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Changeset 3:ff2269d615d9 (2025-01-29)

Previous changeset 2:eddd9befb66d (2025-01-24)

Commit message:
planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34

modified:
irma.xml

added:
test-data/forward.fastqsanger
test-data/reverse.fastqsanger

removed:
test-data/test_reads.fq
test-data/test_reads_copy.fq

diff -r eddd9befb66d -r ff2269d615d9 irma.xml
--- a/irma.xml Fri Jan 24 21:47:10 2025 +0000
+++ b/irma.xml Wed Jan 29 08:19:23 2025 +0000

[

b'@@ -2,7 +2,7 @@\n <description>Construct robust assemblies of highly variable RNA viruses</description>\n <macros>\n <token name="@TOOL_VERSION@">1.2.0</token>\n- <token name="@VERSION_SUFFIX@">2</token>\n+ <token name="@VERSION_SUFFIX@">3</token>\n </macros>\n <xrefs>\n <xref type="bio.tools">irma-virus</xref> \n@@ -44,8 +44,7 @@\n resultDir &&\n ## IRMA does not write empty output files\n ## so the following script makes sure all expected outputs exist unconditionally\n-python3 \'$__tool_directory__/createMissingFiles.py\' &&\n-cat irma_config.sh\n+python3 \'$__tool_directory__/createMissingFiles.py\' \n ]]></command>\n <configfiles>\n <configfile filename=\'irma_config.sh\'><![CDATA[\n@@ -53,10 +52,10 @@\n DOUBLE_LOCAL_PROC=\\$((SINGLE_LOCAL_PROC/2 + (SINGLE_LOCAL_PROC==1)))\n TMP=\\$TMPDIR\n ASSEM_PROG="MINIMAP2"\n+GRID_ON=0\n+SKIP_E=$SKIP_E\n+SORT_PROG="BLAT" ## LABEL is not working in galaxy docker.\n #if $advanced_config.customize == \'yes\':\n- #if $advanced_config.reference == \'yes\':\n-SKIP_E=$advanced_config.reference.SKIP_E\n- #end if\n #if $advanced_config.read_gathering == \'yes\':\n MAX_ROUNDS=$advanced_config.read_gathering.MAX_ROUNDS\t\t \n USE_MEDIAN=$advanced_config.read_gathering.USE_MEDIAN\t\t \n@@ -73,9 +72,6 @@\n MIN_RC=$advanced_config.match_step.MIN_RC\n MIN_BLAT_MATCH=$advanced_config.match_step.MIN_BLAT_MATCH\n #end if\n- #if $advanced_config.sort_step == \'yes\':\n-SORT_PROG=$advanced_config.sort_step.SORT_PROG\n- #end if\n #if $advanced_config.align_step == \'yes\':\n ALIGN_PROG=$advanced_config.align_step.ALIGN_PROG\n DEL_TYPE=$advanced_config.align_step.DEL_TYPE\n@@ -89,11 +85,24 @@\n DEL_T_DEPTH=$advanced_config.assembly.DEL_T_DEPTH\n SILENCE_COMPLEX_INDELS=$advanced_config.assembly.SILENCE_COMPLEX_INDELS\n MIN_AMBIG=$advanced_config.assembly.MIN_AMBIG\n-SSW_M=$advanced_config.assembly.SSW_M\n-SSW_X=$advanced_config.assembly.SSW_X\n-SSW_O=$advanced_config.assembly.SSW_O\n-SSW_E=$advanced_config.assembly.SSW_E\n ALIGN_AMENDED=$advanced_config.assembly.ALIGN_AMENDED\n+MM2_A=$advanced_config.assembly.MM2_A\n+MM2_B=$advanced_config.assembly.MM2_B\n+MM2_O=$advanced_config.assembly.MM2_O\n+ #if $module == "FLU-avian":\n+## respect user choice of A,B,O,E, but configure short read presets otherwise\n+MM2_E="$advanced_config.assembly.MM2_E -x sr"\n+ #else:\n+MM2_E=$advanced_config.assembly.MM2_E\n+ #end if\n+ #else:\n+ #if $module == "FLU-avian":\n+configure short read presets for minimap2 overwriting irma module defaults where necessary\n+MM2_A=2\n+MM2_B=8\n+MM2_O="12,32"\n+MM2_E="2,1 -x sr"\n+ #end if\n #end if\n #if $advanced_config.variant_calling == \'yes\':\n AUTO_F=$advanced_config.variant_calling.AUTO_F\n@@ -106,7 +115,8 @@\n MIN_CONF=$advanced_config.variant_calling.MIN_CONF\n SIG_LEVEL=$advanced_config.variant_calling.SIG_LEVEL\n #end if\n-#end if]]></configfile>\n+#end if\n+]]></configfile>\n </configfiles>\n <inputs>\n <conditional name="input_type_conditional">\n@@ -121,11 +131,12 @@\n <param name="fastq_input" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>\n </when>\n </conditional>\n- <param name="module" type="select" label="Select analysis module">\n- <option value="FLU" selected="true">FLU</option>\n- <option value="FLU-utr">FLU-utr</option>\n- <option value="FLU-pacbio">FLU-pacbio</option>\n+ <param name="module" type="select" label="Select platform">\n+ <option