Following reviewers comments the command line interface has been simplified.
All extra strict validations are performed by default (as before) and the
user has to indicate which one he/she does not want to use with --validationTypeToExclude.
Before he/she was able to indicate the only ones to apply with --validationType but that has been scrapped out.
Stories:
- https://www.pivotaltracker.com/story/show/68725164
Changes:
- Removed validateType argument.
- Improved documentation.
- Added some warnning log message on suspicious argument combinations.
Tests:
- ValidateVariantsIntegrationTest#*
More concretelly Picard's strict VCF validation does not like that there is alternative alleles that are not participating in any genotype call across samples.
This is an issue with GVCF in the single-sample pipeline where this is certainly expected with <NON_REF> and other relative unlikely alleles.
To solve this issue we allow the user to exclude some of the strict validations using a new argument --validationTypeToExclude. In order to avoid the validation
issue with GVCF the user needs to add the following to the command line: '--validationTypeToExclude ALLELES'
Story:
https://www.pivotaltracker.com/story/show/68725164
Changes:
- Added validateTypeToExclude argument to ValidateVariants walker.
- Implemented the selective exclusion of validation types.
- Added new info and improved existing documentation of the ValidateVariants walker.
Tests:
- ValidateVariantsIntegrationTest#testUnusedAlleleError
- ValidateVariantsIntegrationTest#testUnusedAlleleFix
Previously it required you to create a single sample VCF and then to pass that in to the tool, but
Geraldine convinced me that this was a pain for users (because they usually have multi-sample VCFs).
Instead now you can pass in a multi-sample VCF and specify which sample's genotypes should be used
for the IUPAC encoding. Therefore the argument changed from '--useIUPAC' to '--use_IUPAC_sample NA12878'.
Stories:
https://www.pivotaltracker.com/story/show/66263868
Bug:
The problem was due to the way we were calculating the fix penalty of a large deletion or insertion. In this case we calculate the alignment likelihood of the portion
or read or haplotype deletion as the penalty of that deletion/insertion without going through the full pair-hmm process. For large events this resulted in a 0 in
in linear scale computations that ins transformed into an infinity in log scale.
Changes:
- Change to use log10 scale for calculate those penalties.
- Minor addition of .gitignore to hide ./public/external-example/target which is generated by the building process.
- SamPairUtils migrated in Picard r1737
- Revert IndelRealigner changes made in commit 4f4b85
-- Those changes were based on Picard revision 1722 to net/sf/picard/sam/SamPairUtil.java
-- Picard revision 1723 reverts these changes, so we also revert to match
Story:
- https://www.pivotaltracker.com/story/show/67601310
Change:
- Unless recover-danging-heads is active, the threading starting location policy is the original one. i.e. just at already existing unique kmer vertices.
Tests:
- HaplotypeCallerIntegrationTest#testMissingKeyAlternativeHaplotypesBugFix
-- SmartSiteIterator needs to know to span across Chunks when iterating by polling the Chunk list
-- Added KB test to test for this case
-- Removed the maxSites argument in ExtractConsensusSites because it is counterintuitive and not useful.
This is currently my leading suspect for the cause of the
intermittent NoSuchElementException errors on master, since
the maven surefire plugin seems unable to handle errors in
TestNG DataProviders without blowing up.
This test is not, as I had initially thought, the cause of the
maven errors. Our master branch is failing intermittently
regardless of whether this test is enabled or disabled.
This reverts commit 45fc9ff515eec8d676b64a04fb34fb357492ff84.
These tests pass individually and as part of complete test suite runs,
but cause an intermittent NoSuchElementException in maven when the
unit tests are run on their own. Disabling these tests until the
cause of this can be identified.
This test passes when run individually, as part of the commit tests, or as
part of the package tests. However, when running the unit tests in isolation
it causes maven/surefire to throw a NoSuchElementException.
This is clearly a maven/surefire bug or configuration issue. I will re-enable
this test on a branch as Khalid and I try to work through it.
Valentin Ruano-Rubio
Laura Gauthier
Eric Banks
Geraldine Van der Auwera
Khalid Shakir
droazen
jmthibault79
MauricioCarneiro
Ryan Poplin