Commits · 5225e199ea7b1b886ad292adf958b17aa608144b · SVdetection / cnvpipelines

Dec 04, 2018
- - delly ex is now mine · 5225e199
  Thomas Faraut authored 6 years ago
  
  - get_regions to exclude uses not mad
  5225e199
Oct 23, 2018
- removing self._rerun_tools(tools) · b4182d5e
  Thomas Faraut authored 6 years ago
  
  b4182d5e
Oct 19, 2018
- adding batch id to record id in parse · 9408978e
  Thomas Faraut authored 6 years ago
  
  9408978e
Sep 27, 2018
- - implementing a pure pysam bacoverage instead of the pysamstats implementation · cd6a9624
  Thomas Faraut authored 6 years ago
  
  - window width for the detection of high coverage is now 500bp - simplifying gzip of pindel files
  cd6a9624
Aug 23, 2018
- upgrading lib · 5923e4f3
  Thomas Faraut authored 6 years ago
  
  5923e4f3
Aug 21, 2018
- test · 6ba7f9d6
  Thomas Faraut authored 6 years ago
  
  6ba7f9d6
- . and PASS are now PASS · 7919032e
  Thomas Faraut authored 6 years ago
  
  7919032e
Aug 06, 2018
- Make script executable · 2dd074ab
  Floreal Cabanettes authored 6 years ago
  
  2dd074ab
- Try fix: move script in file and run it with shell · 9705f19b
  Floreal Cabanettes authored 6 years ago
  
  9705f19b
- removing duplicate calls from pindel · d9dd88e1
  Thomas Faraut authored 6 years ago and Floreal Cabanettes committed 6 years ago
  
  d9dd88e1
Aug 03, 2018
- . is now PASS in the FILTER column of any filtered vcf · 794b0dd5
  Thomas Faraut authored 6 years ago
  
  794b0dd5
Jul 23, 2018
- Fix genomestrip rerun · dc13d884
  Floreal Cabanettes authored 6 years ago
  
  dc13d884
Jul 20, 2018
- Fix crash · 5163583f
  Floreal Cabanettes authored 6 years ago
  
  5163583f
- Fix chromosomes with no reads for lumpy · 96f3d4d0
  Floreal Cabanettes authored 6 years ago
  
  96f3d4d0
Jul 19, 2018
- Fix insert size distro: change to the 100000 first reads instead of reads of a... · 754a702c
  Floreal Cabanettes authored 6 years ago
  
  Fix insert size distro: change to the 100000 first reads instead of reads of a region to fix bug if regions is composed only by N
  754a702c
Jul 06, 2018
- - change filter to noFilter (by default filtering is done) · cea5dca8
  Thomas Faraut authored 6 years ago
  
  - simplify gcmaskbed and lcmaskebed (erferencebundle) - Update submodule snakecnv/lib to latest
  cea5dca8
Jul 02, 2018
- only pep8 compliance · 7b6ee7cd
  Thomas Faraut authored 6 years ago
  
  7b6ee7cd
Jun 14, 2018
- Fix existing folders on rerun · 18c8e335
  Floreal Cabanettes authored 6 years ago
  
  18c8e335
- Fix command · 2375fbe3
  Floreal Cabanettes authored 6 years ago
  
  2375fbe3
- Multicopy CNVs: sh -> py · efbf8706
  Floreal Cabanettes authored 6 years ago
  
  efbf8706
- Remove unused sh · 906c4967
  Floreal Cabanettes authored 6 years ago
  
  906c4967
- Fix rights · 64e95457
  Floreal Cabanettes authored 6 years ago
  
  64e95457
- Remove unused sh · 2fd0b5ad
  Floreal Cabanettes authored 6 years ago
  
  2fd0b5ad
- Preprocess move to python · 10832e0e
  Floreal Cabanettes authored 6 years ago
  
  10832e0e
- Fix genomestrip script · 26255499
  Floreal Cabanettes authored 6 years ago
  
  26255499
- Remove deprecaded sh file · be24ffa4
  Floreal Cabanettes authored 6 years ago
  
  be24ffa4
- Replace genomestrip sh by a python executor · d87430fb
  Floreal Cabanettes authored 6 years ago
  
  d87430fb
Jun 01, 2018
- Add links to popsim binaries · 2291404c
  Floreal Cabanettes authored 6 years ago
  
  2291404c
May 24, 2018
- adding maxConcurrentRun · 91d9bc6f
  Thomas Faraut authored 6 years ago
  
  91d9bc6f
May 16, 2018
- add doFilter switch to parse, dfault to False in contrast to previous implementation · 2620e274
  Thomas Faraut authored 6 years ago
  
  2620e274
- empty gaps file now treated in a correct manner · 5d283195
  Thomas Faraut authored 6 years ago
  
  5d283195
May 09, 2018
- getChomLength bug corrected; pep8 for referencebundle · 06ddcb30
  Thomas Faraut authored 6 years ago
  
  06ddcb30
May 03, 2018
- bug correction bnd_merge due to duplication of start and en in DellyRecord · 77700be1
  Thomas Faraut authored 6 years ago
  
  77700be1
May 02, 2018
- Fix CNV pipeline · 8c64d91c
  Floreal Cabanettes authored 6 years ago
  
  8c64d91c
Apr 27, 2018
- Port to pysam >= 0.14 · 2cc768ee
  Floreal Cabanettes authored 6 years ago
  
  2cc768ee
- Restore previous code: fix has been done in svtyper · bd7962eb
  Floreal Cabanettes authored 6 years ago
  
  bd7962eb
- Fix genotype svtyper rule · 7325ca13
  Floreal Cabanettes authored 6 years ago
  
  7325ca13
- Fix genotype svtyper rule · 5d52f9cf
  Floreal Cabanettes authored 6 years ago
  
  5d52f9cf
- Fix genotype svtyper rule · fab1d9a0
  Floreal Cabanettes authored 6 years ago
  
  fab1d9a0
- Fix svtyper launcher · 7fae3604
  Floreal Cabanettes authored 6 years ago
  
  7fae3604

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