| Next changeset 1:5ece301faf6b (2020-08-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344 |
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added:
idba_hybrid.xml macros.xml test-data/all_fasta.loc test-data/assembly_sample-R1.fastq test-data/assembly_sample-R2.fastq test-data/merged.fa test-data/out/align-100-0 test-data/out/align-20 test-data/out/align-40 test-data/out/align-60 test-data/out/align-80 test-data/out/begin test-data/out/contig-100.fa test-data/out/contig-20.fa test-data/out/contig-40.fa test-data/out/contig-60.fa test-data/out/contig-80.fa test-data/out/contig.fa test-data/out/end test-data/out/graph-100.fa test-data/out/graph-20.fa test-data/out/graph-40.fa test-data/out/graph-60.fa test-data/out/graph-80.fa test-data/out/kmer test-data/out/local-contig-20.fa test-data/out/local-contig-40.fa test-data/out/local-contig-60.fa test-data/out/local-contig-80.fa test-data/out/log test-data/out/scaffold.fa test-data/reference.fa tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r a81c5169e9fc idba_hybrid.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idba_hybrid.xml Mon Aug 05 15:59:15 2019 -0400 |
| [ |
| @@ -0,0 +1,94 @@ +<tool id="idba_hybrid" name="IDBA-HYBRID" version="@IDBA_VERSION@"> + <description> + Iterative de Bruijn Graph Assembler for hybrid sequencing data + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ + idba_hybrid + + @MAIN_INPUT@ + #if $ref_source.ref_source_sel == "cached" + --reference '${$ref_source.reference.fields.path}' + #else + --reference '$ref_source.reference' + #end if + @LEVELS_INPUT@ + @KMER_OPTIONS@ + @FILTER_OPTIONS@ + --min_region $min_region + --max_gap $max_gap + @MIN_PAIRS_FILTER@ + @OTHER_OPTIONS@ + @THREADS@ + ]]></command> + + <inputs> + <expand macro="main_input"/> + <conditional name="ref_source"> + <param label="Choose the source for the reference genome" name="ref_source_sel" type="select"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param argument="--reference" label="Using reference genome" type="select"> + <options from_data_table="all_fasta"> + <filter column="1" type="sort_by" /> + </options> + <validator message="No reference genome is available" type="no_options" /> + </param> + </when> + <when value="history"> + <param argument="--reference" type="data" format="fasta" label="Reference Annotation" /> + </when> + </conditional> + <expand macro="levels_input"/> + <expand macro="kmer_options" maxk_default="100" step_default="20"/> + <expand macro="filter_options"/> + <param argument="--min_region" type="integer" value="300" label="Minimum size of region in reference genome"/> + <param argument="--max_gap" type="integer" value="3" label="Maximum gap in reference"/> + <expand macro="min_pairs_filter"/> + <expand macro="other_options"/> + </inputs> + <outputs> + <data name="output" from_work_dir="out/scaffold.fa" format="fasta"/> + </outputs> + <tests> + <!-- basic test + check of defaults --> + <test> + <param name="ref_source|reference" value="reference.fa" ftype="fasta"/> + <param name="ref_source|ref_source_sel" value="history"/> + <param name="read" value="merged.fa" ftype="fasta"/> + <output name="output" file="out/scaffold.fa" ftype="fasta"/> + <assert_command> + <has_text text="--min_region 300" /> + <has_text text="--max_gap 3" /> + </assert_command> + </test> + <!-- chached reference test --> + <test> + <param name="ref_source|reference" value="test_id"/> + <param name="ref_source|ref_source_sel" value="cached"/> + <param name="read" value="merged.fa" ftype="fasta"/> + <output name="output" file="out/scaffold.fa" ftype="fasta"/> + </test> + <!-- tool specific parameters --> + <test> + <param name="ref_source|reference" value="reference.fa" ftype="fasta"/> + <param name="ref_source|ref_source_sel" value="history"/> + <param name="read" value="merged.fa" ftype="fasta"/> + <param name="min_region" value="299"/> + <param name="max_gap" value="2"/> + <assert_command> + <has_text text="--min_region 299" /> + <has_text text="--max_gap 2" /> + </assert_command> + <output name="output" file="out/scaffold.fa" ftype="fasta"/> + </test> + </tests> + <expand macro="help" more_help="IDBA-Hybrid is an iterative De Bruijn Graph De Novo Assembler for hybrid sequencing. It is an extension of IDBA-UD algorithm. It aims at using a closed related reference genome to help de novo assembly, especially when sequencing depth is low. IDBA-Hybrid does alignment between reads and reference first to extract similar regions in the reference genome, and then it correct the similar regions based on the alignment results and apply local assembly technique to resolve potential structure virations. Finally, it groups all the reads and the contigs got from those similar regions to do de novo assembly. The expriments showed it outperforms all existing de novo or hybrid assembly algorithms, especilly when the sequencing depth is low and the reference genome is similar to the target genome."/> + <expand macro="citations"> + </expand> +</tool> |
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| diff -r 000000000000 -r a81c5169e9fc macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Aug 05 15:59:15 2019 -0400 |
