| Previous changeset 12:d60c3f704da0 (2024-08-13) Next changeset 14:ecb9f4854617 (2024-11-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d |
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modified:
fastp.xml macros.xml |
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added:
test-data/bwa-mem-fastq-paired-collection/input_forward.fastqsanger.gz test-data/bwa-mem-fastq-paired-collection/input_reverse.fastqsanger.gz test-data/bwa-mem-fastq-paired-collection/output_forward.fastqsanger.gz test-data/bwa-mem-fastq-paired-collection/output_reverse.fastqsanger.gz test-data/bwa-mem-merged-read-include-unmerged.fastqsanger test-data/bwa-mem-merged-reads.fastqsanger test-data/bwa-mem-unmerged-filtered-reads1.fastqsanger test-data/bwa-mem-unmerged-filtered-reads2.fastqsanger test-data/bwa-mem-unmerged-unfiltered-reads1.fastqsanger |
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| diff -r d60c3f704da0 -r dbfc505896e9 fastp.xml --- a/fastp.xml Tue Aug 13 12:18:39 2024 +0000 +++ b/fastp.xml Tue Oct 15 11:45:19 2024 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy1" profile="23.1">\n+<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy2" profile="23.1">\n <description>fast all-in-one preprocessing for FASTQ files</description>\n <macros>\n <import>macros.xml</import>\n@@ -13,11 +13,13 @@\n \n ## Link input files\n \n-#set ext = \'.fastq\'\n+#set ext = \'.fastqsanger\'\n \n-#if $single_paired.single_paired_selector == \'paired_collection\':\n- #if $single_paired.paired_input.forward.is_of_type(\'fastq.gz\'):\n- #set ext = \'.fastq.gz\'\n+#if $single_paired.single_paired_selector == \'paired_collection\'\n+ #if $single_paired.paired_input.forward.is_of_type(\'fastqsanger.gz\')\n+ #set ext = \'.fastqsanger.gz\'\n+ #elif $single_paired.paired_input.forward.is_of_type(\'fastqillumina.gz\')\n+ #set ext = \'.fastqillumina.gz\'\n #end if\n #set $in1 = $single_paired.paired_input.forward\n #set $in2 = $single_paired.paired_input.reverse\n@@ -28,8 +30,10 @@\n ln -sf \'$in1\' \'$in1_name\' &&\n ln -sf \'$in2\' \'$in2_name\' &&\n #else\n- #if $in1.is_of_type(\'fastq.gz\')\n- #set ext = \'.fastq.gz\'\n+ #if $in1.is_of_type(\'fastqsanger.gz\')\n+ #set ext = \'.fastqsanger.gz\'\n+ #elif $in1.is_of_type(\'fastqillumina.gz\')\n+ #set ext = \'.fastqillumina.gz\'\n #end if\n \n #set $in1_name = re.sub(\'[^\\w\\-\\s]\', \'_\', str($in1.element_identifier)) + $ext\n@@ -41,6 +45,7 @@\n #end if\n #end if\n \n+cp \'$c1\' galaxy.json &&\n \n ## Run fastp\n \n@@ -54,14 +59,30 @@\n #end if\n \n -i \'$in1_name\'\n--o first${ext}\n \n-#if str($single_paired.single_paired_selector).startswith(\'paired\'):\n+## Merge reads\n+\n+#if str($single_paired.single_paired_selector).startswith(\'paired\')\n -I \'$in2_name\'\n- -O second${ext}\n+ #if $single_paired.merge_reads.merge\n+ $single_paired.merge_reads.merge\n+ --merged_out \'$merged_reads\'\n+ #if $single_paired.merge_reads.include_unmerged\n+ $single_paired.merge_reads.include_unmerged\n+ #else\n+ --out1 \'$unmerged_out1\'\n+ --out2 \'$unmerged_out2\'\n+ --unpaired1 \'$unpaired1\'\n+ --unpaired2 \'$unpaired2\'\n+ #end if\n+ #else\n+ -o first${ext}\n+ -O second${ext}\n+ #end if\n+#else \n+ -o first${ext}\n #end if\n \n-\n ## Adapter Trimming Options\n \n $single_paired.adapter_trimming_options.disable_adapter_trimming\n@@ -200,14 +221,50 @@\n \n $read_mod_options.base_correction_options.correction\n \n-&&\n-\n-mv first${ext} \'${out1}\'\n-#if str($single_paired.single_paired_selector).startswith(\'paired\'):\n+#if str($single_paired.single_paired_selector).startswith(\'single\')\n+ &&\n+ mv first${ext} \'${out1}\'\n+#elif str($single_paired.single_paired_selector).startswith(\'paired\') and not $single_paired.merge_reads.merge:\n+ &&\n+ mv first${ext} \'${out1}\'\n &&\n mv second${ext} \'${out2}\'\n #end if\n ]]></command>\n+ <configfiles>\n+ <configfile name="c1">\n+ #set $ext1 = "fastqsanger"\n+ #set $ext2 = "fastqsanger"\n+ #if str($single_paired.single_paired_selector) == "single"\n+ #if $in1.ext.endswith("gz")\n+ #set $ext1 = "fastqsanger.gz"\n+ #end if\n+ #elif str($single_paired.single_paired_selector) == "paired"\n+ #if $in1.ext.endswith("gz")\n+ #set $ext1 = "fastqsanger.gz"\n+ #end if\n+ #if $in2.ext.endswith("gz")\n+ #set $ext2 = "fastqsanger.gz"\n+ #end if\n+ #else\n+ #if $paired_input.forward.ext.endswith("gz")\n+ #set $ext1 = "fastqsanger.gz"\n+ #end if\n+ #if $paired_input.reverse.ext.endswith("gz")\n+ #set $ext2 = "fastqsanger.gz"\n+ #end if\n+ #end if\n+ {\n+ "out1": {"ext": "$ext1"},\n+ "out2": {"ext": "$ext2"},\n+ "merged_reads": {"ext": "$ext1"}'..b'param name="paired_input">\n+ <collection type="paired">\n+ <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />\n+ <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />\n+ </collection>\n+ </param>\n+ <param name="merge" value="--merge" />\n+ <param name="include_unmerged" value="--include_unmerged" />\n+ <param name="report_html" value="False" />\n+ <output name="merged_reads" ftype="fastqsanger" file="bwa-mem-merged-read-include-unmerged.fastqsanger" />\n+ <output name="report_json">\n+ <assert_contents>\n+ <has_text text="fastp report"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!--15. Test paired collection in combination with compressed input-->\n+ <test expect_num_outputs="4">\n+ <param name="single_paired_selector" value="paired_collection"/>\n+ <param name="paired_input">\n+ <collection type="paired">\n+ <element name="forward" value="bwa-mem-fastq-paired-collection/input_forward.fastqsanger.gz" ftype="fastqsanger.gz" />\n+ <element name="reverse" value="bwa-mem-fastq-paired-collection/input_reverse.fastqsanger.gz" ftype="fastqsanger.gz" />\n+ </collection>\n+ </param>\n+ <param name="report_json" value="False" />\n+ <output name="report_html">\n+ <assert_contents>\n+ <has_text text="fastp report"/>\n+ </assert_contents>\n+ </output>\n+ <output_collection name="output_paired_coll" type="paired">\n+ <element name="forward" value="bwa-mem-fastq-paired-collection/output_forward.fastqsanger.gz" decompress="True" ftype="fastqsanger.gz"/>\n+ <element name="reverse" value="bwa-mem-fastq-paired-collection/output_reverse.fastqsanger.gz" decompress="True" ftype="fastqsanger.gz"/>\n+ </output_collection>\n+ </test>\n </tests>\n <help><![CDATA[\n .. class:: infomark\n@@ -494,13 +650,13 @@\n \n 6. Trim polyG in 3\' ends, which is commonly seen in NovaSeq/NextSeq data. Trim polyX in 3\' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)\n \n-7. Preprocess unique molecular identifer (UMI) enabled data, shift UMI to sequence name\n+7. Preprocess unique molecular identifier (UMI) enabled data, shift UMI to sequence name\n \n 8. Report JSON format result for further interpreting\n \n 9. Visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative)\n \n-10. Split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file (*Not enabled in this Galaxy tool*)\n+10. Split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limiting the lines of each split file (*Not enabled in this Galaxy tool*)\n \n 11. Support long reads (data from PacBio / Nanopore devices)\n \n@@ -508,13 +664,18 @@\n \n **Inputs**\n \n-Single-end or Paired-end FASTQ or FASTQ.GZ reads\n+Single-end or Paired-end (compressed) fastqsagnger or fastqillumina files\n \n -----\n \n **Outputs**\n \n * Processed reads\n+ * Merged reads\n+ * Unmerged filtered reads1, reads that cannot be merged successfully, but both pass all the filters.