Galaxy |

Changeset 9:4654c51dae72 (2018-05-09)

Previous changeset 8:e9fd173fc7ee (2018-04-20)

Commit message:
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a7add3a4ffc9275f78d4583aac1ef3281c0def21

modified:
bio_hansel.xml

added:
test-data/SRR1002850_SMALL.fasta-match_results.tab
test-data/SRR1002850_SMALL.fasta-results.tab
test-data/SRR1002850_SMALL.fasta-tech_results.tab
test-data/SRR5646583_SMALL-match_results.tab
test-data/SRR5646583_SMALL-results.tab
test-data/SRR5646583_SMALL-tech_results.tab

removed:
test-data/match_results.tab
test-data/results.tab
test-data/tech_results.tab

diff -r e9fd173fc7ee -r 4654c51dae72 bio_hansel.xml
--- a/bio_hansel.xml Fri Apr 20 10:44:35 2018 -0400
+++ b/bio_hansel.xml Wed May 09 15:06:32 2018 -0400

[

b'@@ -1,227 +1,296 @@\n-<tool id="bio_hansel" name="Bio Hansel" version="1.3.1">\n- <description>SNV Subtyping with genome assemblies or reads</description>\n- <requirements>\n- <requirement type="package" version="1.3.1">bio_hansel</requirement>\n- <requirement type="package" version="17.2.0">attrs</requirement>\n- </requirements>\n- <command detect_errors="exit_code"><![CDATA[\n- ## Preparing file input.\n- #if $data_type.type == "paired":\n+<tool id="bio_hansel" name="bio_hansel" version="2.0.0">\n+ <description>SNV subtyping of genome sequence reads or assemblies</description>\n+ <requirements>\n+ <requirement type="package" version="2.0.0">bio_hansel</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code">\n+<![CDATA[\n \n- ln -s \'$data_type.fastq_input1\' \'$data_type.fastq_input1.name\'.fastq &&\n- ln -s \'$data_type.fastq_input2\' \'$data_type.fastq_input2.name\'.fastq &&\n-\n- #elif $data_type.type == "collection":\n+#import re\n \n- ln -s \'$data_type.fastq_input1.forward\' \'$data_type.fastq_input1.name\'_1.fastq &&\n- ln -s \'$data_type.fastq_input1.reverse\' \'$data_type.fastq_input1.name\'_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\' \'$data_type.fastq_input1.name\'.fastq &&\n- #end if\n+#def is_gzipped_fastq($data_input)\n+ ## Is FASTQ data param gzipped type? i.e. either \'fastq.gz\' or \'fastqsanger.gz\'?\n+ #return $data_input.is_of_type(\'fastqsanger.gz\') or $data_input.is_of_type(\'fastq.gz\')\n+#end def\n \n- #if $data_type.fastq_input1.is_of_type(\'fasta\'):\n- ln -s \'$data_type.fastq_input1\' \'$data_type.fastq_input1.name\'.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\' \'$type_of_scheme.scheme_input.name\' &&\n- #end if\n- #end if\n+#def get_fastq_ext($data_input)\n+ ## Get file extension for FASTQ data param\n+ #return \'.fastq.gz\' if $is_gzipped_fastq($data_input) else \'.fastq\'\n+#end def\n \n- ## Start the actual command here\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- enteritidis\n- #elif $type_of_scheme.scheme_type == "custom":\n- \'$type_of_scheme.scheme_input.name\'\n- #end if\n+#def base_sample_name($name)\n+ #if $re.search(r\'_R(1|2)\', $name):\n+ #return $re.sub(r\'(.+)_R(1|2)([^\\.]*)(\\..+)\', r\'\\1\\3\', $name)\n+ #elif $re.match(r\'.+_\\d\\.\', $name):\n+ #return $re.sub(r\'(.+)_(\\d)(\\..+)\', r\'\\1\', $name)\n+ #else\n+ #return $name\n+ #end if\n+#end def\n \n- ## Use Json output\n- #if $dev_args.use_json == "yes":\n- --json\n- #end if\n-\n- #if $kmer_vals.kmer_min\n- --min-kmer-freq $kmer_vals.kmer_min\n- #end if\n-\n- #if $kmer_vals.kmer_max\n- --max-kmer-freq $kmer_vals.kmer_max\n- #end if\n-\n- #if $qc_vals.low_cov_depth_freq\n- --low-cov-depth-freq $qc_vals.low_cov_depth_freq\n- #end if\n-\n- #if $qc_vals.max_missing_tiles\n- --max-missing-tiles $qc_vals.max_missing_tiles\n- #end if\n-\n- #if $qc_vals.min_ambiguous_tiles\n- --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles\n- #end if\n+#def get_paired_fastq_filename($data_input, $name=None, $is_forward=True)\n+ ## Get paired FASTQ filename for a data param with appropriate file extension \n+ ## with \'_1\' or \'_2\' appended if forward or reverse reads, respectively.\n+ #set $name = $name if $name is not None else $data_input.name\n+ '..b'GTTTTACATCCTGCGAAATGCGCAGCGTCAA | 87 | 564 | forward.fastqsanger; reverse.fastqsanger | 691203-2.2.1.1 | True | 2.2.1.1 | 691203 | True | heidelberg |\n- +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n- | CAGGAGAAAGGATGCCAGGGTCAACACGTAAAC | 33 | 564 | forward.fastqsanger; reverse.fastqsanger | 944885-2.2.1.1.1 | True | 2.2.1.1.1 | 944885 | True | heidelberg |\n- +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+ +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+\n+ | tilename | seq | freq | refposition | subtype | is_pos_tile | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message |\n+ +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+\n+ | negative4642573-1.2 | TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT | 62 | 4642573 | 1.2 | False | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |\n+ +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+\n+ | 21097-2.2.1.1.1 | GCAAATCGCGCCAGTCAAGTCCTCTTTTACCGT | 42 | 21097 | 2.2.1.1.1 | True | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |\n+ +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+\n \n- Next 200 lines omitted.\n+ *Next 202 lines omitted.*\n \n-Galaxy wrapper written by Matthew Gopez at the Public Health Agency of Canada, National Microbiology Laboratory.\n+Galaxy wrapper written by Matthew Gopez and Peter Kruczkiewicz at the Public Health Agency of Canada, National Microbiology Laboratory.\n \n ]]></help>\n- <citations>\n- <citation type="bibtex">@ARTICLE{a1,\n- title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.},\n- author = {Genevi\xc3\xa8ve Labb\xc3\xa9, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash.},\n- url = {https://github.com/phac-nml/bio_hansel}\n- }\n- }</citation>\n- </citations>\n+ <citations>\n+ <citation type="bibtex">@ARTICLE{a1,\n+ title = {A robust genotyping scheme for Salmonella enterica serovar Heidelberg clones circulating in North America},\n+ author = {Genevi\xc3\xa8ve Labb\xc3\xa9, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash},\n+ url = {https://github.com/phac-nml/bio_hansel}\n+ }\n+ }</citation>\n+ </citations>\n </tool>\n'

