- Adapted to get the trio information from the SampleDB (i.e. from Pedigree file (ped)) => Multiple trios can be passed as argument
- Mendelian violations and trio phasing possibilities are pre-calculated and stored in Maps. => Runtime is ~3x faster
- Genotype combinations possible only given two MVs are now given a squared MV prior (e.g. 0/0+0/0=>1/1 is given 10^-16 prior if the MV prior is 10^-8)
- Corrected bug: In case the best genotype combination is Het/Het/Het, the genotypes are now set appropriately (before original genotypes were left even if they weren't Het/Het/Het)
- Basic reporting added:
-- mvf argument let the user specify a file to report remaining MVs
-- When the walker ends, some basic stats about the genotype reconfiguration and phasing are output
Known problems:
- GQ is not recalculated even if the genotype changes
Possible improvements:
- Phase partially typed trios
- Use standard Allele/Genotype Classes for the storage of the pre-calculated phase
-- 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
The test was successful -- the packaging error was detected and
prevented from propagating out into the binary/source releases.
This reverts commit 8f2a1462d94ce50fb7c1b1d0c40142b109e9c38e.
This is to test the ability of the new release system
to detect the kinds of packaging errors we couldn't
detect before (in this case, missing codecs). If all goes
as expected, "GSA-Stable: Release" will fail, preventing
the binary release and github from getting updated, while
"GSA-Stable: All Tests" and all of the other old test plans
will pass.
Will revert this in a bit -- if the system works as it should,
our users will never see it until after it's been reverted.
Mauricio Carneiro
Laurent Francioli
Christopher Hartl
Mark DePristo
Eric Banks
Ryan Poplin
Menachem Fromer
David Roazen