\n+ * Unmerged filtered reads2, reads that cannot be merged successfully, but both pass all the filters.\n+ * Unmerged unfiltered reads1, reads that cannot be merged, **read1** passes filters but **read2** doesn\'t.\n+ * Unmerged unfiltered reads2, reads that cannot be merged, **read2** passes filters but **read1** doesn\'t.\n \n Optionally, under **Output Options** you can choose to output\n \n' |
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| diff -r d60c3f704da0 -r dbfc505896e9 macros.xml --- a/macros.xml Tue Aug 13 12:18:39 2024 +0000 +++ b/macros.xml Tue Oct 15 11:45:19 2024 +0000 |
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| @@ -43,12 +43,25 @@ </param> </xml> + <xml name="merge_reads"> + <conditional name="merge_reads"> + <param argument="--merge" type="select" label="Merge forward and revese reads?"> + <option value="">No</option> + <option value="--merge">Yes</option> + </param> + <when value="--merge"> + <param argument="--include_unmerged" type="boolean" truevalue="--include_unmerged" falsevalue="" checked="false" label="Include unmerged outputs into merged output file" /> + </when> + <when value="" /> + </conditional> + </xml> + <xml name="detect_adapter_for_pe"> <param argument="--detect_adapter_for_pe" type="boolean" truevalue="--detect_adapter_for_pe" falsevalue="" checked="false" label="Adapter sequence auto-detection for paired-end" /> </xml> <xml name="in" token_read_number="1" token_argument="-i"> - <param name="in@READ_NUMBER@" argument="@ARGUMENT@" type="data" format="fastq,fastq.gz" label="Input @READ_NUMBER@" help="Input FASTQ file #@READ_NUMBER@"/> + <param name="in@READ_NUMBER@" argument="@ARGUMENT@" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz" label="Input @READ_NUMBER@" help="Input FASTQ file #@READ_NUMBER@"/> </xml> <xml name="poly_g_min_len"> |
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| diff -r d60c3f704da0 -r dbfc505896e9 test-data/bwa-mem-fastq-paired-collection/input_forward.fastqsanger.gz |
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| diff -r d60c3f704da0 -r dbfc505896e9 test-data/bwa-mem-fastq-paired-collection/input_reverse.fastqsanger.gz |
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| Binary file test-data/bwa-mem-fastq-paired-collection/input_reverse.fastqsanger.gz has changed |
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| diff -r d60c3f704da0 -r dbfc505896e9 test-data/bwa-mem-fastq-paired-collection/output_forward.fastqsanger.gz |
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| diff -r d60c3f704da0 -r dbfc505896e9 test-data/bwa-mem-fastq-paired-collection/output_reverse.fastqsanger.gz |
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| Binary file test-data/bwa-mem-fastq-paired-collection/output_reverse.fastqsanger.gz has changed |
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| diff -r d60c3f704da0 -r dbfc505896e9 test-data/bwa-mem-merged-read-include-unmerged.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa-mem-merged-read-include-unmerged.fastqsanger Tue Oct 15 11:45:19 2024 +0000 |
