| .. |
|
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
|
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 |
|
clipreads
|
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 |
|
codecs
|
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 |
|
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
|
gatkdoc now generalized to use @Annotation. Multiple subsystems now use annotation to receive docs
|
2011-07-23 20:00:35 -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
|
Default values now displayed in arguments
|
2011-07-24 22:56:55 -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
|
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 |
|
pileup
|
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 |
|
pileup2
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
sam
|
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 |
|
text
|
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 |
|
threading
|
Removed GATK use of distributed parallelism framework.
|
2011-07-20 16:26:09 -04:00 |
|
variantcontext
|
CombineVariants no longer combines records of different types. So now when combining SNP and indel callsets, overlapping calls get their own records. Useful for Khalid in the pipeline. For those interested, it turns out the previous behavior was doing the wrong thing occasionally (and this was even captured in the integration tests).
|
2011-07-18 13:42:45 -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 |
|
BaseUtils.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -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
|
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 |
|
GenomeLocParser.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 |
|
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
|
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 |
|
MannWhitneyU.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
MathUtils.java
|
Complete refactor of the ReplicationValidation framework, plus the following new functionality:
|
2011-07-21 21:39:00 -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
|
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 |
|
package-info.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
95b48eface