Commit Graph

5 Commits (40a247e86089c8ea9e25f1dcf28f4ff6f6e2c31a)

Author SHA1 Message Date
Guillermo del Angel c78b0eee3a Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller. 2012-04-17 14:22:48 -04:00
Khalid Shakir b80d407dc7 No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
Other minor cleanup.
2011-10-27 14:17:07 -04:00
Khalid Shakir fac9932938 Embedding gsalib source and queueJobReport R scripts in the dist and package jars.
Moved gsalib and queueJobReport.R to embeddable namespaced locations.
Updated packager dependencies/dir to add an @includes which filters the embedded fileset.
RScriptExecutor can now JIT compiles the gsalib.
RScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG.
Refactored ProcessController and IOUtils from Queue to Sting Utils.
Added more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count.
Replaced uses of some IOUtils with Apache Commons IO.
ShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown.
Better QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().
2011-10-24 15:58:34 -04:00
David Roazen bd8bb93811 Split RScriptExecutorUnitTest into public and private test classes.
We can't have a public test that depends on both public and private
code/data -- the new release system needs to do public-only tests,
and will catch this sort of thing.
2011-10-14 20:04:42 -04:00
Mark DePristo 1ceb020fae UnitTests for RScript 2011-08-27 10:50:05 -04:00