Ryan Poplin 5bb0693888 Bug fix for HC GGA mode. Shouldn't try to add an indel into the haplotype if that haplotype already contains the event of interest. Misc minor assembly param changes. Turning off capping of base qualities by base indel qualities until we can evaluate that change.		2012-06-28 12:57:51 -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	Bug fix for HC GGA mode. Shouldn't try to add an indel into the haplotype if that haplotype already contains the event of interest. Misc minor assembly param changes. Turning off capping of base qualities by base indel qualities until we can evaluate that change.	2012-06-28 12:57:51 -04:00
test	Refactored parsing of Rod/IntervalBinding. Queue S/G now uses all interval arguments passed to CommandLineGATK QFunctions including support for BED/tribble types, XL, ISR, and padding.	2012-06-27 01:15:22 -04:00