Repository 'shovill'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/shovill

Changeset 0:196a599ec43d (2017-10-25)
Next changeset 1:57d5928f456e (2018-03-07)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
added:
shovill.xml
test-data/contigs.fa
test-data/mutant_R1.fastq
test-data/mutant_R2.fastq
b
diff -r 000000000000 -r 196a599ec43d shovill.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/shovill.xml Wed Oct 25 03:39:03 2017 -0400
[
b'@@ -0,0 +1,169 @@\n+<tool id="shovill" name="Shovill" version="0.8.0">\n+    <description>Faster SPAdes assembly of Illumina reads</description>\n+    <requirements>\n+        <requirement type="package" version="0.8.0">shovill</requirement>\n+    </requirements>\n+    <version_command>shovill --version</version_command>\n+    <command detect_errors="exit_code"><![CDATA[\n+        shovill\n+            --outdir \'out\'\n+            --cpus \\${GALAXY_SLOTS:-1}\n+            --ram \\${SHOVILL_RAM:-4}\n+            #if str($library.lib_type) == "paired"\n+                --R1 \'$library.R1\'\n+                --R2 \'$library.R2\'\n+            #else if str($library.lib_type) == "collection"\n+                --R1 \'$library.input1.forward\'\n+                --R2 \'$library.input1.reverse\'\n+            #end if\n+            $trim\n+            --namefmt "$adv.namefmt"\n+            --depth \'$adv.depth\'\n+            #if $adv.gsize\n+                --gsize \'$adv.gsize\'\n+            #end if\n+            #if $adv.kmers\n+                --kmers \'$adv.kmers\'\n+            #end if\n+            #if $adv.opts\n+                --opts \'$adv.opts\'\n+            #end if\n+            $adv.nocorr\n+            --minlen $adv.minlen\n+            --mincov $adv.mincov\n+            --asm $adv.asm\n+            \n+    ]]></command>\n+    <inputs>\n+        <conditional name="library">\n+            <param name="lib_type" type="select" label="Input reads type, collection or single library" help="Select \'paired end\' for a single library or \'collection\' for a paired end collection">\n+                <option value="paired" selected="true">Paired End</option>\n+                <option value="collection">Paired Collection</option>\n+            </param>\n+            <when value="paired">\n+                <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>\n+                <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>\n+            </when>\n+            <when value="collection">\n+                <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/> \n+            </when>\n+        </conditional>\n+        <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" />\n+        <param name="log" type="boolean" label="Output log file?" checked="true" help="Return the Shovill log file as part of the output. Default is on" />\n+        <section name="adv" title="Advanced options" expanded="False">\n+            <param name="namefmt" argument="--namefmt" type="text" value="contig%05d" label="Contig name format" help="Format of contig FASTA IDs in \'printf\' style (default: \'contig%05d\')" >\n+                <sanitizer>\n+                    <valid initial="string.printable" />\n+                </sanitizer>\n+            </param>\n+            <param name="depth" argument="--depth" type="integer" value="100" label="Depth" help="Sub-sample --R1/--R2 to this depth. Disable with --depth 0 (default: 100)" />\n+            <param name="gsize" argument="--gsize" type="text" value="" label="Estimated genome size" help="An estimate of the final genome size, it will autodetect if this is blank. (default: \'\')" />\n+            <param name="kmers" argument="--kmers" type="text" value="" label="List of kmer sizes to use" help="List of K-mer sizes to use in SPAdes. Blank is AUTO. default: \'\'" />\n+            <param name="opts" argument="--opts" type="text" value="" label="Extra SPAdes options" help="eg. --plasmid --sc ... (default: \'\')" />\n+            <param name="nocorr" argument="--nocorr" type="boolean" truevalue="--nocorr" falsevalue="" ch'..b'nts>\n+                    <has_text text="&gt;contig00001"/>\n+                </assert_contents>\n+            </output>\n+            <output name="shovill_std_log" ftype="txt" >\n+                <assert_contents>\n+                    <has_text text="Running: seqtk"/>\n+                    <has_text text="Running: kmc"/>\n+                    <has_text text="Running: lighter"/>\n+                    <has_text text="User supplied --nocorr"/>\n+                    <has_text text="Running: flash"/>\n+                    <has_text text="Running: spades"/>\n+                    <has_text text="Done."