Galaxy |

Changeset 1:4deefd708943 (2021-05-06)

Previous changeset 0:e3698ac146d7 (2017-10-03) Next changeset 2:1b88c1cf803d (2024-10-05)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"

modified:
bio_hansel.xml

added:
macros.xml
test-data/SRR1002850_SMALL.fasta.gz
test-data/SRR5646583_SMALL_1.fastq.gz
test-data/SRR5646583_SMALL_2.fastq.gz
test-data/match_results1.tab
test-data/match_results2.tab
test-data/results1.tab
test-data/results2.tab

removed:
test-data/SRR1002850_SMALL.fasta
test-data/SRR5646583_SMALL_1.fastq
test-data/SRR5646583_SMALL_2.fastq

diff -r e3698ac146d7 -r 4deefd708943 bio_hansel.xml
--- a/bio_hansel.xml Tue Oct 03 10:39:11 2017 -0400
+++ b/bio_hansel.xml Thu May 06 18:31:35 2021 +0000

[

b'@@ -1,47 +1,51 @@\n-<tool id="bio_hansel" name="Salmonella Subtyping" version="0.1.0">\n- <requirements>\n- <requirement type="package" version="0.1.0">bio_hansel</requirement>\n- <requirement type="package" version="17.2.0">attrs</requirement>\n- </requirements>\n+<tool id="bio_hansel" name="Salmonella Subtyping" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n <command detect_errors="exit_code"><![CDATA[\n- ## Preparing file input.\n #if $data_type.type == "paired":\n-\n- ln -s \'$data_type.fastq_input1\' fast_q_paired_1.fastq &&\n- ln -s \'$data_type.fastq_input2\' fast_q_paired_2.fastq &&\n-\n+ #if $data_type.fastq_input1.ext.endswith(\'.gz\'):\n+ gunzip -c \'$data_type.fastq_input1\' > fast_q_paired_1.fastq &&\n+ gunzip -c \'$data_type.fastq_input2\' > fast_q_paired_2.fastq &&\n+ #else:\n+ ln -s \'$data_type.fastq_input1\' fast_q_paired_1.fastq &&\n+ ln -s \'$data_type.fastq_input2\' fast_q_paired_2.fastq &&\n+ #end if\n #elif $data_type.type == "collection":\n-\n- ln -s \'$data_type.fastq_input1.forward\' fast_q_paired_1.fastq &&\n- ln -s \'$data_type.fastq_input1.reverse\' fast_q_paired_2.fastq &&\n-\n- #elif $data_type.type == "single":\n-\n- #if $data_type.fastq_input1.is_of_type(\'fastqsanger\') or $data_type.fastq_input1.is_of_type(\'fastq\'):\n- ln -s \'$data_type.fastq_input1\' fast_q_single.fastq &&\n+ #if $data_type.fastq_input1.forward.ext.endswith(\'.gz\'):\n+ gunzip -c \'$data_type.fastq_input1.forward\' > fast_q_paired_1.fastq &&\n+ gunzip -c \'$data_type.fastq_input2.reverse\' > fast_q_paired_2.fastq &&\n+ #else:\n+ ln -s \'$data_type.fastq_input1.forward\' fast_q_paired_1.fastq &&\n+ ln -s \'$data_type.fastq_input1.reverse\' fast_q_paired_2.fastq &&\n #end if\n-\n- #if $data_type.fastq_input1.is_of_type(\'fasta\'):\n- ln -s \'$data_type.fastq_input1\' fast_a_single.fasta &&\n- #end if\n-\n- #end if\n-\n-\n- ## Checking for custom scheme.\n- #if $type_of_scheme.scheme_type == "custom":\n- #if $type_of_scheme.scheme_input.is_of_type(\'fasta\'):\n- ln -s \'$type_of_scheme.scheme_input\' custom_scheme.fasta &&\n+ #elif $data_type.type == "single":\n+ #if $data_type.fastq_input1.ext.startswith("fastq"):\n+ #if $data_type.fastq_input1.ext.endswith(\'.gz\'):\n+ gunzip -c \'$data_type.fastq_input1\' > fast_q_single.fastq &&\n+ #else:\n+ ln -s \'$data_type.fastq_input1\' fast_q_single.fastq &&\n+ #end if\n+ #elif $data_type.fastq_input1.ext.startswith(\'fasta\'):\n+ #if $data_type.fastq_input1.ext.endswith(\'.gz\'):\n+ gunzip -c \'$data_type.fastq_input1\' > fast_a_single.fasta &&\n+ #else:\n+ ln -s \'$data_type.fastq_input1\' fast_a_single.fasta &&\n+ #end if\n #end if\n #end if\n-\n- ## Start the actual command here\n+ #if $type_of_scheme.scheme_type == "custom":\n+ #if $type_of_scheme.scheme_input.ext.startswith(\'fasta\'):\n+ #if $type_of_scheme.scheme_input.ext.endswith(\'.gz\'):\n+ gunzip -c \'$type_of_scheme.scheme_input\' > custom_scheme.fasta &&\n+ #else:\n+ ln -s \'$type_of_scheme.scheme_input\' custom_scheme.fasta &&\n+ #end if\n+ #end if\n+ #end if\n hansel \n-\n-\n- ## Select the scheme\n -s\n-\n #if $type_of_scheme.scheme_type == "heidelberg":\n heidelberg\n #elif $type_of_scheme.scheme_type == "enteritidis":\n@@ -49,36 +53,21 @@\n #elif $type_of_scheme.schem'..b'work_dir="results.tab" label="${tool.name} on ${on_string}: results.tab"/>\n+ <data format="tabular" name="match_results" from_work_dir="match_results.tab" label="${tool.name} on ${on_string}: match_results.tab"/>\n </outputs>\n <tests>\n <test>\n <param name="type" value="single"/>\n <param name="type_of_scheme" value="heidelberg"/>\n- <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/>\n- <output name="results.tab">\n- <assert_contents>\n- \n- <has_text_matching expression="sample\\s+scheme\\s+subtype\\s+all_subtypes\\s+tiles_matching_subtype\\s+are_subtypes_consistent\\s+inconsistent_subtypes\\s+n_tiles_matching_all\\s+n_tiles_matching_all_total\\s+n_tiles_matching_positive\\s+n_tiles_matching_positive_total\\s+n_tiles_matching_subtype\\s+n_tiles_matching_subtype_total\\s+file_path"/>\n- \n- <has_text_matching expression="(heidelberg)\\s+(2.2.2.2.1.4)\\s+(2;)\\s+(2.2;)\\s+(2.2.2;)\\s+(2.2.2.2;)\\s+(2.2.2.2.1;)\\s+(2.2.2.2.1.4)\\s+(1037658-2.2.2.2.1.4;)\\s+(2154958-2.2.2.2.1.4;)\\s+(3785187-2.2.2.2.1.4)\\s+(True)\\s+(202)\\s+(202)\\s+(17)\\s+(17)\\s+(3)\\s+(3)"/>\n- </assert_contents>\n- </output>\n- <output name="match_results.tab">\n- <assert_contents>\n- \n- <has_text_matching expression="negative4738855-1.1"/>\n- </assert_contents>\n- </output>\n+ <param name="fastq_input1" ftype="fasta.gz" value="SRR1002850_SMALL.fasta.gz"/>\n+ <output name="results" ftype="tabular" file="results1.tab" compare="contains"/>\n+ <output name="match_results" ftype="tabular" file="match_results1.tab" compare="contains"/>\n </test>\n <test>\n <param name="type" value="paired"/>\n <param name="type_of_scheme" value="heidelberg"/>\n- <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/>\n- <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/>\n- <output name="results.tab">\n- <assert_contents>\n- \n- <has_text_matching expression="sample\\s+scheme\\s+subtype\\s+all_subtypes\\s+tiles_matching_subtype\\s+are_subtypes_consistent\\s+inconsistent_subtypes\\s+n_tiles_matching_all\\s+n_tiles_matching_all_total\\s+n_tiles_matching_positive\\s+n_tiles_matching_positive_total\\s+n_tiles_matching_subtype\\s+n_tiles_matching_subtype_total\\s+file_path"/>\n- \n- <has_text_matching expression="(heidelberg)\\s+(2.2.1.1.1.1)\\s+(2;)\\s+(2.2;)\\s+(2.2.1;)\\s+(2.2.1.1;)\\s+(2.2.1.1.1;)\\s+(2.2.1.1.1.1)\\s+(1983064-2.2.1.1.1.1;)\\s+(4211912-2.2.1.1.1.1)\\s+(True)\\s+(202)\\s+(202)\\s+(20)\\s+(20)\\s+(2)\\s+(2)"/>\n- </assert_contents>\n- </output>\n+ <param name="fastq_input1" ftype="fastq.gz" value="SRR5646583_SMALL_1.fastq.gz"/>\n+ <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq.gz"/>\n+ <output name="results" ftype="tabular" file="results2.tab" compare="contains"/>\n+ <output name="match_results" ftype="tabular" file="match_results2.tab" compare="contains"/>\n </test>\n </tests>\n <help><![CDATA[\n@@ -264,4 +235,4 @@\n }\n }</citation>\n </citations>\n-</tool>\n\\ No newline at end of file\n+</tool>\n'

