This is a tool that we use internally validate the ReduceReads development. I think it should be
private. There is no need to improve docs.
[delivers #54703398]
* add overall walker GATKDocs
* add explanation for skip parameter and make it advanced
* reverse the logic on exculding unmapped reads for clarity
* fix read length calculation to no longer include indels
ps: I am not sure how useful this walker is (I didn't write it) but the skip logic is poor and
calculates the entire statistic for the reads it is eventually going to skip. This would be an easy
fix, but only worth our time if people actually use this.
The update contains:
1. documentation changes for VariantContext and Allele (which used to discuss the now obsolete null allele)
2. better error messages for VCFs containing complex rearrangements with breakends
3. instead of failing badly on format field lists with '.'s, just ignore them
Also, there is a trivial change to use a more efficient method to remove a bunch of attributes from a VC.
Delivers PT#s 59675378, 59496612, and 60524016.
Basically, it does 3 things (as opposed to having to call into 3 separate walkers):
1. merge the records at any given position into a single one with all alleles and appropriate PLs
2. re-genotype the record using the exact AF calculation model
3. re-annotate the record using the VariantAnnotatorEngine
In the course of this work it became clear that we couldn't just use the simpleMerge() method used
by CombineVariants; combining HC-based gVCFs is really a complicated process. So I added a new
utility method to handle this merging and pulled any related code out of CombineVariants. I tried
to clean up a lot of that code, but ultimately that's out of the scope of this project.
Added unit tests for correctness testing.
Integration tests cannot be used yet because the HC doesn't output correct gVCFs.
-You can now add "minValue", "maxValue", "minRecommendedValue", and "maxRecommendedValue" attributes
to @Argument annotations for command-line arguments
-"minValue" and "maxValue" specify hard limits that generate an exception if violated
-"minRecommendedValue" and "maxRecommendedValue" specify soft limits that generate a warning if violated
-Works only for numeric arguments (int, double, etc.) with @Argument annotations
-Only considers values actually specified by the user on the command line, not default values
assigned in the code
As requested by Geraldine
Renamed it CalculateGenotypePosteriors.
Also, moved the utility code to a proper utility class instead of where Chris left it.
No actual code modifications made in this commit.
In general, test classes cannot use 3rd-party libraries that are not
also dependencies of the GATK proper without causing problems when,
at release time, we test that the GATK jar has been packaged correctly
with all required dependencies.
If a test class needs to use a 3rd-party library that is not a GATK
dependency, write wrapper methods in the GATK utils/* classes, and
invoke those wrapper methods from the test class.
The tests that access the knowledge base are interfering with the basic
ability to run the unit/integration test suite to completion -- these
few tests often take hours to complete.
Created a new class of test ("KnowledgeBaseTest") that runs separately
from the unit/integration test suite, with corresponding build target.
A new bamboo plan will be set up to run these tests independently so
that they don't interfere with unit/integration testing.
With this change, plus the recent changes to the parallel test runner,
unit/integration test suite runtime should be back down to ~30 minutes
on average.
-Run with -W 240 to give tests more time to complete and hopefully
stop jobs from getting killed with TERM_RUNLIMIT
-Switch to /humgen/gsa-hpprojects for test working directories, since
/broad/hptmp has been unacceptably slow lately
Time to create test working directory, 12/5/13:
/broad/hptmp: 19 minutes
/humgen/gsa-hpprojects: 4 minutes
Previously, we would strip out the PLs and AD values since they were no longer accurate. However, this is not ideal because
then that information is just lost and 1) users complain on the forum and post it as a bug and 2) it gives us problems in both
the current and future (single sample) calling pipelines because we subset samples/alleles all the time and lose info.
Now the PLs and AD get correctly selected down.
While I was in there I also refactored some related code in subsetDiploidAlleles(). There were no real changes there - I just
broke it out into smaller chunks as per our best practices.
Added unit tests and updated integration tests.
Addressed reviews.
Eric Banks
Mauricio Carneiro
David Roazen
Jacob Silterra
Valentin Ruano Rubio
Joel Thibault
Bertrand
Geraldine Van der Auwera
amilev