gatk-3.8/public/java
Mauricio Carneiro d16cb68539 Updated and more thorough version of the BadCigar read filter
* No reads with Hard/Soft clips in the middle of the cigar
   * No reads starting with deletions (with or without preceding clips)
   * No reads ending in deletions (with or without follow-up clips)
   * No reads that are fully hard or soft clipped
   * No reads that have consecutive indels in the cigar (II, DD, ID or DI)

 Also added systematic test for good cigars and iterative test for bad cigars.
2012-08-17 17:05:27 -04:00
..
config Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
src Updated and more thorough version of the BadCigar read filter 2012-08-17 17:05:27 -04:00
test Updated and more thorough version of the BadCigar read filter 2012-08-17 17:05:27 -04:00