Mercurial > repos > iuc > sra_tools
changeset 26:f7732611d0fc draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 7632986831e24fcd189a57d824b9e6b1d5dc5c4c
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--- a/fasterq_dump.xml Fri Jun 23 21:31:47 2023 +0000 +++ b/fasterq_dump.xml Mon Aug 26 14:59:07 2024 +0000 @@ -13,8 +13,10 @@ @CONFIGURE_RETRY@ @SET_ACCESSIONS@ while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do - fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1} - --seq-defline '@\$sn/\$ri' + fasterq-dump "\$acc" + -e \${GALAXY_SLOTS:-1} + -t \${TMPDIR} + --seq-defline '$adv.seq_defline' --qual-defline '+' $adv.split #if str( $adv.minlen ) != "": @@ -71,6 +73,7 @@ <inputs> <expand macro="input_conditional"/> <section name="adv" title="Advanced Options" expanded="False"> + <expand macro="defline" defline_param="--seq-defline" defline_default="@$ac.$sn/$ri"/> <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--min-read-len"/> <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end)."> <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option> @@ -186,6 +189,30 @@ </element> </output_collection> </test> + <test expect_num_outputs="4"> + <param name="input_select" value="file_list"/> + <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/> + <section name="adv"> + <param name="seq_defline" value="@$ac.$si/$ri $sn length=$rl"/> + </section> + <output_collection name="list_paired" type="list:paired" count="1"> + <element name="SRR11953971"> + <element name="forward" ftype="fastqsanger.gz" decompress="True"> + <assert_contents> + <!-- TODO replace has_size by has_line --> + <has_size min="56206"/> + <!-- <has_line line="@SRR11953971.2053/1 2053 length=101"/> --> + </assert_contents> + </element> + <element name="reverse" ftype="fastqsanger.gz" decompress="True"> + <assert_contents> + <has_size min="59843"/> + <!-- <has_line line="@SRR11953971.2053/2 2053 length=101"/> --> + </assert_contents> + </element> + </element> + </output_collection> + </test> </tests> <help><![CDATA[ **What it does?**
--- a/fastq_dump.xml Fri Jun 23 21:31:47 2023 +0000 +++ b/fastq_dump.xml Mon Aug 26 14:59:07 2024 +0000 @@ -12,7 +12,7 @@ @SET_ACCESSIONS@ #if $input.input_select == "sra_file": - fastq-dump --log-level fatal --accession '${input.file.name}' + fastq-dump --log-level fatal --accession "\$acc" #else: ## Do not use prefetch if region is specified, to avoid downloading ## the complete sra file. @@ -20,9 +20,9 @@ prefetch -X 200000000 "\$acc" && #end if fastq-dump --accession "\$acc" - --split-files #end if - --defline-seq '@\$sn[_\$rn]/\$ri' + --split-files + --defline-seq '$adv.defline_seq' --defline-qual '+' $adv.split @@ -91,6 +91,7 @@ <option value="fastqsanger.bz2">bzip2 compressed fastq</option> </param> <section name="adv" title="Advanced Options" expanded="False"> + <expand macro="defline" defline_param="--defline-seq" defline_default="@$ac.