| Next changeset 1:c7fda6e88567 (2024-10-01) |
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Commit message:
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303" |
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added:
kmc.xml kmc_tools_filter.xml kmc_tools_simple.xml kmc_tools_transform.xml macros.xml test-data/F3D0_R1.fastq test-data/F3D1_R1.fastq test-data/compact_3_db.kmc_pre test-data/compact_3_db.kmc_suf test-data/contig_kmer27.kmc_pre test-data/contig_kmer27.kmc_suf test-data/contigs.fa test-data/counters_subtract_sum_db.kmc_pre test-data/counters_subtract_sum_db.kmc_suf test-data/db.kmc_pre test-data/db.kmc_suf test-data/dump.txt test-data/filtered_1.fastq test-data/filtered_2.fastq test-data/histogram.txt test-data/intersect_max_db.kmc_pre test-data/intersect_max_db.kmc_suf test-data/intersect_min_db.kmc_pre test-data/intersect_min_db.kmc_suf test-data/kmers_one.kmc_pre test-data/kmers_one.kmc_suf test-data/kmers_two.kmc_pre test-data/kmers_two.kmc_suf test-data/reduce_1_db.kmc_pre test-data/reduce_1_db.kmc_suf test-data/sort_1_db.kmc_pre test-data/sort_1_db.kmc_suf test-data/sort_2_db.kmc_pre test-data/sort_2_db.kmc_suf test-data/union_db.kmc_pre test-data/union_db.kmc_suf |
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| diff -r 000000000000 -r ca2743037241 kmc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kmc.xml Tue Sep 27 05:20:06 2022 +0000 |
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| @@ -0,0 +1,125 @@ +<tool id="kmc" name="KMC Counter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > + <description>K-mer counting and filtering of reads</description> + <xrefs> + <xref type='bio.tools'>kmc</xref> + </xrefs> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + kmc + -t\${GALAXY_SLOTS:-4} + #if $params.k: + -k'$params.k' + #end if + #if $params.m: + -m'$params.m' + #end if + #if $params.j: + -j'$statistic' + #end if + #if $params.exclude_length: + -ci'$params.exclude_length' + #end if + #if $params.max_counter_value: + -cs'$params.max_counter_value' + #end if + #if $input_file.is_of_type("fastq"): + -fq + #elif $input_file.is_of_type("fasta"): + -fm + #elif $input_file.is_of_type("bam"): + -fbam + #elif $input_file.is_of_type("kmc_suf"): + -fkmc + #end if + $input_file + db + . + + ]]></command> + <inputs> + <expand macro="macro_input" /> + <section name="params" title="parameter" expanded="false"> + <param argument="-k" type="integer" value="25" label="k-mer length (k from 1 to 256; default: 25)" /> + <param argument="-m" type="integer" value="12" label="max amount of RAM in GB (from 1 to 1024); default: 12" /> + <param name="signature_length" arguments="-p" type="integer" value="9" label="signature length (5, 6, 7, 8, 9, 10, 11); default: 9"/> + <param name="exclude_length" arguments="-ci" type="integer" value="2" label="exclude k-mers occurring less than [value] times (default: 2)"/> + <param name="max_counter_value" arguments="-cs" type="integer" value="255" label="maximal value of a counter (default: 255)"/> + <param name="exclude_kmer_occurence" arguments="-cx" type="integer" value="1000000000" label="xclude k-mers occurring more of than [value] times (default: 1e9)"/> + <param argument="-j" type="boolean" truevalue="-j" falsevalue="" checked="True" label="file name with execution summary in JSON format"/> + </section> + </inputs> + <outputs> + <data format="json" name="statistic" label="${tool.name} on ${on_string}"> + <filter>params['j']</filter> + </data> + <collection name="kmc_db" type="list" label="${tool.name} on ${on_string}: kmc db"> + <data format="binary" name="db.kmc_suf" label="${tool.name} on ${on_string}" from_work_dir="db.kmc_suf" /> + <data format="binary" name="db.kmc_pre" label="${tool.name} on ${on_string}" from_work_dir="db.kmc_pre" /> + </collection> + </outputs> + + <tests> + <test> + <!-- #1 test fastq with common parameters --> + <param name="input_file" value="F3D0_R1.fastq" ftype="fastq"/> + <param name="k" value="25" /> + <param name="m" value="12" /> + <param name="p" value="9" /> + <param name="ci" value="2" /> + <param name="cs" value="255" /> + <output name="db.kmc_suf" file="db.kmc_suf" ftype="binary" /> + <output name="db.kmc_pre" file="db.kmc_pre" ftype="binary" /> + </test> + <test> + <!-- #2 test fasta with common parameters --> + <param name="input_file" value="contigs.fa" ftype="fasta"/> + <param name="k" value="27" /> + <param name="m" value="24" /> + <param name="ci" value="2" /> + <param name="cs" value="255" /> + <param name="fm" value="-fm" /> + <output name="contig_kmer27.kmc_suf" file="contig_kmer27.kmc_suf" ftype="binary" /> + <output name="contig_kmer27.kmc_pre" file="contig_kmer27.kmc_pre" ftype="binary" /> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +*K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.* + + +**Input** + +- input file - FASTA, FASTQ and BAM. Also, gipped versions of FASTA and FASTQ. + +**Example:** + +- kmc -k27 -m24 NA19238.fastq NA.res /data/kmc_tmp_dir/ +- kmc -k27 -m24 @files.lst NA.res /data/kmc_tmp_dir/ + +**Output** + +- filename.res.kmc_suf +- filename.res.kmc_pre + + +.. class:: infomark + +**References** + +More information are available on `website <http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about>`_. + ]]></help> + <citations> + <citation type="doi">DOI: 10.1093/bioinformatics/btx304</citation> + <citation type="doi">DOI: 10.1093/bioinformatics/btv022</citation> + <citation type="doi">DOI: 10.1186/1471-2105-14-160</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r ca2743037241 kmc_tools_filter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kmc_tools_filter.xml Tue Sep 27 05:20:06 2022 +0000 |
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| @@ -0,0 +1,134 @@ +<tool id="kmc_filter" name="KMC filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > + <description>filtering KMC's database</description> + <xrefs> + <xref type='bio.tools'>kmc</xref> + </xrefs> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + #for $f in $input_collection: + #if '.kmc_suf' in str($f.element_identifier) + ln -s '${f}' db.kmc_suf && + #else + ln -s '${f}' db.kmc_pre && + #end if + #end for + kmc_tools + filter + -t\${GALAXY_SLOTS:-2} + #if $t: + '$t' + #end if + #if $hm: + '$hm' + #end if + db + -ci'$min_kmer_occurrence' + -cx'$max_kmer_occurrence' + $input_read_file + -f'$input_format' + -ci'$exclude_length' + -cx'$exclude_kmer_occurence' + #if str($output_format) == 'q': + $filter_output_fastq + #else + $filter_output_fasta + #end if + -f'$output_format' + + ]]></command> + <inputs> + <param name="input_collection" type="data_collection" collection_type="list" label="KMC db"/> + <param name="input_read_file" type="data" format="fastq,fasta" label="input read file" help="Input file format FASTQ/FASTA [default:FASTQ]"/> + <expand macro="input_option"/> + <param name="input_format" argument="-f" type="select" label="input read file format [default:FASTQ]"> + <option value="q" selected="true">FASTQ</option> + <option value="a">FASTA</option> + </param> + <param argument="-t" type="boolean" truevalue="-t" falsevalue="" checked="false" label="trim reads" help="trim reads on first invalid k-mer instead of remove entirely"/> + <param argument="-hm" type="boolean" truevalue="-hm" falsevalue="" checked="false" label="hard mask" help="hard mask invalid k-mers in a read"/> + <expand macro="general_option"/> + <param name="output_format" argument="-f" type="select" label="output read file format [default:FASTQ]"> + <option value="q" selected="true">FASTQ</option> + <option value="a">FASTA</option> + </param> + </inputs> + <outputs> + <data name="filter_output_fastq" format="fastq" label="${tool.name} on ${on_string}: filter"> + <filter>'q' in output_format</filter> + </data> + <data name="filter_output_fasta" format="fasta" label="${tool.name} on ${on_string}: filter"> + <filter>'a' in output_format</filter> + </data> + + </outputs> + + <tests> + <test> + <!-- #1 test with common parameters --> + <param name="input_collection"> + <collection type="list"> + <element name="db.kmc_suf" value="db.kmc_suf" dbkey="89"/> + <element name="db.kmc_pre" value="db.kmc_pre" dbkey="89"/> + </collection> + </param> + <param name="input_read_file" value="F3D0_R1.fastq" ftype="fastq"/> + <param name="min_kmer_occurrence" value="3" /> + <param name="exclude_length" value="2" /> + <param name="exclude_kmer_occurence" value="10" /> + <output name="filtered_1.fastq" file="filtered_1.fastq" ftype="fastq" /> + </test> + <test> + <!-- #2 test with common parameters --> + <param name="input_collection"> + <collection type="list"> + <element name="db.kmc_suf" value="db.kmc_suf" dbkey="89"/> + <element name="db.kmc_pre" value="db.kmc_pre" dbkey="89"/> + </collection> + </param> + <param name="input_read_file" value="F3D0_R1.fastq" ftype="fastq"/> + <param name="exclude_length" value="10" /> + <param name="exclude_kmer_occurence" value="100" /> + <output name="filtered_2.fastq" file="filtered_2.fastq" ftype="fastq" /> + </test> + + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +*K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.* + +**Input** + +- input file - FASTA, FASTQ and BAM. Also, gipped versions of FASTA and FASTQ. + +**Command line Example:** + +- kmc_tools filter kmc_db -ci3 input.fastq -ci0.5 -cx1.0 filtered_1.fastq +- kmc_tools filter kmc_db input.fastq -ci10 -cx100 filtered_2.fastq + +**Output** + +- filtered_1.fastq +- filtered_2.fastq + + +.. class:: infomark + +**References** + +More information are available on `website <http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about>`_. + ]]></help> + <citations> + <citation type="doi">DOI: 10.1093/bioinformatics/btx304</citation> + <citation type="doi">DOI: 10.1093/bioinformatics/btv022</citation> + <citation type="doi">DOI: 10.1186/1471-2105-14-160</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r ca2743037241 kmc_tools_simple.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kmc_tools_simple.xml Tue Sep 27 05:20:06 2022 +0000 |
