* 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
-- 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
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.
* 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
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.
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.
* 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
Creating a single temporary directory per ant test run instead of a putting temp files across all runs in the same directory.
Updated various tests for above items and other small fixes.
fixed issue where a read starting with an insertion followed by a deletion would break, clipper can now safely clip the insertion and the deletion if that's the case.
note: test is turned off until contract changes to allow hanging insertions (left/right).
* fixed edge case when requested to hard clip beginning of a read that had hanging soft clipped bases on the left tail.
* fixed edge case when requested to hard clip end of a read that had hanging soft clipped bases on the right tail.
* fixed AlignmentStart of a clipped read that results in only hard clips and soft clips
note: added tests to all these beautiful cases...
* expanded the systematic cigar string space test framework Roger wrote to all tests
* moved utility functions into Utils and ReadUtils
* cleaned up unused classes
caught a bug in the hard clipper where it does not account for hard clipping softclipped bases in the resulting cigar string, if there is already a hard clipped base immediately after it.
* updated unit test for hardClipSoftClippedBases with corresponding test-case.
bug: When performing multiple hard clip operations in a read that has indels, if the N+1 hardclip requests to clip inside an indel that has been removed by one of the (1..N) previous hardclips, the hard clipper would go out of bounds.
fix: dynamically adjust the boundaries according to the new hardclipped read length. (this maintains the current contract that hardclipping will never return a read starting or ending in indels).
-- Now properly handles the case where a sample isn't present (no longer adds a null to the genotypes list)
-- Fix for logic failure where if the number of requested samples equals the number of known genotypes then all of the records were returned, which isn't correct when there are missing samples.
-- Unit tests added to handle these cases
Tests are more rigorous and includes many more test cases.
We can tests custom cigars and the generated cigars.
*Still needs debugging because code is not working.
Created test classes to be used across several tests.
Some cases are still commented out.
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
Insertions are a problem so cigar cases with "I" are commented out.
The test works with multiple deletions and matches.
This is still not a complete test. A lot of cigar test cases are commented out.
Added insertions to ReadClipperUnitTest
ReadClipper now tests for all indels.
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
PreQC parses file with spaces in sample names by using tabs only.
PostQC allows passing the file names for the evals so that flanks can be evaled.
BaseTest's network temp dir now adds the user name to the path so files aren't created in the root.
HybridSelectionPipeline:
- Updated to latest versions of reference data.
- Refactored Picard parsing code replacing YAML.
-- VariantSummary now includes novelty of CNVs by reciprocal overlap detection using the standard variant eval -knownCNVs argument
-- Genericizes loading for intervals into interval tree by chromosome
-- GenomeLoc methods for reciprocal overlap detection, with unit tests
-- Performance optimizations
-- Tables now are cleanly formatted (floats are %.2f printed)
-- VariantSummary is a standard report now
-- Removed CompEvalGenotypes (it didn't do anything)
-- Deleted unused classes in GenotypeConcordance
-- Updates integration tests as appropriate
-- Updating MD5s for UG to reflect that what was previously called ./.:.:10:0,0,0 is now just ./. Eric will fix long-standing bug in QD observed from this change
-- VFW MD5s restored to their old correct values. There was a bug in my implementation to caused the genotypes to not be parsed from the lazy output even through the header was incorrect.
This syntax predates the ability to have multiple -L arguments, is
inconsistent with the syntax of all other GATK arguments, requires
quoting to avoid interpretation by the shell, and was causing
problems in Queue.
A UserException is now thrown if someone tries to use this syntax.
-- Now you provide a LazyParsing object
-- LazyGenotypesContext now knows nothing about the VCF parser itself. The parser holds all of the necessary data to parse the VCF genotypes when necessarily, and the LGC only has a pointer to this object
-- Using new interface added LazyGenotypesContext to unit tests with a simple lazy version
-- Deleted VCFParser interface, as it was no longer necessary
-- With our GenotypesContext class we can naturally create a LazyGenotypesContext subclass that does the on-demand loading.
-- This new class was replaced all of the old, complex functionality
-- Better still, there were many cases were the genotypes were being loaded unnecessarily, resulting in efficiency. This was detected because some of the integration tests changed as the genotypes were no longer being parsing unnecessarily
-- Misc. bug fixes throughout the system
-- Bug fixes for PhaseByTransmission with new GenotypesContext
-- We should no longer have md5s changing because of hashmaps changing their sort order on us
-- Added GenotypeLikelihoodsUnitTests
-- Refactored ExactAFCaclculation to put the PL -> QUAL calculation in the GenotypeLikelihoods class to avoid the code copy.
