search

GATB / DiscoSnp

DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.
https://gatb.inria.fr/software/discosnp/
GNU Affero General Public License v3.0
38 stars 20 forks source link

Fix compatibility to gatb-core v1.3.0 #4

Closed ysard closed 5 years ago

ysard commented 7 years ago

Hi, I fixed the compatibility with gatbcore 1.3.0; since the remove of the Vector type members in the Graph class, in favor of GraphVector members.

Best regards.

ysard commented 7 years ago

Hello, i also have another problem with a Segmentation Fault due to a DSK setting. In run_discoSnp++.sh there is a load of a fasta file: graphCmd="${dbgh5_bin} -in ${read_sets}_${kissprefix}_removemeplease -out $h5prefix -kmer-size $k -abundance-min ${c_dbgh5} -abundance-max $C -solidity-kind one ${option_cores_gatb} -mphf none -verbose $verbose"

with this parameter: -solidity-kind one

currently only 'sum' value doesn't generate a segfault. Here there is a report: [DSK: Collecting stats on reads_r1 ] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 11, 11, 11] MB [DSK: Pass 1/1, Step 1: partitioning ] 0 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 13, 13, 13] MB Erreur de segmentation

By switching 'one' to 'sum' the simple unit test fail: diff discoRes_a.vcf discoRes_b.vcf

Here is the diff: 1,12c1,12 < >SNP_higher_path_3|P_1:30_C/G|high|nb_pol_1|left_unitig_length_86|right_unitig_length_261|left_contig_length_169|right_contig_length_764|C1_124|C2_0|Q1_0|Q2_0|G1_0/0:10,378,2484|G2_1/1:2684,408,10|rank_1 < cgtcggaattgctatagcccttgaacgctacatgcacgataccaagttatgtatggaccgggtcatcaataggttatagcctagtagttaacatgtagcccggccctattagtacagtagtgccttcatcggcattctgtttattaagttttttctacagcaaaacgatCAAGTGCACTTCCACAGAGCGCGGTAGAGACTCATCCACCCGGCAGCTCTGTAATAGGGACtaaaaaagtgatgataatcatgagtgccgcgttatggtggtgtcggatcagagcggtcttacgaccagtcgtatgccttctcgagttccgtccggttaagcgtgacagtcccagtgaacccacaaaccgtgatggctgtccttggagtcatacgcaagaaggatggtctccagacaccggcgcaccagttttcacgccgaaagcataaacgacgagcacatatgagagtgttagaactggacgtgcggtttctctgcgaagtacacctcgagctgttgcgttgttgcgctgcctagatgcagtgtcgcacatatcacttttgcttcaacgactgccgctttcgctgtatccctagacagtcaacagtaagcgctttttgtaggcaggggctccccctgtgactaactgcgccaaaacatcttcggatccccttgtccaatctaactcaccgaattcttacattttagaccctaatatcacatcattagagattaattgccactgccaaaattctgtccacaagcgttttagttcgccccagtaaagttgtctataacgactaccaaatccgcatgttacgggacttcttattaattcttttttcgtgaggagcagcggatcttaatggatggccgcaggtggtatggaagctaatagcgcgggtgagagggtaatcagccgtgtccaccaacacaacgctatcgggcgattctataagattccgcattgcgtctacttataagatgtctcaacggtatccgcaa < >SNP_lower_path_3|P_1:30_C/G|high|nb_pol_1|left_unitig_length_86|right_unitig_length_261|left_contig_length_169|right_contig_length_764|C1_0|C2_134|Q1_0|Q2_0|G1_0/0:10,378,2484|G2_1/1:2684,408,10|rank_1 < cgtcggaattgctatagcccttgaacgctacatgcacgataccaagttatgtatggaccgggtcatcaataggttatagcctagtagttaacatgtagcccggccctattagtacagtagtgccttcatcggcattctgtttattaagttttttctacagcaaaacgatCAAGTGCACTTCCACAGAGCGCGGTAGAGAGTCATCCACCCGGCAGCTCTGTAATAGGGACtaaaaaagtgatgataatcatgagtgccgcgttatggtggtgtcggatcagagcggtcttacgaccagtcgtatgccttctcgagttccgtccggttaagcgtgacagtcccagtgaacccacaaaccgtgatggctgtccttggagtcatacgcaagaaggatggtctccagacaccggcgcaccagttttcacgccgaaagcataaacgacgagcacatatgagagtgttagaactggacgtgcggtttctctgcgaagtacacctcgagctgttgcgttgttgcgctgcctagatgcagtgtcgcacatatcacttttgcttcaacgactgccgctttcgctgtatccctagacagtcaacagtaagcgctttttgtaggcaggggctccccctgtgactaactgcgccaaaacatcttcggatccccttgtccaatctaactcaccgaattcttacattttagaccctaatatcacatcattagagattaattgccactgccaaaattctgtccacaagcgttttagttcgccccagtaaagttgtctataacgactaccaaatccgcatgttacgggacttcttattaattcttttttcgtgaggagcagcggatcttaatggatggccgcaggtggtatggaagctaatagcgcgggtgagagggtaatcagccgtgtccaccaacacaacgctatcgggcgattctataagattccgcattgcgtctacttataagatgtctcaacggtatccgcaa < >SNP_higher_path_2|P_1:30_A/T|high|nb_pol_1|left_unitig_length_86|right_unitig_length_52|left_contig_length_881|right_contig_length_52|C1_74|C2_0|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1 < ttgcggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctaggcagcgcaacaacgcaacagctcgaggtgtacttcgcagagaaaccgcacgtccagttctaacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatgactctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtACTAATAGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCGGTCCATacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccgacg < >SNP_lower_path_2|P_1:30_A/T|high|nb_pol_1|left_unitig_length_86|right_unitig_length_52|left_contig_length_881|right_contig_length_52|C1_0|C2_86|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1 < ttgcggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctaggcagcgcaacaacgcaacagctcgaggtgtacttcgcagagaaaccgcacgtccagttctaacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatgactctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtACTAATAGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCGGTCCATacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccgacg < >SNP_higher_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_472|right_unitig_length_261|left_contig_length_472|right_contig_length_461|C1_0|C2_114|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1 < ttgcggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctagGCAGCGCAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCAGTTCTAacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatgactctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtactaatagggccgggctacatgttaactactaggctataacctattgatgacccggtccatacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccgacg < >SNP_lower_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_472|right_unitig_length_261|left_contig_length_472|right_contig_length_461|C1_110|C2_0|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1 < ttgcggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctagGCAGCGCAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCAGTTCTAacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatgactctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtactaatagggccgggctacatgttaactactaggctataacctattgatgacccggtccatacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccgacg

> >SNP_higher_path_3|P_1:30_C/G|high|nb_pol_1|left_unitig_length_86|right_unitig_length_261|left_contig_length_166|right_contig_length_761|C1_124|C2_0|Q1_0|Q2_0|G1_0/0:10,378,2484|G2_1/1:2684,408,10|rank_1
> cggaattgctatagcccttgaacgctacatgcacgataccaagttatgtatggaccgggtcatcaataggttatagccttgtagttaacatgtagcccggccctattagtacagtagtgccttcatcggcattctgtttattaagttttttctacagcaaaacgatCAAGTGCACTTCCACAGAGCGCGGTAGAGACTCATCCACCCGGCAGCTCTGTAATAGGGACtaaaaaagtgatgataatcatgagtgccgcgttatggtggtgtcggatcagagcggtcttacgaccagtcgtatgccttctcgagttccgtccggttaagcgtgacagtcccagtgaacccacaaaccgtgatggctgtccttggagtcatacgcaagaaggatggtctccagacaccggcgcaccagttttcacgccgaaagcataaacgacgagcacatatgagagtgttagaactggacgtgcggtttctctgcgaagaacacctcgagctgttgcgttgttgcgctgcctagatgcagtgtcgcacatatcacttttgcttcaacgactgccgctttcgctgtatccctagacagtcaacagtaagcgctttttgtaggcaggggctccccctgtgactaactgcgccaaaacatcttcggatccccttgtccaatctaactcaccgaattcttacattttagaccctaatatcacatcattagagattaattgccactgccaaaattctgtccacaagcgttttagttcgccccagtaaagttgtctataacgactaccaaatccgcatgttacgggacttcttattaattcttttttcgtgaggagcagcggatcttaatggatggccgcaggtggtatggaagctaatagcgcgggtgagagggtaatcagccgtgtccaccaacacaacgctatcgggcgattctataagattccgcattgcgtctacttataagatgtctcaacggtatccg
> >SNP_lower_path_3|P_1:30_C/G|high|nb_pol_1|left_unitig_length_86|right_unitig_length_261|left_contig_length_166|right_contig_length_761|C1_0|C2_134|Q1_0|Q2_0|G1_0/0:10,378,2484|G2_1/1:2684,408,10|rank_1
> cggaattgctatagcccttgaacgctacatgcacgataccaagttatgtatggaccgggtcatcaataggttatagccttgtagttaacatgtagcccggccctattagtacagtagtgccttcatcggcattctgtttattaagttttttctacagcaaaacgatCAAGTGCACTTCCACAGAGCGCGGTAGAGAGTCATCCACCCGGCAGCTCTGTAATAGGGACtaaaaaagtgatgataatcatgagtgccgcgttatggtggtgtcggatcagagcggtcttacgaccagtcgtatgccttctcgagttccgtccggttaagcgtgacagtcccagtgaacccacaaaccgtgatggctgtccttggagtcatacgcaagaaggatggtctccagacaccggcgcaccagttttcacgccgaaagcataaacgacgagcacatatgagagtgttagaactggacgtgcggtttctctgcgaagaacacctcgagctgttgcgttgttgcgctgcctagatgcagtgtcgcacatatcacttttgcttcaacgactgccgctttcgctgtatccctagacagtcaacagtaagcgctttttgtaggcaggggctccccctgtgactaactgcgccaaaacatcttcggatccccttgtccaatctaactcaccgaattcttacattttagaccctaatatcacatcattagagattaattgccactgccaaaattctgtccacaagcgttttagttcgccccagtaaagttgtctataacgactaccaaatccgcatgttacgggacttcttattaattcttttttcgtgaggagcagcggatcttaatggatggccgcaggtggtatggaagctaatagcgcgggtgagagggtaatcagccgtgtccaccaacacaacgctatcgggcgattctataagattccgcattgcgtctacttataagatgtctcaacggtatccg
> >SNP_higher_path_2|P_1:30_A/T|high|nb_pol_1|left_unitig_length_86|right_unitig_length_49|left_contig_length_878|right_contig_length_49|C1_74|C2_0|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1
> cggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctaggcagcgcaacaacgcaacagctcgaggtgttcttcgcagagaaaccgcacgtccagttctaacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatgagtctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtACTAATAGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCGGTCCATacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccg
> >SNP_lower_path_2|P_1:30_A/T|high|nb_pol_1|left_unitig_length_86|right_unitig_length_49|left_contig_length_878|right_contig_length_49|C1_0|C2_86|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1
> cggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctaggcagcgcaacaacgcaacagctcgaggtgttcttcgcagagaaaccgcacgtccagttctaacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatgagtctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtACTAATAGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCGGTCCATacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccg
> >SNP_higher_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_469|right_unitig_length_261|left_contig_length_469|right_contig_length_458|C1_0|C2_114|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1
> cggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctagGCAGCGCAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCAGTTCTAacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatgactctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtactaatagggccgggctacatgttaactacaaggctataacctattgatgacccggtccatacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccg
> >SNP_lower_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_469|right_unitig_length_261|left_contig_length_469|right_contig_length_458|C1_110|C2_0|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1
> cggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctagGCAGCGCAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCAGTTCTAacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatgactctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtactaatagggccgggctacatgttaactacaaggctataacctattgatgacccggtccatacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccg

Best regards ;-)