value="FLU-avian" selected="true">Illumina</option>\n+ <option value="FLU-minion">MinIon</option>\n+ <option value="FLU-pacbio">PacBio</option>\n </param>\n+ <param name="SKIP_E" type="boolean" falsevalue="1" truevalue="0" checked="true" label="Assemble UTRs, by elongation of reference" />\n <param name="optional_outputs" type="select"'..b' </conditional>\n <conditional name="align_step">\n <param name="customize" value="yes"/>\n <param name="ALIGN_PROG" value="SAM"/>\n@@ -442,10 +421,10 @@\n <param name="DEL_T_DEPTH" value="1"/>\n <param name="SILENCE_COMPLEX_INDELS" value="true"/>\n <param name="MIN_AMBIG" value="0.25"/>\n- <param name="SSW_M" value="2"/>\n- <param name="SSW_X" value="5"/>\n- <param name="SSW_O" value="10"/>\n- <param name="SSW_E" value="1"/>\n+ <param name="MM2_A" value="2"/>\n+ <param name="MM2_B" value="7"/>\n+ <param name="MM2_O" value="12"/>\n+ <param name="MM2_E" value="2"/>\n <param name="ALIGN_AMENDED" value="false"/>\n </conditional>\n <conditional name="variant_calling">\n@@ -473,13 +452,14 @@\n </test>\n <test expect_num_outputs="19">\n <conditional name="input_type_conditional">\n- <param name="fastq_input1" value="test_reads.fq" />\n+ <param name="fastq_input1" value="forward.fastqsanger" />\n <param name="input_type" value="single" />\n </conditional>\n <conditional name="advanced_config">\n <param name="customize" value="no" />\n </conditional>\n- <param name="module" value="FLU-utr" />\n+ <param name="module" value="FLU-avian" />\n+ <param name="SKIP_E" value="1" />\n <param name="optional_outputs" value="amended_consensus,run_info"/>\n <output_collection name="consensus_collection" type="list">\n <element name="HA">\n@@ -504,23 +484,25 @@\n \n IRMA (Iterative Refinement Meta-Assembler) can be used to obtain robust assembly, variant calling, and phasing of highly variable RNA viruses.\n These are obtained after an iterative assembly approach. Visit https://wonder.cdc.gov/amd/flu/irma/ for more information.\n-IRMA offers modules for influenza, RSV, ebolavirus and coronavirus, but this galaxy wrapper currently only supports influenza modules.\n+IRMA offers modules for influenza, RSV, ebolavirus and coronavirus, but this Galaxy wrapper currently only supports influenza modules.\n \n **Inputs**\n \n-Specify the module and provide your read data.\n+Specify the sequencing platform and provide your read data.\n \n **Outputs**\n \n-The default output of the tool is a collection of consensus sequences in FASTA format.\n+The default output of the tool is a collection of majority consensus sequences in FASTA format.\n \n-Optionally, collections of read mapping and variant calling results can be produced as additional outputs.\n+Optionally, collections of ambiguous consensus sequences, of read mapping and variant calling results can be produced as additional outputs.\n \n **Settings**\n \n IRMA provides carefully chosen default settings for its different analysis modes.\n Advanced(!) users have the option to override these through the advanced config section.\n \n+This wrapper always uses *minimap2* at the assembly step (even where the IRMA command line tool would default to SSW). For MinIon and PacBio data it uses minimap2\'s default long reads settings with IRMA-specific modifications of -A, -B, -O and -E parameters. For Illumina data minimap2 is run with its short-reads preset (-x sr) configuration. For all platforms, the minimap2 options -A (match score), -B (mismatch penalty), -O (gap open penalty) and -E (gap extension penalty) are user-configurable via Advanced settings -> Assembly settings.\n+\n .. class:: Warning mark\n \n By enabling any section of the advanced configuration options you will override the default settings for *all* parameters in that section, and the default values of a section may not be IRMA\'s defaults for the selected module, but reflect IRMA\'s global defaults.\n'

