zjshi/gt-pro

Issues

• Question about optimization step for multiple sequencing samples

  #63 opened 2 months ago by fallinwind
  0

• new environment run

  #62 opened 4 months ago by AlsoATraveler
  0

• lmer_index and mmer_bloom

  #61 opened 4 months ago by AlsoATraveler
  0

• GT_pro optimize terminate called after throwing an instance of 'std::length_error' what(): vector::_M_default_append

  #60 opened a year ago by HaimAshk
  0

• Extract sck-mer sequences

  #59 opened a year ago by DaomingWang1
  0

• Segmentation fault when run gt-pro build

  #58 opened a year ago by alienzj
  1

• Optimize.py does not allow for outdir specification

  #50 opened 2 years ago by sophiejwalton
  3

• GT-Pro genotype fails on reads with ambiguous bases other than "N"

  #57 opened 2 years ago by bsmith89
  0

• 0 SNPs reported for longer reads (undocumented maximum read length?)

  #49 opened 2 years ago by bsmith89
  8

• support paired-end reads?

  #55 opened 2 years ago by nick-youngblut
  2

• `GT_Pro parse` => IndexError: string index out of range

  #56 opened 2 years ago by nick-youngblut
  1

• `assert os.path.isdir(in_dir)` => no helpful error message

  #54 opened 2 years ago by nick-youngblut
  2

• MUMmer4 output reformatting code

  #52 opened 2 years ago by nick-youngblut
  5

• list dependency versions

  #51 opened 2 years ago by nick-youngblut
  5

• Error writing file (cl 1067) seems to be result of g++ version

  #48 opened 2 years ago by bsmith89
  2

• Optimize database runs but does not produce any ouputs

  #47 opened 2 years ago by thapasz
  1

• conda?

  #38 opened 4 years ago by wwood
  2

• build database

  #46 opened 3 years ago by Alice-yyt
  13

• Build customize database problem

  #43 opened 3 years ago by wjj666
  25

• Error writing output xxx_gtpro__20190723_881species.tsv.gz cl 1067

  #42 opened 3 years ago by yejunbin
  5

• GT-pro optimize returned Error

  #44 opened 3 years ago by boaty
  9

• GT-pro optimize issues

  #45 opened 3 years ago by wangbaikui
  7

• GT-pro build Error : Multispecies kmers present in input

  #41 opened 3 years ago by majunyeong
  3

• verify if specific SNP/gene is in database

  #39 opened 3 years ago by ramiroricardo
  1

• %{in} not using just base name

  #36 opened 4 years ago by nick-youngblut
  1

• make sure to output the last SNP for each input file

  #13 opened 4 years ago by boris-dimitrov
  2

• Can't download resources - ERROR 403: Forbidden

  #40 opened 4 years ago by LeCray
  1

• Possible to create custom databases?

  #37 opened 4 years ago by wwood
  1

• gtp_parse.py error

  #33 opened 4 years ago by snayfach
  1

• aws tools

  #32 opened 4 years ago by snayfach
  2

• gtp_parse.py output columns

  #35 opened 4 years ago by nick-youngblut
  4

• Assertion `db_data != MAP_FAILED' failed

  #34 opened 4 years ago by nick-youngblut
  1

• Search multiple compressed gzip'ed files

  #3 opened 5 years ago by snayfach
  2

• No output for sample

  #4 opened 6 years ago by snayfach
  5

• Do genotype counts indicate #s of matched reads or # of matched kmers?

  #5 opened 6 years ago by snayfach
  1

• Indicate haplotypes in snp_dict

  #6 opened 6 years ago by snayfach
  1

• wget snp_dict.tsv error

  #1 opened 6 years ago by snayfach
  4

• no chrom in output?

  #2 opened 6 years ago by snayfach
  6