| .. |
|
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 |
|
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
|
UnitTest for reverseAlleleClipping
|
2012-01-18 07:35:11 -05:00 |
|
collections
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
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
|
Fixed NPE in getNextOverlappingBAMScheduleEntry() when mixed mapped/unmapped interval lists are used. Added integrationtest to verify behavior.
|
2012-01-12 13:29:11 -05:00 |
|
io
|
Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc.
|
2012-01-23 16:17:04 -05:00 |
|
pileup
|
GATKSAMRecord refactor
|
2011-11-03 15:43:26 -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
|
HaplotypeCaller now uses insertions and softclipped bases as possible triggers. LocusIteratorByState tags pileup elements with the required info to make this calculation efficient. The days of the extended event pileup are coming to a close.
|
2012-01-26 15:56:33 -05:00 |
|
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
|
Bug fix for incorrect logic in subsetSamples
|
2011-12-14 16:14:26 -05:00 |
|
BaseUtilsUnitTest.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -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 |
|
MWUnitTest.java
|
Reorganized the codebase beneath top-level public and private directories,
|
2011-06-28 06:55:19 -04:00 |
|
MathUtilsUnitTest.java
|
Added knuth-shuffle (KS) and randomSubset using KS to MathUtils
|
2012-01-03 09:29:46 -05:00 |
|
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 |
cdff23269d