 test-data/bduk_outputu1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bduk_outputu1.fastqsanger Thu Nov 11 16:38:09 2021 +0000 |
| b |
| @@ -0,0 +1,102 @@ +@XXXXXXXXXX:7:1101:1582:1835#/1 +NGCTTCAGTTGGTACAGGTGTGTCACCCGTAGTTTGTAGGCTTGGAAGCCTGTAAGCTGTAGGGAACGTGGCAAGAACCAGATCTGGCCTTCCATATCTC ++ +!1=DDDDDAFFDDEFFG@AGHBCFHIFIEGIC?DBFGIFF?FGDFIBFFII8BCFIEEF.@FFIIEFFCE=??B@>A@@@BBBAD>A:?BBBBB@>>>B: +@XXXXXXXXXX:7:1101:1610:1859#/1 +NTTATGTGTTACGTGAATCTCCTGAAGACAGCAGAAACTAGGTTGGTGAATTCTTATCCATTCTGCCATTCTGTATCTTTTAAGTGGAGCATTTAGGCTA ++ +!1=DDFDFHHHHHHJJIJJJJJJJJJJJIJIIJJJIJIJJJJIJJJIIJJJIJJJIIJJJJIIJJJJGIJJJIHJHHHHHHHFFFFFFDDDEEDEDDCDD +@XXXXXXXXXX:7:1101:1743:1871#/1 +NCGGGATGGAGGCAGGGCAAGCGGATGCAGGCCCAGCCCTGCCCTTACAGGTAGCTGGAAGTGACGAAGGAGTGGGGCCCCCGGACTCTGCTCAGGTGGA ++ +!1=DDDFFHHHHHIJJJEGGGIHIGIIGGGIIIJEHHHGGCCHIIIFHHFHADDCDDC@CECECCDDB7?BB9?BA>9<@DDB>>9>CD>:>CA9A:A@A +@XXXXXXXXXX:7:1101:1536:1878#/1 +NGGCCTTTTTGGACAGGTGGTGTGTGGTGGCCTTGGTATGTGCTTTCTCGTGTTACATCGCGCCATCATTGGTATATGGTTAGTGTGTTGGTTAGTAGGC ++ +!1=DDDFEHHHHCGGIJFHIECHEFHIGGGGIJI<BBFGEIFGIIJIIJJJEGGEGGIHCCBHBFFCCEDEEC@CDDDC3>:95>@ABCAA<?C?>CDCC +@XXXXXXXXXX:7:1101:2990:100153#/1 +GCCAGGAGTGACTGTGTTGTTCTTTGCTTTATATACATAAGCGCATCTCTTGCCCAAATAGAATTCTGTTTCATCTCGGGCGTAAACACCTTCAATTTTA ++ +@@@DDDFDBFHDFH<EHGIHGCHEGHGIIGIIEGFEIGGIIIIII<GICCE@4?BBFHGHAEGIHHIICDHEEEAAHFBEDD@B@B@><@D>CDDDDCCB +@XXXXXXXXXX:7:1101:1624:1906#/1 +NCCAGGTTTAAGGCATTACATCGAGGGGCTGAACTTGAGACAGTCCCTGAAAATGTAAGAACAGGAGCTAGAACTTGCTTATGGGAAGGGCCTAGGGAGA ++ +!1=DDFFFHHHHHJJJJJIJJJJJJJJJJJJJJJJJIJJIJIIJJJJJJJGIJJIIJIECGIHHHHFFFFEECEECEDDDDDDCDCDDDDDDDDDDDDD@ +@XXXXXXXXXX:7:1101:1666:1926#/1 +NGCAAACTGGTCAGGACCTGGAGCTGCTTGCCTGGCCTTGGCACAAGAGGCCGACATATGCCCAGCCCCTAGGAGTGACAGATCCGTCCTCTGTGGGAAC ++ +!1BDFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJIJJJJJJIJJJJJJJJJJJJJJJHHHHHHFFFFDDDDDDCCDBDDDDDDDDDDDDDDDDDDDDBCD +@XXXXXXXXXX:7:1101:2921:100163#/1 +CTCCGGATGCCAAAGGATCTGACAGTGTATCTAGCTTTGGAAAACACAGGGGTCTGCCCTGTGAGCTGCTCCAACACCTTGGCTGCTCGCGTCAGTCTGT ++ +CCBFFFFFHHHHHJJJIJIIIJJJJHIFFHGIIHEIJIIIIIJIIGIIIICHHHHIJIIEHHJIHHFHHFFFFFFBDDDDDCDDDDDDDDD@B@@CCDDD +@XXXXXXXXXX:7:1101:1513:1929#/1 +NCACTATCAAGGTTAGTGTCTATATCTACTTGAGANAAAATACTGAAAATTCAGTGTATGAAGCCAAATCCTGATTTAACAAGTTATTGGTAGTATAAGT ++ +!1:ABDDDDFFF:ACGFGFHHFIFAHEEHDFI@F8!1:CFEFFIGEFGIII>GIFICGGII@FFFIEFEADGIIEIFFFFFFFEEDDDDBDAC>>;;BA5 +@XXXXXXXXXX:7:1101:2759:100170#/1 +CTGCTCATCACATTCCAGATGCCATCACAGGCAATGACCATGAATTCATGGTCGTCAGTGAGAGTCAGCACCTTGATGTCAGGAAGGGCTGAAATCATCT ++ +CCCFFFFFHHHHHJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJIJJJIJJJIJJJJJJHIIJJJIJJJJJJJHHHHHHHFFFFFEEDDDDDBCDDDDDDD +@XXXXXXXXXX:7:1101:1708:1937#/1 +NGGTCGGTGTCCTTTTTTGGCGTCAAACTTATAGAGGGAAGCAGGGAATCTACCCAACCAAAGCCAATGAACAGTCAGTCAGTCCATCTAGTTAAGGTTC ++ +!1=BDDDDFDHHHIJJIJIJGIJIGGIJIGAGFHGHIGA=FCDFGHJJHEHFHHEFFFDABCDCDCCCDCDDDDDACDDCDDCAAACCDDDDDDACCACD +@XXXXXXXXXX:7:1101:2981:100211#/1 +GGGGTCAGTGGGAAAGGTGTCAATGGGACTTCGGTCTCCATGCCGAAACACCAAAGTCACAAACTTCAACTCCTTGGCTAGTACACTTCGGTCTAGCCAG ++ +@@CFDDDFFFFHHEIGGHIIIIJJIIDHIGGIJFGBHIIIGGGGGGGIIJJHJGIG=DECEEEFFFFCDCCE@CC@?CDCBDDCDCCCCBB?B@>CACAB +@XXXXXXXXXX:7:1101:1688:1946#/1 +NCCGCCTTCTTTCTCTACTTCGTGACCTTTTGTGGTCCCGAGACCTGCTGCATCTTCTGTCTGATGTTCGGCTTGAGTGTCTACTTCCTGAACGACTTCT ++ +!1:BDAAD<DDDDIEE>DBEEFEEFIIIIIEADEC?C>DD<?D@?@BDDDEEDIEIEDE=CEE>CE?CCC6=?########################### +@XXXXXXXXXX:7:1101:2767:100225#/1 +CGCCTGGTGTCAATGCGCACATCTGGAGTTCCCATCTCCTTCATGGCAAATTTCCGAATCTCTTTGAGTGCCCGAGGTGCACGCTTCTTGAAGCCCACTC ++ +@@@FDFFFGHHHFJJIJIIIIJIJIJIGHBD@DFGGGJIFIJJJJIIIIIGHIIGIJFIJJIJIG@EECCHEEDCAD>ACCCDDDDDACCAC@CDDDDDD +@XXXXXXXXXX:7:1101:1536:1959#/1 +NGATACTGTTGGGTCAGGACCAGGGCCTGCACCACCGAAATTCTGTCTTTTACAAACTGGACCAAGCGGTTGAGAATACAGGGGCCGAAGAGTAGGATTA ++ +!4:BB?DDHHDHAE?ECB@=GGI=<;CG@B;<D@DG:@FFABFBG<=FFGFHIIGGH@>==AEC?DECA<;8;3<AC>CCCC8&-5>@@59?4::>>>CC +@XXXXXXXXXX:7:1101:2797:100234#/1 +GTGCTGGTCTCTCTCCACGATCTCTTACGTGCTAGCAGGGTGAACAAGGACGCCTCGCTGTCATTGCACTCACGCCACAGGAGCCTGGCACATTTCCGCT ++ ++:?BDD8DFFFB8ED;@GF8A3?FH?B<)11?@FG<E<;@F629?BF@?2=A;4C6BE7-,7@;@;@A>;@CBB?=88?5(95983?(8<><AA###### +@XXXXXXXXXX:7:1101:1552:1976#/1 +NTGATGAGTTTGCTAATACAATGCCAGTCAGGCCACCTACGGTGAAAAGAAAGATGAATCCTAGGGCTCAGAGCACTGCAGCAGATCATTTCATATTGCT ++ +!1=DDFFFFHFHGJJJJIJJJJJJJJJJJIIJFGHGIIIJIJGHIEIIJJJHIGIIJGJIIJJJBHIIJHHHHHDEFCECEEEEDDDDDEFEEEEEEEDD +@XXXXXXXXXX:7:1101:1748:1978#/1 +NCGCTGAGCAGGGCAGGCAGTGGTGGAGGCAGCCCCCCAAGACCCCATCTCTATCACAGTGAGAGCATCTGAACTCCAAAGCCACGACAGAACAGCTCCC ++ +!1=DFFFFHHHHHIJJJJIJIJJFHJIIJIJJGJJIIJAHGGGHHHHFFFFFFEEDECE@CDDCDDDCDDDACCCCDDDDCDDDDDDDDBDDCCC@ACDD +@XXXXXXXXXX:7:1101:2779:100239#/1 +TGGGTGCTCTCCTTGGTCAGCTGCTGCTCGAACAGAGCACTTCTAGATACAGAGTTGGACCCAGACACAGCAGGGGTGGCCATGGCGGCTGGGAAAGACC ++ +@@@?DD?DFHHFFHIEEHIBGI9CFHFGCB::CGIGHG@BF<FHFHD@DDDBBDBFGH<C;C;==;C;;?H;;?<>88=@?C################## +@XXXXXXXXXX:7:1101:1593:1980#/1 +NGGCACCAGAAGCATGAGCATAGGCAGAGCCATTTCCACCATGCTGACGGCAGGCAAGAAGAAGACAAAAATGAACCCCTTTCATGCTTGTTTAGAAATG ++ +!1=DFFFFHHHHGJJJJJJJJIJJIJJJIGJIIJJJJGIIIJJJJJIIJJJJJJIIJHHHHHFFFFFEEDDDDDDDDDDDDDDDEDDDEDDDDDDDDDDD +@XXXXXXXXXX:7:1101:2946:100242#/1 +TGGGGATGTTGTTAAAAAAAATACAGGCTCCCCCACAACTGGGGTGCCTGGGGGGAACTTGGTCTGCTTCAGCCCAAGAGGAATCAAAAGATCAAAAGCA ++ +@@@FFDDDHHHHHJIIGIJIGEGIIJJIIJJGJJEECDEA=FHI-=?B?CEDDDD5583:AC3::94:CAACCDBABD8?BA?CCDDDDD@CCACCDCBD +@XXXXXXXXXX:7:1101:1987:1781#/1 +NTTAGCAGGTCCTCGTAGCGTTTCCGCAACTCTCGGAATCTGGAGTCTTCGGAGTGCAACTCTGAGGGTCCCGGGAAACTTGCGCGGCTCGCCTCGGCCA ++ +!1=DDFFFHHHHHJJJJJIJJJJIJJJJJJJJJJJJJJJGJJJJIIHIJJJIJHHGHFFFFFFCEEDDDDDDDDDBDDDDDDDDDDDDDDBBDDD9B?B< +@XXXXXXXXXX:7:1101:3046:100006#/1 +CTGTACAGCATGGATGTGGACAGGGAAAACAGCAAGTGCACACAGTGGGACAGGCCACAGGACAGGCTGGGAGTGAATAAAGAGTTCACACTGCTTCCCT ++ +CCCFFFFFHHHHHJJJIJJJJJJJJJJJJJJJIJJJFHIJJIIJIGGHIJJJJJJIJJIIJJJHHHHFFFD=C;?CDCDDD@>?>@CACDACCDDCDDDD +@XXXXXXXXXX:7:1101:1900:1788#/1 +NCCCGCTGCCCACGCCACTGTCCCGGCGCTGCCCTGGGCGCGGAATGCGCGTTAGGCAATCCCCGGTCTGCGCGTCCCACACGCAGATGTGGCCTGCCAG ++ +!1=DFFFFGHHGHJJJIJJIJJJJGIIJJJIIJJIJJJIHFFDDDDDDDDDBDDDDDDDDDDDDBD@BDDDB>BB<BBDDDDDDDDDDDECDDBDDDDC@ +@XXXXXXXXXX:7:1101:3214:100027#/1 +GGCTGAGGTACTGAATGAGGAACAGCAGGAGGTAACGTCTGAGGGTGCGGCTGGGGAACGGTTTGCACAGGGGTGGCTGTAGGAGCAGGAGGTGAAACAC ++ +@@@FFDFF?DFHHIIIIIIGIIGHGIIGIIII?FHHGDFGIGGIC6?FHIIFIHHH59;=B559=33:55<(830588<((>:(98<CB02&28>CA>98 +@XXXXXXXXXX:7:1101:1848:1879#/1 +NCTTCTTCTTCCTCATGTTTTTTGATCAACTGCTCCACTTCTTTTTGTTTGAGAACTCTGATTACTGTCTTTCCATTCTCTCTTGTTAGTGTTGCAATTT |
| b |
| diff -r 17ad142b56e6 -r e0ca2ec4f5d9 test-data/bduk_outputu2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bduk_outputu2.fastqsanger Thu Nov 11 16:38:09 2021 +0000 |
| b |
| @@ -0,0 +1,102 @@ +@XXXXXXXXXX:7:1101:1582:1835#/2 +GCAATGATGGGGCCGCTCCCGGGGCCACACCTGCTTCTGGATCCGCTGCTTCCAAGTTCCTTTGCCTCCCTCCTGGCATCACTGTCTGCGACTCAGGCCG ++ +@@@DDDADHFHGFEGIGIIIGEGFD@FHA@GIGIJJIJJEAHHEBEDACEAC@CDDDC@@CCCCDCD@AD9?BCCDDCCDDDDDDDDCC99BBDDCACBB +@XXXXXXXXXX:7:1101:1610:1859#/2 +CAATAACACAGTCCAAAATATATGTATGTATGTATATATATATGCAGGCAACAAATAGCACAATGAATAAAATAGTACTTCATCTCAGTACTAACATTGA ++ +C@BFFFFFHHGHDIIJJJJJJIIJHIJJHIJIJJIGIJIJJJJJFIIJJIIIIIJJJIJJJJJJJJIJJJIJJJJEGIIJJIJHHHHHCDFFFFFFEEEE +@XXXXXXXXXX:7:1101:1743:1871#/2 +GCTTCCAAGGGACAAAGTCCTGCCCTTGGGTGTGGAAGACACCGTGGACAAGCTCAAGATGCTGGAAGGCCGCAAGACCAGCATCCGCAAGTCAGTGCAG ++ +CCCFFFFFHHHHHJJJJJIIJHEHJIJJJIEDGIIIJIGGGIJIGEIIIIJIIIIIHGHHHHFFFFFFFDB>B@BDDCDDDDDDDCB?