LohseLab/gIMble

Issues

• When running gimble parse: Samples in SAMPLE_FILE not found in BED_FILE

  #142 opened 6 months ago by kuangzhuoran
  2

• Not enough blocks in Gimble datastore.

  #138 opened 7 months ago by ala98412
  11

• Obtaining delta B estimates

  #140 opened 7 months ago by juanitagutierrez
  1

• Uninformative message: Not enough blocks in datastore

  #139 opened 7 months ago by GertjanBisschop
  1

• Reduce memory usage of the block tally step

  #137 opened 7 months ago by GertjanBisschop
  0

• gimble -info cannot handle minimal sample size

  #135 opened 8 months ago by KLohse
  0

• the unit for recombination rate and methods to estimate global parameter confidence interval

  #133 opened 9 months ago by XieHongX
  1

• too much memory needed during gimble windows

  #131 opened 10 months ago by XieHongX
  1

• choosing the region of the genome for analysis

  #128 opened 10 months ago by XieHongX
  2

• gimbleprep can't create filtered vcf

  #127 opened 10 months ago by juanitagutierrez
  1

• gimble makegrid usage

  #114 opened 10 months ago by juanitagutierrez
  9

• How to interpret the number of anomaly counts?

  #122 opened a year ago by MengLu-flw
  0

• Query and Delete option usage added in manual

  #97 opened a year ago by gotouerina
  0

• How can I query simulation results？

  #119 opened a year ago by hrluo93
  3

• Simulating individual blocks is prohibitively slow

  #117 opened a year ago by A-J-F-Mackintosh
  2

• Problem with llvmlite while running gimble parse

  #101 opened a year ago by pierrebarry
  2

• Missing dependencies when Running 'gimble parse'

  #99 opened a year ago by hrluo93
  13

• Issues with parsing step - even with example_input

  #104 opened a year ago by juanitagutierrez
  5

• carve out gimble-preprocess

  #103 opened a year ago by GertjanBisschop
  1

• making gimble available through conda-forge

  #100 opened a year ago by GertjanBisschop
  2

• naming

  #102 opened a year ago by GertjanBisschop
  0

• KeyError: 'blocks/Contig1/1/starts'

  #98 opened a year ago by gotouerina
  3

• Manual update required

  #96 opened a year ago by gotouerina
  2

• Do block region overlap?

  #95 opened a year ago by gotouerina
  1

• gimble info error

  #91 opened a year ago by gotouerina
  5

• Problems with sync'ing populations

  #74 opened 2 years ago by DRL
  2

• gIMble query error

  #76 opened 2 years ago by DRL
  1

• test_math tests need fixing

  #77 opened 2 years ago by DRL
  0

• preprocess produces empty BED for single-sample VCF

  #72 opened 2 years ago by DRL
  0

• preprocess can't handle directory prefixes for temp folder

  #73 opened a year ago by DRL
  1

• gimble query error

  #92 opened a year ago by gotouerina
  3

• One chromesome test failed, I really suggest split preprocess step of VCF, BAM, and FASTA into individual step

  #89 opened a year ago by gotouerina
  4

• An optimization in index identification

  #88 opened a year ago by gotouerina
  4

• Example file wanted

  #90 opened a year ago by gotouerina
  1

• gimble windows instruction error

  #87 opened a year ago by gotouerina
  1

• Could you write a shell scripts for preprocess step1 and do not write files into .tmp folder?

  #85 opened a year ago by gotouerina
  10

• parse step error

  #86 opened a year ago by gotouerina
  1

• how many mutations per bases

  #84 opened a year ago by DRL
  0

• Preprocess step occurs error

  #83 opened a year ago by aaannaw
  1

• Can the input file vcf(SNP) only be generated with freebayes?

  #81 opened a year ago by kuangzhuoran
  3

• equations with synced Ne values should result in simpler equations

  #68 opened a year ago by GertjanBisschop
  0

• make globally declared sage variables local

  #64 opened 2 years ago by GertjanBisschop
  1

• adapt simulate to work with msprime 1.0

  #66 opened 2 years ago by GertjanBisschop
  1

• Add ability to restrict calculating ETPs to observed cases

  #67 opened 2 years ago by GertjanBisschop
  1

• labelling of lnCls/results (gridsearch/optimize)

  #71 opened 2 years ago by DRL
  0

• changes to simulate with new config

  #69 opened 2 years ago by GertjanBisschop
  2

• Query the probabilities of mutuples for a given model and parameters

  #79 opened 2 years ago by A-J-F-Mackintosh
  2

• Terminated during Infering coverage levels from BAM files

  #80 opened 2 years ago by aaannaw
  1

• optimize

  #65 opened 3 years ago by DRL
  0

• optimize output

  #63 opened 4 years ago by GertjanBisschop
  1