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| b'@@ -0,0 +1,425 @@\n+<tool id="kmc_simple" name="KMC simple" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >\n+ <description>simple operations for two input kmer sets</description>\n+ <xrefs>\n+ <xref type=\'bio.tools\'>kmc</xref>\n+ </xrefs>\n+ <macros>\n+\t <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="stdio" />\n+ <expand macro="version_command" /> \n+ <command><![CDATA[\n+\t mkdir outdir &&\n+\t #for $f in $input_collection_one:\n+\t \t#if \'.kmc_suf\' in str($f.element_identifier)\n+\t \t ln -s \'${f}\' kmers_db_one.kmc_suf &&\n+\t #else\n+\t \t ln -s \'${f}\' kmers_db_one.kmc_pre &&\n+\t #end if\n+\t #end for\n+\t #for $f in $input_collection_two:\n+ #if \'.kmc_suf\' in str($f.element_identifier)\n+ ln -s \'${f}\' kmers_db_two.kmc_suf &&\n+ #else\n+ ln -s \'${f}\' kmers_db_two.kmc_pre &&\n+ #end if\n+ #end for\n+\t kmc_tools \n+\t -t\\${GALAXY_SLOTS:-4}\n+\t simple\n+\t #if $input_options_cond.input_param == "None":\n+\t kmers_db_one\n+\t \t kmers_db_two\n+\t #elif $input_options_cond.input_param == "kmc_one_params":\n+\t kmers_db_one\n+\t \t -ci\'$input_options_cond.kmc_db_one_param.min_kmer_occurrence\'\n+\t -cx\'$input_options_cond.kmc_db_one_param.max_kmer_occurrence\'\n+\t\t kmers_db_two\n+\t #elif $input_options_cond.input_param == "kmc_two_params":\n+\t kmers_db_one \n+\t \t kmers_db_two\n+\t -ci\'$input_options_cond.kmc_db_two_param.min_kmer_occurrence\'\n+ -cx\'$input_options_cond.kmc_db_two_param.max_kmer_occurrence\'\n+\t #elif $input_options_cond.input_param == "both_kmc_params":\n+\t\t kmers_db_one\n+\t -ci\'$input_options_cond.both_db_one_param.min_kmer_occurrence\'\n+ -cx\'$input_options_cond.both_db_one_param.max_kmer_occurrence\'\n+ kmers_db_two\n+ -ci\'$input_options_cond.both_db_two_param.min_kmer_occurrence\'\n+ -cx\'$input_options_cond.both_db_two_param.max_kmer_occurrence\'\n+\t #end if\n+\t #set $operation_arr=[]\n+\t #for $i,$opt in enumerate($operations)\n+\t #silent $operation_arr.append(str($opt.ops.select_operation))\n+\t \t #if str($opt.ops.select_operation) == "intersect":\n+\t \t\t$opt.ops.select_operation\n+\t\t\t#if str($opt.ops.add_output_params.oc) != \'None\': \n+\t \t\t \'${opt.ops.select_operation}_${opt.ops.add_output_params.oc}_db\'\n+\t -oc\'$opt.ops.add_output_params.oc\'\n+\t \t\t#else\n+\t \t\t \'${opt.ops.select_operation}_min_db\'\n+\t \t\t -oc\'min\'\n+\t \t\t#end if\n+\t\t \t#if str($opt.ops.add_output_params.min_kmer_occurrence) != \'\':\n+\t \t\t-ci\'$opt.ops.add_output_params.min_kmer_occurrence\'\n+\t \t#end if\n+\t \t#if str($opt.ops.add_output_params.max_kmer_occurrence) != \'\':\n+\t \t\t-cx\'$opt.ops.add_output_params.max_kmer_occurrence\'\n+\t \t \t#end if\n+\t \t #elif str($opt.ops.select_operation) == "union":\n+\t\t\t$opt.ops.select_operation\n+ #if str($opt.ops.add_output_params.oc) != \'None\':\n+ \'${opt.ops.select_operation}_${opt.ops.add_output_params.oc}_db\'\n+ -oc\'$opt.ops.add_output_params.oc\'\n+ #else \n+\t \t \'${opt.ops.select_operation}_sum_db\' \n+\t \t\t -oc\'sum\'\n+ #end if\n+ #if str($opt.ops.add_output_params.min_kmer_occurrence) != \'\':\n+ -ci\'$opt.ops.add_output_params.min_kmer_occurrence\'\n+ #end if\n+ #if str($opt.ops.add_output_params.max_kmer_occurrence) != \'\':\n+ -cx\'$opt.ops.add_output_params.max_kmer_occurrence\'\n+\t \t\t#end if\n+ \t\t #elif str($opt.ops.select_operation) == "kmers_subtract":\n+ $opt.ops.select_operation\n+\t \t\t'..b'+ </section>\n+ <output_collection name="kmc_db" type="list">\n+ <element name="counters_subtract_sum_db.kmc_suf" file="counters_subtract_sum_db.kmc_suf"/>\n+ <element name="counters_subtract_sum_db.kmc_pre" file="counters_subtract_sum_db.kmc_pre"/>\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+\n+**What it does**\n+\t \n+*KMC simple operation performs set operation on two input KMC\'s databases*\n+\n+**General Syntax**\n+\n+kmc_tools simple <input1 [input1_params]> <input2 [input2_params]> <oper1 output1 [output_params1]> [<oper2 output2 [output_params2]> ...]\n+\n+**Input:**\n+\t \n+- input file - input1 and input2 are the databases generated by KMC ( kmc file suffix - kmc_pre and kmc_suf )\n+\n+**Available Operations:**\n+\n+- intersect - output database will contains only k-mers that are present in both input sets\n+- union - output database will contains each k-mer present in any of input sets\n+- kmers_subtract - difference of input sets based on k-mers. Output database will contains only k-mers that are present in first input set but absent in the second one\n+- counters_subtract - difference of input sets based on k-mers and their counters (weaker version of kmers_subtract). Output database will contains all k-mers that are present in first input, beyond those for which counter operation will lead to remove (i.e. counter equal to 0 or negative number)\n+- reverse_kmers_subtract - same as kmers_subtract but treat input2 as first and input1 as second\n+- reverse_counters_subtract - same as counters_subtract but treat input2 as first and input1 as second\n+\n+**Additional Parameters for inputs:**\n+\n+- ci<value> - exclude k-mers occurring less than <value> times\t\t\n+- cx<value> - exclude k-mers occurring more of than <value> times\n+\n+**Additional Parameters for outputs:**\n+\n+- ci<value> - exclude k-mers occurring less than <value> times\n+- cx<value> - exclude k-mers occurring more of than <value> times\n+- cs<value> - maximal value of a counter\n+- o<kmc|kff> - output in KMC or KFF format (default: kmc)\n+- oc<value> - redefine counter calculation mode for equal k-mers\n+\n+**Available oc<value>**\n+\n+- min - get lower value of a k-mer counter (default value for intersect operation)\n+- max - get upper value of a k-mer counter\n+- sum - get sum of counters from both databases\n+- diff - get difference between counters (default for counters_subtract operation)\n+- left - get counter from first database (input1)\n+- right - get counter from second database (input2)\n+\n+\n+**Example(1):**\n+\n+- kmc -k27 file1.fastq kmers1 kmc_tmp_dir\n+- kmc -k27 file2.fastq kmers2 kmc_tmp_dir\n+- kmc_tools simple kmers1 -ci10 -cx200 kmers2 -ci4 -cx100 intersect kmers1_kmers2_intersect -ci20 -cx150\n+\n+**Output(1)**\n+\n+- kmers1_kmers2_intersect.kmc_suf (i.e intersect_kmc_suf in galaxy)\n+- kmers1_kmers2_intersect.kmc_pre (i.e intersect_kmc_pre in galaxy)\n+\n+**Example(2):**\n+\n+- kmc -k27 file1.fastq kmers1 kmc_tmp_dir\n+- kmc -k27 file2.fastq kmers2 kmc_tmp_dir\n+- kmc_tools simple kmers1 kmers2 intersect inter_k1_k2_max -ocmax intersect inter_k1_k2_min union union_k1_k2 -ci10\n+\n+**Output(2)**\n+\n+- inter_k1_k2_max.kmc_suf (i.e intersect.kmc_suf in galaxy)\n+- inter_k1_k2_max.kmc_pre (i.e intersect.kmc_pre in galaxy)\n+- inter_k1_k2_min.kmc_suf (i.e intersect.kmc_suf in galaxy)\n+- inter_k1_k2_min.kmc_pre (i.e intersect.kmc_pre in galaxy)\n+- union_k1_k2.kmc_suf (i.e union.kmc_suf in galaxy)\n+- union_k1_k2.kmc_pre (i.e union.kmc_pre in galaxy\n+ \n+.. class:: infomark\n+\t \n+**References**\n+\n+More information are available on `website <https://github.com/refresh-bio/KMC/blob/master/kmc_tools.pdf>`_.\n+\t]]></help>\n+ <citations>\n+ <citation type="doi">DOI: 10.1093/bioinformatics/btx304</citation>\n+\t<citation type="doi">DOI: 10.1093/bioinformatics/btv022</citation>\n+\t<citation type="doi">DOI: 10.1186/1471-2105-14-160</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r ca2743037241 kmc_tools_transform.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kmc_tools_transform.xml Tue Sep 27 05:20:06 2022 +0000 |
| [ |
| b'@@ -0,0 +1,320 @@\n+<tool id="kmc_transform" name="KMC transform" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >\n+ <description>single KMC\'s database</description>\n+ <xrefs>\n+ <xref type=\'bio.tools\'>kmc</xref>\n+ </xrefs>\n+ <macros>\n+\t <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="stdio" />\n+ <expand macro="version_command" /> \n+ <command><![CDATA[\n+\t mkdir outdir &&\n+\t #for $f in $input_collection:\n+\t \t#if \'.kmc_suf\' in str($f.element_identifier)\n+\t \t ln -s \'${f}\' db.kmc_suf &&\n+\t #else\n+\t \t ln -s \'${f}\' db.kmc_pre &&\n+\t #end if\n+\t #end for\n+\t kmc_tools \n+\t -t\\${GALAXY_SLOTS:-2}\n+\t transform\n+\t db \n+ #set $operation_arr=[]\n+ #for $i,$opt in enumerate($operations)\n+\t \t #silent $operation_arr.append(str($opt.ops.transform_operation))\n+\t\t #set $i = $i + 1\n+\t \t #if str($opt.ops.transform_operation) == "sort" or str($opt.ops.transform_operation) == "reduce" or str($opt.ops.transform_operation) == "compact":\n+\t \t\t#if str($opt.ops.input_opt.min_kmer_occurrence) != \'\':\n+\t \t\t -ci\'$opt.ops.input_opt.min_kmer_occurrence\'\n+\t\t\t#end if\n+\t \t #if str($opt.ops.input_opt.max_kmer_occurrence) != \'\':\n+\t \t\t -cx\'$opt.ops.input_opt.max_kmer_occurrence\'\n+\t\t #end if\n+\t\t\t $opt.ops.transform_operation\n+\t \t\t \'${opt.ops.transform_operation}_${i}_db\'\n+\t \t\t#if str($opt.ops.output_opt.min_kmer_occurrence) != \'\':\n+\t\t\t -ci\'$opt.ops.output_opt.min_kmer_occurrence\'\n+\t\t\t#end if\n+\t \t\t#if str($opt.ops.output_opt.max_kmer_occurrence) != \'\':\n+\t \t\t -cx\'$opt.ops.output_opt.max_kmer_occurrence\'\n+\t\t\t#end if\n+\t \t\t#if str($opt.ops.output_opt.max_counter_value) != \'\':\n+\t \t\t -cs\'$opt.ops.output_opt.max_counter_value\'\n+\t \t\t#end if\n+\t\t #elif str($opt.ops.transform_operation) == "histogram":\n+\t \t #if str($opt.ops.input_opt.min_kmer_occurrence) != \'\':\n+ -ci\'$opt.ops.input_opt.min_kmer_occurrence\'\n+ #end if\n+ #if str($opt.ops.input_opt.max_kmer_occurrence) != \'\':\n+ -cx\'$opt.ops.input_opt.max_kmer_occurrence\'\n+ #end if\n+ $opt.ops.transform_operation\n+ \'${opt.ops.transform_operation}\'.txt\n+ #if str($opt.ops.output_opt.min_kmer_value) != \'\':\n+ -ci\'$opt.ops.output_opt.min_kmer_value\'\n+ #end if\n+ #if str($opt.ops.output_opt.max_kmer_value) != \'\':\n+ -cx\'$opt.ops.output_opt.max_kmer_value\'\n+\t \t\t#end if\n+\t\t #elif str($opt.ops.transform_operation) == "dump":\n+\t \t\t#if