| Previous changeset 0:10e0e74c83af (2017-10-20) Next changeset 2:633917132c49 (2018-09-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6 |
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modified:
macros.xml test-data/discosnp/vcf_file.vcf test-data/discosnp/vcf_file_paired.vcf |
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added:
test-data/discosnpRAD/fasta.fa test-data/discosnpRAD/loci_reads test-data/discosnpRAD/vcf_file.vcf |
| b |
| diff -r 10e0e74c83af -r 291753bf4013 macros.xml --- a/macros.xml Fri Oct 20 03:14:44 2017 -0400 +++ b/macros.xml Fri Nov 24 12:48:26 2017 -0500 |
| [ |
| @@ -1,18 +1,27 @@ <macros> + <xml name="discosnp_requirements"> + <requirements> + <requirement type="package" version="2.3.0">discosnp</requirement> + </requirements> + </xml> + + <token name="@DISCOSNP_VERSION@">2.3.0</token> + <token name="@discosnp_single_reads@"><![CDATA[ #for $input in $input_type_options.list_reads - #set $filename = str($input) + "." + $input.ext + #set $filename = os.path.basename(str($input)) + "." + $input.ext ln -sf '${input}' '${filename}' && echo '${filename}' >> input.lst && #end for ]]></token> + <token name="@discosnp_paired_reads@"><![CDATA[ #for $i, $paired in enumerate( $input_type_options.list_paired_reads ) - #set $filenameFWD = str($paired.forward) + "." + $paired.forward.ext + #set $filenameFWD = os.path.basename(str($paired.forward)) + "." + $paired.forward.ext ln -sf '${paired.forward}' '${filenameFWD}' && - #set $filenameREV = str($paired.reverse) + "." + $paired.reverse.ext + #set $filenameREV = os.path.basename(str($paired.reverse)) + "." + $paired.reverse.ext ln -sf '${paired.reverse}' '${filenameREV}' && echo '${filenameFWD}' > "paired_${i}.lst" && @@ -21,22 +30,121 @@ #end for ]]></token> + + <xml name="discosnp_inputs"> + <conditional name="input_type_options"> + <param name="input_type" type="select" label="Input options"> + <option value="single">Single end reads</option> + <option value="paired">Paired end reads</option> + <option value="mix">Both single and paired reads</option> + </param> + <when value="single"> + <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" /> + </when> + <when value="paired"> + <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files" /> + </when> + <when value="mix"> + <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" /> + <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files"/> + </when> + </conditional> + </xml> + + <xml name="discosnp_options"> + <param argument="-D" type="integer" label="Deletion size" value="0" help="If different of 0, discoSnp will search for deletions of size from 1 to D included"/> + <param argument="-P" type="integer" label="Maximum SNPs per bubble" value="1" help="discoSnp will search up to P SNPs in a unique bubble"/> + <param