| Next changeset 1:551f8c9bc4cf (2020-05-28) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3" |
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added:
all_fasta.loc.sample macros.xml medaka_consensus.xml test-data/alignment.bam test-data/all_fasta.loc test-data/assembly.fasta test-data/basecalls.fastq test-data/bwa-mem-mt-genome.fa test-data/consensus.hdf tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r ef94bace3a3c all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Sat May 23 13:38:26 2020 -0400 |
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| @@ -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. +# |
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| diff -r 000000000000 -r ef94bace3a3c macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat May 23 13:38:26 2020 -0400 |
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| @@ -0,0 +1,104 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">1.0.1</token> + <token name="@PROFILE@">18.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">medaka</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command>medaka --version</version_command> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex">@online{medaka, + author = {Oxford Nanopore Technologies Ltd.}, + title = {medaka}, + year = 2020, + url = {https://github.com/nanoporetech/medaka}, + urldate = {2020-05-06} + }</citation> + </citations> + </xml> + + <!-- + command + --> + + <token name="@REF_FASTA@"><![CDATA[ + #if $reference_source.reference_source_selector == 'history': + ln -f -s '$reference_source.ref_file' 'reference.fa' && + #else: + ln -f -s '$reference_source.ref_file.fields.path' 'reference.fa' && + #end if + ]]></token> + + <!-- + input + --> + + <xml name="b" token_argument="-b"> + <param argument="@ARGUMENT@" type="integer" value="100" min="1" label="Set inference batch size"/> + </xml> + <xml name="model" token_argument="-m" token_label="Select model"> + <param argument="@ARGUMENT@" type="select" label="@LABEL@"> + <option value="r10_min_high_g303">r10_min_high_g303</option> + <option value="r10_min_high_g340">r10_min_high_g340</option> + <option value="r103_min_high_g345">r103_min_high_g345</option> + <option value="r103_min_high_g360">r103_min_high_g360</option> + <option value="r103_prom_high_g360">r103_prom_high_g360</option> + <option value="r103_prom_snp_g3210">r103_prom_snp_g3210</option> + <option value="r103_prom_variant_g3210">r103_prom_variant_g3210</option> + <option value="r941_min_fast_g303">r941_min_fast_g303</option> + <option value="r941_min_high_g303">r941_min_high_g303</option> + <option value="r941_min_high_g330">r941_min_high_g330</option> + <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option> + <option value="r941_min_high_g344">r941_min_high_g344</option> + <option value="r941_min_high_g351" selected="true">r941_min_high_g351</option> + <option value="r941_min_high_g360">r941_min_high_g360</option> + <option value="r941_prom_fast_g303">r941_prom_fast_g303</option> + <option value="r941_prom_high_g303">r941_prom_high_g303</option> + <option