Galaxy |

Changeset 0:c6e29bb1ab31 (2018-08-15)

Next changeset 1:1f8eccf9d15d (2018-11-05)

Commit message:
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c

added:
biohansel.xml
test-data/SRR1002850_SMALL.fasta
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
test-data/SRR5646583_SMALL_1.fastq
test-data/SRR5646583_SMALL_2.fastq

diff -r 000000000000 -r c6e29bb1ab31 biohansel.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biohansel.xml Wed Aug 15 10:34:50 2018 -0400

[

b'@@ -0,0 +1,423 @@\n+<tool id="biohansel" name="biohansel" version="2.1.0">\n+ <description>SNP subtyping of genome sequence reads or assemblies</description>\n+ <requirements>\n+ <requirement type="package" version="2.1.0">bio_hansel</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code">\n+<![CDATA[\n+\n+#import re\n+\n+## Illumina FASTQ naming regular expression (https://github.com/phac-nml/biohansel/issues/38)\n+#set global $ILLUMINA_REGEX = $re.compile(r\'^([\\w\\-\\_]+)_S\\d+_L\\d{3}_R(\\d)_001\\.fastq(\\.gz)?$\')\n+\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 $data_input.is_of_type(\'fastq.gz\')\n+#end def\n+\n+#def get_fastq_ext($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+#def base_sample_name($name)\n+ ## Get the base sample name and append 1/2 depending on if forward/reverse read\n+ #set $illumina_match = $ILLUMINA_REGEX.match($name)\n+ #if $illumina_match\n+ #return $illumina_match.group(1)\n+ #elif $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 $name\n+ #end if\n+#end def\n+\n+#def get_paired_fastq_filename($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+ #set $name = $base_sample_name($name)\n+ #set $postfix = \'1\' if $is_forward else \'2\'\n+ #set $ending = \'_{}{}\'.format($postfix, $get_fastq_ext($data_input))\n+ #return \'"{}"\'.format($name) if $ending in $name else \'"{}{}"\'.format($name, $ending)\n+#end def\n+\n+## Create symlinks from Galaxy *.dat to <sample_name>(.fasta|.fastq|.fastq.gz)\n+#if $input.type == \'fasta\'\n+ #set $input_files = \'"{}"\'.format($input.fasta.name)\n+ ln -s "$input.fasta" $input_files &&\n+#elif $input.type == \'paired\'\n+ #set $forward_filename = $get_paired_fastq_filename($input.forward)\n+ #set $reverse_filename = $get_paired_fastq_filename($input.reverse, is_forward=False)\n+ #set $input_files = \'{} {}\'.format($forward_filename, $reverse_filename)\n+ ln -s "$input.forward" $forward_filename &&\n+ ln -s "$input.reverse" $reverse_filename &&\n+#elif $input.type == \'single\'\n+ #set $input_files = \'"{}"\'.format($input.single.name)\n+ ln -s "$input.single" $input_files &&\n+#elif $input.type == \'paired_collection\'\n+ #set $forward_filename = $get_paired_fastq_filename($input.paired_collection.forward)\n+ #set $reverse_filename = $get_paired_fastq_filename($input.paired_collection.reverse, is_forward=False)\n+ #set $input_files = \'{} {}\'.format($forward_filename, $reverse_filename)\n+ ln -s "$input.paired_collection.forward" $forward_filename &&\n+ ln -s "$input.paired_collection.reverse" $reverse_filename &&\n+#end if\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\' \'$type_of_scheme.scheme_input.name\' &&\n+ #end if\n+#end if\n+\n+#def get_subtype_metadata_filename($data_input)\n+ ## Ensure that the subtype metadata table file has the proper extension - .tab or .csv\n+ #set $filename = $data_input.name\n+ #if $data_input.is_of_type(\'tabular\')\n+ #return \'{}.tab\'.format($filename)\n+ #elif $data_input.is_of_type(\'csv\')\n+ #return \'{}.csv\'.format($filename)\n+ #else\n+ #return None\n+ #end if\n+#end def\n+\n+## Symlink to subtype metadata table if it is specified\n+#if $subtype_metadata\n+ #set global $subtype_metadata_filename = $get_subtype_metadata_filename($subtype_metadata)\n+ #if $subtype_metadata_filename\n+ ln -s \'$subtype_metadata\' \'$subtype_metadata_filename\' &&\n+ '..b'----+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+\n+\n+Contents of ``match_results.tab``:\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 202 lines omitted.*\n+\n+\n+**Example Subtype Metadata**\n+\n+A column with name `subtype` must exist and should have subtype designations that would appear in your biohansel results. There are no requirements for the number of columns or contents of those columns in the table - they can contain whatever you want.\n+\n+\n+ +-------------+-------+--------+------------------+\n+ | subtype | clade | source | disease_symptoms |\n+ +-------------+-------+--------+------------------+\n+ | 1 | I | geese | death |\n+ +-------------+-------+--------+------------------+\n+ | 1.1 | I | moose | burns |\n+ +-------------+-------+--------+------------------+\n+ | 2.2.1.1.1 | II | mouse | boils |\n+ +-------------+-------+--------+------------------+\n+ | 2.2.2.2.1.4 | IIa | house | rash |\n+ +-------------+-------+--------+------------------+\n+\n+The `biohansel` results table will be joined with the subtype metadata table on the `subtype` field so if there are subtype metadata for your `biohansel` results, it will show up in the final output table. For example, if you have a sample that produces a result with subtype "1", there will also be columns "clade", "source" and "disease_symptoms" with "I", "geese" and "death", respectively.\n+\n+\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+</tool>\n'

diff -r 000000000000 -r c6e29bb1ab31 test-data/SRR1002850_SMALL.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR1002850_SMALL.fasta Wed Aug 15 10:34:50 2018 -0400

b'@@ -0,0 +1,766 @@\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 000000000000 -r c6e29bb1ab31 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 Aug 15 10:34:50 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 000000000000 -r c6e29bb1ab31 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 Aug 15 10:34:50 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 000000000000 -r c6e29bb1ab31 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 Aug 15 10:34:50 2018 -0400

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

diff -r 000000000000 -r c6e29bb1ab31 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 Aug 15 10:34:50 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 000000000000 -r c6e29bb1ab31 test-data/SRR5646583_SMALL-results.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR5646583_SMALL-results.tab Wed Aug 15 10:34:50 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 000000000000 -r c6e29bb1ab31 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 Aug 15 10:34:50 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 000000000000 -r c6e29bb1ab31 test-data/SRR5646583_SMALL_1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR5646583_SMALL_1.fastq Wed Aug 15 10:34:50 2018 -0400

b'@@ -0,0 +1,20000 @@\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 000000000000 -r c6e29bb1ab31 test-data/SRR5646583_SMALL_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR5646583_SMALL_2.fastq Wed Aug 15 10:34:50 2018 -0400