diff -r e9fd173fc7ee -r 4654c51dae72 test-data/SRR1002850_SMALL.fasta-match_results.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR1002850_SMALL.fasta-match_results.tab Wed May 09 15:06:32 2018 -0400

b'@@ -0,0 +1,203 @@\n+tilename\tseq\tis_revcomp\tcontig_id\tmatch_index\trefposition\tsubtype\tis_pos_tile\tsample\tfile_path\tscheme\tscheme_version\tqc_status\tqc_message\n+2154958-2.2.2.2.1.4\tGGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t13732\t2154958\t2.2.2.2.1.4\tTrue\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative2131791-2.2.3.1.3\tGCTGGGCGAAATGATGCAGTTCACCACTTGCTC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t36900\t2131791\t2.2.3.1.3\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+2069216-2.2.2\tATACTTAGGCTGTCAGTAACCCGTGAGGTAGTG\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t99475\t2069216\t2.2.2\tTrue\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative2048364-2.1\tGGTCGCGACAGGCCGAGCCAGAACAGGAAAAGC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t120327\t2048364\t2.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative2045923-2.1.3\tCGACATATTCCCGCACCGTGCCATGGCTCATCT\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t122768\t2045923\t2.1.3\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1983064-2.2.1.1.1.1\tTCCAGCATATCGCCCAGGCGACTGAACGCAGGC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t185627\t1983064\t2.2.1.1.1.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1976727-2.1\tTACTTTATCTTTGTACTTATTCCACAATACGGA\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t191964\t1976727\t2.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1950957-2.2.2.2.2.2\tTTTCCTTGCCCTAATCGCGCCCTACGGCTGGTC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t217734\t1950957\t2.2.2.2.2.2\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1910623-2.2.3.3\tGCTCCGATTTTTGCCTGATAATTATCCAATTAC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t258068\t1910623\t2.2.3.3\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1856421-2.1.1.1\tGTTTGCGCAGCAGGCAGCCCCTGGCGAGCGGCT\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t312270\t1856421\t2.1.1.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1840959-2.2.2.2.7\tCACCATTGAGCCGGTAATAATGCCGACAAAGGC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t327846\t1840959\t2.2.2.2.7\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1831783-2.2.2.1.2\tTTTTCCGGGCTTATCGGCAACGCTATTCTGGCC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t337022\t1831783\t2.2.2.1.2\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1825773-2.2.2.2.2\tCATCCCGGTTCATAGCGGCTCCGCTACGCTAAA\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t343032\t1825773\t2.2.2.2.2\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1760974-2.2.3.1.3\tTCGCGATGCGCAGGTCGGAGAAATCGCGCTAAA\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t407831\t1760974\t2.2.3.1.3\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1697407-2.2.2.2.1.5\tACACTGCCCAGAATAAGCGACACACAGCGCGCC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t471398\t1697407\t2.2.2.2.1.5\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1689446-2.2.2.2.4\tGGGCCGAAGACCTCGCGTTGCACGATGGCATCT\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t479359\t1689446\t2.2.2.2.4\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1649579-2.2.2.2.4\tGCGCATCGCGCATTACTGATGAAATGCTGATGT\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t519226\t1649579\t2.2.2.2.4\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1603329-2.2.2.2.1.1\tATTGGCCAGGGCAAAGTCGCTGACTATATTCCG\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t565476\t1603329\t2.2.2.2.1.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1534092-2.1.1.1\tCCGTCGAGTGGGGGGCAATAGCGATAACCGTCC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t634713\t1534092\t2.1.1.