-- Cut down the size of a few large files in public/testdata that were only used in part
-- Refactor vcf Filename => shadow BCF filename to BCF2Utils. Fix bug in WalkerTest due to the way this was handled previously
-- Fully working version
-- Use -generateShadowBCF to write out foo.bcf as well as foo.vcf anywhere you use -o foo.vcf
-- Moved MedianUnitTest to its proper home in Utils
-- Added reportng to ivy and testng, so build/report/X/html/ is a nicely formatted output for Unit and Integration tests. From this website it's easy to see md5 diffs, etc. This is a vastly better way to manage unit and integration test output
--handle entirely missing GT in a sample in decodeGenotypeAlleles
--Create MAX_ALLELES_IN_GENOTYPES constant in BCF2Utils, and extracted its use inline from the code
-- Generalized genotype writing code to handle ploidy != 2 and variable ploidy among samples
-- Remove special case inline treatment of case where all samples have no GT field values, and moved this into calcVCFGenotypeKeys
-- Removed restriction on getPloidy requiring ploidy > 1. It's logically find to return 0 for a no called sample
-- getMaxPloidy() in VC that does what it says
-- Support for padding / depadding of generic genotype fields
-- fixed final bugs with PL encoding / decoding
-- Ready for testing by other members of the group
-- Current performance numbers aren't so great, but they will improve in the next phase of BCF2 optimizations
-- Fixed a nasty bug in the filter field
-- Not that some (many?) GATK tools won't work with BCF because they internally assume values are Strings not their true types
Read 1500 genotypes file in VCF -> VCF : 11 seconds
Read 1500 genotypes file in VCF -> BCF : 9.5 seconds
VariantEval 1500 genotypes file in VCF : 3 seconds
VariantEval 1500 genotypes file in BCF : 3 seconds
-- Trivial import changes in some walkers
-- SelectVariants has a new hidden mode to fully decode a VCF file
-- DepthPerAlleleBySample (AD) changed to have not UNBOUNDED by A type, which is actually the right type
-- GenotypeLikelihoods now implements List<Double> for convenience. The PL duality here is going to be removed in a subsequent commit
-- BugFixes in BCF2Writer. Proper handling of padding. Bugfix for nFields for a field
-- padAllele function in VariantContextUtils
-- Much better tests for VariantContextTestProvider, including loading parts of dbSNP 135 and the Phase II 1000G call set with genotypes to test encoding / decoding of fields.
-- List<String> is converted inside of the codec to a collapsed string, and exploded in the decoder.
-- Unified the type conversion code in BCFWriter to simply the mapping from VCF type => BCF type and special value recoding
-- Code cleanup and renaming
-- Convenience routine for creating alleles from strings of bases
-- Convenience constructor for VCFFilterHeader line whose description is the same as name
-- VariantContextTestProvider creates all sorts of types of VariantContexts for testing purposes. Can be reused throughtout code for BCF, VCF, etc.
-- Created basic BCF2WriterCodec tests that consumes VariantContextTestProvider contexts, writes them to disk with BCF2 writer, and checks that they come back equals to the original VariantContexts. Actually worked for some complex tests in the first go
-- Moved VCF and BCF writers to variantcontext.writers
-- Updated vcf.jar build path
-- Refactored VCFWriter and other code. Now the best (and soon to be only) way to create these files is through a factory method called VariantContextWriterFactory. Renamed the general VCFWriter interface to VariantContextWriter which is implemented by VCFWriter and BCF2Writer.
-- Refactored VCF writers into vcf.writers package
-- Moved BCF2Writer to bcf2.writer
-- Updates to all of the walkers using VCFWriter to reflect new packages
-- A large number of files had their headers cleaned up because of this as well
This bug will happen in all adapter/wrapper classes that are passed a resource, and then in their close method they ignore requests to close the wrapped resource, causing a leak when the adapter is the only one left with a reference to the resource.
Ex:
public Wrapper getNewWrapper(File path) {
FileStream myStream = new FileStream(path); // This stream must be eventually closed.
return new Wrapper(myStream);
}
public void close(Wrapper wrapper) {
wrapper.close(); // If wrapper.close() does nothing, NO ONE else has a reference to close myStream.
}
The practical differences between version 1.0 and this one (v1.1) are:
* the underlying data structure now uses arrays instead of hashes, which should drastically reduce the memory overhead required to create large tables.
* no more primary keys; you can still create arbitrary IDs to index into rows, but there is no special cased primary key column in the table.
* no more dangerous/ugly table operations supported except to increment a cell's value (if an int) or to concatenate 2 tables.
Integration tests change because table headers are different.
Old classes are still lying around. Will clean those up in a subsequent commit.