str($opt.ops.input_opt.min_kmer_occurrence) != \'\':\n+ -ci\'$opt.ops.input_opt.min_kmer_occurrence\'\n+ #end if\n+ #if str($opt.ops.input_opt.max_kmer_occurrence) != \'\':\n+ -cx\'$opt.ops.input_opt.max_kmer_occurrence\'\n+ #end if\n+\t \t\t $opt.ops.transform_operation\n+\t \t\t#if str($opt.ops.output_opt.sort_output) == "true":\n+\t \t\t -s\n+\t\t \t#end if\n+\t \t\t \'${opt.ops.transform_operation}\'.txt\n+\t \t #elif str($opt.ops.transform_operation) == "set_counts":\n+ #if str($opt.ops.input_opt.min_kmer_occurrence) != \'\':\n+ -ci\'$opt.ops.input_opt.min_kmer_occurrence\'\n+ #end if\n+ #if str($opt.ops.input_opt.max_kmer_occurrence) != \'\':\n+ -cx\'$opt.ops.input_opt.max_kmer_occurrence\'\n+ #end if\n+\t\t\t $opt.ops.transform_operation\n+ $opt.ops.input_opt.kmer_counts_value \n+\t \t\t \'${opt.ops.transform_operation}_${i}_db\'\n+ #end if\n+ #end for\n+\n+\t #for'..b'peat name="operations">\n+ <conditional name="ops">\n+ <param name="transform_operation" value="reduce"/>\n+ </conditional>\n+ <section name="input_opt">\n+ <param name="min_kmer_occurrence" value="2"/>\n+ <param name="max_kmer_occurrence" value="20"/>\n+\t </section>\n+\t </repeat>\n+ <repeat name="operations">\n+ <conditional name="ops">\n+ <param name="transform_operation" value="sort"/>\n+ </conditional>\n+ <section name="input_opt">\n+ <param name="min_kmer_occurrence" value="3"/>\n+ <param name="max_kmer_occurrence" value="30"/>\n+ </section>\n+\t </repeat>\n+ <repeat name="operations"> \n+ <conditional name="ops">\n+ <param name="transform_operation" value="compact"/>\n+ </conditional>\n+ <section name="input_opt">\n+ <param name="min_kmer_occurrence" value="4"/>\n+ <param name="max_kmer_occurrence" value="40"/>\n+ </section>\n+\t </repeat>\n+ <output_collection name="kmc_db" type="list">\n+ <element name="reduce_1_db.kmc_suf" file="reduce_1_db.kmc_suf"/>\n+\t\t<element name="reduce_1_db.kmc_pre" file="reduce_1_db.kmc_pre"/>\n+\t <element name="sort_2_db.kmc_suf" file="sort_2_db.kmc_suf"/>\n+ <element name="sort_2_db.kmc_pre" file="sort_2_db.kmc_pre"/>\n+\t\t<element name="compact_3_db.kmc_suf" file="compact_3_db.kmc_suf"/>\n+ <element name="compact_3_db.kmc_pre" file="compact_3_db.kmc_pre"/>\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+**What it does**\n+\t \n+*This operation transforms single KMC database to one or more KMC database(s) or text file(s).*\n+\t \n+**Input**\n+\t \n+- input file - path to databases generated by KMC (KMC generates 2 files with the same name, but different extensions (i.e kmc_suf and kmc_pre).\n+\n+**Available Operations:**\n+\n+- sort - converts database produced by KMC2.x to KMC1.x database format (which contains k-mers in sorted order)\n+- reduce - exclude too rare and too frequent k-mers\n+- compact - remove counters of k-mers\n+- histogram - produce histogram of k-mers occurrences\n+- dump - produce text dump of kmc database\n+- set_counts <value> - set all k-mer counts to specific value\n+\n+**Generate KMC DB**\n+\n+- kmc -k27 file.fastq kmers_db kmc_tmp_dir\n+\n+**Example 1: split k-mers on a valid and invalid database**\n+\n+*Let\'s suppose k-mers with occurences below 11 are erroneous due to sequencing erros. With reduce we can split k-mer set to one set with valid k-mers and one with invalid:*\n+\n+- kmc_tools transform kmers_db reduce reduce_1_db -cx10 reduce reduce_2_db -ci11 histogram histogram.txt dump dump.txt\n+\n+**Example 2: perform all operations**\n+\n+- kmc_tools transform kmers_db reduce -ci10 reduce_1_db sort sort_2_db compact compact_3_db histogram histogram.txt dump dump.txt\n+\n+**Output**\n+\n+*Example 1:*\n+\n+- reduce_1_db.kmc_suf\n+- reduce_1_db.kmc_pre\n+- reduce_2_db.kmc_suf\n+- reduce_2_db.kmc_pre\n+- histogram\n+- dump\n+\n+*Example 2:*\n+\n+- reduce_1_db.kmc_suf\n+- reduce_1_db.kmc_pre\n+- sort_2_db.kmc_suf\n+- sort_2_db.kmc_pre\n+- compact_3_db.kmc_suf\n+- compact_3_db.kmc_pre\n+- histogram\n+- dump\n+\n+\n+ \n+.. class:: infomark\n+\t \n+**References**\n+\n+More information are available on `website <https://github.com/refresh-bio/KMC/blob/master/kmc_tools.pdf>`_.\n+\t]]></help>\n+ <citations>\n+ <citation type="doi">DOI: 10.1093/bioinformatics/btx304</citation>\n+\t<citation type="doi">DOI: 10.1093/bioinformatics/btv022</citation>\n+\t<citation type="doi">DOI: 10.1186/1471-2105-14-160</citation>\n+ </citations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r ca2743037241 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Sep 27 05:20:06 2022 +0000 |
| [ |
| @@ -0,0 +1,110 @@ +<macros> + <token name="@TOOL_VERSION@">3.2.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">kmc</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <xml name="version_command"> + <version_command><![CDATA[ + kmc --version 2>&1 | head -1 + ]]></version_command> + </xml> + <xml name="macro_input"> + <param name="input_file" type="data" format="fasta,fastq,fasta.gz,fastqsanger,fastq.gz,bam" label="Sequence file"/> + </xml> + <xml name="general_option"> + <param argument="exclude_length" type="integer" value="2" label="exclude k-mers occurring less than [value] times (default: 2)"/> + <param argument="exclude_kmer_occurence" type="integer" value="1000000000" label="exclude k-mers occurring more of than [value] times (default: 1e9)"/> + </xml> + <xml name="transform_option"> + <section name="input_opt" title="Input options" expanded="true"> + <expand macro="input_option"/> + </section> + <section name="output_opt" title="Output options" expanded="true"> + <expand macro="none_counter_calculation_option"/> + </section> + </xml> + <xml name="histogram_option"> + <section name="input_opt" title="Input options" expanded="true"> + <expand macro="input_option"/> + </section> + <section name="output_opt" title="Output options" expanded="true"> + <param name="min_kmer_value" argument="-ci" type="integer" value="2" optional="true" label="minimum value of counter to be stored in the output file"/> + <param name="max_kmer_value" argument="-cx" type="integer" value="255" optional="true" label="maximum value of counter to be stored in the output file"/> + </section> + </xml> + <xml name="set_count_option"> + <section name="input_opt" title="Input options" expanded="true"> + <expand macro="input_option"/> + <param argument="kmer_counts_value" type="integer" value="10" label="set all k-mer counts to specific value"/> + </section> + </xml> + <xml name="misc"> + <param name="misc_output" argument="-o" type="select" label="output in KMC or KFF format (default: kmc)"> + <option value="kmc" selected="true">KMC</option> + <option value="kff">KFF</option> + </param> + </xml> + <xml name="dump_option"> + <section name="input_opt" title="Input options" expanded="true"> + <expand macro="input_option"/> + </section> + <section name="output_opt" title="Output options" expanded="true"> + <param name="sort_output" argument="-s" type="boolean" truevalue="true" checked="false" label="sorted output"/> + </section> + </xml> + <xml name="input_option"> + <param name="min_kmer_occurrence" argument="-ci" type="integer" value="3" optional="true" label="exclude k-mers occurring less than x times"/> + <param name="max_kmer_occurrence" argument="-cx" type="integer" value="30" optional="true" label="exclude k-mers occurring more of than x times"/> + </xml> + <xml name="input_option_two"> + <param name="min_kmer_occurrence_two" argument="-ci" type="integer" value="3" label="exclude k-mers occurring less than x times"/> + <param name="max_kmer_occurrence_two" argument="-cx" type="integer" value="30" label="exclude k-mers occurring more of than x times"/> + </xml> + <xml name="simple_operation"> + <param name="select_operation" type="select" label="Simple Operation" help="redefine counter calculation mode for equal k-mers"> + <option value="intersect" selected="true">intersect</option> + <option value="union">union</option> + <option value="kmers_subtract">kmers_subtract</option> + <option value="reverse_kmers_subtract">reverse_kmers_subtract</option> + <option value="counters_subtract">counters_subtract</option> + <option value="reverse_counters_subtract">reverse_counters_subtract</option> + </param> + </xml> + <xml name="counter_calculation_option"> + <param name="min_kmer_occurrence" argument="-ci" type="integer" optional="true" label="exclude k-mers occurring less than x times"/> + <param name="max_kmer_occurrence" argument="-cx" type="integer" optional="true" label="exclude k-mers occurring more of than x times"/> + <param name="max_counter_value" argument="-cs" type="integer" optional="true" label="maximal value of a counter"/> + <param argument="-oc" name="oc" type="select" optional="true" label="Counter Calculation" help="redefine counter calculation mode for equal k-mers"> + <option value="min">min - get lower value of a k-mer counter</option> + <option value="max">max - get upper value of a k-mer counter</option> + <option value="sum">sum - get sum of counters from both databases</option> + <option value="diff">diff - get difference between counters </option> + <option value="left">left - get counter from first datatabase (KMC db one)</option> + <option value="right">right - get counter from second database (KMC db two)</option> + </param> + </xml> + <xml name="none_counter_calculation_option"> + <param name="min_kmer_occurrence" argument="-ci" type="integer" optional="true" label="exclude k-mers occurring less than x times"/> + <param name="max_kmer_occurrence" argument="-cx" type="integer" optional="true" label="exclude k-mers occurring more of than x times"/> + <param name="max_counter_value" argument="-cs" type="integer" optional="true" label="maximal value of a counter"/> + </xml> + <xml name="transform_operation"> + <param name="transform_operation" type="select" optional="true" label="Transform Operation" help="transforms single KMC database to one or more KMC database(s) or text file(s)"> + <option value="sort" >sort - converts database produced by KMC2.x to KMC1.x database format (which contains k-mers in sorted order)</option> + <option value="reduce">reduce - exclude too rare and too frequent k-mers</option> + <option value="compact">compact - remove counters of k-mers</option> + <option value="histogram">histogram - produce histogram of k-mers occurrences</option> + <option value="dump">dump - produce text dump of kmc database</option> + <option value="set_counts">set counts - set all k-mer counts to specific value</option> + </param> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/F3D0_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/F3D0_R1.fastq Tue Sep 27 05:20:06 2022 +0000 |
