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.
* Downsampling is now a parameter to the walker with default value of 0 (no downsampling)
* Downsampling selects reads at random at the variant region window and strives to achieve uniform coverage if possible around the desired downsampling value.
* Added integration test
* Knuth-shuffle is a simple, yet effective array permutator (hope this is good english).
* added a simple randomSubset that returns a random subset without repeats of any given array with the same probability for every permutation.
* added unit tests to both functions
* Modified cleanCigarShift to allow insertions in the beginning and end of the read
* Allowed cigars starting/ending in insertions in the systematic ReadClipper tests
* Updated all ReadClipper unit tests
* ReduceReads does not hard clip leading insertions by default anymore
* SlidingWindow adjusts start location if read starts with insertion
* SlidingWindow creates an empty element with insertions to the right
* Fixed all potential divide by zero with totalCount() (from BaseCounts)
* Updated all Integration tests
* Added new integration test for multiple interval reducing
-- Automatic detection of most recent version of GATK release (just tell the script now to use 1.2, 1.3, and 1.4)
-- Uses 1.4 now
-- By default we do 9 runs of each non-parallel test
-- In PathUtils added convenience utility to find most recent release GATK jar with a specific release number
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)
David Roazen
Christopher Hartl
Eric Banks
Mauricio Carneiro
Mark DePristo
Matt Hanna