Repository 'salmon'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/salmon

Changeset 6:885d11dc8090 (2018-05-10)
Previous changeset 5:53e9709776a0 (2017-07-12) Next changeset 7:e7e885f718fb (2018-05-30)
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86
modified:
salmon.xml
added:
test-data/reads_1.fastq.bz2
test-data/reads_2.fastq.bz2
test-data/reads_both.fastq
test-data/reads_both.fastq.bz2
test-data/reads_both.fastq.gz
b
diff -r 53e9709776a0 -r 885d11dc8090 salmon.xml
--- a/salmon.xml Wed Jul 12 14:05:10 2017 -0400
+++ b/salmon.xml Thu May 10 06:48:28 2018 -0400
[
b'@@ -10,12 +10,20 @@\n                 <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>\n             </param>\n         </xml>\n-        <token name="@VERSION@">0.8.2</token>\n+        <xml name="orientation">\n+            <param name="orientation" type="select" label="Relative orientation of reads within a pair">\n+                <option value="M">Mates are oriented in the same direction (M = matching)</option>\n+                <option value="O">Mates are oriented away from each other (O = outward)</option>\n+                <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>\n+            </param>\n+        </xml>\n+        <token name="@VERSION@">0.9.1</token>\n     </macros>\n \n     <requirements>\n         <requirement type="package" version="1.0.6">bzip2</requirement>\n         <requirement type="package" version="@VERSION@">salmon</requirement>\n+        <requirement type="package" version="1.2">seqtk</requirement>\n     </requirements>\n \n     <stdio>\n@@ -52,27 +60,52 @@\n             #if $single_or_paired.input_singles.ext == \'fasta\':\n                 #set $ext = \'fasta\'\n             #else:\n-                #if $single_or_paired.input_singles.is_of_type(\'fastq.gz\'):\n+                #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):\n                     #set compressed = \'GZ\'\n-                #else if $single_or_paired.input_singles.is_of_type(\'fastq.bz2\'):\n+                #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n                     #set compressed = \'BZ2\'\n                 #end if\n                 #set $ext = \'fastq\'\n             #end if\n             ln -s $single_or_paired.input_singles ./single.$ext &&\n-        #else:\n+        #else if $single_or_paired.single_or_paired_opts == \'paired\':\n             #if $single_or_paired.input_mate1.ext == \'fasta\':\n                 #set $ext = \'fasta\'\n             #else:\n-                #if $single_or_paired.input_mate1.is_of_type(\'fastq.gz\'):\n+                #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):\n                     #set compressed = \'GZ\'\n-                #else if $single_or_paired.input_mate1.is_of_type(\'fastq.bz2\'):\n+                #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n                     #set compressed = \'BZ2\'\n                 #end if\n                 #set $ext = \'fastq\'\n             #end if\n             ln -s $single_or_paired.input_mate1 ./mate1.$ext &&\n             ln -s $single_or_paired.input_mate2 ./mate2.$ext &&\n+        #else if $single_or_paired.single_or_paired_opts == \'paired_collection\':\n+            #if $single_or_paired.input_1.forward.ext == \'fasta\':\n+                #set $ext = \'fasta\'\n+            #else:\n+                #if $single_or_paired.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):\n+                    #set compressed = \'GZ\'\n+                #else if $single_or_paired.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+                    #set compressed = \'BZ2\'\n+                #end if\n+                #set $ext = \'fastq\'\n+            #end if              \n+            ln -s ${single_or_paired.input_1.forward} ./mate1.$ext &&\n+            ln -s ${single_or_paired.input_1.reverse} ./mate2.$ext &&\n+        #else if $single_or_paired.single_or_paired_opts == \'paired_interleaved\':\n+            #if $single_or_paired.input_1.ext == \'fasta\':\n+                #set $ext = \'fasta\'\n+            #else:\n+                #if $single_or_paired.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n+                    #set compressed = \'GZ\'\n+                #else if $single_or_paired.