| b |
| b'@@ -0,0 +1,31172 @@\n+@M00967:43:000000000-A3JHG:1:1101:18327:1699 1:N:0:188\n+NACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\n++\n+#>>AABABBFFFGGGGGGGGGGGGGGGGHHHHHHHGGGHHHHHGHGGGGGGGHGGGGGGHHHHHHHHHHGGGGGHHHHGHGGGGGGHHBGHGDGGGGGHHHGGGGHHHHHHHHGGGGGHG@DHHGHEGGGGGGBFGGEGGGGGGGG.DFEFFFFFFFDCFFFFFFFFFFFFFFFFFFFFFFFFFFDFDFFFEFFCFF?FDFFFFFFFFAFFFFFFFFFFFBDDFFFFFEFADFFFFFBAFFFA?EFFFBFF\n+@M00967:43:000000000-A3JHG:1:1101:14069:1827 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\n++\n+3AA?ABBDBFFBEGGEGGGGAFFGGGGGHHHCGGGGGGHFGHGGCFDEFGGGHGGGEGF1GGFGHHHHHGGEGGHHHHHFGGGGGGHHHHHGGGGCDDGHHGGGFHHHHHHHHCD@CCHGGGGHEHGGG@GFGGGGGGG@BGGGEGCEBFFFBFFB;9@EFFFEFFFFFFFFFFFFAFBBBFFFFFBBBFFFFBBBFFFFFFFFFFFBBBBBBBFFFFFFFFFDDFAFFFFF.AF9/FBBBBB.EAFFE?F\n+@M00967:43:000000000-A3JHG:1:1101:18044:1900 1:N:0:188\n+TACGGAGGATGCGAGCGTTGTCCGGAATCACTGGGCGTAAAGGGCGCGTAGGCGGTTTAATAAGTCAGTGGTGAAAACTGAGGGCTCAACCCTCAGCCTGCCACTGATACTGTTAGACTTGAGTATGGAAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGATTCTCTGGGCCAAGACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACA\n++\n+BA@BBBABBFFFGGGGGGGGGGHGGGGGHHHHGHHHGGGGHHHGGGGGGGGGHGGGGGGFHFHHHFHHHHHHGFHHHHHHFHGGFGHHGGHGGHHFHHHHHHHHHHHHHHGHHHGHDHHHHHHHHHGHDGFFHHHDHHHHHHHHHHHHFHHHDGHHGGGGGHHHHHGGGGEGGGGGBF0BGGGGGGGGFFFGGGDGFFFFBCFBFFBFFBEEFFEFFFFFFFFBDA9EEFFF>DFFFFDDFFFADDFFFF.\n+@M00967:43:000000000-A3JHG:1:1101:13234:1983 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\n++\n+BCBCCCCCCFFFGGGGGGGGGGHGGGGGHHHHHHHGGGHHHHHGHGGGGGGGGGGGGGHHHHHHHHHHHGGGGGHHHHHHHHHGGHHHHHHHHGHHHGHGGGGGGHHHHHHHGHHGHHHGHHHHHHHGGGGGHHHHHHGGGGGHHGGGGHGHHHHGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFAFFFFFFFFAFFFFFFFFFFFFFFBFFFFFFFFFFEFFFF\n+@M00967:43:000000000-A3JHG:1:1101:16780:2259 1:N:0:188\n+TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGGACGCAAGTCAGATGTGAAAACCACGGGCTCAACCTGTGGCCTGCATTTGAAACTGTGTTTCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACG\n++\n+BBCCBFFCDFCFGGGGGGGGGGHGGGGGHHHHHHHHGGHFHHHGGGEGGHHHGGGGGGGEFGGGHHHHFHHHHGHHHHG/FGGGFGHFHHHGA?CGEHGGGHGHHFBGHHHGGHHHHDGHHFHFHHHHHEC0DDDEDAFFDDEGHHHHHEHHHHHEGGAFFGGGGBDGGGGGGFFFGGFFG.FFFFFFFFFFFFFFFDEFF@=FFFFFF.AFFEFFFFFFFDFFFBFF.:;F-@FFBDAFAAC.;9?FFE.\n+@M00967:43:000000000-A3JHG:1:1101:19378:2540 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\n++\n+CCCCCCCCCFFFGGGGGGGGGGHGGGGGHHHHHHGGGGHHHHHGFFGGGGGGGGGGGGHHHGHHHHHHHGGGGGHHHHHHHHHGGHHGGHHHHHHHHHHGGGGGGGHHHHHHHHHGHHHHHHHHHHHGGGGGGHHHHHGGGGGHHGGGGHGHHHHGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFDFFFFFFADFFFFFFFFAFFFFFFFFF\n+@M00967:43:000000000-A3JHG:1:1101:17674:2779 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAG\n++\n+ABB@BABDAFFFGGGGGGGGGGHGGGGGHHGHHGHGGGHFDHHGHEGCGGGGGGGFEECGHHHHHHHHHGGGGGHHHGGGGGGGGGHGHGHGGGGHHHGGGGDGGEHHHGFHHGGGFHHGHFHFHCGGGGGGGFGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF?FFFFFFFFFFFFFAFEFFFFFFFFFFBFFDFFFFFFFFFDBF/AEFFFF\n+@M00967:43:000000000-A3'..b'FFFFEFFFFFDFBBFBFEFFFFFDDDFFFFFFFFFFFF\n+@M00967:43:000000000-A3JHG:1:2114:17313:26856 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTGTTAAGTCAGCGGTCAAATGTCGGGGCTCAACCCCGGCCTGCCGTTGAAACTGGCGGCCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\n++\n+BBBBBBABBFFFGCEGGGGGGGHGGGGGHHHGHHGGGGHHHHGGHGGGFGGGHGGGGGFHHHGHHHHHHGGGGGHHF4FGE/DGFGHHHHHGGGCGGCFHHGGGGFHHHHHH.<DGGGHGDDHHGEEGGGGGGBFBFGGGGFFBFFFFF.AEFFFAFADFFFFFFFFFBFFFFFFFFEFA=FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFAFFC?BB.DFFFFFFFFBFD?./9.;>D.;BBFFFF;F\n+@M00967:43:000000000-A3JHG:1:2114:19678:27051 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\n++\n+BBABBBBDBFFFGGGGGGGGGGHGGGGGHHHHHHHEGGHHGHHGHGGGGGGGHGGGGGGHHHHHHHHHHGGGGGHHHHHHGGGGGGHHHHHGGGDGGGHHHGGGGHHHHHHHHGGGGGHGGGHHGHGGGGGGG0FFFGGGGGGGGGGGFEFFFFFFFDFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFFBFFFFFFBEFFFFFFFFFFFFFFFFFFFFFFBDDDFFFFFFFFFFFFFFFFFA;A.FFFFFF\n+@M00967:43:000000000-A3JHG:1:2114:14397:27192 1:N:0:188\n+TATGTATGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCAGGGCAAGCCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGGAACTGCCCCGCTCGAGTGCCGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACGGTGTACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAA\n++\n+BABBAFFFFF3AEGGGGG?EGGHG2EFDHBGHHGFHGGHHHBFGFEGCE?EGHGGGEGGGGGGGHEHGHFBDHHFGFHHHGEEGC/GGHHFGGGGCGGHHHHFHHHHGHGHHHHHGGGCGCGFHFEHGC?DCC@BGGGGBG@BGGBFEFFFFBFFFBBDBFEFFFFFFF?ABFFFFFFFFF?FFFFFFFFFFFBBBBDE;<-9AEF/FF?A@;..:BF/9/9.DADFFF.9AB-9AAFFA??B;ABAA//\n+@M00967:43:000000000-A3JHG:1:2114:18736:27579 1:N:0:188\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGAGACAAGTCTGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGCCTGACTGGAGTGCTGGAGAGGCAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAAA\n++\n+BBBBAFFBB@DDGGGGCGGGGGHGFDDFHHHHGHGFEEHHFHCGHGGGGDEGHGGGHG15FGHAHFHFHHGHGHHEFBCHGGGGGGHHHH0EDFC?CGHHHHHH2CCGHHHB10FGHHHHHHHGHF1GFCGFGC.FGEHGFGCGHHHHBCGGGHFHGCEDGGFFFGG?AFGGGGFBFGG0AAFFFFF?.BBF?DFFA?EAFFFFAEFFFFABFFFFFFFFFD9E?EFFE??=DBAAFD..9-9.-..BB.:\n+@M00967:43:000000000-A3JHG:1:2114:12060:27959 1:N:0:188\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTGTGCAAGTCTGAAGTGAAAGCCCGCGGCTCAACTGCGGAACGGCTTTGGAAACTGTGTAACTGGGGGGCTGGAGAGGTAAGCGGAATTCCGGGTGTAGCGGTGAAATGCGTAGAGATCAGGAGGAACACCGGCGGGGAAGGCGGCTTACTGGACAGTAACTGAGGTTGAGGCTCGAAGGCGGGGGGAGGAAAAG\n++\n+AAAAAFFA11ADAFCGFEFGGGHGGGGGHHBGHGGHCEHHHHHG/EFGEGGAGGGA>/B/BGHGHHFHE2FGHHHH1FCHE/EEGGGFHHFFGC//<CG/@<AGHCGHHB1F<<1@<1>G0.>----;?-9BB-9/99/@-@--;///9---9///;--9;/////9----9///;F//EABF?FF-=--@---;-AF-@-@@=/F/;//;/-;;B//9//9;--/9BE9-@@F---9-;@@--9-;B/-/\n+@M00967:43:000000000-A3JHG:1:2114:10980:28089 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATAACACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAG\n++\n+BBBBBABBABFFCGCGEFFEEGHE?E?EFGFHHGEFCDFHFBGGBFCECFGGHGGG?AA3D4GFBGDG3ECE/FFGFHHEFEDHFHHHBGGHBGHFDFFACCADG/GG1?G11CFE0F>FBGFDFHADCC@DHHHFH0<AC@CGHDFDA.;90F;AG.-EGB000C0BFBB00009EBBF-BBF/BDF?DEFD;BDFFFF..9B/FA--9-B-BBAB///9..DDFF/FFA.ADDBA9ADA.;:/AAB.@B\n+@M00967:43:000000000-A3JHG:1:2114:11799:28499 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\n++\n+3AAA?AADAFFFCGCGGGFEGCHA?EG?FHHGHGHGGEFHGFHGHF?EFA?EBFGC?EGEFHHHHHH3EEGEEGHFH@E0BCA/CGFHHHDGGGFFF/@DGGDGFHHHHBGH.<<AGGHHHHGHEGE?-ABGF;FFGGDGGGGGGG.CCFEFFF/9;9BFFFFFFFFFFFFFFFFFFFFFFFFFFBDFFFFFFFFCBAF9.AFF/FFAAFFADAFFEFFFFFBDDFFFF.DFFFFFFDDFA;BFFDEFFFF\n' |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/F3D1_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/F3D1_R1.fastq Tue Sep 27 05:20:06 2022 +0000 |
| b |
| b'@@ -0,0 +1,23476 @@\n+@M00967:43:000000000-A3JHG:1:1101:18954:2112 1:N:0:189\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTCCCGGCGCGCAAATGACGCTCATGCACGAAAGCGTGGGTATCGAAACG\n++\n+BBBBAA@B2CFF2EFGGGGGGGHGGGGGGHHGHFHEEEFHHHHG11AEFGGGGGGEGG3G3FGHHHGHHFGG/EHHHH/?/EFGGG/GHHHG?DAHHBDFGGGGGCGHBD0GH...C/C/00;C0@-;B-AGGFGG00-B>F.9BA9A-9:A;/B-@A>AFFFBB//BF/B9FBFBDFF--;.//B.@AAFF.@D-.9.:.EF..A.B-@B>--;@//9/...../;9//A.9A./..:@C.///.;F.-.\n+@M00967:43:000000000-A3JHG:1:1101:14117:2137 1:N:0:189\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAGGGGGGGGAGACGGGTTTGGCAGGCTGGTGGGGAAACCCGGGGCTCCACCCCCGGGATGCATTTGAAAATGGAAGGCTGGAGTGCCGGGGAGGGAAGGGGAATTCCTAGTGTAACGGGGAAATGGGGTGGTTTTAAGGGGGACCACCAGGGGGGAAGCGGGTTTATGGGCCGGAAATGAAGGTGGGGCTCGGAAGGGGGGGGGGGAAAAAG\n++\n+BBBBBFFBBBBBGFGGGGGAGGFGFDGGHHH5FHHAEAFH5BG00/----...;-@EF../;.-..../..--;A./;D-;DF--..;.;DF-@F--...//;/;/;F///////..9;A../;//-;----;-9A...;.;.B/;///99////9;.--;A///;..--...;//;/.;-;-..;....;---;.9.-;-9A.///;...---;-//////;/.9;.-.9-;A...--;BFA---;A99A\n+@M00967:43:000000000-A3JHG:1:1101:14312:2436 1:N:0:189\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTGTTAAGTCAGCGGTCAAATGTCGGGGCTCAACCCCGGCCTGCCGTTGAAACTGGCGGCCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\n++\n+BCCCCCCCCFFFGFGGGGGGGGHGGGGGHHHHHHHGGGHHHHHGHGGGGGGGHGGGGGGHHHHHHHHHHGGGGGHHHHHHHGGGGGHHHHHGGGGGGGGHHGGGGHHHHHHHHGGGGGHGGGHHGGGGGGGGGFGGGGGFFFFFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFAFFFFEFFFF\n+@M00967:43:000000000-A3JHG:1:1101:13783:2582 1:N:0:189\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCGCGGCAAGTCTGAAGTGAAAGGCAGGGGCTTAACCCCTGAACTGCTTTGGAAACTGCCATGCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACG\n++\n+ABBBBFFBBBBBGGGGGGGGGGHGGCGGHHHHHHHHGGHHGHHGHGGGGGGGHGGGGGGGGGGGHHHHHHHHHHHHHHHHGGGGGGHHHHHHGGGHHHFHHHHHHGHHGHHHGHHHGHHHHEHHHFHHGHHHGGGHHHHHHHHGHHGHHHHHHHGHGGGGGHHHHHGGGG?FFFGGGGGGGFGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFAFFFBF9:>DC.D.A//:.\n+@M00967:43:000000000-A3JHG:1:1101:16452:2947 1:N:0:189\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\n++\n+CBCBBCCCCFFFGGGGGGGGGGHGGGGGHHHHHHHGGGFHHHHGHGGGGGGGGGGGGGHHHHHHHHHHHGGGGGGHHHHHHHHGGHHHHHHHHHHHHHHGGGGGGHHHHHHHHHHGHHHHHHHGHHHGGGGGHHHHHHGGGGGHHGGGGHGHHHGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFF;FFFFFDFFFBEFFFF\n+@M00967:43:000000000-A3JHG:1:1101:14168:3426 1:N:0:189\n+TACGTAGGGAGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGATGGCATAGTAAGTCTTTTGTAAAAATGCTGGGCTCAACCCAGTAGGGCAAAAGATACTGCAAAGCTAGAGTATGACAGAGGCAAGTGGAACTACATGTGTAGCGGTAAAATGCGTAAATATATGTAAGAACACCAGTGGCGAAGGCGGCTTGCTGGGTCGATACTGACATTGAGGCACGAAAGCGTGGGGAGCAAACAG\n++\n+BB@BAFFB@CABEGGGGGGGGGHGGG2FHHHHHHHAEEEGHHHGGFGGGGGC5GFCEGFF5FGHHHGFHHHHGHHG313E4GFEHHHHHHHG/FCGEFFG/?02BF3BGHG3?3BCFHFHBHHF3GF3GHHBEGGFGFFEGH1CBFBGGDGFHGEGGA.FHHHHH?A.A<DGHEDG0<GHHHG/CF.C0CG:CFGGFFA?D?F?EBFFF;B-@AA;BFF//;9FBFFAEFFFFFFFBAFCC;AAD?B9.AF\n+@M00967:43:000000000-A3JHG:1:1101:10678:3505 1:N:0:189\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAG\n++\n+B@ABBBBBBFFFGGGGGGGFCGHGGGGGGHHHHGHFGGHHHFHGGGGGGGGCHGGGFGGHHHHGHHHHHGGGGGHHHHHFBFHHHHHHHGBHHGHHGHGGGGDGGHHHHHHHFGFEFGHHHHGFG.FCGCFGHGHHGHGGGGGHHGGACEGGGGGGGGGGGGBFFGGGGGGGGGGGGGFFAFFBFFDFDFEFFFFFFFFFBFFFFFFFFFFCA-BFFFEFDFFBA/;/99-.ADDFDDF-B.BFFDE/.9B\n+@M00967:43:000000000-A3'..b'/;/BFB//.;EF?FF/./9/:BF/.