Galaxy |

Changeset 0:fd974c5df8bc (2021-02-17)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"

added:
optitype.xml
test-data/exome/NA11995_SRR766010_1_fished.fastq
test-data/exome/NA11995_SRR766010_2_fished.fastq
test-data/rna/CRC_81_N_1_fished.fastq
test-data/rna/CRC_81_N_2_fished.fastq

diff -r 000000000000 -r fd974c5df8bc optitype.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/optitype.xml Wed Feb 17 08:10:24 2021 +0000

[

b'@@ -0,0 +1,213 @@\n+<tool id="optitype" name="OptiType" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+ <description>HLA genotyping predictions from NGS data</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">1.3.5</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">optitype</requirement>\n+ </requirements>\n+ <command detect_errors="aggressive">\n+<![CDATA[\n+export MPLCONFIGDIR=\\$TEMP &&\n+#set $fastqs = []\n+#if str( $fastq_input.fastq_input_selector ) == "paired":\n+ ln -s \'${fastq_input.fastq_input1}\' reads_1.fastq\n+ && ln -s \'${fastq_input.fastq_input2}\' reads_2.fastq\n+ #set $fastqs = [\'reads_1.fastq\',\'reads_2.fastq\']\n+#elif str( $fastq_input.fastq_input_selector ) == "paired_collection":\n+ ln -s \'${fastq_input.fastq_input1.forward}\' reads_1.fastq\n+ && ln -s \'${fastq_input.fastq_input1.reverse}\' reads_2.fastq\n+ #set $fastqs = [\'reads_1.fastq\',\'reads_2.fastq\']\n+#elif str( $fastq_input.fastq_input_selector ) == "single":\n+ ln -s \'${fastq_input.fastq_input1}\' reads.fastq\n+ #set $fastqs = [\'reads.fastq\']\n+#end if\n+&& RAZERS3=`which razers3`\n+&& sed "s#path_to_razers3#\\$RAZERS3#" \'$optitype_config\' | sed "s/threads=16/threads=\\${GALAXY_SLOTS}/" > config.ini\n+#set $input_fq = \' \'.join($fastqs)\n+&& OptiTypePipeline.py \n+$read_type --input ${\' \'.join($fastqs)}\n+#if str($beta) != \'\': \n+ --beta $beta\n+#end if\n+#if str($enumerations) != \'\': \n+ --enumerate $enumerations\n+#end if\n+--config "`pwd`/config.ini"\n+--outdir outdir\n+&& cp outdir/*/*_coverage_plot.pdf \'$coverage_plot\'\n+&& cp outdir/*/*_result.tsv \'$result\'\n+]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="optitype_config"><![CDATA[\n+[mapping]\n+\n+# Absolute path to RazerS3 binary, and number of threads to use for mapping\n+\n+razers3=path_to_razers3\n+threads=16\n+\n+[ilp]\n+\n+# A Pyomo-supported ILP solver. The solver must be globally accessible in the\n+# environment OptiType is run, so make sure to include it in PATH.\n+# Note: this is NOT a path to the solver binary, but a keyword argument for\n+# Pyomo. Examples: glpk, cplex, cbc.\n+\n+solver=$solver\n+threads=1\n+\n+[behavior]\n+\n+# tempdir=/path/to/tempdir # we may enable this setting later. Not used now.\n+\n+# Delete intermediate bam files produced by RazerS3 after OptiType finished\n+# loading them. If you plan to re-analyze your samples with different settings\n+# disabling this option can be a time-saver, as you\'ll be able to pass the bam\n+# files to OptiType directly as input and spare the expensive read mapping\n+# step.\n+\n+deletebam=true\n+\n+# In paired-end mode one might want to use reads with just one mapped end (e.g.,\n+# the other end falls outside the reference region). This setting allows the\n+# user to keep them with an optionally reduced weight. A value of 0 means they\n+# are discarded for typing, 0.2 means single reads are "worth" 20% of paired\n+# reads, and a value of 1 means they are treated as valuable as properly mapped\n+# read pairs. Note: unpaired reads will be reported on the result coverage plots\n+# for completeness, regardless of this setting.\n+\n+unpaired_weight=$unpaired_weight\n+\n+# We call a read pair discordant if its two ends best-map to two disjoint sets\n+# of alleles. Such reads can be either omitted or either of their ends treated\n+# as unpaired hits. Note: discordant read pairs are reported on the coverage\n+# plots as unpaired reads, regardless of this setting.\n+\n+use_discordant=$use_discordant\n+ ]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <conditional name="fastq_input">\n+ <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">\n+ <option value="paired">Paired</option>\n+ <option value="single">Single</option>\n+ <option value="paired_collection">Paired Collection</option>\n+ </param'..b'end falls outside the reference region). This setting allows the\n+user to keep them with an optionally reduced weight. A value of 0 means they\n+are discarded for typing, 0.2 means single reads are "worth" 20% of paired\n+reads, and a value of 1 means they are treated as valuable as properly mapped\n+read pairs. Note: unpaired reads will be reported on the result coverage plots\n+for completeness, regardless of this setting. ]]>\n+ </help>\n+ </param>\n+ <param name="use_discordant" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use_discordant">\n+ <help><![CDATA[\n+We call a read pair discordant if its two ends best-map to two disjoint sets\n+of alleles. Such reads can be either omitted or either of their ends treated\n+as unpaired hits. Note: discordant read pairs are reported on the coverage\n+plots as unpaired reads, regardless of this setting. ]]>\n+ </help>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data