QScript accessor to QSettings to specify a default runName and other default function settings.
Because log files are no longer pseudo-random their presense can be used to tell if a job without other file outputs is "done". For now still using the log's .done file in addition to original outputs.
Gathered log files concatenate all log files together into the stdout.
InProcessFunctions now have PrintStreams for stdout and stderr.
Updated ivy to use commons-io 2.1 for copying logs to the stdout PrintStream. Removed snakeyaml.
During graph tracking of outputs the Index files, and now BAM MD5s, are tracked with the gathering of the original file.
In Queue generated wrappers for the GATK the Index and MD5s used for tracking are switched to private scope.
Added more detailed output when running with -l DEBUG.
Simplified graphviz visualization for additional debugging.
Switched usage of the scala class 'List' to the trait 'Seq' (think java.util.ArrayList vs. using the interface java.util.List)
Minor cleanup to build including sending ant gsalib to R's default libloc.
-- You can create (and drop the old) GATK_LOG table with the setupDB command
-- You can load data into the database with the loadToDB command
Currently I'm pushing up all of the GATK logs into the new MySQL server setup for the gsa group. Details of the server are in the code, for those interested. All of this is part of my experimentation with Tableau for visualizing GATK run logs.
To support this, refactored code that computes consensus alleles. To ease merging of mulitple alt alleles, we create a single vc for each alt alleles and then use VariantContextUtils.simpleMerge to carry out merging, which takes care of handling all corner conditions already. In order to use this, interface to GenotypeLikelihoodsCalculationModel changed to pass in a GenomeLocParser object (why are these objects to hard to handle??).
More testing is required and feature turned off my default.
-- Call sets with indels > 50 bp in length are tagged as CNVs in the tag (following the 1000 Genomes convention) and were unconditionally checking whether the CNV is already known, by looking at the known cnvs file, which is optional. Fixed. Has the annoying side effect that indels > 50bp in size are not counted as indels, and so are substrated from both the novel and known counts for indels. C'est la vie
-- Added integration test to check for this case, using Mauricio's most recent VCF file for NA12878 which has many large indels. Using this more recent and representative file probably a good idea for more future tests in VE and other tools. File is NA12878.HiSeq.WGS.b37_decoy.indel.recalibrated.vcf in Validation_Data
This error was due to the ReadClipper change of contract. Before the read utils would return null if a read was entirely clipped, now it returns an empty (safe) GATKSAMRecord.
Some tests in this class were intermittently not being executed due
to being randomly scheduled before tests whose results they depend on.
Now the serial dependencies are enforced to avoid problematic orderings.
Previously, the initial release of a new GATK version had a version
number with only one part (eg., "1.4"). This could potentially mislead
people into thinking it's the most recent revision of a release, instead
of the least recent.
Now, initial releases will have full, three-part version numbers
(eg., "1.4-0-g472fc94") like everything else.
* outputs only the groups of read groups necessary, avoiding multiple pileup creations every call to map
* now also counts the number of variants associated with a given ROD (dbSNP) exist in the interval
* new column: interval size
Eric Banks
Matt Hanna
Menachem Fromer
Mauricio Carneiro
Mark DePristo
Khalid Shakir
Guillermo del Angel
Ryan Poplin
Christopher Hartl
David Roazen