/>\n+                </assert_contents>\n+            </output>\n+        </test>\n+        <test> <!-- Test 1: Auto everything + trim + different name format test -->\n+            <param name="lib_type" value="paired" />\n+            <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />\n+            <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />\n+            <param name="trim" value="true" />\n+            <section name="adv">\n+                <param name="depth" value="0"/>\n+                <param name="minlen" value="0"/>\n+                <param name="mincov" value="0"/>\n+                <param name="nocorr" value="false"/>\n+                <param name="namefmt" value="contig%03d"/>\n+            </section>\n+            <output name="contigs" ftype="fasta">\n+                <assert_contents>\n+                    <has_text text="&gt;contig001"/>\n+                </assert_contents>\n+            </output>\n+            <output name="shovill_std_log" ftype="txt" >\n+                <assert_contents>\n+                    <has_text text="Running: seqtk"/>\n+                    <has_text text="Running: kmc"/>\n+                    <has_text text="Running: trimmomatic"/>\n+                    <has_text text="Running: lighter"/>\n+                    <has_text text="Running: flash"/>\n+                    <has_text text="Running: spades"/>\n+                    <has_text text="Running: bwa index"/>\n+                    <has_text text="Running: (bwa mem"/>\n+                    <has_text text="Running: _JAVA"/>\n+                    <has_text text="Done."/>\n+                </assert_contents>\n+            </output>\n+        </test>\n+    </tests>\n+    <help><![CDATA[\n+Synopsis:\n+  Faster de novo assembly pipeline for Illumina paired end reads based around Spades\n+\n+Details and options:\n+    - Takes paired end Illumina fastq reads\n+    - Trim reads:   Use Trimmomatic to remove common adaptors first (default: OFF)\n+    - Output log file:  If set to "Yes", tool will return Shovill\'s log file as part of the output\n+    \n+Advanced options:    \n+    - Name format:          Format of output contig FASTA IDs in \'printf\' style (default: \'contig%05d\')\n+    - Depth:                Sub-sample the reads to this depth. Disable with *Depth: 0* (default: 100)\n+    - Estimated genomesize: An estimate of the final genome size, it will autodetect if this is blank. (default: \'\')\n+    - List of kmers to use: List of K-mer sizes to use in SPAdes. Blank is AUTO. (default: \'\')\n+    - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: \'\')\n+    - Disable post-assembly correction: Disable post assembly correction with pilon (default: ON)\n+    - Minimum contig length:    Minimum length of contig to be output. 0 is AUTO (default: 0)\n+    - Minimum contig coverage:  Minimum coverage to call part of a contig. 0 is AUTO (default: 2)\n+    - Spades result to correct: Spades result to correct: before_rr, contigs or scaffolds (default: \'contigs\')\n+\n+Documentation can be found at Torsten Seemann `site <https://github.com/tseemann/shovill>`_.\n+    ]]></help>\n+    <citations>\n+        <citation type="bibtex">\n+@UNPUBLISHED{Seemann2017,\n+    author = {Seemann, Torsten},\n+    title = {Shovill: Faster SPAdes assembly of Illumina reads},\n+    year = {2017},\n+    url = {https://github.com/tseemann/shovill},\n+}\n+        </citation>\n+    </citations>\n+</tool>\n'
b
diff -r 000000000000 -r 196a599ec43d test-data/contigs.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.fa Wed Oct 25 03:39:03 2017 -0400