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1462807-2.2.3\tATAATGTTGCCGACGGCGCACACAAACGCCACA\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t705998\t1462807\t2.2.3\tFalse\tSRR100'..b'61770\t3090898\t1.2\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3113857-1.2\tTTCATGACGTCATCCCAGTCTTTTTCCGTGAAA\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t84729\t3113857\t1.2\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3118525-2.2.3.1.3\tCCTGGCCTCTAACATACTGGCCGCATAAGGCGC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t89397\t3118525\t2.2.3.1.3\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3159204-2.2.1.1.3\tCCGCCTCGCCAACCTGCGGCGGAGTCGCGAGCT\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t130070\t3159204\t2.2.1.1.3\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3187428-2.2.3.1.1\tCTTTATCAGCGCGCAGTGTCCCATTCCATCATC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t158294\t3187428\t2.2.3.1.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3200083-2.1\tACCCGGTCTACCGCAAAATGGAAAGCGATATGC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t170949\t3200083\t2.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3204925-2.2.3.1.5\tCTCGCTGGCAAGCAGTGCGGGTACTATCGGCGG\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t175791\t3204925\t2.2.3.1.5\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+3212817-2.2.2.2\tCAAAACTACGAATACGACGCAGCGGGCGACCGT\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t183683\t3212817\t2.2.2.2\tTrue\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3230678-2.2.2.1.1.1\tAGCGGTGCGCCAAACCACCCGGAATGATGAGTG\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t201544\t3230678\t2.2.2.1.1.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3233869-2.1.1.1.1\tCAGCGCTGGTATGTGGCTGCACCATCGTCATTA\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t204735\t3233869\t2.1.1.1.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3254229-2.2.3.1.3\tCGCCACCACGCGGTTAGCGTCACGCTGACATTC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t225095\t3254229\t2.2.3.1.3\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3257074-2.2.1\tCGGCAACCAGACCGACTACGCCGCCAAGCAGAC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t227940\t3257074\t2.2.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3264474-2.2.2.1.1.1\tAATGGCGCCGATCGTCGCCAGATAACCGTTGCC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t235340\t3264474\t2.2.2.1.1.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3267927-2.2.2.2.2.1\tAAAGAGAAATATGATGCCAGGCTGATACATGAC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t238793\t3267927\t2.2.2.2.2.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3278067-1.1\tTGTGAGTAAGTTGCGCGATATTCTGCTGGATTC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t248933\t3278067\t1.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3299717-2.2.3.1.4\tATGCCGGACAGCAGGCGAAACTCGAACCGGATA\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t270583\t3299717\t2.2.3.1.4\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3305400-2.1.1.1\tCATCGTGAAGCAGAACAGACGCGCATTCTTGCT\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t276266\t3305400\t2.1.1.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+3324813-2.2.2.2\tCAGATGAAGCGGGCGCAGGATAACTTCAAGGCC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t295679\t3324813\t2.2.2.2\tTrue\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3373069-2.2.2.2.1.1\tCTCTCCAGAAGATGAAGCCCGTGATGCGGCGCA\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t344042\t3373069\t2.2.2.2.1.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3408895-2.1.1\tACAGTAAAAACAGGATCTGCTGCGAGGCCAGAC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t379868\t3408895\t2.1.1\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3436797-2.2.2.1.2\tATGCGGTATTCCTTGGCGTCGGCACCTATCAGT\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t407770\t3436797\t2.2.2.1.2\tFalse\tSRR1002850_SMALL\tSRR1002850_SMALL.fasta\theidelberg\t0.5.0\tPASS\t\n'