diff -r eddd9befb66d -r ff2269d615d9 test-data/forward.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/forward.fastqsanger Wed Jan 29 08:19:23 2025 +0000

b'@@ -0,0 +1,3348 @@\n+@FS10001248:222:BRL95618-1622:1:1101:3720:1000/1\n+AGAAATACACCAGGACAACGTACTGGTGGGATGGGCTCCAATCCTCAGACGATTTTGTCCAAGATTCAGTATCGAGACTCCCAAAACTGTACTTAGCATGTTGAACATGCCCATCATCATTCCAGGGCTCAATGATGCTGTTCCAT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:F:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1101:8590:1000/1\n+CTACAAGCCTCCCATTGTAAATGAAGCTAGCAGTTGCATTTTTATCATCCCCCGTTATACAAACATGCAGCCATGCTTTTCCATCGTGACAACTTGAGCTGGACCATGCTATGCACACTTGCTTGGTCCCCAGATGGAAAGGAACAC\n++\n+FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FFFFFFFF:FFFFFFF,FFF:FFFFFFFFFFFFFF:FFFFFFFF::FF:FFFF\n+@FS10001248:222:BRL95618-1622:1:1101:9450:1000/1\n+GGGGGAAACTGTCAACTAGAGGAGTACAAATTGCTTCAAATGAGAACATGGATAATATGGGATCAAGCACTCTTGAACTGAGAAGCGGGTACTGGGCCATAAGGACCAGGAGCGGAGGAAACACTAATCAACAGAGGGCCTCCGCAGG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1101:4990:1240/1\n+ATAGTATGTCCTGGAAAAGAAGGCAATGGTGAGATTTCGCCAACAATTGCTCCCTCTTCGGTGAAAGCCCTTAGCAATACTATGGTCTCTAGCCGGCCAAAAATCACATTGAAATTCGCTTTTAACATGATGTTTTTCTCCATGATT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1101:6720:1330/1\n+AAATTGGAATGCCAAATCATCATGTGGGTTAGACCAGATGTAGCATCCTCACCATTGTTGGCTTGGCGCCAGATTCGCCTTATTTCCTCTTTGTCATTAAGGACGAGTTCCCTCATCCATTTTCCATCGTCTCTTCTGTATAT\n++\n+FF:FF:FFF:FFF:F:FFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FF,FFFFFFFF:FFF:FFFFF:FF,FF:F,F:F:FFFFF:FF:FFFFFFF:FFFFFFF:FF,FFFFFFF:FFF,F\n+@FS10001248:222:BRL95618-1622:1:1101:14230:1350/1\n+GTTCTGTCTAAGAATGTCCACCATCCTTGTTCCGCCAATTTGCGTGCTGTGGCACATCTCCAATAAAGATGCTAGTGGGTCTGCTGACACTGCGGCTCTTCTTACTATGTTCCTGGCCGCAATAATTAGGCTTTGGTCAACATCGTC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF\n+@FS10001248:222:BRL95618-1622:1:1101:5170:1430/1\n+GAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCGTTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACCCTGAAATTGGC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1101:11160:1460/1\n+TCTCATGACTGCTTCTCCAAGCGAATCTCTGTAGATTTTTAGAGACTCGAACTGTGTTATCATTCCATTCAAGTCCTCCGATGAGGACCCCAATTGCATTTTTGACATCCTCAATAGTATGTCCTGGAAATGAAGGCAATGGTGAGAT\n++\n+,F:FFFFFFFF:F:FFFFFF:FFFFFFFFFFFFFFFF:F:F:F:FFFFF,FFFFFFFF,FF,FF:FFFFF,F:FFFFFFF,F:,FFFFFFF:FFF:FF:FF::FFFFFFFFFFF:FFFF::FFFFFF:,F,FFFF::,::FFFF,FFF\n+@FS10001248:222:BRL95618-1622:1:1101:13970:1490/1\n+GTTCTGTCTAAGAATGTCCACCATCCTTGTTCCGCCAATTTGCGTGCTGTGGCACATCTCCAATAAAGATGCTAGTGGGTCTGCTGACACTGCGGCTCTTCTTACTATGTTCCTGGCCGCAATAATTAGGCTTTGGTCAACATCGTC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1101:10980:1510/1\n+GAGTGTAAGGGAATTGAATAGAATCAATCCGAATGTAATGGAAAGGAATGGAAC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1101:9890:1590/1\n+AGTCTGCCCTTGTGGCCATTTCCTCCCCAGTGAATGAAAAAATGTGAATGTGTGTGTTCTCTGATTTAATTTTATTGGCCTTTTCAAGGTAATATATGTGGACTTCTCTCCTTGTCACTCCAATTTCGATGAATCTGTTTTCTTTGTA\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFF\n+@FS10001248:222:BRL95618-1622:1:1