Khalid Shakir 9801dd114f Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped ... The GATK -L unmapped is for GenomeLocs with SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, not SAMRecord.getReadUnmappedFlag() Previously unmapped flag reads in the last bin were being printed while also seeking for the reads without a reference contig.		2012-04-27 09:58:38 -04:00
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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	Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped	2012-04-27 09:58:38 -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	Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped	2012-04-27 09:58:38 -04:00
BaseTest.java	Bug fix: BaseTest change shouldn't have been committed, first cleanup of SNP pool code (more to follow)	2012-04-03 18:55:52 -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	New way to handle exceptions in multi-threaded GATK	2012-04-13 09:23:33 -04:00