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| b'@@ -0,0 +1,400 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/1\n+ATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT\n++\n+BCCCCFFFFFFFGGGGGGGGGGGHHHHGHGHHHHHHHHHGGGGGGHHHHGHHHHHHHHHHGHHHHHHGGHGGHHHGHHHHFHHGHHHHHHHHHGHEHEFFGHHEGGCEFGGFHHHBGHHGHHHHGHFHHHGHGHGHGGCDFDDACGGGGGGGAAFFFFFFFFFBAFFFFFB;FFFFFFADDFFFFFFFFFFEFFFFFFFFFFBFFFFFFFFFFFFFFEFFFFFFFFBFEFFFFEFE;DFFFDFBFF/9BFB\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/1 merged_251_1\n+GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATG\n++\n+AAAAAFFFFFFFGGGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB.H:@ABFF//;BFFFFFBF/9D:A//C\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/1 merged_251_57\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAG\n++\n+CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF.HHEHHHHHHHHGGGGHHHHHHHHHHHHHHHHGHHHGGGGGGGGGGFFFFCFFCCCCB\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/1 merged_251_78\n+ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTAGCTACCCCCAAGTGTTATGGGC\n++\n+33AA?DFD5BDFGGGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/A<C@EGFDCGGGHFHHHEGFGHBFHG0:CEHFCHGGED.;0CEF.F99B0CFFEEFGGG0FBFBBF0F/FFBDE?/9/H9B.FFBFFFFFFBF..AG.;@B-FGGBHFGGHEHHHGFBEAHGGGHFHFFFGF5DBGGDCGGFGHFHGFHGCHHHHGHHHGCGGGCGGCGFFFFFB43AAA3\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/1 merged_251_40\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGAT\n++\n+CCCCDFFFFCCFGGGGGGGGFGHHHHHGGGGHHHHHHHHHHHHHHHHGBGHGGHGGHHHHHHHHHHGHGHGGGGGHHHHHHHHGHHHHHHHHHGGGGGHHHHFFGHHHGGGGGGHHHGFGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGGHHHHHHHHHHHHHFHGGGHHHHGGGGGG:FE;EGEGGGGG/;?FGGGGGGGFFFFGGFFFFFFFFFBFFFFFFFFFFBFFFFFFEFFFFFEFFFHHHGHHHHHHHHGHHHHHGGGGGGGGGGFFFCCCCDDDCC\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/1 merged_251_65\n+ATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTTTTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATAA\n++\n+ABCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHGHHHHGHHHHHHHHHHHGGGGHHHHHHHHFHHHHHHGGHGHGGHGGHHHHHHHGGHFHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHHEGGHHGGGGGGHHHGGGGHGGGGGHHHHHHGGGDCGHHHHGGGGGGGHEFGGGGHGHHHGHGGGFGGGGGGGEGGGGGGG?E0CEFGGGGGFEE9EEFFFFFBFFFFFFFBFFBD.AFFFFFFF0HHGHHHHHHHHGGGGHHHHHHHHHHHGHHHHHHHHHHHHHHHHGGGGGGGGGGFCCCBBFCCCCB\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/1 merged_251_21\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTA'..b'AAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATAC\n++\n+>AAAAFFFBFFFGGGGGGGGGGHHFHGHHHHGHHHHHHHHHHHGGGGHHHHFHHHHFHGHHHHGAFFEFHEGHHHHHHHHGHEHHGGFGGGHHHHHHFHHHHHGGHHHHGGGGGHFHHFF?HHGGFECEFFGHFFGFHGECDGHGBGFHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFFHHHHGGGGHHHHHHHHHGHGHHHHHHHHHHHHHHHHGGGGGGGGGGFCCCCCFCBAAB\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/1 merged_251_29\n+TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATAC\n++\n+ABBBBFFFFFFFGGGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0<C;CGGGGEFF/.;0;FFFBF/0;0CFGFFB..9B/;0CBFFBBFFFFBAC?DED9;B9AD;.FFFB/B/;FBA/B//HHHHHHHGGGGGGGGGGFCCCCCFCBBBB\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/1 merged_166_0\n+CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGAT\n++\n+>A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/1 merged_251_57\n+CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTAGCTACCCCCAAGTG\n++\n+AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;AG-=A--:BBFB90;;FEHHGHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGGGGGGGGGGCCDCCFFCCCCC\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/1 merged_251_9\n+TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGGGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA\n++\n+BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<<AHHHGGGGGGGFHH0GHFCCCADGGG?.9/A-???DGGFFF.9F9/EE-;;BBBFFBFFFFFFFFFEFFFFBFFBBFFFFF/BFFBFFFFF-DBFFF;/BFF//BB//9/BEA---9:BFFFFFF/FH.;H:@9.BBFF/;BFFH;/////9/////.FFFFCCCCC\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/1 merged_251_33\n+CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGCGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA\n++\n+11>>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9D:-/;;FFFE9BF?