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+                    #set compressed = \'BZ2\'\n+                #end if\n+                #set $ext = \'fastq\'\n+            #end if     \n+            ln -s $single_or_paired.input_1 ./mate1.$ext && \n   '..b'bz2" ftype="fastqsanger.bz2" />\n+            <param name="biasCorrect" value="False" />\n+            <param name="TranscriptSource" value="history" />\n+            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />\n+            <output name="output_quant">\n+                <assert_contents>\n+                    <has_text text="EffectiveLength" />\n+                    <has_text text="TPM" />\n+                    <has_text text="NM_001168316" />\n+                    <has_text text="NM_174914" />\n+                    <has_text text="NM_018953" />\n+                    <has_text text="NR_003084" />\n+                    <has_text text="NM_017410" />\n+                    <has_text text="NM_153693" />\n+                    <has_text text="NR_031764" />\n+                    <has_n_columns n="5" />\n+                </assert_contents>\n+            </output>\n+        </test>\n+        <test> <!-- interleaved gz input -->\n+            <param name="single_or_paired_opts" value="paired_interleaved" />\n+            <param name="input_1" value="reads_both.fastq.gz" ftype="fastqsanger.gz" />\n+            <param name="biasCorrect" value="False" />\n+            <param name="TranscriptSource" value="history" />\n+            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />\n+            <output name="output_quant">\n+                <assert_contents>\n+                    <has_text text="EffectiveLength" />\n+                    <has_text text="TPM" />\n+                    <has_text text="NM_001168316" />\n+                    <has_text text="NM_174914" />\n+                    <has_text text="NM_018953" />\n+                    <has_text text="NR_003084" />\n+                    <has_text text="NM_017410" />\n+                    <has_text text="NM_153693" />\n+                    <has_text text="NR_031764" />\n+                    <has_n_columns n="5" />\n+                </assert_contents>\n+            </output>\n+        </test>\n         <test>\n             <param name="single_or_paired_opts" value="paired" />\n             <param name="input_mate1" value="reads_1.fastq" />\n@@ -421,6 +535,43 @@\n                 </assert_contents>\n             </output>\n         </test>\n+        <test>\n+            <param name="single_or_paired_opts" value="paired_collection" />\n+            <param name="input_1">\n+                <collection type="paired">\n+                    <element name="forward" value="reads_1.fastq" ftype="fastqsanger" />\n+                    <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" />\n+                </collection>    \n+            </param> \n+            <param name="TranscriptSource" value="history" />\n+            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />\n+            <param name="geneMap" value="gene_map.tab" ftype="tabular" />\n+            <output name="output_quant">\n+                <assert_contents>\n+                    <has_text text="EffectiveLength" />\n+                    <has_text text="TPM" />\n+                    <has_text text="NM_001168316" />\n+                    <has_text text="NM_174914" />\n+                    <has_text text="NM_018953" />\n+                    <has_text text="NR_003084" />\n+                    <has_text text="NM_017410" />\n+                    <has_text text="NM_153693" />\n+                    <has_text text="NR_031764" />\n+                    <has_n_columns n="5" />\n+                </assert_contents>\n+            </output>\n+            <output name="output_gene_quant">\n+                <assert_contents>\n+                    <has_text text="EffectiveLength" />\n+                    <has_text text="TPM" />\n+                    <has_text text="baz" />\n+                    <has_text text="bar" />\n+                    <has_text text="2283" />\n+                    <has_text text="1640" />\n+                    <has_n_columns n="5" />\n+                </assert_contents>\n+            </output>\n+        </test>\n     </tests>\n \n     <help><![CDATA[\n'