101:11700:1640/1\n+ATCCTATTGTATATGAGGCCCATGCAACTGGCAAGTGCACCAGCAGAATAACTGAGAGCTATTTCTTTGGCCCCGTGGAACGTTATCTCCCTCTTAAGTTTCCTATACAGTTTAACTGCTTTGTCCATGTTATTTGGGTCTCCATTC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL9'..b'ACTACTGTAACATTGCATTTCAAGCAATATGAATTCAACTCCCCTCCAAATAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGAAACATAACAGAGATAGTGTATTTG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF,FFF\n+@FS10001248:222:BRL95618-1622:1:1116:2860:3220/1\n+GCATGTATGCGACCATCAAGGGGGAAATTTTGCAATCTCGGAGTTCTTCTTTTTTCTCTTTAGTTATTGTTAGCTGTGATTCTGATGTTAGTATTCTGGCTCCCACTTCATTGGGAAAAACAACTTCCATAATTACATCTTGTGCC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFF:FFFF:FF:FFF\n+@FS10001248:222:BRL95618-1622:1:1116:5990:3250/1\n+CACTGATATTGAGAGGATCAGTTGCTCACAAATCTTGCCTACCTGCCTGTGCATATGGACCTGCAGTATCCAGTGGTTACGAC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:16430:3260/1\n+GTATAGGAAACTTAAGAGGGAGATAACGTTCCACGGGGCCAAAGAAATAGCTCTCAGTTATTCTGCTGGTGCACTTGCCAGTTGCATGGGCCTCATATACAATAGGATGGGGGCTGTAACCACTGAAGTGGCA\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:13420:3270/1\n+TGCCTGGTCCATTCTGATGCAAAGAGGTCCTTCCACTTTCTGCTTGGGCATTAGCATGAACCAGTTTCTTGAC\n++\n+F:F,:,F::FFFF:FF,FFF:FF,:F:FFF:F:FFFFFFFF:FFF,::FFF,FFFF,FF:FF:FF,:FFF:,F\n+@FS10001248:222:BRL95618-1622:1:1116:2860:3310/1\n+GGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCC\n++\n+FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:8620:3440/1\n+GGGAAGATCTCATCTGAGGAATGACACAGACGTGGTAAACTTTGTGAGCATGGAGTTTTCTCTCACAGACCCGAGACTTGAACCACATAAATGGGAGAAATATTGTGTCCTTGAGATAGGAGATATGTTACTAAGGAGTGCCATAGG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:8400:3630/1\n+CCTACAGACTTTCCCAATGGAACCTTCTTCCACTCCTTTGGGGGACTCCCCAATGGGCCATGCTTCTGATTTATTCTCAAAAAACTCTTTAGTCATGTCTTTCTCTTTAACTGAGGACTCGGCTTCAATCATGCTCTCGATCTGCTGG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:7680:3710/1\n+CAAGTGCACCAGCAGAATAACTGAGAGCTATTTCTTTGGCCCCGTGGAACGT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:15270:3730/1\n+GAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAGATGTAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCGTTCCA\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:3780:3940/1\n+GCACTTGTCTGAACGTTACCCATAACCTCAATATGTTTCATTGTAGCCAGAGGGCTTAGAAGATAAATAGACAAGAATAAGATTAGAAAGCTAGGGACGAGGATCGTAAC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:12760:3990/1\n+GCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAAC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:4260:4040/1\n+GGCCTTTCTTTACCTCTCCCTGCTCCCGGGCTCTGCCAAAG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:9400:4040/1\n+TCTGAGACCATTGAATTTTGACAGCTTCCCAATTCCTGATGATCCATTGATAGGTATTGACCAAAACCGACTCAGGGCCGTTAATCTCCCACATCATCGATGATGAATAAGTTATGGTCAGTCTTTCAGTTCCCTGTGTTTCACCTG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:2720:4080/1\n+AACTAACCCAAGGTCGCCAAACTTATGATTGGACATTAAACAGGAACCAACCGGCAGCAACTGCATTAGCCAACACCATAGAAGTCTTTAGATCGAACGGATTAACAGCTAATGAATCAGGAAGGCTAATAGATTTCCTCAAGGATGG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFF:\n'