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| @@ -0,0 +1,128 @@ +<macros> + <token name="@IDBA_VERSION@">1.1.3</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@IDBA_VERSION@">idba</requirement> + <yield/> + </requirements> + </xml> + + <xml name="main_input"> + <param argument="--read" type="data" format="fasta" label="Fasta read file. Lower or equal to 600b"/> + <param argument="--long_read" type="data" format="fasta" optional="true" label="Fasta long read file. More than 600b"/> + </xml> + + <token name="@MAIN_INPUT@"> + --read '$read' + #if $long_read: + --long_read '$long_read' + #end if + </token> + + <xml name="levels_input"> + <param argument="--read_level_2" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for second level scaffolds"/> + <param argument="--read_level_3" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for third level scaffolds"/> + <param argument="--read_level_4" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fourth level scaffolds"/> + <param argument="--read_level_5" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fifth level scaffolds"/> + </xml> + <token name="@LEVELS_INPUT@"> + #if $read_level_2: + --read_level_2 '$read_level_2' + #end if + #if $read_level_3: + --read_level_3 '$read_level_3' + #end if + #if $read_level_4: + --read_level_4 '$read_level_4' + #end if + #if $read_level_5: + --read_level_5 '$read_level_5' + #end if + </token> + + <xml name="kmer_options" token_maxk_default="" token_step_default=""> + <param argument="--mink" type="integer" value="20" max="312" label="Minimum k value. Lower or equal to 312"/> + <param argument="--maxk" type="integer" value="@MAXK_DEFAULT@" max="312" label="Maximum k value. Lower or equal to 312"/> + <param argument="--step" type="integer" value="@STEP_DEFAULT@" label="Increment of k-mer of each iteration"/> + <param argument="--inner_mink" type="integer" value="10" label="Inner minimum k value"/> + <param argument="--inner_step" type="integer" value="5" label="Inner increment of k-mer"/> + <param argument="--prefix" type="integer" value="3" label="Prefix length used to build sub k-mer table"/> + <param argument="--min_count" type="integer" value="2" label="Minimum multiplicity for filtering k-mer when building the graph"/> + <param argument="--min_support" type="integer" value="1" label="Minimum supoort in each iteration"/> + <param argument="--seed_kmer" type="integer" value="30" label="Seed kmer size for alignment"/> + </xml> + <token name="@KMER_OPTIONS@"> + --mink $mink + --maxk $maxk + --step $step + --inner_mink $inner_mink + --inner_step $inner_step + --prefix $prefix + --min_count $min_count + --min_support $min_support + --seed_kmer $seed_kmer + </token> + + <xml name="filter_options"> + <param argument="--min_contig" type="integer" value="200" label="Minimum size of contig"/> + <param argument="--similar" type="float" value="0.95" label="Similarity for alignment"/> + <param argument="--max_mismatch" type="integer" value="3" label="Max mismatch of error correction"/> + </xml> + <token name="@FILTER_OPTIONS@"> + --min_contig $min_contig + --similar $similar + --max_mismatch $max_mismatch + </token> + + <xml name="min_pairs_filter"> + <param argument="--min_pairs" type="integer" value="3" label="Minimum number of pairs"/> + </xml> + <token name="@MIN_PAIRS_FILTER@"> + --min_pairs $min_pairs + </token> + <xml name="other_options"> + <param name="other" type="select" display="checkboxes" multiple="true" label="Other options"> + <yield/> + <option value="--no_local">Do not use local assembly (--no_local)</option> + <option value="--no_coverage">Do not iterate on coverage (--no_coverage)</option> + <option value="--no_correct">Do not do correction (--no_correct)</option> + <option value="--pre_correction">Perform pre-correction before assembly (--pre_correction)</option> + </param> + </xml> + <token name="@OTHER_OPTIONS@"> + #if $other: + ${" ".join(str($other).split(","))} + #end if + </token> + + <token name="@THREADS@"> + --num_threads \${GALAXY_SLOTS:-1} + </token> + + <xml name="help" token_more_help=""> + <help><![CDATA[ +IDBA is an iterative De Bruijn Graph De Novo Assembler for sequence assembly. Most assemblers based on de Bruijn graph build a de Bruijn graph with a specific k-mer size to perform the assembling task. For all of them, it is very crucial to find a specific value of k. If k is too large, there will be a lot of gap problems in the graph. If k is too small, there will a lot of branch problems. IDBA uses not only one specific k but a range of k values to build the iterative de Bruijn graph. It can keep all the information in graphs with different k values. + +@MORE_HELP@ + +Input: IDBA-* take interleaved paired end data in the FASTA format as input, +i.e. paired-end reads need to be stored in the same FASTA file such that a pair +of reads should be in two consecutive lines. +In Galaxy paired reads in separate FASTQ files can be converted into interleaved +FASTA using the tools: + +* `FASTQ interlacer on paired end read <https://toolshed.g2.bx.psu.edu/view/devteam/fastq_paired_end_interlacer>`_ +* `Samtools extract FASTA or FASTQ from a SAM file <https://toolshed.g2.bx.psu.edu/view/devteam/fastq_to_fasta>`_ + +Note that, IDBA-* assumes that the paired-end reads are in order (->,<-). +If your data is in reverse order (<-,->), please convert it by yourself. + ]]></help> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1007/978-3-642-12683-3_28</citation> + <yield/> + </citations> + </xml> + +</macros> |
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| diff -r 000000000000 -r a81c5169e9fc test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Mon Aug 05 15:59:15 2019 -0400 |
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| @@ -0,0 +1,20 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# +test_id test_dbkey test display name ${__HERE__}/merged.fa + |
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| diff -r 000000000000 -r a81c5169e9fc test-data/assembly_sample-R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assembly_sample-R1.fastq Mon Aug 05 15:59:15 2019 -0400 |