name="low_complexity" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Remove low complexity bubbles" /> + <param argument="-k" type="integer" label="Size of kmers" value="31" /> + + <conditional name="coverage_options_type" > + <param name="coverage_options" type="select" label="Coverage option"> + <option value="auto"></option> + <option value="custom"></option> + </param> + <when value="auto" /> + <when value="custom"> + <param argument="-c" type="text" label="Minimal coverage per read set" value="4" help="e.g. 4 / 4,5,17 / 4,auto,auto"/> + </when> + </conditional> + + <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" /> + <param argument="-d" type="integer" label="Max number of errors per read" value="1" help="Max number of errors per read" /> + + </xml> + + <token name="@discosnp_inputs@"><![CDATA[ + -r input.lst + -b ${b} + -D ${D} + -P ${P} + ${low_complexity} + -k ${k} + + #if str($coverage_options_type.coverage_options) == 'auto' + -c auto + #else + -c '${coverage_options_type.c}' + #end if + -C ${C} + -d ${d} + ]]></token> + <token name="@lordec_inputs@"><![CDATA[ -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }" -i '${program_type_choice.i}' -k ${program_type_choice.k} -s ${program_type_choice.s} ]]></token> + <xml name="lordec_inputs"> <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" /> <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" /> <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/> <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" /> </xml> + + <token name="@discosnp_help@"><![CDATA[ +------- + +.. class:: warningmark + +**Input parameters** + +-Sequences files in fasta or fastq each allele will be counted in each file individually + +-Use collections: data list and/or data list paired + +-Fasta sequence of a genome if case of you are willing to map the sequence extension on a reference in order to get a compliant VCF + +------- + +.. class:: warningmark + +**Ouput parameters** + +-VCF file with coordinates on the higher branch sequences or on a reference genome if provided + +-Fasta file with sequence extensions around the SNP. + + +------- + +**Web site** + +https://colibread.inria.fr/software/discosnp/ + + ]]></token> + <xml name="citations"> <citations> <yield/> <citation type="doi">10.1186/s13742-015-0105-2</citation> </citations> </xml> + + <xml name="discosnp_citation"> + <citation type="doi">10.1101/209965</citation> + </xml> + </macros> |
| b |
| diff -r 10e0e74c83af -r 291753bf4013 test-data/discosnp/vcf_file.vcf --- a/test-data/discosnp/vcf_file.vcf Fri Oct 20 03:14:44 2017 -0400 +++ b/test-data/discosnp/vcf_file.vcf Fri Nov 24 12:48:26 2017 -0500 |
| b |
