-- samtools can emit alleles where the ref is 42M Ns and this caused the GATK (via tribble) to hang in several places.
-- Tribble was updated so we actually could read the line properly (rev. to 51 here).
-- Still the parsing algorithms in the GATK aren't happy with such a long allele. Instead of optimizing the code around an improper use case I put in a limit of 2^16 bp for any allele, and throw a meaningful exception when encountered.
CalibrateGenotypeLikelihoods supports using an external VCF as input for genotype likelihoods. Currently can be a per-sample VCF, but has un-implemented methods for allowing a read-group VCF to be used.
Removed the old constrained genotyping code from UGE -- the trellis calculated is exactly the same as that done in the MLE AC estimate; so we should just re-use that one.
* using the filter() instead of map() makes for a cleaner walker.
* renaming the unit tests to make more sense with the other unit and integration tests
* if the adaptor boundary is more than MAXIMUM_ADAPTOR_SIZE bases away from the read, then let's not clip anything and consider the fragment to be undetermined for this read pair.
* updated md5's accordingly
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.
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.
* 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)
Mark DePristo
Ryan Poplin
Matt Hanna
Christopher Hartl
Mauricio Carneiro
Eric Banks
Khalid Shakir
Guillermo del Angel
David Roazen
Laurent Francioli