-- New approach to making VariantContexts modeled on StringBuilder
-- No more modify routines -- use VariantContextBuilder
-- Renamed isPolymorphic to isPolymorphicInSamples. Same for mono
-- getChromosomeCount -> getCalledChrCount
-- Walkers changed to use new VariantContext. Some deprecated new VariantContext calls remain
-- VCFCodec now uses optimized cached information to create GenotypesContext.
-- Major change to how chromosomeCounts is computed. Now NO_CALL alleles are always excluded. So ChromosomeCounts(A/.) is 1, the previous result would have been 2.
-- Naming changes for getSamplesNameInOrder()
-- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4
-- 1.3 VC and associated utilities copied wholesale into test directory under v13
-Modified the SnpEff parser to work with the SnpEff 2.0.4 VCF output format
-Assigning functional classes and effect impacts now handled directly
by SnpEff rather than the GATK
-Removed support for SnpEff 2.0.2, as we no longer trust the output of that
version since it doesn't exclude effects associated with certain nonsensical
transcripts. These effects are excluded as of 2.0.4.
-Updated unit and integration tests
This support is based on a *release-candidate* of SnpEff 2.0.4, and so is subject
to change between now and the next GATK release.
compressed the representation of the reduce reads counts by offset results in 17% average compression in final BAM file size.
Example compression -->
from : 10, 10, 11, 11, 12, 12, 12, 11, 10
to: 10, 0, 1, 1,2, 2, 2, 1, 0
-- I have no idea why I named this InferredGeneticContext, a totally meaningless term
-- Renamed to CommonInfo.
-- Made package protected, as no one should use this outside of VariantContext and Genotype
-- UGEngine was using IGC constant, but it's now using the public one in VariantContext.
-- Enables further sophisticated optimizations, as this class can be smarter about storing the data and will directly support operations like subset to samples
-- All instances in the gatk that used Map<String, Genotype> now use GenotypeMap type.
-- Amazingly, there were many places where HashMap<String, Genotype> is used, so that the order of the genotypes is technically undefined and could be dangerous. Now everything uses GenotypeMap with a specific ordering of samples (by name)
-- Integrationtests updated and all pass
* Generalized the concept of a synthetic read to cread both running consensus and a synthetic reads of filtered data.
* Synthetic reads can now have deletions (but not insertions)
* New reduced read tag for filtered data synthetic reads *(RF)*
* Sliding window header now keeps information of consensus and filtered data
* Synthetic reads are created simultaneously, new functionality is controlled internally by addToSyntheticReads
The GATK engine will now provide a GATKSAMRecord to all tools which incorporates the functionality used by the GATK to the bam file (ReadGroups, Reduced Reads, ...).
* No tools should create SAMRecord anymore, use GATKSAMRecord instead *
-- scatterLocusIntervals master utility
-- Moved around some general functionality from GenomeLocSortedSet to GenomeLoc
-- Util function for reversing a list (List<T> -> List<T>, unlike Collections version)
-- DoC is PartitionType.INTERVAL
-- Significant unit tests on new functionality (all passing)
-- Ready for real-world testing, as soon as I can get LocusScatterFunction.scala to actually work
-- Supports ReadBackedPileup -> FragmentCollection as before
-- Added support for List<SAMRecord> -> FragmentCollection for Ryan's haplotype caller
-- General cleanup, renaming, move to separate package, more extensive unit tests, etc.
-- Added toFragment() function to ReadBackedPileup interface
Moved gsalib and queueJobReport.R to embeddable namespaced locations.
Updated packager dependencies/dir to add an @includes which filters the embedded fileset.
RScriptExecutor can now JIT compiles the gsalib.
RScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG.
Refactored ProcessController and IOUtils from Queue to Sting Utils.
Added more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count.
Replaced uses of some IOUtils with Apache Commons IO.
ShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown.
Better QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().
-- removed intermiate functions. Now only original version and best optimized new version remain
-- Moved general artificial read backed pileup creation code into ArtificialSamUtils
-- Uses mayOverlapRoutine in ReadUtils
-- Attempts to be smart when doing overlap calculation, to avoid unnecessary allocations
-- PileupElement now comparable (sorts on offset than on start)
-- Caliper microbenchmark to assess performance
-- Creates all combinatinos of overlapping and non-overlapping read pair pileups in all orientations and first/second pairings to validate fragment detection.
