Commits · c6f3940396bb4ac91da3ebd6fb0dd4532f76031e · Klinische Genetica / capture-lumc / vtools · GitLab

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Dec 03, 2019
- Merge branch 'testing' into devel · c6f39403
  van den Berg authored 5 years ago
  
  c6f39403
Dec 02, 2019
- Make sure the parent output folder exists · 7b50bc24
  van den Berg authored 5 years ago
  7b50bc24
Nov 26, 2019
- Merge branch 'testing' into 'devel' · 335925d5
  van den Berg authored 5 years ago
  335925d5
Nov 25, 2019
- The discordant VCF file is gzipped · e6309163
  van den Berg authored 5 years ago
  
  e6309163
- Use get_header_type to determine if RGQ is present · e62c9164
  van den Berg authored 5 years ago
  
  e62c9164
- Write to stats file instead of using print · 257600ce
  van den Berg authored 5 years ago
  
  257600ce
- Update min-depth to integer · 3c789431
  van den Berg authored 5 years ago
  3c789431
- tox automatically calls pip install '.' · d6779d59
  van den Berg authored 5 years ago
  
  d6779d59
Nov 19, 2019
- Write discordant variants to valid vcf file · b151b5db
  van den Berg authored 5 years ago
  
  b151b5db
Nov 12, 2019
- Merge branch 'testing' of git.lumc.nl:klinische-genetica/capture-lumc/vtools into testing · c76505da
  van den Berg authored 5 years ago
  
  c76505da
- Add support for RQC annotations to be used as GQ · d37115cc
  van den Berg authored 5 years ago
  d37115cc
Nov 04, 2019
- Add test cases for missing ALT in call vcf · 955802ec
  van den Berg authored 5 years ago
  955802ec
Oct 25, 2019
- Fixed bug with partial no calls · 0ab4c701
  van den Berg authored 5 years ago
  0ab4c701
- Add test for a rare bug with partial variants · bbb226bc
  van den Berg authored 5 years ago
  
  bbb226bc
- Add test cases where the ALT and REF differ · b63f7cb0
  van den Berg authored 5 years ago
  b63f7cb0
Oct 24, 2019
- Add support for parital calls · f9aadab3
  van den Berg authored 5 years ago
  
  f9aadab3
- Extract genotypes to support conflicting ALT calls · d6a8d0e5
  van den Berg authored 5 years ago
  
  d6a8d0e5
- Add check for non-diploid calls · 8786b514
  van den Berg authored 5 years ago
  8786b514
- Clean up test data · 05ade21d
  van den Berg authored 5 years ago
  
  05ade21d
- Add check for decomposed calls · 86bd745b
  van den Berg authored 5 years ago
  86bd745b
- Convert single use fixtures to regular tests · 3479a77a
  van den Berg authored 5 years ago
  
  3479a77a
- Add check for phased calls · 9e87861b
  van den Berg authored 5 years ago
  9e87861b
Oct 23, 2019
- Compare allele genotypes directly · fb075df9
  van den Berg authored 5 years ago
  fb075df9
Oct 22, 2019
- Merge branch 'testing' of git.lumc.nl:klinische-genetica/capture-lumc/vtools into testing · 2fda84f6
  van den Berg authored 5 years ago
  
  2fda84f6
- Do not use '-' as a stand in for stdout · 51eb6db9
  van den Berg authored 5 years ago
  
  51eb6db9
- Update .gitlab-ci.yml · 6a0b5cf5
  Ruben Vorderman authored 5 years ago
  
  6a0b5cf5
- Update .gitlab-ci.yml · 7b191690
  Ruben Vorderman authored 5 years ago
  
  7b191690
- Update .gitlab-ci.yml · 3a634675
  Ruben Vorderman authored 5 years ago
  
  3a634675
- Add comment for decomposed variants · 34801b91
  van den Berg authored 5 years ago
  
  34801b91
- Add test cases for truncated call vcf · c2d64d27
  van den Berg authored 5 years ago
  c2d64d27
- Properly count 'no call' sites · 895f7541
  van den Berg authored 5 years ago
  895f7541
Aug 27, 2019
- Add tests for quality and depth filter · 336a5a94
  van den Berg authored 5 years ago
  
  336a5a94
- Add testcase for every field in the output · 26922303
  van den Berg authored 5 years ago
  
  26922303
- Add gatk test file and rename test script · 368545f7
  van den Berg authored 5 years ago
  
  368545f7
- Add real test for site_concordancy · 65623106
  van den Berg authored 5 years ago
  
  65623106
Aug 26, 2019
- Add dummy test with tox · fdaf72ab
  van den Berg authored 5 years ago
  
  fdaf72ab
- Add option to filter records based on read depth · d5dd7f1a
  van den Berg authored 5 years ago
  
  d5dd7f1a
Aug 14, 2019
- Merge pull request #1 from LUMC/devel · ec9bba93
  Redmar van den Berg authored 5 years ago
  ec9bba93
Aug 08, 2019
- Write stats to stdout by default · 70d3ac7f
  van den Berg authored 5 years ago
  70d3ac7f
Jul 31, 2019
- Reword usage message for --discordant · 5b51b794
  van den Berg authored 5 years ago
  
  5b51b794