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diff -r 53e9709776a0 -r 885d11dc8090 test-data/reads_1.fastq.bz2
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Binary file test-data/reads_1.fastq.bz2 has changed
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diff -r 53e9709776a0 -r 885d11dc8090 test-data/reads_2.fastq.bz2
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Binary file test-data/reads_2.fastq.bz2 has changed
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diff -r 53e9709776a0 -r 885d11dc8090 test-data/reads_both.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads_both.fastq Thu May 10 06:48:28 2018 -0400
b
b'@@ -0,0 +1,80000 @@\n+@1:NM_014620:16:182\n+GTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAACCATTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@1:NM_014620:16:182\n+CCCCAGCTGCCCCCAGCTTCGGCAACTCCACCTGGGAGGAAAAAAAATTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@2:NM_014620:1094:172\n+ATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@2:NM_014620:1094:172\n+AGAGGCACAGCGAGTGGGCGATCTCGATCCTTCTCCTTCGGGTCAGGTAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@3:NM_022658:294:172\n+TGTACGGGCCCGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@3:NM_022658:294:172\n+CTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTCCGTGGCAGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@4:NM_022658:1362:195\n+ACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAAAATGAAGAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@4:NM_022658:1362:195\n+ACCCACATCTCCTTCAGGTTTCCATCAGGTTCCTAGAGAAAGTCAAGGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@5:NM_173860:323:180\n+GCGTGAGGAGCGCGGGCGCGACCCGGGAGCCGGGCCCGGGGCAGCGCTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@5:NM_173860:323:180\n+GATTCCAGCGACTGGCAGGAGGGCGGGTCGTGCGGAGGTCCTGCGCCGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@6:NM_022658:1062:146\n+GGAAGGACTCAGAAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@6:NM_022658:1062:146\n+GTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@7:NM_022658:1912:184\n+CTACCTATAGAAAGAAATCCTGCTTTGAGAGTATTTGTAATGCGGTTTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@7:NM_022658:1912:184\n+GTTAACTATACATTCAGTGCAATTTAGTTCTACTCTACTGGGGTTAGAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@8:NM_022658:304:172\n+AAGGGACTGTCTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@8:NM_022658:304:172\n+CGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCACGTTCAAGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9:NM_174914:46:212\n+ATAACATCCAAGAAAGACACCTTGCATATTCTTTCAGTTTCTGTTTTGTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9:NM_174914:46:212\n+GAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10:NM_022658:25:186\n+CCAACCTGCCCAGCCCCCAGCCCACCAGCCCAGCCCAGTCCCGGGGAGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10:NM_022658:25:186\n+GAGAACAGGGGGTTGACGAAGTAGGAGCTCATGCTGGGTACATGAAAACC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@11:NM_022658:1031:165\n+AAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGAGTGAGACAGAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@11:NM_022658:1031:165\n+TCTAACTACCTGTCAGATACTTGCAGCTCTGGTTTTATTACCTTTGGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@12:NM_022658:1090:157\n+CTTTATTTGTTTGGGGGCTGGAGGGGGGAGACGGAGAAACAGTGAAAAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@12:NM_022658:1090:157\n+CGAGGAGCACGGAGGCCAGGTCTCAGACCTTAAAATCCAGGAAGGACTCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@13:NM_173860:524:97\n+CAACGAGGGCAACAAGGGCGCCGGCGCAGGCGACCCCGGCAGCTTGGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@13:NM_173860:524:97\n+CCAGGGCGCGCCGCTGGCCGAGAGCCCGCCGCCGGGGTTCAACGGCGATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@14:NM_022658:1471:182\n+CCCTCCCCCTCCCCAGGGCTCCCTGCTTAGAAAAACCCCCTTGACTTTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@14:NM_022658:1471:182\n+AGGCATGGGCCCGAGTGACCATGGGATGGTTAGGTAGGATTTTAGAGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@15:NM_022658:1173:198\n+CACTTGTCCCTGCCCCCACCCTTCTGAGTCCTTCCTGGATTTTAAGGTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@15:NM_022658:1173:198\n+ACATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@16:NM_022658:1052:179\n+CAGGTCTCAGACCTTAAAATCCAGGAAGGACTCAGAAGGGTGGGGGCAGG\n++\n+IIIIIIIII'..b'IIIIIIIIIIIIIIIIII\n+@9986:NM_022658:1194:170\n+TTCTGAGTCCTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9986:NM_022658:1194:170\n+GTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTGCATTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9987:NM_174914:1475:158\n+GTCGAGCAAAATCAAAGGCAAAGTCAGAGTTAATGAACCACAACTCTGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9987:NM_174914:1475:158\n+CTTTAGTTTCTGCAGGAGGCAACAGCACATGCAGTCTACATTTGACAACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9988:NM_004503:167:199\n+GAGAGCATGTCTTTCTCCTGGTAAAAGGAATTAGATCCATAGTCATACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9988:NM_004503:167:199\n+ACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9989:NM_022658:1203:166\n+CTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCCTCGGTCTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9989:NM_022658:1203:166\n+ATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9990:NM_006897:430:179\n+TTTGTGCTTGCTGCCGGCGAGCGCGTCCGCCTCGGGCGAGGGCAGTGTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9990:NM_006897:430:179\n+GGGGCCGTCACTACGCCCTCAAGCCGGACGCCTACCCCGGGCGCCGCGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9991:NM_173860:200:188\n+ACGGCTCCAGCGGGAGCAGCGCTGCCCCGGGCCCGGCTCCCGGGTCGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9991:NM_173860:200:188\n+CTACCTCGGCAGCCCAGTGTCTCTCAACCCTCCCTTCGGCCGCACGTGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9992:NM_022658:826:161\n+TAAACTTCTCAATTTATCTGCTACCATAAAACGAAACTTCAAGGGAGTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9992:NM_022658:826:161\n+CCGAGATGAGGAGAAGGTGGAGGAAGAAGGAAATGAGGAAGAGGAGAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9993:NM_014620:1162:157\n+AGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9993:NM_014620:1162:157\n+CTTCTTCCATTTCATGCGACGGTTTTGGAACCAGATTTTGATCTGCCTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9994:NM_022658:752:194\n+AGGGAGTTGCTAAGGGGGGGGGGGTCTTTCTTTTTTGCTTAGTCCTTGTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9994:NM_022658:752:194\n+CAAGTGAAGATCTGGTTCCAGAACCGAAGGATGAAGTGGAAAAAGGAGAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9995:NM_022658:1888:191\n+AGAAACCTCCAGCGTATTTTATCACTACCTATAGAAAGAAATCCTGCTTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9995:NM_022658:1888:191\n+TGCAATTTAGTTCTACTCTACTGGGGTTAGAAGCACAATAAAAGCGCACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9996:NM_014620:1559:191\n+ATATATATATATATATATATATAGGTTCTTTTCTCTCTTCCTCTCACCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9996:NM_014620:1559:191\n+GGCCTTTTAAAAAAAAACACCCAGCAGGTACCATGCTAAGACAACATCAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9997:NM_006897:223:164\n+GAGCCAAGTCCGCATGTAGCGCGTGTCGGCGCCGAGGTGGGGCTGGGGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9997:NM_006897:223:164\n+TGGTGCCGGACTGTAGCGATTTTCCGTCCTGTAGCTTCGCGCCCAAGCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9998:NM_022658:1995:180\n+ACCCAACAACTGAGACTGCCTAGCCCGCCGGTCCTGTGCGCTTTTATTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9998:NM_022658:1995:180\n+CAAAAAATTATTATTATAGATATATTTTTAACATTTTTTTCTTTCGAGCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9999:NM_022658:1773:182\n+GCATTACAAATACTCTCAAAGCAGGATTTCTTTCTATAGGTAGTGATAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9999:NM_022658:1773:182\n+TACCTAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10000:NM_014620:1728:181\n+GGAAGGAGGAGGAGGAGAAGGATGAGAATTGGCTTTAAAATTTCTTTCCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10000:NM_014620:1728:181\n+GGGTGTTTTTTTTTAAAAGGCCATTTTGGGGGGTTATTTATTTTTTAAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n'
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diff -r 53e9709776a0 -r 885d11dc8090 test-data/reads_both.fastq.bz2
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Binary file test-data/reads_both.fastq.bz2 has changed
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diff -r 53e9709776a0 -r 885d11dc8090 test-data/reads_both.fastq.gz
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Binary file test-data/reads_both.fastq.gz has changed