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Mauricio Carneiro f73ad1c2e2 Bugfix/Rewrite: Algorithm to determine adaptor boundaries 
The algorithm wasn't accounting for the case where the read is the reverse strand and the insert size is negative.

    * Fixed and rewrote for more clarity (with Ryan, Mark and Eric).
    * Restructured the code to handle GATKSAMRecords only
    * Cleaned up the other structures and functions around it to minimize clutter and potential for error.
    * Added unit tests for all 4 cases of adaptor boundaries.
 		2011-12-20 17:48:39 -05:00
..
R Protect ourselves when iteration is present but there's only a single iteration in queueJobReport.R 2011-12-19 10:08:38 -05:00
c Reinitialize random seed in the bwa bindings from the fixed seed stored in the 2011-07-22 13:41:53 -04:00
chainFiles Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
doc Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
java Bugfix/Rewrite: Algorithm to determine adaptor boundaries 2011-12-20 17:48:39 -05:00
packages Revved Picard to incorporate tfennell's AsyncSAMFileWriter. 2011-12-06 10:37:42 -05:00
perl Update to the bindings for liftOverVCF.pl (to -V from -B) 2011-09-15 15:33:09 -04:00
scala General improvements to Queue 2011-12-20 14:05:09 -05:00
testdata Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00