b
b'@@ -0,0 +1,3361 @@\n+>contig00001 len=14151 cov=4.0 corr=0 spades=NODE_1_length_14151_cov_3.95289_pilon\n+GAAGAAGTAAAAAAGGGCTATTTTCCAATCAAACGTGCGATTGACTTGGTATTAAGTATC\n+GTTTTATTATTTTTAACATTTCCGATTATGTTCATATTCGCCATTGCTATCGTCATAGAT\n+TCGCCAGGAAACCCTATTTATAGTCAGGTTAGAGTTGGGAAGATGGGTAAATTAATTAAA\n+ATATACAAATTACGTTCGATGTGTAAAAACGCAGAGAAAAACGGTGCGCAATGGGCTGAT\n+AAAGATGATGATCGTATAACAAATGTCGGGAAGTTTATTCGTAAAACACGCATTGATGAA\n+TTACCACAACTAATTAATGTTGTTAAAGGGGAAATGAGTTTTATTGGACCACGCCCGGAA\n+CGTCCAGAATTTGTAGAATTATTTAGTTCAGAAATAATAGGATTTGAGCAAAGATGTCTT\n+GTTACACCAGGATTAACAGGTCTTGCGCAAATTCAAGGTGGATATGACTTAACACCACAA\n+CAAAAATTAAAATATGACATGAAATATATACATAAAGGTAGCTTAATGATGGAATTATAT\n+ATATCAATTAGAACATTGATGGTTGTTATTACAGGGGAAGGCTCAAGGTAGTCTTAATTT\n+GCTTAATAAGTTTAAATAAAAGTTACATTTTAAAGATTGTGACCAATTGTTACAGTATAA\n+CGAGGAATCCCTTGAGACAGTATCAAATGGCATTAAGAAATATTTGCCATCATTGATTTG\n+CATGGCTATAAATACTATTCATCTGATGAGATAGCCATGTTAAGAAATTGAAAGTATAGC\n+ATTAAAGGGGTTTGTAACAGTTGAAAATTATATATTGTATTACTAAAGCAGATAATGGTG\n+GTGCACAAACACATCTCATTCAACTCGCTAACCATTTTTGCGTACACCATGATGTTTATG\n+TCATTGTAGGCAATCATGGACCAATGATTGAACAACTAGATGCAAGAGTCAATGTAATTA\n+TTATCGAACATTTAGTAGGTCCAATTGACTTTAAACAAGATATTTTAGCTGTCAAAGTGT\n+TAGCACAGTTATTCTCGAAAATTAAACCTGATGTTATCCATCTACATTCTTCCAAAGCTG\n+GAACGGTCGGACGAATTGCGAAGTTCATTTCGAAATCGAAAGACACACGTGTAGTTTTTA\n+CTGCGCATGGATGGGCTTTTACAGAGGGTGTTAAACCAGCTAAAAAATTTCTATATCTAG\n+TTATTGAAAAATTAATGTCACGTATTACAGATAGCATTATTTGTGTTTCAGATTTCGATA\n+AACAGTTAGCGTTAAAATATCGATTTAATCGATTGAAATTAACCACTATACATAATGGAA\n+TTGCAGATGTTCCCGCTGTTAAGCAAACGCTAAAAAGCCAATCACATAACAATATTGGCG\n+AAGTTGTTGGAATGTTGCCTAATAAACAAGATTTACAGATTAATGACTCGACAAAACATC\n+AATTTGTTATGATTGCAAGATTTGCTTATCCAAAATTGCCACAAAATCTAATCGCGGCAA\n+TAGAGATATTGAAATTACATAACAGTAATCATGCGCATTTTACATTTATAGGCGATGGAC\n+CTACATTAAATGATTGTCAGCAACAAGTTGTACAAGCTGGGTTAGAAAATGATGTCACAT\n+TTTTGGGCAATGTCATTAATGCGAGTCATTTATTATCACAATACGATACGTTTATTTTAA\n+TAAGTAAGCATGAAGGTTTGCCAATTAGCATTATCGAAGCGATGGCTACAGGGTTGCCTG\n+TCATCGCTAGTCATGTTGGTGGCATTTCGGAATTAGTAACTGATAATGGTATATGTATAG\n+TGAACAATCAACCTGAAACTATTGCCAAAGTCCTGGAAAAATATTTAATAGACAGTGATT\n+ACATCAAAATGAGTAACCAATCTAGAAAACGTTATTTAGAATGTTTTACAGAGGAGAAAA\n+TGATTAAAGAAGTGGAAGACGTTTATAATGGAAAATCAACACAATAGTAAATATCTAACA\n+TTGTTACTTATCGGTTTAGCGGTTTTTATTCAGCAATCTTCGGTTATTGCCGGTGTGAAT\n+GTTTCTATAGCTGACTTTATCACATTACTAATATTAGTTTATTTACTGTTTTTCGCCAAC\n+CATTTATTAAAGGCAAATCATTTTTTACAGTTTTTCATTATTTTGTATACATATCGTATG\n+ATTATTACGCTTTGTTTACTATTTTTTGATGATTTGATATTTATTACGGTTAAGGAAGTT\n+CTTGCATCTACAGTTAAATATGCATTTGTAGTCATTTATTTCTATTTAGGGATGATCATC\n+TTTAAGTTAGGTAATAGCAAAAAAGTGATCGTTACCTCTTATATTATAAGCAGTGTGACT\n+ATAGGTCTATTTTGTATTATAGCTGGTTTGAACAAGTCCCCTTTACTAATGAAATTATTA\n+TACTTTGATGAAATACGTTCAAAAGGATTAATGAATGACCCTAACTATTTCGCGATGACA\n+CAGATTATTACATTGGTACTTGCTTACAAGTATATTCATAATTACATATTCAAGGTCCTT\n+GCATGTGGTATTTTGCTATGGTCTTTAACTACAACGGGGTCTAAGACTGCGTTTATCATA\n+TTAATCGTCTTAGCCATTTATTTCTTTATTAAAAAGTTATTTAGTAGAAATGCAGTAAGT\n+GTTGTGAGTATGTTAGTGATTATGTTAATTCTACTTTGTTTTACCTTTTATAATATAAAC\n+TACTATTTATTCCAATTAAGCGACCTTGATGCCTTACCGTCATTAGATCGAATGGCGTCT\n+ATTTTTGAAGAGGGGTTTGCATCATTAAATGATAGTGGATCTGAGCGAAGTGTTGTATGG\n+ATAAATGCCATTTCAGTAATTAAATATACATTAGGTTTTGGTGTTGGCTTAGTGGATTAT\n+GTACATATTGGCTCGCAAATTAATGGTATTTTACTTGTTGCCCATAATACATATTTGCAA\n+ATTTTTGCGGAATGGGGCATTTTATTCGGTGCGTTATTTATCATATTTATGATTTATTTA\n+TTATTTGAATTATTTAGATTCAATATTTCTGGGAAAAATGTAACAGCAATTGTTGTAATG\n+TTGACGATGCTGATTTACTTTTTAACAGTATCGTTTAATAACTCAAGATATGTCGCTTTT\n+ATTTTAGGAATTATCGTCTTTATTGTTCAATATGAAAAGATGGAAAGGGATCGTAATGAA\n+GAGTGATTCACTAAAAGAAAATATTATTTATCAAGGGCTATACCAATTGATTAGAACGAT\n+GACACCGCTGATTACAATACCCATTATTTCACGTGCATTTGGTCCCAGTGGTGTGGGTAT\n+TGTTTCATTTTCTTTCAATATCGTGCAATACTTTTTGATGATTGCAAGTGTTGGCGTTCA\n+GTTATATTTTAATAGAGTTATCGCGAAGTCCGTTAACGACAAACGGCAATTGTCTCAGCA\n+GTTTTGGGATATCTTTGTCAGTAAATTATTTTTAGCGTTAACAGTTTTTGCGATGTATAT\n+GGTCGTAATTACTATATTTATAGATGATTACTATCTTATTTTCCTACTACAAGGAATCTA\n+TATTATAGGTGCAGCACTCGATATTTCATGGTTTTATGCTGGAACTGAAAAGTTTAAAAT\n+ACCTAGCCTTAGTAATATTGTTGCGTCTGTTATTGTATTAAGTGTCGTTGTTATCTTTGT\n+GAAAGATCAATCAGATTTATCATTGTATGTATTTACTATTGCTATTGTGACAGTATTAAA\n+CCAATTACCTTTGTTTATCTATTTAAAACGATACATTAGCTTTGTTTCGGT'..b'CAGACATTTAAAAAATACATGGCTTACACTACG\n+ATTGGTTTG\n+>contig00092 