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| b'@@ -0,0 +1,604 @@\n+@HWI-ST745_0097:7:1101:1001:1000#0/1\n+GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTT\n++HWI-ST745_0097:7:1101:1001:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1002:1000#0/1\n+AAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTA\n++HWI-ST745_0097:7:1101:1002:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1003:1000#0/1\n+AAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAG\n++HWI-ST745_0097:7:1101:1003:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1004:1000#0/1\n+AAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGT\n++HWI-ST745_0097:7:1101:1004:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1005:1000#0/1\n+AACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTG\n++HWI-ST745_0097:7:1101:1005:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1006:1000#0/1\n+ACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGG\n++HWI-ST745_0097:7:1101:1006:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1007:1000#0/1\n+CGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGT\n++HWI-ST745_0097:7:1101:1007:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1008:1000#0/1\n+GCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTG\n++HWI-ST745_0097:7:1101:1008:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1009:1000#0/1\n+CGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGA\n++HWI-ST745_0097:7:1101:1009:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1010:1000#0/1\n+GCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAG\n++HWI-ST745_0097:7:1101:1010:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1011:1000#0/1\n+CTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGT\n++HWI-ST745_0097:7:1101:1011:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1012:1000#0/1\n+TTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTC\n++HWI-ST745_0097:7:1101:1012:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1013:1000#0/1\n+TGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCG\n++HWI-ST745_0097:7:1101:1013:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1014:1000#0/1\n+GCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGT\n++HWI-ST745_0097:7:1101:1014:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1015:1000#0/1\n+CAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTC\n++HWI-ST745_0097:7:1101:1015:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1016:1000#0/1\n+AGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCG\n++HWI-ST745_0097:7:1101:1016:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1017:1000#0/1\n+GATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGG\n++HWI-ST745_0097:7:1101:1017:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1018:1000#0/1'..b'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1135:1000#0/1\n+GACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCA\n++HWI-ST745_0097:7:1101:1135:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1136:1000#0/1\n+CCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATC\n++HWI-ST745_0097:7:1101:1136:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1137:1000#0/1\n+GTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCG\n++HWI-ST745_0097:7:1101:1137:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1138:1000#0/1\n+TTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCA\n++HWI-ST745_0097:7:1101:1138:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1139:1000#0/1\n+GGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACT\n++HWI-ST745_0097:7:1101:1139:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1140:1000#0/1\n+TTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCC\n++HWI-ST745_0097:7:1101:1140:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1142:1000#0/1\n+CCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGA\n++HWI-ST745_0097:7:1101:1142:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1141:1000#0/1\n+CGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAA\n++HWI-ST745_0097:7:1101:1141:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1145:1000#0/1\n+AACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGT\n++HWI-ST745_0097:7:1101:1145:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1143:1000#0/1\n+ACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTT\n++HWI-ST745_0097:7:1101:1143:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1144:1000#0/1\n+CTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTG\n++HWI-ST745_0097:7:1101:1144:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1146:1000#0/1\n+CTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTG\n++HWI-ST745_0097:7:1101:1146:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1147:1000#0/1\n+TGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGC\n++HWI-ST745_0097:7:1101:1147:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1148:1000#0/1\n+CCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACC\n++HWI-ST745_0097:7:1101:1148:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1149:1000#0/1\n+CATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCA\n++HWI-ST745_0097:7:1101:1149:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1150:1000#0/1\n+ATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAG\n++HWI-ST745_0097:7:1101:1150:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1151:1000#0/1\n+TGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC\n++HWI-ST745_0097:7:1101:1151:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/assembly_sample-R2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assembly_sample-R2.fastq Mon Aug 05 15:59:15 2019 -0400 |
| b |
| b'@@ -0,0 +1,604 @@\n+@HWI-ST745_0097:7:1101:1001:1000#0/2\n+GCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTC\n++HWI-ST745_0097:7:1101:1001:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1002:1000#0/2\n+TTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAA\n++HWI-ST745_0097:7:1101:1002:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1003:1000#0/2\n+ATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAG\n++HWI-ST745_0097:7:1101:1003:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1004:1000#0/2\n+CAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGC\n++HWI-ST745_0097:7:1101:1004:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1005:1000#0/2\n+CCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCC\n++HWI-ST745_0097:7:1101:1005:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1006:1000#0/2\n+CCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTC\n++HWI-ST745_0097:7:1101:1006:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1007:1000#0/2\n+AAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGC\n++HWI-ST745_0097:7:1101:1007:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1008:1000#0/2\n+TGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGT\n++HWI-ST745_0097:7:1101:1008:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1009:1000#0/2\n+GCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTC\n++HWI-ST745_0097:7:1101:1009:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1010:1000#0/2\n+GGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGG\n++HWI-ST745_0097:7:1101:1010:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1011:1000#0/2\n+TTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGG\n++HWI-ST745_0097:7:1101:1011:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1012:1000#0/2\n+CTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATA\n++HWI-ST745_0097:7:1101:1012:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1013:1000#0/2\n+CAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGC\n++HWI-ST745_0097:7:1101:1013:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1014:1000#0/2\n+CCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGA\n++HWI-ST745_0097:7:1101:1014:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1015:1000#0/2\n+CTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTA\n++HWI-ST745_0097:7:1101:1015:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1016:1000#0/2\n+GTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCG\n++HWI-ST745_0097:7:1101:1016:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1017:1000#0/2\n+CATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGA\n++HWI-ST745_0097:7:1101:1017:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1018:1000#0/2'..b'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1135:1000#0/2\n+ACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCAT\n++HWI-ST745_0097:7:1101:1135:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1136:1000#0/2\n+TTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTAC\n++HWI-ST745_0097:7:1101:1136:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1137:1000#0/2\n+GTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGA\n++HWI-ST745_0097:7:1101:1137:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1138:1000#0/2\n+CTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCT\n++HWI-ST745_0097:7:1101:1138:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1139:1000#0/2\n+GCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCT\n++HWI-ST745_0097:7:1101:1139:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1140:1000#0/2\n+CGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGG\n++HWI-ST745_0097:7:1101:1140:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1142:1000#0/2\n+GAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTC\n++HWI-ST745_0097:7:1101:1142:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1141:1000#0/2\n+TGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTG\n++HWI-ST745_0097:7:1101:1141:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1145:1000#0/2\n+GATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAG\n++HWI-ST745_0097:7:1101:1145:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1143:1000#0/2\n+AGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGC\n++HWI-ST745_0097:7:1101:1143:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1144:1000#0/2\n+TGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCG\n++HWI-ST745_0097:7:1101:1144:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1146:1000#0/2\n+TGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAA\n++HWI-ST745_0097:7:1101:1146:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1147:1000#0/2\n+CTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCC\n++HWI-ST745_0097:7:1101:1147:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1148:1000#0/2\n+GATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAG\n++HWI-ST745_0097:7:1101:1148:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1149:1000#0/2\n+CTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATG\n++HWI-ST745_0097:7:1101:1149:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1150:1000#0/2\n+TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACC\n++HWI-ST745_0097:7:1101:1150:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1151:1000#0/2\n+AACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCG\n++HWI-ST745_0097:7:1101:1151:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/merged.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| b'@@ -0,0 +1,604 @@\n+>HWI-ST745_0097:7:1101:1001:1000#0/1\n+GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTT\n+>HWI-ST745_0097:7:1101:1001:1000#0/2\n+GCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTC\n+>HWI-ST745_0097:7:1101:1002:1000#0/1\n+AAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTA\n+>HWI-ST745_0097:7:1101:1002:1000#0/2\n+TTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAA\n+>HWI-ST745_0097:7:1101:1003:1000#0/1\n+AAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAG\n+>HWI-ST745_0097:7:1101:1003:1000#0/2\n+ATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAG\n+>HWI-ST745_0097:7:1101:1004:1000#0/1\n+AAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGT\n+>HWI-ST745_0097:7:1101:1004:1000#0/2\n+CAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGC\n+>HWI-ST745_0097:7:1101:1005:1000#0/1\n+AACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTG\n+>HWI-ST745_0097:7:1101:1005:1000#0/2\n+CCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCC\n+>HWI-ST745_0097:7:1101:1006:1000#0/1\n+ACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGG\n+>HWI-ST745_0097:7:1101:1006:1000#0/2\n+CCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTC\n+>HWI-ST745_0097:7:1101:1007:1000#0/1\n+CGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGT\n+>HWI-ST745_0097:7:1101:1007:1000#0/2\n+AAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGC\n+>HWI-ST745_0097:7:1101:1008:1000#0/1\n+GCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTG\n+>HWI-ST745_0097:7:1101