$sn[_$rn]/$ri"/> <param name="minID" type="integer" label="Minimum spot ID" optional="true" help="Minimum spot id to be dumped." argument="--minSpotId"/> <param name="maxID" type="integer" label="Maximum spot ID" optional="true" help="Maximum spot id to be dumped." argument="--maxSpotId"/> <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--minReadLen"/> @@ -225,6 +226,64 @@ </element> </output_collection> </test> + <test expect_num_outputs="2"> + <param name="input_select" value="accession_number"/> + <param name="outputformat" value="fastqsanger.gz"/> + <param name="accession" value="ERR086330, SRR11953971"/> + <section name="adv"> + <param name="defline_seq" value="@$ac.$si/$ri $sn length=$rl"/> + </section> + <output_collection name="list_paired" type="list:paired" count="2"> + <element name="ERR086330"> + <element name="forward" ftype="fastqsanger.gz" decompress="True"> + <assert_contents> + <!-- decompressed content assertions only work from 23.1 + therefore we test for size being at least one byte + larger than the results of the previous test which + uses the shorter default deflines + TODO replace has_size by has_line--> + <has_size min="147"/> + <!-- <has_line line="@ERR086330.1/1 1 length=76"/> --> + </assert_contents> + </element> + <element name="reverse" ftype="fastqsanger.gz" decompress="True"> + <assert_contents> + <has_size min="141"/> + <!-- <has_line line="@ERR086330.1/2 1 length=76"/> --> + </assert_contents> + </element> + </element> + <element name="SRR11953971"> + <element name="forward" ftype="fastqsanger.gz" decompress="True"> + <assert_contents> + <has_size min="56206"/> + <!-- <has_line line="@SRR11953971.1/1 1 length=101"/> --> + </assert_contents> + </element> + <element name="reverse" ftype="fastqsanger.gz" decompress="True"> + <assert_contents> + <has_size min="59843"/> + <!-- <has_line line="@SRR11953971.1/2 1 length=101"/> --> + </assert_contents> + </element> + </element> + </output_collection> + </test> + <test expect_num_outputs="2"> + <param name="input_select" value="sra_file"/> + <param name="sra_file" value="SRR522874.sra"/> + <param name="split" value="True"/> + <param name="skip_technical" value="True"/> + <section name="adv"> + <param name="defline_seq" value="@$sn/$ri"/> + </section> + <output_collection name="list_paired" type="list:paired" count="1"> + <element name="SRR522874.sra"> + <element name="forward" file="SRR522874.sra_2_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> + <element name="reverse" file="SRR522874.sra_4_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> + </element> + </output_collection> + </test> </tests> <help><![CDATA[ **What it does?**
--- a/macros.xml Fri Jun 23 21:31:47 2023 +0000 +++ b/macros.xml Mon Aug 26 14:59:07 2024 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">3.0.5</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">3.1.1</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">22.01</token> <xml name="edam_ontology"> <edam_topics> @@ -15,8 +15,8 @@ <macro name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">sra-tools</requirement> - <requirement type="package" version="2.6">pigz</requirement> - <requirement type="package" version="1.17">samtools</requirement> + <requirement