diff -r e3698ac146d7 -r 4deefd708943 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu May 06 18:31:35 2021 +0000

@@ -0,0 +1,9 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.6.1</token>
+    <token name="@PROFILE@">20.01</token>
+    <xml name="requirements">
+    <requirements>
+        <requirement type="package" version="2.6.1">bio_hansel</requirement>
+    </requirements>
+    </xml>
+</macros>

diff -r e3698ac146d7 -r 4deefd708943 test-data/SRR1002850_SMALL.fasta
--- a/test-data/SRR1002850_SMALL.fasta Tue Oct 03 10:39:11 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,766 +0,0 @@\n->NODE_384_length_56_cov_34125_ID_767\n-CTAGCCTGATTCAGTTTTATCTTTCGTCGGTGAGCGACGGTACTTTCTGACCTCGG\n->NODE_383_length_56_cov_335_ID_765\n-CAATTGTGATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGCCCCGAAAA\n->NODE_382_length_56_cov_201_ID_763\n-CCGTCGCTCACCGACGAAAGATAAAACGGAATCAGGCTAGCGGGGTGTCGGGGTGC\n->NODE_377_length_57_cov_34097.5_ID_753\n-AAACCGAGGTCAGAAAGTACCGTCGCTCACCGACGAAAGATAAAACTGAATCAGGCT\n->NODE_376_length_57_cov_200_ID_751\n-GAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTAGTGCCGCCAGGCAAATTCTTT\n->NODE_375_length_58_cov_19568.3_ID_749\n-TAATACCGTCACACGCGACGCTATCACAATTGCCATCTGGTCAGGGGTGCACCCCGAC\n->NODE_374_length_58_cov_29262.3_ID_747\n-GCACCCCGACACCCCGCTAGCCTGATTCAGTTTTATCTTTCGTCGGTGAGCGACGGTA\n->NODE_372_length_59_cov_291.25_ID_743\n-TAGCCTGATTCAGTTTTATCTTTCGTCGGTGAGCGACGGGACTTTCTGACCTCGGTTTT\n->NODE_369_length_60_cov_34761.2_ID_737\n-GCGGTGGCCGAAACCCTGAAATATTCCACGAAGCCGGCTGACATGGTGGCCGATCCTGAA\n->NODE_367_length_60_cov_167.2_ID_733\n-CCGAGGGCGACGATGACGGTTCACGAATCGCGTTCGAGTGGAAACCCGAGGTCAGAAAGT\n->NODE_365_length_61_cov_228.5_ID_729\n-TCGCGTTCGAGTGGAAAACCGAGGTCAGAAAGTCCCGTCGCTCACCGACGAAAGATAAAAC\n->NODE_360_length_62_cov_66.7143_ID_719\n-CAGGGGTGCACCCCGACACCCCGCTAGCCTGATTCAGTTTTATCTTTCGTCGGTGGGCGACG\n->NODE_357_length_63_cov_202.375_ID_713\n-GGGGTGTGGGGGTGCACCCCTGACCAGATGGCAATTGTGATAGCGTCGCGTGTGACGGTATTA\n->NODE_356_length_63_cov_142.75_ID_711\n-TGTAATTGTAATAACGTCACACGCGACGCTATCACAATTGCCATCTGGTCAGGGGGGCACCCC\n->NODE_355_length_64_cov_127.667_ID_709\n-CGTCGCTCCCCGACGAAAGATAAAACTGAATCAGGCTAGCGGGGTGTCGGGGTGCCCCCCTGAC\n->NODE_352_length_64_cov_30.6667_ID_703\n-CGTCGCTCCCCGACGAAAGATAAAACTGAATCAGGCTAGGGGGGTGTCGGGGTGCACCCCTGAC\n->NODE_351_length_64_cov_104.444_ID_701\n-ATGATATTTCCGAGGGCGACGATGACGGTTCACGAATCGCGTTCGAGTGGAAACCCGAGGTCAG\n->NODE_349_length_64_cov_29.3333_ID_697\n-GTCAGGGGGGCACCCCGACACCCCCCTAGCCTGATTCAGTTTTATCTTTCGTCGGGGAGCGACG\n->NODE_347_length_64_cov_32_ID_693\n-GTCAGGGGGGCACCCCGACACCCCGCTAGCCTGATTCAGTTTTTTCTTTCGTCGGGGAGCGACG\n->NODE_346_length_65_cov_38729.2_ID_691\n-CTGACCTCGGTTTTCCACTCGAACGCGATTCGTGAACCGTCATCGTCGCCCTCGGAAATATCATC\n->NODE_342_length_66_cov_28.1818_ID_683\n-CTGACCTCGGGTTTCCACTCGAACGCGATTCGTGAACCGTCATCGTCGCCCTCGGGAATATCATCA\n->NODE_340_length_67_cov_71.3333_ID_679\n-CCGACGAAAGATAAAACTGAATCAGGCTAGGGGGGTGTCGGGGTGCCCCCCTGACCAGATGGCAATT\n->NODE_336_length_67_cov_56_ID_671\n-CTTGAATATGGCGGTGAGGGGGGGATTGACTCGCTTTGCTCGCCCCTTCGGGGCAGCCCGTTCGCTG\n->NODE_335_length_68_cov_32300.2_ID_669\n-CCCCGACACCCCGCTAGCCTGATTCAGTTTTATCTTTCGTCGGTGAGCGACGGTACTTTCTGACCTCG\n->NODE_333_length_69_cov_126.429_ID_665\n-GGTGTCGGGGTGCCCCCCTGACCAGAGGGCAATTGTGATAGCGTCGCGTGTGACGGTATTACAATTACA\n->NODE_332_length_69_cov_101.286_ID_663\n-GGTGTCGGGGTGCCCCCCTGACCAGATGGCATTTGTGATAGCGTCGCGTGTGACGGTATTACAATTACA\n->NODE_327_length_71_cov_31.375_ID_653\n-GCACCCCGACACCCCCCTAGCCTGATTCAGTTTTATCTTTCGTCGGGGAGCGACGGTACTTTCTGACCTCG\n->NODE_326_length_71_cov_108.125_ID_651\n-CCGAGGTCAGAAAGTCCCGTCGCTCCCCGACGAAAGATAAAACTGAATCAGGCTAGCGGGGTGTCGGGGTG\n->NODE_324_length_71_cov_35.75_ID_647\n-TGTAATTGTAATACCCTCACACGCGACGCTATCACAATTGCCATCTGGTCAGGGGGGCACCCCGACACCCC\n->NODE_318_length_74_cov_355.895_ID_635\n-GTAGGCGTTATTGGCGCAGCCAGTTTGGACACGGACAGCGCGCAAAAACCGGAGCGTACACGTAGTACGTGAGG\n->NODE_316_length_76_cov_59.5714_ID_631\n-CGTCGCTCACCGACGAAAGAAAAAACTGAATCAGGCTAGGGGGGTGTCGGGGTGCACCCCTGACCAGATGGCAATT\n->NODE_315_length_76_cov_76.8571_ID_629\n-CGTCGCTCACCGACGAAAGATAAAACTGAATCAGGCTAGCGGGGTGTGGGGGTGCACCCCTGACCAGATGGCAATT\n->NODE_314_length_76_cov_172.333_ID_627\n-AATTGCCATCTGGTCAGGGGTGCACCCCGACACCCCGCTAGCCTGATTCCGTTTTATCTTTCGTCGGTGAGCGACG\n->NODE_313_length_76_cov_35231.5_ID_625\n-AAACGGCAAAATGATTTACTCGCCGTTTGTGTGGGTTGTTTTGTGGGGTGTCAATGGGGTTGTGGTCTTTTTTGTG\n->NODE_312_length_76_cov_28.9048_ID_623\n-CGTCGCTCACCGACGAAAGAAAAAACTGAATCAGGCTAGGGGGGTGTCGGGGTGCCCCCCTGACCAGATGGCAATT\n->NODE_310_length_79_cov_105.5_ID_619\n-CTCAAAAAACCGAGAAACGGCGGGGATTTTCGGGACAGGATGTGTAATTGTAATAACGTCACACGCGACGCTATCACAA\n->NODE_306_length_82_cov_64.2963_ID_611\n-TATCACAATTGCCATCTGGTCAGGGGGGCACCCCGACACCCCGCTAGCCTGATTCCGTTTTATCTTTCGTCGGTGAGCGACG\n->NODE_294_length'..b'GGATGGCCGCGTCTTTGAAGCGCTACTGGTTGGCTCCGATTCGCTTACCGATCTGGCGGTGCTGAAGATCAACGCCACTGGCGGGCTGCCTACCATCCCGATTAATACAAAGCGTACACCGCATATTGGCGACGTCGTACTGGCTATCGGCAACCCATATAATCTGGGACAGACCATTACCCAGGGGATCATCAGCGCAACGGGTCGTATCGGCCTGAACCCGACGGGGCGACAGAATTTTCTCCAGACCGACGCCTCGATTAACCACGGTAATTCCGGCGGCGCGCTGGTCAACTCGTTAGGCGAACTGATGGGGATCAACACCCTCTCTTTTGATAAGAGTAACGATGGTGAAACGCCGGAAGGCCTTGGTTTTGCGATTCCCTTCCAGCTAGCCACGAAAATTATGGATAAGCTTATCCGCGACGGTCGTGTGATTCGCGGCTATATCGGTATTGGCGGACGAGAAATCGCGCCGCTGCACGCGCAGCAGGGTAGCGGCATGGACCCGATTCAGGGCATTGTCGTTAATGAAGTGACGCCAAACGGCCCCGCCGCGCTTGCCGGTATTCAGGTTAATGATTTGATTATTTCGGTCAATAATAAACCCGCCGTGTCCGCGCTGGAGACAATGGATCAGGTGGCGGAAATCCGCCCGGGCTCCGTCATTCCGGTCGTGGTAATGCGGGATGATAAGCAACTCACGTTCCAGGTGACGGTGCAGGAATACCCGGCGTCGAACTAAAACGACGCGGCTTTTGCCTGCGTCGTTCGACGGCTAGTCAATAAAGACTGGCCCTGCCGGAAAATGCGCCAGGAAACTCGTGAAGATCAGCAGAGCGGGGAGACTTTTCTCCCCGACGGCTTCTTCACGCAGCGCCTTATCCAGTGCAAGCAGGCTGTGCTCCCCCCCTTCCCCCAAAATGCCGCCCATCCAGAGCAGTCGTTGCGCCTGTTGACGCGCATACTGCGATGCGCTTTTCCAGGCGACCAGATGCAGCAACGTTTGTAACAGCAGGACCCGAGACGCGTGACCATCGCGTTGCAATCGCCTGAATACGGGTAATGCAATACTACGTACCGTCGAGAAACCGCTCGCCGCCTCCCCCTCAATCGGCGATAAACCAACAGCCGCCTGTTTGACGAAATCGCATAACTGATTGTGTGTTAATGGCCGCTCGCCTGCGCTCATATACCCTGCGGCAAAACAGAGTAACCCGATACCCTGAGCCCAATCGGTCGATGGCAGAATCCCCTGCGGAACATTCGGTGCCGACGTCTGTGCGGCACAAAGCCCCTCGTCGTAACACTGTGCAAAACGTTGCTCATATATTGCTGAGTTGATGCCAGACCACGGCAGTAAATGCAGCGCTGGCTCAAGCTCAGTTATCTGATTCACCGTCTCAACAACATAACGCAAGATGGTTTCTCTGGATGGCATGGATGTACCTTGCCGAAACGCAACCATTTCACTCATTACTGTGTCCTCATTTTGCGGGAGCAGAATCACTGCTCCCGATTAGATTGGATTACATTGCCAGCACGTACTTCAGCATCACGCCCGCCGCAATGGCCGAACCGATAACCCCCGCCACGTTCGGGCCCATCGCGTGCATCAGCAGGAAGTTCTGCGGGTCCGACTCCAGGCCCACCTTGTTCGATACGCGGGCCGCCATCGGCACCGCCGACACCCCCGCCGAACCGATAAGCGGGTTGATTTTGTTCTTACTGCACAGGTTCAGCAGCTTCGCCATCAGCACCCCGGCGGCAGTCCCGATACCAAAGGCAATCACACCCAGCAGCAGAATGCCCAGCGTCTGCGGCTGCAGGAACTTGTCCGCCACCAGCTTCGCCCCTACCGACAGCCCGAGGAAAATGGTGACGATGTTGATCAGCCCGTTCTGCACTGTGTCGCTCAGGCGCTCCACCACGCCGCTTTCACGCATCAGATTGCCGAAGCAGAACATCCCCAGCAGCGGCGCGGCGTCCGGCAGCAGCAGCGCCACCAGTAGTAACAGCACTACCGGGAAGAGGATTTTTTCCCGCTTACTCACCGTGCGCAGCTGCACCATGCGGATTTTCCGCTCCGTCTCCGTGGTCAGCGCGCGCATAATCGGCGGCTGGATTAACGGCACCAGCGCCATATACGAGTACGCCGCCACCGCGATGGCCCCCAGCAGCTCCGGCGCCAGTTTGCCCGACAGATAAATGGCCGTCGGACCGTCCGCGCCGCCGATGATGCCTATCGCCGCCGCCTGCGGCAGGGTGAAGGAAATCAGGCCGAAGTAATTCAGCGTCAGCGCCCCCAGCACCGTGGCGAAGATGCCGAACTGCGCCGCCGCGCCGAGCAGCAGGGTACGCGGGTTGGCCAGCAGCGGGCCGAAGTCGGTCATCGCGCCGACGCCCATAAAGATGACCAGCGGCGCGACGCCGGAGCCAATCGCCACTTTATAGAACAGCGCCAGCACCCCCGGCGTGTAGCCCATGTCCACCGCCAGGTTCTCCATCTGGCTCTGAACGGAGGGCAGCGCCAGCGCTAACGCCTCCTTGATGGCGTGCACGTCCGGCGCGCAGTTAAGCTTCGCGGCAATCACCGCCAGCTGCCCGGCGTCGTGGTGCGCCAGCAGGCTTTCCAGCGCGGTCAGCGCCATGCCCGCTTCCGGGATGTTGGAGAGCAGGCCGCCGAAGCCAATCGGCAACAGCAACAACGGCTCGAACTTTTTCGCAATCGCCAGCCACAGCAGCAGCAGGCTGACCAGCAGCATGATGGCCTGGCCTGCGCCAAGGTGCATCAGCCCCATGCCCTGAAGCAGGGCGTTCAGACTTTCCATTCGTCCTCTCCGTTACGCAAGCTGCATCAGGGTGTCGCCCACCGCCACCGCATCCCCGGCTTTCACCGCGATGCCGCGTACCGTCCCGGCCTGCGCGGCGCGGATTTCGGTTTCCATTTTCATGGCTTCCAGAATCAGCAGCACATCGCCTTCGGCCACCGTCTGGCCTTCCGTCGCCACCACTTTCCAGATATTGCCCGCCAGCGGCGCGCTGACCGGGGTGCCCGCGCCCGCCGGGGCGGCGGCAGGCGCCGCGGTCTGAACCGGCGCAGAACTGGCCGTGGCCAGCTGGCTGATATCGCCGCCGTCGCTGACTTTCACCACAAAGGCTTTGCCTTCCACTTCGACGGTGTAGATACCGGAAGCGGCGGGTTTTGCGGCTTTTTCCTCTTTCACGGCAGGTTTCGCGGCTTCCGCCTGCGGCAGTGGCTCAAACGCCGCCGGGTTATGGCGGTTTTCGAGGAATTTCAGCCCGACCTGCGGGAACAGTGCCACGGTGAGGACGTCATCAATGGCGTTCTCTGCAAGCCGGATGCCTTTTTCTGCCGCCTGGCGTTTAATGTCCGCTTCCAGTTGCGCCAGTTCCGGTTTCAGTAAATCCGCCGGGCGGCAGGTGACGGCCTCTTCGCCGTCCAGCACTCTGGCCTGTAACGCCGCGTTGACCGGCGCTGGCGTGTGGCCGTATTCGCCCTTCAGTATCCCGGCGGTTTCTTTGGCGATGGTTT\n->NODE_216_length_189_cov_23403.1_ID_431\n-CCTGATTCAGTTTTATCTTTCGTCGGTGAGCGACGGTACTTTCTGACCTCGGTTTTTCACTCGAACGCGATTCGTGAACCGTCATCGTCGCCCTCGGAAATATCATCACCGATCACCATGTCGGCGTCAGTTTCCTGATCGAGTTTCAGCACGTCTTTGAGTGCGCCGCCGGTCGCCACAAAGCGGCGC\n->NODE_222_length_167_cov_18131.6_ID_443\n-CACTCAAAGACGTGCTGAAACTCGATCAGGAAACTGACGCCGACATGGTGATCGGTGATGATATTTCCGAGGGCGACGATGACGGTTCACGAATCGCGTTCGAGTGAAAAACCGAGGTCAGAAAGTACCGTCGCTCCCCGACGAAAGATAAAACTGAATCAGGCTAG\n'

