-- removed intermiate functions. Now only original version and best optimized new version remain
-- Moved general artificial read backed pileup creation code into ArtificialSamUtils
-- Uses mayOverlapRoutine in ReadUtils
-- Attempts to be smart when doing overlap calculation, to avoid unnecessary allocations
-- PileupElement now comparable (sorts on offset than on start)
-- Caliper microbenchmark to assess performance
-- Creates all combinatinos of overlapping and non-overlapping read pair pileups in all orientations and first/second pairings to validate fragment detection.
This commit contains:
- IntronLossGenotyper is brought into its current incarnation
- A couple of simple new filters (ReadName is super useful for debugging, MateUnmapped is useful for selecting out reads that may have a relevant unaligned mate)
- RFA now matches my current local repository. It's in flux since I'm transitioning to the new traversal type.
+ the triggering read stash pilot required me to change the scope of some of the variables in the ReadClipping code, private -> protected. Those are all the changes there.
- MendelianViolation restored to its former glory (and an annotator module that uses the likelihood calculation has been added)
+ use this rather than a hard GQ threshold if you're doing MV analyses.
- Some miscellaneous QScripts
-- all of the methods in the class must be synchronized or the internal state can be inconsistent with the contract invariant when entering the class in a non-synchronized method, even when that method doesn't care about the object's internal state
We can't have a public test that depends on both public and private
code/data -- the new release system needs to do public-only tests,
and will catch this sort of thing.
The public integration test VariantContextIntegrationTest was dependent on the
private walker TestVariantContextWalker. Moved this walker to public/java/test
(NOT public/java/src, since this walker is only used by the test suite) to avoid
errors during public-only tests.
-- MD5 db had spelling error; fixed
-- Bug in AlignmentUtils resulted in some bases not being color space corrected. The integration test caught the change, and it's clear that the new version is correct, as the prev. version was not considering the last the N qualities for reads with a ND operation.
-- SimpleTimer is now threadsafe using synchronized method keywords
-- Bug fix for alignmentToByteArray() where the N case was refPos++ not the now correct refPos += elementLength
Mark DePristo
Christopher Hartl
Eric Banks
Mauricio Carneiro
Ryan Poplin
David Roazen