type="package" version="2.8">pigz</requirement> + <requirement type="package" version="1.20">samtools</requirement> <yield/> </requirements> </macro> @@ -36,11 +36,6 @@ <token name="@COPY_CONFIGFILE@"><![CDATA[ mkdir -p ~/.ncbi && cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg && - vdb-config -s "/repository/user/main/public/root=\$PWD" && - vdb-config -s "/repository/user/ad/public/root=\$PWD" && - vdb-config -s "/repository/user/default-path=\$PWD" && - vdb-config -s "/repository/user/main/public/root=\$PWD" && - vdb-config -s /http/timeout/read=10000 && ]]></token> <token name="@SET_ACCESSIONS@"><![CDATA[ #if $input.input_select == "sra_file": @@ -69,6 +64,11 @@ /config/default = "false" /libs/temp_cache = "." /tools/prefetch/download_to_cache = "false" +/http/timeout/read = "1000" +/repository/user/main/public/root = "." +/repository/user/ad/public/root = "." +/repository/user/default-path = "." +/repository/user/main/public/root = "." ]]></configfile> </configfiles> </macro> @@ -116,13 +116,42 @@ <param name="minMapq" type="integer" min="0" max="42" label="Minimum mapping quality" optional="true" help="Minimum mapping quality an alignment has to have, to be dumped." argument="--min-mapq"/> </macro> <macro name="region"> - <param format="text" name="region" type="text" label="aligned region" optional="true" + <param name="region" type="text" label="aligned region" optional="true" help="Filter by position on genome. Can be either accession.version (ex: NC_000001.10), chromosome name (ex:chr1 or 1) or 1-based coordinates (ex: chr1:1-101)." argument="--aligned-region"/> </macro> <macro name="matepairDist"> <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true" help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference" argument="--matepair-distance"/> </macro> + <macro name="defline" tokens="defline_param,defline_default"> + <param argument="@DEFLINE_PARAM@" value="@DEFLINE_DEFAULT@" type="text" label="Defline format specification for sequence"> + <help>A string of characters and/or variables. The variables can be one of: + $ac: accession, $si: spot id, $sn: spot name, $sg: spot group (barcode), $sl: spot length in bases, $ri: read number, $rn: read name, $rl: read length in bases. + '[]' could be used for an optional output: if all vars in [] yield empty values whole group is not printed. Empty value is empty string or for numeric variables. + Ex: @$sn[_$rn]/$ri '_$rn' is omitted if name is empty"</help> + <!-- allow many chars, but quotes and backslash --> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="@" /> + <add value="$" /> + <add value="[" /> + <add value="]" /> + <add value="_" /> + <add value="-" /> + <add value="+" /> + <add value="." /> + <add value=";" /> + <add value=":" /> + <add value="/" /> + <add value="?" /> + <add value=" " /> + <add value="=" /> + </valid> + </sanitizer> + <validator type="regex" message="Must start with @">^.*</validator> + + </param> + </macro> <macro name="citation"> <citations> <citation type="doi">10.1093/nar/gkq1019</citation>