@BDCCDDDDDDD +@XXXXXXXXXX:7:1101:1536:1878#/2 +TGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCC ++ +@@@DFFFFHGFHGIJJJJJJJAFDHICDFHGIJIIJEEIJGIJGHJIJJIFAAAFGBGGFFFHGHFDFDFBCBDDDD<ACDDDCADEDDDDCD:>CDDCC +@XXXXXXXXXX:7:1101:2990:100153#/2 +TGGAGGCCTGCTGGGAACGGGACTTCTAAAAGGAACTATGTCTGGAAGGCTGTGGTCCAAGGCCATTTTTGCTGGCTATAAGCGGGGTCTCCGGAACCAA ++ +@@@DDDDFHHFDHJJIGGHIJHIJJJJJGGGHJEGIIJJJIJJJIJJII?=FFHIHGGIJIHHHHFFC@BBCCEDDDDDECCDBDBD09CDDDDBBB??1 +@XXXXXXXXXX:7:1101:1624:1906#/2 +GGCTGGTCTGTCCCCTCTGCATCTGGGGCTCCTCCTGGCCCTTCTCCCGCTGCCTGTCCTGCCTCCTGGCCCTGCAGCAGCACCTTGCCCAGTGATCTTT ++ +CCCFFFFFHGHHHJJJJJJJIJJJIJJJIJIJJIJJIJIJJJJJJGGIJJFGIJGHHIFHHHHHFFDFDEEDDDD?CDDDDDDDDDCCDCDDCCCDCCCD +@XXXXXXXXXX:7:1101:1666:1926#/2 +GGCTGTGGGAACTCTAGCTGCTGTCAGCCCCTCCTGTAGGAGCTGGCCCTGCCCAGGCTCCTGACTTCCCTCAGGAAGTCTTTCTGTCTTTCTCCATCAG ++ +CCCFFFFFHHFHHJJIJJJJJJIJJJJJJJJJJJJJJJJIIJJJJIJJJJIJJIJJIIJJJIHCHHGHFFFFBEE>@B>CDDDCDDDDDDDDDACDDCCD +@XXXXXXXXXX:7:1101:2921:100163#/2 +GAAAAGGAGAACCCCATGCGGGAACTTCGCATCCGCAAACTCTGTCTCAACATCTGTGTTGGGGAGAGTGGAGACAGACTGACGCGAGCAGCCAAGGTGT ++ +CCCFFFFFHHGHHJJIJJJJJJIIJJJIIIGDHIGIJJJIJJ>HHGEHHGEHFFFFCDEEDCBDDDBB>C@DDCDDDDDDDDDDB@BD@BDDDBDDD:@@ +@XXXXXXXXXX:7:1101:1513:1929#/2 +AAAATGAGGGCCCGTAACAGAACCAGTGTGTGTATAACGAAAACCATGTATAAAATGGGCCTATCACCCTTGTCAGAGATATAAATTACCACATTTGCCT ++ +?@@;;D>DFH:;?EFD:F<FE?;CBF:DCG?FD4?FIGHIGIJJGFGIFG@FGGDHIHIGHHGFFFFFECEDADCDACA>CAADACDDCDCC<ACDDDDD +@XXXXXXXXXX:7:1101:2759:100170#/2 +GGTCACCATGGATGGGCGAGTCAACGGGGGCCTCAACCTCTCCAGAGCCATTGGGGACCACTTCTATAAGAGAAACAAGAACCTGCCACCTGAGGAACAG ++ +CC@FFFFFHHHHHJJJJJIJGIIJJJJJJIJJGGHHCEFFFFEEEEDDDDDDDDDDDDDDDDDDDDEEDDDDCDDDDDDDDDDDDDDDDDDDDCDC?ABD +@XXXXXXXXXX:7:1101:1708:1937#/2 +GAATACTTTGTGTTTACCCACTGCCCCCTGACCACTGCTGAAGGCAGAAAGGGACGATCACCTACAGTACCTGGTTTGGGTCTTTATTCTCTCATTCTAG ++ +B@BFFFFFHHCFHIJIHGIGIIJJGGIJJGIIIGIGGIJJEIGIHHJJJJIHIIJJIJHHHGFBEFFCCEEDCD;@A?BB?ACCCCCCCCACD@DADA@C +@XXXXXXXXXX:7:1101:2981:100211#/2 +TTCCTCCTAACTCCTGCCAGAAACAGCTCTCCTCAACATGAGAGCTGCACCCCTCCTCCTGGCCAGGGCAGCAAGCCTTAGCCTTGGCTTCTTGTTTCTG ++ +@@BFFFFFHBDHHIHIIIIGGGADGGIGIEHIIIIJJIIIE<BHAHHHIGFGIJJJJIIHIBDGGEAEFFF;>CCABCDCDDCACDCCAA?@CD4:<@AC +@XXXXXXXXXX:7:1101:1688:1946#/2 +GAGAAAGGGAAGAAAGAGAAAGGAAAAGACGAAGGGAAGAGGAAGAAAGAGAAAAAGAAAGGGCTCGTGACAGAGAAAGAAGAAAGAGAAGTCGTTCACG ++ +BB@ADFFFHDDHAGGHGHGGHEHGIJJIIJIIJJJJ<FH;FGDEGEGHGIFHEGIJFFHHFDFFEDDBDDDDCCCACCDABDDDDDCCCCDCCD@B?CDD +@XXXXXXXXXX:7:1101:2767:100225#/2 +TGCAGAATGGCTCCCGCAAAGAAGGGTGGCGAGAAGAAAAAGGGCCGTTCTGCCATCAACGAAGTGGTAACCCGAGAATACACCATCAACATTCACAAGC ++ +@@@FFFFF<FFHHGGIJIIGGGIII>):?FF:FGGGIJIJIHCHHHFBCE;ACDDDDDCA@<@DBDDCDDCDDDDDDDDD@CCCDAA@>ACC>>A@@C1< +@XXXXXXXXXX:7:1101:1536:1959#/2 +GAGACAAAAATTGTTTGAATCAGGACAAGGGAGGTTTGAGGGACTGTTTAACAGGTCCCCATGGTTCACGACCCTGATATCCACCATTATGGGCCCTCTG ++ +@8@1:?:=DD>D<CE+A:+C?+AF++++281)?D):?HD=FG6((?88=CFFCHG7=@HH@9?3.)7772?3,9;A(((5>;5>BBAA:>CCD?8@BD9A +@XXXXXXXXXX:7:1101:2797:100234#/2 +GGAAACGCTGGAGAAGACAGTGTTGCTAGTCTGTTCCTGTTCGTGAGAATGCTTTGAATGGAGGCTCACTGTGCTGCGGCGGCTGCGGCCGTAGCGGGCG ++ +B1=+:A+0A::A2+2A2A3A<+2<?9<*119:9:1CC:DDFF<)800//9/>8E=<)/8@@@6C(6==737==>>@######################## +@XXXXXXXXXX:7:1101:1552:1976#/2 +TGTGAGCACACCATATATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAGT ++ +CCCFFFFFHHHHHIIGIGGIHJIGHHJIECGGGHJIJJJJJJJJJGHIJJGGHGIIEHIIJDIJFHFFFFF@CCCEECDDDDDCDDDB@BDDBBBDDCD> +@XXXXXXXXXX:7:1101:1748:1978#/2 +CAAGGAGCTGTTCTGTCGTGGCTTTGGAATTCAGATGCTCTCACTGTGATAGAGATGGGGTCTTGGGGGGCTGGGAGCTGTTCTGTCGTGGCTTTGGAGT ++ +B@@FFFFFHHHHHJJIIJHIJIJJJJJIIJJIJJJJJIJJJJIJJJGHFGGHHIIIJIJJ@GIIJJIHFDDDDDDABBDCCDDEDDDB?BDDDDCCDCDA +@XXXXXXXXXX:7:1101:2779:100239#/2 +GCTGTGGTTACCTGTCCCCTGCCCCTGGCCTCCAGCCAGCTGCCAGTGGCCCCTCAGCTGCCTGTGGTGAGGCAATACTTAGCTAGGTTCTTAGACGGCC ++ +?