| @@ -12,6 +12,7 @@ ##INFO=<ID=CR,Number=1,Type=Integer,Description="length of the contig right"> ##INFO=<ID=Genome,Number=1,Type=String,Description="Allele of the reference;for indel reference is . "> ##INFO=<ID=Sd,Number=1,Type=Integer,Description="Reverse (-1) or Forward (1) Alignement"> +##INFO=<ID=XA,Number=0/1,Type=String,Description="Other mapping positions (chromosome_position). Position is negative in case of Reverse alignment. The position designs the starting position of the alignment, not the position of the variant itself."> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Cumulated depth accross samples (sum)"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled Genotype Likelihoods"> |
| b |
| diff -r 10e0e74c83af -r 291753bf4013 test-data/discosnp/vcf_file_paired.vcf --- a/test-data/discosnp/vcf_file_paired.vcf Fri Oct 20 03:14:44 2017 -0400 +++ b/test-data/discosnp/vcf_file_paired.vcf Fri Nov 24 12:48:26 2017 -0500 |
| b |
| @@ -12,6 +12,7 @@ ##INFO=<ID=CR,Number=1,Type=Integer,Description="length of the contig right"> ##INFO=<ID=Genome,Number=1,Type=String,Description="Allele of the reference;for indel reference is . "> ##INFO=<ID=Sd,Number=1,Type=Integer,Description="Reverse (-1) or Forward (1) Alignement"> +##INFO=<ID=XA,Number=0/1,Type=String,Description="Other mapping positions (chromosome_position). Position is negative in case of Reverse alignment. The position designs the starting position of the alignment, not the position of the variant itself."> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Cumulated depth accross samples (sum)"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled Genotype Likelihoods"> |
| b |
| diff -r 10e0e74c83af -r 291753bf4013 test-data/discosnpRAD/fasta.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/discosnpRAD/fasta.fa Fri Nov 24 12:48:26 2017 -0500 |
| b |
| @@ -0,0 +1,28 @@ +>SNP_higher_path_7|P_1:30_C/T,P_2:49_C/G|high|nb_pol_2|left_unitig_length_1|right_unitig_length_16|C1_49|Q1_0|G1_0/1:702,15,702|rank_0 +gATTGGATGCGAGCTTCTTTACCCGATCATACGTCCAGCGAAGGGATTAGCTGTCGTTAGGGCCCTAATTCCTGCCTGGAGcggacaacaaagtagt +>SNP_lower_path_7|P_1:30_C/T,P_2:49_C/G|high|nb_pol_2|left_unitig_length_1|right_unitig_length_16|C1_49|Q1_0|G1_0/1:702,15,702|rank_0 +gATTGGATGCGAGCTTCTTTACCCGATCATATGTCCAGCGAAGGGATTAGGTGTCGTTAGGGCCCTAATTCCTGCCTGGAGcggacaacaaagtagt +>SNP_higher_path_6|P_1:30_C/G|high|nb_pol_1|left_unitig_length_1|right_unitig_length_8|C1_49|Q1_0|G1_0/1:702,15,702|rank_0 +tATGATCGGGTAAAGAAGCTCGCATCCAATCCCTATTGACTAAGTAGGACACTAATTATCGGacgctccc +>SNP_lower_path_6|P_1:30_C/G|high|nb_pol_1|left_unitig_length_1|right_unitig_length_8|C1_49|Q1_0|G1_0/1:702,15,702|rank_0 +tATGATCGGGTAAAGAAGCTCGCATCCAATCGCTATTGACTAAGTAGGACACTAATTATCGGacgctccc +>SNP_higher_path_5|P_1:30_A/C|high|nb_pol_1|left_unitig_length_5|right_unitig_length_51|C1_44|Q1_0|G1_0/1:632,15,632|rank_0 +ctatcGCGGCTGTTCGTATGATGACCTATGCGGAGAGGGGAAACCAGATGGGTGACCCAAAAACGCacgcgacctctgtaatagggctccaggtgggaattaggcgtggtccgtcag +>SNP_lower_path_5|P_1:30_A/C|high|nb_pol_1|left_unitig_length_5|right_unitig_length_51|C1_44|Q1_0|G1_0/1:632,15,632|rank_0 +ctatcGCGGCTGTTCGTATGATGACCTATGCGGAGCGGGGAAACCAGATGGGTGACCCAAAAACGCacgcgacctctgtaatagggctccaggtgggaattaggcgtggtccgtcag +>SNP_higher_path_4|P_1:30_A/G|high|nb_pol_1|left_unitig_length_51|right_unitig_length_0|C1_44|Q1_0|G1_0/1:632,15,632|rank_0 +ggggaaaccagatgggtgacccaaaaacgcacgcgacctctgtaatagggcTCCAGGTGGGAATTAGGCGTGGTCCGTCAGAAATATAGGAGACGAAAACATAGCTCTTCTT +>SNP_lower_path_4|P_1:30_A/G|high|nb_pol_1|left_unitig_length_51|right_unitig_length_0|C1_44|Q1_0|G1_0/1:632,15,632|rank_0 +ggggaaaccagatgggtgacccaaaaacgcacgcgacctctgtaatagggcTCCAGGTGGGAATTAGGCGTGGTCCGTCAGGAATATAGGAGACGAAAACATAGCTCTTCTT +>SNP_higher_path_3|P_1:30_A/C|high|nb_pol_1|left_unitig_length_23|right_unitig_length_0|C1_42|Q1_0|G1_0/1:604,15,604|rank_0 +ccctttatattggctagacggtcTAGTTTTCAATAACCCCTGAGGAGCGGCACAGTATGATACAGGGAGTGAAGGAGGGA +>SNP_lower_path_3|P_1:30_A/C|high|nb_pol_1|left_unitig_length_23|right_unitig_length_0|C1_42|Q1_0|G1_0/1:604,15,604|rank_0 +ccctttatattggctagacggtcTAGTTTTCAATAACCCCTGAGGAGCGGCACCGTATGATACAGGGAGTGAAGGAGGGA +>SNP_higher_path_2|P_1:30_C/T|high|nb_pol_1|left_unitig_length_8|right_unitig_length_0|C1_49|Q1_0|G1_0/1:702,15,702|rank_0 +ctattgacTAAGTAGGACACTAATTATCGGACGCTCCCCGGGGGAGGTCAAC +>SNP_lower_path_2|P_1:30_C/T|high|nb_pol_1|left_unitig_length_8|right_unitig_length_0|C1_49|Q1_0|G1_0/1:702,15,702|rank_0 +ctattgacTAAGTAGGACACTAATTATCGGACGCTCCCTGGGGGAGGTCAAC +>SNP_higher_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_23|right_unitig_length_39|C1_42|Q1_0|G1_0/1:604,15,604|rank_0 +gtgccgctcctcaggggttattgAAAACTAGACCGTCTAGCCAATATAAAGGGAACTTGTAAGATCGCCTCTCCTGTCCAGGGCgagtgagctggtcgttggcttatgagctgactcaacgac +>SNP_lower_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_23|right_unitig_length_39|C1_42|Q1_0|G1_0/1:604,15,604|rank_0 +gtgccgctcctcaggggttattgAAAACTAGACCGTCTAGCCAATATAAAGGGTACTTGTAAGATCGCCTCTCCTGTCCAGGGCgagtgagctggtcgttggcttatgagctgactcaacgac |
| b |
| diff -r 10e0e74c83af -r 291753bf4013 test-data/discosnpRAD/loci_reads --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/discosnpRAD/loci_reads Fri Nov 24 12:48:26 2017 -0500 |
| b |
| b'@@ -0,0 +1,1000 @@\n+>read0_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TCTAGCGATTAACGTCAACGGACTTAACGGGGGATAATTTTTCGGGAGAATACAGTTACCGGGTGACTCCAACGCAGGGGACAACGAAAGCGGTTTAGGGGGGAATGCACGCTACGTCGCATTTTGAGTGAAAACCGGATCCACACTCAG\n+>read1_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+ACTACTTTGTTGTCCGCTCCAGGCAGGAATTAGGGCCCTAACGACACCTAATCCCTTCGCTGGACATATGATCGGGTAAAGAAGCTCGCATCCAATCGCTATTGACTAAGTAGGACACTAATTATCGGACGCTCCCCGGGGGAGGTCAAC\n+>read2_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+AAGAAGAGCTATGTTTTCGTCTCCTATATTTCTGACGGACCACGCCTAATTCCCACCTGGAGCCCTATTACAGAGGTCGCGTGCGTTTTTGGGTCACCCATCTGGTTTCCCCGCTCCGCATAGGTCATCATACGAACAGCCGCGATAGGA\n+>read3_