value="r941_prom_high_g330">r941_prom_high_g330</option> + <option value="r941_prom_high_g344">r941_prom_high_g344</option> + <option value="r941_prom_high_g360">r941_prom_high_g360</option> + <option value="r941_prom_snp_g303">r941_prom_snp_g303</option> + <option value="r941_prom_snp_g322">r941_prom_snp_g322</option> + <option value="r941_prom_variant_g303">r941_prom_variant_g303</option> + <option value="r941_prom_variant_g322">r941_prom_variant_g322</option> + </param> + </xml> + <xml name="reference"> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> + <option value="cached">Use a built-in genome</option> + <option value="history">Use a genome from history</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No reference genomes are available" /> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" /> + </when> + </conditional> + </xml> + + <!-- + Help + --> + + <token name="@WID@"><![CDATA[ +medaka is a tool suite to create a consensus sequence from nanopore sequencing data. + +This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster. + ]]></token> + <token name="@REFERENCES@"><![CDATA[ +More information are available in the `manual <https://nanoporetech.github.io/medaka/index.html>`_ and `github <https://github.com/nanoporetech/medaka>`_. + ]]></token> +</macros> |
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| diff -r 000000000000 -r ef94bace3a3c medaka_consensus.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/medaka_consensus.xml Sat May 23 13:38:26 2020 -0400 |
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| @@ -0,0 +1,168 @@ +<tool id="medaka_consensus_pipeline" name="medaka: Consensus pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>Assembly polishing via neural networks</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"><![CDATA[ + medaka_consensus + ## optional + -m '${m}' + -b $b + -o 'results' + #if 'draft' in str($out).split(',') or 'variants' in str($out).split(',') or 'polished' in str($out).split(',') + -v + #end if + -t \${GALAXY_SLOTS:-4} + ## required + -i '$i' + -d '$d' + + |& tee 'log.txt' + #if 'variants' in str($out).split(',') + && bgzip -d 'results/variants.vcf.gz' + #end if + ]]></command> + <inputs> + <param argument="-i" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select basecalls"/> + <param argument="-d" type="data" format="fasta,fasta.gz" label="Select assembly" help="The input assembly should be preprocessed with racon."/> + <expand macro="model"/> + <expand macro="b"/> + <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="'Draft To Consensus', 'Variants' and 'Polished regions in draft coordinates' are generated using the parameter -v."> + <option value="consensus" selected="true">Consensus</option> + <option value="probs" selected="true">Consensus probabilities</option> + <option value="calls" selected="true">Calls to draft</option> + <option value="draft">Draft to consensus</option> + <option value="variants">Variants</option> + <option value="polished">Polished regions in draft coordinates</option> + <option value="log">Log</option> + </param> + </inputs> + <outputs> + <!