name="coverage_plot" format="pdf" label="${tool.name} on ${on_string} coverage_plot.pdf"/>\n+ <data name="result" format="tabular" label="${tool.name} on ${on_string} result.tsv">\n+ <actions>\n+ <action name="column_names" type="metadata" default="Solution,A1,A2,B1,B2,C1,C2,Reads,Objective"/>\n+ </actions>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <conditional name="fastq_input">\n+ <param name="fastq_input_selector" value="paired"/>\n+ <param name="fastq_input1" ftype="fastqsanger" value="rna/CRC_81_N_1_fished.fastq"/>\n+ <param name="fastq_input2" ftype="fastqsanger" value="rna/CRC_81_N_2_fished.fastq"/>\n+ </conditional>\n+ <param name="read_type" value="--rna"/>\n+ <param name="solver" value="glpk"/>\n+ <output name="result">\n+ <assert_contents>\n+ <has_text_matching expression="0\\tA\\*31:01\\tA\\*68:01\\tB\\*40:01\\tB\\*51:01\\tC\\*03:04\\tC\\*15:02\\t13\\d+.\\d+\\t12\\d+.\\d+"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <conditional name="fastq_input">\n+ <param name="fastq_input_selector" value="paired"/>\n+ <param name="fastq_input1" ftype="fastqsanger" value="exome/NA11995_SRR766010_1_fished.fastq"/>\n+ <param name="fastq_input2" ftype="fastqsanger" value="exome/NA11995_SRR766010_2_fished.fastq"/>\n+ </conditional>\n+ <param name="read_type" value="--dna"/>\n+ <param name="solver" value="glpk"/>\n+ <param name="enumerations" value="2"/>\n+ <param name="unpaired_weight" value="0.2"/>\n+ <output name="result">\n+ <assert_contents>\n+ <has_text_matching expression="0\\tA\\*01:01\\tA\\*01:01\\tB\\*08:01\\tB\\*57:01\\tC\\*06:02\\tC\\*07:01\\t3\\d+.\\d+\\t3\\d+.\\d+"/>\n+ <has_text_matching expression="1\\tA\\*01:01\\tA\\*01:01\\tB\\*08:01\\tB\\*08:01\\tC\\*06:02\\tC\\*07:01\\t3\\d+.\\d+\\t3\\d+.\\d+"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+**OptiType**\n+============\n+\n+OptiType_ is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.\n+\n+**INPUTS** \n+\n+ RNA or DNA sequences in fastq format.\n+\n+**OUTPUTS**\n+\n+ result.tsv A TAB-separated file of HLA genotyping predictions:\n+\n+ ::\n+\n+\t\tA1\tA2\tB1\tB2\tC1\tC2\tReads\tObjective\n+\t0\tA*31:01\tA*68:01\tB*40:01\tB*51:01\tC*15:02\tC*03:04\t132\t128.43599999999998\n+\n+\n+ coverage_plot.pdf Plots of coverage of HLA genotyping predictions\n+\n+.. _OptiType: https://github.com/FRED-2/OptiType\n+]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btu548</citation>\n+ </citations>\n+</tool>\n'

diff -r 000000000000 -r fd974c5df8bc test-data/exome/NA11995_SRR766010_1_fished.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exome/NA11995_SRR766010_1_fished.fastq Wed Feb 17 08:10:24 2021 +0000

b'@@ -0,0 +1,4000 @@\n+@SRR766010.692\n+TACAAAAAAATTAGCTGGGCGTGGTGGCACATGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATTGCTTGAATCTGGGAGGCAGAGCTTGCA\n++SRR766010.692\n+3BBBCCC>>::CABB@?====66.)B@C?ECCIGEA=ECF=IHGGGHDDHDFDDGHHHBGGGF<GEIG?4HGEGGEIGIIHDGEHFEFFHHHHDDA+D<@@\n+@SRR766010.944\n+CATCGTTGCTGGCCTGGCTGTCCTGGTTGTCCTAGCTGTCCTTGGAGCTGTGGTCACCGCTATGATGTGTAGGAGGAAGAGCTCAGGTAGGGAAGGGGTGA\n++SRR766010.944\n+<ADDDDDDBBBBB<99(<C<5=DBBCBCCCFEFED=HC<IHECHAFCAIIHEHDA:IHGIGHDIIIIIGIGHGGIIIHFECGGEIHFDDHHHFBDEDF@@@\n+@SRR766010.1469\n+AGTCTCCCTCTGTCGCCCAGGCTGGAGTGCAGTGGTGCGATCTTGGCTCACTGCAACCTCTGCCTCCCAGGTTGATGCCATTCTCCTGCCTCAGCCTCCCT\n++SRR766010.1469\n+CCCFFFFFHHGHFGHIIJJJIJJJIJJHHIIJHIIIHGGGIIIJJIIJIGIJIIJIJIJGGIJHHHHFFFF;@CEEEEDCCDDEDDDDDDDDDCDDDDDD<\n+@SRR766010.2064\n+AGTGGCAACATCTCGGCTCACTGCAAGCTCCACCTCCTGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCTAGTAGCTGGGACTACAGGCGCCCACCACCA\n++SRR766010.2064\n+CCBFFFFFHHHHGIJJJJJJJIEIIIIJJIJJJJJJJ9HIJFGGJJJIJDIJJJJJJIJJJJGIGHGHFFFCFCCCCECDDDDDDDDCDDDDDDDDDDDD?\n+@SRR766010.3628\n+TGCTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCACCTCGGCCTCCCAAGTGCTGGGATGACAGGCGTGAGCCACTGCGCCTGGCCTAATT\n++SRR766010.3628\n+CCBCCCCCCCCCCBBBBCBCCBB@CCCC@CCCCCBBBBBB?CCC?FHEIIIIEGIIIHIIGIIIIIHF@IIIIIGGGBIIGIGHIIIHAHHDHFFEFFC@C\n+@SRR766010.3766\n+CGCGCGCCACCATGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGCGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCTGCCC\n++SRR766010.3766\n+CCCFFFFFHHHHGIJJJIGIJIIJJJJJIBFIGJJJGIHIIJJJJJJGJ:BDFFFFDDDDDDBDDABDDCDDCCDCCCDBDDDCDDDDDCDBBDDEC>CD?\n+@SRR766010.3790\n+TGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGACGGGTGGATCACGAGGTCAGGAGACCTAGACCATCCTGGCTAACAAGGTGAAACCCCGTCT\n++SRR766010.3790\n+9DDDDDDDDDDDDDDCDDDDEDDCCBDDDDEFFFFFFHHHJIGJJJJJJIHJJIJJJJJJJJJIJJJJHFJJJJJJJJJJJJJJJJJJGHHFDFFFFFCCC\n+@SRR766010.3927\n+TCCTAGCTAACATGGTGAAACCCTGTCTCTACTAAAAATACAAAAAACTAGCTGGGCGTGGTGGCAGGTGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGG\n++SRR766010.3927\n+CCCFFFFFHGHHHJJEHIJIGIIJJJJJGJJJIJJJJIJJJJJJJJIIIJJJJGJJJJGIHHHHBDFDACAEDDDACACCDDCBDCCCC>CD?BDB??BD?