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

Changeset 4:de387b2b2803 (2019-02-18)
Previous changeset 3:98242353faa4 (2018-05-14) Next changeset 5:7518ee87b53d (2020-09-08)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit d44d890566efb82b4ce8a9ed2903b0902f3884ca
modified:
megahit_wrapper.xml
test-data/paired_result.fa
added:
test-data/interleaved-fq.fa
test-data/interleaved_result.fa
b
diff -r 98242353faa4 -r de387b2b2803 megahit_wrapper.xml
--- a/megahit_wrapper.xml Mon May 14 06:11:34 2018 -0400
+++ b/megahit_wrapper.xml Mon Feb 18 12:14:46 2019 -0500
[
b'@@ -1,8 +1,8 @@\n <?xml version=\'1.0\' encoding=\'utf-8\'?>\n-<tool id="megahit" name="MEGAHIT" version="@VERSION@.3">\n+<tool id="megahit" name="MEGAHIT" version="@VERSION@.4">\n     <description>for metagenomics assembly</description>\n     <macros>\n-        <token name="@VERSION@">1.1.2</token>\n+        <token name="@VERSION@">1.1.3</token>\n     </macros>\n     <requirements>\n         <requirement type="package" version="@VERSION@">megahit</requirement>\n@@ -22,15 +22,20 @@\n             -1 \'${input_option.batchmode.pair_input.forward}\'\n             -2 \'${input_option.batchmode.pair_input.reverse}\'\n         #end if\n+    #else if $input_option.choice == \'interleaved\'\n+        --12 \'${input_option.interleaved_file}\'\n     #else\n         -r \'${input_option.single_files}\'\n     #end if\n     ##basic assembly\n     --min-count \'${basic_section.min_count}\'\n-    --k-min \'${basic_section.k_min}\'\n-    --k-max \'${basic_section.k_max}\'\n-    --k-step \'${basic_section.k_step}\'\n-    --min-contig-len \'${basic_section.min_contig_len}\'\n+    #if $basic_section.k_mer.k_mer_method == "klist_method":\n+        --k-list \'${basic_section.k_mer.k_list}\'\n+    #else:\n+        --k-step \'${basic_section.k_mer.k_step}\'\n+        --k-min \'${basic_section.k_mer.k_min}\'\n+        --k-max \'${basic_section.k_mer.k_max}\'\n+    #end if\n     ##advanced assembly\n     ${advanced_section.nomercy}\n     --bubble-level \'${advanced_section.bubble_level}\'\n@@ -40,17 +45,22 @@\n     --low-local-ratio \'${advanced_section.low_local_ratio}\'\n     ${advanced_section.nolocal}\n     ${advanced_section.kmin1pass}\n+    --min-contig-len \'${output_section.min_contig_len}\'\n && cat megahit_out/log\n     ]]></command>\n     <inputs>\n         <conditional name="input_option">\n             <param name="choice" type="select" label="Select your input option">\n                 <option value="single" selected="true">Single</option>\n+                <option value="interleaved">Interleaved-paired-end</option>\n                 <option value="paired">Paired-end</option>\n                 <option value="paired_collection">Paired-end collection</option>\n             </param>\n             <when value="single">\n-                <param name="single_files" argument="-r" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Single-end file(s)" help="FASTQ/FASTA/FASTQ.GZ files accepted" />\n+                <param name="single_files" argument="-r" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz,fastq.bz2" multiple="true" label="Single-end file(s)" help="Accepts fasta (.fasta, .fa) and fastq (.fastq) formats as well as gzip (.gz) and gzip2 (.bz2) files" />\n+            </when>\n+            <when value="interleaved">\n+                <param name="interleaved_file" argument="--12" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz,fastq.bz2" multiple="true" label="Interleaved-paired-end file(s)" help="Accepts fasta (.fasta, .fa) and fastq (.fastq) formats as well as gzip (.gz) and gzip2 (.bz2) files" />\n             </when>\n             <when value="paired">\n                 <param name="fastq_input1" argument="-1" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 1 input reads"/>\n@@ -72,14 +82,24 @@\n             </when>\n         </conditional>\n         <section name="basic_section" title="Basic assembly options" expanded="True">\n-            <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" />\n-            <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/>\n-            <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size" max="255" help="must be odd number"/>\n-            <param