diff -r e9fd173fc7ee -r 4654c51dae72 test-data/SRR1002850_SMALL.fasta-results.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR1002850_SMALL.fasta-results.tab Wed May 09 15:06:32 2018 -0400

@@ -0,0 +1,2 @@
+sample scheme scheme_version subtype all_subtypes tiles_matching_subtype are_subtypes_consistent inconsistent_subtypes n_tiles_matching_all n_tiles_matching_all_expected n_tiles_matching_positive n_tiles_matching_positive_expected n_tiles_matching_subtype n_tiles_matching_subtype_expected file_path qc_status qc_message
+SRR1002850_SMALL 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 2154958-2.2.2.2.1.4; 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 True 202 202 17 17 3 3 SRR1002850_SMALL.fasta PASS

diff -r e9fd173fc7ee -r 4654c51dae72 test-data/SRR1002850_SMALL.fasta-tech_results.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR1002850_SMALL.fasta-tech_results.tab Wed May 09 15:06:32 2018 -0400

@@ -0,0 +1,2 @@
+sample subtype qc_status qc_message
+SRR1002850_SMALL 2.2.2.2.1.4 PASS

diff -r e9fd173fc7ee -r 4654c51dae72 test-data/SRR5646583_SMALL-match_results.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR5646583_SMALL-match_results.tab Wed May 09 15:06:32 2018 -0400