--- a/test-data/DRR015708_forward.fastqsanger Fri Jun 23 21:31:47 2023 +0000 +++ b/test-data/DRR015708_forward.fastqsanger Mon Aug 26 14:59:07 2024 +0000 @@ -1,20 +1,20 @@ -@HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/1 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/1 NTATTGTAGCGCACTATGAGGTCGCTCATTANTNTACATCNNCATCCAAATTTCAGCATNANTTTNNNNNTGTTTGATATTCTCAAAGNGATNAACGTTT + #1=DDFFFHGHHHJIIIIGIJFHIJJJJJJI#0#08DFII##-7@FHIIJJJJGEHEEE#,#,,;#####,,;?DCCDEFEEFCDDDD#+2+#+2<?<CC -@HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/1 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/1 NTTCTAAACTCATTCCAGAAGTAATTGATGCGTCACCAATAATTGCAATATGTTTTCTATTGATTTGATTGATTTTATCTGCTGTTGCCATCCCAACAAT + #4=DDFFFHHHHHJJJJJJIIHIJJJJJJJJIHJJJJJIJJJJJJJJJJJJJIJJJJJJJJJJJJJJIIIICHHGEHHGIFEHHHHFFDFFFDDCEB@AC -@HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/1 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/1 NTCACCTACAACTCGAATATTCGAATGATATGTGATATTGTTAGATGATTTTGGCATGCTTGCAGAAAGTGCATAAACACCTGTATTGATTCCCGAATTT + #4=DFFFFHHHHHIJIJJIHIIJIIJJJJIJIHIIGGIIJHIEHGGHGHIIJJJIIJJJJJHHCHGGGE@FHGHIIJIEHHEDCCDCCDEEED@AB/=A# -@HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/1 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/1 NCTTAAAACTTATTAAATGAATCAATTAGATAAAAGACTTTTTTTGTTAGATGCTTATGCCTTAATTTTTAGAGGATATTATGCATTTATCAAAAATCCA + #4=DFFFFHHHHHJJJIJJJJJJJJJJJJJJJJIHGDGHIJJJJJJGHHJGIJIJJJJJJJIJIJJJJJHFFHGFDDFEEFEECCEEDEEDDCC3<A5>C -@HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/1 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/1 NTAAAGGTTATTGTGCTTCACAGAAAATGCATTATTATGGGTATAAACTTCATGCGGTTTGCTCAGCGGAAGGTGTCTTTCAAAGTTTGGATATTAGTCC + #1=DDFFEHHHHHGIJJJJGIJJJJJJJJJJJJIJJJJJJJCFGFIIHJIJHIJJJJHIJJJJIJIJIFHBDE;@ACEEEDDCCCCCDDDCCDCCFECCC
--- a/test-data/DRR015708_reverse.fastqsanger Fri Jun 23 21:31:47 2023 +0000 +++ b/test-data/DRR015708_reverse.fastqsanger Mon Aug 26 14:59:07 2024 +0000 @@ -1,20 +1,20 @@ -@HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/2 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/2 CATTANNAGNNANNNTTNNNNGANNNNNTCGANNNNNANTTTTAANCGNNNNNCTCTTNGAGAATATCAAANAGNTNAAAAATTANGCTGANNNTNGNAT + CCCFF##4<##2###32####22#####11?F#####0#07CHGI#.;#####--;BB#,;?ADDDEEDDD#,8#,#,58<?BD:#+2?@?######### -@HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/2 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/2 GAAAGATGGTATTTCTGGTTTTCCAACGCGTACAGAAAGTGAGTTTGATACATTTGGAACGGGACATTCTTCTACATCTATTTCAGCAATTGTTGGGATG + BBCFFDFFHCFHHJJJJJIJJJJJJJIJJJJJJJIHGIIDHGIFIIJIIGHIIHIIJDHIIJH=DFFFFFEEEEEDEDDDEDEDDDDDCDDDCDDDBBDB -@HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/2 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/2 AAATATAATTGGAGAATCAACTTTATTTTCGAATACAATTCCAAATCAAAAAGAAGATAAAACACTAGAATTATCTCAAAAGAATTCAACTCAAAAAGAT + CCCFFFFFHHHHGJIJIJJIJJJJJJJJJJJIJJJJJJJJJJJJEIJJJJHIJJIJJJIJJJIJJIJJJIJIJJJHHHGEHFFDFF>C@C>CEC;A538: -@HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/2 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/2 ATTGAAACCTTTTGAGTTGATTCGTGGATTTTTGATAAATGCATAATATCCTCTAAAAATTAAGGCATAAGCATCTAACAAAAAAAGTCTTTTATCTAAT + CCCFFFFFHHHHHJEGGHIHIIJJHHJHIJIJJJGJIJJJJJJJJJJJJJIIIJIJJIJIJJIJJJJIGHEHIIHHHHFHFFEDDDDCDEEDDDDDDEDD -@HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/2 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/2 TTGGTATTCTGCGGATAAATATCCTTTATCAGCTAAGAGCGTACAATTTTTAAACTGCTGTTTTATATCTTTCAGATAATGAATGTCATGCACTGAAGCT + BCCFBDFFHHHHHJJJJJJJJJJJJJJJJJJJJJIJIFIJJHHIIIJJJJGHJJJJJJJJHIIJJIJJHHHHHHGEFFFFFFCDCEEEFDDDDCDD>CDD
