Commits · 09197f5706f8b03c3e3d88e15418ebf9b7c2d96c · Thomas Weber / Mosaicatcher Update · GitLab

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Jun 17, 2018
- Fixed small typo · 09197f57
  Sascha Meiers authored 6 years ago
  
  09197f57
- Hopefully fixed bug that messed up `None` bins during counting of observed reads · 5c2e6b1f
  Sascha Meiers authored 6 years ago
  
  5c2e6b1f
- Deprecated warning for old normalization · 1d37914e
  Sascha Meiers authored 6 years ago
  
  1d37914e
- Clean up old entries · 1d52cf23
  Sascha Meiers authored 6 years ago
  
  1d52cf23
Jun 16, 2018
- Unified logging · 58983392
  Sascha Meiers authored 6 years ago
  
  58983392
Jun 15, 2018
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · 93e8d1c5
  Sascha Meiers authored 6 years ago
  
  93e8d1c5
- Fixed integer problem during mosaiClassifier · 53625fc7
  Sascha Meiers authored 6 years ago
  
  53625fc7
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · 81e158c2
  Sascha Meiers authored 6 years ago
  
  81e158c2
- Use more recent SV plot script + do not black list counts based initially · 3ca02902
  Sascha Meiers authored 6 years ago
  
  3ca02902
- Fixing segment coordinates during SV classification · b21cacc7
  Sascha Meiers authored 6 years ago
  
  b21cacc7
- solve off-by-one error in segment breakpoint. Those are reported in 0-based coordinates · 8916a913
  Sascha Meiers authored 6 years ago
  
  8916a913
Jun 14, 2018
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · 9dd6405d
  Sascha Meiers authored 6 years ago
  
  9dd6405d
- Use more recent version of qc.R · 44c28d26
  Sascha Meiers authored 6 years ago
  
  44c28d26
Jun 13, 2018
- removed analysis folder · 2cf6a35d
  Maryam Ghareghani authored 6 years ago
  
  2cf6a35d
Jun 12, 2018
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · 2351e570
  Sascha Meiers authored 6 years ago
  
  2351e570
- Enable new segmentation · 6e5c73f6
  Sascha Meiers authored 6 years ago
  
  6e5c73f6
- Add new way of normalization (right at the start). Remove old one · f07cf7eb
  Sascha Meiers authored 6 years ago
  
  f07cf7eb
- added a directory containing scripts for the analysis of pipeline results · a565b288
  maryamghr authored 6 years ago
  
  a565b288
Jun 05, 2018
- removed expectation-level normalization by default · f6123fc7
  Sascha Meiers authored 6 years ago
  
  f6123fc7
- New and better function to annotate expected and observed counts. Ignores bins · 09070990
  Sascha Meiers authored 6 years ago
  
  09070990
Jun 04, 2018
- Further fixes to read counting · 8873314a
  Sascha Meiers authored 6 years ago
  
  8873314a
- Replaced old function for counting reads and fixed the new one · 0cabe6c6
  Sascha Meiers authored 6 years ago
  
  0cabe6c6
- New (hoefully faster and more correct) function to add read counts and expectation · 2bea9646
  Sascha Meiers authored 6 years ago
  
  2bea9646
- More realistic count calculation - fixing bugs · 53017894
  Sascha Meiers authored 6 years ago
  
  53017894
- Ignore counts from None bins both during counting and in expectation! · e56f887b
  Sascha Meiers authored 6 years ago
  
  e56f887b
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · 74d6ab6d
  Sascha Meiers authored 6 years ago
  
  74d6ab6d
- Include log-likelihood-ratio filter and normalization · c6ab4003
  Sascha Meiers authored 6 years ago
  
  c6ab4003
May 30, 2018
- Add more info in plot titles · e8bcaae9
  Sascha Meiers authored 6 years ago
  
  e8bcaae9
- added a function for translating haplotype code to genotype class · a8fa0baa
  maryamghr authored 6 years ago
  
  Unverified
  
  a8fa0baa
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · e4ea25e5
  maryamghr authored 6 years ago
  
  e4ea25e5
- Added normalization file for 50 kb based on HGSVC trio coverage. Enable 50kb in pipeline · 2b6b6b06
  Sascha Meiers authored 6 years ago
  
  2b6b6b06
- adding an Rscript for computing jump probs · c6a62d21
  maryamghr authored 6 years ago
  
  c6a62d21
- IMPORTANT UPDATE: don't really *force* bi-allelic, just give a prior aginst other states · db955384
  Sascha Meiers authored 6 years ago
  
  db955384
- Propagate information about scalars into the final table (normalization) · 480a3cdf
  Sascha Meiers authored 6 years ago
  
  480a3cdf
- Adjust scalar to length of segment · 3d0c2f7c
  Sascha Meiers authored 6 years ago
  
  3d0c2f7c
- Added normalization on the level of NB expectation · 00d026b3
  Sascha Meiers authored 6 years ago
  
  00d026b3
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · bd2b4630
  Sascha Meiers authored 6 years ago
  
  bd2b4630
- fixed color in plot script · 4da3c7f0
  Sascha Meiers authored 6 years ago
  
  4da3c7f0
May 29, 2018
- added function to estimate mappability in user defined bins · ed1c2fe7
  daewoooo authored 6 years ago
  
  ed1c2fe7
May 26, 2018
- Fixed plot error · d52951cc
  Sascha Meiers authored 6 years ago
  
  d52951cc