b'@@ -0,0 +1,204 @@\n+tilename\tseq\tfreq\trefposition\tsubtype\tis_pos_tile\tis_kmer_freq_okay\tsample\tscheme\tscheme_version\tqc_status\tqc_message\n+negative4642573-1.2\tTACCAGGAAGTGCTGGAAGAGTTTAACGAACAT\t62\t4642573\t1.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+21097-2.2.1.1.1\tGCAAATCGCGCCAGTCAAGTCCTCTTTTACCGT\t42\t21097\t2.2.1.1.1\tTrue\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3647258-2.2.2.2.2.1\tTACGGGTAACTGTTATCGGTAACATTGTCCAAC\t64\t3647258\t2.2.2.2.2.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3931056-2.2.3.2.1\tATATTCATCATCAAACTACCGTCGCCGGAAAAA\t26\t3931056\t2.2.3.2.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3540924-2.2.2.2.2.2\tACCGCCGCTATTACAAGCGGCGGCTCTCAGTTT\t52\t3540924\t2.2.2.2.2.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3062689-2.2.2.2.2.2\tCCAGAACCGACCGCACGCAAAAGCTTCTGAACC\t32\t3062689\t2.2.2.2.2.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3113857-1.2\tTTCATGACGTCATCCCAGTCTTTTTCCGTGAAA\t50\t3113857\t1.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3011381-2.1.1.3\tGTTGAGCCACAGCTTGCGCCAGAGCGGCGTTTG\t38\t3011381\t2.1.1.3\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3230678-2.2.2.1.1.1\tAGCGGTGCGCCAAACCACCCGGAATGATGAGTG\t66\t3230678\t2.2.2.1.1.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative2482056-2.2.3.1\tGGATCGGCCATTATTGCCTGCTGAACATAATAC\t28\t2482056\t2.2.3.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative2045923-2.1.3\tCGACATATTCCCGCACCGTGCCATGGCTCATCT\t20\t2045923\t2.1.3\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1831783-2.2.2.1.2\tTTTTCCGGGCTTATCGGCAACGCTATTCTGGCC\t30\t1831783\t2.2.2.1.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative2217680-2.2.2.2.1\tTCCCTGATTGCGGTGCTGATCCCGTTGCTCTTT\t34\t2217680\t2.2.2.2.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative2592097-2.2.1.1.2\tTGCAAACTATCACGACGCGGCGCAAGAGTTTGT\t68\t2592097\t2.2.1.1.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3523461-2.2.2.2.4\tCGATTTTACCGCCAGCAGCTTCGATAGCAGCAC\t54\t3523461\t2.2.2.2.4\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative4157035-2.2.2.2.1.2\tCCCAGGACTCCAGGCACATCTGCTCTTCTTCAC\t56\t4157035\t2.2.2.2.1.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3696399-2.2.2.2.2\tTCATTTGTATAATAACCTATTGATCAGGCTAAT\t90\t3696399\t2.2.2.2.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1840959-2.2.2.2.7\tCACCATTGAGCCGGTAATAATGCCGACAAAGGC\t30\t1840959\t2.2.2.2.7\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3802645-2.1\tATCGCGCCAGCCGCAGACGCTAACGTTCATTCC\t38\t3802645\t2.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3090898-1.2\tCGCATGGCTTTCCAGTTCAAGGATGTCCGCCTG\t42\t3090898\t1.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative4136269-2.2.2.2.2\tCCGCTGCTGGAAGATGAAAAAGTGCGCAAAGTG\t38\t4136269\t2.2.2.2.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3691258-2.2.2.1.1\tGCACGTGACGTTTAGAGACGGAGTCCAGCTCAG\t44\t3691258\t2.2.2.1.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative2658490-2.2.1.1.3\tGCTGGTCAGCCACAACGCTGACGCTATTTCTGA\t48\t2658490\t2.2.1.1.3\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3819645-2.2.2.2.3\tTCGAATCTGGATACCCGCGTCACCAATATCGAA\t46\t3819645\t2.2.2.2.3\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1288160-2.2.2.2.4\tGCGTGGTATCGTCCTGCGCCAGATTTTGTGGCG\t50\t1288160\t2.2.2.2.4\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3939049-2.1.1.2\tGAGATCATTGCGATTGCCATTGGTTCCGGCGCC\t52\t3939049\t2.1.1.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative4136928-2.1.2\tGATTTTGGAGTATCGTGGTCTGGCGAAGCTAAA\t34\t4136928\t2.1.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative4542157-2.1.1.1.1\tTGGGTGATGCGTATAGTTGGGTAGGCTACGCGG\t42\t4542157\t2.1.1.1.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative3373069-2.2.2.2.1.1\tCTCTCCAGAAGATGAAGCCCGTGATGCGGCGCA\t44\t3373069\t2.2.2.2.1.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative2048364-2.1\tGGTCGCGACAGGCCGAGCCAGAACAGGAAAAGC\t40\t2048364\t2.1\t'..b'2.2.2.1.1.1\tGTACCGTCAACGGTAATATCCGCCAGCGTCGGC\t30\t198398\t2.2.2.1.1.