<?BBDDEFADA?ECCFFGEHDIDB;;FBG>GDHFGGGAFEHE?F@8?>F;CFCEADEEG@EEHAEFBDEEED7A>CACDECD>C@A(5>>C@>A##### +@XXXXXXXXXX:7:1101:1593:1980#/2 +GGCTGTTCTCGAACTCCTGACCTCAGGTGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCGCCTAGCCGTCACATTTC ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJFHIIJJJJJIIJJJJJJJJJJJJJJJIHIJJJJJHIJJJJJJJHEEEFEEEEDECDDDDDDDDDBDDDCDDEE +@XXXXXXXXXX:7:1101:2946:100242#/2 +AATCCCTTCACCCCAGTTGCCAAACAGACCCCCCACCCCCTGGATTTTCCTTCTCCCTCCATCCCTTGACGGTTCTGGCCTTCCCAAACTGCTTTTGATC ++ +C@CFFFFFHHHFFHBHHHEIJJIIIJIIJCGGIIGIHHIJIG@D;DCE>>?AEEFF@@DB(.;>?;CC@>=',5<CC>ADCDCCDA>B?CDD>ACCC0>C +@XXXXXXXXXX:7:1101:1987:1781#/2 +GCCGCAACCTGCACAGCCATGCCCGGGCAAGAACTCAGGACGCTGAATGGCTCTCAGATGCTCCTGGTGTTGCTGGTGCTCTCGTGGCTGCCGCATGGGG ++ +CCCFFFFFHHHHHJJJJJJIJJJJJJJJJJJJJJJJJJIIJIJJJJJHHHHHFFFFFFEEEEEEDDDCCBDDDDDDDDDDDDDDDDDDDDDD<@BBDBBD +@XXXXXXXXXX:7:1101:3046:100006#/2 +GACGAGATGGAGTTCACCGAGGCCGAGAGCAACATGAATGACCTGGTGTCCGAGTACCAGCAGTACCAGGATGCCACAGCCGAGGAGGAGGGCGAGTTCG ++ +CCCFFFFFHHHHFIJJJJJIIJIJJIHIIIJJJIIJJJGIJJJIJJIJHGEHFFFEEEEEDDDDDDDDDDDCDDDDDDDDDDDDDDDDBDDBDD<B9@CB +@XXXXXXXXXX:7:1101:1900:1788#/2 +CGGCTATGCGCCACCCGAGACGGAGATCGTGCCGCTTGTGCTGCGCGGCCACCTCATGGACATCGAGTGCCTGGCCAGCGACGGCATGCTGCTGGTGAGC ++ +CCCFFFFFGHHHHJJJJJJHHJJIFHIJJHHIIIJJJIIIJJJJJHFDDD@@DDDDCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCDD<?C@C +@XXXXXXXXXX:7:1101:3214:100027#/2 +CACAACAACTGCTACTTCAGTTGCGCAGACAGTATCAACACCCACAACACAAGATCAGACCCCAAGTTCTGCTGTTTCAGTTGCCACGCCTACAGTTAGT ++ +@CCFFFFFGFHHHIIJJJIIHIIIIIJ<GIIG?DHIJJGIIJBHJJJJJIGCGGHHJJHHHHFDEF;ACEEEDDDDDCEDDDDCDCDDDDDDDCCDDDD> +@XXXXXXXXXX:7:1101:1848:1879#/2 +GGAGAAATGACCTTGAAGTCAGCACTTGCTTTAGCTATCAAAGTACTAAATAAGACCATGGATGTTAGTAAACTCTCTGCTGAAAAAGTGGAAATTGCAA |