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  • 4ab1fa249b Simplification and commenting. hanna 2009-03-11 22:58:22 +0000
  • 4af5e54411 Replay changes that were obliterated by the move. hanna 2009-03-11 21:43:31 +0000
  • c3f74f46c4 Oops! Restore changes that were clobbered during the move. hanna 2009-03-11 21:26:29 +0000
  • ec8a555cae Added a dependency on JUnit to the playground aaron 2009-03-11 21:21:07 +0000
  • 5031875507 Move to new directory organization. hanna 2009-03-11 20:58:01 +0000
  • 25ddc0f5ea Skeleton of new directory structure. hanna 2009-03-11 20:05:05 +0000
  • 6a0a45950e First swipe at autogeneration of the classpath. hanna 2009-03-11 19:44:02 +0000
  • 3c605e95cb First inklings of a unified allele caller! andrewk 2009-03-11 17:54:24 +0000
  • 150610d63d Move to ivy for dependency management. hanna 2009-03-11 17:14:04 +0000
  • 393400deea Documented TraveralEngine depristo 2009-03-10 22:09:12 +0000
  • 716af47dd5 Added NullWalker module (do nothing). Added SingleSampleGenotyper module (old-school single sample genotyping). jmaguire 2009-03-10 21:26:07 +0000
  • 6b8650b0c0 Patch up scripts to use new directory structure. hanna 2009-03-10 19:54:46 +0000
  • ea0a826f8f Clean up 3rd party dependencies. hanna 2009-03-10 19:34:00 +0000
  • e4bde58353 Fix for inaccurate and misleading timing information, now only prints estimated time to completion when the location flag isn't set depristo 2009-03-10 14:59:42 +0000
  • 17c94a8c5c make build.xml work from within the java directory. jmaguire 2009-03-06 22:58:12 +0000
  • e938dbda47 Check for the existence of the module name and return error rather than throwing an exception if not found. andrewk 2009-03-04 00:15:35 +0000
  • a81a1bdbb4 Minor bug fixed to progress meter depristo 2009-03-02 22:19:39 +0000
  • 851e1df072 reconciled TraversalEngine depristo 2009-03-02 21:51:25 +0000
  • 46c3f1a0ac Support for progress tracking during parsing of SAM files. depristo 2009-03-02 21:49:08 +0000
  • 49a84c965e Added basic GenomeLoc class Support for operating on any location in genome (albeit slowly) Improvements to dbSNP support depristo 2009-03-02 18:18:48 +0000
  • 63f8d82e36 Fix for ROD in TraversalEngine depristo 2009-03-02 02:46:34 +0000
  • b19e4b502b Continuing to expand support for ROD. These edits add a program, PrepareROD, that sorts and prepares RODs for consumption by the analysis TK. depristo 2009-03-01 23:32:23 +0000
  • fd447d7c1d Renamed Empty to Count methods in analysisTK depristo 2009-03-01 23:31:33 +0000
  • a5c76f7666 Renamed Empty to Count methods in analysisTK depristo 2009-03-01 23:31:23 +0000
  • 0ee2375292 Working on reference ordered data; added build.xml for ant! depristo 2009-03-01 18:27:32 +0000
  • f64f3e2d90 Phase II support for generic reference order data set parsing. Can read GFF and dbSNP files correctly. Traversal engine now supports keeping moving window of reference ordered data along with the locus iterator. Tested by walking through a sam file keeping track of the dbSNP positions encountered -- they definitely look right... depristo 2009-02-28 20:47:48 +0000
  • dee840efa5 Moved out of java/src depristo 2009-02-28 17:52:34 +0000
  • 69e9a467d0 Wrong directory depristo 2009-02-28 17:52:16 +0000
  • bd1fadd9fe Validating walker for lots of bam files depristo 2009-02-28 17:05:08 +0000
  • e892c3fd98 Shouldn't be in the tree depristo 2009-02-28 15:31:17 +0000
  • 17aabb38f9 Basic reorganization of tree depristo 2009-02-28 15:28:56 +0000
  • c9f0161e24 Initial support for reference ordered data sets depristo 2009-02-27 17:07:57 +0000
  • bb55947e2e Better organization of AnalysisTK modules depristo 2009-02-26 22:15:41 +0000
  • 5e3adc76fc Initial Analysis toolkit depristo 2009-02-26 21:50:51 +0000
  • 59083a47d5 Initial Analysis toolkit depristo 2009-02-26 21:50:29 +0000