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative202001-1.1\tCTGGAAGAGGCGGAAATGCTGTGCCGCAATATC\t40\t202001\t1.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative205838-2.1.1.1.1\tCTGTTCGCTGCCGTCGGTTTCTTTTACCGTCAC\t32\t205838\t2.1.1.1.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative227831-2.2.3.2.1\tTCCCGGCGAATTTACCGTGCAGGCCAATAGCAT\t40\t227831\t2.2.3.2.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative239152-2.2.2.2.2.1\tTTCCGTCGATGTCACCCATTCCCGTGCGACGCT\t20\t239152\t2.2.2.2.2.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative271435-2.2.1.1.3\tTCGGGTGCAAATGGGATGGTAAGGAGTTTATTG\t50\t271435\t2.2.1.1.3\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative467662-2.2.3.1.2\tCTAACTTATGTCATAACGCCGTTGACCGCTGGC\t26\t467662\t2.2.3.1.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative484993-2.2.2.2.1.2\tCGGGAATGGTTAAAGTCTGCGGATATGGCGCTT\t30\t484993\t2.2.2.2.1.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative489687-2.2.3.2.1\tCCTTGTCGTTAAATCCAGGCGGTATAGTAACGA\t48\t489687\t2.2.3.2.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative508759-2.2.2.2.1.3\tCCTGGTGATTTCCAGCCAGAGCGGTAATCAACT\t38\t508759\t2.2.2.2.1.3\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative573259-2.2.2.2.5\tACCACAACGTCTGGCGGTACGTTTTTTATCACC\t26\t573259\t2.2.2.2.5\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative600350-2.1.2\tGTCGGAAAATAAAAAACAGGTGAATTACGTACC\t40\t600350\t2.1.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative600783-1.1\tAGCGGCGGCGGTATTCGCGACTCGATTGAGGCG\t46\t600783\t1.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative649988-2.2.2.1\tGGAGCCGACAGGATGCCGAAACCGGGTGTGTGT\t28\t649988\t2.2.2.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative691203-2.2.1.1\tCAGTTTTACATCCTGCAAAATGCGCAGCGTCAA\t2\t691203\t2.2.1.1\tFalse\tFalse\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative720751-2.2.1.1.2\tATGGCCATCTGCATACCTGGGGCTTTAACTATA\t30\t720751\t2.2.1.1.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative775920-2.2.2.2\tGTTCAGGTGCTACCGATGATCGTTTTTGGTGCG\t46\t775920\t2.2.2.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative842143-2.1.1.1.1\tTGCCCAGCTCTTTCAGCACTTCGTGGCAGGTTT\t30\t842143\t2.1.1.1.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative848800-2.2.3.1\tTCGTTATCAACAACCAGGTGGGTTTCACCACCT\t50\t848800\t2.2.3.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative869993-2.2.1.1.3\tCGGACTACTGAATCCCAGGTTCATCGCGAACTG\t34\t869993\t2.2.1.1.3\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1036874-2.2.2.1\tGACAATGAGCAGAATTGTAGGGAATTTACAGAC\t40\t1036874\t2.2.2.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1037658-2.2.2.2.1.4\tGATGTGTTTGAACAGTTTAATGCCGCCGTGCAA\t56\t1037658\t2.2.2.2.1.4\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1037736-2.2.2.1.1\tGACTACCTGTTGAAAACCCGTGTACCGGATATG\t52\t1037736\t2.2.2.1.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1049933-1.1\tCCAGCTAACGCGTTGACGCGCATTCGGCCTGCA\t30\t1049933\t1.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1052031-2.2.2.2.1.3\tACCGTCGTTGCCTTGCAGGGGCTGACGCTGGCA\t30\t1052031\t2.2.2.2.1.3\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1061770-2.2.2.1\tAAAATAAAGACGTTAAGCCGGGGTTAAGCATTC\t24\t1061770\t2.2.2.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1062011-2.1.2\tTGTTGTGTGACGCATGCCGCATTTTCTCCTCGC\t34\t1062011\t2.1.2\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1091342-2.2.3.1\tTTAAAACCAATCTGGGCATAAGTCTGGTCGGCA\t20\t1091342\t2.2.3.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1155229-2.2.3.1.5\tGCTGACTGACGATCTGACCCACGTACAAATCAA\t40\t1155229\t2.2.3.1.5\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1174327-2.2.2.2.6\tCCATTAACATACCGCCCAGGAAAGACATATCCT\t36\t1174327\t2.2.2.2.6\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n+negative1193219-1.1\tGGTACAGATTAAGCAACTGCTCGACGTCGGCGC\t32\t1193219\t1.1\tFalse\tTrue\tSRR5646583_SMALL\theidelberg\t0.5.0\tPASS\t\n'