\n+@SRR766010.4145\n+TGAATACTGCTAGATATTTTCATCCACAAAGACTGGTATAATCAAGTATCTTCCTCTCTTAGGTTACACTCCTCTTCCTGGGTCCAATTATTCAGAAGGTA\n++SRR766010.4145\n+CCCFFFFFHHHHHJJIJJJJJJJJJJJJJIJJJJJJHIJJJJJJJJIJJJJJJJJJJJJJJJJIJJJJJJIJJJIFHIJJIHHHHHFFFFFFFEECEEEDC\n+@SRR766010.4767\n+AGCCTGGCCAACATGGTGAAACCCCATCTCTACCAAAAATACAAAAATTAGCCAGGCGTGGTGGCCCGTGCCTGTAATCCCAGCTACTTGGGAGGCTGAGG\n++SRR766010.4767\n+CCCFFFFFHFHHHIJJAGHIGIJJJJJIJIJJJJJJIJJJJJJIJIJIIJJIIJJIFJAGHAHGFFFDADDDDD@>CDECCDDDDDDDDDDDBBDDBDDB<\n+@SRR766010.5393\n+TGGGGGCAAGTTGGGTTGAAGCCTCATTATCTCCCTTTTATTTATTCTGTAGGATGGCACATTTCCTAGAGGCAGAATCCTACAACTTCCACTCCAAAGAT\n++SRR766010.5393\n+CCCFFFFFHHHHHJJHJIIJJJJJJGIJGIJJJJJJJJJJJJJJJJIJIIIJJGIJJJJJGHHHHHHFFFFFDDDDDDDDDDDDDDDDDDDDDDDDCDDDD\n+@SRR766010.5446\n+CTCTTCAGCAGGGTCAGGGCTGAGGCCTGGAGATCAGGGCCCCTCACCTTCCCTTCCTTTCCCAGAGCAGTCTCCCCAGCCCACCATCCCCATCGTGGGCA\n++SRR766010.5446\n+BDDCCDDDDDDDDDDDDDDDDDDDBCCDDDEDDDDB?DDDDECCFDFFHHHHGJIHGIGIJJIJJJJJIHIJJJJJJJJJIHFJJIIJHHHHHFFFFFCCC\n+@SRR766010.5918\n+CCTAAACAAAGCTCTGCTGCTGGGGGCCCTCGCCCTGACTGCCGTGATGAGCCCCTGTGGAGGTGAAGACATTGTGGGTGAGTGCATGAGTGAGGAATGTT\n++SRR766010.5918\n+@C@FFFDDHFBCFGEHGGIGHIJIJI:@FFIIIJIIIJIGJJJJ@EEHD=@DFFDDC>CCCDB5?AACCCCCDD>>@>9-8A(:A@CC@C:ACD@CA:>:>\n+@SRR766010.6183\n+AACACCCTCATCTGTCTTGTGGACAACATCTTTCCTCCTGTGGTCAACATCACATGGCTGAGCAATGGGCACGCAGTCACAGAACGTGTTTCTGAGACCAG\n++SRR766010.6183\n+;==AD?DDDDFHBE<EAGHACGHCD3F8;FBDBGHBDFE@HGEIIIBHEIIII<?<=BGB(.847@CE@>E;-</9A@>;;A###################\n+@SRR766010.6358\n+TAGGCTGGGCGCGTTAGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCGGGCAGATCACAAGGTCAAGAGATCGAGACCATCCTAGCCAACATG\n++SRR766010.6358\n+438?8><502=8;(C;5;(2CAA@@;7@>EEEAC=@@.@GDF@AHFBB=3H@?))BD<?C?9HFD>EEC<H<FACCG@CFAHDA<GDAHDF?BDDDDD@?;\n+@SRR766010.6782\n+TGGCACATTTCCTAGAGGCAGAATCCTACAACTTCCACTCCAAGTGAGAAGGAGATTCAAACTCAATGATGCTACCATGCCTCTCCAACATCTTCAACCCC\n++SRR766010.6782\n+>>;;>CAC@;;:@CECCA<D@@;;E?=7EC@<GAEC=HFGGIJJJIHGHHF9IGIIGIHGBGGJIIIJJJIHCFJJIIDIJIJJJJJJHDFHHDFDBFC@@\n+@SRR766010.6826\n+CGGCTAGTTTTTTGTAGTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGTCTCAATCTCCTGACCTCGTGATCTGCCCGCCTCGGCCTCCCAA\n++SRR766010.6826\n+DDDDDC'..b'DDDDDDDDDEDDCDCDDCAA?BBDDDDFFHHHIJIJJJJJJJJJJJJJJJJIIJIHJJJJJJJJJJJJJJJJJJJJJIIIIHHHHHFFFFFCCC\n+@SRR766010.411631\n+CATTGTGTTGGGAGAATAGATTTGCTTCCATACCTTTTAAGTGTATATCTTTTCCTCTTTTTCCCAGGGCACTCTGGACTTCACCCAACAGGTAATACCTT\n++SRR766010.411631\n+@@CFDDEDHHHHHIIJGIIIIJJGGJIJIIIIJJIIIIGHIIJIGIGJJIJJJJHIIJJJJICEHEHGIJIJJHFHHHHFFFDFDEDDDBDBCCDEFDDDC\n+@SRR766010.411864\n+GATGGGGTTTCACCATGTTGGCCAGGTTGGTTTCGAACTCCTGACCTCAGGTGATCCACTTGCCTAAGCCTCCCAAAGTGCTGGAATTACAGGCATGAGCC\n++SRR766010.411864\n+BCCFFFFDHHHHHJJJJJIIJJJJJJHIJJGHIJJJGHIIHIJEIJIJIGI4CGHIHJIIIIIIGHGGHHFFFFECEE:@CDDDDDDDDDDDC?ACBACC?\n+@SRR766010.412206\n+TGGCTCACGCCTGTAATCCCAGCACTTTGAGAGACCGAGGCGGGCAGATTATGAGGTCAGGAGTTTGAGACCAGCCTGACCAACACGGTGAAACTCTGTCT\n++SRR766010.412206\n+9AABB>5DDC@@C@CCBBCC@CCCEAAECFDDECHEIGHIIIJHGJIIHGIEIIJJHGIJJJJJJIGHHGJJIJJIJHEJJIHHGJJJHGHHHFFFFFCCB\n+@SRR766010.412680\n+GAAGTCAGGTGGTTCCGGAACAGCCAGGAAGAGAAGGCTGGGGTGGTGTCCACAGGCCTGATTCAGAATGGAGACTGGACCTTCCAGACCCTGGTGATGCT\n++SRR766010.412680\n+CA>CCCB@8?5;2??;>5>;CCAA;C;CD@;;ACEEGIIIIIHCCHDDAFB96@B3@BGGBDFAFAGDGHHGGGEA<<9DEIIHGCAA@ADA?BDDD?<?@\n+@SRR766010.414169\n+TTTCACCATATTGGCGAGGCTGGTCTCAAACTCCTGACCTTGTGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCTACCACGCCC\n++SRR766010.414169\n+=@;A=DDDDF8CCFE:<C:AEFD:CDFA<9?F<9*9?9BDD4BB?*8=FBFI;;(8=@D=7=?=?A>@B;;@3>;(,55@;;((,88=<?AA#########\n+@SRR766010.414638\n+TGTGGAGCGGGGCCAGCCCAACACCCTCATCTGCCACATTGACAAGTTCTTCCCACCAGTGCTCAACGTCACGTGGCTGTGCAACGGGGAGCTCGTCACTG\n++SRR766010.414638\n+=<?DAA32)@@060B)6D;;BCDD7@@C>AA)=7?))6=AD9A?AA>>;@A9-;5=6;<>A<A35:?2<????2(252(++44>A59>??>>1(09<>>A>\n+@SRR766010.416298\n+AAACCATGAGTGAACTCCCATTCACAATTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACAAGGGATGTGAAGGCCCTCTTCAAGGAGAACTAC\n++SRR766010.416298\n+#######A>CD@@=B;EE@C;C?@===9CDDADGGG@BFBFC?8:FB90HF?FB?::*EDD:?14?HHFGFAEF9GGHF1@1GGCFFEFDHHHDDABB@@@\n+@SRR766010.416894\n+CGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCAGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACATGTGCCATGTGCAGCATG\n++SRR766010.416894\n+@DDCDDDCDBDDB?DCBDCA?BDDC;@HEGHHGGDBJJJJJIJIIIIHGIIJJIJIIIJJIGJJJJJJIGGJIIIIIHIGHJJIJJIJFHHHGFFFDFCC@\n+@SRR766010.417198\n+GTCTTGATGTGGAGGCTGCTGAAGCTCTCCAGGCCGGACCTGCCTCTCCTCGTTGCCGCCTTCTTCTTCCTTGTCCTTGCTGTTTTGGGTGAGTCAGGAGA\n++SRR766010.417198\n+CBBFFFFFGHHHGJIIIJJJJJJIIJIGIJIIJIJIJBHHIIGJJJJIIIIIHIJEHHFFCDCEDDDDDDDDDDCCCDACCDCCDCA<B<@ABCCDDD@B8\n+@SRR766010.417544\n+AATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGATCAGACGGTCAGGAGTTCGAGACCAGCTTGACCAAGATGGTGAAACCTCGTCTCTACTAAAAATACA\n++SRR766010.417544\n+ADBDDDEDDCDBCDDDDDDECDEECEDFFHHHHHHJJJJJJJJJJJJJJJJIJJHGJJJIJJJJHGIIJJJJJJJJJIHJJJJJJJJJHHHHHFFFFFBCC\n+@SRR766010.418008\n+GTGGTGCCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAAGCGGGCAGATCATGAGGTCAGGAGTTCGAGACCAGCTTGGCCAACATAGTGAAACCCC\n++SRR766010.418008\n+<B@A?<DDCDDDBCDDDCDDDBCACAC>DEEFFEDHHHHIIHGGBHBIJJIGGGIEIIJJGIJJIIJJIGHG@CIGFIJJIJIIIJHJHFHFDFDDDFC@@\n+@SRR766010.418267\n+GTAGAGAAGGTGTTTCACCGTGTTAGCCAGGATGGTCTTGATCTCCTGACATCGTGATCTGTCTGCCTCGGACTCCCAAAGTGCTGGGATTACAGGTGTGA\n++SRR766010.418267\n+@B@FFDFFHHFFHIJJIJJJJIIJIIJJJJJIGIG3CFGAGAHIIHIBGHHJIJFHGIGJJIIICFHGGBHE=DD@BEECE5>ADDCDDDDDDDDDCCCDC\n+@SRR766010.420147\n+GCCTGCTATGTGTGGGGCTTCTATCCAGCAGAAGTGACTATCACGTGGAGGAAGAACGGGAAGCTTGTCATGCCTCACAGCAGTGCGCACAAGACTGCCCA\n++SRR766010.420147\n+DDDDDDDDDDDDDDDDCDDDDEEDEEEEFFFFFFHHHHHHHJIJJJJJJJJJJJJJJJJHIJIJJJJJJJJJJJJJIJIJJJJIJIJIHHHHHFFFFFCCC\n+@SRR766010.420400\n+AGAGATGGGGTTTCATTATGTTGCCCAGGCTGGTCTCAAACTCCTGAGCTCAGGCAATCCACTCACCTTGGCCTCCCAAAGTGCTAGGATTACAGGCGTGA\n++SRR766010.420400\n+CCA<CDDBDDDDDCCADC?DDDDCBBEB=B@CHHHEEJIHGGHEHAEGHGJJIJIJHGHFDJIHDIJIGIGHGFDAFJJIHEIJJJJJHGGHGFFFDFCCC\n+@SRR766010.420849\n+GAGTGTGCAGTGGCACAATCTCTGCTCACTGCAACCTCTGCCTCCCGGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCGAGTAGCTTGGATTACAGGCACA\n++SRR766010.420849\n+DDDDDDDDDC>@DCCCDCCAAC@DDCC>DDDDBCDDDBDDDDFFHJJIIJJJJJJJJJJIIIJJJJJJJJJJJJIJJJJJJJJJJJJIGHHHHFFFFFBC@\n+@SRR766010.422204\n+TCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACGAGGTCAAAAGATTGAGACCATCCTGACCAACATGGTGAAACCCCATCTCTAC\n++SRR766010.422204\n+?5@DBDDDCCAD@DDDDDC>DECECDFFFGFFJIJJJIJJJJJJJIHGJJIGGFEJJJJIJIGHGGIJJJIJIHGIHIGGIJJJIJIHFHHHFFDFFF@@C\n'