We can't have a public test that depends on both public and private
code/data -- the new release system needs to do public-only tests,
and will catch this sort of thing.
The public integration test VariantContextIntegrationTest was dependent on the
private walker TestVariantContextWalker. Moved this walker to public/java/test
(NOT public/java/src, since this walker is only used by the test suite) to avoid
errors during public-only tests.
-- MD5 db had spelling error; fixed
-- Bug in AlignmentUtils resulted in some bases not being color space corrected. The integration test caught the change, and it's clear that the new version is correct, as the prev. version was not considering the last the N qualities for reads with a ND operation.
This allows the annotation classes to perform any necessary initialization/validation.
For example, it allows the SnpEff annotator to (among other things) validate its rod binding.
This will prevent a NullPointerException when SnpEff annotation is requested but no rod binding
is present.
Added an integration test to cover this case so that it doesn't break again.
-- Changes associated code throughout the codebase
-- Updated necessary (but minimal) UnitTests to reflect new behavior
-- Much better makealleles() function in VC.java that enforces a lot of key constraints in VC
classloading of bcel*.jar/ant-apache-bcel*.jar. Switching instead to manually
specifying a minimal set of packages/classes to include in the vcf.jar via
build.xml, and adding a unit test which creates a limited classloader
only aware of vcf.jar and tribble.jar and tries to use it to load the core
classes in the vcf jar.
Hopefully third time's the charm.
-- the underlying data structure is still present, but until I decide what to do for the extensible system I've completely disabled the subsystem
-- Added code to merge Samples, so that a mostly full record can be merged with a consistent empty record. If the two records are inconsistent, an error is thrown
-- addSample() in Sample.class now invokes mergeSample() when appropriate
-- Validation types are now only STRICT or SILENT
-- Validation code implemented in SampleDBBuilder
-- Extensive unit tests for SampleDBBuilder
-- Passes significiant unit tests
-- Implicit sample creation for mom / dad when you create single samples
-- Continuing cleanup of Sample and SampleDataSource
* Includes tests that include HardClip to Read and Reference Coords.
* Changed ReadUtils.HardClipByReferenceCoordinates from private to protected to allow for testing
-- UnitTests for key functions on reduced reads
-- PileupElement calls static functions in ReadUtils
-- Simple routine that takes a reduced read and fills in its quals with its reduced qual
b) Change md5 to reflect records that are now merged correctly.
c) Change unit merge alleles test to reflect the fact that a null non-variant vc object is not valid and not supported because there's no way to codify such object in a vcf. The code correctly converts this to a non-variant single-base event with whatever the reference is at that location.
b) First reimplementation of new vc merger of different types. Previous version did it in two steps, first merging all vc's per type and then trying to see if resulting vc's would be merged if alleles of one type were a subset of another, but this won't work when uniquifying genotypes since sample names would be messed up and GT sample names wouldn't match VC sample names. Now, it's actually simpler: when splitting vc's by type before merging, we check for alleles of one vc being a subset of alleles of vc of another type and if so we put them together in same list.
-We now assign a functional class (nonsense, missense, silent, or none) to each SnpEff effect, and add a
SNPEFF_FUNCTIONAL_CLASS annotation to the INFO field of the output VCF.
-Effects are now prioritized according to both biological impact and functional class, instead of impact only.
-Many of SnpEff's "low-impact" effects are now classified as "modifiers" with lower priority than every
other effect. This includes such "effects" as DOWNSTREAM, UPSTREAM, INTRON, GENE, EXON, and others that
really describe the location of the variant rather than its biological effect.
This code will be short-lived (likely 1.2-only), as the next version of SnpEff will include most of these
features directly.
Checking this change into Stable+Unstable instead of Unstable because the current functional class stratification
in VariantEval is basically broken and urgently needs to be fixed for production purposes.
-- Old code required qual to be <64, which isn't strictly necessary. Now uses the Picard SAMUtils.MAX_PHRED_SCORE constant
-- Unittest to enforce this behavior
-- Now handles multiple records at a site, so that you don't see records like set=dbsnp-dbsnp-dbsnp when combining something with dbsnp
-- Proper handling of ids. If you are merging files with multiple ids for the same record, the ids are merged into a comma separated list
This change is urgently required for production, which is why it's going into Stable+Unstable
instead of just Unstable.
