3 Commits (4a84ff4fcecadc2db57d265876bee32d034e6fc4)

Author	SHA1	Message	Date
David Roazen	d2f3d6d22f	Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)" ... This reverts commit 075c56060e0ffcce39631693ef39cf5f8c3a4d5a.	2012-09-10 15:52:39 -04:00
Menachem Fromer	0b717e2e2e	Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)	2012-09-10 15:32:41 -04:00
Christopher Hartl	d795437202	- New UserExceptions added for when ReadFilters or Walkers specified on the command line are not found. When -rf xxxx cannot find the class corresponding to xxxx, all read filters are printed in a better formatted way, with links to their gatk docs. ... - VariantAnnotatorEngine changed to call genotype annotations even if pilups and allele -> likelihood mappings are not present. Current genotype annotations altered to check for null pilupes and null mappings.	2012-09-04 16:41:44 -04:00