gatk-3.8/public
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
..
R Add warning message about ratios in variantQCreport, give ratio for MAF > 10% 2012-04-25 12:22:32 -04:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
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 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
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages build system overhaul 2012-05-17 15:16:29 -04:00
perl Update to the bindings for liftOverVCF.pl (to -V from -B) 2011-09-15 15:33:09 -04:00
scala Removed old GATKReport code and moved the new stuff in its place. 2012-05-18 01:44:31 -04:00
testdata Extensive refactoring of the GATKReports. This was a beast. 2012-05-18 01:11:26 -04:00