len=300 cov=4.5 corr=0 spades=NODE_92_length_300_cov_4.53039_pilon\n+ACTAAACCTAAATTGCACTTCACTAAAATAACGGTTATCACCGATTGTTCTTTTAAATAA\n+GTAGGTAGATTCATATATATGTTGATTCTTGTTCACACTAACCACAAGCTCTCTGATATC\n+GAACACTATATATTACTTGTCCTACGAACAATGTCTTATTAAGTTATTTTTAATATAGCA\n+AACTATATTTGCTTTTTCAAGTAACGATTTCAAACATCAATCATGTCGATTTAGTGACAT\n+GCAGTCGTTTGATAAATTGATTGCTTTAAATACTGTGCAACCGCTTCAATATCTTTATGA\n+>contig00093 len=299 cov=9.8 corr=0 spades=NODE_93_length_299_cov_9.77222_pilon\n+AGGTTAAAACAGCATGTTAGAAATCTCATGAGTACTGATATGGCGAGAGAATATAAAAAA\n+TTAAGTAAAGAACATGGGCAAGTTAAAGAAAAATATAGTGGTCTTGTAGAGCGATTTAAT\n+GAAAATGTAAATGATTATAATGAGTTGCTTGAAGAAAACAAGTCTTTAAAGTCTAAAATA\n+AGCGATTTAAAGCGTGATGTGAGTTTAATCTATGAAAGCACTAAGGAATTCCTTAAGGAA\n+CGTACAGACGGCTTAAAAGCCTTTAAAAACGTTTTTAAGGGGTTTGTAGACAAGGTAAA\n+>contig00094 len=284 cov=4.4 corr=0 spades=NODE_94_length_284_cov_4.44242_pilon\n+CAAGCACCAAAAGAGGAAGACAACAACAAGCCTGGCAAAGAAGACAACAACAAGCCTGGT\n+AAAGAAGACGGCAACAAACCTGGTAAAGAAGACAACAAAAAACCTGGCAAAGAAGATGGC\n+AACAAACCTGGTAAAGAAGACGGCAACAAGCCTGGTAAAGAAGATGGCAACAAGCCTGGT\n+AAAGAAGACGGCAACGGAGTACATGTCGTTAAACCTGGTGATACAGTAAATGACATTGCA\n+AAAGCAAACGGCACTACTGCTGACAAAATTGCTGCAGATAACAA\n+>contig00095 len=243 cov=4.3 corr=0 spades=NODE_104_length_243_cov_4.33871_pilon\n+ACCTAACTTAAATGAAGAACAACGCAATGGTTTCATCCAAAGCTTAAAAGATGACCCAAG\n+CCAAAGCGCTAACCTTTTAGCAGAAGCTAAAAAGCTAAATGATGCACAAGCACCAAAAGC\n+TGACAACAAATTCAACAAAGAACAACAAAATGCTTTCTATGAAATTTTACATTTACCTAA\n+CTTAACTGAAGAACAACGTAACGGCTTCATCCAAAGCCTTAAAGACGATCCTTCAGTGAG\n+CAA\n+>contig00096 len=219 cov=2.2 corr=0 spades=NODE_156_length_219_cov_2.18_pilon\n+TGCTAACCTTTTAGCAGAAGCTAAAAAGTTAAATGAATCTCAAGCACCGAAAGCTGATAA\n+CAAATTCAACAAAGAACAACAAAATGCTTTCTATGAAATCTTACATTTACCTAACTTAAC\n+TGAAGAACAACGTAACGGCTTCATCCAAAGCCTTAAAGACGATCCTTCAGTGAGCAAAGA\n+AATTTTAGCAGAAGCTAAAAAGCTAAACGATGCTCAAGC\n+>contig00097 len=213 cov=2.0 corr=0 spades=NODE_157_length_213_cov_2_pilon\n+TTTACCAGGTTTGTTGCCGTCTTCTTTACCAGGCTTGTTGTTGTCTTCTTTGCCAGGCTT\n+GTTGTTGTCTTCCTCTTTTGGTGCTTGAGCATCGTTTAGCTTTTTAGCTTCTGCTAAAAG\n+GTTAGCGCTTTGGCTTGGGTCATCTTTTAAGCTTTGGATGAAACCATTGCGTTGTTCTTC\n+ATTTAAGTTAGGTAAATGTAAGATTTCATAGAA\n+>contig00098 len=207 cov=3.8 corr=0 spades=NODE_158_length_207_cov_3.75_pilon\n+TGCTAACCTTTTAGCAGAAGCTAAAAAGTTAAATGAATCTCAAGCACCGAAAGCTGATAA\n+CAAATTCAACAAAGAACAACAAAATGCTTTCTATGAAATCTTACATTTACCTAACTTAAA\n+TGAAGAACAACGCAATGGTTTCATCCAAAGCTTAAAAGATGACCCAAGCCAAAGCGCTAA\n+CCTTTTAGCAGAAGCTAAAAAGCTAAA\n+>contig00099 len=191 cov=2.1 corr=0 spades=NODE_161_length_191_cov_2.06944_pilon\n+TTGTTGCCGTCTTCTTTACCAGGCTTGTTGTTGTCTTCTTTGCCAGGCTTGTTGTTGTCT\n+TCCTCTTTTGGTGCTTGAGCATCGTTTAGCTTTTTAGCTTCTGCTAAAATTTCTTTGCTC\n+ACTGAAGGATCGTCTTTAAGGCTTTGGATGAAGCCGTTACGTTGTTCTTCAGTTAAGTTA\n+GGTAAATGTAA\n+>contig00100 len=184 cov=3.0 corr=0 spades=NODE_162_length_184_cov_3_pilon\n+TGCTTTTAACTTACCTCTTATCTGCAATTTTACTTAGGATTGCTTTTAACTTACCCCTTA\n+TCAGCAATTTTACTGAGAACTGCTTTTAACAAACCTCTTATCTGCAATTTTACTTAGAAC\n+TGCTTTTAACAAACCTCTTATCTGCAATTTTACTTAGAATTGCTTTTACTATTCCTCTTA\n+TTAG\n+>contig00101 len=181 cov=5.9 corr=0 spades=NODE_163_length_181_cov_5.8871_pilon\n+CTAAGTAAAATTGCAGATAAGAGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAA\n+GGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTA\n+AAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATT\n+T\n+>contig00102 len=172 cov=3.8 corr=0 spades=NODE_164_length_172_cov_3.84906_pilon\n+GTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTA\n+AAATTGCAGATAAGAGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTAC\n+AGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTT\n+>contig00103 len=161 cov=2.6 corr=0 spades=NODE_165_length_161_cov_2.64286_pilon\n+GCTTGAGCATCGTTTAGCTTTTTAGCTTCTGCTAAAATTTCTTTGCTCACTGAAGGATCG\n+TCTTTAAGGCTTTGGATGAAGCCGTTACGTTGTTCTTCAGTTAAGTTAGGTAAATGTAAA\n+ATTTCATAGAAAGCATTTTGTTGTTCTTTGTTGAATTTGTT\n+>contig00104 len=151 cov=6.2 corr=0 spades=NODE_166_length_151_cov_6.1875_pilon\n+TTTTAGCAGAAGCTAAAAAGCTAAACGATGCTCAAGCACCAAAAGAGGAAGACAACAACA\n+AGCCTGGCAAAGAAGACAACAACAAGCCTGGTAAAGAAGACGGCAACAAACCTGGTAAAG\n+AAGACAACAAAAAACCTGGCAAAGAAGATGG\n'
b
