| Previous changeset 3:297e9d318b48 (2020-01-22) Next changeset 5:fd98c5af5a6c (2021-05-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166" |
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modified:
discosnp_pp.xml macros.xml test-data/discosnp/multifasta.fa test-data/discosnp/multifasta_paired.fa test-data/discosnp/vcf_file.vcf test-data/discosnp/vcf_file_paired.vcf test-data/discosnpRAD/fasta.fa test-data/lordec/stat_file.txt |
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| diff -r 297e9d318b48 -r 912d042e4f1e discosnp_pp.xml --- a/discosnp_pp.xml Wed Jan 22 17:31:42 2020 -0500 +++ b/discosnp_pp.xml Mon Aug 17 10:39:36 2020 -0400 |
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| @@ -25,14 +25,15 @@ run_discoSnp++.sh @discosnp_inputs@ - ${t} ${T} + -b ${b} #if str($VCF_option.mapping) == 'reference' -G '${reference_file}' - -M ${VCF_option.M} ${VCF_option.R} #end if + --max_threads \${GALAXY_SLOTS:-1} + ]]></command> <inputs> @@ -48,7 +49,6 @@ <expand macro="discosnp_options" /> - <param argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Extends each polymorphism with left and right unitigs" /> <param argument="-T" type="boolean" checked="false" truevalue="-T" falsevalue="" label="Extends each polymorphism with left and right contigs" /> <conditional name="VCF_option" > @@ -59,7 +59,6 @@ <when value="default"></when> <when value="reference"> <param argument="-G" type="data" format="fasta,fastq" label="Reference genome file" /> - <param argument="-M" type="integer" value="4" label="Maximal number of mapping errors" help="during BWA mapping phase" /> <param argument="-R" type="boolean" truevalue="-R" falsevalue="" checked="false" label="Use the reference genome also in the variant calling, not only for mapping results" /> </when> </conditional> |
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| diff -r 297e9d318b48 -r 912d042e4f1e macros.xml --- a/macros.xml Wed Jan 22 17:31:42 2020 -0500 +++ b/macros.xml Mon Aug 17 10:39:36 2020 -0400 |
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| @@ -1,12 +1,12 @@ <macros> + <token name="@DISCOSNP_VERSION@">2.5.4</token> + <xml name="discosnp_requirements"> <requirements> - <requirement type="package" version="2.3.0">discosnp</requirement> + <requirement type="package" version="@DISCOSNP_VERSION@">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 $filename = os.path.basename(str($input)) + "." + $input.ext @@ -64,7 +64,7 @@ </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"/> + <param argument="-c" type="text" label="Minimal coverage per read set" value="3" help="e.g. 3 / 3,5,17 / 3,auto,auto"/> </when> </conditional> @@ -75,7 +75,6 @@ <token name="@discosnp_inputs@"><![CDATA[ -r input.lst - -b ${b} -D ${D} -P ${P} ${low_complexity} |
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| diff -r 297e9d318b48 -r 912d042e4f1e test-data/discosnp/multifasta.fa --- a/test-data/discosnp/multifasta.fa Wed Jan 22 17:31:42 2020 -0500 +++ b/test-data/discosnp/multifasta.fa Mon Aug 17 10:39:36 2020 -0400 |