diff -r e9fd173fc7ee -r 4654c51dae72 test-data/SRR5646583_SMALL-results.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR5646583_SMALL-results.tab Wed May 09 15:06:32 2018 -0400

[

@@ -0,0 +1,2 @@
+sample scheme scheme_version subtype all_subtypes tiles_matching_subtype are_subtypes_consistent inconsistent_subtypes n_tiles_matching_all n_tiles_matching_all_expected n_tiles_matching_positive n_tiles_matching_positive_expected n_tiles_matching_subtype n_tiles_matching_subtype_expected file_path avg_tile_coverage qc_status qc_message
+SRR5646583_SMALL 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 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1 True 202 202 20 20 2 2 ['SRR5646583_SMALL_1.fastq', 'SRR5646583_SMALL_2.fastq'] 42.631 PASS

diff -r e9fd173fc7ee -r 4654c51dae72 test-data/SRR5646583_SMALL-tech_results.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR5646583_SMALL-tech_results.tab Wed May 09 15:06:32 2018 -0400

@@ -0,0 +1,2 @@
+sample subtype avg_tile_coverage qc_status qc_message
+SRR5646583_SMALL 2.2.1.1.1.1 42.631 PASS

diff -r e9fd173fc7ee -r 4654c51dae72 test-data/match_results.tab
--- a/test-data/match_results.tab Fri Apr 20 10:44:35 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,203 +0,0 @@\n-tilename\tseq\tis_revcomp\tcontig_id\tmatch_index\trefposition\tsubtype\tis_pos_tile\tsample\tfile_path\tscheme\tscheme_version\tqc_status\tqc_message\n-2154958-2.2.2.2.1.4\tGGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t13732\t2154958\t2.2.2.2.1.4\tTrue\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative2131791-2.2.3.1.3\tGCTGGGCGAAATGATGCAGTTCACCACTTGCTC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t36900\t2131791\t2.2.3.1.3\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-2069216-2.2.2\tATACTTAGGCTGTCAGTAACCCGTGAGGTAGTG\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t99475\t2069216\t2.2.2\tTrue\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative2048364-2.1\tGGTCGCGACAGGCCGAGCCAGAACAGGAAAAGC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t120327\t2048364\t2.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative2045923-2.1.3\tCGACATATTCCCGCACCGTGCCATGGCTCATCT\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t122768\t2045923\t2.1.3\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative1983064-2.2.1.1.1.1\tTCCAGCATATCGCCCAGGCGACTGAACGCAGGC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t185627\t1983064\t2.2.1.1.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative1976727-2.1\tTACTTTATCTTTGTACTTATTCCACAATACGGA\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t191964\t1976727\t2.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative1950957-2.2.2.2.2.2\tTTTCCTTGCCCTAATCGCGCCCTACGGCTGGTC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t217734\t1950957\t2.2.2.2.2.2\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative1910623-2.2.3.3\tGCTCCGATTTTTGCCTGATAATTATCCAATTAC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t258068\t1910623\t2.2.3.3\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative1856421-2.1.1.1\tGTTTGCGCAGCAGGCAGCCCCTGGCGAGCGGCT\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t312270\t1856421\t2.1.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative1840959-2.2.2.2.7\tCACCATTGAGCCGGTAATAATGCCGACAAAGGC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t327846\t1840959\t2.2.2.2.7\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative1831783-2.2.2.1.2\tTTTTCCGGGCTTATCGGCAACGCTATTCTGGCC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t337022\t1831783\t2.2.2.1.2\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative1825773-2.2.2.2.2\tCATCCCGGTTCATAGCGGCTCCGCTACGCTAAA\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t343032\t1825773\t2.2.2.2.2\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative1760974-2.2.3.1.3\tTCGCGATGCGCAGGTCGGAGAAATCGCGCTAAA\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t407831\t1760974\t2.2.3.1.3\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative1697407-2.2.2.2.1.5\tACACTGCCCAGAATAAGCGACACACAGCGCGCC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t471398\t1697407\t2.2.2.2.1.5\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\thei'..b'L.