diff -r 000000000000 -r fd974c5df8bc test-data/exome/NA11995_SRR766010_2_fished.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exome/NA11995_SRR766010_2_fished.fastq Wed Feb 17 08:10:24 2021 +0000

b'@@ -0,0 +1,4000 @@\n+@SRR766010.600\n+TCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGTTGCGACTACAGGCGCCCACCACCACGCCCAGCTAATTTTTTTTTTTTTTTTT\n++SRR766010.600\n+CCCFFFFFHHHHHIIJJJJJJGJJIJJJJJJJJJJJFIJJJJGAHFGGFFFIIGGFFFFEDDDDDBBDDBDDDDDDDDBBDD@CDEDDDDDDDDDBDBDB5\n+@SRR766010.666\n+AGACCAGCCTGGGCAACATGGCGAAACCCCGTCTCTACAAAAAATACAAAAAATGTAGCTGGGCGTGGTGGCACGGGCCTGTAGTCCCAGCTCCTCGGGAG\n++SRR766010.666\n+@@@DADDFHHHHHIJGGG@FBGEHIIIGI@H6BFHDHGHIGGEHGIIIJHGHFDECDECCC?BBDDDBA@DDDDDDBBB@?:CCA@CDCCDDDDCC5595<\n+@SRR766010.944\n+GGGCCCCTCACCTTCTCCTCCTTTCCCAGAGCCATCTTCCCAGCCCACCATCCCCATCATGGGCATCGTTGCTGGCCTGGCTGTCCTGGTTGTCCTAGCTG\n++SRR766010.944\n+@@@@BDDDFFFDHIIIIGGIGHIJDBBG?FADFGHGG@>@FHDCEBFGIFBFFDHH9;7@CDCE?CHFDFFCEEDBD@=?AC@9@:;@C5:89:@A:>>>:\n+@SRR766010.1295\n+CACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTTGTGATCCGCTCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCAGC\n++SRR766010.1295\n+CCCFFFFFHHHHHJJJJJJJGIJJJJIIJJJIIFJJJJJHGIJIJJIIGHFGIJIIIHEHHFFFDACCEECDDDDDCCDDDDD?B?@??CCD05>BBD9A?\n+@SRR766010.1469\n+TCTTGGCTCACTGCAACCTCTGCCTCCCAGGTTGATGCCATTCTCCTGCCTCAGCCTCCCTCGTAGCTGGAACTACAGGCACCTGCCACCACGCCTGGCTA\n++SRR766010.1469\n+A?A9DCADDCCCDC<(D@@DBDBDBBBAADDCCDDCBDCC@CDCFFECHAHIGIIHBIIJIIIGIFJJIJIHIGGEEIGHEJIHGGECHHDHHFFFFD@@@\n+@SRR766010.1570\n+TCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCTCCCGCCACCACGCCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCA\n++SRR766010.1570\n+@><B@DC@A8B?DDDBDBADDBD?<DCCDDDCDDDDDDDACDDDC@?B@DGGIIHFJHFIIJIJJJJJJJIJIIGIIJJJIJJJJJJIHFHHHFFDFF@B@\n+@SRR766010.2064\n+AGGCATGGTGGCTCACACCTGTAATCCCAGCACTTTAGGAGGCTGAGGTGGGCGGATCACAAGGTCAAGAGATCAAGACCATCCTGGCCAACATGGTGAAA\n++SRR766010.2064\n+@CCFFFFFFHHHHJIJJJJJJJJJJJJJJJJGGIIIIJJIGIIJJJJJEHHHHGHBCDDDDDDDCDDDDDBDCDDDDDDDDDDDDDDDDDDDBDDD>CAA>\n+@SRR766010.3039\n+CTAAAAATACAAAAATTAGCTGGGCATGGTGGCACGCACCTGTAGTCCCACCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGCGGAGG\n++SRR766010.3039\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJHIJIJJJJJJJJJJJIJJJJIGHIJJJJJIJJJHHHFFFFDDDDBDBBCDDDDD@ADDDDDDDDDB?BDBDB\n+@SRR766010.3628\n+GGTGAAACCCCATCTCTACTAAAAATACAAAAAATTAGCCGGGTATGCTGGCAGGCTCCTATAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATTGCG\n++SRR766010.3628\n+CDEDB90BBAC@CCADACCBDEDDDC@DDEEEEFEDFHFJIHIGGIIGDGGIIJIIJJJIJJJIIFIIGHGFFJIGJIIJJIGJIGIJHGHFHFFFFFCCC\n+@SRR766010.3766\n+GGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGCGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCTGCCCGTCTCGGCCTCCCAAAG\n++SRR766010.3766\n+AA>@:BBDDDDCC?CCDDCDC@DCB@@DDDDDDDB>5BBDBDDDDDEEEECDDFFEGHJJIJJJJIIHFIJIIIIGGIJJIIJIJJJJGHHHHFFFFFCCC\n+@SRR766010.3927\n+TGTCTCTACTAAAAATACAAAAAACTAGCTGGGCGTGGTGGCAGGTGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGG\n++SRR766010.3927\n+DCCADDDCCBDEEEEEDDDDDDEDDDDDDDDFFHHHHJJIIHHEIIJJIIHJIJIJJJJJJJIIJJJJJJJJIEIGJIJJJJIEJJJJHHGHHFDFFFCCC\n+@SRR766010.4145\n+AATTATTCAGAAGGTAACATCTCTGTTGGTCTGTTTCCCTACTTGCCCTTTGGTAGGGGTGCGGGTTAGAGGGGTCAGTGTTGGGTTCAACTAATCTTGAT\n++SRR766010.4145\n+AEDEDDEDDDDDDDEDEDCDDDDDDDDDDDDDDDEEDEEFFFFHHHHJJIHIG?JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJIHHHHHFFFFFCCC\n+@SRR766010.4221\n+TGAGGCAAGAGAATCGCTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAAATCACATCACTGCACTCCAGCCTGGGTGACAGAGGAGACTCTGTCTCAA\n++SRR766010.4221\n+CC@FFFFFHHHHHJJJJIIJGGJJIJJJIJF?FGGJJDFHIIJGGHGGIIHIJFHGEHCDCFFFEEEEEEDDDDCDDD9?ACCCDCDBB?BCDACCDDDED\n+@SRR766010.5393\n+ATCTTGGGGGCAAGTTGGGTTGAAGCCTCATTATCTCCCTTTTATTTATTCTGTAGGATGGCACATTTCCTAGAGGCAGAATCCTACAACTTCCACTCCAA\n++SRR766010.5393\n+ABBDDDDDDDDDCDDCDFFEDFHHHHHJJJJJIGJIJJIIJJIIJJIJJIIJJIJJJJJJIIGJJJJJJJJJJJJJJJIJGHJJJJJIHHHGHDDFFFCCB\n+@SRR766010.5446\n+AGAGATACACATGCCATGTGCAGCACGAGGGGCTGCCCCAGCCCCTCATCCTGAGATGGGGTAAGGAGGGAGATGGGTAAAGAGGGGAACGAGGGGTCATG\n++SRR766010.5446\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJIJJJJIJJHJJJIGIJJJIJJIJDDCHHHGGFFF9>CEECDDD@D@DDDD9ACDCCCDDD>BBB<@DBB&58A>\n+@SRR766010.5758\n+TAGAGATGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCAGCTTCCCAAAGTGCTGGGATTACAGGCGTGAG\n++SRR766010.5758\n+==114B4A?BDF>G?F@:<3<HA?9A1?:?9D@7BGB?3*??D<FH@@BABCC==3@FAH1B4=49=AAC:>C5>=@CAC>@CCC:<AA?C::>CB@BB@B\n+@SRR766010.5918\n+CGCCCTGACTGCCGTGATGAGCCCCTGTGGAGGTGAAGACATTGTGGGTGAGTGCATGAGTGAGGAATGTTCTCTGGAGCTGAAAAACAGTAAATTAAAGG\n++SRR766010.5918\n+BBBADCDC'..b'FGHHHHJJJJJJJJIIIIIJJIJJJJJJJJIJJJJIIJJHDDD@BDDD?BDDDDDDDDDDDDDDDDDDDDDDDEEDDDDDDDDDDDDDDDDEDC\n+@SRR766010.423587\n+GTTTACCGAGAATGATGATTTCCAATTTCATCCATGTGCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGC\n++SRR766010.423587\n+CCCFFFFFHHHHHIJJJIJIIIIJIJIJIGJIJJJJGHHIGJJIIJJJDGFEIJJIIJJJJJJJJJJJGHHHHHFDBDDC6>@CAC@@@C5@=@CCC@B>C\n+@SRR766010.423589\n+TCGCTCTGTCACCCAGGCTGGGGTGCAGTGGTGCAATCTCGGCTCACTGCAAGCTCCACCTCCCTGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTA\n++SRR766010.423589\n+<@<DDFDAHFBHFIIBHHDHHIG1CAHF:CGDHBG>@FDHICEHHHJGIGGDEHIGGCGHHCED;?