-- Moved previously inner class to MRUCachingSAMSequenceDictionary, and unit test to 100% coverage
-- Fully document all functions in GenomeLocParser
-- Unit tests for things like parsePosition (shocking it wasn't tested!)
-- Removed function to specifically create GenomeLocs for VariantContexts. The fact that you must incorporate END attributes in the context means that createGenomeLoc(Feature) works correctly
-- Depreciated (and moved functionality) of setStart, setStop, and incPos to GenomeLoc
-- Unit test coverage at like 80%, moving to 100% with next commit
-- The new version is roughly 2x faster than the previous version. The key here was to cleanup the workflow for validateGenomeLoc and remove the now unnecessary synchronization blocks from the CachingSequencingDictionary, since these are now thread local variables
-- #resolves https://jira.broadinstitute.org/browse/GSA-724
-- All functions tested. In the testing / review I discovered several bugs in the ActiveRegion routines that manipulate reads. New version should be correct
-- Enforce correct ordering of supporting states in constructor
-- Enforce read ordering when adding reads to an active region in add
-- Fix bug in HaplotypeCaller map with new updating read spans. Now get the full span before clipping down reads in map, so that variants are correctly placed w.r.t. the full reference sequence
-- Encapsulate isActive field with an accessor function
-- Make sure that all state lists are unmodifiable, and that the docs are clear about this
-- ActiveRegion equalsExceptReads is for testing only, so make it package protected
-- ActiveRegion.hardClipToRegion must resort reads as they can become out of order
-- Previous version of HC clipped reads but, due to clipping, these reads could no longer overlap the active region. The old version of HC kept these reads, while the enforced contracts on the ActiveRegion detected this was a problem and those reads are removed. Has a minor impact on PLs and RankSumTest values
-- Updating HaplotypeCaller MD5s to reflect changes to ActiveRegions read inclusion policy
Please check that your commit hook is properly pointing at ../../private/shell/pre-commit
Conflicts:
public/java/test/org/broadinstitute/variant/VariantBaseTest.java
-Moved some of the more specialized / complex VariantContext and VCF utility
methods back to the GATK.
-Due to this re-shuffling, was able to return things like the Pair class back
to the GATK as well.
One of the fixes was critical: SlidingWindow was not converting between global and relative positions correctly.
Besides not being correct, it was resulting in a massive slow down of the RR traversal.
That fix definitely breaks at least one of the integration tests, but it's not worth changing md5s now because I'll be
changing things all over RR for the next few days, so I am going to let that test fail indefinitely until I can confirm
general correctness of the tool.
a) Add option to stratify CalibrateGenotypeLikelihoods by repeat - will add integration test in next push.
b) Simulator to produce BAM files with given error profile - for now only given SNP/indel error rate can be given. A bad context can be specified and if such context is present then error rate is increased to given value.
c) Rewrote RepeatLength covariate to do the right thing - not fully working yet, work in progress.
d) Additional experimental covariates to log repeat unit and combined repeat unit+length. Needs code refactoring/testing
With LegacyLocusIteratorByState deleted, the legacy downsampling implementation
was already non-functional. This commit removes all remaining code in the
engine belonging to the legacy implementation.
-- New algorithm will only try to create an active region if there's at least maxREgionSize + propagation distance states in the list. When that's true, we are guaranteed to actually find a region. So this algorithm is not only truly correct but as super fast, as we only ever do the search for the end of the region when we will certainly find one, and actually generate a region.
-- Helped ID more bugs in the ActivityProfile, necessitating a new algorithm for popping off active regions. This new algorithm requires that at least maxRegionSize + prob. propagation distance states have been examined. This ensures that the incremental results are the same as you get reading in an entire profile and running getRegions on the full profile
-- TODO is to remove incremental search start algorithm, as this is no longer necessary, and nicely eliminates a state variable I was always uncomfortable with
-- Now records the position of the current locus, as well as that of the last read. Necessary when passing through regions with no reads. The previous version would keep accumulating empty active regions, and never discharge them until end of traversal (if there was no reads in the future) or until a read was finally found
-- Protected a call to logger.debug with if ( logger.isDebugEnabled()) to avoid a lot of overhead in writing unseen debugger logging information
-- Allows us to avoid doing a lot of misc. work to set up the genotype when we don't have any data to genotype. Valuable in the case where we are passing through large regions without any data
- directionality only influences 'chop' operation (since split will maintain all bases of the original read)
- added directional unit test
GSATDG-25 #resolved
- Fixed shell glob limitation that was failing license updates on big commits
- Hook will now force user to re-commit after updating the licenses (pre-commit hook can't update and commit in the same process)
- Moved all scripts to bash/zsh
- Separated the license utilities in a separate python module to avoid copying code
GSATDG-28 #resolve
Eric Banks
Mark DePristo
Mauricio Carneiro
David Roazen
Ami Levy-Moonshine
Guillermo del Angel
Ryan Poplin
Tad Jordan