From tribble logs:
Binary feature support in tribble
-- Massive refactoring and cleanup
-- Many bug fixes throughout
-- FeatureCodec is now general, with decode etc. taking a PositionBufferedStream
as an argument not a String
-- See ExampleBinaryCodec for an example binary codec
-- AbstractAsciiFeatureCodec provides to its subclass the same String decode,
readHeader functionality before. Old ASCII codecs should inherit from this base
class, and will work without additional modifications
-- Split AsciiLineReader into a position tracking stream
(PositionalBufferedStream). The new AsciiLineReader takes as an argument a
PositionalBufferedStream and provides the readLine() functionality of before.
Could potentially use optimizations (its a TODO in the code)
-- The Positional interface includes some more functionality that's now
necessary to support the more general decoding of binary features
-- FeatureReaders now work using the general FeatureCodec interface, so they can
index binary features
-- Bugfixes to LinearIndexCreator off by 1 error in setting the end block
position
-- Deleted VariantType, since this wasn't used anywhere and it's a particularly
clean why of thinking about the problem
-- Moved DiploidGenotype, which is specific to Gelitext, to the gelitext package
-- TabixReader requires an AsciiFeatureCodec as it's currently only implemented
to handle line oriented records
-- Renamed AsciiFeatureReader to TribbleIndexedFeatureReader now that it handles
Ascii and binary features
-- Removed unused functions here and there as encountered
-- Fixed build.xml to be truly headless
-- FeatureCodec readHeader returns a FeatureCodecHeader obtain that contains a
value and the position in the file where the header ends (not inclusive).
TribbleReaders now skip the header if the position is set, so its no longer
necessary, if one implements the general readHeader(PositionalBufferedStream)
version to see header lines in the decode functions. Necessary for binary
codecs but a nice side benefit for ascii codecs as well
-- Cleaned up the IndexFactory interface so there's a truly general createIndex
function that takes the enumerated index type. Added a writeIndex() function
that writes an index to disk.
-- Vastly expanded the index unit tests and reader tests to really test linear,
interval, and tabix indexed files. Updated test.bed, and created a tabix
version of it as well.
-- Significant BinaryFeaturesTest suite.
-- Some test files have indent changes
-- Other tribble contributors did major refactoring / simplification of tribble, which required some changes to GATK code
-- Integrationtests pass without modification, though some very old index files (callable loci beds) were apparently corrupt and no longer tolerated by the newer tribble codebase
Updated ReadFilter abstract class to implement (via UnsupportedOperationException) the new SamRecordFilter.filterOut().
In IndelRealignerIntegrationTest updates for Picard fixes to SAMRecord.getInferredInsertSize() in svn r1115 & r1124.
- Ran FixMates to create new input BAM since running IR with variable maxReadsInMemory means all reads weren't realigned leading to different outputs.
- Updated md5s to match new expectations after looking at TLEN diff engine output.
a) Add ability for ErrorModel to be specified by external log-probability vector for testing.
b) For a given depth and ploidy(=2*samples/pool), create artificial high quality pileup testing from AC=0 to AC=ploidy, and test that pool GL's have expected content.Misc. refactorings and cleanups
c) Misc. cleanups and beautification.
a) Utility class called Probability Vector that holds a log-probability vector and has the ability to clip ends that deviate largely from max value.
b) Used this class to hold site error model, since likelihoods of error model away from peak are so far down that it's not worth computing with them and just wastes time.
c) Expand unit tests and add an exhaustive test for ErrorModel class.
d) Corrected major math bug in ErrorModel uncovered by exhaustive test: log(e^x) is NOT x if log's base = 10.
e) Refactored utility functions that created artificial pileups for testing into separate class ArtificialPileupTestProvider. Right now functionality is limited (one artificial contig of 10 bp), can only specify pileups in one position with a given number of matches and mismatches to ref) but functionality will be expanded in future to cover more test cases.
f) Use this utility class for IndelGenotypeLikelihoods unit test and for PoolGenotypeLikelihoods unit test (the latter testing functionality still not done).
g) Linearized implementation of biallelic exact model (very simple approach, similar to diploid exact model, just abort if we're past the max value of AC distribution and below a threshold). Still need to add unit tests for this and to expand to multiallelic model.
h) Update integration test md5's due to minor differences stemming from linearized exact model and better error model math
The GATK -L unmapped is for GenomeLocs with SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, not SAMRecord.getReadUnmappedFlag()
Previously unmapped flag reads in the last bin were being printed while also seeking for the reads without a reference contig.
Mark DePristo
Khalid Shakir
Eric Banks
Guillermo del Angel
Laurent Francioli
Mauricio Carneiro