-- Added VCFHeader() constructor that makes an empty header, and updated VariantRecalibrator to use it
-- Update build.xml to build vcf.jar with updated paths and bcf2 support.
-- 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
-- Update code to name new, more general decodeSingleValue
-- Update MISSING_VALUE constants to be 0xFFFFFF80 vs. 0x00000080 as these are equivalent for a byte and handle the two complement cast from byte to int
-- Fix decoding of byte and short values which were screwing up missing values
-- Code cleanup in decoder
-- Generalize bestIntegerType function
-- Handle the encoding of boolean FLAG fields
-- Test the encoding of vectors of values
-- BCF2 encoder and BCF2 decoder are now fully tested, and are working correctly.
-- Code cleanup and reorganization to fix bugs encountered during testing.
-- Decoder is a low-level reader of underlying data from a BCF2 encoded stream
-- Codec uses the decoder to build a VC from the stream
-- Separation key for upcoming UnitTest framework that will ensure correctness of low-level decoder / encoder before optimization of the encoder / decoder starts
-- Restructured code to separate the MISSING value in java (currently everywhere a null) from the byte representation on disk (an int).
-- Now handles correctly MISSING qual fields
-- Refactored setting of contigs from VCFWriterStub to VCFUtils. Necessary for proper BCF working
-- Added VCFContigHeaderLine that manages the order for sorting, so we now emit contigs in the proper order.
-- Cleaned up VCFHeader operations
-- BCF now uses the right header files correctly when encoding / decoding contigs
-- Support for string dictionary at standard positions in the VCF
-- Refactored setting of contigs from VCFWriterStub to VCFUtils. Necessary for proper BCF working
-- Added VCFContigHeaderLine that manages the order for sorting, so we now emit contigs in the proper order.
-- Cleaned up VCFHeader operations
-- BCF now uses the right header files correctly when encoding / decoding contigs
-- Clean up unused tools
-- Refactored header parsing routines to make them more accessible
-- More minor header changes from Intellij
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.
}
* For some reason, the original implementor decided to use Booleans instead of booleans and didn't always check for null so we'd occasionally get a NPE. Switched over to booleans.
* We'd also generate a NPE if SAMRecord writing specific arguments (e.g. --simplifyBAM) were used while writing to sdout.
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.
* Added support for a protected directory whose contents are only made public in binary form
* Simplified and reorganized build.xml to improve readability and maintainability
* build.xml now autodetects most build properties:
-Includes private/protected if they exist
-No more STING_BUILD_TYPE or specialized targets for public-only, etc.
* Build targets have changed! There are now two main build options:
"ant" build everything (GATK and Queue)
"ant gatk" build just the GATK
It was too hard to build everything before -- now it is the default.
* To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line.
Much better than the old comment/uncomment method!
Mark DePristo
Joel Thibault
Guillermo del Angel
Ryan Poplin
Christopher Hartl
Khalid Shakir
Eric Banks
David Roazen