-- standard --> + <data name="out_consensus" format="fasta" from_work_dir="results/consensus.fasta" label="${tool.name} on ${on_string}: Consensus"> + <filter>'consensus' in out</filter> + </data> + <data name="out_probs" format="h5" from_work_dir="results/consensus_probs.hdf" label="${tool.name} on ${on_string}: Consensus probabilities"> + <filter>'probs' in out</filter> + </data> + <data name="out_calls" format="bam" from_work_dir="results/calls_to_draft.bam" label="${tool.name} on ${on_string}: Calls to draft"> + <filter>'calls' in out</filter> + </data> + <!-- optional with parameter -v --> + <data name="out_draft" format="txt" from_work_dir="results/draft_to_consensus.chain" label="${tool.name} on ${on_string}: Draft to consensus"> + <filter>'draft' in out</filter> + </data> + <data name="out_variants" format="vcf" from_work_dir="results/variants.vcf" label="${tool.name} on ${on_string}: Variants"> + <filter>'variants' in out</filter> + </data> + <data name="out_polished" format="bed" from_work_dir="results/polished_regions_in_draft_coords.bed" label="${tool.name} on ${on_string}: Polished regions in Draft"> + <filter>'polished' in out</filter> + </data> + <!-- optional --> + <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt"> + <filter>'log' in out</filter> + </data> + </outputs> + <tests> + <!-- #1 default --> + <test expect_num_outputs="3"> + <param name="i" value="basecalls.fastq"/> + <param name="d" value="assembly.fasta"/> + <output name="out_consensus"> + <assert_contents> + <has_n_lines n="2"/> + <has_line line=">4_segment0 4:1.0-3792.0"/> + <has_text_matching expression=".+GTCAGAATCGCGTTCAGCGCGTTTCAGCGGTGCGTACAATT.+"/> + </assert_contents> + </output> + <output name="out_probs"> + <assert_contents> + <has_size value="194782" delta="100"/> + </assert_contents> + </output> + <output name="out_calls"> + <assert_contents> + <has_size value="533139" delta="100"/> + </assert_contents> + </output> + </test> + <!-- #2 --> + <test expect_num_outputs="7"> + <param name="i" value="basecalls.fastq"/> + <param name="d" value="assembly.fasta"/> + <param name="m" value="r941_min_fast_g303"/> + <param name="b" value="99"/> + <param name="out" value="consensus,probs,calls,draft,variants,polished,log"/> + <output name="out_consensus"> + <assert_contents> + <has_n_lines n="65"/> + <has_line line=">4 length=3792 depth=114.52x circular=true"/> + <has_line line="CATCTCTTT"/> + </assert_contents> + </output> + <output name="out_probs"> + <assert_contents> + <has_size value="192710" delta="100"/> + </assert_contents> + </output> + <output name="out_calls"> + <assert_contents> + <has_size value="533163" delta="100"/> + </assert_contents> + </output> + <output name="out_draft"> + <assert_contents> + <has_n_lines n="6"/> + <has_line line="chain 3789 4 3792 + 0 3792 4 3789 + 0 3789 1"/> + <has_line line="1204"/> + </assert_contents> + </output> + <output name="out_polished"> + <assert_contents> + <has_size value="9"/> + </assert_contents> + </output> + <output name="out_variants"> + <assert_contents> + <has_n_lines n="9"/> + <has_line line="##fileformat=VCFv4.1"/> + <has_text_matching expression="4	.