diff -r e3698ac146d7 -r 4deefd708943 test-data/SRR1002850_SMALL.fasta.gz

Binary file test-data/SRR1002850_SMALL.fasta.gz has changed

diff -r e3698ac146d7 -r 4deefd708943 test-data/SRR5646583_SMALL_1.fastq
--- a/test-data/SRR5646583_SMALL_1.fastq Tue Oct 03 10:39:11 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,20000 +0,0 @@\n-@32927/1\n-GTGAGTAAGTTGCGCGATATTCTGCTGGATTCGGTAGTAACCAGCTCTATTGTTCTCTTACTGGTCGGCTGCTCAATGGGAATGTCATGGGCGATGACCAATGCCGATGTTCCTGAACTGATTAATGAAATGATTACCAGCGTGTCCGAAA\n-+\n-AAA?ADD5F5BFGGGCCFFGGGGHHGHHHGFFFHGHGHHGCHHHHFHGHHGHEGHFHHHHHFHHHG?AEGGGEHHFGFGHGHFHFFFHHHHHGGGCHHHFGHFHHGCGFFGFGHHHHHGHHHHHBGFHHHHHGFHHFFHGHFED<FFD?ED\n-@351952/1\n-GGATTACCAGGAAGTGCTGGAAGAGTTTAACGAACATCGTAATGAGCCTGTTGATACTAACGACTTTATTGAGGCGATTGAGCGAAGTAAACGTCGCTTCCATGTTGTTGAAAATGAACAGGAGCTACTGCAAATGCTCAATGCGCCA\n-+\n-CCCCCFFFBFCBFGFGFGGGGGHHHHHHHHHGGFGGGHGHHHDHHHHHHHHHHHGHHHHHHFFGGGHHHHGHFHGGGGHGHGHGGGGFGHHHGHHGGGGGGHHHHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHGHGGHHHHGGGGG\n-@37856/1\n-GCGCAGGAACGTATCGGCTTACCGTACCGGTACTGGCGAATGATGAGATGCAAATCGCGCCAGTCAAGTCCTCTTTTACCGTTACGCTGCAATCCGGCGATGCCGCCGCGCAGGTCCAGGTATCCTGTCTGCCGATTGTCCGTTATGCCAG\n-+\n-CCCCCCCCFFCBG5GGGGGGGGHGGHGGGGGGGHHHHGGGGHHGHHHHHHHHGHHHGGGGGGGHHHHHHHHHHHHHHHHHGGGGGGGGGGHHHHHGGGGGGGGHGGGGGGGGGGHHHHHGGHHHHHHHHHHHHGGGGGHHHGHHGHHHHHF\n-@844740/2\n-GATCATGATTAGTCGTGCTCAAAGCGGGCCCCCACTCTACAAGTTGCAAAATTTGTTACGGGTAACTGTTATCGGTAACATTGTCCAACCGCACCATTCACGACGCAATGACCATTCGTGCCAAAAGTGAATAAGTGTGAGCTACTTCAAA\n-+\n-BBBBBFFFFFFFGGFGGGGGGGGHGGGFGGGGGCFCGHHHCHHHHFFGHHFHFHHFFFHGGGEEHHHHHHHFHHGAHGHHGHFHHHHHHGGGGFFAGHFFFEGGGGCCFFFGHHHFHFFFGHHHHEHGHFFHFFF1GDFF<GHHEHFHEGG\n-@1034303/1\n-CCTGAATATTCATCATCAAACTACCGTCGCCGGAAAAACACAGCACCTTGTTGCCCGGATTCGCCAGCGCCGCGCCAATCGCCGCGGGCAGACCAAACCCCATGGTGCCCAGCCCGCCGGAAGTCAGCCACTGACGCGGACGGTTGAGCGG\n-+\n-CCCCCFFFFFFFGGGGGGGGGGHHHGGGGGGGGGGGHHGHHHHHHHHHHHHHHHHHGGGGGGGGGGGGGGGGGGGGGGHHGGGGGGGGGGGGHHHHGHGGGGHGHFGFHHHHHGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFF\n-@79331/2\n-CCCTGGTATTCGACGTAGAGCTGCTGGATATCAAACCAGCGCCGAAAGCGGATGCTAAACCTGCCGATGCGGCTGACGCTAAAGCCGCAGATGCTGCTAAAAAATAAAAACTGAGAGCCGCCGCTTGTAATAGCGGCGGTTTTTTTTTTTT\n-+\n-AAABCCFFFFFFGGGGGGGGGGHGHGGHGHHHHHHGGHHHGGGGGGGGHGGGGGGHHHHHFHHHHGGGGGGGGGGFHGGGGGHHHHGGGGGHHEGHHHHHHHHGHHHHHHGHHHHHHHHGGGGGGGGHHEHHHGGGGGG-;AEGGGAFF--\n-@234915/1\n-CACCTAATTTAACGGTCTGGTGACCAGAACCGACCGCACGCAAAAGCTTCTGAACCGATGAGGATGCTATGGGAAACACAACAATACAAACACAGAGTTTTCGTGCTGTGGATGCAGAGCAAAGCAAAAGCAAGCGCTACATTATTCCATT\n-+\n-DDCDCFFFFFFFGGGGGGGGGGHHHGHHHHHGGGGGGGGGGGGGHHHHHHHHHHHHGGGGHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHGHHHHHHHHHHHGHGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHFGGGGHHHHHHHHHHH\n-@238890/1\n-GTACTGGCGAATGATGAGATGCAAATCGCGCCAGTCAAGTCCTCTTTTACCGTTACGCTGCAATCCGGCGATGCCGCCGCGCAGGTCCAGGTATCCTGTCTGCCGATTGTCCGTTATGCCAGCGCGCGTCTGATGATTGACGCCCCTGCG\