diff -r eddd9befb66d -r ff2269d615d9 test-data/reverse.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reverse.fastqsanger Wed Jan 29 08:19:23 2025 +0000

b'@@ -0,0 +1,3348 @@\n+@FS10001248:222:BRL95618-1622:1:1101:3720:1000/2\n+AAATAAGGCCTCTTCTAATAGATGGAACAGCATCATTGAGCCCTGGAATGATGATGGGCATGTTCAACATGCTAAGTACAGTTTTGGGAGTCTCGATACTGAATCTTGGACAAAATCGTCTGAGGATTGGAGCCCATTCCACCAG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF,,FFFFFF\n+@FS10001248:222:BRL95618-1622:1:1101:8590:1000/2\n+CTATTGATGAATGAGTTGGGTGTTCCTTTCCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGCTCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAATGCAACTGCTAGCTTCATTT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:F,F:FFFFFFFF:FFFFFFFFFFFFF:FFFFF:F:FFF:FFFF::FFFF:FF,FFF,FF:FFF:FFFFFFFF:,F,:FFFFFF,FFFFFFFF:FF,FF,FFFFFFFFFF:\n+@FS10001248:222:BRL95618-1622:1:1101:9450:1000/2\n+AACGTAGGTTGCACACTGGTTTGGCCTGCGGAGGCCCTCTGTTGATTAGTGTTTCCTCCGCTCCTGGTCCTTATGGCCCAGTACCCGCTTCTCAGTTCAAGAGTGCTTGATCCCATATTATCCATGTTCTCATTTGAAGCAATTTGT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFF,FFFFFF:FFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1101:4990:1240/2\n+CATCAAATCAGCCACCCATGTTGGAAAGCAAATCGTAGAAAAGATTCTGAAAGGAGAATCTGATGAGACACTTAAAATGACCATGGTCTCAACACCTGCTTCGCGATACATAACTGACATGACTATTGAGGAATTGTCAAGAAACTGG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFF\n+@FS10001248:222:BRL95618-1622:1:1101:6720:1330/2\n+ATATACAGAAGAGTCGATGGAAAATGGATGAGGGAACTCGTCCTTTATGACAAAGAGGAAATAAGGCGAATCTGGCGCCAAGCCAACAATGGTGAGGATGCTACATCTGGTCTAACCCAC\n++\n+,F:F,FF:F,FFFFFFFFFF:,FFF,F:FFFFFF:FFFF:F:FFFFFF:FF,FF:FF:FFFF:FFFFF:FFFFFFF,FFFF,FF,FF,F:FFFFFFF:F:FFF::FFFFFFFF,FFF,,F\n+@FS10001248:222:BRL95618-1622:1:1101:14230:1350/2\n+AAACAAGGTTTCTCCCAGTTGCTGGCGGAACAAGCAGTATATACATTGAAGTTTTACATTTGACTCAAGGAACGTGTTGGGAACAAATGTACACTCCAGGTGGAGGAGTGAGGAATGACGATGTTGACCAAAGCCTAATTATTGCGG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF\n+@FS10001248:222:BRL95618-1622:1:1101:5170:1430/2\n+GCCAATTTCAGGGTGCTTTGCTTAACATATCTGGGACAGGCCCCGTATGTGATCCTGTTTACATTTTGGAACGGTTTGTCATTGGGAATGCTTCCATTTGGAGTGATGCATTC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1101:11160:1460/2\n+GAGCAATTGTTGGCGAAATCTCACCATTGCCTTCTTTTCCAGGACATACTATTGAGGATGTCAAAAATGCAGTTGGGGTCCTCATTGG\n++\n+FFFFFFFFFFF,FFF,FFF:FFF:,F,F,FFF:FF,F:F:F:FFFFF:FF::F:,FFFFF:FF:F:FFFFF,FF::FFF,FFFFF,,F\n+@FS10001248:222:BRL95618-1622:1:1101:13970:1490/2\n+AAACAAGGTTTCTCCCAGTTGCTGGCGGAACAAGCAGTATATACATTGAAGTTTTACATTTGACTCAAGGAACGTGTTGGGAACAAATGTACACTCCAGGTGGAGGAGTGAGGAATGACGATGTTGACCAAAGCCTGATTATTGCGG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF,FFF\n+@FS10001248:222:BRL95618-1622:1:1101:10980:1510/2\n+GTTCCATTCCTTTCCATTACATTCGGATTGATTCTATTCAATTCCCTTACACTC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1101:9890:1590/2\n+GGACAGTAGTAAACAGTATCTGCAACACTACTGGAGCTGGAAAACCGAAGTTTTTACCGGATCTGTATGATTACAAAGAAAACAGATTCATCGAAATTGGAGTGACAAGGAGAGAAGTCCACATATATTACCTTGAAAAGGCCAATAA\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFFFFFFFF:\n+@FS10001248:222:BRL95618-1622:1:1101:11700:1640/2\n+GATTTGTTTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTAAATGGGAATGGAGACCCAAATAACATGGACAAAGCAGTTAAACTGTATAGGAAACTTAAGAGGGAGATAACGTTCCG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1101:6420:1680/2\n+CTCTGTCTGATCCAGCATCACTCATTTTACTCCATAGAGTTTGTCCTTGTTCATTTCTCTCCGGAACCATTTCTGTTATCCTTTTGTCAGCAGTAATTGGATATTTCATTGCCATCATCCATTTCATTCTAAGT'..b'248:222:BRL95618-1622:1:1116:10870:3190/2\n+CAAATACACTATCTCTGTTATGTTTCTTTCTATTATTGTTGGTTCACACAGCATCACTTGGTTATTTGGAGGGGAGTTGAATTCATATTGCTTGAAATGCAATGTTACAGTAGTTATCAGG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:2860:3220/2\n+GTCCATTTTAGAAATCAAGTCAAAATACGAAGACGAGTAGACATAAATCCTGGTCATGCAGACCTCAGTGCCAAAGAGGCACAAGATGTAATTATGGAAGTTGTTTTTCCCAATGAAGTGGGAGCCAGAATACTAACATCAGAATCA\n++\n+FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFF,FFFFFFF,FF:FFFFFF,F\n+@FS10001248:222:BRL95618-1622:1:1116:5990:3250/2\n+GTCGTAACCACTGGATACTGCAGGTCCATATGCACAGGCAGGTAGGCAAGATTTGTGAGCAACTGATCCTCTCAATATCAGTG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:16430:3260/2\n+TGCCACTTCAGTGGTTACAGCCCCCATCCTATTGTATATGAGGCCCATGCAACTGGCAAGTGCACCAGCAGAATAACTGAGAGCTATTTCTTTGGCCCCGTGGAACGTTATCTCCCTCTTAAGTTTCCTATAC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F:FFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:13420:3270/2\n+AGGCAATACTCTCGGTCTAGACATCAAATCAGCCACCCATGTTGGA\n++\n+F::FFFFF:FFF:F:FF:FFFF,FFFFFFFFF:FF:,FFF::,:::\n+@FS10001248:222:BRL95618-1622:1:1116:2860:3310/2\n+GGCGATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:8620:3440/2\n+AATTTGGCCTATGGCACTCCTTAGTAACATATCTCCTATCTCAAGGACACAATATTTCTCCCATTTATGTGGTTCAAGTCTCGGGTCTGTGAGAGAAAACTCCATGCTCACAAAGTTTACCACGTCTGTGTCATTCCTCAGATGAGAT\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:8400:3630/2\n+GTTCTTGTATGTGAGGACAAACGGAACATCAAAAGTCAAAATGAAATGGGGAATGGAGATGAGACGTTGCCTCCTTCAGTCACTCCAGCAGATCGAGAGCATGATTGAAGCCGAGTCCTCAGTTAAAGAGAAAGACATGACTAAAGAG\n++\n+F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFF:\n+@FS10001248:222:BRL95618-1622:1:1116:7680:3710/2\n+ACGTTCCACGGGGCCAAAGAAATAGCTCTCAGTTATTCTGCTGGTGCACTTG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:15270:3730/2\n+TGGAACGGTTTGTCATTGGGAATGCTTCCATTTGGAGTGATGCATTCAGACTTACATCTGCCAATGGGTGCATCTGATCTCATTATTGAGCTTTTCCCACTTCGTATTTTGAAGTAACCCCTAGGAGCAATTAGATTC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:3780:3940/2\n+GTTACGATCCTCGTCCCTAGCTTTCTAATCTTATTCTTGTCTATTTATCTTCTAAGCCCTCTGGCTACAATGAAACATATTGAGGTTATGGGTAACGTTCAGACAAGTGC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:12760:3990/2\n+GTTCCATTGATCTATATCTCTGTTTTGGTACCAGTACCATGC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:4260:4040/2\n+CTTTGGCAGAGCCCGGGAGCAGGGAGAGGTAAAGAAAGGCC\