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| @@ -1,12 +1,12 @@ ->SNP_higher_path_3|P_1:24_A/T|high|nb_pol_1|C1_74|C2_0|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1 -AGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCG ->SNP_lower_path_3|P_1:24_A/T|high|nb_pol_1|C1_0|C2_86|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1 -AGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCG ->SNP_higher_path_2|P_1:24_C/G|high|nb_pol_1|C1_0|C2_134|Q1_0|Q2_0|G1_1/1:2484,378,10|G2_0/0:10,408,2684|rank_1 -ATTACAGAGCTGCCGGGTGGATGACTCTCTACCGCGCTCTGTGGAAGTG ->SNP_lower_path_2|P_1:24_C/G|high|nb_pol_1|C1_124|C2_0|Q1_0|Q2_0|G1_1/1:2484,378,10|G2_0/0:10,408,2684|rank_1 -ATTACAGAGCTGCCGGGTGGATGAGTCTCTACCGCGCTCTGTGGAAGTG ->SNP_higher_path_1|P_1:24_A/T|high|nb_pol_1|C1_0|C2_114|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1 -CAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCA ->SNP_lower_path_1|P_1:24_A/T|high|nb_pol_1|C1_110|C2_0|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1 -CAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCA +>SNP_higher_path_3|P_1:24_A/T|high|nb_pol_1|left_unitig_length_92|right_unitig_length_55|C1_74|C2_0|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1 +tctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtactaatAGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCGgtccatacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccg +>SNP_lower_path_3|P_1:24_A/T|high|nb_pol_1|left_unitig_length_92|right_unitig_length_55|C1_0|C2_86|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1 +tctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtactaatAGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCGgtccatacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccg +>SNP_higher_path_2|P_1:24_C/G|high|nb_pol_1|left_unitig_length_267|right_unitig_length_92|C1_0|C2_134|Q1_0|Q2_0|G1_1/1:2484,378,10|G2_0/0:10,408,2684|rank_1 +cttcgcagagaaaccgcacgtccagttctaacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctATTACAGAGCTGCCGGGTGGATGACTCTCTACCGCGCTCTGTGGAAGTGcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtactaatagggccgggctacatgttaactac +>SNP_lower_path_2|P_1:24_C/G|high|nb_pol_1|left_unitig_length_267|right_unitig_length_92|C1_124|C2_0|Q1_0|Q2_0|G1_1/1:2484,378,10|G2_0/0:10,408,2684|rank_1 +cttcgcagagaaaccgcacgtccagttctaacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctATTACAGAGCTGCCGGGTGGATGAGTCTCTACCGCGCTCTGTGGAAGTGcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtactaatagggccgggctacatgttaactac +>SNP_higher_path_1|P_1:24_A/T|high|nb_pol_1|left_unitig_length_475|right_unitig_length_267|C1_0|C2_114|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1 +cggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctaggcagcgCAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCAgttctaacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatga +>SNP_lower_path_1|P_1:24_A/T|high|nb_pol_1|left_unitig_length_475|right_unitig_length_267|C1_110|C2_0|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1 +cggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctaggcagcgCAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCAgttctaacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatga |
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| diff -r 297e9d318b48 -r 912d042e4f1e test-data/discosnp/multifasta_paired.fa --- a/test-data/discosnp/multifasta_paired.fa Wed Jan 22 17:31:42 2020 -0500 +++ b/test-data/discosnp/multifasta_paired.fa Mon Aug 17 10:39:36 2020 -0400 |
| b |