n-+\n-BBCCCFFCCBCCGFGGGGGGGGHHHHHGGGGGGGHHHHHHHHHHHHHHHHHGGGGGGGGGGHGHHHGGGGGGGGHGGGGGGGGGGHHHHHHHHHHHHHHHHHHHGGGGGHHHGGHGHHHHHHGGGGGGGGGGHHHHHHFHHFGGGGGGGG\n-@238964/2\n-ATCGGCAGACAGGATACCTGGACCTGCGCGGCGGCATCGCCGGATTGCAGCGTAACGGTAAAAGAGGACTTGACTGGCGCGATTTGCATCTCATCATTCGCCAGTACCGGTACGGTAAGCCGATACGTTCCTGCGCTAAGATCGCTTATTG\n-+\n-AAA3AB?DBFBFCGGGGGFBFFHHHHFFGGGGGCFGGHGGGGGGGGHHHGHGGGGGGGG/CGHHGHGHHHHHHGHHHHFGGFCHGHGEHGHHHHHGGEFFDGGGCFHFGC<-CAGBAEFHGG?@CCGHHH/GFECGCBCFGGF.DACEFF0\n-@135672/1\n-GAATACGGTCATATTGATATTCTGGTGAATAACGCGGGTTTGATCCGTCGTGAAGATGCGATTGATTTCACGGAAAAAGACTGGGATGACGTCATGAACCTGAACATCAAGAGCGTGTTCTTTATGTCTCAGGCGGCGGCAAAACTTTTTA\n-+\n-BA@AAFBAFB?FGGGGFGGGGGHHFB4FGGFHGGGGGGEFGDHHHGHFGGGGHGHFFHHGGHHGGHFFHHHHGGGGGFGGHHHHEHHGHHGFEFHGGHHFFHHGFHHHFFFFHHC/CEFHHHHGHHHHBGHHHGCCCD-@DCAFEG0GG0.\n-@1027688/2\n-GTCTTCTATGTTACCGTCAATCAACCCGGAACTGGCCCGTATCGCTCCCGGCTTTCGTGCATTAATTATTAATGTTATTGCCGCTCCGATTCGCGATGCGCAGGTCGGAGCAATCGCGCTAAAAGAGGCCTGTCAGGCCGTATTTAACGGG\n-+\n->A11>333F33DEGGGFE1EF111BAAA000A1B0FBEEAEFG//0/A//A/EA01/0??EF211222B2222BGFH2@111/E///?EE/1>?//<<E/////0B<B@?/<0FHEECCC?CHG1.0<.<1.0/00CHC-<<.:CFHH.@.\n-@278520/1\n-GTACTGGCGAATGATGAGATGCAAATCGCGCCAGTCAAGTCCTCTTTTACCGTTACGCTGCAATCCGGCGATGCCGCCGCGCAGGTCCAGGTATCCTGTCTGCCGATTGTCCGTTATGCCAGCGCGCGTCTGATGATTGACGCCCCTGCG\n-+\n-BABBBFFBBBBBGGGGGGGGGGHHHHHGGGGGGGHHGHHHHHHHHHHHHHHGGGGGFGGGGHHHHHGGGGGGGGHGGGGGGGGGGHHHHHHFGHHHGHHHHHHGGCGGGHHHGGFDEHHHHHGGGGGGGGGGHHHHHHHHHGGGGGGGGG\n-@1088790/2\n-GCTCCGGCGTGGTAACGGCATTCGCCTGCTCGCTGGTCCGCGTCGCGGCAAGCCACGGGAAAACGGTCGCATCACACTGGTCTGGTAAAGGCAGATCCGCAGTATCCTGCGGCATCACGTTGAGCCACAGCTTGCGC'..b'CGGG\n-+\n-1>AAAF@>AABBFFBFEFGBGGH0A3EAEEAEA0/E///AE//0AEGCECGHHF1GEEECEGFBCGFBF111E/>EF>GBE/EECCGFCC?/CCECGCCFH??-<@?EH0EECGHH.@@-:CCG/.-@---;-;-BAA=@-@@??F?F-99\n-@47237/1\n-ATGGAATTAATTGGACTTAGTGAGAAGTGTTCATGGTGTCCCCTGCAGGAATCGAACCTGCAACTAGCCCTTAGGAGGGGCTCGTTATATCCATTTAACTAAGGGGACAACGCGGCGCCAGTATAGCGTTTTTTATTCGCCGGAGTAAGTG\n-+\n-ABBBAFFFFFFFGFGGGGGGGFFHHHHHHGGHHHHFGHHHHHHHGHHHGGHGHHHHHGHHHHHHGHFHHHHHHHHHHGGGGCHFFEHHHHHHGHHHHHHHHCFEGGEGGHHFGGGGGGD/B?GFHHHGGGGGGGHHFHFGFCGDCGHHHFH\n-@1474189/1\n-TGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATAATCCTTAGCATCTGCTAAGGATTTTTTTTTGCCTAAAATTACCTGATTATCTGATCAGGTAATCGTAAGTTCCCTTCTTTTTCTT\n-+\n-AABAB5DFBFFBGAEEEGGGGGGEEECGE?EEHHGHGEHFDGHEGHHHECEGDEEFGFCGFHEEG4FGHHHFG3FFFBGHHHGHFB3FHHFFEGGGGFHHHH11DGHHHHH0FBFG2FGHHFG<GFG2F</G0?<FF1FDDFFDGGGHBGH\n-@343204/2\n-CTAAGGAGGCATTCAGTGCGGATTCATATTCTCTTTGACCTCAATTTCCCTGGTCAGTTTCCCCATTCGTCCAGAAATGCTCCCTGCGCTCCGCCATGCGCACTAATTGTTCACAAGGCGCGTAACGAGGACCGTAAAGTGCGGCCAGGCG\n-+\n-3ABBBFFA??AFGFFGGGGGGGGGCFHFHHHGHHHHHHFHHHHHFFBGHHGGHHHHHHGGHHHHHHEHHHGGGGHHHGFFHFHEHHGECFGEDEFCAGFEF?EECBGBFGHHGGFFGAGGGGDDDGGGFGGHHCCGDGFFGHGGFGCE.CC\n-@707874/1\n-GATTAAGCAACTGCTCGACGTCGGCGCGCAAACGCTTCTGATACCGATGGTGCAGAATGCCGATGAAGCGCGAAACGCCGTAGCGGCTACGCGTTATCCGCCTGCCGGTATTCGCGGCGTGGGCAGCGCGCTGGCGCGGGCATCGCGCTGG\n-+\n-A>AAAFFFFF?FGFGGCG1EEF0EEEGGCGFECE/F/A1DGHGD1EFC/E@FGFEDC1@1@E>EEFGHHECEGGC@C//C</CF??