--- a/test-data/ERR027433_forward.fastqsanger Fri Jun 23 21:31:47 2023 +0000 +++ b/test-data/ERR027433_forward.fastqsanger Mon Aug 26 14:59:07 2024 +0000 @@ -1,20 +1,20 @@ -@IL4_4847:5:1:1051:7109/1 +@ERR027433.IL4_4847:5:1:1051:7109/1 GCCGCCAACGTCCGACGGCGCGTCCCGCACGACTTGAACCGATCTCACCGAGACAGAACTAT + C@CC@@@C2BBCBB:>@8@@5@>>@@@@@>@97@@==<@>>@4<'@8>:35=%&B####### -@IL4_4847:5:1:1058:16093/1 +@ERR027433.IL4_4847:5:1:1058:16093/1 AAGGTCGGGCATTCGTTCGAGCCGACGACCGCGAGGAAGCGGTTCGGCCGGGCGTAGAATCC + ?ABBABB;<@>@=<?@CBBB:@2>BCBB,,?):7@/3$54'818->1-+=+()$6--C8+?1 -@IL4_4847:5:1:1111:15034/1 +@ERR027433.IL4_4847:5:1:1111:15034/1 TCGATCCGCAGGGCAATCTGTGGATCCCGGCGTTCGACGACGGCGGGCGGGTGGCTCGGCAT + 2524;@@@/4<@6@;9?C@@93@>BAB2>>C@>B>C4BC4@-+B<@525++%=)######## -@IL4_4847:5:1:1122:6048/1 +@ERR027433.IL4_4847:5:1:1122:6048/1 ATCTCCTCGACGCGCACCAGATAGCGGTCGTAGCAATCGCCGTCCACGCCGACGGGCCCACT + BBB@@@@@@@AB.<@2)7;B-@==:@>@@@A7@<AA4:A3'@9+4;&00'9+AC5--DA5,? -@IL4_4847:5:1:1138:20693/1 +@ERR027433.IL4_4847:5:1:1138:20693/1 CTGCTCGCGCGAGAACGCGCGCAAGCTCGGGGGCGGTGGCGGGGTCGGGCGACACCGATGTA + CB<C7@>);9@@@@=1B@@@@2@=*:4@@@0%(-$,'3%%'%$%$,44%3&$=$C;CC-C##
--- a/test-data/ERR027433_reverse.fastqsanger Fri Jun 23 21:31:47 2023 +0000 +++ b/test-data/ERR027433_reverse.fastqsanger Mon Aug 26 14:59:07 2024 +0000 @@ -1,20 +1,20 @@ -@IL4_4847:5:1:1051:7109/3 +@ERR027433.IL4_4847:5:1:1051:7109/3 AACGCACTGCGCGCGGACTCGCCCCCGCGGCCACTCCGTGGGCCGGCGTACGGA + )(664;(>>/:1<+/'())0)',8%'*7'+9904)'(+()'''':+4+'.7)'( -@IL4_4847:5:1:1058:16093/3 +@ERR027433.IL4_4847:5:1:1058:16093/3 GCATAGCTGCCCTCGCCTTCTACTCGCACCGAACAAGCGGCCCGCCTACGCGGG + ;=>1(/2(:/=@(:'9/<(*'&.(?.6)(';+.5''-3.&''7(96%0:+($2$ -@IL4_4847:5:1:1111:15034/3 +@ERR027433.IL4_4847:5:1:1111:15034/3 GAGTGGAGCCGCGGACGGGAGCGCGGCGGCTGCCTCACAGCACCCGGGGGGTCG + ::3+:2655(*('((3*&&&4+')6'3/2,+++*.+')-/)4((<-+&&'&%<( -@IL4_4847:5:1:1122:6048/3 +@ERR027433.IL4_4847:5:1:1122:6048/3 GAGGTCGGCGTTCTGGATGACAGGCGCGAAGCCCCCGCCGTCGGTGCCTTCACG + =8+(-(,(3.5*=99+;).)8'(,(/(+(-6@'-3<6&,%/4++)')1/)>(.& -@IL4_4847:5:1:1138:20693/3 +@ERR027433.IL4_4847:5:1:1138:20693/3 TGGACGTTGTGGTGGTTGTAAGAGATTTCGCTCCCCATGTTGGCGAGCTGCGAT + ;)?5;=9996@((((097:41=,A((+)5>9,:''''67+9)=(968-(8;8)3
--- a/test-data/SRR1993644.fastqsanger Fri Jun 23 21:31:47 2023 +0000 +++ b/test-data/SRR1993644.fastqsanger Mon Aug 26 14:59:07 2024 +0000 @@ -1,20 +1,20 @@ -@1/2 +@SRR1993644.1/2 TATACTACTGTCATGTTTGCTTTTTTCGTGCTCATTACCTTATCGTATGCTTCCATCCAAAGATCTAGTTGTTTATAATATTCTCCCGGCCTTACTTCAAC + ?@<DDDADDFAAC@>GG<FDCBHIIGB:8??DEAHGAFEDF<B?F9DBFFCDHF>48BBCF)8877=@=@C7=E??EBD:AADA;>C3;BB6:A@>>@:3> -@2/2 +@SRR1993644.2/2 AAAAAAACTTTCTTTACAGGCGTAAAGAAAGTGAAATTGACAGTATTTATACATGAAATAGCAATGTCTTTCCCACTTCCCTACGCTGGCATTAACCAGAT + <@@DA6DDF42ABGF9F?F@C<EDDDFBGI>04BGC>BFF><?