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3 Commits (c1eaf7cf81e8606a43b3cc43b2d2b4eb255667ea)

Author SHA1 Message Date
Mauricio Carneiro 731a463415 Updated IntegrationTests with new adaptor clipper 
phew!
 2011-12-20 17:48:52 -05:00
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
David Roazen 3c9497788e Reorganized the codebase beneath top-level public and private directories, 
removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
 2011-06-28 06:55:19 -04:00