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative3204925-2.2.3.1.5\tCTCGCTGGCAAGCAGTGCGGGTACTATCGGCGG\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t175791\t3204925\t2.2.3.1.5\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-3212817-2.2.2.2\tCAAAACTACGAATACGACGCAGCGGGCGACCGT\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t183683\t3212817\t2.2.2.2\tTrue\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative3230678-2.2.2.1.1.1\tAGCGGTGCGCCAAACCACCCGGAATGATGAGTG\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t201544\t3230678\t2.2.2.1.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative3233869-2.1.1.1.1\tCAGCGCTGGTATGTGGCTGCACCATCGTCATTA\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t204735\t3233869\t2.1.1.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative3254229-2.2.3.1.3\tCGCCACCACGCGGTTAGCGTCACGCTGACATTC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t225095\t3254229\t2.2.3.1.3\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative3257074-2.2.1\tCGGCAACCAGACCGACTACGCCGCCAAGCAGAC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t227940\t3257074\t2.2.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative3264474-2.2.2.1.1.1\tAATGGCGCCGATCGTCGCCAGATAACCGTTGCC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t235340\t3264474\t2.2.2.1.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative3267927-2.2.2.2.2.1\tAAAGAGAAATATGATGCCAGGCTGATACATGAC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t238793\t3267927\t2.2.2.2.2.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative3278067-1.1\tTGTGAGTAAGTTGCGCGATATTCTGCTGGATTC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t248933\t3278067\t1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative3299717-2.2.3.1.4\tATGCCGGACAGCAGGCGAAACTCGAACCGGATA\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t270583\t3299717\t2.2.3.1.4\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative3305400-2.1.1.1\tCATCGTGAAGCAGAACAGACGCGCATTCTTGCT\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t276266\t3305400\t2.1.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-3324813-2.2.2.2\tCAGATGAAGCGGGCGCAGGATAACTTCAAGGCC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t295679\t3324813\t2.2.2.2\tTrue\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative3373069-2.2.2.2.1.1\tCTCTCCAGAAGATGAAGCCCGTGATGCGGCGCA\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t344042\t3373069\t2.2.2.2.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative3408895-2.1.1\tACAGTAAAAACAGGATCTGCTGCGAGGCCAGAC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t379868\t3408895\t2.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n-negative3436797-2.2.2.1.2\tATGCGGTATTCCTTGGCGTCGGCACCTATCAGT\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t407770\t3436797\t2.2.2.1.2\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n'

diff -r e9fd173fc7ee -r 4654c51dae72 test-data/results.tab
--- a/test-data/results.tab Fri Apr 20 10:44:35 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-sample scheme scheme_version subtype all_subtypes tiles_matching_subtype are_subtypes_consistent n_tiles_matching_all n_tiles_matching_all_expected n_tiles_matching_positive n_tiles_matching_positive_expected n_tiles_matching_subtype n_tiles_matching_subtype_expected file_path qc_status qc_message
-SRR1002850_SMALL.fasta 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 2154958-2.2.2.2.1.4; 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 True 202 202 17 17 3 3 /tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta PASS

diff -r e9fd173fc7ee -r 4654c51dae72 test-data/tech_results.tab
--- a/test-data/tech_results.tab Fri Apr 20 10:44:35 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-sample subtype qc_status qc_message
-SRR1002850_SMALL.fasta 2.2.2.2.1.4 PASS