-9@BB-B.9/9.9\n+@M00967:43:000000000-A3JHG:1:2114:18156:26651 1:N:0:189\n+TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGCATGGCAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTGCCAGGCTAGAGTGTCGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACGATCACTGACGCTGAGGCTCGAAAGCGTGGGGATCGAACG\n++\n+ABABBCFFFFFCGGGGGGGFGFHEGGGGHHHGHHHC?AGHFHHGHGCECCGGEECGGGHGHHHGHHHHGFHHEFHFHGHGGGGGGGHHGHHGGGGGGGHFGHGHH1DHHFHHHHHFHGHHHBF1GHGFGCGCGD.EHGHHHHFHHFHHGHHH:CGFGCFBGGGGGEDADGGGGGFFGGGGGAFFEFFFF/;FF>@BBFEBBBBBBEFFFFFB=EA.BBFEFFFFD?AEFEFBBFFFFB;:9BB...9DFF-\n+@M00967:43:000000000-A3JHG:1:2114:18845:26698 1:N:0:189\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\n++\n+CCCBBCABCFFFGGGGGGGGGGHGGEGGHHHHHHHGGGHHGCHGHGGGGGGGGGGGGGGHGHHHHHHHHGGGDFHHHHGGHHHGGHHHHHHHHHHHHGHGGGGGGHHHGHHHHHHGHHHHHHGHHFFGGGGGHHHHHHGGGGGHHGGDCCEEHHHGGFGGGBFGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDFDFFFFFFFDFFFFFFFFF\n+@M00967:43:000000000-A3JHG:1:2114:12787:26750 1:N:0:189\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGACGGCTGTGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCGGGACTGCTCTGGAAACTGTAAAGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGCAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACA\n++\n+AAAABFFBBBBBGGFGGGGCGGHGCGGGHHGHHHHGG0GFGHHGHGGGCGGGHGGGGG1FHHHHHHFHFGHHHHHHDGHGGGGGGGGGHGGGGGGG@FHHHFFFBGHHHHHHBFFGHFFGGGGFFFBFGEG.EG/;BBF-BGFEFFFFFFBFFFFFFFDFEFFFFFF.9DEFFFFFFBFFFABFFFFFFFFFFFFFFFFFF-@DFFFFFBFFFFFFFFFFFA;EFFFFEFFF;BADFF.AACF.BD.BBF.\n+@M00967:43:000000000-A3JHG:1:2114:16284:26978 1:N:0:189\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATTCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAG\n++\n+AAAAAAADA11C1EEE0EAEEGBEEEGGHHHHHHHG/EBGHFB?BF/EE/EEEGCC?EBFHHHFHGHBE/EGCGHGGHCGECCGGGFCB<GCCCCGHFACCC@EGGHH0GDHHHG?.GGHHF00:::A@--9BBFF00A@@@-BFF-A=FE-FFF----;FBF//BBFFEFFFFF/-99@@F-9F/A-B--/-@@@FEF-A?B/9F@?-99--9@@F/9/-A9A-/;/9:-9:B9/-;9=@-BB9-AFF<F\n+@M00967:43:000000000-A3JHG:1:2114:10613:27683 1:N:0:189\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGAGTAGGTGGCATAGTAAGTAGCTAGTGAAATCTGGTGGCTCAACCATTCAGACTATTAGCTAAACTGCTAAGCTCGAGACCGTTAGGGGTAACTGGAATTTCTAGTGTAGGAGTGAAATCCGTAGATATTAGAAGGAACACCGATAGCGTAGGCAGGATACTGGGACGGTTCTGACACTAAGGCACGAAAGCGTAGGGAGCAAA\n++\n+BB?ABFFAA?D2EFFFGFGGAFGEEGGGFHGHHGGBAABGHB3AFE1ABEGD5FEHHGBFDGHFEGFFH5EFEGHHG3GGE3BEFFHHEFHGFFHHEHEFHEFHFFBGFGHEFHHEFFFHGG?EH?FCG/AFGHGDDHBG@0?GHEHB1DGGHHEHH1GFF>GGGBGCFGFG0D0DDDDB0<.<<</AC?--;GCAEADFF.9.;CFGFG?F?BGAE?FFFFBFBBFBBBFFD..ADBD9;=D./9AEFF\n+@M00967:43:000000000-A3JHG:1:2114:14684:27826 1:N:0:189\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTGTTAAGTCAGCGGTCAAATGTCGGGGCTCAACCCCGGCCTGCCGTTGAAACTGGCGGCCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATGGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGCGTGGGGAGCGAACAG\n++\n+@ABBBBBBBFFFGGGGGGCFGGHEGGGGGHHHHGHGGGHHHHHCHEGGFFGGGGGGGGEHHHHHHGHGHFCE?EHGHFHHHGGGGCEFHHHGG@/CDGGHHGGGGGHHGFGHEGGGGGFEDCCCE.CDBAGGECBFGGGGG;FEF9AAA9;EFFEFFDFFFFFFFFFBFFFFFFF/;:-9@BF/FF9-A.9BD;=AFFADD.F/;/;B;-9---@DFFEFFAFD??EA.ADFFFB/DFFFF-E-99@C;@F\n+@M00967:43:000000000-A3JHG:1:2114:14493:28703 1:N:0:189\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGCAGCCGGAGAGACAAGTCAGATGTGAAATCCACGGGCTCAACCCGTGAACTGCATTTGAAACTGTTTCCCTTGAGTGTCGGAGAGGTAATCGGAATTCCTTGTGTAGCGGTGAAATGCGTAGATATAAGGAAGAACACCAGTGGCGAAGGCGGATTACTGGACGATAACTGACGGTGAGGCGCGAAAACGTGGGGAGCAAACA\n++\n+>AA11BC1BB>FFFFCFAEEGFGG0AEEHFGHBE0BEGBBB2B?CC/ECHBBGE/ECG/FGGHGGHF1@GHEGHFBEGHHF/EECGEGHHFG/A/FFF1F11GB22BFFB1GF2DGFFGH0BCGF1@?/<>@CGGGFHHGGCEAFBGHHB11<1FGC?CCGGG0=D.;AC.;CFGB000;.:GHFG...00;.9A--A.;-9--//;B//-9-E9AB/:/BA--9;A-9-9=@---9-9-9-9---9B/;-\n' |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/compact_3_db.kmc_pre |
| b |
| Binary file test-data/compact_3_db.kmc_pre has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/compact_3_db.kmc_suf |
| b |
| Binary file test-data/compact_3_db.kmc_suf has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/contig_kmer27.kmc_pre |
| b |
| Binary file test-data/contig_kmer27.kmc_pre has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/contig_kmer27.kmc_suf |
| b |
| Binary file test-data/contig_kmer27.kmc_suf has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/contigs.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.fa Tue Sep 27 05:20:06 2022 +0000 |
| b |
| b'@@ -0,0 +1,16971 @@\n+>000000F\n+CGATGTCATAGAGTACGTGTCATCGTTTGAGTGACGTTCTCGCTCAATAATCTCACAGGACTGCCTAATTCCACTTTTTT\n+TATTACTTGAGGCACCAACAACACTAGAACTCATCCGATAATTTATTTACTTGATTATTTTTTTTTTTTTTTTTCTCTTT\n+CCAGTCCATAAAACTATTTTACTTTTCTTATTTATGTAAATAGTATTTAAGATTCTACGGTCGCTACATCTGCTAGAAAT\n+GGAATTACTTTAATACATTCCATGTTCTCATATATACTTTTACTGACACCTTTCGTCACTATTTTTTGTTTAACTTTTTT\n+TTTGGAAGTACTAAAATTATATGCTCGTAATTATTGAGTATCAAAAAAAAAAAAAAAATTGCTGTGACACCCCTTCAATG\n+TGGTGTCTATACACCTGGTGACTTTAACTTTAACTTTGACCTGTCGTCGTACAATCAACTTAGTTTCCGAAAATCCACAA\n+CGAACCAGTTATACCGAAGACTTTTGTACGACAAGAATACTGTACCGTCGAAACTATCTCTTTTCAAACTGATGAGTGAA\n+GCTTGTGTTTATGTCTGTTGAAACAAGGAAAAAAATGCGGTGCCTGTCGACAGGATATGCGCACAAGTGCAAAATCATCA\n+AAAAATTGAGTACCTAGATCCGGTGGTGTAGGACGAGCAAAGTTCCTTCATAAACAAACCGTAAGGGTTACTGATACACA\n+ATTTCCTTTTTGTAAAGAGTATTTGAGCAAATTAGTCAGCGATTGAAAACAACACCCTTTTTTCTATATATAGTAGGTGA\n+AAGTTAACATGCGAGTAAAAGTAGTGCCACATTTCCTTTGCAGCAGGTGCAAATTGGTACATATTTAACAGATAGCGCCG\n+CACCTCATATGCAGCGCGTACATGATACGAGACGACAAGATATGCAAAAGATAATAGTGTCATCACACCTTTATGAGAAG\n+CGAATTTTTTTTTTTTTTTGGTTTAAATATATATATACATATATATAGATATAGATATACACATGTATAGATGTATTCTA\n+GTTACTTATACCTAGAACTGATCAGACCAGATCATACCTGGTATAGAGCTTAATCGATAGAAATTCAAAAATATGGAGGA\n+AACTAAGTACTCTTCGCAGCAGGAGATAGAAGAAGCATGTGGTTCAGACGTTTCATTGAATGCTAGAGGTAGCAATGATT\n+CTCCAATGGGACTTTCCTTGTACCTCTGCCTGGCTTCGTAACTCTTGTACTATTCATAACTGCACTGGATATTTTGATAG\n+TGGGAACTATTATTGACGTGGTCGCAGAACAGTTCGGAAACTACTCCAAAACAGGTTGGCTCGTTACAGGCTACAGTTTA\n+CCAAATGCTATTCTGAGTCTCATTTGGGGAAGATTCGCATCTATCATAGGTTTCCAGCATAGTCTCATTTTAGCAATACT\n+TATTTTTGAAGCCGGATCCCTAATTGCTGCCCTTGCCTCTTCAATGAATATGCTCATTGTCGGTAGAGTTGTTGCTGGTG\n+TTGGGGGAAGCGGACTTCAAACGCTTTGCTTTGTTATTGGTTGTACGATGGTTGGTGAAAGGTCACGTCCATTGGTGATT\n+TCCATCCTAAGTTGTGCATTTGCTGTAGCTGCTATCGTTGGTCCTATAATCGGAGGTGCCTTTACAACCCATGTTACCTG\n+GAGGTGGTGCTTCTATATCAATCTTCCTATCGGTGGTCTTGCCATTATTATGTTTTTACTCCTATAAGCCGAGAATAAGG\n+GTATACTTCAACAAATTAAAATGCTATAGGAACAATCTCGAGCTTTACTTTTAGTAAGTTCAGACACCAAGTTAATTTTA\n+AAAGACTTATGAATGGCATAATCTTCAAGTTTGACTTCTTTGGTTTTGCCCTCTGCTCTGCAGGGCTGGTCCTTTTCCTA\n+CTGGGGCTAACCTTTGGCGGTAATAAATATAGTTGGAACTCTGGCCAAGTCATCGCATATTTGGTTTTGGGTGTCTTACT\n+TTTTATTTTTTCATTGGTGTACGATTTCTTCTATTCGATAAATTCAACCCGGAACCTGATAATATATCCTACAGGCCTCT\n+CCTTCTAAGAAGATTGGTAGCAAAACCAGCCATAATAATAGTAAACATGGTAACATTTCTATTATGTACCGGTTACAATG\n+GGCAAATGATATACTCTGTCCAGTTTTTCCAACTTATATTTGCGTCGAGTGCATGGAAAGCCGGTCTTCACTTGATACCA\n+ATCGTTATTACCAACGTTATTGCGGCCATTGCAAGTGGTGTGATTACCAAAAAGCTCGGTTTAGTTAAACCACTCTTAAT\n+ATTTGGAGGCGTTCTTGGGGTAATTGGAGCAGGGCTTATGACACTTATGACAAATACGTCCACGAAGTCAACTCAAATTG\n+GTGTTTTGCTATTACCGGGGTTTTCCCTTGGATTTGCTCTACAAGCATCGCTCATGAGTGCACAGCTTCAAATTACCAAA\n+GATCGTCCAGAAGCTGCTATGGACTTTATTGAAGTAACAGCTTTCAATACATTCATGAAGTCATTAGGTACAACTCTTGG\n+TGGTGTGCTTTCAACCACTGTTTTTTCCGCCTCCTTTCACAACAAAGTATCACGAGCTCATCTAGAGCCTTACGAAGGAA\n+AAACGGTTGATGACATGATTTTGTATCGTCTTCAAAACTACGACGGTTCTCATTCGACTATTGGAAACATTTTAAGCGAC\n+TCCATTAAGAACGTATTTTGGATGGATCTAGGGTTTTATGCCTTAGGATTTTTGTTTTGTAGTTTTTCATCCAATAAGAA\n+ATTAATCATACCAAAAAAAGGACGAGACACCAGAAGATAATTTAGAAGACAAGTAGCGCAGTTATTTTCTTATTTTCATT\n+TTTTAGATTATCCTTATTTCAACAAGAATATTTAAAATATGCTATAAAAATCAATACTAGGCTTAGGGTTTGGCCAACAC\n+TTTTTGTGTAACGTGAAAACTTTGAAACATGGTACACGTATTTTTTTTGATAGAATACCAGCAATAATTTAGTAAAATTG\n+GGCAAGGAGATCAAGTAGTAACAAGCGCTCTAATTACCAGTGATGAAAAAATATTTGTTTTTTTTTTTTTACACAAAATA\n+GCATTTATACGCATCTTATAATTCAAATATCTTGTATAGCGACAACTAAGACACAGACTAGTTCTCAATAGTTTCTTAAA\n+ATTCTTTTTTTTTTTTATTCGGCTCCGCTCAGCAAAAATGACAATGACCATTATACTTAATATTTCATGACTGCACTCGG\n+ATCTAATAAGAATTGTGTTCTTATTAAGTTTGAATGAAGTGTGTTTCAACATATAATAGCTTCATTTTTGAAAAATCAGA\n+GGAGATTAAAAGAATTCAAACACACCTTTTTCGCAGAAAAAAATTTTTTTTTTTATTCTCCTGTAACAGTTTTGTTAGTT\n+TCAAAGGAAGAATTTAATCAAATACATTCATGTGAAGTATTTTCTGCAATTCATTACTACGGTATGATAGCTATTCTAAG\n+AATTTACAGAAAAGTTTCTTCAGTGCTTTCTAAATCTACACAGCATCTTATGAATGGGTTTTTGATTTTTTATGTTTTTT\n+TTAAAATATTAAAGTTTTCGGTACGGACATTTTAGGAATTCAATTTATTAATGAAAAACAATTAACTAATTGATGTACTT\n+AGTATTTGGCCATTATTATCGATTTCGGGGGCAAAATCTAATCAAATTCAACCTACATTTTTTCAAGCTGATTTAAACAC\n+CTTTCACAATAAGATTTTTATATCTAGCGCACATAGAATGAAAGTAAACAAAGATTTCAGAAAAAGTCGTCATTCAAACT\n+TGTATTAGACGAGGGACGGGAGATTTTTGTGT'..b'GCGGCAGGAGGTTTCAACATGCCAACAATGGAAGTGGTTAAGAGACGTTTTCTGGTTTCTGGGCAGCTGTTA\n+CATAGAATCTCTGATTTACATGCTCAAGTATTCGCAAAGATCGGTATGATGGGAAAATAGGTGAATTTTGGGATAATGAC\n+TGAGATTATACCGTTGTTAATGCTATAATATTAATTATACAGAATATATTAGAAGTTCTCCTCGAGGATATGGGAACCCA\n+CAGAAGCGAATCGATGTTTCTACATAAAAAGAAAAAAATAATCTCATTTTATCTTCGGTTTTGAATCTTTTCATTTTTTT\n+TTCCTATTACATTATCAATTCTGGCATTTCAGTGTTTATAAAAAGATCAAATTGCTGTTTGAAACTCATTGCGCTAATTC\n+CATAATTTTGCACCATGTATGCTCATGACTCCATATAGGACAACATACTGGTAGGAATATTATCAAGTGAACGATAACGG\n+TTCTTCTCCCAACAAGAAGTAAGCCTGGTGAGTGTATTTTGAAGCTTTTTGGAGGGGCGGCCACGGAATAAGATATGAAC\n+ACATACTGGCAATTGGGCTGAGATCTGATTACATTGTCGACAGATTCCCATGAAGGTGTTTGAGAGAATTTTGATTGAGT\n+CGTTATACAAATTGCTGTGGACACGTACGCATAAAGTAGTTCGGGCAGCTATGTTTGCCACGTAGTAGCTACAATATTAA\n+GCATAGCAGACTAAATGCAATTGGCTGTGTTGAAAGAAACTTCTGAACTGAGATTCAAGTAACGTGATTGTGTGCGCCAT\n+TTTACACAGGCTGCGCGGCAAATCAAAACCAAAGATACTTCTCCGGAGGTATACGTGTTGCATTTTCAACAGACTATACG\n+AGTTTTTTCTGATCGTTGTATATTTAAGTGCAGCTTGGACTTACAAGCTCTATACTAGGATAATGATCTCATTGGATTCA\n+AGAGAAAGAAACTCTATACTGGCGCCAAATTAGCAGTGTCAAATTTCGAAAAGGTGATGACGCCCTATGCAGTAGCAATT\n+ACCGTGGCCTTACTAATTGTAACAGTGAGCGCACTCCAGGTCAACAATTCATGTGTCGCTTTTCCGCCATCAAATCTCAG\n+AGGCAAAAATGGAGACGGTACTAATGAACAGTATGCAACTGCACTACTTTCTATTCCCTGGAATGGACCTCCTGAGTCAT\n+TGAGGGATATTAATCTTATTGAACTCGAACCGCAAGTTGCACTCTATTTGCTCGAAAATTATATTAACCATTACTACAAC\n+ACCACAAGAGACAATAAGTGCCCTAATAACCACTACCTAATGGGAGGGCAGTTGGGTAGCTCATCGGATAATAGGAGTTT\n+GAACGATCCGCAAACGATGCTATGGCCGGAAAAGAAGGAAGACGAAAAAAACTGCCAAGAAACTTTTAAAGGGGCCTGTT\n+CGTGTACCAAAAGGTTTTGCAAGGGTTATTTCTCTGTAAATATTTTTGGGATAAACCTGAATATATCTTATAGCTCTGGA\n+AAGTGATTGACATGTCATTTTTTGGAAATTAGTTATAGATACATAGAATATACTAAAGAATTCTCCTTGAAGACCATGGT\n+CACCGAAAATTTCACAGAATACTACAAACTATTCTCTTATTGATGTTTCTCCTTAACACCCAGGGTGCTTTAGCTACAAT\n+GAAGTTAATAGCAATATCTATATGGTTGCACTGGCCTCTAGCTGCGAATACGATAATACGAATGCGTAGGTAAATGATAA\n+TTATCATCTATCGATTAGTGTTTCTTCCTACTAATATATCATTATATGGGTATAAGAAGATGGCATAAAAGTTGAGAAAC\n+AACCATCGGATTTAATGGAGGCTGAAATGCAAGGATTGGTAATGGAATAGGATAATGAATGACAGCATATAAAATGGAGG\n+AAGAGGTGATAATATTATTACGTAGAATTCTCTTTTTTGGATTCAGGATCAGTGAGGACAGCTTCTAGTATATTCTGCAT\n+ACCTAAATGCTATTCTTTTTTTTATCAATTTGATTTACTAAATGCTATTTATCCCAAATAATCCATATAAGATTTTAATC\n+TAGATGGAGGGTAAAAGCGCGGAAACATGAGTGTAAACTGATTGTGCAGATATTTACACATTTGAGTAGCTCGTCAAGGG\n+CAATCAAGCTTTCAATCTTGCCGGTTTCATACATGTTGATAAGCTAATGAAACTACTAATGTCTTGCTGTAAAGTAAACC\n+TGTATCATTTCTGTTTGGAAGATTTCAACAAACGTTCGGGCGTGTGGCGTAGTCGGTAGCGCGCTCCCTTAGCATGGGAG\n+AGGTCTCCGGTTCGATTCCGGACTCGTCCATTTAAATTTTTTTTTTTTTTTGTCAAATCTCTCTATCTATAGAGATAATC\n+TCTATCAACTCAAATGATACTGGATATTATATGTACATTTTCCATTTCCCGTACAATCTTTCCCTTTCAAACACATTTTA\n+GTACTTCTTGATACGTACAATTCAGTAAAAATCCTCGAGGTCATGCACTCACACCATTCACACTCCGGTGACTATAGTGC\n+CCACGGTACGGACCCTTTGGATTCCGTGGTCGATCAAGTGGTCAACCTCAACTTTCACACGTACTGTTTGACAGAGCACA\n+TACCAAGAATTGAGGCCAAGTTTATATACCCCGAAGAGCAGTCATTGGGCAAGAATCCTGAGGAAGTCATAACCAAGCTA\n+GAAACATCGTTCAAGAATTTCATGAGTCATGCGCAAGAAATCAAGACTCGTTATGCTGATAGACCCGATGTGCGGACTAA\n+ATTCATTATAGGAATGGAGATCGAAAGTTGTGACATGGCTCATATCGAATATGCAAAGCGACTCATGAAGGAGAATAATG\n+ATATTTTGAAGTTTTGTGTGGGTTCGGTCCATCACGTCAACGGGATCCCTATTGATTTCGACCAACAACAATGGTACAAT\n+TCATTGCATTCCTTCAATGATAATTTGAAACATTTTCTCCTGTCTTACTTCCAATCACAGTACGAAATGCTGATCAATAT\n+TAAACCGTTGGTCGTGGGTCACTTCGACCTTTACAAATTATTTTTGCCCAATGACATGCTAGTAAACCAGAAATCGGGCA\n+ACTGCAACGAAGAAACCGGAGTTCCTGTAGCTTCACTGGACGTCATCAGTGAATGGCCAGAAATATACGATGCAGTTGTA\n+AGAAATTTACAATTTATAGACTCCTATGGCGGCGCAATTGAAATCAATACGTCCGCATTAAGAAAGCGCCTCGAGGAGCC\n+GTACCCCAGCAAAACCTTATGTAATCTGGTCAAGAAGCACTGTGGATCCAGATTTGTTCTAAGTGATGACGCACACGGCG\n+TGGCGCAAGTGGGTGTGTGCTATGACAAGGTAAAGAAATACATAGTAGACGTGCTACAATTAGAGTATATTTGCTACCTT\n+GAGGAAAGCCAATCACCAGAGAATCTGTTAACTGTAAAGAGATTACCCATTTCGCAATTCGTTAATGATCCCTTTTGGGC\n+CAATATATAATCTGATTATCTTGAACTGGATGTACATAAAAAAAAACTGTCATATAAACTCATGTACAGCTGTGTAGAAG\n+TGAATGATCTTTCCAAGAAAAAAATTTCACACTGAATTGATTGAATTGACTGCTCATTTTATATTGGGTGCCCAAATTGT\n+CTTTCTTTATTGTTCGTTTAGTAGCAGCACCCTGTTTGCTCGCCGACTCGGCCGCATCTGGAAGTTCAACATGAAAGAGT\n+ATAAACTATCGAAGAAATCTAGAACGGCTTTGGATCACGGGTGGCAAAGAAATCAAAAACAAAAGCTGTATCACACGCAA\n+TGGGTATTAACAATCCTATTCCAAGGAGTTTAAAGAGTGAGACAAAGTATGTTTTATACGGGTTTGGCTG\n' |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/counters_subtract_sum_db.kmc_pre |
| b |
| Binary file test-data/counters_subtract_sum_db.kmc_pre has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/counters_subtract_sum_db.kmc_suf |
| b |
| Binary file test-data/counters_subtract_sum_db.kmc_suf has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/db.kmc_pre |
| b |
| Binary file test-data/db.kmc_pre has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/db.kmc_suf |
| b |
| Binary file test-data/db.kmc_suf has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/dump.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dump.txt Tue Sep 27 05:20:06 2022 +0000 |
| b |
| b'@@ -0,0 +1,15013 @@\n+AAAAAAGTTTCCAAAGCCATTCCGC\t4\n+AAAAACAGTTTCAAATGCAGGCCAC\t22\n+AAAAACAGTTTTGAACGCTTGTACA\t3\n+AAAAAGTGGCGGAATGCTCTCGAAA\t4\n+AAAAAGTTTCCAAAGCCATTCCGCG\t4\n+AAAAATTCGGGGCTCAACCCCGGCC\t4\n+AAAAATTCGGGGCTCAACCCCGTAC\t4\n+AAAACAGTTTCAAATGCAGGCCACA\t22\n+AAAACAGTTTTGAACGCTTGTACAG\t3\n+AAAACCACGGGCTCAACCTGGGGCC\t3\n+AAAACCAGTGGCGAAGGCGGCCTGC\t10\n+AAAACCATGGGCTCAACCCGTGGAC\t3\n+AAAACCATGGGCTCAACCTGTGGCC\t20\n+AAAACCCAAAGCTCAACTATGGGAA\t10\n+AAAACCCAGGGCTCAACCTTGGGAC\t16\n+AAAACCCGAGGCTCAACCACGGGAG\t5\n+AAAACCCGGGGCCCAACCCCGGGAG\t14\n+AAAACCCGGGGCTCAACTCCGGGAT\t3\n+AAAACCCGGGGCTTAACCCCGCGGA\t10\n+AAAACTACCGGCTCAACCGATAGTC\t3\n+AAAACTACGGGCTTAACCTGTAGAC\t21\n+AAAACTATCGGCTCAACTGGTAGAT\t5\n+AAAACTATGGGCTCAACCCATAGCC\t19\n+AAAACTCCGATTGCGAAGGCAGCAT\t3\n+AAAACTGACGTTGAGGCTCGAAAGC\t4\n+AAAACTGACTGACTAGAGTATGGTA\t10\n+AAAACTGAGGGCTCAACCCTCAGCC\t29\n+AAAACTGCAATTCTTGAGTGAAGTA\t9\n+AAAACTGCAGCTCTTGAGTGAAGTA\t6\n+AAAACTGCAGTTCTTGAGTGAAGTA\t14\n+AAAACTGCGATTCTTGAGTGAAGTA\t5\n+AAAACTGCGGGCTCAACCCGGAGAG\t5\n+AAAACTGGGAGGCTGGAGTGCAGGA\t4\n+AAAACTGGGGAGCTGGAGTGCAGGA\t12\n+AAAACTGGTAAGCTGGAGTGCAGGA\t14\n+AAAACTGTATGACTTGAGTGCAGTA\t27\n+AAAACTGTGAGGCTGGAGTGCAGGA\t4\n+AAAACTGTTGAACTTGAGTGCAGGA\t3\n+AAAACTGTTGAGCTGGAGTGCAGGA\t3\n+AAAACTGTTGGACTCGAGTGCAGGA\t12\n+AAAACTGTTGGACTTGAGTGCAGGA\t11\n+AAAACTGTTTTTCTTGAGTGGAGTA\t3\n+AAAAGCAATCCGCGGGGTTAAGCCC\t14\n+AAAAGCAGTCCCAAGGTTGAGCCCT\t16\n+AAAAGCCACCTACAGACGCTTTACG\t3\n+AAAAGCCCAGCAAGCCGCCTTCGCC\t5\n+AAAAGCCCAGCAGGCCGCCTTCGCC\t16\n+AAAAGCGAAGGCAGCTCTCTGGGTC\t4\n+AAAAGGCCGCCTACACTCCCTTTAC\t4\n+AAAAGTGGCGGAATGCTCTCGAAAC\t4\n+AAAAGTTTCCAAAGCCATTCCGCGG\t4\n+AAAATCCGGGGCCCAACCCCGGAAT\t9\n+AAAATTCGGGGCTCAACCCCGGCCG\t3\n+AAAATTCGGGGCTCAACCCCGTACA\t4\n+AAAATTGAGGGGCTCAACCTCTTCG\t3\n+AAACACAGTTTCAAATGCAGGCCAC\t17\n+AAACAGCCTACGCACGCTTTACGCC\t11\n+AAACAGTTTCAAATGCAGGCCACAG\t22\n+AAACAGTTTCAAATGCAGTTCGCAG\t11\n+AAACAGTTTTGAACGCTTGTACAGG\t3\n+AAACATCCAACTTGCATCCCCGCCT\t3\n+AAACCAATTCACTTGAGTGAGACAG\t4\n+AAACCACCTACGCACCCTTTACGCC\t25\n+AAACCACCTACGCGCGCTTTACGCC\t9\n+AAACCACGGGCTCAACCTGGGGCCT\t3\n+AAACCAGTGGCGAAGGCGGCCTGCT\t10\n+AAACCATGGGCTCAACCCGTGGACT\t3\n+AAACCATGGGCTCAACCTGTGGCCT\t20\n+AAACCCAAAGCTCAACTATGGGAAT\t10\n+AAACCCAATAAATCCGGATAACGCC\t4\n+AAACCCAATAAATCCGGATAATGCT\t3\n+AAACCCAATAAATCCTGATAACGCT\t5\n+AAACCCAATGAATCCGGATAACGCT\t4\n+AAACCCAGGGCTCAACCTTGGGACT\t16\n+AAACCCAGTAAATCCGGATAACGCT\t3\n+AAACCCAGTTTCAACGGCTCGAAGA\t4\n+AAACCCATGGGCTCAACCCATGGCC\t9\n+AAACCCCGGGGCTCAACCCCGGGCA\t3\n+AAACCCCGGGGCTTAACCCCGCGGA\t4\n+AAACCCGAGGCTCAACCACGGGAGT\t5\n+AAACCCGGGGCCCAACCCCGGGAGT\t14\n+AAACCCGGGGCTCAACTCCGGGATT\t3\n+AAACCCGGGGCTTAACCCCGCGGAT\t10\n+AAACCCTGCGCTTAGGTTGCCACCT\t6\n+AAACCGCCTACGCGCCCTTTACGCC\t29\n+AAACCGCCTACGCTCCCTTTACACC\t16\n+AAACCGCCTGCGTGCGCTTTACGCC\t6\n+AAACCGGGCAACTTGAGTGCAGAAG\t6\n+AAACGCAGGCTATGGGTTGAGCCCA\t6\n+AAACGCAGTCCACGGGTTGAGCCCA\t3\n+AAACGCAGTTCCAGGGTTGAGCCCT\t23\n+AAACGTCAGTTACAGTCCAGCAGGC\t4\n+AAACTACCGGCTCAACCGATAGTCG\t3\n+AAACTACGGGCTTAACCTGTAGACT\t21\n+AAACTAGGAATTCCGCCTGCCTCTC\t3\n+AAACTATCGGCTCAACCGGTAATTG\t3\n+AAACTATCGGCTCAACTGGTAGATG\t5\n+AAACTATGGGCTCAACCCATAGCCT\t19\n+AAACTATGTGACTGGAGTGCAGGAG\t15\n+AAACTCCGATTGCGAAGGCAGCATA\t3\n+AAACTGACACTGAGGCTCGAAAGCG\t4\n+AAACTGACGCTGAGGTACGAAAGCG\t3\n+AAACTGACGCTGAGTCACGAAAGCG\t10\n+AAACTGACGGTCTTGAGTGGGCGAG\t3\n+AAACTGACTGACTAGAGTATGGTAG\t10\n+AAACTGAGGGCTCAACCCTCAGCCT\t29\n+AAACTGAGTAGCTAGAGTGCAGGAG\t17\n+AAACTGCAATTCTTGAGTGAAGTAG\t9\n+AAACTGCAGCTCTTGAGTGAAGTAG\t6\n+AAACTGCAGTTCTTGAGTGAAGTAG\t14\n+AAACTGCATATCTAGAGTGTCGGAG\t8\n+AAACTGCCAGGCTAGAGTGTCGGAG\t30\n+AAACTGCCAGGCTGGAGTGCCGGAG\t9\n+AAACTGCCAGGCTGGAGTGTCGGAG\t24\n+AAACTGCCATGCTAGAGTGCTGGAG\t28\n+AAACTGCCCGGCTAGAGTGCTGGAG\t19\n+AAACTGCCCGGCTGGAGTGCGGGAG\t3\n+AAACTGCCGGACTAGAGTGTCGGAG\t3\n+AAACTGCCGGGCTAGAGTATCGGAG\t5\n+AAACTGCCGGGCTCGGGTGGGCGAG\t3\n+AAACTGCCGGGCTGGAGTGCAGGAG\t25\n+AAACTGCCGTTCTTGAGTGAAGTAG\t3\n+AAACTGCGAGGCTGGAGTGCTGGAG\t8\n+AAACTGCGATTCTTGAGTGAAGTAG\t5\n+AAACTGCGGGACTGGAGTGTCGGAG\t5\n+AAACTGCGGGCTCAACCCGGAGAGT\t5\n+AAACTGCGTCGCTGGAGTACGGGAG\t6\n+AAACTGCTAAGCTCGAGACCGTTAG\t3\n+AAACTGCTCAGCTAGAGTGCAGGAG\t10\n+AAACTGCTTTTGGAACTGCGTGTCT\t4\n+AAACTGGCGAGCTGGAGTGCCGGAG\t3\n+AAACTGGCGGCCTTGAGTGGGCGAG\t3\n+AAACTGGCGGGCTCGAGTGGGCGAG\t3\n+AAACTGGCGGGCTGGAGTGCCGGAG\t3\n+AAACTGGCGGTCTTGAGTGGGCGAG\t4\n+AAACTGGCGTCCTA'..b'AACACCA\t7\n+TGCGTAGATATAGGAAGGAACACCA\t10\n+TGCGTAGATATATGGAGGAACACCA\t3\n+TGCGTAGATATTAGGAGGAAAACCA\t12\n+TGCGTAGATATTAGGAGGAACAACA\t3\n+TGCGTAGATATTAGGAGGAACCCCA\t4\n+TGCGTAGATATTAGGAGGGACACCA\t4\n+TGCGTAGATATTAGGGGGAACACCA\t6\n+TGCGTAGATATTGGGAAGAACACCA\t3\n+TGCGTAGATATTGGGAGGAACACCA\t8\n+TGCGTAGATATTTGGAGGAACACCA\t3\n+TGCGTGGATATTAGGAGGAACACCA\t5\n+TGCTCCCCACCCTTTCGAGCCTCAA\t5\n+TGCTCCCCACGCTCTCGAGCCTCAA\t7\n+TGCTCCCCACGCTTCCGAGCCTCAA\t8\n+TGCTCCCCACGCTTGCGAGCCTCAA\t3\n+TGCTCCCCACGCTTTCGCGCCTCAA\t5\n+TGCTCCCCACGCTTTCGGGCCTCAA\t13\n+TGCTCCCCACTCTTTCGAGCCTCAA\t3\n+TGCTCCCCCCCCTTTCGAGCCTCAA\t3\n+TGCTCCCCCCGCCTTCGAGCCTCAA\t3\n+TGCTCCCCCCGCTTTCGTGCCTCAA\t4\n+TGCTCCCCTCGCTTTCGAGCCTCAA\t3\n+TGCTCGAAAGTGTGGGTATCGAACA\t3\n+TGGAACTGGAGTGCTGGAGAGGCAA\t3\n+TGGAATGCGCAGATATCGGGAAGAA\t5\n+TGGAATGCGTAGATATATGGAGGAA\t5\n+TGGAATGCGTAGATATTAGGAAGAA\t13\n+TGGAATGCGTAGATATTGGGAAGAA\t7\n+TGGAATGTGTAGATATCGGGAAGAA\t24\n+TGGAATTCCATGTGTAGCGGTGGAA\t5\n+TGGAATTCCCAGTGTAGCGGTGAAA\t4\n+TGGAATTCCCAGTGTAGCGGTGGAA\t3\n+TGGAATTCCCGGTGTAACGGTGGAA\t23\n+TGGAATTCCTAGTGAAGCGGTGAAA\t3\n+TGGAATTCCTAGTGTAGCGGGGAAA\t4\n+TGGAATTCCTGGTGTAGCGGTGAAA\t13\n+TGGAATTCTTAGTGTAGCGGTGAAA\t11\n+TGGAATTTCCTGTGTAGCGGTGAAA\t9\n+TGGAATTTCGTGTGTAGGGGTGAAA\t4\n+TGGACTCGAGTGCAGGAGGGGCAAA\t12\n+TGGACTTGAGTGCAGGAGGGGCAAA\t10\n+TGGAGCTAGAGTGCTGGAGAGGTAA\t3\n+TGGAGTACCGGAGAGGTAAGCGGAA\t6\n+TGGAGTACGGGAGGGGCAGGCGGAA\t9\n+TGGAGTACGGTAGGGGCAGAGGGAA\t3\n+TGGAGTACTGGAGAGGCAGGCGGAA\t4\n+TGGAGTGCAGGAGAGGAAAGTGGAA\t3\n+TGGAGTGCAGGAGAGGTGAGCAGAA\t4\n+TGGAGTGCAGGAGAGGTGAGCGGAA\t11\n+TGGAGTGCAGGGGAGGTAAGTGGAA\t6\n+TGGAGTGCCGGAGAGGTAAGCGGAA\t9\n+TGGAGTGCCGGAGAGGTAAGTGGAA\t8\n+TGGAGTGCCGGAGAGGTAGGCGGAA\t8\n+TGGAGTGCCGGAGGGGCAGGCGGAA\t21\n+TGGAGTGCCGGAGGGGTAGGCGGAA\t6\n+TGGAGTGCGGGAGAGGTAAGCGGAA\t4\n+TGGAGTGCGGGAGGGGCAGGCGGAA\t26\n+TGGAGTGTCGGAGAGGCAGGCGGAA\t12\n+TGGCAGAGCAAGTCCGAAGTGAAAA\t10\n+TGGCAGGGCAAGTCAGATGTGAAAA\t4\n+TGGCATGGCAAGCCAGAAGTGAAAA\t9\n+TGGCATGGTAAGCCAGAAGTGAAAA\t4\n+TGGCGAAGGCGACCACCTGGACTAA\t9\n+TGGCGAAGGCGATTCTCTGGGCCAA\t29\n+TGGCGAAGGCGGCCCCCTGGACGAA\t5\n+TGGCGAAGGCGGCTTGCTGGACGAA\t4\n+TGGGAACTGCATCTGATACTGGCAA\t5\n+TGGGAGTGCATTGGAAACTGTAGAA\t3\n+TGGGCTCAACCCAGGAACCGCATAA\t11\n+TGGGCTTTCACATCAGACTTGTACA\t3\n+TGGGCTTTCACTTCAGACTTGCACA\t3\n+TGGTGTTCTTCCCGATATCTACACA\t26\n+TGTAACTGACGTTGAGGCTCGAAAA\t4\n+TGTAACTGGAGTGCTGGAGAGGTAA\t21\n+TGTAACTTGAGTGCAGGAGAGGTAA\t6\n+TGTACAGGTTGAGCCCGTACCTTAA\t3\n+TGTACTCTAGTTACACAGTTTCCAA\t26\n+TGTAGCTAGAGTGCAGGAGAGGTAA\t10\n+TGTGAAAGCCTTAAGCTTAACTTAA\t12\n+TGTGAAAGCCTTAGGCTTAACCAAA\t20\n+TGTGACTGGAGTGCAGGAGAGGTAA\t11\n+TGTTCTTCGGAATGACTGGGCGTAA\t3\n+TGTTGCTAGATTGCAGGAGAGGTAA\t4\n+TTAACCCCGCGGATTGCTTTTGGAA\t14\n+TTAAGCCGCGGGATTTCACATATAA\t12\n+TTAAGCCGCGGGATTTCACATCTAA\t16\n+TTAAGCCGTAGGATTTCACATCTAA\t4\n+TTAAGCCTCGGAGTTACGCTACCAA\t11\n+TTAAGCTAGAGTGCTGGAGAGGTAA\t13\n+TTACCGGTTGAGCCGATAGTTTAAA\t3\n+TTACCTCTACTCCACTCAAGAAAAA\t3\n+TTACCTCTCCGGTACTCCAGCAAAA\t6\n+TTACCTCTCCTGCAATCTAGTTCAA\t20\n+TTAGATGTGAAATCCCGCGGCTCAA\t3\n+TTAGCAGTTTAGCTAATAGTCTGAA\t3\n+TTATGTGTGAAAGCCCACGGCTCAA\t4\n+TTCAAAACTGCGATTCTTGAGTGAA\t5\n+TTCACTCAAGAACGGCAGTTTAGAA\t3\n+TTCACTCAAGCCTCACAGTTTCAAA\t3\n+TTCCACTAACCTCTACTGCACTCAA\t27\n+TTCCACTCTCCCCTTCTGCACTCAA\t5\n+TTCCACTCTCCTCTGTCTCACTCAA\t3\n+TTCCAGTCTCCCCTACCGCACTCAA\t25\n+TTCCATTCACCCCTCCTGCACTCAA\t4\n+TTCCATTCTCCTCTTCCATACTCAA\t28\n+TTCCATTTGCCCCTCCTGCACTCAA\t10\n+TTCCCTCAAGCCCTACAGTTTCAAA\t3\n+TTCCGATGACCTCTCCGATACTCAA\t11\n+TTCCGATGACCTCTCCGGTACTCAA\t29\n+TTCCGATTGCCTCTCCAGCACTCAA\t20\n+TTCCGCATACTTCTCGCCCCCTCAA\t6\n+TTCCGCCAACCTCTACTTCACTCAA\t21\n+TTCCGCCTACCTCTACTTCACTCAA\t4\n+TTCCGCCTACTTCTCGCCCACTCAA\t8\n+TTCCGCCTGCCTCTCCAGTACTCAA\t30\n+TTCCGCTTACCTCTACTCCACTCAA\t3\n+TTCCGCTTACCTCTCCTGCACTCAA\t6\n+TTCCGCTTACCTCTCCTGTACTCAA\t11\n+TTCCGCTTGCCTCTACTTCACTCAA\t5\n+TTCCGCTTGCCTCTCCATCACTCAA\t5\n+TTCCGCTTTCCTCTCCTGCACTCAA\t11\n+TTCTACCCCCCTCTACGAGACTCAA\t6\n+TTCTCCCCACGCTTTCGAGCCTCAA\t3\n+TTGAATGTGAAATCTATGGGCTCAA\t3\n+TTGAATGTTTAAGGTACGGGCTCAA\t3\n+TTGAGCCCCGGAGTTACGCTACCAA\t10\n+TTGAGCCCCGGGATTACGCTACCAA\t3\n+TTGAGCCCGCAGTTTTCACATCCAA\t5\n+TTGAGCCCGGGGATTTCACATCCAA\t9\n+TTGAGCCGATAGTTTAAACATCCAA\t3\n+TTGAGCCGATAGTTTTAACAATCAA\t9\n+TTGAGCCGGTAGATTTGACACCCAA\t14\n+TTGAGCCGGTAGTTTTGACACCCAA\t3\n+TTGCCCCTCCTGCACTCAAGTCCAA\t11\n+TTGCCCCTCCTGCACTCGAGTCCAA\t12\n+TTGCCTCTCCAGCACTCAAGAAAAA\t7\n' |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/filtered_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered_1.fastq Tue Sep 27 05:20:06 2022 +0000 |
| b |
| b'@@ -0,0 +1,1040 @@\n+@M00967:43:000000000-A3JHG:1:1101:18044:1900 1:N:0:188\n+TACGGAGGATGCGAGCGTTGTCCGGA\n++\n+BA@BBBABBFFFGGGGGGGGGGHGGG\n+@M00967:43:000000000-A3JHG:1:1101:4164:14549 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTATTGG\n++\n+ABBBBFFBBFBBGGGGGGGGGGHGGGGGHFHHHH\n+@M00967:43:000000000-A3JHG:1:1101:13124:16196 1:N:0:188\n+TACGGAGGGGGCAAGCGTTATCCGGATT\n++\n+BCCCCCCCCBCCGGGGGGGGGGHGGGGG\n+@M00967:43:000000000-A3JHG:1:1101:5053:23863 1:N:0:188\n+TACGGAGGATGCGGGCGTTATCCGGATTTATTGGGTTT\n++\n+>AAAAA@DAFFF?1AAEE/EABGGGGCGHHHHFCHEA/\n+@M00967:43:000000000-A3JHG:1:1102:14793:3762 1:N:0:188\n+TACAGAGGTCTCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGGAGCGAAAG\n++\n+CCCCCFFCFFFFGGGGGGGGGGHGGGGGHHHHHHGGGEFGGHHGGGGGGGGGHHHHHHHGGFHHHHGGGHHHHHHHHHHGGGGGGGHHHHHGGGGGGGGGGGGHHHHHHHHHGGGFFGHGHHHHHHHHHHHGGGGGGGGGGGGGGGGGGGCDFFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFEFFFCCFAEFFCCFFB0FE/AFFFFEBBFFBFFDFFFEAEFFFFFFFFFFFF@?CDACFCD\n+@M00967:43:000000000-A3JHG:1:1102:13449:7439 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+CCCBBFFAFFCCGGGGGGGGGGHGGGGGHHHHHGGHGEFGHHHGGE\n+@M00967:43:000000000-A3JHG:1:1102:20777:10045 1:N:0:188\n+TACGGAGGATGCGGGCGTTATCCGGATTTATTGGGTTT\n++\n+BABCBCCCCFFFGGGGGGGGGGHGGGGGHHHHHHHGGG\n+@M00967:43:000000000-A3JHG:1:1102:15058:11924 1:N:0:188\n+TACGTAGGATCCGAGCGTTATCCGGATTT\n++\n+CCCCCFFBFFFFGGGGGGGGGGHGGGGGH\n+@M00967:43:000000000-A3JHG:1:1102:8426:19244 1:N:0:188\n+TACGTAGGATTCAAGCGTTATCCGGATTT\n++\n+CCCDCFFBFFFFGGGGGGGGGGHGGGGGH\n+@M00967:43:000000000-A3JHG:1:1102:10315:19580 1:N:0:188\n+TACAGAGGTCTCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGGAGCGAAAG\n++\n+CCCCCFFCFFFFGGGGGGGGGGHGGGGGHHHHHHHHGGGGHHHGGGGGFGGGHHHHHHHGHHHHHHGGGHHHHHHHHHHGGGGGGGHHHHHGGGGGGGGGGGGHHHHFHHHHHGGGGGHHHHHHHHHHHHHGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFF\n+@M00967:43:000000000-A3JHG:1:1102:10011:20138 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+B@BBBFFABFBBGGGGGGGGGGHGGGGGHHHHGHGHF\n+@M00967:43:000000000-A3JHG:1:1102:9218:23401 1:N:0:188\n+TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACTGACTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGAT\n++\n+BBBBBFFBBBBBGGGGGGGGCGHGCGEFHHHHHHHCEEE2GGFGGGGGGGEF5BFEGHGGHHHHHHHHGHHHHHHHHFFHGGGGGGHHHHHHHGGHHGHHHHHHGHHHHHHHHHEHHHHGHFB>GGFHDGHFHGGCFGAGGFFBGFDFHFGGHFHHGCGGGHEFFGD..;.:\n+@M00967:43:000000000-A3JHG:1:1102:14380:24828 1:N:0:188\n+TACGTAGGATCCGAGCGTTATCCGGATTT\n++\n+ABBAAFF@FFFFGGGGGGGGGGGGGGGGH\n+@M00967:43:000000000-A3JHG:1:1102:15024:26862 1:N:0:188\n+TACGGAGGGTGCAAGCGTTAATCGGA\n++\n+BBBBBBBBBBBBGGGGGGGG2FGGGG\n+@M00967:43:000000000-A3JHG:1:1103:18198:2609 1:N:0:188\n+TACGGAGGTGGCAAGCGTTGTCCGGATTT\n++\n+CCCCCCCCBCCFGGGGGGGGGGHGGGGGH\n+@M00967:43:000000000-A3JHG:1:1103:17798:3752 1:N:0:188\n+TACGGAGGGAGCGAGCGTTATCCGGA\n++\n+BBBBABBBBBBBCGGGGGGGGGHGGG\n+@M00967:43:000000000-A3JHG:1:1103:8515:3790 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+BBBBBFFBBFBBGGGGGGGGGGHGGGGGHHHHHHHCF\n+@M00967:43:000000000-A3JHG:1:1103:22803:5970 1:N:0:188\n+TACGTAAGGGGCAAGCGTTATCCGGATTTAC\n++\n+CCCCBFFFFFCCGGGGGGGGGGHGGGGGHHH\n+@M00967:43:000000000-A3JHG:1:1103:7671:14378 1:N:0:188\n+TACGTAGGGAGCAAGCGTTATCCGGATTTAC\n++\n+BCBCCFFCCFCCGGGGGGGGGGHGGGGGHHH\n+@M00967:43:000000000-A3JHG:1:1103:7329:17775 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+BBBBBFFBFFBBGGGGGGGGGGHGGGGGHHHHHHHGCEEGHHHGCG\n+@M00967:43:000000000-A3JHG:1:1104:3247:11917 1:N:0:188\n+TACGTAGTGGGCAAGCGTTATCCGGATTTA\n++\n+?AABBFF3>C4AFEFGGFCFGG5AEFGFGG\n+@M00967:43:000000000-A3JHG:1:1104:25138:12414 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+BBCCCFFCFFCCGG'..b'ATTACTGGGTG\n++\n+BBBBAFFBAFBAFGGGGGGGGGHGGGGGHHHGHHGH2\n+@M00967:43:000000000-A3JHG:1:2111:9881:3810 1:N:0:188\n+GACGTAGGGGGCAAGCGTTATCCGG\n++\n+1>AAA@FAAAD?AA0A0AEGGGHGC\n+@M00967:43:000000000-A3JHG:1:2111:28102:9219 1:N:0:188\n+TACGGAGGGGGCAAGCGTTATCCGGAAT\n++\n+AABB3>ABDD?DAFFGGGGGGGHGGG2F\n+@M00967:43:000000000-A3JHG:1:2111:23451:9225 1:N:0:188\n+TACGTAGGGAGCAAGCGTTATCCGGATTTAC\n++\n+CCCCCFFCCFCCGGGGGGGGGGHGGGGGHHH\n+@M00967:43:000000000-A3JHG:1:2111:19869:15034 1:N:0:188\n+TACGGAGGGGGCAAGCGTTATCCGGAATT\n++\n+BBBBBABDBBBBGGGGGEGGGGHGGGGGH\n+@M00967:43:000000000-A3JHG:1:2111:20910:15547 1:N:0:188\n+TACGGAGGGGGCAAGCGTTATCCGGAATT\n++\n+AAAA1>ADD1ADGGGGGGGGGGHGGGEGH\n+@M00967:43:000000000-A3JHG:1:2111:20158:16824 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+CCCDCFFDCFCCGGGGGGGGGGHGGGGGHHHHHHHGF\n+@M00967:43:000000000-A3JHG:1:2111:8008:19696 1:N:0:188\n+TACGGAGGGGGCAAGCGTTATCCGGATTT\n++\n+BCCCCCCCBCCCGGGGGGGGGGHGGGGGH\n+@M00967:43:000000000-A3JHG:1:2111:14251:26147 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGA\n++\n+AAAA>FFA1>AACGGGGGGGGGGEGF\n+@M00967:43:000000000-A3JHG:1:2112:12931:12612 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+BCCBAFFCCFCCGGGGGGGGFGHGGGGGHHHGHHHHG\n+@M00967:43:000000000-A3JHG:1:2112:10839:15096 1:N:0:188\n+TACGTAGGTCCCGAGCGTTATCCGGATTTATTGG\n++\n+CCCCCFFCFFFFGGGGGGGGGGHGGGGGHHHHHH\n+@M00967:43:000000000-A3JHG:1:2112:25157:19286 1:N:0:188\n+TACGTAGGATCCGAGCGTTATCCGGATTT\n++\n+CCCCCFFCFFFFGGGGGGGGGGHGGGGGG\n+@M00967:43:000000000-A3JHG:1:2112:24834:22079 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+BBBBAFFBFFBBGGGGEGGGGGHGGGEFHHFHHHHGCGGGHHGGHG\n+@M00967:43:000000000-A3JHG:1:2113:14457:3580 1:N:0:188\n+TACGGAGGATGCGAGCGTTGTCCGGATTTACTGG\n++\n+AAAAB?ABBFFFGGGCGGGGGCHFGGGGGFHHHG\n+@M00967:43:000000000-A3JHG:1:2113:20030:3857 1:N:0:188\n+TACGTAAGGGGCAAGCGTTATCCGGATTTAC\n++\n+BBBBAFFFFFBBGCAGGGGGGGHGGGGGH5G\n+@M00967:43:000000000-A3JHG:1:2113:25338:6570 1:N:0:188\n+TACGGAGGATGCGGGCGTTATCCGGATTTATTGGGTTT\n++\n+BBBB@ABBBFFFGGGGGGGGGGHGGGGGHGHHHHHGGG\n+@M00967:43:000000000-A3JHG:1:2113:25467:7322 1:N:0:188\n+TACGGAGGAGGCGAGCGTTATCCGGATTTATTGG\n++\n+AAAA??AD11>A0EEGGGG0AGHGGGGGHH2FGH\n+@M00967:43:000000000-A3JHG:1:2113:5038:9324 1:N:0:188\n+TACGGAGGTGGCGAGCGTTGTCCGGATTT\n++\n+>AAA1>ADAAAFGG0EEGGGFGHGEFGGH\n+@M00967:43:000000000-A3JHG:1:2113:28731:11914 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTATTGG\n++\n+BBBBBFFB@BAAGGGGGEGGGGHGGGGGHHHHHH\n+@M00967:43:000000000-A3JHG:1:2114:22327:5513 1:N:0:188\n+TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTG\n++\n+BBBBBFFBAFBBEGFGFGGCFGHGGGGGBFHHGFHHGEGFHHHGHG\n+@M00967:43:000000000-A3JHG:1:2114:7852:9583 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTAC\n++\n+ABCCBFFCCFBCGGGGGGGGGGHGGGGGHHH\n+@M00967:43:000000000-A3JHG:1:2114:16606:9609 1:N:0:188\n+TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACTGACTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGAT\n++\n+BCCBCFFBCABCGGGGGGGGGGHGGGGGHHHHHGGGGEGGHGHGGGGGGGGGFGGEFHGHHHHHHHHHHHHHHGHHHHHHGGGGGGHHHHHHHHGHHGHHHHHHGHGHHHHHHHHHHHHHHHHHHHHHFHHHHHGDFGGGGHHHHHHGHHHHHHHHGGGGGHGHHHGGGGGH\n+@M00967:43:000000000-A3JHG:1:2114:4360:11353 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTATTGG\n++\n+AAAA>CFBCFABGGGGGGGGGGHGGGGGHHHHHG\n+@M00967:43:000000000-A3JHG:1:2114:28521:18445 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTATTGG\n++\n+BBBBBFFB@>ABGGGG?FFGGGHGG2EGHHHGHG\n+@M00967:43:000000000-A3JHG:1:2114:16773:20452 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTATTGG\n++\n+ABCAAFFCCFCCGGGGGGGGGGHGGGGGGHHHHH\n+@M00967:43:000000000-A3JHG:1:2114:23924:23696 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+>AAB3BFBFFCCGGGGGGGGGGHGGGGGCBDFHHHFFEGGHHHGFF\n+@M00967:43:000000000-A3JHG:1:2114:9786:25559 1:N:0:188\n+TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACTGACTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGAT\n++\n+BBBBBFFBABBBGGGGGGGG2AGFEGAFGHFHHHHAAEGGHHFG?EGGEGGG@BFEF1EHGHHHHHHHH3GHFHHHH3EGAEECGGHHHHHHFE/GF/2GFBGHFHHHDCCGF2GDFCGFF2@@G2FG<1?GFBACFCAFFHGFHBGHFFGB0=DFGFA@EHFCGHDA.@.:\n' |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/filtered_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered_2.fastq Tue Sep 27 05:20:06 2022 +0000 |
| b |