*88BDFDEAFFDGCGEFEEFIFFFEF>EBDBB@@:ACCCAB8@?=;B<@BABBBBB?# -@3/2 +@SRR1993644.3/2 GTGCCATCATTTTCTATCCATTATTATGGATTATTGGCTCATCGTTTAATCCGGGTGATAGTTTATCTGGATCAAGTATTATTCCACAAAATGCAACGTTA + =BBFFFFFHHHHHJJJJJJJJJJJJIJIJEIIGIJJJHGIGGIIGHIDIJGHIIJ?FFHGIIJJJJJJJJHGIHHHCEHFFFFFFFFEAECCDADDDDDDD -@4/2 +@SRR1993644.4/2 TTCAAAACACATAAAGCTAATTGCCGCATATGACAATATTGCTAAAATAATTTTTTTACCAGATATCGGTGTTAATCGAAATAATGTACTTTCGGTCATTT + BBCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJIJJJJJJIIJJJJJJJIJJHHHHHFFDDCDEEEDDDDDDDDEDDDFFFEDDDDDDDDE -@5/2 +@SRR1993644.5/2 ACTTGCCAATGCGATGCACCAATCTTTTCAGCAATAATCGGCAAAATTGGGTCGACTACTCCTATACCTGAAAAGGCAAGGAAAGTAGCCAACACTGTAAT + BCCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIHIIJIJHHHHFFFFFFEEEEEEDDDDDDDDDDDDDCDDDDDDDDDDDDDED
--- a/test-data/SRR925743_forward.fastqsanger Fri Jun 23 21:31:47 2023 +0000 +++ b/test-data/SRR925743_forward.fastqsanger Mon Aug 26 14:59:07 2024 +0000 @@ -1,20 +1,20 @@ -@1/1 +@SRR925743.1/1 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT + EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<EDDE?2@?AEEDEED=D+C?5@A=6:>BA8:>@:4+36945&4354445>/B>@ -@2/1 +@SRR925743.2/1 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGT + HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFGGEEAEEEDD0ADDBD9BDBDDA@6?BA;?CD=:-7<<::)1;5,6-6A@?=9 -@3/1 +@SRR925743.3/1 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCA + HHHHFHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHGEFHGEGGFGGGGGGHHHHEFEIDDEEEEEDD4DD;??:6>6<@.<==@?.@@<?##### -@4/1 +@SRR925743.4/1 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTA + HHGBHHHHGFHHHHHFDHHFHGEHHHHHEFHHHHEGEGEFFFAFFFDCFGF?@GCDFGFEFHHEFDF*F6DC4DD:A8>@D@CD8->=>=<@CB@##### -@5/1 +@SRR925743.5/1 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTCACACTCACCCTA + GGGFGFFGGGFBGGEGGFFGGGCFFGGGGGEGFFFFFGFFGFFFDFFB+FGGFEE?FCF::7B5A?+BB###############################
--- a/test-data/SRR925743_reverse.fastqsanger Fri Jun 23 21:31:47 2023 +0000 +++ b/test-data/SRR925743_reverse.fastqsanger Mon Aug 26 14:59:07 2024 +0000 @@ -1,20 +1,20 @@ -@1/2 +@SRR925743.1/2 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA + GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF?EHGGHHHGHFHEHDEHGHFFEEE9BDDBEBAD.AD:ACBBC=4@>?5>=+? -@2/2 +@SRR925743.2/2 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA + HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHHHHHHHHHHGHHHGHHBHGHHFDBDDED5FCFCEEGF<@>>>@,<5<@@?>;D -@3/2 +@SRR925743.3/2 ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT + HHHHHHHHHFIEGFHFHDHHHHGFFHGEGDIGGEGGHHHAGEGGGDHHHHHHHHHHHFGDGGGEGDFFF>BEEEE3B;BB;>B7C@DA=DFBDD.BEE=9 -@4/2 +@SRR925743.4/2 ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT + GFFFHHFFHHHFHHFEFGGBGEEEE?<9?6=>>:=DDDD@DBGDB;DBDBA.ADD8<2<>6A@=A5>550=>>>>BE;EEEDEEE79+336<68=BCEB@ -@5/2 +@SRR925743.5/2 ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTAGGGTTAGGGGTAGGGT + 479<.>><:<A7BABBE8@=:<<:@BB?C75:2?;.5<<3FEFGEEC88FEDEE=AB><AA@B<ABDC8.27<9:58.58??6<:@>+?=9@########