=;A@CECDDBBCDC>ACCCDC>C>393(88<C?##\n+@SRR766010.423768\n+TGTTAGTCAGGATGGTCTTGATCTCCTGACCTTGTGATCTTCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACTGGCATGAGCCACCGCGCCCTGCCTGTT\n++SRR766010.423768\n+CCCFFFDFHHHHHHJCHIJJIJJJJJJJJJJJJJHIIJJJJJJJJIJJJJHGIIHHJIIIIGIHIIHHHHFFFFFFDEEEEDDDDDDDDDBDBDDBBCD>>\n+@SRR766010.424087\n+AGACGGGGTTTCACCATGTTAGCCAGTATGGTCTCAATCTCCTGACCTCGTGATCAGCCTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTAAGCCA\n++SRR766010.424087\n+@@@FFFFFCFHHDIJIIJFFHIIIIJHCFGIGIIIIJJJIJJJJGIEGGJHHBGCFHIDGIGIGAEHFFFFFCCEED-;@ACCDDCDCCCDDDDBDD?CC?\n+@SRR766010.424252\n+GAGGCAGGAAAAGTGCTTGAACCCGGGAGGCGGAAGTTGTGGTGAGCCGAGATGGCGCCATTGCACTCCAGCCTGGGCAACAAGAGCAAAACTCCATCTCA\n++SRR766010.424252\n+DDDDDDDDDDDDDDDDCC@@=DDDDDDDDDDFFFFFHHHHJJJJJJJJIHIJJIJJJIHIJJIIHJIIJJJJJJJJIJJIJJJJJJJJHHHHHFFFFFCCC\n+@SRR766010.424423\n+CCTCCTTTCTCTGCTGCACATGCCCTTCACAATAGCAGCGGAGAAGGTGTACAACACCCGCCATCAGGTGAGCGTGCATGTAAGGGAACCCCAAAGGGAGA\n++SRR766010.424423\n+DBDDDDCCDDDDDDECCCBC?BBDDEDDEDDDDDDDDDDDDDCDDDDDDDCBB>=3FJJJJIJJJJJJJJJJJJIJJIIJJJJJJIGCHHHHHFFFFFCCC\n+@SRR766010.425860\n+TAGTAGAGACAGGGTTTCTCCATGTTGGTCAGGCTGGTCTCGAACTCCCAACCTCAGGTGATCCACCTGCCTCGGCCTCCCAAAGTGCTGGATTACAGGCA\n++SRR766010.425860\n+@CCDFFDFHHDHHIEGIJIHIIJIJJGJEHHIJJJIIHIJGGHIIIIIJIGGIIABHIFGEIIIGADCHHHHFF<ABC;ABCCDD@CCDDD?ACCCCCDD@\n+@SRR766010.425929\n+ATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGTCGCAATAAACATACATGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTAT\n++SRR766010.425929\n+BCCFFFFDHHHHHJJHIJJJJJJIJJIIJJGIJJJJJJJJJJJIJJJJJJIIIJJJJHJJJJJIJIJJJJJJJHHHHHFFFFFFFEEEEFEEDDDDDD@CC\n+@SRR766010.426081\n+TGGAGAGCTTTAGCAGGGTCAGGGTCCCTCACCTTCCCCCCTTTTCCCAGAGCCATCTTCCCAGCCCACCATCCCCATCGTGGGCATCGTTGCTGGCCTGG\n++SRR766010.426081\n+CCCFFFFFGHHHHJJJJJFGIJJIIJJIJIJJJJJJJJJJJJJJJHIJJJHIJJIIHHHHHHFFFFDDDDDDDDDDCDDDBB@BB?CDBDDDDDDD@BCBB\n+@SRR766010.426224\n+GTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTA\n++SRR766010.426224\n+???DDFFFDHFDBEDAHHIBG@FG>GGGCBG<FHGIIIGGBEHG<?FHHG;BBD87@CFGCEGC?C3=AEFBD>A>>;88?BB?ADCCDA4>C@CCB8>C>\n+@SRR766010.426521\n+TCCTATACACCAAGAACAGACAAACAGAGACCCAAATCATGAGTGAACTCCCATTCACAATTACTACAAAGAGAATAAAATATCTAGGAATACAACTTACA\n++SRR766010.426521\n+EEEEDCBDDFHHHHHEHJIHJJJHJIIIGBJJJJIIIJJJJJJJIHEIHHD?:::HFJJJJIHIIHJJJJJIJJIJJJJJJJJJJJJHGHGHHEDFFFB@@\n+@SRR766010.426560\n+TGAGGAATCGCCACACTGTGTTTCACAATGGTTGAACTAATTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCATCTG\n++SRR766010.426560\n+DDDDCBBBDA@@>>;DCDEACCB@BDDFHFHHGIH@HEGIIGGGEGFBFCFFIJGHGGGIEIIHGIIIIIGHEIGCGHFGHEHHBEBF?HFHFDBEDA@CB\n+@SRR766010.426805\n+ATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACTATGT\n++SRR766010.426805\n+CCCFDFFFFHHGHJJIJJIIJGAFBFGGIIIIIIIIJIJGBGEGHIHJBHHHHHFFFDDDDD@CDEDDDDDEDEDDDBC@@:4@CCDBDB5>?CCDDCCCD\n+@SRR766010.428346\n+AGGTGGCGACGTAGGGGCCATGGGGCTGGGCCGGGTCCTGCTGTTTCTGGCCGTCGCCTTCCCTTTTGCACCCCCGGCAGCCGCCGCTGGTGAGTGGGGAT\n++SRR766010.428346\n+?DB?DDDB?DDB?DDDAC?C@DDBBB@D@BBBBDB@DDCBCCCDDBDBB<7BBBBBDBB?DDDDDDC@:0DDFHGIJIGJJJGJJJJJHHGHHFFFFFCCC\n+@SRR766010.429642\n+CTCACCCAACAGGTAATACCTTTTAATCCTCTTTTAGAAACAGATTCAGTTTTCCTAGAATGATGGCAGAGGTGATAAGGCATGAGACAGAAATAGCAGGA\n++SRR766010.429642\n+#########?7@CD@E??5)GHDG@=8.)1CAIGB80***B8994HB?9)0:*HGAHDD?D?::9AAHF@C@HF?DFBHF@F<EHE<A<A,??;DDD?;<B\n+@SRR766010.429831\n+AATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTTCAGGGACTTGGATGAAGCTGGAAACCATCATTCTCAGCAAACTAACACAGGAACGGAAA\n++SRR766010.429831\n+DC>5:AA??BDDCEECDFHHHHHHHJJJIHIJJJJJJJJJJIJJJIIHHFFJJJJJJJJJJJJJIHJJJJJJJJJJJJJJJJJJJJJIFHHHHFFFFFCCC\n'

diff -r 000000000000 -r fd974c5df8bc test-data/rna/CRC_81_N_1_fished.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rna/CRC_81_N_1_fished.fastq Wed Feb 17 08:10:24 2021 +0000

b'@@ -0,0 +1,6276 @@\n+@SRR397217.2404\n+TCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGAGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACAT\n++SRR397217.2404\n+9FEEBF?DDEE?F?ECFHDHHHHHHHEAFFF@FFHHFHHFFFHDHFHFHHFHHHHFHFHFHFHHHHHHHHHHHHHHHEHHHHHHHHHHHHHHGGHHHHHHH\n+@SRR397217.3931\n+GAGGAGGAAGAGCTCAGATAGAAAAGGAGGGAGCTACTCTCAGGCTGCAAGCAGTGACAGTGCCCAGGGCTCTGATGTGTCTCTCACAGCTTGTAAAGTGT\n++SRR397217.3931\n+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHFHHFHHHHFFHHHFFED<>CEBEEDFDFHEF<EEEDEFFEFHGHHCHHAFCCED?BBFC:>7\n+@SRR397217.7193\n+AGCCCCCAAAGACACACGTGACTCACCACCCCATCTCTGAACATGAGGCCACCCTGAGGTGCTGGGACCTGAGCTTCTACCCTGCGGAGATCACACTGACC\n++SRR397217.7193\n+DEGGFCGCEAFGGG@CFFBFF=6FBDC?BFE@6C=B>@E?.EEEED>-DADDD?7*33**<B;5503:2*4*:8*@@-=B.@3.>/-24(@7CD#######\n+@SRR397217.16054\n+CGGTTCCTGGACAGATACTTCTATCACCAAGAGGAGTACGTGCGCTTCGACAGCGACGTGGGGGAGTACCGGGCGGTGACGGAGCTGGGGCGGCCTGATGC\n++SRR397217.16054\n+@5>><::@;DA4:CCD4DF<FFBCHDAC?CD;C9?