diff -r 000000000000 -r 196a599ec43d test-data/mutant_R1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mutant_R1.fastq Wed Oct 25 03:39:03 2017 -0400
b
b'@@ -0,0 +1,49920 @@\n+@mutant-no_snps.gff-24960/1\n+AATGTTGTCACTTGGATTCAAATGACATTTTAAATCTAATTATTCATGAATCGAACTAGTACGAAATGCAATGAGCATCTTGTCTAGTTCGATTTTTTAATGTCTAAAAATGTCGTATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTT\n++\n+5??A9?BBBDDDBEDDBFF+FGHHIIHHHEIHIIHIIAHDHIIHIG#IIHIFHHHFGIII*IHHHIHFIIHGICIHHIHFFFHHHIIIIIHIHDHIIIAHHH?GHHHHHF@HGGH6GGHEEGBGGGGGFGFE6FGFEFE?GF5EGGEEAC\n+@mutant-no_snps.gff-24958/1\n+CAAAGTCGTTGGTCATATAAAAAACCGCGTACAGTCAACTATAGATACAATCAAGATAAACTCATGCACAGATTGGGAGATATTTTAGTGCAATATGGAATTCAACATGACACAGGGTTATTACCACATGAATGGCATTATCACATTTCG\n++\n+?A????@?DDDABDE9FGGGFGICFHIIIBGHIIIGICHHIFH=IHAFIHIHHHHIFCIIEIHAIFGIHIDDIHEIIFIIIIHHHICIIIHIH=@HFHEHBFHIHHHH-HHHFCBHHDGHHEHGEH<GDEEEFHDEGGDGE*FGBGG,GD\n+@mutant-no_snps.gff-24956/1\n+TATAAATTCAACTTTGCAACAGAACCATCTAATCTTCAACAAACTGGCCCGTTTGTTGAACTACTCTTTAATAAAATAATTTTTCCGTTCCCAATTCCACATTGCAATAATAGAAAATCCATCTTCATCGGCTTTTTCGTCATCATCTGT\n++\n+?????BBADD5DDDDDGFGCFFEECFBBICIII,IIHIICHIHIIFHHHHHIHIIIIIIIAHHIHHH5FHDHHHHFIIHFGF5IIIHIIHHI@<IHHHHHDHDHFHHIGGEHHFHGEEFBHH?HH*FEGBHGH@EDG?C*FEGBGEGGGG\n+@mutant-no_snps.gff-24954/1\n+CATGATCAAAAAGCAGCTGATTTATTATTACAAGCACAACGTTTTGGTGTAAAAGAAGATGGTTCAGCAAGTAAAGAACTTGTAGATAGTTATAAATCAGAAATTCTTGTTAAAAAAGACTCAAAAATTAAAAGCTTGAAAGATTTAAAA\n++\n+<A?=?<?BBDDDDDDDFGGGAFEHIIIBIFH/CFCHFFIH9IHIHIIIHHIIIIIHHIHH>FHDHHHHIH+IFHIIGHHICHHIHHHIHFHHHCHHHFFHHFGHHCHIH<HHGGHHBEHGFE9HFGGAHGGF;:EGCGGGGFEE,B:AEG\n+@mutant-no_snps.gff-24952/1\n+CTCAATATCATCGGTGGATTTATTCATCCATCATCTGGTCGTGTCATTATTGATAACGAAATTAAACAACAGCCGTCTCCAGATTGTTTAATGCTATTTCAACATCATAATCTGCTGCCATGGAAAACGATTAATGACAACATTAGGATT\n++\n+=?<????BDDDDDDDDFGCFFFHB>H0FHHHIIIHDIHIHHH.CHIHHIIDEIHFIIFEHIIFIHIIGGIIIFIIHHHFDCHGIIHIIHIHHHHFEHCHHIDHCHFHFHHFHFHHFBGEHGHEEFGFHGHGF*?GGEE88DEGF6FGBA*\n+@mutant-no_snps.gff-24950/1\n+TTTCTTTCTTTAAAAATGGTCTCATAAAATGGTTTCGACTGTATTCTTTGCATGTCACCAATTACATAAAACTCTTTTTTAGCCCTTGTCACTGCAACATTTAACAAGTTTGGTTTTTCGCATGACCAGTTCACAGCACCATCTTGAGTA\n++\n+A5???BBBD@DDDDDDGGFGGFHEFB+HIIGIIIGHGIIFIHIHCI>IIFHHHAHIDHFICHHIFICHHIIHHHIHHIHCFIHIIIH=HHIH<HEFEFHHFHIHHHFDHHEIGHHFGDFHHEEHGF=HGHGGEFFCEGEDFFCGAGEG8G\n+@mutant-no_snps.gff-24948/1\n+ACATCGATGTTATTAAAGGCATTATCGCCTTTTCATCAAACAAAAAAAATAATTCAGAATTAGATGAGCTATATTCCATTTATATGAATGATGATTCTATCACATCCATTGTTCACCCTGACTTAATAGAAAGTATAGAGCTTATCCATA\n++\n+?AA?ABBBDDEBDDDDFCFGCCICFHHFFHIHHIEFHHHIGHCIIIH,IIIAIHEEEHHGIFHH5IHHHAHHHHHHGIHFHFGHIHHIIIFIDIEDHHH?H.HFH.HHH?HDFEHAHD:G=EEDEFEHCHHHHGDFGGCEG@FDE?EGEE\n+@mutant-no_snps.gff-24946/1\n+GATCCGATTCAAATTGAACCTGTTGTTACTTTAGAAAGCCATTTAATTGATAATATTCGTAAAAATTATAATGTTCCGGAATATCTAGTTTCTAAAGAAGCTTCTGTGCAGTCTGTCGCTGACAACGCTAATCAATATGGCTTTTGGAAA\n++\n+?A???BABDBADDDDDCGCGGGHHIIIFHCHIIFHH/IIHI=IGIEIIIIIHIAIIIHIEIHIIHHDHD?ICBIHIIEIIAHFIH?HHHHHHHHDFIFHCFHEGHHFFHEIHHEGGEH*HFGF>EFEEGCFHGFEE8FFGGFEFGG8HG9\n+@mutant-no_snps.gff-24944/1\n+CCGATTGGCGTCGTAGGTGCTGTTGTTGCTTGGAACTTCCCAATGCTATTAGCTGCATGGAAGATTGCGCCAGCCATTGCTGCAGGTAATACAATTGTGATTCAACCTTCGTCTTCAACACCATTAAGTTTATTGGAAGTTGCTAAAATT\n++\n+??A??7B>DDDDDDDDAGCFG-HFHEIH.HHICHIHHIHIIIIGHHDHFFIIFFFHHIIHHHAH=IIHHHHFEEHHHH>IIIIIF7HHIH*G.@I>IHHH.6HEDEHHHHHGHGGHG,GFGGGGGGGFEDHEDGFEGC@GHG@GCGGGGB\n+@mutant-no_snps.gff-24942/1\n+TCACTACATTATTTTAAATATCTTTTACTTCTGCAGAAACTTTCATCCCATTTTGAACATCCATATTTTTGAACGGGACAGTTAACACATATTGTTTTAAATAATAATTAAGCGTCTCTAAACTAAGCGTGTTATATCTTGTATTATCAC\n++\n+?AA??=BBDDB<BDDEFFFDGCH0E-HFHHIIHI=CI/HHHIHHGDHIGIID@FEFFHHIEGHHDHH@IEH>IFHBHDIHCHIEIIHIHHHHIGECIHDHIHHH.FHFGHIGIHHHGHGHGEGGGGGGFHDFGGBGBGHFEGGEGG=EFG\n+@mutant-no_snps.gff-24940/1\n+GACTTAATTTCACAATATGCTCAACTGTCTCACGATCTTTAACGTGTGGCACAATAATACCTCTCGCACCCATATCCAACACTTTAATGATATCTCTATCTATCACTGCAGTGACACGTACAATTGGTATAATATGCGCTGCTTCAGCTG\n++\n+?????BBB@D@9DDEDGGFFGGIHHHIHIFHIIIHIIGIIIIIHFIIIGHDFFIHHHHIEHHIHBHHIIAHHIFIIIIIFD4HHICIHHIHCGHHH=ICHIHGHHFHHDHHFHFHGGGHHGGHH*FE:EEHDGEGGGGEGCBGGFFEG@E\n+@mutant-no_snps.gff-24938/1\n+ATGAGTATGGATGTTATGGGAATTTCAAAAGAAGAATTAAGAGATGAAGTCGATTATGGTGGCGTAGGTACTTATATTGGACATGCTGAGCAAGCAAATCATAACTTATTTATCTAATCAATAAAATCTATTTTAAAAAGGAGTTTTTTT\n++\n+????