@;-9-99/B9F/:///G/99/;HHHHHHHHHHHGGGGGGGGGGFFFFFFFCCCDC\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/1 merged_233_0\n+TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCAT\n++\n+CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFF\n' |
| b |
| diff -r d60c3f704da0 -r dbfc505896e9 test-data/bwa-mem-merged-reads.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa-mem-merged-reads.fastqsanger Tue Oct 15 11:45:19 2024 +0000 |
| b |
| b'@@ -0,0 +1,388 @@\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/1 merged_251_1\n+GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATG\n++\n+AAAAAFFFFFFFGGGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB.H:@ABFF//;BFFFFFBF/9D:A//C\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/1 merged_251_57\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAG\n++\n+CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF.HHEHHHHHHHHGGGGHHHHHHHHHHHHHHHHGHHHGGGGGGGGGGFFFFCFFCCCCB\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/1 merged_251_78\n+ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTAGCTACCCCCAAGTGTTATGGGC\n++\n+33AA?DFD5BDFGGGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/A<C@EGFDCGGGHFHHHEGFGHBFHG0:CEHFCHGGED.;0CEF.F99B0CFFEEFGGG0FBFBBF0F/FFBDE?/9/H9B.FFBFFFFFFBF..AG.;@B-FGGBHFGGHEHHHGFBEAHGGGHFHFFFGF5DBGGDCGGFGHFHGFHGCHHHHGHHHGCGGGCGGCGFFFFFB43AAA3\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/1 merged_251_40\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGAT\n++\n+CCCCDFFFFCCFGGGGGGGGFGHHHHHGGGGHHHHHHHHHHHHHHHHGBGHGGHGGHHHHHHHHHHGHGHGGGGGHHHHHHHHGHHHHHHHHHGGGGGHHHHFFGHHHGGGGGGHHHGFGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGGHHHHHHHHHHHHHFHGGGHHHHGGGGGG:FE;EGEGGGGG/;?FGGGGGGGFFFFGGFFFFFFFFFBFFFFFFFFFFBFFFFFFEFFFFFEFFFHHHGHHHHHHHHGHHHHHGGGGGGGGGGFFFCCCCDDDCC\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/1 merged_251_65\n+ATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTTTTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATAA\n++\n+ABCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHGHHHHGHHHHHHHHHHHGGGGHHHHHHHHFHHHHHHGGHGHGGHGGHHHHHHHGGHFHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHHEGGHHGGGGGGHHHGGGGHGGGGGHHHHHHGGGDCGHHHHGGGGGGGHEFGGGGHGHHHGHGGGFGGGGGGGEGGGGGGG?E0CEFGGGGGFEE9EEFFFFFBFFFFFFFBFFBD.AFFFFFFF0HHGHHHHHHHHGGGGHHHHHHHHHHHGHHHHHHHHHHHHHHHHGGGGGGGGGGFCCCBBFCCCCB\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/1 merged_251_21\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCC\n++\n+>A@AAAAD2ADDFFGGGGGFGGHA?EAEFBEAGHFABFGG5FDF5DB1EEGAFDFB53FF5FH@G5FFEHGHEFHFFHBE333GF43GCGGGGE@0?BFGGB0B?FHGFDGGHHHBFFDEGGHGFFFDFE@<1>@FFFGHHHHFHEFGDABFFGG/@DCE<CG1<GF0/DD000=<DHGBDFDCECE/:AC?-;-;9B/ABBB-AD9BFB99AB?BDFBAD-.9..