gatk-3.8/public/java/test/org/broadinstitute/sting
Khalid Shakir e57cd78bba Killed two more resource leakers that ignored requests to close wrapped file pointers, and added Unit Tests for each.
This bug will happen in all adapter/wrapper classes that are passed a resource, and then in their close method they ignore requests to close the wrapped resource, causing a leak when the adapter is the only one left with a reference to the resource.

Ex:

public Wrapper getNewWrapper(File path) {
  FileStream myStream = new FileStream(path); // This stream must be eventually closed.
  return new Wrapper(myStream);
}

public void close(Wrapper wrapper) {
  wrapper.close(); // If wrapper.close() does nothing, NO ONE else has a reference to close myStream.
}
2012-05-21 15:41:56 -04:00
..
alignment Reinitialize random seed in the bwa bindings from the fixed seed stored in the 2011-07-22 13:41:53 -04:00
commandline Added ability to specify arguments in files via -args/--arg_file 2011-10-24 15:58:34 -04:00
gatk Killed two more resource leakers that ignored requests to close wrapped file pointers, and added Unit Tests for each. 2012-05-21 15:41:56 -04:00
jna When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter. 2011-12-16 18:09:25 -05:00
utils New annotation for indels that describe if they're STR's and their characteristics. If an indel is a STR, 3 fields are added to INFO: STR (boolean), RU = repeat unit (String), RPA = number of repetitions per allele. So, for example, if ATATAT* context gets changed to ATAT and ATATATAT, then RU=AT and RPA=3,2,4. Will be made standard annotation shortly. Added unit tests for new functionality. Pending: refactor VariantContextUtils.isRepeat() to unify code, and fix VariantEval functionality. 2012-05-17 15:28:19 -04:00
BaseTest.java Revert bad part of last commit that shouldn't have been pushed 2012-05-10 10:41:08 -04:00
MD5DB.java Merged bug fix from Stable into Unstable 2011-10-13 18:02:06 -04:00
MedianUnitTest.java Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably. 2012-03-05 08:28:42 -05:00
StingTextReporter.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
WalkerTest.java Rev'ing Tribble from 53 to 94 2012-05-03 07:31:47 -04:00