Eric Banks d6277b70d8 Forgot to consider the optimized case in hasAllele		2012-04-24 11:32:28 -04:00
..
R	Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.	2012-04-17 14:22:48 -04:00
activeregion	Fixing a bug when breaking up active regions where the resulting regions would overlap by one base. Adding quality score manipulation from the UG into the haplotype caller (qual capped by mapping quality, min qual threshold).	2012-04-20 14:02:55 -04:00
analysis	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
baq	On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live.	2012-02-13 12:35:09 -05:00
classloader	Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.	2011-09-27 14:33:57 -04:00
clipping	BitSet implementation of the on-the-fly recalibration using the CSV format file.	2012-03-16 13:02:15 -04:00
codecs	If we are subsetting alleles in the UG (either because there were too many or because some were not polymorphic), then we may need to trim the alleles (because the original VariantContext may have had to pad at the end). Thanks to Ryan for reporting this. Only one of the integration tests had even partially covered this case, so I added one that did.	2012-04-20 17:00:05 -04:00
collections	Standalone common Pair HMM utility class with associated unit tests.	2012-03-01 22:41:13 -05:00
crypt	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
duplicates	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
exceptions	Catch poorly formatted PL/GL fields	2012-04-23 09:33:50 -04:00
fasta	Fix for ref 0 bases for Chris	2012-01-24 10:55:09 -05:00
file	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
fragments	BitSet implementation of the on-the-fly recalibration using the CSV format file.	2012-03-16 13:02:15 -04:00
gcf	Vastly better way of doing on-demand genotyping loading	2011-11-20 08:23:09 -05:00
help	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -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	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	Adding read position rank sum test to the list of annotations that get produced with the HaplotypeCaller	2012-04-17 17:00:00 -04:00
pileup2	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
recalibration	BQSR bug triage #3	2012-04-19 17:31:04 -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	BQSR triage and test routines	2012-04-23 11:23:00 -04:00
text	Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.	2012-04-17 14:22:48 -04:00
threading	Removed GATK use of distributed parallelism framework.	2011-07-20 16:26:09 -04:00
variantcontext	Forgot to consider the optimized case in hasAllele	2012-04-24 11:32:28 -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
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	laying groundwork to have insertions and deletions going through the system.	2012-02-07 18:11:53 -05:00
BitSetUtils.java	BitSets keys to lower BQSR's memory footprint	2012-03-16 13:01:48 -04:00
ContigComparator.java	Documented following the new gatkdoc framework	2011-07-25 00:25:08 -04:00
GenomeLoc.java	make the size of a GenomeLoc int instead of long	2012-02-03 17:12:42 -05:00
GenomeLocComparator.java	Optimized interval iteration	2011-09-28 16:07:34 -04:00
GenomeLocParser.java	Merged bug fix from Stable into Unstable	2011-12-08 13:11:39 -05:00
GenomeLocSortedSet.java	Active region walkers can now see the reads in a buffer around thier active reigons. This buffer size is specified as a walker annotation. Intervals are internally extended by this buffer size so that the extra reads make their way through the traversal engine but the walker author only needs to see the original interval. Also, several corner case bug fixes in active region traversal.	2012-01-19 22:05:08 -05:00
Haplotype.java	Adding function call in HaplotypeCaller right before the VariantContext gets written out to disk which partitions all the reads by which allele gave the read the highest likelihood. This will allow variants to be annotated by the refactored VariantAnnotator. Uninformative reads are mapped to Allele.NO_CALL	2012-04-06 00:22:52 -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	Improvements to indel analysis capabilities of VariantEval	2012-04-06 16:07:46 -04:00
MannWhitneyU.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
MathUtils.java	minor misc optimizations to PairHMM	2012-04-18 15:02:26 -04:00
Median.java	ReadGroupProperties walker and associated infrastructure	2012-03-01 15:01:11 -05:00
MendelianViolation.java	Cleaned up unused import statements	2011-11-30 15:30:30 +01:00
NGSPlatform.java	BQSR with indels integrated!	2012-02-09 18:46:45 -05:00
PairHMM.java	Revert some bad merge changes	2012-04-18 16:35:09 -04:00
PathUtils.java	GATKPerformanceOverTime script update	2012-01-02 09:58:46 -05:00
QualityUtils.java	BQSR bug triage #3	2012-04-19 17:31:04 -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	Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.	2012-04-17 14:22:48 -04:00
SequenceDictionaryUtils.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
SimpleTimer.java	Removing contracts for the SimpleTimer	2011-11-06 22:22:49 -05:00
Utils.java	Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.	2012-04-17 14:22:48 -04:00
package-info.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00