@;=;;..9..9/9;BEF;A:9/BFFCFFGGGGBEDAA>FB43A?AA\n+@M01368:8:000000000-A3GHV:1:1102:106'..b'AAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATAC\n++\n+>AAAAFFFBFFFGGGGGGGGGGHHFHGHHHHGHHHHHHHHHHHGGGGHHHHFHHHHFHGHHHHGAFFEFHEGHHHHHHHHGHEHHGGFGGGHHHHHHFHHHHHGGHHHHGGGGGHFHHFF?HHGGFECEFFGHFFGFHGECDGHGBGFHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFFHHHHGGGGHHHHHHHHHGHGHHHHHHHHHHHHHHHHGGGGGGGGGGFCCCCCFCBAAB\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/1 merged_251_29\n+TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATAC\n++\n+ABBBBFFFFFFFGGGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0<C;CGGGGEFF/.;0;FFFBF/0;0CFGFFB..9B/;0CBFFBBFFFFBAC?DED9;B9AD;.FFFB/B/;FBA/B//HHHHHHHGGGGGGGGGGFCCCCCFCBBBB\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/1 merged_166_0\n+CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGAT\n++\n+>A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/1 merged_251_57\n+CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTAGCTACCCCCAAGTG\n++\n+AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;AG-=A--:BBFB90;;FEHHGHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGGGGGGGGGGCCDCCFFCCCCC\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/1 merged_251_9\n+TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGGGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA\n++\n+BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<<AHHHGGGGGGGFHH0GHFCCCADGGG?.9/A-???DGGFFF.9F9/EE-;;BBBFFBFFFFFFFFFEFFFFBFFBBFFFFF/BFFBFFFFF-DBFFF;/BFF//BB//9/BEA---9:BFFFFFF/FH.;H:@9.BBFF/;BFFH;/////9/////.FFFFCCCCC\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/1 merged_251_33\n+CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGCGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA\n++\n+11>>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9D:-/;;FFFE9BF?@;-9-99/B9F/:///G/99/;HHHHHHHHHHHGGGGGGGGGGFFFFFFFCCCDC\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/1 merged_233_0\n+TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCAT\n++\n+CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFF\n' |
| b |
| diff -r d60c3f704da0 -r dbfc505896e9 test-data/bwa-mem-unmerged-filtered-reads1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa-mem-unmerged-filtered-reads1.fastqsanger Tue Oct 15 11:45:19 2024 +0000 |
| b |
| @@ -0,0 +1,4 @@ +@M01368:8:000000000-A3GHV:1:1103:14528:12993/1 +GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGAT ++ +BBBBBFFFBDFFGFBCG2EGFFGHHCF5AFHHHFHFHHHGG?CEHBHHDGFHHGHHGHBGHABFFBGHGDGGGFHGHHGGHHHGGG@E1GEHHHGHHFHH3FEDHHHHGFGHGFHHGHFBGA?FGHHHHHGHHFFGHFDFGGHHH2??<ECFHHGHHHHHHHHHGHH<1DFGHGC<.FCB/<=@DCFFFFFEDA=-AAB9B/9B9B-@?.-;A-AFF.=-=BFEFEDEFFFBFEA-A.B//9F9F//;BBB |
| b |
| diff -r d60c3f704da0 -r dbfc505896e9 test-data/bwa-mem-unmerged-filtered-reads2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa-mem-unmerged-filtered-reads2.fastqsanger Tue Oct 15 11:45:19 2024 +0000 |
| b |
| @@ -0,0 +1,4 @@ +@M01368:8:000000000-A3GHV:1:1103:14528:12993/2 +CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCCACGTGATGTCTTAGTTAAGGGGAACGGGTGGGCTCTTTAGGTTTTT ++ +BBBBBBFFFFFFGGGGGGGGGGHHHGHHHFHGHHHHHGFHHGGHGGGHHHHHHHHHEEHGGGGGGHGHHHHGBGCHFHHHHHHGGGGGHGFHGFGHHHGGEGFGHHEGFFGHFEGG?HEBFHHF?FGGGEDG0CFGGG?E..<<-.CGGHHH0GHEGGDDC0/CA.0G/:;.;.;;;C09;BBFGBA.--./9;0C0/00;0;/./99.:9///:/9//;//;BF.D.AAD.;--@B9../;;:BF/;/.. |
| b |
| diff -r d60c3f704da0 -r dbfc505896e9 test-data/bwa-mem-unmerged-unfiltered-reads1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa-mem-unmerged-unfiltered-reads1.fastqsanger Tue Oct 15 11:45:19 2024 +0000 |
| b |
| @@ -0,0 +1,4 @@ +@M01368:8:000000000-A3GHV:1:1101:6911:8255/1 +ATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT ++ +BCCCCFFFFFFFGGGGGGGGGGGHHHHGHGHHHHHHHHHGGGGGGHHHHGHHHHHHHHHHGHHHHHHGGHGGHHHGHHHHFHHGHHHHHHHHHGHEHEFFGHHEGGCEFGGFHHHBGHHGHHHHGHFHHHGHGHGHGGCDFDDACGGGGGGGAAFFFFFFFFFBAFFFFFB;FFFFFFADDFFFFFFFFFFEFFFFFFFFFFBFFFFFFFFFFFFFFEFFFFFFFFBFEFFFFEFE;DFFFDFBFF/9BFB |