=B>BDDDDDDDDFFFGGGIHCIIFFHIII0HIIIH?HGIHIHI>7GHI>HFEHDHHHFHHFIFIHIIE-IHIHFIHHHFHFHIHHDCGGHHHHI'..b'GGGGEG\n+@mutant-no_snps.gff-24/1\n+ACAATCTACTGTATCTGAAGATGGTACTGAACAACAACGTGAAGCGGTTGTAAATGATGAAACACCAGGAAATGCAATTCATACTGAAGTGATTGATTCAGAAGTAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGA\n++\n+9??AA?BBDDDEDDD=?GGGGGIICIHAIFFIHHIHHHHH=EHHHGIHIFGIEEHF9IGIFHIIIIGHHHIHIFAGHIIGIEI?GHGGHHFH=FHI?HGHFDIIF5FHHD,HFHHGFHHHGAFGEGFEFHGG(GGEGG8F::CE*GGEGG\n+@mutant-no_snps.gff-22/1\n+ACGACACAATTTATTCCCCATTGGGAACAACCAGAGCATATTCAGTCACTTACGTTTCATAGTGCTTTTGCAACACTTCAACAACACTTACCTGAAATGAAGCGATATGCAGATATCATTGTGGTTTGTTACCATGGTGGATTTGAAAAG\n++\n+???A?BBBD<EDDDBBGFGGGGFCH-IIAHFIIHIHHHIFHII@HIFHFFIICFIHFHFFDHI/IHGHFFHIEGIHE-IHFIEH=:IFH+HHHHHHD?HFFF8HHHIHHH.=HDFHECHHCGGG,EHCEGFGGF,EE)=@G?CFEFEFGE\n+@mutant-no_snps.gff-20/1\n+AGGAGTATCCGCTTGTTAAATGTACATAGCTTATATTTAGCTGTTTAACATGCCACATAATGATTCGAATTATTCCAAGTCCCGCACCTCAGAATCAAAAAACATTCGAGTGATAAAATTTTAAAAATCAAAAATATAAAAATGATCTAA\n++\n+?AA??ABABDDDDDDEGFGGFFEIHHHHIHHHGHIIIHBIIIGEGHCIIIIHFIEHHHFHIIIAFHIIIIIHH0HIHIIHHHIIFDHHHIIHHHHHEFHIEGHHG=HIHGHFHGF?HHHEGGG?F2GGEEFFGHE;.G.GEF@=?ECGEG\n+@mutant-no_snps.gff-18/1\n+ATAAAGTTACTTAATCATTCTCATCATACAATAATTTTTACTCGAATTGGAAAAATTATAAAAATTAAACATAGAAACAACTTGAACATTGGTTTTATGCAAGATCAGTAGAGATAACTGTAAAATGTTCTTAATATTGTCAAAATGTAA\n++\n+?AA??AB?D9<DBDDDFCGFFFHHIIFIIHIHGHHIIHBGHDHHHIII-HHHIIIHIIHHFCIHIGHHIHI@HHHFHHCHIHIIFHGIHHFHIIEHGHA)CI=HGHHH=H,.FHHGD@GGHHDGGFB+HD+,@;GFGFAGFBGGGFE;GG\n+@mutant-no_snps.gff-16/1\n+GTATTTTCGGTGCATTAAAATTGATTGAAACGACACATATGCCAAAATCACAAACACCAAATATTAATAAAGGTATTCGCCGTTCATTTCAATGTCTATTATGCACACAACAAACATGTCGATTTATTATCGTTGGCGTTTTAGCAAACT\n++\n+??=9?5BBBDDDDDDDGFGFFFCHIHCHIFHH+HHFHFFIIEHHHEGFHFHIHHGHIHIIHFFHIHIFIIIHCH-HHGIIHGHEIIHIEHHHHIGGHAHD5GHCHHHEIHIGHGHHFAGFFDD2.FFFFHFFEEGIGEAGG?EGG*EG@G\n+@mutant-no_snps.gff-14/1\n+TTAAATATTATGCAAGATCAACAAACGTTAGCGGGCATTACGGCGAATGCGCTTGCTAAACTTGATAGCATCATTAATGAGGAACAGCCGGATATGATTTTAGTACATGGTGATACTACAACGACTTTTGTAGGAAGCTTGGCAGCATTT\n++\n+?????BBBDDBDED<BAFFGF@EEHIHHIHIHCHIHIHHHIHHIIHAIIHHFHIHFHHHGDFIFIHHHIIEIHHHFBHAIEHFIHHIIFHFHHIHGHFIHE,FHHHHHHHHHGHFHGEHHGH>EHGGFHFH+FEGABEGGBEEGEGEGG2\n+@mutant-no_snps.gff-12/1\n+TTTCACAAAACTACTCAATTTATTAAAACATGAACAAGTGACTTACCTCATAGATGCTAATCCATCTATATTAACACCATCTTTTTATGAGCATCTTCGACAATATGATGCACAATTTATGATTCGTATCGATCATAGTACATCAATTGA\n++\n+A??==BBBDDDD@D<DGFFGFGIFHIIHHFHHIIIIFFHIHFHHIHFHIIH9GFGI=ICHFHEBFIIHIHGHIHIIIEFIIHIEI+III7HFHHGHHFDGHHHHIHEHHGHHHFHHEHGEHHFFGHBH;EDGGGEGFGFE(*8GEGGFGC\n+@mutant-no_snps.gff-10/1\n+TCACCATAATGATGAGCCGCTTCCTTTGTTGGCGGTACTTGTTGCTTATCTGTTGTTGCTTTGTCTATCGTTGTTACTGCATGTGCTTTCATTGGTGTATGTTGCTCAGCCGCGCTCGAGACTCGCCATAATCCCATTGCACTAAAAAGC\n++\n+?A??ABBBBDDDEDD<FGGGFFHEIFHHHIEIIH9HIIFIDHHAHIDIIIHIFICIDHGHHHHDIHHIGIIHHFHIIHHIHIHIIHHIFIHHG=HFHH?HEHEH-HE*DHHHHFFFHHFEHHH6HGEFHEEBCFGCAGCEFGGCBCG@<G\n+@mutant-no_snps.gff-8/1\n+ATGGTGTACTTAGCTTAAGTAAGAATCCTGATATTTCAATTGCTGAGTTAATGGAAGATATTGAAGGTCCTGATTTCCCAACTGCTGGACTTATTTTAGGTAAGAGTGGTATTAGACGCGCATATGAAACAGGTCGTGGTTCAATTCAAA\n++\n+?????BB?DEEDDDDBF?FGCGIIHIIIIIICHIHHIIIHIIFHFIHHIIFBIIIFIHIHHHHIHIHHIHFH5HAFHIHGHIHHIEIHIHIFHGFIDIHIEHHEDHGGDHHHHBFFFDH6HGEEHGD@FGHGFEGFG=H1GGGFGEG@EG\n+@mutant-no_snps.gff-6/1\n+TTACCTTTGCCTAACTTTTCCCCCAGTGCACCGAATGGTTCGGCTACAGAATACCCTGTAATTCTGTGTTCACTTAATGCGGCTGGCATTTCTGCTGGCGACATTTCATGATAGCTAAAATGCCCCGGTTTAATCTTTAATTGTTCTCGT\n++\n+??<??BBBDDDDDDDDCGFEGGICIIHIFIIIGIIHIHIHFI:IHIHIIIIHHHHHGIHHHFHIFFHIHGHICHHHGIGAH@HEHDHI7IHHFIHHFHFHCHHEI=HFH?FHCHHHHFG+EHGGH7H8HDGHGEBGEGHEHEG@@FG?GD\n+@mutant-no_snps.gff-4/1\n+CCAAACCAAGATAATCCATTAACAGAAGGCAAAACACCAATCTTACTATTTGATGTTTGGGAGCATGCCTACTATCTGAAATATCAAAATAAACGTCCAGACTATATGACTGCATTTTGGAATATTGTTAACTGGAAAAAAGTTGATGAA\n++\n+??????BBDDBD@DDDFFGFECHIIIIH>IDGHIH@IGIIII>:IIHE,CHFFIE.H-HHIHIEFGF5HIIHIIHIHIIHIHIEFIFHIHFHFIHHGIHIIEHHIIGHHE?HHH;HGEFFHG*;GGFHGHHF?ED=EGGCGG8EF?C5EG\n+@mutant-no_snps.gff-2/1\n+AATTTAAATTTAACTGGGTGGTCATTGTATCGCAATATATTATTTCCCGGGGCATTTAAACAAATCATGGCTGGGATACATATGGCGGTAGGAACAAGTTGGATATTTTTAGTTTCTGGTGAAATGATTGGTGCACAATCGGGATTAGGT\n++\n+????A9BBDDDDDDDDFGGFEGFHHIHHHIHCHIGH,EGIIIFHIHIFEHHGFIHIIE5CIHFHHHIHHIFHIHIIII5IFHGHHIFF?FGIHHHIICFHCHI7HHHHHHHHGHFHHGDHGFHEHEDHFFEFGEFG@EEGC-EGHGGGEG\n'
b
