This module was causing failures during the release packaging tests. After discussing with Khalid, we've decided to disable it for now until a fix can be developed.
…Pipeline upadte the script (for RNA pipeline and comment out RR from it)
Add flag to GenotypeConcordance to output sites; add error checking to CalculateGenotypePosteriors
…ic variants with wrong number of ACs -- throws UserException; added tests in PosteriorLikelihoodsUtilsUnitTests Add error handling to CalculateGenotypePosteriors for cases where MLEAC>AN; add tests in PosteriorLikelihoodsUtilsUnitTests Add unit tests to confirm that CalculateGenotypePosteriors has the ability to switch genotypes for four cases
…t genotypes (to System.out) Revised ConcondanceMetrics tests to adapt to change Added comments to PosteriorLikelihoodsUtils
Log to STDERR instead of STDOUT
Maven doesn't currently create the necessary private/testdata symlinks when private is not being built. This script is a temporary workaround to allow manual creation when doing public/protected-only testing.
- order if statements and error message in increasing severity
…aplotypes Added a more efficient implementation of the KBest haplotype finder code...
…Test -created a Pivotal ticket to eventually redesign this test
…ode (CONT.) Changes: 1. Addressed review comments on new K-best haplotype assembly graph finder. 2. Generalize KBestHaplotypeFinder to deal with multiple source and sink vertices. 3. Updated test to use KBestHaplotypeFinder instead of KBestPaths 4. Retired KBestPaths to the archive. 5. Small improvements to the code and documentation.
…ode. Story: https://www.pivotaltracker.com/story/show/66238286 Changes: 1. Created a new k-best haplotype search implementation in class KBestHaplotypeFinder. 2. Changed HC code to use the new implementation. This seems to fix the original problem without causing significant changes in outputs using some empirical data test cases 3. Moved haplotype's cigar calculation code from Path to CigarUtils; need that in order to gain independence from Path in some parts of the code. In any case that seems like a more natural location for that functionality.
Added code to retrieve dangling heads from the read threading graph (pre...
… the graph. Added unit tests to cover this case. Delivers PT#66690470.
…previously we were rescuing just the tails). The purpose of this is to be able to call SNPs that fall at the beginning of a capture region (or exon). Before, the read threading code would only start threading from the first kmer that matched the reference. But that means that, in the case of a SNP at the beginning of an exome, it wouldn't start threading the read until after the SNP position - so we'd lose the SNP. For now, this is still very experimental. It works well for RNAseq data, but does introduce FPs in normal exomes. I know why this is and how to fix it, but it requires a much larger fix to the HC: the HC needs to pass all reads and bases to the annotation engine (like UG does) instead of just the high quality ones. So for now, the head merging is disabled by default. As per reviewer comments, I moved the head and tail merging code out into their own class.
…gs_for_ami Add the capability to the N-cigar splitter to also hard-clip off overhan...
Moving Reduce Reads to the archive.
…hangs based on observed split positions. We use a "manager" to keep track of observed splits and previous reads. This can be extended/modified in the future to try to salvage those overhangs instead of hard-clipping them and/or try other possible strategies. Added unit tests and more integration tests.
The GATK now fails with a user error if you try to run with a reduced bam. (I added a unit test for that; everything else here is just the removal of all traces of RR)
…individual_filters Add an option to AssessNA12878 to be able to ignore one or more specific...
…fic filters (instead of either all or none). Useful in conjunction with ROCCurveNA12878 in determining a good VQSR cut.
Attempting to limit GC during Maven tests
…4436 Added command line checks for duplicate files in ROD lists
-- Keep a list of processed files in ArgumentTypeDescriptor.getRodBindingsCollection -- Throw user exception if a file name duplicates one that was previously parsed -- Throw user exception if the ROD list is empty -- Added two unit tests to RodBindingCollectionUnitTest
Fixes test counts, and full paths of diff commands
… from any directory.
…am_patches Ks pd queuelogdir gatherbam patches