| @@ -1,12 +1,12 @@ ->SNP_higher_path_3|P_1:30_C/G|high|nb_pol_1|C1_124|Q1_0|G1_0/1:1927,18,1727|rank_0 -CAAGTGCACTTCCACAGAGCGCGGTAGAGACTCATCCACCCGGCAGCTCTGTAATAGGGAC ->SNP_lower_path_3|P_1:30_C/G|high|nb_pol_1|C1_134|Q1_0|G1_0/1:1927,18,1727|rank_0 -CAAGTGCACTTCCACAGAGCGCGGTAGAGAGTCATCCACCCGGCAGCTCTGTAATAGGGAC ->SNP_higher_path_2|P_1:30_A/T|high|nb_pol_1|C1_74|Q1_0|G1_0/1:1260,18,1020|rank_0 -ACTAATAGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCGGTCCAT ->SNP_lower_path_2|P_1:30_A/T|high|nb_pol_1|C1_86|Q1_0|G1_0/1:1260,18,1020|rank_0 -ACTAATAGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCGGTCCAT ->SNP_higher_path_1|P_1:30_A/T|high|nb_pol_1|C1_114|Q1_0|G1_0/1:1548,17,1628|rank_0 -GCAGCGCAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCAGTTCTA ->SNP_lower_path_1|P_1:30_A/T|high|nb_pol_1|C1_110|Q1_0|G1_0/1:1548,17,1628|rank_0 -GCAGCGCAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCAGTTCTA +>SNP_higher_path_3|P_1:30_C/G|high|nb_pol_1|left_unitig_length_86|right_unitig_length_261|C1_124|Q1_0|G1_0/1:1927,18,1727|rank_0 +gtagttaacatgtagcccggccctattagtacagtagtgccttcatcggcattctgtttattaagttttttctacagcaaaacgatCAAGTGCACTTCCACAGAGCGCGGTAGAGACTCATCCACCCGGCAGCTCTGTAATAGGGACtaaaaaagtgatgataatcatgagtgccgcgttatggtggtgtcggatcagagcggtcttacgaccagtcgtatgccttctcgagttccgtccggttaagcgtgacagtcccagtgaacccacaaaccgtgatggctgtccttggagtcatacgcaagaaggatggtctccagacaccggcgcaccagttttcacgccgaaagcataaacgacgagcacatatgagagtgttagaactggacgtgcggtttctctgcgaag +>SNP_lower_path_3|P_1:30_C/G|high|nb_pol_1|left_unitig_length_86|right_unitig_length_261|C1_134|Q1_0|G1_0/1:1927,18,1727|rank_0 +gtagttaacatgtagcccggccctattagtacagtagtgccttcatcggcattctgtttattaagttttttctacagcaaaacgatCAAGTGCACTTCCACAGAGCGCGGTAGAGAGTCATCCACCCGGCAGCTCTGTAATAGGGACtaaaaaagtgatgataatcatgagtgccgcgttatggtggtgtcggatcagagcggtcttacgaccagtcgtatgccttctcgagttccgtccggttaagcgtgacagtcccagtgaacccacaaaccgtgatggctgtccttggagtcatacgcaagaaggatggtctccagacaccggcgcaccagttttcacgccgaaagcataaacgacgagcacatatgagagtgttagaactggacgtgcggtttctctgcgaag +>SNP_higher_path_2|P_1:30_A/T|high|nb_pol_1|left_unitig_length_86|right_unitig_length_52|C1_74|Q1_0|G1_0/1:1260,18,1020|rank_0 +tctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtACTAATAGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCGGTCCATacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccgacg +>SNP_lower_path_2|P_1:30_A/T|high|nb_pol_1|left_unitig_length_86|right_unitig_length_52|C1_86|Q1_0|G1_0/1:1260,18,1020|rank_0 +tctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtACTAATAGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCGGTCCATacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccgacg +>SNP_higher_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_472|right_unitig_length_261|C1_114|Q1_0|G1_0/1:1548,17,1628|rank_0 +ttgcggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctagGCAGCGCAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCAGTTCTAacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatga +>SNP_lower_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_472|right_unitig_length_261|C1_110|Q1_0|G1_0/1:1548,17,1628|rank_0 +ttgcggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctagGCAGCGCAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCAGTTCTAacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatga |
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| diff -r 297e9d318b48 -r 912d042e4f1e test-data/discosnp/vcf_file.vcf --- a/test-data/discosnp/vcf_file.vcf Wed Jan 22 17:31:42 2020 -0500 +++ b/test-data/discosnp/vcf_file.vcf Mon Aug 17 10:39:36 2020 -0400 |
