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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Ami Levy-Moonshine c103623cf6 bug fix in my new function at SampleUtils.java 2013-01-28 19:04:39 -05:00
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R Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
activeregion Fixed NPE in ActiveRegionUnitTest by allowing null supporting states in ActiveRegion 2013-01-24 13:48:00 -05:00
analysis Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
baq Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
classloader Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
clipping getAdaptorBoundary returns an int, not an Integer, as this was taking 30% of the allocation effort for LIBS 2013-01-14 16:30:15 -05:00
codecs Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
collections Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
crypt Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
duplicates Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
exceptions Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
fasta Added tests for changing IUPAC bases to Ns, for failing on bad ref bases, and for the HaplotypeCaller not failing when running over a region with an IUPAC base. 2013-01-16 14:55:33 -05:00
file Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
fragments Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
genotyper Moving lots of walkers back from protected to public (along with several of the VA annotations). 2013-01-24 11:42:49 -05:00
help Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
instrumentation Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
interval Re-committing the following changes from Dec 18: 2013-01-16 12:43:15 -05:00
io Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
locusiterator LIBS optimization for adapter clipping 2013-01-25 16:05:17 -05:00
nanoScheduler Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
pairhmm Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
pileup The CachingIndexedFastaSequenceFile now automatically converts IUPAC bases to Ns and errors out on other non-standard bases. 2013-01-16 10:22:43 -05:00
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
progressmeter Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
recalibration Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
runtime Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
sam Add contract to ensure that getAdapterBoundary returns the right result 2013-01-25 16:05:17 -05:00
text Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
threading Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variant Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
wiggle Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
AutoFormattingTime.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
BitSetUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ContigComparator.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLoc.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLocComparator.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLocParser.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLocSortedSet.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Haplotype.java I finally gave up on trying to get the Haplotype/Allele merging to work in the HaplotypeCaller. 2013-01-18 01:21:08 -05:00
HasGenomeLocation.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
HeapSizeMonitor.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
IndelUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
LRUCache.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
LegacyReservoirDownsampler.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MannWhitneyU.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MathUtils.java Making band pass filter size, sigma, active region max size and extension all accessible from the command line 2013-01-24 13:47:59 -05:00
Median.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MendelianViolation.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MultiThreadedErrorTracker.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
NGSPlatform.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
PathUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
QualityUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
SWPairwiseAlignment.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
SampleUtils.java bug fix in my new function at SampleUtils.java 2013-01-28 19:04:39 -05:00
SequenceDictionaryUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
SimpleTimer.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Utils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
package-info.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00