| b'@@ -0,0 +1,624 @@\n+@M00967:43:000000000-A3JHG:1:1101:4164:14549 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTATTGG\n++\n+ABBBBFFBBFBBGGGGGGGGGGHGGGGGHFHHHH\n+@M00967:43:000000000-A3JHG:1:1101:13124:16196 1:N:0:188\n+TACGGAGGGGGCAAGCGTTATCCGGATT\n++\n+BCCCCCCCCBCCGGGGGGGGGGHGGGGG\n+@M00967:43:000000000-A3JHG:1:1102:14793:3762 1:N:0:188\n+TACAGAGGTCTCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGGAGCGA\n++\n+CCCCCFFCFFFFGGGGGGGGGGHGGGGGHHHHHHGGGEFGGHHGGGGGGGGGHHHHHHHGGFHHHHGGGHHHHHHHHHHGGGGGGGHHHHHGGGGGGGGGGGGHHHHHHHHHGGGFFGHGHHHHHHHHHHHGGGGGGGGGGGGGGGGGGGCDFFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFEFFFCCFAEFFCCFFB0FE/AFFFFEBBFFBFFDFFFEAEFFFFFFFFFFFF@?CDAC\n+@M00967:43:000000000-A3JHG:1:1102:13449:7439 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+CCCBBFFAFFCCGGGGGGGGGGHGGGGGHHHHHGGHGEFGHHHGGE\n+@M00967:43:000000000-A3JHG:1:1102:10315:19580 1:N:0:188\n+TACAGAGGTCTCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGGAGCGA\n++\n+CCCCCFFCFFFFGGGGGGGGGGHGGGGGHHHHHHHHGGGGHHHGGGGGFGGGHHHHHHHGHHHHHHGGGHHHHHHHHHHGGGGGGGHHHHHGGGGGGGGGGGGHHHHFHHHHHGGGGGHHHHHHHHHHHHHGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFF\n+@M00967:43:000000000-A3JHG:1:1102:10011:20138 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+B@BBBFFABFBBGGGGGGGGGGHGGGGGHHHHGHGHF\n+@M00967:43:000000000-A3JHG:1:1103:8515:3790 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+BBBBBFFBBFBBGGGGGGGGGGHGGGGGHHHHHHHCF\n+@M00967:43:000000000-A3JHG:1:1103:22803:5970 1:N:0:188\n+TACGTAAGGGGCAAGCGTTATCCGGA\n++\n+CCCCBFFFFFCCGGGGGGGGGGHGGG\n+@M00967:43:000000000-A3JHG:1:1103:7329:17775 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+BBBBBFFBFFBBGGGGGGGGGGHGGGGGHHHHHHHGCEEGHHHGCG\n+@M00967:43:000000000-A3JHG:1:1104:25138:12414 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+BBCCCFFCFFCCGGGGGGGGGGHGGGGGHHHHHHHHGGGGHHHGHG\n+@M00967:43:000000000-A3JHG:1:1104:24665:17168 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTATTGG\n++\n+BBBB?FFBAFBBFGGGGGGGGGHGGGGGHHHHHH\n+@M00967:43:000000000-A3JHG:1:1104:17315:20406 1:N:0:188\n+TACGTAAGGGGCAAGCGTTATCCGGA\n++\n+DDDDDFFFFFCDGGGGGGGGGGHGGG\n+@M00967:43:000000000-A3JHG:1:1105:18572:8415 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+ABBBAFFB3CABGGGGGGGCGGHGGGEFHHGHHHHHA\n+@M00967:43:000000000-A3JHG:1:1105:5622:9401 1:N:0:188\n+TACGGAGGGGGCAAGCGTTATCCGGATTT\n++\n+ABCCCCCCBBCCGGGGGGGGGGHGGGGGH\n+@M00967:43:000000000-A3JHG:1:1105:5580:9621 1:N:0:188\n+TACAGAGGTCTCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGGAGCGA\n++\n+BCBCCFFCBFFFGGGGFGGGFGHGGGGGHHHHHHHHGGCGHHHGDGGGAEGGHHHHHHGGAGHHHHGG1FGHGHGHHFG@ECEFGCHHHHHG@@GC@<C@DGGHHFFFDGHHHGCGCDHHGGHDDDDHGCGEGG?DFGGGGGGGFFFFGGEGAFBFFFFBFFFFFFF.ABFFFF/A..;CDFF?BFFFFAADC>FCF?EDB;=EFFFFFFFFFBFFFFBFFDD..9A9A?FFF..AEEEFFF;.-.-@\n+@M00967:43:000000000-A3JHG:1:1105:23025:12058 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+BCCDCFFDFFDDGGGGGGGGGGHGGGGGHHHHHHHGGEFEHHHGHG\n+@M00967:43:000000000-A3JHG:1:1105:7380:21363 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+ABBAAFFBBFBBFFEGGGG?FGHGGGGFHHHHHHGFE\n+@M00967:43:000000000-A3JHG:1:1105:10286:23294 1:N:0:188\n+TACGGAGGGGGCAAGCGTTATCCGGATTT\n++\n+CCCCCCBBCCCCGGGGGGGGGGHGGGGGH\n+@M00967:43:000000000-A3JHG:1:1105:12965:26634 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTATTGG\n++\n+BBBBBFFBB4AAGFBGGGGGGGHGGGGGHGHHHH\n+@M00967:43:000000000-A3JHG:1:1106:24475:12056 1:N:0:188\n+TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTG\n++\n+BCCCBFFCCFDDGGGGGGGGGGHGGGGGHHHHHHHGG'..b'GGGGHGHHHHHHGGGGHFFGGGGGGFGGHHHHHHHGHHGHHHGFGHHHHHHGHAGE@EGGGGHHHHHGGGGGGGGGGGGGHHHHHHHHHGGGGGHGHHHHHHHGGHHGGGGAEGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFEFFFF?EFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFEFFFFFFFFFFFFFFFFFEFFFFFDDDFFFFEFF?DFF-\n+@M00967:43:000000000-A3JHG:1:2108:27580:8673 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGA\n++\n+>>AA3CFA44AACGGGGGGGGGHCCG\n+@M00967:43:000000000-A3JHG:1:2108:27846:15702 1:N:0:188\n+TACGTAAGGGGCAAGCGTTATCCGGA\n++\n+BBBABF4CFFBBFGGGGGGGGGGGGD\n+@M00967:43:000000000-A3JHG:1:2109:15993:1967 1:N:0:188\n+TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTG\n++\n+CBCCCFFCCFCCGGGGGGGGGGGGGGGGHGHHGGGHGEEGCGHGHG\n+@M00967:43:000000000-A3JHG:1:2109:12598:17782 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+CBCBCFFCCFCCGGGGGGGGGGHGGGGGHHHHHHHHG\n+@M00967:43:000000000-A3JHG:1:2109:16424:18256 1:N:0:188\n+TACGGAGGGGGCAAGCGTTATCCGGATTT\n++\n+BBBBBBA@BBBBGGGGGGGGGGHGGGGGH\n+@M00967:43:000000000-A3JHG:1:2109:28147:21081 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+>AAA>F4A4CABGGFGGGGGGGHGGGGGGHHGGHHHGGGGHGHFCF\n+@M00967:43:000000000-A3JHG:1:2109:11980:24372 1:N:0:188\n+TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTG\n++\n+CCCCCFFCCFCCGGGGGGGGGGHGGGGGFHHGHHHGGGGGHHHGHG\n+@M00967:43:000000000-A3JHG:1:2110:24580:11767 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+BBBCCFFCDFBCGGGGGGGGGGHGGGEGHHHHHGHFGEFGHHHGAF\n+@M00967:43:000000000-A3JHG:1:2110:6116:13104 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+BBBBBFFBFFBBGGGGGGFGGGHGGGGGHHHHHHHHGGGGHHGGHG\n+@M00967:43:000000000-A3JHG:1:2110:23162:17853 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+BCCCCFFCCFCCGGGGGGGGGGHGGGGGHHHGHHHGF\n+@M00967:43:000000000-A3JHG:1:2110:17767:25669 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+AABB3CFBAFBBGGGGGGGGGFHFGG?FHHFHHHHHG\n+@M00967:43:000000000-A3JHG:1:2110:21271:27854 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+BBBBAFFBAFBAFGGGGGGGGGHGGGGGHHHGHHGH2\n+@M00967:43:000000000-A3JHG:1:2111:28102:9219 1:N:0:188\n+TACGGAGGGGGCAAGCGTTATCCGGA\n++\n+AABB3>ABDD?DAFFGGGGGGGHGGG\n+@M00967:43:000000000-A3JHG:1:2111:19869:15034 1:N:0:188\n+TACGGAGGGGGCAAGCGTTATCCGGA\n++\n+BBBBBABDBBBBGGGGGEGGGGHGGG\n+@M00967:43:000000000-A3JHG:1:2111:20910:15547 1:N:0:188\n+TACGGAGGGGGCAAGCGTTATCCGGA\n++\n+AAAA1>ADD1ADGGGGGGGGGGHGGG\n+@M00967:43:000000000-A3JHG:1:2111:20158:16824 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+CCCDCFFDCFCCGGGGGGGGGGHGGGGGHHHHHHHGF\n+@M00967:43:000000000-A3JHG:1:2111:8008:19696 1:N:0:188\n+TACGGAGGGGGCAAGCGTTATCCGGATTT\n++\n+BCCCCCCCBCCCGGGGGGGGGGHGGGGGH\n+@M00967:43:000000000-A3JHG:1:2111:14251:26147 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGA\n++\n+AAAA>FFA1>AACGGGGGGGGGGEGF\n+@M00967:43:000000000-A3JHG:1:2112:12931:12612 1:N:0:188\n+TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTG\n++\n+BCCBAFFCCFCCGGGGGGGGFGHGGGGGHHHGHHHHG\n+@M00967:43:000000000-A3JHG:1:2112:24834:22079 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+BBBBAFFBFFBBGGGGEGGGGGHGGGEFHHFHHHHGCGGGHHGGHG\n+@M00967:43:000000000-A3JHG:1:2113:20030:3857 1:N:0:188\n+TACGTAAGGGGCAAGCGTTATCCGGA\n++\n+BBBBAFFFFFBBGCAGGGGGGGHGGG\n+@M00967:43:000000000-A3JHG:1:2113:28731:11914 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTATTGG\n++\n+BBBBBFFB@BAAGGGGGEGGGGHGGGGGHHHHHH\n+@M00967:43:000000000-A3JHG:1:2114:22327:5513 1:N:0:188\n+TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTG\n++\n+BBBBBFFBAFBBEGFGFGGCFGHGGGGGBFHHGFHHGEGFHHHGHG\n+@M00967:43:000000000-A3JHG:1:2114:7852:9583 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTA\n++\n+ABCCBFFCCFBCGGGGGGGGGGHGGGGGHH\n+@M00967:43:000000000-A3JHG:1:2114:4360:11353 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTATTGG\n++\n+AAAA>CFBCFABGGGGGGGGGGHGGGGGHHHHHG\n+@M00967:43:000000000-A3JHG:1:2114:28521:18445 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTATTGG\n++\n+BBBBBFFB@>ABGGGG?FFGGGHGG2EGHHHGHG\n+@M00967:43:000000000-A3JHG:1:2114:16773:20452 1:N:0:188\n+TACGTAGGGTGCAAGCGTTATCCGGATTTATTGG\n++\n+ABCAAFFCCFCCGGGGGGGGGGHGGGGGGHHHHH\n+@M00967:43:000000000-A3JHG:1:2114:23924:23696 1:N:0:188\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTG\n++\n+>AAB3BFBFFCCGGGGGGGGGGHGGGGGCBDFHHHFFEGGHHHGFF\n' |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/histogram.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/histogram.txt Tue Sep 27 05:20:06 2022 +0000 |
| b |
| @@ -0,0 +1,28 @@ +3 3770 +4 2131 +5 1589 +6 956 +7 390 +8 549 +9 538 +10 694 +11 493 +12 328 +13 198 +14 331 +15 171 +16 130 +17 135 +18 240 +19 176 +20 236 +21 230 +22 220 +23 207 +24 133 +25 203 +26 211 +27 165 +28 252 +29 186 +30 151 |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/intersect_max_db.kmc_pre |
| b |
| Binary file test-data/intersect_max_db.kmc_pre has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/intersect_max_db.kmc_suf |
| b |
| Binary file test-data/intersect_max_db.kmc_suf has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/intersect_min_db.kmc_pre |
| b |
| Binary file test-data/intersect_min_db.kmc_pre has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/intersect_min_db.kmc_suf |
| b |
| Binary file test-data/intersect_min_db.kmc_suf has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/kmers_one.kmc_pre |
| b |
| Binary file test-data/kmers_one.kmc_pre has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/kmers_one.kmc_suf |
| b |
| Binary file test-data/kmers_one.kmc_suf has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/kmers_two.kmc_pre |
| b |
| Binary file test-data/kmers_two.kmc_pre has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/kmers_two.kmc_suf |
| b |
| Binary file test-data/kmers_two.kmc_suf has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/reduce_1_db.kmc_pre |
| b |
| Binary file test-data/reduce_1_db.kmc_pre has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/reduce_1_db.kmc_suf |
| b |
| Binary file test-data/reduce_1_db.kmc_suf has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/sort_1_db.kmc_pre |
| b |
| Binary file test-data/sort_1_db.kmc_pre has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/sort_1_db.kmc_suf |
| b |
| Binary file test-data/sort_1_db.kmc_suf has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/sort_2_db.kmc_pre |
| b |
| Binary file test-data/sort_2_db.kmc_pre has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/sort_2_db.kmc_suf |
| b |
| Binary file test-data/sort_2_db.kmc_suf has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/union_db.kmc_pre |
| b |
| Binary file test-data/union_db.kmc_pre has changed |
| b |
| diff -r 000000000000 -r ca2743037241 test-data/union_db.kmc_suf |
| b |
| Binary file test-data/union_db.kmc_suf has changed |