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| @@ -1,5 +1,5 @@ ##fileformat=VCFv4.1 -##filedate=2017102 +##filedate=2020814XX ##source=VCF_creator ##SAMPLE=file://discoRes_k_25_c_auto_D_0_P_1_b_0_coherent.fa ##REF=<ID=REF,Number=1,Type=String,Description="Allele of the path Disco aligned with the least mismatches"> @@ -12,13 +12,13 @@ ##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."> +##INFO=<ID=XA,Number=.,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"> ##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Depth of each allele by sample"> ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G1 G2 -SNP_higher_path_3 24 3 A T . . Ty=SNP;Rk=1;UL=.;UR=.;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 0/0:74:8,227,1484:74,0:0,0 1/1:86:1724,263,8:0,86:0,0 -SNP_higher_path_2 24 2 C G . . Ty=SNP;Rk=1;UL=.;UR=.;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 1/1:124:2484,378,10:0,124:0,0 0/0:134:10,408,2684:134,0:0,0 -SNP_higher_path_1 24 1 A T . . Ty=SNP;Rk=1;UL=.;UR=.;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 1/1:110:2204,335,9:0,110:0,0 0/0:114:9,347,2284:114,0:0,0 +SNP_higher_path_3 116 3 A T . . Ty=SNP;Rk=1;UL=92;UR=55;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 0/0:74:8,227,1484:74,0:0,0 1/1:86:1724,263,8:0,86:0,0 +SNP_higher_path_2 291 2 C G . . Ty=SNP;Rk=1;UL=267;UR=92;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 1/1:124:2484,378,10:0,124:0,0 0/0:134:10,408,2684:134,0:0,0 +SNP_higher_path_1 499 1 A T . . Ty=SNP;Rk=1;UL=475;UR=267;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 1/1:110:2204,335,9:0,110:0,0 0/0:114:9,347,2284:114,0:0,0 |
| b |
| diff -r 297e9d318b48 -r 912d042e4f1e test-data/discosnp/vcf_file_paired.vcf --- a/test-data/discosnp/vcf_file_paired.vcf Wed Jan 22 17:31:42 2020 -0500 +++ b/test-data/discosnp/vcf_file_paired.vcf Mon Aug 17 10:39:36 2020 -0400 |
| b |
| @@ -1,5 +1,5 @@ ##fileformat=VCFv4.1 -##filedate=2017102 +##filedate=2020814XX ##source=VCF_creator ##SAMPLE=file://discoRes_k_31_c_auto_D_0_P_1_b_0_coherentBWA_MEM.sam ##REF=<ID=REF,Number=1,Type=String,Description="Allele of the path Disco aligned with the least mismatches"> @@ -12,13 +12,13 @@ ##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."> +##INFO=<ID=XA,Number=.,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"> ##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Depth of each allele by sample"> ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G1 -read661_contig0_position139_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0 62 3 C G . MULTIPLE Ty=SNP;Rk=0;UL=.;UR=.;CL=.;CR=.;Genome=C;Sd=1 GT:DP:PL:AD:HQ 0/1:258:1927,18,1727:124,134:0,0 -read780_contig0_position26_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1 43 2 A T . MULTIPLE Ty=SNP;Rk=0;UL=.;UR=.;CL=.;CR=.;Genome=A;Sd=1 GT:DP:PL:AD:HQ 0/1:160:1260,18,1020:74,86:0,0 -read656_contig0_position454_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1 62 1 T A . MULTIPLE Ty=SNP;Rk=0;UL=.;UR=.;CL=.;CR=.;Genome=T;Sd=1 GT:DP:PL:AD:HQ 0/1:224:1628,17,1548:110,114:0,0 +read661_contig0_position139_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0 62 3 C G . MULTIPLE