//<FC/<CCCHGHCACCEAGCG--CGBC.A--@-??AEFGGG;9@@?=B-:@@@?>F/9A---;@\n-@737981/2\n-GATTAAGCAACTGCTCGACGTCGGCGCGCAAACGCTGCTGATACCGATGGTGCAGAATGCCGATGAAGCGCGAAACGCCGTAGCGGCTACGCGTTATCCGCCTGCCGGTATTCGCGGCGTGGGCAGCGCGCTGGCGCGGGCATCGCGCTTG\n-+\n->11A1F1DFFF1BGFCEGG0EE0A0E?/EE//B/A/E?1111@F1/?@??1FBBF10BBD1>E//BF1@>//></</E///<///<B@C0<//>CCEHE..<..<.<--::CH/.;@@G?A-A.B.CA@@<---9;A-----;/A-@=---\n-@156200/2\n-GTCATACAGCGGCGTTGACGGCCAGGTCTGATCAACCAGTTCGCTGCCTTCATCGCTGGCGATCAGGAATCCGCCGGGAGCGGGGCTATTCAGCGACTGGGCGGCACGCGCGGTCTCGCGAGAAATAAACGGCGCCGTTGAGGTCGTGAC\n-+\n-CBABCFFFFFCCGGGGGGGGEGGGHCGHHHGHHHFGHGGFHHGGGGGHHGHHGHHGHGGGGGGGGGHHEHHHGGGGGG//DGC?FGGEHFHGFHGGFCGHHHGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFF@FFFEF/BABFFF\n-@530652/2\n-ACCTTATCAGGCCTACATAAGCACTCGGCTGGTAGGCCTGATAAGCGCAGCGCCATCAGACATTGATTGGCAATTAAGCCTGTTTAGCAGCTTCTGCTGCTTTCACGATCACCGCGAAGGCGTCAGCTTTCAGAGAAGCGCCGCCTACCAG\n-+\n-BBCCCFFFFFFFGGGGGGGGGGHHHHGGGGGGHHHGHHHGHHHHHHGGGGGGGGGGGHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHCGFGHHGGGEGGGHGGGGGHHHHHHHGHHHGGGGGGGGGGGHHH\n-@424544/1\n-ACTACGAATACGGCGCAGCGGGCGACCGTTTTCATCAAATTCCGGTGAAATGACGTCGTTTTTCATAAAAGTGTAGTCTGCTGTGTTTGAGTTCTGAAAACGGGCATTATCCAAAGTTAGTTGCCGGATGCAAGCATGAAGCGCACTGCGG\n-+\n-DDCCDDCCCDFCGGGGGGGGGGGGGGGGGGHGHHHHHHHHHHHHGGGGHHHHHHGGGGGGGGGHHHHHHHHHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHGGGGGHHHHHHHHHGHHGHHHHHHGGGGGHHHHHHHHHHHGGGGGGHGGF\n-@788695/2\n-CTGCTGGTGGTTGAGCCGCCCTATGATCCTGAGTTGGACTTTCATTACCGCATCTTCAACGCCGACGGCAGTGAAGTCTCGCAGTGCGGCAATGGCGCGCGCTGTTTCGCGCGATTTGTTCGCCTGAAAGGGCTAACCAATAAACGCGACA\n-+\n-BBBBBFFFF@ABGGFGGGGGGGGHHHHHHHGHHHHHHHHHHHHHHHHHHGGGGGHHHHGHGGGGGGGGGCGGHGHHGHHHHGGGGHHEGGGGHHHHGGGGGGGGGHFHGGGGGGGHGHHHHGGGGHHEHHGGGGFHHHHHGGGGGGGGGC-\n-@1399297/2\n-TTCATACAGAGATCATGACCACACATGCAACAAAAAAGCCTGCAACTCATTGAAGTTACAGGCTTTTTTAAGGTTCATGATGCATCATGAATGAATGTTTGGTGGAGCTGGCGGGAGTTGAACCCGCGTCCGAAATTCCTACATCCTCGGT\n-+\n-AAABBFFFFFFCGGGGGGGGFGHGGHGHHCHHHHHHGGHGHHGHHHFFFHGHHFHGHHHHHEGHHHGHGHFHG@GFHHFHHGHFHHHHHHHHHHHHHHGHHG?FFEEFEFBE?CCCGDFFHHGFDFC@DGG@DGG.1>GG11<F0GGFGD<\n-@52275/1\n-GTCACAGTCGACGTTGGCCCCCAAATCAAGCACTACCGTTTTGCCCTTTTGCTGGTGCGGTAATACCGTCACCAACGCCGGACGCTCAATCCCCTCAAGAGGCTTGAGCAATAATTTCGCCAGCCCCATCAGCGCCCCGGTATTACCGGCG\n-+\n-BBBBBFFDFA?DCEGGGGGGGGGCHHHHHGGFHHHGHGGGHGHHHHHHHHGGHHHHHH?EE?FHHHHGFFDGHHHGDGG@ECGGGDGGEHHHHGHGHHHBCHGHHCHHGFBGHHHHHHHGGGFGGGGGHHHHHGGCC?GCC-EHHEHFFG?\n-@384298/2\n-GTGTTTACACAGGAGCTGCTCCAGTTCGCTTAATGACGCCACAGTCCAGGTTGGATGAATACCCGCGGGCTGCTCGCGATGATGCGCGTTAAGCCAGCAGGTCGACAGCCCGGCGTTAATGCCGCCAAGAATATCGGATTCCGCGGTATCG\n-+\n-AAABBFFFFFFFGG2GGGGGGGHHHHGGGGHGGHGHHGGGGGHHHHFHHGCGHGFHHHHHHHHHGGGGGGGGGHHGGG?FGHHHHFGGGGGEHHHHHGHFG0FCCGGGEHGGFDFCFGGGHHHFC?:@CGHBGFHGCD.EBFFGDA.9EF.\n'

