Eric Banks 40618ac471 A bunch of BQSR changes: 1) by default we do not emit indel quals, but they can be turned on with --enable_indel_quals. 2) We check whether or not we are running in Lite mode (not done yet) and if so and the user is trying to recalibrate indels, we throw a User Error (not supported). 3) Like v1 we now allow the user to set the qual value below which we don't recalibrate (this was the remaining source of differences in the v1 vs. v2 plots).		2012-07-17 10:52:43 -04:00
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arguments	A bunch of BQSR changes: 1) by default we do not emit indel quals, but they can be turned on with --enable_indel_quals. 2) We check whether or not we are running in Lite mode (not done yet) and if so and the user is trying to recalibrate indels, we throw a User Error (not supported). 3) Like v1 we now allow the user to set the qual value below which we don't recalibrate (this was the remaining source of differences in the v1 vs. v2 plots).	2012-07-17 10:52:43 -04:00
contexts	Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.	2012-06-15 15:55:03 -04:00
datasources	Added a --no_indel_quals argument that when used with -BQSR inhibits the writing of base insertion and base deletion quality tags.	2012-07-04 01:22:20 -04:00
downsampling	Make downsampler classes themselves generic (instead of just the Downsampler interface)	2012-06-13 16:43:39 -04:00
examples	As promised in the release notes for 1.6, I am removing the old deprecated genotyping framework revolving around the misordering of alleles and have moved the fixed version in its place in preparation for release 1.7 (or 2.0?).	2012-05-01 16:18:24 -04:00
executive	Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.	2012-04-17 14:22:48 -04:00
filters	Bug fix in BadCigar read filter for index out of bounds exception when used with a bam file that contains unmapped reads.	2012-05-21 16:46:59 -04:00
io	BCF2 cleanup	2012-06-26 15:28:33 -04:00
iterators	Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.	2012-06-15 15:55:03 -04:00
phonehome	Capture the class of the exception in GATKRunReport	2012-03-14 12:16:22 -04:00
refdata	BCF2 cleanup	2012-06-26 15:28:33 -04:00
report	Fix a NullPointerException that could occur in DoC if the user requested an interval summary but never provided a -L argument. This situation is now checked for and a UserError thrown instead. Also (after a great struggle) pushing some old VR3 code into the central repository which had been improperly pushed (e.g. with rsync rather than git push) into my repository on the server, and never migrated to unstable. In addition, minor convenience function added to the GATKReport that allows an entire row to be added, and a walker that parses out annotations from a tool called VariantEffectPredictor and summarizes annotations across transcripts, and consensus annotations.	2012-06-19 07:50:13 -04:00
resourcemanagement	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
samples	Added function to get founders IDs in SampleDB	2012-04-25 12:49:36 -04:00
traversals	Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.	2012-06-15 15:55:03 -04:00
walkers	Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2012-07-17 00:32:53 -04:00
CommandLineExecutable.java	Old -B syntax is long gone at this point. Safe to remove the warning.	2012-04-02 22:25:16 -04:00
CommandLineGATK.java	OutOfMemory exceptions are User Errors	2012-04-02 22:46:56 -04:00
DownsampleType.java	…
DownsamplingMethod.java	…
GenomeAnalysisEngine.java	A bunch of BQSR changes: 1) by default we do not emit indel quals, but they can be turned on with --enable_indel_quals. 2) We check whether or not we are running in Lite mode (not done yet) and if so and the user is trying to recalibrate indels, we throw a User Error (not supported). 3) Like v1 we now allow the user to set the qual value below which we don't recalibrate (this was the remaining source of differences in the v1 vs. v2 plots).	2012-07-17 10:52:43 -04:00
ReadMetrics.java	Counts of records failing filters are displayed sorted	2011-10-06 18:42:26 -07:00
ReadProperties.java	Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.	2012-06-15 15:55:03 -04:00
WalkerManager.java	Removed support for RMD in @Requires and @Allows	2011-08-03 15:36:55 -04:00
package-info.java	…