ce55ba98f4
Don't try to left align indels in unmapped reads (which for some reason can still have CIGARs) because the ref context is null.
2012-08-29 15:01:11 -04:00
677babf546
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
08fab49d30
Added function to get bases from the current base forward in the window in ReferenceContext
2012-04-06 16:07:46 -04:00
533c283783
Deprecating AlignmentContext.getExtendedEventPileup(). At this point the only walkers left with any relaiance on extended events are Guillermo's pooled code (he'll update soon) and the Pileup walker. David, I'll leave that last one for you (it should be easy). We can now officially rip the extended event code from the engine.
2012-03-30 10:37:14 -04:00
a12bc63e5c
Get rid of support for bams without sample information in the read groups. This hidden option wasn't being used anyways because it wasn't hooked up properly in the AlignmentContext.
2011-11-05 23:54:28 -04:00
e89ff063fc
GATKSAMRecord refactor
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The GATK engine will now provide a GATKSAMRecord to all tools which incorporates the functionality used by the GATK to the bam file (ReadGroups, Reduced Reads, ...).
* No tools should create SAMRecord anymore, use GATKSAMRecord instead *
2011-11-03 15:43:26 -04:00
54331b44e9
New way of looking at the size of a pileup: there's a physical number of elements in the data structure and there's a representative depth of coverage (since a reduced read represents depth >= 1). The size() method has been removed because its meaning is ambiguous. Updated several annotations and the UG engine to make use of the representative depths.
2011-11-02 12:47:30 -04:00
30d23942b1
Renamed ReadBackedPileup getXSampleName() functions to getXSample
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-- now that we don't have Sample objects floating around we don't have to have all of the Name extensions on our functions
2011-09-30 10:02:57 -04:00
2a0cd556d3
Further cleanup of Sample
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-- Cleaned up interface functions in GAE
-- Added Walker.getSampleDB() function which is an easier option for tools to get the samples db
2011-09-29 10:34:51 -04:00
e76f381628
Moved sample package from DataSources to gatk, and renamed it samples
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-- All associated changes to the codebase are just header updates
2011-09-29 09:57:15 -04:00
9992c373be
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
2011-07-17 20:29:58 -04:00
3c9497788e
Reorganized the codebase beneath top-level public and private directories,
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removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
2011-06-28 06:55:19 -04:00
Eric Banks
Mark DePristo
Mauricio Carneiro
David Roazen