-- Missing BAMs were appearing as StingExceptions
-- Missing VCFs were showing up as CommandLineErrors, but it's clearer for them to be CouldNotReadInputFile exceptions
-- Added integration tests to ensure missing BAMs, VCFs, and -L files are properly thrown as CouldNotReadInputFile exceptions
-- Added path to standard b37 BAM to BaseTest
-- Cleaned up code in SAMDataSource, removing my parallel loading code as this just didn't prove to be useful.
-- 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.
Turns out that because the RTC is the first walker to 'correctly' tree reduce according to functional programming
standards, the RTC has revealed a few problems with the tree reducer holding on to too much data. This is the first
and smaller of two commits to reduce memory consumption. The second commit will likely be pushed after GATK1.4 is
released.
* Creates an empty GATKSAMRecord with empty (not null) Cigar, bases and quals. Allows empty reads to be probed without breaking.
* All ReadClipper utilities now emit empty reads for fully clipped reads
* Described the ReadClipper contract in the top of the class
* Added contracts where applicable
* Added descriptive information to all tools in the read clipper
* Organized public members and static methods together with the same javadoc
These functions are methods of the read, and supplement getAlignmentStart() and getUnclippedStart() by calculating the unclipped start counting only soft clips.
* Removed from ReadUtils
* Added to GATKSAMRecord
* Changed name to getSoftStart() and getSoftEnd
* Updated third party code accordingly.
* Removed all clipping functionality from ReadUtils (it should all be done using the ReadClipper now)
* Cleaned up functionality that wasn't being used or had been superseded by other code (in an effort to reduce multiple unsupported implementations)
* Made all meaningful functions public and added better comments/explanation to the headers
For simplified access to the hard clipping utilities. No need to create a ReadClipper object if you are not doing multiple complicated clipping operations, just use the static methods.
examples:
ReadClipper.hardClipLowQualEnds(2);
ReadClipper.hardClipAdaptorSequence();
The algorithm wasn't accounting for the case where the read is the reverse strand and the insert size is negative.
* Fixed and rewrote for more clarity (with Ryan, Mark and Eric).
* Restructured the code to handle GATKSAMRecords only
* Cleaned up the other structures and functions around it to minimize clutter and potential for error.
* Added unit tests for all 4 cases of adaptor boundaries.
-- Support for collecting resources info from DRMAA runners
-- Disabled the non-standard mem_free argument so that we can actually use our own SGE cluster gsa4
-- NCoresRequest is a testing queue script for this.
-- Added two command line arguments:
-- multiCoreJerk: don't request multiple cores for jobs with nt > 1. This was the old behavior but it's really not the best way to run parallel jobs. Now with queue if you run nt = 4 the system requests 4 cores on your host. If this flag is thrown, though, it will only request 1 and you'll just use 4, like a jerk
-- job_parallel_env: parallel environment named used with SGE to request multicore jobs. Equivalent to -pe job_parallel_env NT for NT > 1 jobs
* New ClippingOp REVERT_SOFTCLIPPED_BASES turns soft clipped bases into matches.
* Added functionality to clipping op to revert all soft clip bases in a read into matches
* Added revertSoftClipBases function to the ReadClipper for public use
* Wrote systematic unit tests
Minor changes to ValidationSiteSelector logic (SampleSelectors determine whether a site is valid for output, no actual subset context need be operated on beyond that determination). Implementation of GL-based site selection. Minor changes to EJG.
UGBoundAF has to go in at some point. In the process of rewriting the math for bounding the allele frequency (it was assuming uniform tails, which is silly since i derived the posterior distribution in closed form sometime back, just need to find it)
Mark DePristo
Matt Hanna
Eric Banks
Mauricio Carneiro
David Roazen
Christopher Hartl
Laurent Francioli