Eric Banks 6df43f730a Fixing ReadBackedPileup to represent mapping qualities as ints, not (signed) bytes. ... Having them as bytes caused problems for downstream programmers who had data with high MQs.		2013-07-23 23:47:15 -04:00
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src/org/broadinstitute/sting	Fixing ReadBackedPileup to represent mapping qualities as ints, not (signed) bytes.	2013-07-23 23:47:15 -04:00
test/org/broadinstitute/sting	Last feature request from Reich/Paavo labs: the allSitePLs feature in UG worked but not quite filled requirements. What's needed is the ability to have all 10 PLs for EVERY site, regardless of whether they are variant or not. Previous version only emitted the 10 PLs in reference sites. Problem is that, if all PLs are emitted in all sites and every single site is quad-allelic (only way to have the PLs printed out in a valid way) then the ability to filter variants and to use the INFO fields may be compromised.	2013-07-18 12:54:52 -04:00