diff -r 000000000000 -r 196a599ec43d test-data/mutant_R2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mutant_R2.fastq Wed Oct 25 03:39:03 2017 -0400
b
b"@@ -0,0 +1,49920 @@\n+@mutant-no_snps.gff-24960/2\n+TCCATTCATCGGTACAACTGTATTTGGTGGATTATCATTAGCGTTAGGTGCAGCGTTATTAGCTGGACGTCGTCGCGAACTATAAAAACAAACAATACACAACGATAGATATCATTTTATCCAAACCAATTTTAACTTATATACGTTGAT\n++\n+????9BBB@DBD@B<DGFFEFAIHFHEH>FIHHHHICIHFIIIIC9H9H8FCCAHHI=DIG?HEHC?I5HEIGEHHFHHIH?=HEIFA/H<HHHHHIIG,HHH-+HHF@FEHGFFHEH*FF;HDHGGHGDHD*GE-E-EFEGD;;G*EG-\n+@mutant-no_snps.gff-24958/2\n+TGTAAAACTTTCTTTTTGTGTCCATATTTGATAAAAATCATTTAAACTACATATTTGATGTGCTTCGTTTGTAGAGAAACACGTCACTAATGTACGCCAGTCTAAACGTAGTGATATCTTTTCGATATCAATACCAACTGGTTCTTTATC\n++\n+?????B?BDDDDDBDDFFGGC+IIHIHE+FHICIEHIHAD+IIHAHHHIEHBEGIIFGDGIHD-HHHF.HH5HHHH6FH-HCC(HCI@HDHHIHHHFC-FIHGHDDFFH,FEDGEHHE+FFG(FFF9HG=DGGGE;)GEFGG':ED*CF2\n+@mutant-no_snps.gff-24956/2\n+CTACGTGAATCAAAAACAATGGATTCAATTTTGGAAAAAGGCAATGAAATTAGACTATGATCCAAATGTAAAAGTTCAAATGATTCGACCGAAAAATAATTATACATCGGATATACAATCGGCAGTTGACGAAACTGCAAAATAGCCTGT\n++\n+A??,9B7B-DDDBD9DGGGGGEFFG/H>IF/IHIIIH+FHH.H-HHHFEGFIHHFCHAEHHFHDCH+HHFEDFIE-FIGHFIHCH@FHEHEHII+CG,I+FCDH+GHFFECHCH4H+FFD9G;7F=D1?@8FEEDEG;GEE2CF'EE*G*\n+@mutant-no_snps.gff-24954/2\n+AGAAATTGTGTCATTCGGAATAGCTTGTGTTAATTTTAAAATTCGTGTGTCTTTAAATACATTTGGTTGGTCTTTTTTCACAGTATTACGTGCATCGTTAAATACAGCTGCAGCATCTACATCTCCATTTAATAATGAGATAACTGCTTG\n++\n+??9??BA<D@DBDEBDGFGFCFIHIIII.CHHIIGHEIHIIH9HHFHEHFH/IHHHFHHGHECH5HEFFIBFHD+@HHFFI5GIHDH>HBHHGHEHGHHHH+D=DDDHHHEHHHHE*DFHE=FHHGEEECDHCF+FGCEGGGFFEC5EEE\n+@mutant-no_snps.gff-24952/2\n+GATAAATAGCTTCATCAATATCGTGAGTGACTAATATAATAGTTGATTCCGTTTTATGTTTTAGTTGTACTAGTTGATCTTGAAGTTTATAGCGTGTAAATGCATCTAATGCATCTAATGGCTCATCCATCAATATAACGTTAGGCTTAT\n++\n+A???,>BB9BBDDBDDCCGCCGH8HHHEIHFIHI+HCHIE9FIIHHEII+9CIHEFFIHEHI5=I5H5HGFIHEHF55D-5ED,-HGGG9H=+HCIIH+HCEHIHFEHFGHFH#FHFHEH,:42HD)G**FBE9?(EEFG*EEGEGGHG9\n+@mutant-no_snps.gff-24950/2\n+TGAGCCGAGTTCATTTGTAATATCACCATTTTCAGCAGTACAAAAACAGGTTAAACGTATATTAAAGCAACAACTACCGACTAGAATTGATATTGAACGTACAAAAATTAATCAATGGGTCGATAAATCCATTGGTACTGTTCATACTTT\n++\n+??,??BBBDDD@DDD+8AGFFFIHF-HHHHGIFHHIDHHICA+H-HH9IGFCIFHBFCHIHDI5HHII@HHEHHIHFHHD+EFIHC4IFIIA>IDHGCHHHFHG.HDFE-HEEBCHEDHH@HHDG>5CEGG=8GF=EGFGGEABEE?GG3\n+@mutant-no_snps.gff-24948/2\n+AAATTAAAATGAAGTGTTCTCGGTCAGCATTTCCTATGAAGTCACGCATAATATCAGCAGCGTCTTGTGGTTCTTCAATACGTCTTTTTAAATACCAAAGTGTATCTTCTTTAACCATTCGGACTTTGACAACATGTATTCTTTTTCTAC\n++\n+?????B>BDBDDBDDDC>FFFEHIHI8IIECEHI+-HDIGHHCHEHCGHGH?HE9EAA=IFDDI-D+HFHAIFFHHII5HGIHEDHHFIHFFIHFIHFHDCHDGBI=6HCHF;EHE=DH.H=EHGGHF?FGEE4GF2HF*>DECF;FGEE\n+@mutant-no_snps.gff-24946/2\n+CAATACTTTTTCGCCATGCTCTTTCACAAATTGTTTTTGTACTGAGTTTCCTTTAACGTCATACCAACCGGTCTTACCTACGTTTGTAATATTACTAGGTAGCACCATTTTATTATTATAAGCAATTTGATTAGCTATCGTGAACATGGG\n++\n+?=???/BBBBDDBDBDGFCF.+CFHIFHICHIGG@HHIFIDBHHIIDHCGFDGHH5FIHFBFDHHFEEAH5FHHIHGCFHHIIBFHDIHIEHEHF7HHFIEFF6.EHGF?D?ICEEHFDFFFBG,FHH@@HEFCFFEB@*EE=EFEGE**\n+@mutant-no_snps.gff-24944/2\n+AACTGAATACCTTCAACTGCAAGGTCTAAATTAGCATCATCTAATATGATATTGGCGCTTTTACCACCAAGCTCTAAAGTAGCAGGTACTAGATGTTTCGCTGCAGCTTCGGCATCTTGATAACCTACATCAGTTGAGCCCGTAAATGAT\n++\n+,9?????>DDBDDDD@GFF8GFI/-IHHHEIHFHFIHHDH.HCHBHI>IEBIHIIHIGEHH5B@HG>D-EH5III-HHAF<FEHEDFEHHHHHIHDGHFG.@HI+FIGC=#EFE+HFE+D*HGGHEHD>EGAEE=FG95(B6CGEDEGGE\n+@mutant-no_snps.gff-24942/2\n+CATCAAAGTTTGATTCAGCACACCAACAAATGCACCAATCATTACGACAGCTATAACACGGTTCCGTTGTTTCAAATCTATATTAAAGGCATATACATTCCTCAAATTTTGACGTCTCCCTCTCTTTTAAGTGGAACCTACTATCATTTA\n++\n+=<A??BBB<DBBBD@DFFFFGGHIBCFEFIIH/IGIHIDHHHI9F?HIGIHFH5AHDH8HG+EHIHEFGHID*IEFIIFFHIHG+IEEHFIIFEHEIHHFEHHEGIHGHAHG<H+=GEFBGE@9GGEFF8*GGG?CFGGE6G2@E8D=EG\n+@mutant-no_snps.gff-24940/2\n+TCGATTATTAAGTGACTCCGAGTTAAGAATTCATCATGTTACAAATCCATTAGGTGTAGGAGGTATTACTGATGCAACAACTATCTCTGAAACATAGATTAAACAATGGTGATTCAGTTTATGGCATTTTTAATTCTATACCGGACCCAT\n++\n+?????B>BDD-DDD-DFFAGEFIEAFIHFII@HHI-H>HHHHEDHEH/IIHCDHFF)DIE@IFHHEHCFFHIAICHEIHCIHFACIHD7GHDEIIIDH.HIHH@HHHIHHBHDGHFFEHFHCG??F+E=5(=GFDEE?E;GGGACFGG.E\n+@mutant-no_snps.gff-24938/2\n+CTCTAATACCTGAAGCAAAATCAGCATGAATATGTGTTTCTGCAGCTTTAGTAATTGTGAATCCTTCTTTATCTGCAACTTTTAAATATTTTGTTAAATCTCGTATAGGGTCAATAATCATTGCTTCTCCTGTACGTTGACATCCAATTC\n++\n+???A?BBBD?DDBDD@6GFCGFHFCIIC/FIIHGIGFHI+HIHIHHAHHHIF=HHEFHGG'FFHIF@?H5@FIIFHGHE5ECHFHEHDICHIH@HFGH"..b"G<GF;E\n+@mutant-no_snps.gff-24/2\n+GTGGTGCCACCATCAAGACTTATCAATGAAATACCTTACGCAATGAAACAATTAGAAAGTTAGTCATTACTAATCATTGAATATAGTATAGCATTACTTTCTAGCATAAAAATAAGACCCCCCTACATATAGGGAAGTCTTATTTTTTTA\n++\n+9???,<?BDDBBBB<DGGGGFGIHEIHBCFIFIHIII-FEHHHI9HIHHHG0HEH+@ECFH.HHHGFHHHHAGF7HIIFHHIHHCFHEHHHFHE)GHF.ECHFHDGDCGGHEFFHGHEHF,FHHHHDGEE)FBEAE*EFE/EGEGF:F,/\n+@mutant-no_snps.gff-22/2\n+TACTCAAGACAACTTTGCCTACAGTTGTACCTCTCGTACCAGGTTGAATCACAGCCGTTTGCTTAAACCTTTCAGCAATTTGTCGATGTTGGTGACCCGTAATAAAGATATCTATATCTTTAGAAAACGCTTCTAACATGCCATATCCTT\n++\n+=????B/?DBDBEDDEAA+CEGFHFHIH.HIFHH7IF?@FHIHGHGFHHF.IEFEHIEFIIEDGIEFEFFHIFCF>HHIECI@HFGDEHHDHIGDHHH5CIH3FHFGF?FHEFHHHE=04GDHGG0EFFFGF:G*GAEDD)2GEGFAAGC\n+@mutant-no_snps.gff-20/2\n+GAATCTTAGAACCTTCCATTTGACCATCCCTTATTAAAAAACAAGCTGCAGCAAGTGAAGCTAGACCAGATCCGATTAAGTAAGCGGATTTGTTTTCTACATTTTCAGGTTTTTTAGGGCGCGCAAATGCTTCATAATTTCCATAACTGT\n++\n+A????BBBBD-DDDDDGGFGFGFIIHC-EFIEDGI=EHHHGHHIGGGEF+?+HGHH+IHEFHGHIFHCIFIDBF5HIHIDH5DFH++HIHIFEFIDHHFH,EHCHHHGFHHIH+EF,E=+.HEEEEF3(HF+BECID8EGHCGGD-EEEE\n+@mutant-no_snps.gff-18/2\n+AATTAATTCATAAGAGTAAATGCCAATAGATGGCATACCGATTCCTGAACCCATGACAGAAACTTTTTTACCTTTATATGTTCCGGTAAAACCAAACATATTTCGCACTGTATTGAACTGTTCCACATCGTCCAAATATGTTTCTGCAAT\n++\n+????,?>=B<BB?DBDG-F-GGCHH6I/AHIHIHHIHHA'IHFIIHHHHCHF-IIH+IH@GHIF?GFIDHI;*A;IHIHF=GIAGHIGHHH6DGHEIICBG+DGAFFHD4FFGDFIHEFFH*G;F@EE9FFFFG4GAEGEE=G8EE8EGE\n+@mutant-no_snps.gff-16/2\n+AAAAATTCTACATTCGTCGCTAAACCTTGCGGTATCGCACTACAACCACATGCAATCGTGGCAAATATATATACTGATTTAACATATGATTTATCATTAAAGCGACCCCATAAAGGCGCGCTTAATATCGAAGCCGTCCAAAATGCGGAC\n++\n+??,??7BBDDD-,-BDGC/?AGCHHIH?HH,/D9HHAHHHIHHIHIHG@HHDHHHEHEFFIFFAGIIHFHDF5IEHII3IHHDCG-G7FIFEEHGHHFF.IHF+HHHFHHFBEHEHHHH.GDE++HGGBBG?G=AEGGGEECFGH*EFGE\n+@mutant-no_snps.gff-14/2\n+AACTGTTGTTGACAATGCGTCGATAACTGTATTTCCGGTAATGAAGATACTCTCTTTGTCTTTGTTTTCAAAAAGTAAATTTTTAGCTGCAATTACTGTTGGCGCAAAATTCAATTCAGCAATATTACTTACCATGACTCGATTTAATTC\n++\n+??A??B9B@D5?DDDDGFGFC-IHHC;III+FHIHGHIIIHI-HHGDE.=HD?HHHIHHHHH5EHHHFHHDFHD=?HFFHFBIHIHEHH*HEHHHFGDH8HIGFDHGHHHHF;HHIEDHHDE@HHGEEH;FG6(BDFGBEFGGGFGG,4E\n+@mutant-no_snps.gff-12/2\n+CATATATTTGTGCCTTTGGATTAAATTGATAAATGAGTTCATTTTTCTTATTGACCAAGTCAACAGATAATCCCGTATCTGGTCTTGGATAATAGTTATGACAAAATGAAAGTAATGTAAAATCATTCAATTGTTGATGTAACCTTGTTA\n++\n+??9??B/BD<ADDDDBF?G+FG,HIEFHI;HHHIIFHIFIIHHIGBEIEEIHDIEBDHH8HHHFFHHIF(HFHFFIHHIIIIHCIIFCHAEFHIH.GFIHFHEH@HHHEHHDHDFH@HHHHC=F@GGG@FFFDGEEEE@GBG(.8EGB@G\n+@mutant-no_snps.gff-10/2\n+GATACGGATAAAGCTATTCCAACGCCAATATATACAATATAAATGAGAGTCACCCGATAAAGTTCCGCACTGCTGTGAAACGACTTTATCGGGTGTTTTTTTATGTTGTTGGTGGGAAATGGCTGTTGTTGAGGTTAAGGTTCTAGTTGA\n++\n+???<?BB=@DDDDD-DGCF.FGIF90HHBHHHGFHE-FGDIIHHHHDFIHFFGFHHF@DHHHI9?HFAIHFIH5HCIIHHF-=IFHHHIHEHHEHHH,HHHAHFD?H4IDHFDHEGHHEGGGB@HHHGHFEGG+;+?G7;)GECGGGEGC\n+@mutant-no_snps.gff-8/2\n+AAGAGGTGTTTGTTTGTATAAGTTATTTAAAATGACACTAGCATTGGCATCCTTACGCACATCAATAACGACACGCACACCAGTACGTAAACTTGTTTCATCACGTAAATCAGTAATACCGTCAATTTTCGTGTCACGAACAAGCTCTGC\n++\n+<????>+BBDDBDDDDFFGFFG>FFIHC-7ICF/HIEHHH.IH+HFHAIGGFDHHHGFHHHHHIHFHHIEFIE@I-HHCFCHIFEHIHBHFHD.HHFEHEHIDH-DHHH=,=HHG=GFHHDDFFE+DGEH*HGDGGEGEEGEFFE?G.GG\n+@mutant-no_snps.gff-6/2\n+GCATCAACTTTAATAGAGCTCGCGATGAAATCAAAGCAGAAGGGCTCGAATATAAAAGCTGTGGCATTGGGGCATCATGAAGGCAATGTCATTATGGGACAAAAAGGTATGCACTTAAATGAATTTAATAATAATGGCGATGATTACCAT\n++\n+595??BBBDDDDDD<DCFFCGFHHIH>HHIHI9IHHHEEHIIHGGHCH/IIHGEFDIGHHFGEGEHCI-GHIFCFIHHHIGGHII-EHH+DIGHGHEHHF?FEHHHGFF=CHGHHFH8?E:EEFHHEBF2FFEGB3FGE*GFGEEGGEG2\n+@mutant-no_snps.gff-4/2\n+TACTTATTTTGTCAATTTATTTAATGTCAATATGTTGATTAATCAATAGTGTTGTCTGATGTATATAGCATTTAAGTCATCGTTATAGTCAACAATAATAAGGTATTTCGAGTTGAAATTTATCGTATTATTTTTCCACTTTTAAGCGCT\n++\n+?<???B>BDDDDBD<DGFCFF86HHHHHH-F(DHHHHHBHHHEIGFGDHHHEHHIC@HIHHCHIHAEFIFIFC=DHGHIDFFH-7GED5AIHFHHAHHGGDEHFF65HHH?6EH=F=EGBFFHH+E+GDFCFG8)D?0@G)D*D*=G=EE\n+@mutant-no_snps.gff-2/2\n+CTCGGATAATACGTCCCTTCATCAACTTCTACTAAATGAGGATCTAATTGTTCTTTGATAAGTGTTTCTAAAGTCATCATCATCTCTCCTTATTCACCAAATCTTCTAAGTATAAACTGCTCAATATAACTAATGAATCGATCAATAATA\n++\n+????<>B?6BDDDDDDFGGGFGHIHHHFHIAFIG5,H/FHG>@FHIH9HHHDGGDABIGHIH>I-AIHCBFHEGI+FH;4EIEHFHIHHFEH-FF4HCHHF.FHGFHH?HHFGDCHH?FEFHHF@CGGEEFGEHEID,GEGGGE(8EGBG\n"