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TCCTATCGCGGCTGTTCGTATGATGACCTATGCGGAGCGGGGAAACCAGATGGGTGACCCAAAAACGCACGCGACCTCTGTAATAGGGCTCCAGGTGGGAATTAGGCGTGGTCCGTCAGAAATATAGGAGACGAAAACATAGCTCTTCTT\n+>read4_contig0_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AAGCAGATTAGGACGACTCGGTGCTTTCGTGGATATGCTGTGGCCCGAGTGATGGGCGTCGTGTATGCAGAGGCCGTCGATGACTAAAGTTCCCTTGGCTTCGGTCAAGCCGTTTACATTATACCCGTATTTGGGACTGAGACCGTGTTG\n+>read5_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GTTGACCTCCCCCGGGGAGCGTCCGATAATTAGTGTCCTACTTAGTCAATAGCGATTGGATGCGAGCTTCTTTACCCGATCATATGTCCAGCGAAGGGATTAGGTGTCGTTAGGGCCCTAATTCCTGCCTGGAGCGGACAACAAAGTAGT\n+>read6_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+ACTACTTTGTTGTCCGCTCCAGGCAGGAATTAGGGCCCTAACGACACCTAATCCCTTCGCTGGACATATGATCGGGTAAAGAAGCTCGCATCCAATCGCTATTGACTAAGTAGGACACTAATTATCGGACGCTCCCCGGGGGAGGTCAAC\n+>read7_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GTTGACCTCCCCCGGGGAGCGTCCGATAATTAGTGTCCTACTTAGTCAATAGCGATTGGATGCGAGCTTCTTTACCCGATCATATGTCCAGCGAAGGGATTAGGTGTCGTTAGGGCCCTAATTCCTGCCTGGAGCGGACAACAAAGTAGT\n+>read8_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TCCCTCCTTCACTCCCTGTATCATACGGTGCCGCTCCTCAGGGGTTATTGAAAACTAGACCGTCTAGCCAATATAAAGGGAACTTGTAAGATCGCCTCTCCTGTCCAGGGCGAGTGAGCTGGTCGTTGGCTTATGAGCTGACTCAACGAC\n+>read9_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+AAGAAGAGCTATGTTTTCGTCTCCTATATTTCTGACGGACCACGCCTAATTCCCACCTGGAGCCCTATTACAGAGGTCGCGTGCGTTTTTGGGTCACCCATCTGGTTTCCCCGCTCCGCATAGGTCATCATACGAACAGCCGCGATAGGA\n+>read10_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TCCTATCGCGGCTGTTCGTATGATGACCTATGCGGAGCGGGGAAACCAGATGGGTGACCCAAAAACGCACGCGACCTCTGTAATAGGGCTCCAGGTGGGAATTAGGCGTGGTCCGTCAGAAATATAGGAGACGAAAACATAGCTCTTCTT\n+>read11_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TCCCTCCTTCACTCCCTGTATCATACGGTGCCGCTCCTCAGGGGTTATTGAAAACTAGACCGTCTAGCCAATATAAAGGGAACTTGTAAGATCGCCTCTCCTGTCCAGGGCGAGTGAGCTGGTCGTTGGCTTATGAGCTGACTCAACGAC\n+>read12_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TCCCTCCTTCACTCCCTGTATCATACGGTGCCGCTCCTCAGGGGTTATTGAAAACTAGACCGTCTAGCCAATATAAAGGGAACTTGTAAGATCGCCTCTCCTGTCCAGGGCGAGTGAGCTGGTCGTTGGCTTATGAGCTGACTCAACGAC\n+>read13_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TCTAGCGATTAACGTCAACGGACTTAACGGGGGATAATTTTTCGGGAGAATACAGTTACCGGGTGACTCCAACGCAGGGGACAACGAAAGCGGTTTAGGGGGGAATGCACGCTACGTCGCATTTTGAGTGAAAACCGGATCCACACTCAG\n+>read14_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+CTGAGTGTGGATCCGGTTTTCACTCAAAATGCGACGTAGCGTGCATTCCCCCCTAAACCGCTTTCGTTGTCCCCTGCGTTGGAGTCACCCGGTAACTGTATTCTCCCGAAAAATTATCCCCCGTTAAGTCCGTTGACGTTAATCGCTAGA\n+>read15_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+ACTACTTTGTTGTCCGCTCCAGGCAGGAATTAGGGCCCTAACGACACCTAATCCCTTCGCTGGACATATGATCGGGTAAAGAAGCTCGCATCCAATCGCTATTGACTAAGTAGGACACTAATTATCGGACGCTCCCCGGGGGAGGTCAAC\n+>read16_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TCCCTCCTTCACTCCCTGTATCATACGGTGCCGCTCCTCAGGGGTTATTGAAAACTAGACCGTCTAGCCAATATAAAGGGAACTTGTAAGATCGCCTCTCCTGTCCAGGGCGAGTGAGCTGGTCGTTGGCTTATGAGCTGACTCAACGAC\n+>read17_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+AAGAAGAGCTATGTTTTCGTCTCCTATATTTCTGACGGACCACGCCTAATTCCCACCTGGAGCCCTATTACAGAGGTCGCGTGCGTTTTTGGGTCACCCATCTGGTTTCCCCGCTCCGCATAGGTCATCATACGAACAGCCGCGA'..b'g2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+GTCGTTGAGTCAGCTCATAAGCCAACGACCAGCTCACTCGCCCTGGACAGGAGAGGCGATCTTACAAGTACCCTTTATATTGGCTAGACGGTCTAGTTTTCAATAACCCCTGAGGAGCGGCACAGTATGATACAGGGAGTGAAGGAGGGA\n+>read233_contig0_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+CAACACGGTCTCAGTCCCAAATACGGGTATAATGTAAACGGCTTGACCGAAGCCAAGGGAACTTTAGTCATCGACGGCCTCTGCATACACGACGCCCATCACTCGGGCCACAGCATATCCACGAAAGCACCGAGTCGTCCTAATCTGCTT\n+>read234_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+GTCGTTGAGTCAGCTCATAAGCCAACGACCAGCTCACTCGCCCTGGACAGGAGAGGCGATCTTACAAGTACCCTTTATATTGGCTAGACGGTCTAGTTTTCAATAACCCCTGAGGAGCGGCACAGTATGATACAGGGAGTGAAGGAGGGA\n+>read235_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TTCTATCGCGGCTGTTCGTATGATGACCTATGCGGAGAGGGGAAACCAGATGGGTGACCCAAAAACGCACGCGACCTCTGTAATAGGGCTCCAGGTGGGAATTAGGCGTGGTCCGTCAGGAATATAGGAGACGAAAACATAGCTCTTCTT\n+>read236_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TCCCTCCTTCACTCCCTGTATCATACTGTGCCGCTCCTCAGGGGTTATTGAAAACTAGACCGTCTAGCCAATATAAAGGGTACTTGTAAGATCGCCTCTCCTGTCCAGGGCGAGTGAGCTGGTCGTTGGCTTATGAGCTGACTCAACGAC\n+>read237_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TCTAGCGATTAACGTCAACGGACTTAACGGGGGATAATTTTTCGGGAGAATACAGTTACCGGGTGACTCCAACGCAGGGGACAACGAAAGCGGTTTAGGGGGGAATGCACGCTACGTCGCATTTTGAGTGAAAACCGGATCCACACTCAG\n+>read238_contig0_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+CAACACGGTCTCAGTCCCAAATACGGGTATAATGTAAACGGCTTGACCGAAGCCAAGGGAACTTTAGTCATCGACGGCCTCTGCATACACGACGCCCATCACTCGGGCCACAGCATATCCACGAAAGCACCGAGTCGTCCTAATCTGCTT\n+>read239_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GTTGACCTCCCCCAGGGAGCGTCCGATAATTAGTGTCCTACTTAGTCAATAGGGATTGGATGCGAGCTTCTTTACCCGATCATACGTCCAGCGAAGGGATTAGCTGTCGTTAGGGCCCTAATTCCTGCCTGGAGCGGACAACAAAGTAGT\n+>read240_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+GTCGTTGAGTCAGCTCATAAGCCAACGACCAGCTCACTCGCCCTGGACAGGAGAGGCGATCTTACAAGTACCCTTTATATTGGCTAGACGGTCTAGTTTTCAATAACCCCTGAGGAGCGGCACAGTATGATACAGGGAGTGAAGGAGGGA\n+>read241_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GTTGACCTCCCCCAGGGAGCGTCCGATAATTAGTGTCCTACTTAGTCAATAGGGATTGGATGCGAGCTTCTTTACCCGATCATACGTCCAGCGAAGGGATTAGCTGTCGTTAGGGCCCTAATTCCTGCCTGGAGCGGACAACAAAGTAGT\n+>read242_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TCTAGCGATTAACGTCAACGGACTTAACGGGGGATAATTTTTCGGGAGAATACAGTTACCGGGTGACTCCAACGCAGGGGACAACGAAAGCGGTTTAGGGGGGAATGCACGCTACGTCGCATTTTGAGTGAAAACCGGATCCACACTCAG\n+>read243_contig0_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AAGCAGATTAGGACGACTCGGTGCTTTCGTGGATATGCTGTGGCCCGAGTGATGGGCGTCGTGTATGCAGAGGCCGTCGATGACTAAAGTTCCCTTGGCTTCGGTCAAGCCGTTTACATTATACCCGTATTTGGGACTGAGACCGTGTTG\n+>read244_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TCTAGCGATTAACGTCAACGGACTTAACGGGGGATAATTTTTCGGGAGAATACAGTTACCGGGTGACTCCAACGCAGGGGACAACGAAAGCGGTTTAGGGGGGAATGCACGCTACGTCGCATTTTGAGTGAAAACCGGATCCACACTCAG\n+>read245_contig0_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+CAACACGGTCTCAGTCCCAAATACGGGTATAATGTAAACGGCTTGACCGAAGCCAAGGGAACTTTAGTCATCGACGGCCTCTGCATACACGACGCCCATCACTCGGGCCACAGCATATCCACGAAAGCACCGAGTCGTCCTAATCTGCTT\n+>read246_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+CTGAGTGTGGATCCGGTTTTCACTCAAAATGCGACGTAGCGTGCATTCCCCCCTAAACCGCTTTCGTTGTCCCCTGCGTTGGAGTCACCCGGTAACTGTATTCTCCCGAAAAATTATCCCCCGTTAAGTCCGTTGACGTTAATCGCTAGA\n+>read247_contig0_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AAGCAGATTAGGACGACTCGGTGCTTTCGTGGATATGCTGTGGCCCGAGTGATGGGCGTCGTGTATGCAGAGGCCGTCGATGACTAAAGTTCCCTTGGCTTCGGTCAAGCCGTTTACATTATACCCGTATTTGGGACTGAGACCGTGTTG\n+>read248_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GTTGACCTCCCCCAGGGAGCGTCCGATAATTAGTGTCCTACTTAGTCAATAGGGATTGGATGCGAGCTTCTTTACCCGATCATACGTCCAGCGAAGGGATTAGCTGTCGTTAGGGCCCTAATTCCTGCCTGGAGCGGACAACAAAGTAGT\n+>read249_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+AAGAAGAGCTATGTTTTCGTCTCCTATATTCCTGACGGACCACGCCTAATTCCCACCTGGAGCCCTATTACAGAGGTCGCGTGCGTTTTTGGGTCACCCATCTGGTTTCCCCTCTCCGCATAGGTCATCATACGAACAGCCGCGATAGAA\n' |
| b |
| diff -r 10e0e74c83af -r 291753bf4013 test-data/discosnpRAD/vcf_file.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/discosnpRAD/vcf_file.vcf Fri Nov 24 12:48:26 2017 -0500 |
| b |
| @@ -0,0 +1,8 @@ +cluster_0_size_4 . SNP_higher_path_1 A T . . Ty=SNP;Rk=0;UL=23;UR=39;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 0/1:84:604,15,604:42,42:0,0 +cluster_0_size_4 . SNP_higher_path_3 A C . . Ty=SNP;Rk=0;UL=23;UR=0;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 0/1:84:604,15,604:42,42:0,0 +cluster_1_size_6 . SNP_higher_path_2 C T . . Ty=SNP;Rk=0;UL=8;UR=0;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 0/1:98:702,15,702:49,49:0,0 +cluster_1_size_6 . SNP_higher_path_6 C G . . Ty=SNP;Rk=0;UL=1;UR=8;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 0/1:98:702,15,702:49,49:0,0 +cluster_1_size_6 . SNP_higher_path_7 C T . . Ty=SNP;Rk=0;UL=1;UR=16;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 0|1:98:702,15,702:49,49:0,0 +cluster_1_size_6 . SNP_higher_path_7 C G . . Ty=SNP;Rk=0;UL=1;UR=16;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 0|1:98:702,15,702:49,49:0,0 +cluster_2_size_4 . SNP_higher_path_4 A G . . Ty=SNP;Rk=0;UL=51;UR=0;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 0/1:88:632,15,632:44,44:0,0 +cluster_2_size_4 . SNP_higher_path_5 A C . . Ty=SNP;Rk=0;UL=5;UR=51;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 0/1:88:632,15,632:44,44:0,0 |