+"/> + </assert_contents> + </output> + <output name="out_log"> + <assert_contents> + <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +@WID@ + +The *medaka_consensus* pipeline performs assembly polishing via neural networks. + +**Input** + +An *assembly* in .fasta format and *basecalls* in .fasta or .fastq format are required. See `Creating a Draft Assembly <https://nanoporetech.github.io/medaka/walkthrough.html#basecalling-and-draft-assembly>`_ for a detailed example of one method of obtaining these. + +**Output** + +- Consensus polished assembly (FASTA) +- Consensus Probabilities (H5/HDF) +- Calls To Draft (BAM) +- Draft To Consensus (chain, TXT) +- Variants: VCF of changes (VCF) +- Polished: BED file of polished regions (BED) + +**References** + +@REFERENCES@ + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r ef94bace3a3c test-data/alignment.bam |
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| Binary file test-data/alignment.bam has changed |
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| diff -r 000000000000 -r ef94bace3a3c test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Sat May 23 13:38:26 2020 -0400 |
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| @@ -0,0 +1,1 @@ +bwa-mem-mt-genome bwa-mem-mt-genome bwa-mem-mt-genome ${__HERE__}/bwa-mem-mt-genome.fa \ No newline at end of file |
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| diff -r 000000000000 -r ef94bace3a3c test-data/assembly.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assembly.fasta Sat May 23 13:38:26 2020 -0400 |
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| @@ -0,0 +1,56 @@ +>4 length=3792 depth=114.52x circular=true +TTGCGGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTCAGCGGTGCGTACAATTACAGCATTATGTTAAA +TTTTATAATTGTCTTTAGTCATTGCGCTATGATTTTGTAGGTGGAGTTGTTTCATATTTTTGATATAAAT +TCTTTTATCTCACTGAAGCAGTCATCGTCAGTATCAATGGTTTTGTTCTTCATTGATATGCCTATTCTAG +AATCTGATTCCTTATTACAACTAAGGTAAACTTGAACTTTTGCTTTCTTTTCATTATTTGGGTAAGCGTA +ATCAGGATCTAAGGATGTAATAATAGATTCTTGTTCTTTTATTTTATTGAATAGATCGTCTATATATCTA +AACACCTCTTTCTTACACGCGTGAGCAATGATTAGATCTTCTATTGCGCCATTCTTGTTTTTTCCTGGCA +TGATAAAGAAAGATATTTTTGTGCTTCCGTTAATGGCTATTTCATTATGCGAGCTTGGTGATGAAATGTT +AAGCTCATTTAATGTTGAAATTATCGATCTTTCCGTGTCAGAAAACGATTCGTCGGCATCGATGATTAAG +AATATACTTTCTTTTTCATTAAAAGACTCTATGCTTTTAAATGCTCTAAGGGTTTGTTTTAGTTTTGTCT +TTCCATTTATTTTTTCAACATAAACATCATTAATTCCTTCTATTTCAAGTAGATTGCAAAGGAAGTGAAA +ATCATCATCACCCTCAACGAAAATGACTTTTTTATAATCATTTATTTTTCTCGGTTTCATTTATCTCACC +TCCCAGCCATTTTCAACTGAAAAAGAAAAATCATCCATGTTAAATTGCATTGCTGTAGGTTTTTGAGATT +CCTTGTCTCTTCCCAGTCTTATGTAAGATATATCTTTTCTTTTTTCATCTAATTCGTTTATCGCACATAT +TACATCATGGCTGTGTGTTGTTGTAAATATTTGATTATTATTGGTTTTTGCTGCTTCTATCAAAGCGTTG +ATCATATCTTTGATTACTGAGTAATGAATTCCATTTTCTATCTCATCAATGAGAATAATTGAGTCTTTTT +GAACTAAGATTGAGCTAATGAAAGACAGCGCTCTGCTTACTCCTTCACCAAGCATTGATATTTCATTTAA +TTCACTTAGTCCTATATCTAAAAAAATCTCTTTGTTTTGATCTGTTGCTATTATTGCAATATCGTTAATT +CTATTATCTATTCTTTTTAGGTTGCCTATTATTTCATCTTTTCTTTTTTGTGTTAGTAGTTTTGATACGT +TTTTTATCGTTGCTTCTTTGTTTATGTTTCTTGATGTGGTTATTATCGCTGCGGTTTTGAATTCATATAG +CTTACCTTTTTTAGTTTGTTTTATTTCTCCGTTTATTTCTTGTGCTTTTTGTGTTATTTTTATAGTAATC +AATTCTTCTGGGGGGGTTCTTTTTCCGTTCTGTGTTTCACTAACCTTAATCATTAAAACATTCCCCTTTT +CCTGAGAGCCGAGGGTTTGTCGCAATGGAGGGGTGTTTGATAATATTGACTCAACATTGAGGGACACGCT +TGATTCACTTTGTGTGTTATCTATCGTTGAGTATTTTTGTGTTACTTCTGACCTTTCATCTCTTATTGTT +ATGGACATTTCTTTGGATGTGTCCATGTTATAAAAATAGCTATCCCAAAATGAGTTTTCTTTATTTAAAA +GAGATGCTTCATTTCTAAAGCTTTTTACTTTTAACAGAGCTGCTGGGTTTTTTACGTCATAAAATGAAAA +TATCGCGTCTAATATCGATGTTTTCCCAAAGTTGTTTTTTCCGGATATTACATTAAGTGTTTTTAGTTGT +TTGAGAGTTATGCTCTCGAAACACTTAAAATTTTTTAAGTGGATATCTTTTATCATGTTTAAACTTGCTC +TCCATTTCTGTTTACGTTTACATAGTAATAATGTGTTTATTTATGCATCACTATGCCACTGTTTCTTTTC +TAGAAGTATAATCAAAATAATATTACTTTATAGTCCTGTTTGGATTGATTTTAACCAGTTTGTCGGAGTT +TCTTCTTGTGATTATTGTGTTCTGGTCGTAATCTCCTAAACTGAAAACGAAAAAACCACCTGGGGAGGTG +GTTTGATCGAAGGTTAAGTCAGTTGGGGAACTGCTTAACCAGGTAACTGTCTTGTGCGAGACGAGTCACC +AAAACTGTCCTTTCAGTGTAGCTGTAGTCAGGCCATCACTTCAAGTACTCTCTTGAACCTCTCGCACATC +GACTTTTACCAATGGCTGCTGCCAGTGGCGCTTTGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTT +ACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACC +TACACCGAACCGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGG +ACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACACCTG +GTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGGCTTGAGCGTCGATTTTTGTGATGCTCGTCAGGG +GGGCGGAGCCTATGGAAAAACGCCTGCGGCGCTGGCTTCCTCCGGTGCTTTGCTTTTTGCTCACATGTTC +TTTCCGACTTTATCCCCCGATTCTGTGGATAACCGTATTACCGCTTTTGAGTGAGCTGACACCGCTCGCC +GCAGTCGAACGACCGAGCGTAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCTTATGTGACATTTTCT +CCTTACGCTCTGTTGTGCCGTTCGGCATCCTGTCCTGAGCGTTATCTCTCTGTGCTATTTTCTACTTCAA +AGCGTGTCTGGATGCTGTTCTGGAGTTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGCAGCCTGTTC +GTCAGCATCGGGTGCGTCCAGTTTTTCGAGCAGCGTCAGGCTCTGACTTTTTATGAATCCCGCCATGTTG +AGTACGGCTTGCTGCTGCTTGTTCATCTTTTCGTTTTCTCCGTTCTGTCTGTCATCTGCGTTGTGTGATT +ATATCGCGTACCACTTTTCGACTGTTTTGCTGCCGTTATTCTGCCGCTTGGCTTTTTGACGGGCATTTCT +GTCAGACAACACTGTCACTGCCAAAAAACTGCCGTGCCTTTGTCGGTAATTCGAGCTTGCTGACAGGACA +GGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTGCCCTGGTCAGGGCTTTGCCCCGA +CACCCATGTCAGATACGGAGCCATGTTTTATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTAT +CAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAG +ACCGTTTCCGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGATCGGGTAC +TGAAAGAAGTTATGAGACTGGGGGCGTTACAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAG +GGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGACTTATGGCAGAT +TAGCTTCCCGGAGAGAAAACTGTCGAAAACAGACGGTATGAACACCGTAAGCTCCCAAAGTGATCACCAT +TCGCTTTCATGCATAGCTATGCAGCGAGCTGAAAACGATCCTGACGCATCCTTCCTGTTTTCCCGGGGTA +AAACATCTCTTT \ No newline at end of file |
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| diff -r 000000000000 -r ef94bace3a3c test-data/basecalls.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/basecalls.fastq Sat May 23 13:38:26 2020 -0400 |
| b |
