This change is urgently required for production, which is why it's going into Stable+Unstable
instead of just Unstable.
The keys for the SnpEff version and command header lines in the VCF file output by
VariantAnnotator (OriginalSnpEffVersion and OriginalSnpEffCmd) are intentionally
different from the keys for those same lines in the SnpEff output file (SnpEffVersion
and SnpEffCmd), so that output files from VariantAnnotator won't be confused
with output files from SnpEff itself.
-- Previously, on the fly indices didn't have dictionary set on the fly, so the GATK would read, add dictionary, and rewrite the index. This is now fixed, so that the on the fly index contains the reference dictionary when first written, avoiding the unnecessary read and write
-- Added a GenomeAnalysisEngine and Walker function called getMasterSequenceDictionary() that fetches the reference sequence dictionary. This can be used conveniently everywhere, and is what's written into the Tribble index
-- Refactored tribble index utilities from RMDTrackBuilder into IndexDictionaryUtils
-- VCFWriter now requires the master sequence dictionary
-- Updated walkers that create VCFWriters to provide the master sequence dictionary
Now the functions getRefCoordSoftUnclippedStart and getRefCoordSoftUnclippedEnd will return getUnclippedStart if the read is all contained within an insertion. Updated the contracts accordingly. This should give the same behavior as the GenomeLocParser now.
-- No functional changes (my algorithm wouldn't work)
-- Major structural cleanup (returning more basic data structures that allow us to development new algorithm)
-- Unit tests for the efficiency of interval partitioning
The ClippingOp clip cigar function would run into a endless loop if the parameter were out of the reads range, I stopped the bug.
* There is no check to make sure the read coordinate are covered by the read though
When Hard clipping to interval, I added a check for deletions.
NOTE: method works for NA12878 WEx but needs to be more thoroughly tested/optimized
After discussing this with Mark, it seems clear that the old version of the
VariantEval FunctionalClass stratification is preferable to this version.
By reverting, we maintain backwards compatibility with legacy output files
from the old GenomicAnnotator, and can add SnpEff support later without
breaking that backwards compatibility.
This reverts commit b44acd1abd9ab6eec37111a19fa797f9e2ca3326.
This is a temporary and hopefully short-lived solution. I've modified
the FunctionalClass stratification to stratify by effect impact as
defined by SnpEff annotations (high, moderate, and low impact) rather
than by the silent/missense/nonsense categories.
If we want to bring back the silent/missense/nonsense stratification,
we should probably take the approach of asking the SnpEff author
to add it as a feature to SnpEff rather than coding it ourselves,
since the whole point of moving to SnpEff was to outsource genomic
annotation.
-Rewrote SnpEff support in VariantAnnotator to support the latest SnpEff release (version 2.0.2)
-Removed support for SnpEff 1.9.6 (and associated tribble codec)
-Will refuse to parse SnpEff output files produced by unsupported versions (or without a version tag)
-Correctly matches ref/alt alleles before annotating a record, unlike the previous version
-Correctly handles indels (again, unlike the previous version
David Roazen
Mauricio Carneiro
Mark DePristo
Christopher Hartl
Roger Zurawicki
Guillermo del Angel
Menachem Fromer
Eric Banks
Ryan Poplin