Mauricio Carneiro 32ee2c7dff Refactored the compression interface per sample in ReduceReadsa ... The CompressionStash is now responsible for keeping track of all intervals that must be kept uncompressed by all samples. In general this is a list generated by a tumor sample that will enforce all normal samples to abide. - Updated ReduceReads integration tests - Sliding Window is now using the CompressionStash (single sample). DEV-104 #resolve #time 3m		2012-10-17 16:40:40 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Refactored the compression interface per sample in ReduceReadsa	2012-10-17 16:40:40 -04:00
test	Bringing CMI changes into the main GATK repo.	2012-10-17 15:23:19 -04:00