:1008:1000#0/2\n+TGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGT\n+>HWI-ST745_0097:7:1101:1009:1000#0/1\n+CGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGA\n+>HWI-ST745_0097:7:1101:1009:1000#0/2\n+GCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTC\n+>HWI-ST745_0097:7:1101:1010:1000#0/1\n+GCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAG\n+>HWI-ST745_0097:7:1101:1010:1000#0/2\n+GGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGG\n+>HWI-ST745_0097:7:1101:1011:1000#0/1\n+CTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGT\n+>HWI-ST745_0097:7:1101:1011:1000#0/2\n+TTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGG\n+>HWI-ST745_0097:7:1101:1012:1000#0/1\n+TTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTC\n+>HWI-ST745_0097:7:1101:1012:1000#0/2\n+CTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATA\n+>HWI-ST745_0097:7:1101:1013:1000#0/1\n+TGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCG\n+>HWI-ST745_0097:7:1101:1013:1000#0/2\n+CAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGC\n+>HWI-ST745_0097:7:1101:1014:1000#0/1\n+GCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGT\n+>HWI-ST745_0097:7:1101:1014:1000#0/2\n+CCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGA\n+>HWI-ST745_0097:7:1101:1015:1000#0/1\n+CAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTC\n+>HWI-ST745_0097:7:1101:1015:1000#0/2\n+CTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTA\n+>HWI-ST745_0097:7:1101:1016:1000#0/1\n+AGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCG\n+>HWI-ST745_0097:7:1101:1016:1000#0/2\n+GTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCG\n+>HWI-ST745_0097:7:1101:1017:1000#0/1\n+GATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGG\n+>HWI-ST745_0097:7:1101:1017:1000#0/2\n+CATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGA\n+>HWI-ST745_0097:7:1101:1018:1000#0/1'..b'TCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAG\n+>HWI-ST745_0097:7:1101:1135:1000#0/1\n+GACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCA\n+>HWI-ST745_0097:7:1101:1135:1000#0/2\n+ACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCAT\n+>HWI-ST745_0097:7:1101:1136:1000#0/1\n+CCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATC\n+>HWI-ST745_0097:7:1101:1136:1000#0/2\n+TTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTAC\n+>HWI-ST745_0097:7:1101:1137:1000#0/1\n+GTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCG\n+>HWI-ST745_0097:7:1101:1137:1000#0/2\n+GTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGA\n+>HWI-ST745_0097:7:1101:1138:1000#0/1\n+TTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCA\n+>HWI-ST745_0097:7:1101:1138:1000#0/2\n+CTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCT\n+>HWI-ST745_0097:7:1101:1139:1000#0/1\n+GGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACT\n+>HWI-ST745_0097:7:1101:1139:1000#0/2\n+GCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCT\n+>HWI-ST745_0097:7:1101:1140:1000#0/1\n+TTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCC\n+>HWI-ST745_0097:7:1101:1140:1000#0/2\n+CGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGG\n+>HWI-ST745_0097:7:1101:1142:1000#0/1\n+CCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGA\n+>HWI-ST745_0097:7:1101:1142:1000#0/2\n+GAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTC\n+>HWI-ST745_0097:7:1101:1141:1000#0/1\n+CGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAA\n+>HWI-ST745_0097:7:1101:1141:1000#0/2\n+TGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTG\n+>HWI-ST745_0097:7:1101:1145:1000#0/1\n+AACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGT\n+>HWI-ST745_0097:7:1101:1145:1000#0/2\n+GATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAG\n+>HWI-ST745_0097:7:1101:1143:1000#0/1\n+ACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTT\n+>HWI-ST745_0097:7:1101:1143:1000#0/2\n+AGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGC\n+>HWI-ST745_0097:7:1101:1144:1000#0/1\n+CTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTG\n+>HWI-ST745_0097:7:1101:1144:1000#0/2\n+TGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCG\n+>HWI-ST745_0097:7:1101:1146:1000#0/1\n+CTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTG\n+>HWI-ST745_0097:7:1101:1146:1000#0/2\n+TGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAA\n+>HWI-ST745_0097:7:1101:1147:1000#0/1\n+TGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGC\n+>HWI-ST745_0097:7:1101:1147:1000#0/2\n+CTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCC\n+>HWI-ST745_0097:7:1101:1148:1000#0/1\n+CCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACC\n+>HWI-ST745_0097:7:1101:1148:1000#0/2\n+GATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAG\n+>HWI-ST745_0097:7:1101:1149:1000#0/1\n+CATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCA\n+>HWI-ST745_0097:7:1101:1149:1000#0/2\n+CTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATG\n+>HWI-ST745_0097:7:1101:1150:1000#0/1\n+ATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAG\n+>HWI-ST745_0097:7:1101:1150:1000#0/2\n+TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACC\n+>HWI-ST745_0097:7:1101:1151:1000#0/1\n+TGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC\n+>HWI-ST745_0097:7:1101:1151:1000#0/2\n+AACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCG\n' |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/align-100-0 |
| b |
| Binary file test-data/out/align-100-0 has changed |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/align-20 |
| b |
| Binary file test-data/out/align-20 has changed |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/align-40 |
| b |
| Binary file test-data/out/align-40 has changed |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/align-60 |
| b |
| Binary file test-data/out/align-60 has changed |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/align-80 |
| b |
