| Next changeset 1:2ed5c0795f99 (2019-08-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb |
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added:
idba_ud.xml macros.xml 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 |
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| diff -r 000000000000 -r fdaf2375d405 idba_ud.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idba_ud.xml Fri Sep 21 15:25:56 2018 -0400 |
| [ |
| @@ -0,0 +1,107 @@ +<tool id="idba_ud" name="IDBA-UD" version="1.1.3"> + <description> + Iterative de Bruijn Graph Assembler <!--for sequencing data with highly uneven depth--> + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command><![CDATA[ + + idba_ud + + --read '$read' + #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 + #if $long_read: + --long_read '$long_read' + #end if + --mink $mink + --maxk $maxk + --step $step + --inner_mink $inner_mink + --inner_step $inner_step + --prefix $prefix + --min_count $min_count + --min_support $min_support + --num_threads \${GALAXY_SLOTS:-1} + --seed_kmer $seed_kmer + --min_contig $min_contig + --similar $similar + --max_mismatch $max_mismatch + --min_pairs $min_pairs + #if $other: + ${" ".join(str($other).split(","))} + #end if + ]]></command> + + <inputs> + <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"/> + + <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"/> + + <param argument="--mink" type="integer" value="20" max="312" label="Minimum k value. Lower or equal to 312"/> + <param argument="--maxk" type="integer" value="100" max="312" label="Maximum k value. Lower or equal to 312"/> + <param argument="--step" type="integer" value="20" 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"/> + <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"/> + <param argument="--min_pairs" type="integer" value="3" label="Minimum number of pairs"/> + + <param name="other" type="select" display="checkboxes" multiple="true" label="Other options"> + <option value="--no_bubble">Do not merge bubble (--no_bubble)</option> + <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> + </inputs> + <outputs> + <data name="output" from_work_dir="out/scaffold.fa" format="fasta"/> + </outputs> + <tests> + <test> + <param name="read" value="merged.fa" ftype="fasta"/> + <output name="output" file="out/scaffold.fa" ftype="fasta"/> + </test> + </tests> + <help><![CDATA[ + IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions. + + +Input: IDBA-UD takes interleaved paired end data in the FASTA format as input, +i.e. paired-end reads need to be stored in the same FASTA file suc h 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-UD assumes that the paired-end reads are in order (->,<-). +If your data is in reverse order (<-,->), please convert it by yourself. + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/bts174</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r fdaf2375d405 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Sep 21 15:25:56 2018 -0400 |
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| @@ -0,0 +1,8 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.1.3">idba</requirement> + <yield/> + </requirements> + </xml> +</macros> |
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| diff -r 000000000000 -r fdaf2375d405 test-data/assembly_sample-R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assembly_sample-R1.fastq Fri Sep 21 15:25:56 2018 -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#0/1\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 fdaf2375d405 test-data/assembly_sample-R2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assembly_sample-R2.fastq Fri Sep 21 15:25:56 2018 -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 fdaf2375d405 test-data/merged.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged.fa Fri Sep 21 15:25:56 2018 -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 fdaf2375d405 test-data/out/align-100-0 |
| b |
| Binary file test-data/out/align-100-0 has changed |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/align-20 |
| b |
| Binary file test-data/out/align-20 has changed |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/align-40 |
| b |
| Binary file test-data/out/align-40 has changed |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/align-60 |
| b |
| Binary file test-data/out/align-60 has changed |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/align-80 |
| b |
| Binary file test-data/out/align-80 has changed |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/contig-100.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/contig-100.fa Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-100_0 length_749 read_count_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/contig-20.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/contig-20.fa Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-20_0 length_747 read_count_300 +AACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTT |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/contig-40.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/contig-40.fa Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-40_0 length_749 read_count_302 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTTC |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/contig-60.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/contig-60.fa Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-60_0 length_749 read_count_302 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/contig-80.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/contig-80.fa Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-80_0 length_749 read_count_302 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/contig.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/contig.fa Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>contig-100_0 length_749 read_count_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/graph-100.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/graph-100.fa Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/graph-20.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/graph-20.fa Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +AACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTT |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/graph-40.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/graph-40.fa Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTTC |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/graph-60.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/graph-60.fa Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/graph-80.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/graph-80.fa Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/kmer |
| b |
| Binary file test-data/out/kmer has changed |
| b |
| diff -r 000000000000 -r fdaf2375d405 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 Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>local_contig_20_0 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTN +>local_contig_20_1 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTN |
| b |
| diff -r 000000000000 -r fdaf2375d405 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 Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>local_contig_40_0 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACN +>local_contig_40_1 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCN |
| b |
| diff -r 000000000000 -r fdaf2375d405 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 Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>local_contig_60_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCN +>local_contig_60_1 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACN |
| b |
| diff -r 000000000000 -r fdaf2375d405 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 Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>local_contig_80_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCN +>local_contig_80_1 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACN |
| b |
| diff -r 000000000000 -r fdaf2375d405 test-data/out/log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/log Fri Sep 21 15:25:56 2018 -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 fdaf2375d405 test-data/out/scaffold.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/scaffold.fa Fri Sep 21 15:25:56 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>scaffold_0 +GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA |