The migration of org.broadinstitute.variant into the Picard repo is
complete. This commit deletes the org.broadinstitute.variant sources
from our repo and replaces it with a jar built from a checkout of the
latest Picard-public svn revision.
This is a necessary prerequisite for the org.broadinstitute.variant migration.
-Picard and sam-jdk go from version 1.67.1197 to 1.84.1337
-Picard-private goes from version 2375 to 2662
-Tribble goes from version 119 to 1.84.1337
-RADICALLY trimmed down the list of classes we extract from Picard-private
(jar goes from 326993 bytes to 6445 bytes!)
-- New tribble library now uses 64 bit sizes. The 26K VCF has so much data that low-level tribble block indices where overflowing their int size values. This includes a to-be-committed tribble jar that fixes this problem
-- See https://jira.broadinstitute.org/browse/GSA-652
-- Minor cleanup of error messages that were useful on the way to solving this monster problem
Added targets to build.xml to effectively 'mvn install' packaged GATK/Queue from ant.
TODO: Versions during 'mvn install' are hardcoded at 0.0.1 until a better versioning scheme that works with maven dependencies has been identified.
We will use DocumentedGATKFeatures to create categories in our documentation. Eric I guess will be in charge of this. We need to remove walkers and think how to categorize everything.
Tools can be hidden from GATKdocs with the @Hidden annotation
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
GATKDocs looks for a key on gsa4, and updates the forum with new walker if it exists.
More changes were made to the GATKDocs. Works nicely with bootstrap on and offline.
Cleaned up the code as well
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
* Did not touch archived walkers... those can be named whatever.
* Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...)
* Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats.
Optimization for PositionalBufferedStream with specialized read(byte, int, int) method
-- For binary codecs having an efficient reader of lots of bytes that doesn't fall back into read() itself vastly improves performance. The old version was 10x slower than InputStream, while the new version is +30%.
-- Generalize PositionalBufferedStream main() method for performance testing, now accepts cmdline arguments for the file to read, how many iterations, etc
Generalize AsciiLineReader main() method for performance testing
-- Now accepts cmdline arguments for the file to read, how many iterations, etc
AsciiLineReaderTest and PositionBufferedStreamTest were in src not test/src
Scalability bugfixes; can issues tens of thousands of queries to an reader
without opening too many files
-- Fixed missing close() statement in TribbleIndexedFeatureReader
-- Fixed NPE in TabixIteratorLineReader
-- Added scalability test that confirms .query() failure and subsequent fix
Note this actually fixes a tested and reproducible scability issue. Might not be the only one but I believe it should do the trick. Sorry everyone for the inconvenience. Note that we now have a test in Tribble to ensure this doesn't happen again.
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.
-- 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.
-- ProfileRodSystem now has a just load index mode, allowing us to optimize the profiler
-- assessFarmNodes R script for making nice plots of performance of jobs on the farm
-- Rev. tribble to use new, optimized index loading (performance win when loading many many indices)
David Roazen
Mark DePristo
kshakir
Roger Zurawicki
Mauricio Carneiro
Matt Hanna
Eric Banks