| Binary file test-data/out/align-80 has changed |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/contig-100.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/contig-100.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-100_0 length_749 read_count_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/contig-20.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/contig-20.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-20_0 length_747 read_count_300 +AACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTT |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/contig-40.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/contig-40.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-40_0 length_749 read_count_302 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTTC |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/contig-60.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/contig-60.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-60_0 length_749 read_count_302 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/contig-80.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/contig-80.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-80_0 length_749 read_count_302 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/contig.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/contig.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-100_0 length_749 read_count_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/graph-100.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/graph-100.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/graph-20.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/graph-20.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +AACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTT |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/graph-40.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/graph-40.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTTC |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/graph-60.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/graph-60.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/graph-80.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/graph-80.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/kmer |
| b |
| Binary file test-data/out/kmer has changed |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/local-contig-20.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/local-contig-20.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>local_contig_20_0 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTN +>local_contig_20_1 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTN |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/local-contig-40.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/local-contig-40.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>local_contig_40_0 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACN +>local_contig_40_1 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCN |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/local-contig-60.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/local-contig-60.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>local_contig_60_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCN +>local_contig_60_1 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACN |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/local-contig-80.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/local-contig-80.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>local_contig_80_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCN +>local_contig_80_1 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACN |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/log Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,47 @@ +number of threads 4 +reads 302 +long reads 0 +extra reads 0 +read_length 76 +kmer 20 +kmers 728 727 +merge bubble 0 +contigs: 1 n50: 747 max: 747 mean: 747 total length: 747 n80: 747 +aligned 300 reads +confirmed bases: 690 correct reads: 230 bases: 0 +distance mean 214 sd 49.643 +seed contigs 1 local contigs 2 +kmer 40 +kmers 710 709 +merge bubble 0 +contigs: 1 n50: 749 max: 749 mean: 749 total length: 749 n80: 749 +aligned 302 reads +confirmed bases: 692 correct reads: 231 bases: 0 +distance mean 213.649 sd 49.4062 +seed contigs 1 local contigs 2 +kmer 60 +kmers 690 689 +merge bubble 0 +contigs: 1 n50: 749 max: 749 mean: 749 total length: 749 n80: 749 +aligned 302 reads +confirmed bases: 692 correct reads: 231 bases: 0 +distance mean 213.649 sd 49.4062 +seed contigs 1 local contigs 2 +kmer 80 +kmers 670 669 +merge bubble 0 +contigs: 1 n50: 749 max: 749 mean: 749 total length: 749 n80: 749 +aligned 302 reads +confirmed bases: 692 correct reads: 231 bases: 0 +distance mean 213.649 sd 49.4062 +seed contigs 1 local contigs 2 +kmer 100 +kmers 650 649 +merge bubble 0 +contigs: 1 n50: 749 max: 749 mean: 749 total length: 749 n80: 749 +reads 302 +aligned 302 reads +distance mean 213.649 sd 49.4062 +expected coverage 0.448071 +edgs 0 +contigs: 1 n50: 749 max: 749 mean: 749 total length: 749 n80: 749 |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/out/scaffold.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/scaffold.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>scaffold_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a81c5169e9fc test-data/reference.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fa Mon Aug 05 15:59:15 2019 -0400 |
| b |