>DDAFFBCC==EEFBFEFEFAHHFHHHHHHFHFFHHHG@HHHGFHHHHHHHHHHHHHHHHHHHHHH\n+@SRR397217.16506\n+GGAAATCATGACAAAGCGCTCCAACTATACTCCGATCACCAATGTACCTCCAGAGGTAACTGTGCTCACGAACGGCCCTGTGGAACTGAGAGAGCCCAACG\n++SRR397217.16506\n+51<@>=>AAC3BEE55GFFEEEDD@ED@=FB=FFEAFBFFFFCFD<BF;FHHHFHHHHFBFHHFHFFCFFFEE5HHHHHHHHHHHHHHHHHHHHHHFHHHH\n+@SRR397217.26902\n+CTCCAAGCCCTCTCCCAGAGACTACAGAGAACGTGGTGTGTGCCCTGGGCCTGACTGTGGGTCTGGTGGGCATCATTATTGGGACCATCTTCATCATCAAG\n++SRR397217.26902\n+####CBCDC<@D0FBFFGFFE>?EFGEEE@BFHCBHFFFEBHHEHHHHFFFFHFFHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHGHHGHGHHHHGHHHH\n+@SRR397217.34824\n+GTGGTCGCTGCTGTGATGTGGAGGAGGAAGAGCTCAGATAGAAAAGGAGGGAGCTACTCTCAGGCTGCAAGCAGTGACAGTGCCCAGGGCTCTGATGTGTC\n++SRR397217.34824\n+HHHHHHHHHHHHHHHEFEBGGCGGDGFEEFFFHFHFHEEHFDC@FHEBFEH@HHEEHDFFF@FFDFHD@E??:@7D>DDAC8BDC0BCCCCFECBCC6@##\n+@SRR397217.35267\n+CTGGCCTGGCTGTCCTAGCAGTTGTGGTCATCGGAGCTGTGGTCGCTGCTGTGATGTGTAGGAGGAAGAGTTCAGGTGGAAAAGGAGGGAGCTACTCTCAG\n++SRR397217.35267\n+D:BEEBBFEDEBADDEFGBEGFEGFGDACC?EFBEECEFFHEEECDBEHHHHHHFHCHHFHHHHHHHHHHHBBHHHFHGHHHHHHFHHHHHHHHHHHHHHH\n+@SRR397217.41512\n+GGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGGACCCCCCAAAACGCATATGACTCACCACGCTGTCTCTGACCATGAAGCCCCCC\n++SRR397217.41512\n+HHHHHHHHHHGHHHHHHHHHHHHGHHHHGFGHHHHEFHGFDEDC<F@F=FFDHHHBFBGFEFDFEC79D4A9>A09>@4<CD?ED2AEDB>7@>@?:13B3\n+@SRR397217.45346\n+GTGGCGGAGCAGTTGAGAGCCTACCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAAACGGGAGGAGGCGCGGCGGCGCACCGGACCCCC\n++SRR397217.45346\n+HHHHHHHBHHEFCGFFFBE<HFDHHDFHCFDEFFBFBFEFCFFBE@ED?>D?#################################################\n+@SRR397217.46100\n+TTTCTACCCAGGCAGCATTCAAGTCCGATGGTTCCTGAATGGACAGGAGGAAACAGCTGGGGTCGTGTCCACCAACCTGATCCGTAATGGAGACTGGACCT\n++SRR397217.46100\n+DCDEDAF@CFGHHHHFFHEHFEIFFFHFFHHA<EFHFHEHHFBFHHHHHHHHHHFHHHHFHHHEHFHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+@SRR397217.55350\n+AGCAGAGATACACGTGCCATGTGCAGCACGAGGGGCTGCCGGAGCCCCTCACCCTGAGATGGGAGCCCTCTTCCCAGCACACCACCCCCATCGCGGGCATC\n++SRR397217.55350\n+HHHHEHHHHHHHHCFFGGGFH?HHHDHHHEHFF?DDDF@G?A6A9DAD;<3,=A+827*3<?C######################################\n+@SRR397217.56880\n+GTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTTCTCACACCATCCAGATGATGTATGGCTGCGACGTGGGGTCGGACGGGGGCTT\n++SRR397217.56880\n+HHHHHHHHHHHHHHHHHFHFHHHHHHHHHHGHEFEHFH?HEDGDFHGFHFHDHEHEHB@FFFHDEE?FFD@<BA@EE:E<ED9CDDB0?AF;<CC######\n+@SRR397217.60691\n+TGCGGTTCGACAGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGGGGATAGAGCAGGGGAGGCCTGGGGATTGGGACCAGGGGGCACGGGAAGGG\n++SRR397217.60691\n+HHHHHHGHHGHHHHGFHHFHGGHHHHHHHHHHHHHHADFFC>BDF55+?####################################################\n+@SRR397217.67670\n+GGCGCCGTGGATAGAGCAGGAGAGGCCTGAGTATTGGGACCAGGAGACACGGAATGTGAAGGCCCACTCACAGATTGACCGAGTGGACCTGGGGACCCTGC\n++SRR397217.67670\n+HHHHHGHFHHHHGHAHHDHHFG?DEFEEFCD2DBDAD?@CDA?D9EBEBECF7CCC>CBB6A6D?.>>>>DCA33CAA?BBCB>CB5@E@AA<D85B@###\n+@SRR397217.68114\n+GGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACTAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGTGGCTGGGGTGGGGCCTTCTGGA\n++SRR397217.68114\n+HHHHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHEFFEDDF1ECCBFBFDDFEEE6EF@6D@EBEDEE@(@7,:?3.<>65>4<@##############\n+@SRR397217.69566\n+AGCGGGCCGCGGTGGACACCTACTGCAGACACAACTACGGGGTTGTGGAGAGCTTCACAGTGCAGCGGCGAGTCCATCCTAAGGTGACCGTGTAT'..b"HHHHHHHHHHHHHHHHFHHHFFBHHHHFHHHHEFHFHFHHHHHHFHCHEHEFCHFFFHHH7F@FBD3F@B>A@=DADD+0?#############\n+@SRR397397.936597\n+TACAGCATGGGGGGCTGCCGAAGCCCCTCACCCTGAGATGGGAGCCATCTTCCCAGTCCACCATCCCCATCGTGGGCATTGTTGCTGGCCTGGCTGTCCTA\n++SRR397397.936597\n+###############?>@@:5EEFEBCCA=::>@<9E>?AE?A;.??=FBGBGFGEDBFEEG@FBGFGEGGGGGGGEGFFGFFFDEFGFGGEDFDFBEEEE\n+@SRR397397.936627\n+AGAGTATTGGGACCGGGAGACACGGAGCGCCAGGGACACCGCACAGATTTTCCGAGTGAACCTGCGGACGCTGCGCGGCTACTACAATCAGAGCGAGGCCG\n++SRR397397.936627\n+DFDGFDDEEEE<9GGGEHHEHFDDHHDFB:FFFFFFFDCFFD@EDFCE7E@HHHHHHHFEHHHHHHHHHHHHHHHHHHHHHHHDGHHHHHHHHHHHHHHHH\n+@SRR397397.941041\n+CACCACAGGAGTGTCAGAGACAGTCTTCCTGCCCAGGGAAGACCACCTTTTCCGCAAGTTCCACTATCTCCCCTTCCTGCCCTCAACTGAGGACGTTTACG\n++SRR397397.941041\n+GHGHFHHHFGHHHHHHHEHHHHHHHHFHHHFHFHHHHHHFHFHFCHHHHHHGHHHHHHHHHHHHHFGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+@SRR397397.941972\n+GAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCAGCTCAGACCACCAAGCACAAGTGGGAGGCGGCCCATGTGGCGGAGGAGTGGAGAGGCTAACTGGG\n++SRR397397.941972\n+HHHHFFDEGEHHGFHHHGEHHHBHHHHCFHFGFEEEE4=3:>:9=BCA8D<,<6'?>8AA#########################################\n+@SRR397397.944374\n+AGCCACTTGCAGGGAGAGGTGTTTGGGGCTGTCCTGCGCCAGGAGACGGAGTTTTTCCAACAGAACCAGACAGGTAACATCATGTCTCGGGTAACAGAGGA\n++SRR397397.944374\n+GGGGGGGGGGGGGG?C;CC;EEEEEGGGGGGEFGGGEGGGDGGEGFGGGFGCFDGFFFCFDFF<C?FEFDGGGCDFGGGGDGGGGDGGGFGBGDGFB=EF8\n+@SRR397397.945721\n+CCGGGTCTCACATCATCCAGACGATGTATGGCTGCGACGTGGGGCCCGACGGGCGCCTCCTCCGCGGGTATGACCAGTACGCCTACGACGGCACGGATTAC\n++SRR397397.945721\n+DDBDAAFFFFFGFGFFGFBGFGGDEFCDBCEFEGFD@EFEADEB@CD?1@?=AAA=A>A<3>733128.*73/9:*5333DCD@?################\n+@SRR397397.946086\n+TGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCAGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACGTGCCATGTGCAGCATGAG\n++SRR397397.946086\n+HHHHHHHHHHHHHHHHHHHHHHEHHHHHHFHHHHHGGHFGHHHHHHHHFHFCGGCHHHHHHGEHHHHHHFHHHHHHHEHHHHHFHHHHGHFHHHHHHGFHH\n+@SRR397397.946163\n+ATACTCCGATCACCAATGTACCTCCAGAGGTAACTGTGCTCACGAACAGCCCTGTGGAACTGAGAGAGCCCAACGTCCTCATCTGTTTCATCGACAAGTTC\n++SRR397397.946163\n+HGHHHHHHHHHGHHHHHGHHGFHHHFHFGHDHHHFGBFGGHEHHFHGGHFHFDFFGDBFGGF?E9GDBFF@EEGFCGGGFHFHFFFGFHDGHHCHGDH?H?