Alec Wysoker 0369f93b24 GATK changes to conform to Tribble refactoring as part improving Tabix support in Tribble (among other things). ... 1. Enable on-the-fly indexing for vcf.gz. 2. Handle on-the-fly indexing where file to be indexed is not a regular file, thus index should not be created. 3. Add method setProgressLogger to all SAMFileWriter implementations. 4. Revved picard to 1.109.1722 5. IndelRealigner md5s change because the MC tag is added to records now. Fixed up and signed off by ebanks.		2014-03-17 11:56:22 -04:00
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gatk-protected	GATK changes to conform to Tribble refactoring as part improving Tabix support in Tribble (among other things).	2014-03-17 11:56:22 -04:00
pom.xml	Update pom versions to mark the start of GATK 3.1 development	2014-03-06 00:05:58 -05:00