VCFGenotypeWriterAdapter now explicitly uses the passed reference base instead of deriving it from VatriantContext (in SNP mode as well!), other writers simply ignore that additional argument.
SimpleIndelCalculationModel now WORKS (or rather, it does produce calls :) )
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unicode quote characters embedded in it. These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset. Fixed.
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from a stream (see Vitter 1985). Thanks to Eric and Andrey for the pointer.
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sorting and merging interval lists, and creating RODs from intervals. This
gives Doug the ability to keep using our interval list parsing code when
sorting intervals on our behalf.
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Most of the changes occur in GenomeAnalysisEngine.java and GenomeLocParser.java:
-- parseIntervalRegion and parseGenomeLocs combined into parseIntervalArguments
-- initializeIntervals modified
-- some helper functions deprecated for cleanliness
Includes new set of unit tests, GenomeAnalysisEngineTest.java
New restrictions:
-- all interval arguments are now checked to be on the reference contig
-- all interval files must have one of the following extensions: .picard, .bed, .list, .intervals, .interval_list
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a caveat: for anyone asking for all of the ROD's back from the RefMetaDataTracker (if your not using the facilities to get the track by name), you'll now be getting back a collection of GATKFeature objects. This object will contain the track name, and a method for getting the underlying object (getUnderlyingObject()), which will be the traditional RodVCF, rodDbSNP, etc. This layer is needed so we can integrate Tribble tracks (which don't natively have names). Calls that ask for RODs by name will still get back the traditional reference ordered data objects (RodVCF, rodDbSNP, etc).
Sorry for the inconvenience! More changes to come, but this is by far the largest (as has the greatest effect on end users).
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of public interfaces. This won't be the last Picard patch, but it should be the last big one.
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Picard patch, including move of some of the Picard private classes we use to Picard public.
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quicker runtime. Making change as minimal as possible to avoid conflicts
with BT's incoming patch.
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This is *NOT* an ideal implementation. One day when we have lots of free time (or a greater desire), we will implement this correctly and sophisticatedly using all the power of JEXL. For now, though, this will have to do.
Docs coming tonight.
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1. Annotations can now be "decorated" with any arbitrary interface description - not just standard or experimental.
2. Users can now not only specify specific annotations to use, but also the interface names from #1. Any number of them can be specified, e.g. -G Standard -G Experimental -A RankSumTest.
3. These same arguments can be used with the Unified Genotyper for when it calls into the Annotator.
4. There are now two types of annotations: those that are applied to the INFO field and those that are applied to specific genotypes (the FORMAT field) in the VCF (however, I haven't implemented any of these latter annotations just yet; coming soon).
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now do the minimum validation rather than the more rigorous only-within-the-contig-bounds
header validation.
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+ -L all now walks over all intervals
+ if a -L argument is passed with a .list extension, and file does not exist, returns a \
File Not Found error instead of "bad interval" error. We plan to soon revisit interval \
lists and generate a concrete list of filenames, so this is likely temporary.
+ Error is thrown if the start position on an interval is higher number than the end position.
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-Check that base and qual strings are the same lengths
-Fix one more bug in the clipper.
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weisburd
aaron
ebanks
hanna
asivache
bthomas
depristo
rpoplin