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@FS10001248:222:BRL95618-1622:1:1116:9400:4040/2\n+GTGAAACACAGGGAACTGAAAGACTGACCATAACTTATTCATCATCGATGATGTGGGAGATTAACGGCCCTGAGTCGGTTTTGGTCAATACCTATCAATGGATCATCAGGAATTGGGAAGCTGTCAAAATTCAATGGTCTCAGACTG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FFFFFFFFFF:FFFF:FFFFFFFFFFFF:FFF:F\n+@FS10001248:222:BRL95618-1622:1:1116:2720:4080/2\n+AAAGTGTGTTGTTATCTCCATTTCCTCCTTATCCATTGATTCCATCACATCCTTGAGGAAATCTATTAGCCTTCCTGATTCATTAGCTGTTAATCCGTTCGATCTAAAGACTTCTATGGTGTTGGCTAATGCAGTTGCTGCCGGTTGG\n++\n+FFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFF::FF:FFFFFFFF:\n'

diff -r eddd9befb66d -r ff2269d615d9 test-data/test_reads.fq
--- a/test-data/test_reads.fq Fri Jan 24 21:47:10 2025 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,4000 +0,0 @@\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-AGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGG\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-TAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCA\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-TTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGAT\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-ATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGT\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-GAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTC\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-CCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACT\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-CCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCAT\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-TATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGT\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIII'..b'GCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCA\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-AGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTG\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-ACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGG\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-ACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGT\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-GCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAA\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-AAGGTAAGAAGCCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTT\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-ACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCA\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-CAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCT\n-+0cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n'

diff -r eddd9befb66d -r ff2269d615d9 test-data/test_reads_copy.fq
--- a/test-data/test_reads_copy.fq Fri Jan 24 21:47:10 2025 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000