diff -r e3698ac146d7 -r 4deefd708943 test-data/SRR5646583_SMALL_1.fastq.gz

Binary file test-data/SRR5646583_SMALL_1.fastq.gz has changed

diff -r e3698ac146d7 -r 4deefd708943 test-data/SRR5646583_SMALL_2.fastq
--- a/test-data/SRR5646583_SMALL_2.fastq Tue Oct 03 10:39:11 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r e3698ac146d7 -r 4deefd708943 test-data/SRR5646583_SMALL_2.fastq.gz

Binary file test-data/SRR5646583_SMALL_2.fastq.gz has changed

diff -r e3698ac146d7 -r 4deefd708943 test-data/match_results1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/match_results1.tab Thu May 06 18:31:35 2021 +0000

@@ -0,0 +1,10 @@
+kmername seq is_revcomp contig_id match_index refposition subtype is_pos_kmer sample file_path scheme scheme_version qc_status
+2154958-2.2.2.2.1.4 GGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG True NODE_1_length_726282_cov_40.4705_ID_1 13732 2154958 2.2.2.2.1.4 True
+3212817-2.2.2.2 CAAAACTACGAATACGACGCAGCGGGCGACCGT False NODE_3_length_427905_cov_48.1477_ID_5 183683 3212817 2.2.2.2 True
+3766668-2.2 GGCCGTACCGTCGGTCTTGCCCAAAAGATAGTC False NODE_4_length_411654_cov_48.8368_ID_7 231109 3766668 2.2 True
+3785187-2.2.2.2.1.4 TTAAAAAGCACCTCAGAGAATAGTCTTAATCCG False NODE_4_length_411654_cov_48.8368_ID_7 249628 3785187 2.2.2.2.1.4 True
+3791096-2.2.2 AACTGCCGGTGGACGGAGGTTTCGACGATAACG False NODE_4_length_411654_cov_48.8368_ID_7 255537 3791096 2.2.2 True
+2217680-2.2.2.2.1 TCCCTGATTGCGGTGCAGATCCCGTTGCTCTTT True NODE_7_length_178659_cov_40.3043_ID_13 130643 2217680 2.2.2.2.1 True
+4744778-2.2 CTGCTTTAATTTTTGATCATGAGTTGGTGACGT True NODE_6_length_203546_cov_46.7874_ID_11 66508 4744778 2.2 True
+3827083-2.2.2.2.1 ACCGGGGAAATGCTGAACAGTTTCCGGGAACAC False NODE_4_length_411654_cov_48.8368_ID_7 291524 3827083 2.2.2.2.1 True
+3479768-2.2 CGCCTTGCCGCCGCCGTGCGCCACACAGGTCAG True NODE_26_length_45055_cov_50.2073_ID_51 23364 3479768 2.2 True

diff -r e3698ac146d7 -r 4deefd708943 test-data/match_results2.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/match_results2.tab Thu May 06 18:31:35 2021 +0000

@@ -0,0 +1,10 @@
+kmername seq freq refposition subtype is_pos_kmer is_kmer_freq_okay total_refposition_kmer_frequency kmer_fraction is_kmer_fraction_okay file_path sample scheme scheme_version qc_status
+4241351-2.2 GGGATTACGTCCATAAAGAATCCATGTTTTTTG 40 4241351 2.2 True True 40 1.000 True
+1983064-2.2.1.1.1.1 TCCAGCATATCGCCCAAGCGACTGAACGCAGGC 46 1983064 2.2.1.1.1.1 True True 46 1.000 True
+944885-2.2.1.1.1 GTTTACGTGTTGACCCTGGCATCCTTTCTCCTG 20 944885 2.2.1.1.1 True True 20 1.000 True
+4744778-2.2 CTGCTTTAATTTTTGATCATGAGTTGGTGACGT 66 4744778 2.2 True True 66 1.000 True
+2438389-2.2 TAGGCCAGCCGCCAGGTAATACCCGCTGCATTT 46 2438389 2.2 True True 46 1.000 True
+293728-2.2.1.1 GTTGAAACGACGCGCGATTTCAGAAAGCAGCGG 42 293728 2.2.1.1 True True 42 1.000 True
+157792-2.2.1.1.1 ACGGTACTTTTACCGCAGCCAATACCGCCGGTT 48 157792 2.2.1.1.1 True True 48 1.000 True
+1047714-2.2.1.1.1 GCGAACTGGCGAAACGCCTTGGCGTGGAACAAC 44 1047714 2.2.1.1.1 True True 44 1.000 True
+691203-2.2.1.1 CAGTTTTACATCCTGCGAAATGCGCAGCGTCAA 38 691203 2.2.1.1 True True 40 0.950 True

diff -r e3698ac146d7 -r 4deefd708943 test-data/results1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/results1.tab Thu May 06 18:31:35 2021 +0000

@@ -0,0 +1,2 @@
+sample scheme scheme_version subtype all_subtypes kmers_matching_subtype are_subtypes_consistent inconsistent_subtypes n_kmers_matching_all n_kmers_matching_all_expected n_kmers_matching_positive n_kmers_matching_positive_expected n_kmers_matching_subtype n_kmers_matching_subtype_expected file_path qc_status qc_message
+fast_a_single heidelberg 0.5.0 2.2.2.2.1.4 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 2.2.2.2.1.4 True 202 202 17 17 3 3

diff -r e3698ac146d7 -r 4deefd708943 test-data/results2.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/results2.tab Thu May 06 18:31:35 2021 +0000

@@ -0,0 +1,2 @@
+sample scheme scheme_version subtype all_subtypes kmers_matching_subtype are_subtypes_consistent inconsistent_subtypes n_kmers_matching_all n_kmers_matching_all_expected n_kmers_matching_positive n_kmers_matching_positive_expected n_kmers_matching_subtype n_kmers_matching_subtype_expected file_path avg_kmer_coverage qc_status qc_message
+fast_q_paired heidelberg 0.5.0 2.2.1.1.1.1 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 2.2.1.1.1.1 True 202 202 20 20 2 2