\n+@SRR397397.946639\n+TGTCTCTCACAGCTTGAAAAGCCTGAGACAGCTGTCTTGTGAGGGACTGAGATGCAGGATTTCTTCACGCCTCCCCTTTGTGACTTCAAGAGCCTCTGGCA\n++SRR397397.946639\n+FEGHEHGHGHHGHHHHHHHHGGGBGGEDHFHGGGHHHHHHHFHHHHHHHHHHGHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHGHHHHHH\n+@SRR397397.946901\n+CCTACCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGGACCCCCCCAAGACGCATATGACTCAC\n++SRR397397.946901\n+#E:ABE9ECAEAFEEFFFCFFBD0EDECEECCABDDDD5=??EGFFHDEHFDFDHFHHDFHEFEEFAEHEFEFE?DHFEGHHGGHAHHHHHHHHHHHGHHG\n+@SRR397397.947568\n+GCGCCGTGGGTGGAGCAGGAGGGGCCGGAGTATTGGGACCGGGAGACACAGAACTACAAGCGCCAGGCACAGACTGACCGAGTGAACCTGCGGAAACTGCG\n++SRR397397.947568\n+HHHHHHHHHHEHHEHHHHHFHHHHHHHHEHDHFFFHHFHHFHHCHEFFHEFFHHFFHHHHFEH?EFBFFFDFAFDFHHDHBFBFDF?G?DDGDBA;>?ABD\n+@SRR397397.956846\n+AAGCACTGGGAGGCCCAAGAGCCAATCCAGATGCCTGAGACAACGGAGACTGTGCTCTGTGCCCTGGGCCTGGTGCTGGGCCTAGTCGGCATCATCGTGGG\n++SRR397397.956846\n+=EDD@C/FEBDCHHHGHHHHB@HHHF@HFFFFD?FEFFFBFFFHHFHFEFFHFEFCEEEA?EFHDFHFFFHFHHFFFHHHDHHFHFFHHHHGHHHHHHHHH\n+@SRR397397.957737\n+TGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGT\n++SRR397397.957737\n+0EGGGGGG@GEHFGHHFHHHHHHHHGFFHFHHHEHHFHFFHHHFHHHHHHHHHHHFHFHDHHHHHHHHHHHHFFHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+@SRR397397.958005\n+GAGTTCTATCTGAATCCTGACCAATCAGGCGAGTTTATGTTTGACTTTGATGGTGATGAGATTTTCCATGTGGATATGGCAAAGAAGGAGACGGTCTGGCG\n++SRR397397.958005\n+BCEE@BA8GGGEEEEEGGGFFFFFEFDD?D<FFBDDFEFDEDFBFEFGGGGCDFFEGGDGFFFEGGGGFGGGFFFFGEEGDEEBEEFFFFCEEGEGGGFGG\n+@SRR397397.958479\n+GACAGGAGCAGAGATACACCTGCCATGTGCAGCATGAGGGTCTCCCCAAGCCCCTCACCCTGAGATGGGAGCCGTCTTCCCAGCCCACCATCCCCATCGTG\n++SRR397397.958479\n+HHHHHHHHHHHHHHHHHHHHHHHGFHHHHHHHHHHHHFHHHFGHHHHHHHEHHHF@FHFHHHD@FHHHHFHHHEFGFGFFGHHFHHHHHFEGGGGHHHEBE\n+@SRR397397.958714\n+GATGCGGGTCACGGCACCCCGAACCGTCCTCCTGCTGCTCTCGGCGGCCCTGGCCCTGACCGAGACCTGGGCCGGCTCCCACTCCATGAGGGATTTCCACA\n++SRR397397.958714\n+HHHHHHHHFHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHG<DFEDEEHC4CCCF;B=C<.:5'6>8;<BCB9ADCEED.52:@7@>>=?%8;=DADDD?\n"

diff -r 000000000000 -r fd974c5df8bc test-data/rna/CRC_81_N_2_fished.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rna/CRC_81_N_2_fished.fastq Wed Feb 17 08:10:24 2021 +0000

b"@@ -0,0 +1,6060 @@\n+@SRR397217.1805\n+GGAAACAGTTCCTCGGAGTGGAGAGGTTTACACCTGCCAAGTGGAGCACCCAAGCCTGACGAGCCCTCTCACAGTGGAATGGAGAGCACGGTCTGAATCTG\n++SRR397217.1805\n+HHHHHHHHHHHHHHHHFHEHHHHFHHFHFEHHHHHFFHHFHHHHEFHFHCIGCGIHHHFHHHHFFHFHHHFHAHEHHFFHH@HEED.@EEFBGFE@EFDEA\n+@SRR397217.2316\n+TTGTCGGGAGGTTCGCCAGCGACGCCACGAGTCCGAGGAAGGAGCCGCGGGCGCCATGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCGGGAGACACAG\n++SRR397217.2316\n+################################@@?<D@C.DFF?GFBFFGFEEEEE>FGF;FHFHGFHFEHFDFFFHHFHHFGHHHHHHHHHHHHHEFHHH\n+@SRR397217.6690\n+TTACGGTCCCTCTGGCCAGTTCACCCATGAATTTGATGGAGATGAGCAGTTCTACGTGGACCTGGAGAAGAAGGAGACTGCCTGGCGGTGGCCTGAGTTCA\n++SRR397217.6690\n+FACD=C+<DA6DEHHFBHE?BHFHHHHHFHFHHEHHGEHHHEHCHHGGGGGFFDGEFHFHHHFFHHHHGHHHHHFHBGBHFGEGHEDHHHFHHEHHHHHHH\n+@SRR397217.7193\n+AGAAGTGGGCAGCGGTGGTGGTGCCTTCTTGAGAGGAGCAGAGATACACGTGCCATGTGCAGCATGAGGGGCTACCCGAGCCCGTCCCCCTGAGATGGAAG\n++SRR397217.7193\n+##################D:D@=>05:>.'>;B9(;>D8A70CDA9<CF?D9?E<EDDB;B:A@@;6?7@>5>,3A6F?BF@BD>@'@@B<D?BE??A>@D\n+@SRR397217.9669\n+AAGAACATGTGATCATCCAGGCCGAGTTCTATCTGAATCCTGACCAATCAGGCGAGTTTATGTTTGACTTTGATGGTGATGAGATTTTCCATGTGGATATG\n++SRR397217.9669\n+3@9A=:?=/>?6FG?EBHHHHGGGGGBFGGGGFGGBHHHHFHHHHHGFFEGFHEHGHHHHHHHHHHFHHHEHHHHHHEHHHHHHHHHHHHHGHHHHHHHHH\n+@SRR397217.14316\n+TATCAAAGAAGAGCATGTGATCAGCCAGGCCGAGTTCTATCTGAATCCTGACCAATCAGGCGAGTTTATGTTTGACTTTGATGGTGATGAGATTTTCCATG\n++SRR397217.14316\n+##B9?GBE?EE;.56.D>CB;>8.;5EEEB?F8FFCFDF@FGDEE@DDBDD@AC>:DDDD?:GEB9D>;DDC@C?C>A:C=8GGDGD=B8D938===C=:B\n+@SRR397217.16398\n+GGGCCGGAGTATTGGGACCGGAACACACGGAATGTGAAGGCCCAGTCACAGACTGACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGT\n++SRR397217.16398\n+@8.66815=7759<DD?EEBEED>BEDCCCBE6E.EFEDFDEEEGB@?@BBA7<@>BDDDDGEGEGGEEE?G?GCGGEIBGFEEEFFHEFHGGFGDGFFEF\n+@SRR397217.16506\n+GTGATCATCCAGGCCGAGTTCTATCTGAATCCTGACCAATCAGGCGAGTTTATGTTTGACTTTGATGGTGATGAGATTTTCCATGTGGATATGGCAAAGAA\n++SRR397217.16506\n+HHHHHHHHHHHHHHHHHHFHHHFHHHHHDHHCEHFHHHDFHHHDHFBHEFGGGHGGHGHHHGF@HGGF9GCEFDFFHHHHHFHHADF>DGFF6ED5@DAD:\n+@SRR397217.26902\n+CGAAATGGAAAACCTGTCACCACAGGAGTGTCAGAGACAGTCTTCCTCCCAGGGAAGACCACCTTTTCCGCAAGTTCCACTATCTCCCCTTCCTGCCCTCA\n++SRR397217.26902\n+HHHHHHHHHHHHHHHHHHHHHHHFGFGHFHFDHHFHHHHHEHHHEHHHHHHHHHFHHBHHHHHHHHHHHHHH<@FBEEFEFFF<DFF>DBEBCE5@EEEEC\n+@SRR397217.31222\n+ATCTTCCCAGTCCACCATCCCCATCGTGGGCATTGTTGCTGGCCTGGCTGTCCTAGCAGTTGTGGTCATCGGAGCTGTGGTCGCTACTGTGATGTGTAGGG\n++SRR397217.31222\n+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCFDHFFHHHFHHHFHFDE?<F?<@?>DD5DB;<?@;6,9<9:<4;/>>7@A#####################\n+@SRR397217.35267\n+TGGCGAGGACCAAACTCAGGACACTGAGCTTGTGGAGACCAGACCAGCAGGAGATAGAACCTTCCAGAAGTGGGCAGCTGTGGTGGTGCCTTCTGGAGAAG\n++SRR397217.35267\n+HHHHHHHHHHHHHHHHHHHHEHHHHHEHHHHHHHHHHBHHHHGHHHHHHHFHFEHHHHFHHHHEHHHHHGEEGFE>GEGG9BEAEC(CACBEAEE@#####\n+@SRR397217.41512\n+CCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGTGGCTGTGGTGGTGCCTTCTGGACAGGAGCAGAGAT\n++SRR397217.41512\n+BDCD3CCBBHFDFDEEGC?EBEHFHEHHFFHHHHFHFGEFGGEBEGGGGEGEBEEBFHEFHFHFHFHFFFHHHHHHHDFHFHFEHHHCEHHGHHHFHHHHH\n+@SRR397217.45346\n+GAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCGTCTGTGGTGGTGCCTTCTGGACAGGAGCA\n++SRR397217.45346\n+CC;BBFBFF<FBDADB4BFHHH?GHDFHHBHHH?HHHHEHHHFEHHHGHHHFEFDFHHHHHFHFHFFHHHHHHHFHCHHGFHACHHHHHHHHHHHGHHHEH\n+@SRR397217.46100\n+TGGAACAGCCAGAAGGACCTCCTGGAGGAGAAGCGGGCAGTGCCGGACAGGGTATGCAGACACAACTACGAGCTGGACTAGGCCGTGACCCTGCAGCGCCG\n++SRR397217.46100\n+HHHHHHHHHHHHHHGHHHHHHHHHHHGHFDHEHHHEHHHHHHHHHHFHHHHHDFDHHHHHHHEDHGHHHHHEHHDHFHEHHHFHG=@7ADGEFG?BCF<F<\n+@SRR397217.56880\n+ACCGCGGCGGACATGGCGGCTCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGTGGCGGAGCAGTTGAGAGCCTACCTGGAGGGCACGTGCGTGGAGTG\n++SRR397217.56880\n+8DEFFBFD?GG;HHHFHHHGFGGGEEG=GHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFDHHHFGHEHHHHHGHHHHHHHHHHHHHHH\n+@SRR397217.56882\n+TACGTCTGAGTGTCATTTCTTCAATGGGACGGAGCGGGTGCGGTTCCTGGACAGATACTTCCATAACCAGGAGGAGAACGTGCGCTTCGACAGCGACGCGG\n++SRR397217.56882\n+D=A8>:EE6AFCFDDDDCED?BGF?FHHEHHFHHEFFHHGHEHHDHDEHHGFEEFEDHHCHHHHHHHHHHHHHHHHHEBHHGDHFHHHHHHHHHHHHHHHH\n+@SRR397217.60691\n+TCCAGATGATGTATGGCTGCGACGTGGGGTCGGACGGGCGCTTCCTCCGCGGGTACCAGCAGGACGCCTACGACGGCAAGGATTACATCGCCTTGAACG"..b'HHHHHHHHHHEHHHHHHHHHHHHHHHHHGHHHHHHHHHHGEHHHEHHFHHHHGHFHHHHFHEHGFFGBFEEGFEGIEFHHHH8FEFGGHGBHG@\n+@SRR397397.931239\n+TCTTCCGATCTGACGGTCTGGCGGCTTGAAGAATTTGGACGATTTGCCAGCTTTGAGGCTCAAGGTGCATTGGCCAACATAGCTGTGGACAAAGCCAACCT\n++SRR397397.931239\n+@F?FDCGHFGGGEHDHHEHGH=HFHHGFHHFGEEDFGGGFGFHHHHIGGFBFEGGIHH@HHFHHHHHFHHHHHHFHFHHEHFGFHHHHHDGGHEHEGEGGG\n+@SRR397397.933885\n+GCGCGGCTACTACAACCAGAGCGAGGCCGGTTCTCACACCATCCAGATGATGTATGGCTGCGACGTGGGGTCGGACGGGCGCTTCCTCCGCGGGTACCAGC\n++SRR397397.933885\n+@FHFFHHFEEFGGE?DHGHHHHEHEHBEFHFEGEGFDFHFHHHHGHHHHHHFFHHHEHHHHE?HHFHFFHHHFHFHHFFGDFHHGHHHHHHHHFFEGGGFI\n+@SRR397397.936597\n+TGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGCGAGGACCAAACTCAGGATACTGAGCTTG\n++SRR397397.936597\n+C>A<B>D@>D95:@@=0=<>75348DDA=9<DDADED5DBDA>>>ADCGAFEBBB@@B>B.B?;@####################################\n+@SRR397397.936627\n+CTCCTTTTACTCCTCTCGGAGGCCCTGGCCCTTACCCAGACCTGGGCGGGCTCCCACTCCTTGAAGTATTTCCACACTTCCGTGTCCCGGCCCGGCCGCGG\n++SRR397397.936627\n+HHHHHHHHHHHGHHHHHHHHHHHHHHFFHHHHHHHHHHHHHHHHFBDFCFE1EEEGGGGGHHHDHHFEFFDGFFDHHHHHH@EFHBCE;/GAEADFCFHED\n+@SRR397397.940142\n+CCGTCACCCTGAGATGGAAGCCGGCTTCCCAGCCCACCATCCCCATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGATCTGTGGTCTCTGGAGCTGTG\n++SRR397397.940142\n+HHHHHHHHHHHHHFHHHHHHHHHHHHH=FHBDBEEBFE2FDFGG9DD?BDGGF=FGFDGEGGGGFHH=HFGFFFIDEAE;DFGBC8E4EECCADAFEFEBG\n+@SRR397397.941041\n+TGGAAATCATGACAAAGCGCTCCAACTATACTCCGATCACCAATGTACCTCCAGAGGTAACTGTGCTCACGAACAGCCCTGTGGAACTGAGAGAGCCCAAC\n++SRR397397.941041\n+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFHGHHHEGEFFHHHHBHHFGHHHHEHHHHDHHDHHHHFHHGDCGE@HHHFEEFEFHBHEFF@\n+@SRR397397.941972\n+CCCCCAAAACGCATATGACTCACCACGCTGTCTCTGACCATGAAGCCACCCTGAGGTGCTGGGCCCTGAGCTTCTACCCTGCGGAGATCACACTGACCTGG\n++SRR397397.941972\n+E69.-<EEHGCGGGGFFAFBFFDGDGHDHEFHEGHGEE@=EAGE?EEFEFFFGFFEGDGFFDADDCD>=5D>>BB9DDDCBGGGGGEEEDEADFEDFIGGG\n+@SRR397397.944374\n+AGCTTATTTCTGTGGTACCTGGTGCGAGGCCTATGTCTCTTGGGGATCATGCTCTGGGGATCAGTGTCCCTCACCATGGTCACCCTGGTCACCCTGCCCCT\n++SRR397397.944374\n+@A8;;BB34A5FGFFD>EEFF:@BB@BE:GEEBEEDGGDGDHHHHHFFFFFFEFFFGFG@HGCGGFB=GFFG:EEEEFF?G<GDCDGHHHDHHGHHHGFHH\n+@SRR397397.945721\n+GCCTACCTGGAGGGCCTGTGCGTGGAGTGGCTCCGCAGATACCTGAAGAATGGGAAGGAGACGCTGCAGCGCGCGGAACACCCAAAGACACACGTGACCCA\n++SRR397397.945721\n+#######EBGE@=?>6CD8CBFFDFFF8=FFDBD/DBEEBE=GE<B=>BBFDCC@CCC@DDB7B@;CD=/DDDBDCGDBDDCCCD@EEE?EFGFEFHGEDH\n+@SRR397397.946086\n+TGGCCTGGTTCTCCTTGGATCTGTGGTCTCTGGAGCTGTGGTTGCTGCTGTGATATGGAGGAAGAAGAGCTCAGGTGGAAAAGGAGGGAGCTACTCTAAGG\n++SRR397397.946086\n+BDFB?FFCBFAGF:BGHHHHHEHHHHHGEHDHHEHHHGHHHHHHHHHGHGHHHBHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+@SRR397397.946163\n+AGTGTCAGAGACAGTCTTCCTGCCCAGGGAAGACCACCTTTTCCGCAAGTTCCACTATCTCCCCTTCCTGCCCTCAACTGAGGACGTTTACGACTGCAGGG\n++SRR397397.946163\n+HGG=BGEEG@GBDBB@HBGHHHGDGHGFFEGFDFFBHHHGHHGHEHFEDCFGFCBEHHHGHHHHHFHHHHHHHHHHHHFHHHHHHHEHHHHHHHHHHHHHH\n+@SRR397397.946901\n+GGTCGGACGGGCGCTTCCTCCGCGGGTACCAGCAGGACGCCTACGACGGCAAGGATTACATCGCCTTGAACGAGGAACTGCGCTCTTGGACCGCGGCGGAC\n++SRR397397.946901\n+GGFDGCBFFBHGHBG@CCBDGEGGDGEDGEGHGHG8DF???@D<DCDD?D=DDDDCGCG?GFG<GHHFHEHEHFF5;@5?@?>?C>CC=A.CC:@A;BB##\n+@SRR397397.952578\n+TGAACGAGGACCTGCGCTCCTGGACCGCCGCGGACACGGCGGCTCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGAGGCGGAGCAGCTGAGAGCCTAC\n++SRR397397.952578\n+5DCBEGBE;CBFHFHH?DDDDGD5EGGHHHFHHEHFHHHHHHHHHHHHHHHHHHHHHHHHFHHHHHFHHHHHHHHHHHGHHGHHHHHHHHGHHHHHHHHHH\n+@SRR397397.956846\n+GAGAGCCTCTTCCTGCCCAGAACAGATTACAGCTTCCACAAGTTCCATTACCTGACCTTTGTGCCCTCAGCAGAGGACTTCTATGACTGCAGGGTGGAGCA\n++SRR397397.956846\n+HHHGHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHFFHHHHHHHHHHHHHHFHHFFHFHHFHHHFGH8HGHHHGEHDHHHHHHHHHFHEHGCGB5\n+@SRR397397.957737\n+TGGCGGAGCAGTTGAGAGCCTACCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGGACCCCCCC\n++SRR397397.957737\n+HHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGEG6H8EBEEE8CDG8DEAEE@EDEEE@7B3B@>>>==<768>..;A=A4E\n+@SRR397397.958714\n+CGGAGTATTGGGACCGGGAGACACAGATCTCCAAGACCAACACACAGACTTACCGAGAGAGCCTGCGGAACCTGCGCGGCTACTACAACCAGAGCGAGGCC\n++SRR397397.958714\n+GBH=GHHBHHHH>BGFHHHDHGEHHHHHHHEHHHHHHHHHEDHHFFEGEGGFHGHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n'