| b'@@ -0,0 +1,303 @@\n+>reference\n+GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTT\n+GCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTC\n+AAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTA\n+TTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAA\n+AAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAG\n+ATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAG\n+AAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGT\n+CAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGC\n+AACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTG\n+CCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCC\n+ACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGG\n+CCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTC\n+CGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGT\n+AAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGC\n+GCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTG\n+TGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGT\n+CGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGA\n+GCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTC\n+GCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAG\n+GGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGG\n+CTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGT\n+TTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGG\n+TTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTC\n+CTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATA\n+TGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCG\n+CAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGC\n+GCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGT\n+CCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGA\n+CAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTC\n+CTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTA\n+AGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCG\n+GTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCG\n+GATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGG\n+CATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGA\n+ATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGT\n+AGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGC\n+TGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTA\n+CAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGA\n+GGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTAT\n+AGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGA\n+GGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATA\n+TGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCC\n+GTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATAT\n+GTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCG\n+TCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATC\n+CAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTC\n+CGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCT\n+CATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGAT\n+GCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTG\n+AGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCAT\n+CAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGT'..b'AGTCCCAACATCCGGGCGAA\n+CGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCG\n+AGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAA\n+ACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGC\n+CTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACT\n+CGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGC\n+TCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTG\n+TCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACG\n+CTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGG\n+CCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCC\n+TCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGC\n+GTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGA\n+CTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCG\n+AACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAG\n+GGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGC\n+CGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCG\n+GGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGC\n+AACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAG\n+GACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCA\n+ACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCAT\n+CCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATC\n+TTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTAC\n+GTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCG\n+GTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGA\n+TTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCA\n+CTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCT\n+GGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACT\n+GCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCT\n+TTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCC\n+CGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGG\n+CCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGA\n+GAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTC\n+CGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAA\n+TGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTG\n+AACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGT\n+GATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAG\n+ACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTT\n+AGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGC\n+CTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTG\n+TGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCG\n+CTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTG\n+TGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAA\n+TGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGC\n+CTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCC\n+CCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACC\n+GATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAG\n+CATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCA\n+CTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATG\n+ATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAG\n+TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACC\n+TGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC\n+AACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCG\n' |
| b |
| diff -r 000000000000 -r a81c5169e9fc tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# |
| b |
| diff -r 000000000000 -r a81c5169e9fc tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r a81c5169e9fc tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Aug 05 15:59:15 2019 -0400 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables> |