| b"@@ -0,0 +1,1016 @@\n+@215f1e0c-27d1-4446-bca5-cb0fd6a8c054\n+TTGCAGTATCTGCGTCAGAATCGCATTCCAGCCGCAGGTGTTCAGCGGTGCGTACAATTACAGCATTATGTTAAATTTTATAATTGTCTTTAGTCATTGCGCTATGATTTGTAGGTGGAGTTGTTTCATATTTTGATATAAATTCTTTTATCTCACCAAACAGTCATCGTCAGTATCAATGGTTTTGTTCTTCATTGATATTACCTATTCTAGAATCTGATTCCTTGTACAACTAAGGTAAACTTGAACTTTGCTTTCTTTTCATTATTTGGGTAAGCGTAATGATGTAGGATCTAGGATATATCTATAATAATAATTCTTGTTCTTTTTTTATTTTATTGAATATGAATCAATACCTGTCTAAGCACACCTCTTTCTTACGCGTGAGCAATGGTTAGATGGATCTTCTGGCGGCCTTGCGCCATTCCTGTTTGTTC\n++\n+?B4-)&'%<ABC>:883110,;*-$/+%)(.(($$#%&$$#%14+6-/=1@5@A>GE@F@<B8B..0F>?AA13EJHTIDHBDAJB@BOM908=B;=>49/(?>>?>?@?(004?C57/9<B>DEEE@@@C?=>=<912+,*'1/1396;78+&$&,15(85::C@>BA>9(,</(B:;G?B;@K=<HF?JF5**+&&0/#%$;>BCB=(4<.=91<4@ADC9:AC$=9>555=3412;6;+=>?@>2$%+839@BH=CAOHFCI<.98<-0/*$%)0**()(')&$)$474)+/,'267432&&'&''''$%&'*')>?C3=;467===95489G:./5229,$$&$(&&$%%(''')+8%/0%.-%0$')&'*=566(-(685''57./4%)44+/*$$$'42:;6($$##$$$'-0(%67112$$'$())'7;:\n+@baf1c4f7-8f02-4c92-be5f-0431ca399c18\n+GGTATTACTTCGTTCAGTTACGTATTGCTGCGCGCACTCTCTGTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACAGGGGAGTTCGTGCACACAGCCCGAAGCTTGGAGCGAACGACCTACGCGAACCGAGATACCTACAGCGTGAGCTATGAAAGCGCCACGCTTCCCGAAGGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCGGGGGAAACACACCTGGTATCTTTTTATAGTCCTGTCCGGGTTTCGCCACCTCTGGCAGGCGTCGATTTTTGTGATGCTCGTCAGAGCGGAATTTATGGAAACGCCTGCGGCGCTGGCTTCCTCCGATGCTGCTTTTTGCTCACATATTCTTTCCGACTTTATCCCCCGATTCTGTGGATAACCGTATTACCGCTGCAGGTGAGCTGACACGCTCGCCGCAGTCGAACGACCGAGAGCGTAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCTATGTGACATTTTCTCCTTACGCTCTGTTGTGCCGTTCGGCATCCTGTCTGAGCGTTATCTCTCTGTGCTATTTTTACTTCAAAGCGTGTCTGGATGCTGTTCTGGAGTTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGCAGCCTGTTCGTCAGCATCGGGTGCGTCCAGTTTTCGAGCAGCATTCAGGCTCTGACTTTTATGAATCCCGCCATGTTGGTACGGCTTTTCTTTCTTGTTCATCTTTTCGTTTTCTCCGTTCTGTCTGTCATCTGCGTTGTGTATGATTATATCGCGTACCACTTTTCGGCTGTTTGCTGCCGTTATTCTGCGCCGCTTGGCTTTTTGACGGGCATTTCTGTCAGACAACACTGTCACTGCCAAAAAACTGCCGTGCCTTTGTCGGTAATTCGAGCTTGCTGACAGGACAGGATGTACAATTGTTATACCGCGCATACATGCACGCTATTACAATTGCCCTGGTCAGGAGCTTTGCCCCGACACCCATGTCCAGATACGGAGCCATGTTTTGCTGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCCCCTGTTCGTCTGACGGCAGAGAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCGGTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACCCACTGACTGATGATCGGGTACTGAAAGAAGTTATGAGACTGGGAGCGTTACAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGGAGTATGCGTTTGATCGCTATTACGGGTATCACGTGCCCTGTTATCAGACTTATGGCAGATTGGCTTCCCGGAGAGAAAACTGTCGAAAACAGACGGTATGAACACCGTAAGCTCCCAAAGTGATCACCATTCGCTTTCATGCATAGCTATGCAGCGAGCTGAAAACGATCCTGACGCATCCTTCCTGTTTTCCCGGGGTAAACATCTTTTTTGCAGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTCAGCAGTGCGTACAATTACAGCATTATGTTAAATTTTATAGTGTCTTTAGTCATTTGCGCTATGATTTTGTAGGTGGAGTTGCTTCATATTTTTGATATAAAGTTCTTTTCCCATCTGCTAGAGCAGTCATCGTCAGTATCAATGGTTTGTTCTTCATTGATATGCCTATTCTAGAATCTGGTCCTTATTACAACTAAGGTAAACTTGAACTTTTGCTTTCTTTTCATTATTTGGGTAAGCGTAATCAGGATCTAAGGATGTAATAATAGATTCTTGTTCTTTTTTATTTTATTGAATAGATCGTCTATATATCTAAACACCTCTTTCTTACACGCGTGAGCAATAGTTGGAGTCTTCTATTGCGCCATTCTTGTTTTTCCTGGCATGATAAAGAAGATATTTTTGTGCTTCCCGTTAATGGCTATTTCATTGTGCGAGCTTGGTGATAAATGTTAAGCTCATTTAATGTTGAAATTATCTGATCTTTCCGTGTCAGAAAAACGATTCCGTCGGCATCGATGATTAAGAATATACTTTCTTTTCCATTAAAGACTCTATGCTTTTAAATGCTCTAAGGGTTTGTTTTAGTTTGTCTTTCCATTTTATTTTTTCAACATAAACATCATTAATTCCTTCTATTTCAAGTAGATTTAGGAAGTGAAAATCATCATCACCCTCAACAAAAAATGACTTTTTTATAATCATTTATTTTCTCGGTTTCATTTATCTCACCTCCCAGCCATTTTCAACTGAAAAGGAAAATCATCCATGTTAAATTGCATTGCTGTAGGTTTTGGGAATTGCTTGTCTCTTCCCAGTCTTATGTAAGATATATCTTTCTTTTTCATCTAATTCGTTTATCGCACATATTACATCATGGCTGTGTGTTGTTGTAAATATTTGATTATTATTGGTTTTGCTGCTTCTATCAAAGCGTTGATCATATCTTTGATTACTGAGTAATGAATTCCATTTTCTATCTCATCAATGAGAATAATTGAGTCTTTTTGAACTAAGATTGAGCTAATGAAAGACAGCGCTCTGCTTACTCCTTCACCAAGCATTGATATTTCATTTAATTCACTTAGTCCTATATCTAAAAAAATCTCTTTGTTTTGATCTGTTGCTATTATTGCAATATCGTTAATTCTATTATCTATTCTTTTAGGTTGCCTATTATTTCATCTTTCTTTTGTGTTAGTAGTTTGACCGTTTTTATCGTTGCTTCTTTGTTTATGCTTCTTGATGTGGTTATTACCGCGCTGCGGTTTTGAACTCATATAGCTTACACACTTTTTAGTTTGTTTTATTTCTCCGTTTATTTCTTGTGCTTTTTGTGTTATTTTTATAGTAATCAATTCTTCTGGGGGTTCTTTTCCGTTCTGTGTTTCACTAACCTTAATCGTTAAAACATTCCCCTTTTCCTGAGAAT"..b"TCCTGTTTTCGGGGTAAAACATCTCTTT\n++\n+(?A@=CE-3()(49))6,69>H>::/(79,%3(0:&&%*3)-0/23-5$)**+&6;<),%:CC=5?7562**'%%61>=?:;FDF@?:4>56>?3/(<;)0*02/36<<;AAABCDFE::JIF<9;5:4<:?>@-)'3'.1$&&$&,;:00C?'4=>((,@D9H?<B<>@B<;=HG=<L(=()(&7<>@=F<;CB>D?=\n+@7a97d860-e33a-4e27-b5be-c4754a2eb907\n+ATTACGAAGTATCACGTGCCCTGTTATCCAGACTTATGGCAGATTAGCTTCCCGGAGAGAAAACTGTCGAAAACAGACGGTATGAACACCGTAAGCTCCAAAGTGATCACCATTCGCTTTCATGCGCCTTGGCTATGCAGCGAGCTGAAAACGATCCTGACGCATCCTTCCTGTTTTCCCGAAGGGTAAAACATCTCTTT\n++\n+?>A?'-$%+?'%8$03F;;;=8*57>((?3:E?E?65%,0,.,B>77?AA6<G<9C(,):0IGAD=;AEIJLC@'?3A+/68966>9?<>??:</:<-.'(%32228@;:=CGDA>78:@97424%%$'%')460((8,:;1/4////@;5;?@//5896:.+?:<ACA>@KEA@LD=C22.+01849?D<>@;A=<K5/\n+@cc6e152f-3be2-4154-95c1-265c4f77a7ac\n+TACGGAGTATCACCGTGCCTGTTATCCAGACTTATGGCAGATTAGCTTCCCGGAGAAAACTGCTCCAACAGACGGTATGAACACCGTAAGCTCCCAGAAGTGATCACCATTCGCTTTCTCATGCATAGCTATGCGGCGAGCTGAAAAGCTGATCCTGACGCATCCTTCCTGTTTTTCCCGGGAGTAAAACATCTCTTT\n++\n+,*635,44()6,87.6'66=(@;0**E=DFCL?77-56732,/(-./1-.//17&(5EE;:)')(6,,4=8>C29;5>8832,>>459;+;;)-(+$%$*77;6CAABDB?-0*+,(&$+&**8:85=??@))?%.7+*4/+(*.'($#%,,++4;EBB:B>78=8<=@GBDCGB@5;A+1<$6:EGDAG;:>>@@?H\n+@749ba682-4ec2-4367-8bb3-51878f06992d\n+CCGGGAAAGCGGAAGGATCGTCAGGATCGTTGCTACAGCTCTGCTACATATGCATGAAAGCGAATGGTGATGCTTTGGGACTTTACGGTGTTTCATACCGTCTGTTTTCGACAGTTTTCTCTCCAGGGAAACTAATCTGCCAGCAAGTCTGGATAACAGGG\n++\n+#$$(+('&%,$)5;:8/&(,121165++.-/$$(%)(%#%'#$$$$&&%$%(3/1<222(666:=8<47/&$&)),&'&',-/.39=B>B?=-89;=>=;;;335686E;=9499=PA@-8<%/'/*+,)$77=7/-5//.-&(()**7',./102,&,&'\n+@3d6bdcab-ef5c-4ff8-a928-23066fb4e887\n+CTGTTATCAGACTTATGGCAGATTAGCTTCCCGGAGAAGAAAACTGTCGAAAACAGACGGTATGAACACCGTAAGCTCCCAAAAGTGATCACCATTCATCATGCATAGCTATGCGGGCAGACTGCGAAAACGATCCTGACTCCTTCCTGTTTTCCGGGGTAAAACATCTCTTT\n++\n+12551)$>,,/,,,AE??>==?6/.'''-8>B03<+,,-=CA@<A@<A98=<17581:*0<BC66@AA<>;;/09:6470999-%171+98==8<;6#'36;AC;7:689<<89%*./(&$++$-+--<-;=>55:4;*%&%*%/454@CAHA/318?G?4599=9?DEA@?E\n+@0b41ea60-ea37-43ef-a912-260c4d33a356\n+CTGTTATCCAGACTTATGGCAGATTAGCTTCCGGAGAAAACTGCTTCGAAAAACAGACGGTATGAACACCGTAAGCTCCCAAAGTGATCACCATTCGCTTTCATGCATAGCGCTATGCAGCGAGCTGAAAACGATCTGACGCATCCTTCCTGTTTTCCCGGGGTAAAACATCTCTTT\n++\n+=B>B3+++7-2-))%&.