- Brought over exact AF estimation from branch (which is now dead). Exact model is default in UnifiedGenotyperV2.
- Implemented completely new genotyping algorithm given best AF estimate using dynamic programming, which in theory should be better than both greedy search and any HWE-based genotyper.
- Integrated and added new Dindel likelihood estimation model.
- Corrected annotators that would call readBasePileup: since we can be annotating extended events, best way is to interrogate context for kind of pileup and either readBasePileup or readExtendedEventPileup.
All changes above except last one are still in playground since they require more testing.
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where, when the system can't find a plugin of the correct name, the system
prefers to crap all over itself and throw an unintelligible NullPointerException
rather than displaying an intelligent error.
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the empty list. Score another victory for the integration tests.
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argument. Brought it back, and added an integrationtest to make sure it
stays around.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4390 348d0f76-0448-11de-a6fe-93d51630548a
the pileup at the next alignment start is large, we don't add as many of those
incoming reads as we should. No integration tests were affected.
Thanks, Chris!
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-- getToolkit().subContextFromSampleProperty(): filters a VariantContext to genotypes that come from samples that have a given property value
-- getToolkit().getSamplesWithProperty(): gets all samples with a given property
-- getToolkit().getSamplesFromVariantContext(): sample objects that are referenced by name in a VariantContext
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This will allow other programs like Queue to reuse the functionality.
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pieces of core that depend on playground. Most of these have been eliminated by
(temporarily) promoting Aaron's report system to core in this checkin. I'll
follow up with other changes in separately.
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The GAE half has all the walker specific code. The new "Abstract" GAE has the rest of the logic.
More refactoring to come, with the end goal of having a tool that other java analysis programs (Queue, etc.) can use to read in genomic data.
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Thanks to Ryan for identifying the problem.
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is. Required to fix bug ZjhCJAdwhtFq1x54ZlmlN8pFNcbrRpdJ and similar. We
might want to change this particular case to a ReviewedStingException after
we gain a bit more experience with it.
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mOVsxGfDiiSMxVs2PPTVjzYTVbizlD6e
f9kUHUADFsZ0LiTGxRL5zPmq9kZcA4cQ
8eGHWJFAlBVmgxwPi3sMd1RmiN2PwHOf
iLhvHWveypKb2F8vKS5irHylc3pYvlOb
HDttXKUMEVoPrvVeWrH7E0htxYyNydMx
plus a bit of cleanup of custom exceptions in the sharding system.
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Added a pipeline java bean and YAML utility to serialize java beans.
Added a getFirehosePipelineYaml.sh that can pull firehose data into the pipeline yaml file format.
Updated the fullCallingPipeline.q to begin using the pipeline yaml file format for bams and reference.
More changes to come as this code gets tested out in the fullCallingPipeline.
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Changed integration tests, adding the -NO_HEADER argument, for walkers that previously did not include the command-line
arg headers.
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delangel
hanna
fromer
rpoplin
ebanks
kshakir
chartl
bthomas
aaron
corin
depristo