The keys for the SnpEff version and command header lines in the VCF file output by
VariantAnnotator (OriginalSnpEffVersion and OriginalSnpEffCmd) are intentionally
different from the keys for those same lines in the SnpEff output file (SnpEffVersion
and SnpEffCmd), so that output files from VariantAnnotator won't be confused
with output files from SnpEff itself.
-- Previously, on the fly indices didn't have dictionary set on the fly, so the GATK would read, add dictionary, and rewrite the index. This is now fixed, so that the on the fly index contains the reference dictionary when first written, avoiding the unnecessary read and write
-- Added a GenomeAnalysisEngine and Walker function called getMasterSequenceDictionary() that fetches the reference sequence dictionary. This can be used conveniently everywhere, and is what's written into the Tribble index
-- Refactored tribble index utilities from RMDTrackBuilder into IndexDictionaryUtils
-- VCFWriter now requires the master sequence dictionary
-- Updated walkers that create VCFWriters to provide the master sequence dictionary
-- No functional changes (my algorithm wouldn't work)
-- Major structural cleanup (returning more basic data structures that allow us to development new algorithm)
-- Unit tests for the efficiency of interval partitioning
After discussing this with Mark, it seems clear that the old version of the
VariantEval FunctionalClass stratification is preferable to this version.
By reverting, we maintain backwards compatibility with legacy output files
from the old GenomicAnnotator, and can add SnpEff support later without
breaking that backwards compatibility.
This reverts commit b44acd1abd9ab6eec37111a19fa797f9e2ca3326.
This is a temporary and hopefully short-lived solution. I've modified
the FunctionalClass stratification to stratify by effect impact as
defined by SnpEff annotations (high, moderate, and low impact) rather
than by the silent/missense/nonsense categories.
If we want to bring back the silent/missense/nonsense stratification,
we should probably take the approach of asking the SnpEff author
to add it as a feature to SnpEff rather than coding it ourselves,
since the whole point of moving to SnpEff was to outsource genomic
annotation.
-Rewrote SnpEff support in VariantAnnotator to support the latest SnpEff release (version 2.0.2)
-Removed support for SnpEff 1.9.6 (and associated tribble codec)
-Will refuse to parse SnpEff output files produced by unsupported versions (or without a version tag)
-Correctly matches ref/alt alleles before annotating a record, unlike the previous version
-Correctly handles indels (again, unlike the previous version
b) More useful AC,AF logging in VariantsToTable with multiallelic sites: instead of logging comma-separated values, log max value by default. Hidden, experimental argument -logACSum to log sum of ACs instead. This is due to extreme slowness of R in parsing strings to tokens and computing max/sum itself (~100x slower than gatk).
c) Added integrationtest for new SelectVariants commands
- Ability to pass a different resident memory reservation and limits. Useful for large pileups of low pass genome data that sometimes need high -Xmx6g but usually don't exceed 2-3g in actual heap size.
- Fixed jobPriority to work for all job runners. Now must be a integer between 0 and 100- even for GridEngine- and will be mapped to the correct values.
- Passing parallel environment and job resource requests to LSF and GridEngine. Useful for passing tokens like iodine_io=1 and -pe pe_slots 8
- Refactored GridEngine JobRunner to also provide basic support for other job dispatchers with DRMAA implementations such as Torque/PBS. Should work for basic running but advanced users must pass their own jobNativeArgs from the command line or in customized QScripts until someone maps properties like jobQueue, jobPriority, residentRequest, etc. into a Torque/PBS/etc. dispatcher.
Misc updates to WholeGenomeIndelCalling.scala
Bug fix in VariantEval (may be temporary, need more investigation): if -disc option is used in sites-only vcf's then a null pointer exception is produced, caused by recent introduction of -xl_sf options.
VariantEval module CountVariants is corrected and an additional column is added so that we log mixed events and complex indels separately (before they were being conflated).
VariantEval module IndelStatistics is considerably simplified as the sample stratification was wrong and redundant, now it should work with the VE-generic Sample stratification. Several columns are renamed or removed since they're not really useful
-- refdata/features now in utils/codecs with the other codecs
-- Deleted dbsnpHelper. rsID function now in VCFutils. Remaining code either deleted or put into VariantContextAdaptors
-- Many associated import updates due to code move
-- Verified now to be correct at runtime
-- UnitTest covers this
-- createTypeDefault now takes a Type, not a Class, so that parameterized classes can have their parameter fetched in the defaults.
