passed in as a Tribble SAM text feature. If the generated pileup contains a valid set of reads according to
the downsampling rules, the test passes.
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as walker attributes or from the command-line. Not ready yet! Downsampling/deduping
works in a general sense, but this approach has not been completely optimized or validated.
Use with caution.
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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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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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ReferenceContext: constructor does not throw an excepion anymore when locus is not fully contained inside the window. So now we can have a reference context associated with a locus such that the window/actual bases do not cover the whole locus. Scary. I am not sure I like this...
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simplification of some of the locus traversal code.
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support batched intervals in a single shard, but intervals are not yet compressed into a single
shard.
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Also deleted the FixBamSortOrder package that isn't used anymore.
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up being outside the reference. Force the blowup elsewhere.
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shard for cases when the index file isn't available. Works for the case in question, but is not
guaranteed to work in general. Will be replaced once the new sharding system comes online.
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in GenomeAnalysisTK.jar. Still no support for actually displaying the archived javadoc. Also change the approach
to providing package javadocs: retired the deprecated package.html file in favor of Java1.5-style package-info.java.
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relationship between these two classes needs to be rethought; see JIRA
GSA-207.
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all the updated classes now make use of new SeekableRodIterator instead of RODIterator. RODIterator class deleted. This batch makes only trivial updates to tests dictated by the change in the ROD system interface. Few less trivial updates to follow. This is a partial commit; a few walkers also still need to be updated, hold on...
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The user is warned if a locus exceeds this threshold, and no more reads are added.
Also CombineDup walker had an incorrect package name.
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from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.
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rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.
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depristo
hanna
aaron
asivache