%,3**749689:=1B0.3&)(-'$$%#%(*(((('$,)+(/+,,/48:>;62+7:)*.<;9>@DE75@?<?GFGD@DDA$$=>;>?::>-043+).2?;<(&551.;><:8G@6E@<6@7<6@1CE78BDB>?=?57I@'-G3;@B=>@F@?8<?>794-\n+@cd8d2944-a807-434b-92d5-bfa925697c85\n+GTTATCCAGACTTATGGCAGATTAGCTTCCCGGAGAGAAAACTGGCATGAAAACAGACAGGTATGAACACCGTAAACTCGGTGATCACCATTCGCTTTCATGCATAGCTATGCAGCGAGCTGAAAACGATCCTGACGCATCTCCTTCCTGTTTTCCGGGGTAAAACATCTCTTT\n++\n+8?>>%%06/B@FEFG7=854742')9<=+3B9:<98%;<>3..-(&$*/13,*;8;1+&59ADB55<94<<:;99(&)+#&62-'('668:7855;=C><24B=>==>;B<:30=;=1;9575IF9A=E55<:@?GC;77=069<=25152/56)/,45?>@BE162;>:9DCE\n+@a492dd23-2c03-4d9b-a606-dee7268bd4fa\n+AAAGAGATGTTTTTGCGGAAAACAGGAAGGATGCGTCAGGATCGTTTTCAGCGCTATAGCTATGCATGAAAGCGAATGGTGATCCTTTGGGAGCTTACGGTGTTCATGCCAATCTGTTTTCGACAGTTTCTCTCCGAGGAAGCTAATCTGCCGCAAGTCTAGTTAAC\n++\n+F:&-/77;:@??=8%%$(#'+()%+9.99AB?==<<7/;;4/;;B>?-+(*2%%&0-1-=5;99GD=88>9>??=IC2:B?:%%*#*-&.1**,--;A::8BID?4&&%8'(<AE3??;C@>B64>:;31&*,(5('7A04.>@CC;AA7%1-1%&-/5'%*%-+,/\n+@4a58265a-1d25-47a1-b851-e7687203734f\n+GGGAAACCCAGGAGGATCGTCAGGATCGTTTTTTCAGCTCGCTGCTATGTATGCGCTGAAAGCGAATGGTGATCACTTTGGGGAGCTTACGGTGTTCATACTGTCTGTTTTCGACAGTTTTCTCTCCGGGAAGCTAATCTGCCATAAGTCTGGATAAC\n++\n+)**%&&%5'%)*$..5%$$,70?B?:>?GBLB<0))%&'-78>.11/$$+($&$&%***2),=88=@,1A=:3<25;<959E;.9?BB*A<CCHBBB==BCC>=B>B9?LL;AA74C>CNEDF<C%?7<D78.=>C=4=?@BB9@>>2-A14:C;..5\n+@f9a56724-1fa4-4807-bacc-f0a85587afd7\n+GAACACCGTAAGCTCCCAAAGTGATCACCATTCGCTTTTTCATGCATAGCTATGCAGCGACTGGCGATCCTGACGCATCTTCTGTTTTCC\n++\n+414===BA;3-.21$+&')'%-20-,((+6:57(*+,139@@?A534546/24022**)$$$#&(--++-7<+6*.*(())(,-03<:(,\n+@e525f31a-e4d6-4fe6-a703-7038efa2f178\n+GCTATGCAGCGAGCTGAAAACGATCCTGACGCATCCTTCCTGTTTCCCGGGTAAAACATCTCTTT\n++\n+;B@E::0+5511=2122@>52((''*<G=E:?A45:79$=JFCC?AJG*024<>HECB@C@?KHI\n+@eeef3ccf-2188-4382-8399-a9442bbbf40a\n+GCTATGCAGCGAGCTGAAAACGATCCTGACGCATCCTTCCTGTTTTCCCGGGGTAAAACATCTCTTT\n++\n+@=:3335937))43378KC?<?A<>CKMEH?BC55=4C>?KDFCLC4@G363877800+7<=;3;;>\n" |
| b |
| diff -r 000000000000 -r ef94bace3a3c test-data/bwa-mem-mt-genome.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa-mem-mt-genome.fa Sat May 23 13:38:26 2020 -0400 |
| b |
| b'@@ -0,0 +1,238 @@\n+>gi|251831106|ref|NC_012920.1|\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCA'..b'CAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n' |
| b |
| diff -r 000000000000 -r ef94bace3a3c test-data/consensus.hdf |
| b |
| Binary file test-data/consensus.hdf has changed |
| b |
| diff -r 000000000000 -r ef94bace3a3c tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat May 23 13:38:26 2020 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<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="all_fasta.loc" /> + </table> +</tables> \ No newline at end of file |
| b |
| diff -r 000000000000 -r ef94bace3a3c tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sat May 23 13:38:26 2020 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<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> \ No newline at end of file |