| .. |
|
R
|
No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
|
2011-10-27 14:17:07 -04:00 |
|
activeregion
|
Fixing a bug identified by the ActivityProfile unit tests
|
2012-03-15 14:24:30 -04:00 |
|
baq
|
Putative fix for BAQ array out of bounds
|
2011-09-21 11:25:08 -04:00 |
|
clipping
|
Add support for reads starting with insertion
|
2012-01-03 09:29:45 -05:00 |
|
codecs
|
Adding test for reading samtools VCF file
|
2012-02-27 17:05:50 -05:00 |
|
collections
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
crypt
|
Do not fail tests that require the GATK private key if the user does not have permission to read it
|
2012-03-06 15:57:02 -05:00 |
|
fasta
|
Reduced the number of combinations being tested here, which was overkill
|
2011-09-01 10:42:43 -04:00 |
|
fragments
|
GATKSAMRecord refactor
|
2011-11-03 15:43:26 -04:00 |
|
genotype/vcf
|
Change interface to getNegLog10PError to getLog10PError
|
2011-11-18 21:07:30 -05:00 |
|
interval
|
make the size of a GenomeLoc int instead of long
|
2012-02-03 17:12:42 -05:00 |
|
io
|
Public-key authorization scheme to restrict use of NO_ET
|
2012-03-06 00:09:43 -05:00 |
|
pileup
|
GATKSAMRecord refactor
|
2011-11-03 15:43:26 -04:00 |
|
recalibration
|
BitSet implementation of the on-the-fly recalibration using the CSV format file.
|
2012-03-16 13:02:15 -04:00 |
|
report
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
runtime
|
No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
|
2011-10-27 14:17:07 -04:00 |
|
sam
|
BitSet implementation of the on-the-fly recalibration using the CSV format file.
|
2012-03-16 13:02:15 -04:00 |
|
text
|
GATKReport v0.2:
|
2011-08-03 00:24:47 -04:00 |
|
threading
|
Removed GATK use of distributed parallelism framework.
|
2011-07-20 16:26:09 -04:00 |
|
variantcontext
|
Merged bug fix from Stable into Unstable
|
2012-03-16 14:33:53 -04:00 |
|
BaseUtilsUnitTest.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
BitSetUtilsUnitTest.java
|
BitSets keys to lower BQSR's memory footprint
|
2012-03-16 13:01:48 -04:00 |
|
GenomeLocParserUnitTest.java
|
During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice.
|
2011-11-17 13:56:42 -05:00 |
|
GenomeLocSortedSetUnitTest.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
GenomeLocUnitTest.java
|
Support for list of known CNVs in VariantEval
|
2011-11-30 17:05:16 -05:00 |
|
HaplotypeUnitTest.java
|
Minor misc updates
|
2012-03-06 10:14:45 -05:00 |
|
MWUnitTest.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
MathUtilsUnitTest.java
|
BitSets keys to lower BQSR's memory footprint
|
2012-03-16 13:01:48 -04:00 |
|
PathUtilsUnitTest.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
ReservoirDownsamplerUnitTest.java
|
Moving reduced read functionality into GATKSAMRecord
|
2011-10-21 13:28:05 -04:00 |
|
SimpleTimerUnitTest.java
|
The right fix for this test is just to delete it.
|
2011-11-15 14:53:27 -05:00 |
|
UtilsUnitTest.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
be9e48ba29