| .. |
|
R
|
AnalyzeCovariates uses the general RScript system now
|
2011-08-27 12:54:13 -04:00 |
|
analysis
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
baq
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
bed
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
classloader
|
Improvements to GATKDocs
|
2011-08-18 21:20:09 -04:00 |
|
clipreads
|
Bringing Reduce Reads bug fixes to the main repository
|
2011-09-07 12:25:53 -04:00 |
|
codecs
|
Now only prints 1 warning message about duplicate headers in simpleMerge
|
2011-08-29 14:41:29 -04:00 |
|
collections
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
duplicates
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
exceptions
|
Fixed bug that required symbolic alleles to be padded with reference base and added integration test to test parsing and output of symbolic alleles
|
2011-08-12 12:23:44 -04:00 |
|
fasta
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
file
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
genotype
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
help
|
Final documented version of GATKDoclet and associated classes
|
2011-08-19 16:52:17 -04:00 |
|
instrumentation
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
interval
|
Intermediate commit cleaning up scatter intervals
|
2011-09-09 12:56:45 -04:00 |
|
pileup
|
ReducedRead flag cached in GATKSAMRecord. 20% performance improvement
|
2011-09-06 15:11:38 -04:00 |
|
pileup2
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
sam
|
ReducedRead flag cached in GATKSAMRecord. 20% performance improvement
|
2011-09-06 15:11:38 -04:00 |
|
text
|
Now provides type-specific user feedback
|
2011-08-18 10:47:16 -04:00 |
|
threading
|
Removed GATK use of distributed parallelism framework.
|
2011-07-20 16:26:09 -04:00 |
|
variantcontext
|
We already had isPolymorphic and isMonomorphic in the VariantContext, but the implementation was incorrect for many edge cases (e.g. sites-only files, sites with samples who were no-called). Fixing. Moving on to VE now.
|
2011-09-07 14:01:42 -04:00 |
|
wiggle
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
yaml
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
AminoAcid.java
|
Removing the Genomic Annotator and its supporting classes
|
2011-07-25 15:10:25 -04:00 |
|
AminoAcidTable.java
|
Removing the Genomic Annotator and its supporting classes
|
2011-07-25 15:10:25 -04:00 |
|
BaseUtils.java
|
Functional VCF output.
|
2011-08-04 17:49:08 -04:00 |
|
ContigComparator.java
|
Documented following the new gatkdoc framework
|
2011-07-25 00:25:08 -04:00 |
|
DisjointSet.java
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
GenomeLoc.java
|
Performance bugfix for GenomeLoc.hashcode
|
2011-09-09 14:25:37 -04:00 |
|
GenomeLocParser.java
|
Removed getFeaturesAsGATKFeature and created createGenomeLoc(Feature) in genomeLocParser
|
2011-08-03 16:04:51 -04:00 |
|
GenomeLocSortedSet.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
HasGenomeLocation.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
HeapSizeMonitor.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
IndelUtils.java
|
Fixing up and refactoring usage of indel categories. On a variant context, isInsertion() and isDeletion() are now removed because behavior before was wrong in case of multiallelic sites. Now, methods isSimpleInsertion() and isSimpleDeletion() will return true only if sites are biallelic. For multiallelic sites, isComplex() will return true in all cases.
|
2011-08-18 16:17:38 -04:00 |
|
MannWhitneyU.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
MathUtils.java
|
Added RMS calculation for consensus MQ
|
2011-08-30 02:45:20 -04:00 |
|
MendelianViolation.java
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
PathUtils.java
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
QualityUtils.java
|
This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation.
|
2011-07-12 14:11:53 -04:00 |
|
ReservoirDownsampler.java
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
SWPairwiseAlignment.java
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
SampleUtils.java
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
SequenceDictionaryUtils.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
SimpleTimer.java
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
Utils.java
|
Moved ResolveHostname to general utils as a static function
|
2011-08-28 12:04:16 -04:00 |
|
package-info.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
3c8445b934