| Next changeset 1:33f00ff1cb22 (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_tran.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 a30d991a3fdd idba_tran.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idba_tran.xml Mon Aug 05 15:58:44 2019 -0400 |
| [ |
| @@ -0,0 +1,64 @@ +<tool id="idba_tran" name="IDBA-TRAN" version="@IDBA_VERSION@"> + <description> + Iterative de Bruijn Graph Assembler for transcriptome data + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ + idba_tran + + @MAIN_INPUT@ + @KMER_OPTIONS@ + @FILTER_OPTIONS@ + --min_transcript $min_transcript + --max_isoforms $max_isoforms + --max_component_size $max_component_size + @OTHER_OPTIONS@ + @THREADS@ + ]]></command> + <inputs> + <expand macro="main_input"/> + <expand macro="kmer_options" maxk_default="60" step_default="10"/> + <expand macro="filter_options"/> + <param argument="--min_transcript" type="integer" value="300" label="Minimum size of transcript"/> + <param argument="--max_isoforms" type="integer" value="3" label="Maximum number of isoforms"/> + <param argument="--max_component_size" type="integer" value="30" label="Maximum size of component"/> + <expand macro="other_options"/> + </inputs> + <outputs> + <data name="output" from_work_dir="out/scaffold.fa" format="fasta"/> + </outputs> + <tests> + <!-- basic test + tool specific defaults --> + <test> + <param name="read" value="merged.fa" ftype="fasta"/> + <assert_command> + <has_text text="--maxk 60" /> + <has_text text="--step 10" /> + <has_text text="--min_transcript 300" /> + <has_text text="--max_isoforms 3" /> + <has_text text="--max_component_size 30" /> + </assert_command> + <output name="output" file="out/scaffold.fa" ftype="fasta" compare="sim_size"/> + </test> + <!-- tool specific parameters --> + <test> + <param name="read" value="merged.fa" ftype="fasta"/> + <param name="min_transcript" value="299"/> + <param name="max_isoforms" value="2"/> + <param name="max_component_size" value="29"/> + <assert_command> + <has_text text="--min_transcript 299" /> + <has_text text="--max_isoforms 2" /> + <has_text text="--max_component_size 29" /> + </assert_command> + <output name="output" file="out/scaffold.fa" ftype="fasta" compare="sim_size"/> + </test> + </tests> + <expand macro="help" more_help="IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler for transcriptome. It is purely de novo assembler based on only RNA sequencing reads. IDBA-Tran uses local assembly to reconstructing missing k-mers in low-expressed transcripts and then employs progressive cutoff on contigs to seperate the graph into components. Each component corresponds to one gene in most cases and contains not many transcripts. A heuristic algorithm based on pair-end reads is then used to find the isoforms."/> + <expand macro="citations"> + <citation type="doi">10.1093/bioinformatics/btt219</citation> + </expand> +</tool> |
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| diff -r 000000000000 -r a30d991a3fdd macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Aug 05 15:58:44 2019 -0400 |
| [ |
| @@ -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 a30d991a3fdd test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Mon Aug 05 15:58:44 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 a30d991a3fdd 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 15:58:44 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 a30d991a3fdd 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 15:58:44 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 a30d991a3fdd test-data/merged.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged.fa Mon Aug 05 15:58:44 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 a30d991a3fdd test-data/out/align-100-0 |
| b |
| Binary file test-data/out/align-100-0 has changed |
| b |
| diff -r 000000000000 -r a30d991a3fdd test-data/out/align-20 |
| b |
| Binary file test-data/out/align-20 has changed |
| b |
| diff -r 000000000000 -r a30d991a3fdd test-data/out/align-40 |
| b |
| Binary file test-data/out/align-40 has changed |
| b |
| diff -r 000000000000 -r a30d991a3fdd test-data/out/align-60 |
| b |
| Binary file test-data/out/align-60 has changed |
| b |
| diff -r 000000000000 -r a30d991a3fdd test-data/out/align-80 |
| b |
| Binary file test-data/out/align-80 has changed |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-100_0 length_749 read_count_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-20_0 length_747 read_count_300 +AACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTT |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-40_0 length_749 read_count_302 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTTC |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-60_0 length_749 read_count_302 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-80_0 length_749 read_count_302 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a30d991a3fdd test-data/out/contig.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/contig.fa Mon Aug 05 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-100_0 length_749 read_count_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +AACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTT |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTTC |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a30d991a3fdd test-data/out/kmer |
| b |
| Binary file test-data/out/kmer has changed |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>local_contig_20_0 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTN +>local_contig_20_1 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTN |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>local_contig_40_0 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACN +>local_contig_40_1 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCN |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>local_contig_60_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCN +>local_contig_60_1 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACN |
| b |
| diff -r 000000000000 -r a30d991a3fdd 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 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>local_contig_80_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCN +>local_contig_80_1 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACN |
| b |
| diff -r 000000000000 -r a30d991a3fdd test-data/out/log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/log Mon Aug 05 15:58:44 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 a30d991a3fdd test-data/out/scaffold.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/scaffold.fa Mon Aug 05 15:58:44 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>scaffold_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r a30d991a3fdd test-data/reference.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fa Mon Aug 05 15:58:44 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 a30d991a3fdd 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 15:58:44 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 a30d991a3fdd 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 15:58:44 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 a30d991a3fdd 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 15:58:44 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> |