Ty=SNP;Rk=0;UL=86;UR=261;CL=.;CR=.;Genome=C;Sd=1;XA=read547_51,read624_39,read871_45,read688_36,read201_34,read45_68,read71_47,read728_35,read302_36,read492_42,read901_69,read237_35,read912_67,read120_38,read779_39,read161_45,read63_55,read872_67,read281_36,read900_43,read891_67,read943_45,read793_31,read300_58,read168_52,read315_58,read650_53,read918_70,read839_58,read215_68,read388_62,read479_63,read543_64,read418_35,read515_39,read661_62,read77_54,read241_35,read427_43,read268_67,read115_36,read915_50,read838_45,read382_44,read811_38,read438_35,read503_52,read472_46,read804_70,read510_30,read500_30,read759_70,read855_70,read171_70,read51_28,read464_70,read36_27,read579_70,read140_70,read720_26,read906_25,read454_24,read187_70,read75_24,read5_24,read729_24,read702_23,read433_23,read118_22,read377_22,read914_70,read691_21,read270_21,read112_70,read459_20,read240_20 GT:DP:PL:AD:HQ 0/1:258:1927,18,1727:124,134:0,0 +read780_contig0_position26_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1 43 2 A T . MULTIPLE Ty=SNP;Rk=0;UL=86;UR=52;CL=.;CR=.;Genome=A;Sd=1;XA=read653_58,read292_70,read858_59,read808_53,read335_36,read233_53,read596_53,read132_33,read721_66,read378_67,read103_53,read928_33,read998_31,read484_51,read834_38,read387_38,read182_41,read111_60,read272_70,read325_59,read853_44,read480_37,read559_67,read244_32,read642_43,read780_43,read8_32,read170_49,read602_66,read973_58,read475_46,read347_69,read843_49,read612_65,read153_51,read78_30,read85_70,read420_30,read899_70,read805_70,read303_70,read104_27,read970_27,read328_70,read806_70,read202_70,read757_26,read521_26,read962_70,read696_23,read566_70,read321_70,read649_20,read253_20 GT:DP:PL:AD:HQ 0/1:160:1260,18,1020:74,86:0,0 +read656_contig0_position454_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1 62 1 T A . MULTIPLE Ty=SNP;Rk=0;UL=472;UR=261;CL=.;CR=.;Genome=T;Sd=1;XA=read639_58,read567_37,read836_63,read727_33,read44_68,read625_48,read121_42,read298_56,read840_35,read62_69,read868_60,read38_56,read629_55,read896_35,read213_36,read897_67,read837_50,read994_50,read756_48,read113_59,read32_52,read129_38,read575_68,read957_34,read765_69,read94_41,read218_34,read297_51,read437_50,read256_48,read322_70,read716_52,read101_62,read254_50,read198_36,read12_44,read905_61,read760_67,read185_52,read761_66,read311_51,read357_43,read260_70 GT:DP:PL:AD:HQ 0/1:224:1628,17,1548:110,114:0,0 |
| b |
| diff -r 297e9d318b48 -r 912d042e4f1e test-data/discosnpRAD/fasta.fa --- a/test-data/discosnpRAD/fasta.fa Wed Jan 22 17:31:42 2020 -0500 +++ b/test-data/discosnpRAD/fasta.fa Mon Aug 17 10:39:36 2020 -0400 |
| b |
| @@ -1,28 +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 +>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|left_contig_length_40|right_contig_length_16|C1_49|Q1_0|G1_0/1:702,15,702|rank_0 +gggagcgtccgataattagtgtcctacttagtcaatagggATTGGATGCGAGCTTCTTTACCCGATCATACGTCCAGCGAAGGGATTAGCTGTCGTTAGGGCCCTAATTCCTGCCTGGAGcggacaacaaagtagt +>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|left_contig_length_40|right_contig_length_16|C1_49|Q1_0|G1_0/1:702,15,702|rank_0 +gggagcgtccgataattagtgtcctacttagtcaatagggATTGGATGCGAGCTTCTTTACCCGATCATATGTCCAGCGAAGGGATTAGGTGTCGTTAGGGCCCTAATTCCTGCCTGGAGcggacaacaaagtagt +>SNP_higher_path_6|P_1:30_C/G|high|nb_pol_1|left_unitig_length_1|right_unitig_length_8|left_contig_length_67|right_contig_length_8|C1_49|Q1_0|G1_0/1:702,15,702|rank_0 +actactttgttgtccgctccaggcaggaattagggccctaacgacagctaatcccttcgctggacgtATGATCGGGTAAAGAAGCTCGCATCCAATCCCTATTGACTAAGTAGGACACTAATTATCGGacgctccc +>SNP_lower_path_6|P_1:30_C/G|high|nb_pol_1|left_unitig_length_1|right_unitig_length_8|left_contig_length_67|right_contig_length_8|C1_49|Q1_0|G1_0/1:702,15,702|rank_0 +actactttgttgtccgctccaggcaggaattagggccctaacgacagctaatcccttcgctggacgtATGATCGGGTAAAGAAGCTCGCATCCAATCGCTATTGACTAAGTAGGACACTAATTATCGGacgctccc +>SNP_higher_path_5|P_1:30_A/C|high|nb_pol_1|left_unitig_length_5|right_unitig_length_51|left_contig_length_5|right_contig_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 +>SNP_lower_path_5|P_1:30_A/C|high|nb_pol_1|left_unitig_length_5|right_unitig_length_51|left_contig_length_5|right_contig_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 +>SNP_higher_path_4|P_1:30_A/G|high|nb_pol_1|left_unitig_length_51|right_unitig_length_0|left_contig_length_87|right_contig_length_0|C1_44|Q1_0|G1_0/1:632,15,632|rank_0 +ctatcgcggctgttcgtatgatgacctatgcggagcggggaaaccagatgggtgacccaaaaacgcacgcgacctctgtaatagggcTCCAGGTGGGAATTAGGCGTGGTCCGTCAGAAATATAGGAGACGAAAACATAGCTCTTCTT +>SNP_lower_path_4|P_1:30_A/G|high|nb_pol_1|left_unitig_length_51|right_unitig_length_0|left_contig_length_87|right_contig_length_0|C1_44|Q1_0|G1_0/1:632,15,632|rank_0 +ctatcgcggctgttcgtatgatgacctatgcggagcggggaaaccagatgggtgacccaaaaacgcacgcgacctctgtaatagggcTCCAGGTGGGAATTAGGCGTGGTCCGTCAGGAATATAGGAGACGAAAACATAGCTCTTCTT +>SNP_higher_path_3|P_1:30_A/C|high|nb_pol_1|left_unitig_length_23|right_unitig_length_0|left_contig_length_93|right_contig_length_0|C1_42|Q1_0|G1_0/1:604,15,604|rank_0 +gtcgttgagtcagctcataagccaacgaccagctcactcgccctggacaggagaggcgatcttacaagttccctttatattggctagacggtcTAGTTTTCAATAACCCCTGAGGAGCGGCACAGTATGATACAGGGAGTGAAGGAGGGA +>SNP_lower_path_3|P_1:30_A/C|high|nb_pol_1|left_unitig_length_23|right_unitig_length_0|left_contig_length_93|right_contig_length_0|C1_42|Q1_0|G1_0/1:604,15,604|rank_0 +gtcgttgagtcagctcataagccaacgaccagctcactcgccctggacaggagaggcgatcttacaagttccctttatattggctagacggtcTAGTTTTCAATAACCCCTGAGGAGCGGCACCGTATGATACAGGGAGTGAAGGAGGGA +>SNP_higher_path_2|P_1:30_C/T|high|nb_pol_1|left_unitig_length_8|right_unitig_length_0|left_contig_length_106|right_contig_length_0|C1_49|Q1_0|G1_0/1:702,15,702|rank_0 +actactttgttgtccgctccaggcaggaattagggccctaacgacagctaatcccttcgctggacgtatgatcgggtaaagaagctcgcatccaatcgctattgacTAAGTAGGACACTAATTATCGGACGCTCCCCGGGGGAGGTCAAC +>SNP_lower_path_2|P_1:30_C/T|high|nb_pol_1|left_unitig_length_8|right_unitig_length_0|left_contig_length_106|right_contig_length_0|C1_49|Q1_0|G1_0/1:702,15,702|rank_0 +actactttgttgtccgctccaggcaggaattagggccctaacgacagctaatcccttcgctggacgtatgatcgggtaaagaagctcgcatccaatcgctattgacTAAGTAGGACACTAATTATCGGACGCTCCCTGGGGGAGGTCAAC +>SNP_higher_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_23|right_unitig_length_39|left_contig_length_23|right_contig_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 +>SNP_lower_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_23|right_unitig_length_39|left_contig_length_23|right_contig_length_39|C1_42|Q1_0|G1_0/1:604,15,604|rank_0 gtgccgctcctcaggggttattgAAAACTAGACCGTCTAGCCAATATAAAGGGTACTTGTAAGATCGCCTCTCCTGTCCAGGGCgagtgagctggtcgttggcttatgagctgactcaacgac |
| b |
| diff -r 297e9d318b48 -r 912d042e4f1e test-data/lordec/stat_file.txt --- a/test-data/lordec/stat_file.txt Wed Jan 22 17:31:42 2020 -0500 +++ b/test-data/lordec/stat_file.txt Mon Aug 17 10:39:36 2020 -0400 |
| b |
| @@ -3,7 +3,7 @@ 0 1821 -1 1821 0 11808 -1 11808 0 6928 -1 6928 -79 6317 61 6134 58 21 +0 6317 -1 6317 0 6872 -1 6872 0 6308 -1 6308 0 1314 -1 1314 |