name="k_max" argument="--k-max" type="integer" value="141" label="maximum kmer size" max="255" help="must be odd number"/>\n-            <p'..b'of length " value="20,0.95" />\n             <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="3" label="strength of low depth pruning" />\n@@ -88,9 +108,17 @@\n             <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="disable local assembly" />\n             <param name="kmin1pass" type="boolean" checked="false" truevalue="--kmin-1pass" falsevalue="" label="use 1pass mode to build SdBG of k_min" />\n         </section>\n+        <section name="output_section" title="Output options" expanded="True">\n+            <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" />\n+            <param name="show_intermediate_contigs" type="boolean" checked="false" label="Return intermediate contigs?"/>\n+        </section>\n     </inputs>\n     <outputs>\n         <data format="fasta" name="output" from_work_dir="megahit_out/final.contigs.fa" label="Assembly with ${tool.name} on ${on_string}" />\n+        <collection name="intermediate_contigs" type="list" label="Intermediate contigs from ${tool.name} on ${on_string}">\n+            <filter>output_section[\'show_intermediate_contigs\']</filter>\n+            <discover_datasets pattern="(?P&lt;designation&gt;.*\\d)\\.contigs\\.fa$" ext="fasta" directory="megahit_out/intermediate_contigs" />\n+        </collection>\n     </outputs>\n     <tests>\n         <test>\n@@ -105,6 +133,13 @@\n             </output>\n         </test>\n         <test>\n+             <conditional name="input_option">\n+                <param name="choice" value="interleaved"/>\n+                <param name="interleaved_file" value="interleaved-fq.fa"/>\n+            </conditional>\n+            <output name="output" file="interleaved_result.fa"/>\n+        </test>\n+        <test>\n             <conditional name="input_option">\n                 <param name="choice" value="paired"/>\n                 <param name="fastq_input1" value="paired-fq1.fa"/>\n@@ -113,23 +148,23 @@\n             <output name="output" file="paired_result.fa"/>\n         </test>\n         <test>\n-          <conditional name="input_option">\n-            <param name="choice" value="paired_collection"/>\n-            <conditional name="batchmode">\n-              <param name="processmode" value="merge"/>\n-              <param name="pair_input_list">\n-                <collection type="list:paired">\n-                <element name="Pair1">\n-                  <collection type="paired">\n-                    <element name="forward" value="paired-fq1.fa" ftype="fasta"/>\n-                    <element name="reverse" value="paired-fq2.fa" ftype="fasta"/>\n-                  </collection>\n-                </element>\n-                </collection>\n-              </param>\n+            <conditional name="input_option">\n+                <param name="choice" value="paired_collection"/>\n+                <conditional name="batchmode">\n+                    <param name="processmode" value="merge"/>\n+                    <param name="pair_input_list">\n+                        <collection type="list:paired">\n+                        <element name="Pair1">\n+                          <collection type="paired">\n+                            <element name="forward" value="paired-fq1.fa" ftype="fasta"/>\n+                            <element name="reverse" value="paired-fq2.fa" ftype="fasta"/>\n+                          </collection>\n+                        </element>\n+                        </collection>\n+                    </param>\n+                </conditional>\n             </conditional>\n-          </conditional>\n-          <output name="output" file="paired_result.fa"/>\n+            <output name="output" file="paired_result.fa"/>\n         </test>\n     </tests>\n     <help><![CDATA[\n@@ -149,4 +184,4 @@\n     <citations>\n         <citation type="doi">10.1093/bioinformatics/btv033</citation>\n     </citations>\n-</tool>\n+</tool>\n\\ No newline at end of file\n'
b
diff -r 98242353faa4 -r de387b2b2803 test-data/interleaved-fq.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/interleaved-fq.fa Mon Feb 18 12:14:46 2019 -0500
b