New class handles (vastly more cleanly) the db of tribble codecs, features, and names for use throughout the GATK.
Added SelfScopingFeatureCodec interface that allows a FeatureCodec to examine a file and determine if the file can be parsed. This is the first step towards allowing the GATK to dynamically determine the type of a RodBinding.
-- CombineVariants now uses the new RodBinding syntax, -V / --variants. Passed all integration tests on first run
-- Exposed gapping bug in the List<RodBinding<T>> system now fixed. ParserEngine now has a addRodBinding() that is called by RodBindingArgumentTypeDescriptor when it encounters each RodBinding. This allows the system to work with collection types that are recursively parsed by the system.
-- Cleaning up old interface to RMDT, docs and contracts added
-- Proper type checking for RodBinding for cases where the Tribble type isn't found or is the wrong type
- Floating point column widths are measured correctly
- Using fixed width columns instead of white space separated which allows spaces embedded in cell values
- Legacy support for parsing white space separated v0.1 tables where the columns may not be fixed width
- Enforcing that table descriptions do not contain newlines so that tables can be parsed correctly
Replaced GATKReportTableParser with existing functionality in GATKReport
-- support for explicit naming of bindings (-X:name,type x)
-- support for automatic naming of bindings in lists (-X:vcf foo.vcf -X:vcf bar.vcf will generate internal names X and X2)
-- ParserEngineUnitTest expanded to cover all of the Rodbinding cases
-- RodBindingUnitTest tests all of the low-level accessors
-- Parsing engine throws UserExceptions when bad bindings are provided on the command line
RodBinding no longer duplicates the get() methods in RMDT. This is just an object now that connects the command line system to the RMDT.
Updated programs to use new style
Added UnitTests for the RodBinding accessors.
You know have to provide an explicit list of RODRecordLists upfront to the constructor. RefMetaDataTracker is now immutable. Changes in engine to incorporate these differences
Extensive UnitTests for RefMetaDataTracker now.
On the path towards converging getVariantContext() and getValues() in tracker so that we can have a single approach to get values from RODs with the new RodBinding() types
Problem is that Novelty sees multiple records at a site (SNP, INDEL) to calculate whether a site is novel, but VariantEvalWalker makes an arbitrary decision which to use for analysis and CompOverlap may not see a comp record of the same type as eval. So you get lines where the stratification is known but there are 10 novel sites!
Renamed many functions to more clearly state what they are actually doing
Removed unnecessary / unused functionality, reducing interface complexity
Updated all uses of this code in GATK
Added generic, type-safe accessors to RefMetaDataTracker such as public <T> List<T> getValues(final String name, Class<T> clazz)
Added standard refMetaDataTracker accessors to RodBinding, so you can do everything you can for generic rods with the tracker directly with with the RodBinding
Removing unused files RODRecordIterator, ReferenceOrderedData, QueryableTrack, RMDTrackCreationException, GATKFeatureIterator, ReferenceOrderedDataUnitTest
Refactored dbSNP and refseq utilities to be closer to the other files implementing these features
System has the concept of a local and a global MD5 db. The local one is like it operated previously. The global one lives in /humgen/gsa-hpprojects/GATK/data/integrationtests. If the system can find this directory then MD5s will also be read / written to this location. This means that gsabamboo will print differences as appropriate. And all users will in effect have access to a complete history of MD5 file results.
A few minor code reshuffles changed VariantRecalibration and VCFHeader test files.
printSummaryReport now uses GATKReport for nice formating
Moved print formatting arguments into inner class provided to printing functions themselves, not the class
BAMDiffableReader only reads 1000 entries to avoid performance issue. Work around for BAM files with non-unique names
Uncommented all of the incorrectly commented out CombineVariants integrationtests
BaseTest now uses DiffEngine to provide inline differences to VCF and BAM files
non-static to avoid problems when multiple references are used within the same
thread (eg., during integration tests). This should kill the intermittent
IndelRealignerIntegrationTest failures.
Eric Banks
Ryan Poplin
Mark DePristo
Mauricio Carneiro
Matt Hanna
Guillermo del Angel
David Roazen
Laurent Francioli
Khalid Shakir
Roger Zurawicki
Menachem Fromer
Kiran V Garimella
Christopher Hartl