b'@@ -0,0 +1,400 @@\n+>megahit_ref_example_454_1062_2:0:0_1:0:0_c8/1\n+GTCCGTCCAAATCTCGCAACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTAT\n+>megahit_ref_example_454_1062_2:0:0_1:0:0_c8/2\n+CCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTAAGCCAATATCAGCGATGCCGAACGTATTTTTGCCG\n+>megahit_ref_example_183_711_2:0:0_2:0:0_c9/1\n+AACATCCATGAAACGCATTAGCACCACCATTACGACCACCAACACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCC\n+>megahit_ref_example_183_711_2:0:0_2:0:0_c9/2\n+ACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCGAACAAACTAATGGCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATCGACGAAA\n+>megahit_ref_example_447_926_3:0:0_0:0:0_ca/1\n+CTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCTGCCAGGATGCTTTACCCAATATCATCGATGCGGAACGTATT\n+>megahit_ref_example_447_926_3:0:0_0:0:0_ca/2\n+GCCACTGATGTACCGCCGGTGAAACCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGG\n+>megahit_ref_example_35_557_3:0:0_4:0:0_cb/1\n+TCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTTGTAACCAGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTT\n+>megahit_ref_example_35_557_3:0:0_4:0:0_cb/2\n+AGTTCGGCAAAAATACGTTCGGCATCGCAGATATTGGGTAACGCATGCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGTGGTAGGTGATTTTGG\n+>megahit_ref_example_423_941_6:0:0_1:0:0_cc/1\n+GCAGGGGCAGGAGGCGAGCGTCCTCTCTGCCCCCGCCAAAATCACCAAGCACCTGGTTGCGATGATTGAAAAACCCATTAGCGGCCAGGATGCTTTACCC\n+>megahit_ref_example_423_941_6:0:0_1:0:0_cc/2\n+AAACGTTCTGCATTTGCCACTGATGTACCGCCGGTGAAAGCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACT\n+>megahit_ref_example_683_1208_1:0:0_1:0:0_cd/1\n+TGGAACTGGGCGATGGGGGTAATGGTGCGGGGGTGAAGAACATTAGCGCCGAAGTAGGAAAGCTCCATCGCTTCCTGGTAGGACATCGACTTCAACAACC\n+>megahit_ref_example_683_1208_1:0:0_1:0:0_cd/2\n+ATAGCCTCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGA\n+>megahit_ref_example_102_568_2:0:0_1:0:0_ce/1\n+GTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCAAATGGTTTTTTCAATCATCGCCACCAGGTGGTT\n+>megahit_ref_example_102_568_2:0:0_1:0:0_ce/2\n+AAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGCGTACACAACATCCATGACACGCATT\n+>megahit_ref_example_435_844_3:0:0_2:0:0_cf/1\n+ACTCAGCAATCTCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATACCAGTAACGTTGTGACCGCGCGCTTCTAATAC\n+>megahit_ref_example_435_844_3:0:0_2:0:0_cf/2\n+GGCCACCGTCCTCTCTGCCCCCGCCACAATCACCACCCACCTGGTGGCGATGATTGCAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGAT\n+>megahit_ref_example_551_990_1:0:0_2:0:0_d0/1\n+CCGAACTTTTGAGGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCT\n+>megahit_ref_example_551_990_1:0:0_2:0:0_d0/2\n+GCGTCCAAGCACCACCAGTTCGCCTTTTTCATTACCGGCAACACGCCGAAAACGTTCTGCATTTGCCACTGATGTCCCGCCGGTGAAACCTGCCATCAGC\n+>megahit_ref_example_446_903_2:0:0_2:0:0_d1/1\n+ACCTGCCATCAGCACCATGTGATCAGCCGGAAAGCGGCTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTACTGCCCCACT\n+>megahit_ref_example_446_903_2:0:0_2:0:0_d1/2\n+TCTCTGCCCCCGCCAAAATCACCAACCACCAGGTGGCGATGATTGAACAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTAT\n+>megahit_ref_example_274_766_8:0:0_1:0:0_d2/1\n+TGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCCA\n+>megahit_ref_example_274_766_8:0:0_1:0:0_d2/2\n+AAAAAATCCCGCACCTTACAGTGCGGGCTTTTTTTTTCGACCAACGGTAACGCGGAAACAAGCAAGCGAGTTTTGAAGTTCGGCGGTACATCAGTGGCAA\n+>megahit_ref_example_302_779_3:0:0_4:0:0_d3/1\n+TATTTTTTTCGACCAAAGGTAACGAGGTAAGAACCATGCGAGTGTTGAAGTTCGGCGGTACCTCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGA\n+>megahit_ref_example_302_779_3:0:0_4:0:0_d3/2\n+ATAACCGTACCGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGATCGACATTTTCTCGGCACGGCAAATCAGCGCAGCGTTGATTCTATCCG\n+>megahit_ref_example_664_1070_2:0:0_5:0:0_d4/1\n+CCGTCACCGTCCGTCCAAATCTCGCAACAAACGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCTTTGCGTCCAAGGACCCCCAGTT\n+>megahit_ref_example_664_1070_2:0:0_5:0:0_d4/2\n+TTGTTGGGGCAGTTCCCGGATAGCATCAACGCTGCGCTGATTTTCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTC\n+>megahit_ref_example_190_676_5:0:0_0:0:0_d5/1\n+ATGAAACGCATTAGCACCACCATAACCCCCACCAACACGATTACCAGAGGTAACG'..b'AATTTGCCCAAATAAAACATGTCCTGCATGGCATAAGATTGTTGGGGCAGTGCCCGGATAGCAT\n+>megahit_ref_example_175_730_3:0:0_2:0:0_11f/1\n+GAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCAGCATTACGACAGGTAACGGTGCGGGCTGACGCTTACAGGAAACACAGA\n+>megahit_ref_example_175_730_3:0:0_2:0:0_11f/2\n+CGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCGGGGCACTGCCCCAACAAACTAATTCCATGCAGGACATGTTTTATTTGGGC\n+>megahit_ref_example_694_1127_1:0:0_1:0:0_120/1\n+GCTGCGCTTATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAA\n+>megahit_ref_example_694_1127_1:0:0_1:0:0_120/2\n+GACATCGACTTCAACAACCTCGCATCGGGCACCTGACGCGGGTCGCAGGTATAGACCCGGTCAACGTCCGTCCAAATCTCGCAACAATCGGCGCGTAAAC\n+>megahit_ref_example_539_991_1:0:0_3:0:0_121/1\n+TGCGTCCAAGCACCACCAGTTCGCCTTTTTCATTACCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATTTACCGCCGGATAAACCTGCCATCAG\n+>megahit_ref_example_539_991_1:0:0_3:0:0_121/2\n+AACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGTGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAAT\n+>megahit_ref_example_689_1161_1:0:0_0:0:0_122/1\n+GCCGAAGTAGGAAAGCTCCATCGCTTCCTGGTAGGACATCGACTTCAACAACCTCGCATCGGGCACCTGACGCGGGTCGCAGGTATAGACCCCGTCAACG\n+>megahit_ref_example_689_1161_1:0:0_0:0:0_122/2\n+TCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTAGTGTTATCGATCCGGT\n+>megahit_ref_example_371_878_3:0:0_1:0:0_123/1\n+CAAATGCAGAACTTTTTCAGCGTGTTGCCGATATACTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAA\n+>megahit_ref_example_371_878_3:0:0_1:0:0_123/2\n+GCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGCAGTATTTCGACCGGATCGA\n+>megahit_ref_example_407_902_2:0:0_2:0:0_124/1\n+CCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGGTCGATTCGATGTAATGCCCCACTG\n+>megahit_ref_example_407_902_2:0:0_2:0:0_124/2\n+TGGAAAGCAATTCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACGAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGG\n+>megahit_ref_example_496_1063_2:0:0_1:0:0_125/1\n+ACCATTAGCGGCCAGGATGCTTTACCCCATATCAGCGATGCCGAACGAATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGC\n+>megahit_ref_example_496_1063_2:0:0_1:0:0_125/2\n+CGTCCGTCCAAATCTCGCAACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGAAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTT\n+>megahit_ref_example_529_1002_0:0:0_1:0:0_126/1\n+GTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTTTTCATTACCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACGGCCGGTGAAA\n+>megahit_ref_example_529_1002_0:0:0_1:0:0_126/2\n+AGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAAT\n+>megahit_ref_example_486_996_1:0:0_5:0:0_127/1\n+ACCGTTGCGTCCAAGCAGCACCAGTTCGCCTTTTTCATAACCGGCAACACGCAGAAAACTTTCTGCATTTGCGACTGATTTACCGCCGGTGAAACCTGCC\n+>megahit_ref_example_486_996_1:0:0_5:0:0_127/2\n+GATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGAATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCG\n+>megahit_ref_example_200_640_1:0:0_0:0:0_128/1\n+TTATTTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACG\n+>megahit_ref_example_200_640_1:0:0_0:0:0_128/2\n+TTAGCCCCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGG\n+>megahit_ref_example_370_888_2:0:0_2:0:0_129/1\n+GGAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGGAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCA\n+>megahit_ref_example_370_888_2:0:0_2:0:0_129/2\n+CATGTGATCATCCGGAATGCGGCTTGCCGCAATACGGGGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCG\n+>megahit_ref_example_335_841_1:0:0_2:0:0_12a/1\n+CCATGCGATTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGT\n+>megahit_ref_example_335_841_1:0:0_2:0:0_12a/2\n+CAGCAATATCGACGGTAGATTGGAGGTAATGCCGCACTGCCAGCAGTTTTTCGACCGGATCGATAACAGTAACGTTGTGACCGCGCGCTTCTAATACGCC\n+>megahit_ref_example_42_498_1:0:0_2:0:0_12b/1\n+GGTTTTTTCAATCATCGCCACCAGGTGGTTGGTGATTTTGGGGGGGGCAGAGATGACGGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATATCG\n+>megahit_ref_example_42_498_1:0:0_2:0:0_12b/2\n+GGATTAAAAAAAGAGTGTCTGAAAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAAT\n\\ No newline at end of file\n'
b
diff -r 98242353faa4 -r de387b2b2803 test-data/interleaved_result.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/interleaved_result.fa Mon Feb 18 12:14:46 2019 -0500
b
@@ -0,0 +1,2 @@
+>k59_1 flag=1 multi=8.7336 len=1215
+TGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCCCTTCGCCCAGTTCCAGATCCCTTGCCTGATTAAA
b
diff -r 98242353faa4 -r de387b2b2803 test-data/paired_result.fa
--- a/test-data/paired_result.fa Mon May 14 06:11:34 2018 -0400
+++ b/test-data/paired_result.fa Mon Feb 18 12:14:46 2019 -0500
b
@@ -1,2 +1,2 @@
->k141_1 flag=1 multi=107.0000 len=390
+>k141_1 flag=1 multi=106.0000 len=390
 CATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCAAGTGTAGTGCTCGGGGGGG