Ryan Poplin b8709d8c67 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable		2012-08-06 11:41:28 -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	HaplotypeCaller now use an excessive number of high quality soft clips as a triggering signal in order to capture both end points of a large deletion in a single active region.	2012-07-27 12:44:02 -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	Cleanup BQSR classes	2012-07-31 08:11:03 -04:00
clipping	Cleanup BQSR classes	2012-07-31 08:11:03 -04:00
codecs	Prevent NumberFormatExceptions when parsing the VCF POS field	2012-08-06 11:19:54 -04:00
collections	Refactored/renamed the nested integer array; cleaned up code a bit.	2012-07-03 00:12:33 -04:00
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	Requested by Geraldine: adding a utility to register deprecated walkers (and the major version of the first release since they were removed) so that the User Error printed out for e.g. CountCovariates now states: Walker CountCovariates is no longer available in the GATK; it has been deprecated since version 2.0.	2012-08-01 09:50:00 -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	First pass of implementation of Reduced Reads with HaplotypeCaller. Main changes: a) Active region: scale PL's by representative count to determine whether region is active. b) Scale per-read, per-haplotype likelihoods by read representative counts. A read representative count is (temporarily) defined as the average representative count over all bases in read, TBD whether this is good enough to avoid biases in GL's. c) DeBruijn assembler inserts kmers N times in graph, where N is min representative count of read over kmer span - TBD again whether this is the best approach. d) Bug fixes in FragmentUtils: logic to merge fragments was wrong in cases where there is discrepancy of overlaps between unclipped/soft clipped bases. Didn't affect things before but RR makes prevalence of hard-clipped bases in CIGARs more prevalent so this was exposed. e) Cache read representative counts along with read likelihoods associated with a Haplotype. Code can/should be cleaned up and unified with PairHMMIndelErrorModelCode, as well as refactored to support arbitrary ploidy in HaplotypeCaller	2012-08-03 12:24:23 -04:00
help	Removed Categories.	2012-07-25 13:46:24 -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	Refactored parsing of Rod/IntervalBinding. Queue S/G now uses all interval arguments passed to CommandLineGATK QFunctions including support for BED/tribble types, XL, ISR, and padding.	2012-06-27 01:15:22 -04:00
io	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
pileup	Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.	2012-06-15 15:55:03 -04:00
pileup2	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
recalibration	Ready for full-scale evaluation adaptive BQSR contexts	2012-08-03 16:02:53 -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	Fixed AlignmentUtils bug for handling Ns in the CIGAR string. Added a UG integration test that calls a BAM with such reads (provided by a user on GetSatisfaction).	2012-07-31 15:37:22 -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	Update BCF2 to include a minor version number so we can rev (and report errors) with BCF2	2012-08-02 17:30:30 -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	Initial checkpoint commit of VariantContext/Allele refactoring. There were just too many problems associated with the different representation of alleles in VCF (padded) vs. VariantContext (unpadded). We are moving VC to use the VCF representation. No more reference base for indels in VC and no more trimming and padding of alleles. Even reverse trimming has been stopped (the theory being that writers of VCF now know what they are doing and often want the reverse padding if they put it there; this has been requested on GetSatisfaction). Code compiles but presumably pretty much all tests with indels with fail at this point.	2012-07-26 01:50:39 -04:00
BitSetUtils.java	Refactoring of BQSRv2 to use longs (and standard bit fiddling techniques) instead of Java BitSets for performance improvements.	2012-06-12 09:19:36 -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	As a user pointed out, it is not valid for a GenomeLoc to have a start or stop equal to 0.	2012-07-17 22:18:43 -04:00
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	Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2012-08-06 11:41:28 -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	First pass of implementation of Reduced Reads with HaplotypeCaller. Main changes: a) Active region: scale PL's by representative count to determine whether region is active. b) Scale per-read, per-haplotype likelihoods by read representative counts. A read representative count is (temporarily) defined as the average representative count over all bases in read, TBD whether this is good enough to avoid biases in GL's. c) DeBruijn assembler inserts kmers N times in graph, where N is min representative count of read over kmer span - TBD again whether this is the best approach. d) Bug fixes in FragmentUtils: logic to merge fragments was wrong in cases where there is discrepancy of overlaps between unclipped/soft clipped bases. Didn't affect things before but RR makes prevalence of hard-clipped bases in CIGARs more prevalent so this was exposed. e) Cache read representative counts along with read likelihoods associated with a Haplotype. Code can/should be cleaned up and unified with PairHMMIndelErrorModelCode, as well as refactored to support arbitrary ploidy in HaplotypeCaller	2012-08-03 12:24:23 -04:00
Median.java	ReadGroupProperties walker and associated infrastructure	2012-03-01 15:01:11 -05:00
MendelianViolation.java	Efficient Genotype object Intermediate commit	2012-06-14 16:42:24 -04:00
NGSPlatform.java	Stabilized NGSPlatform code: don't assume all reads have read groups (e.g. artificial SAM records)	2012-06-06 15:17:30 -04:00
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	Extensive unit tests, contacts, and documentation for RecalDatum	2012-07-31 08:11:03 -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	Phase I commit to get shadowBCFs passing tests	2012-06-21 15:16:26 -04:00
SequenceDictionaryUtils.java	Cleanup Genotypes	2012-06-14 16:42:36 -04:00
SimpleTimer.java	Removing contracts for the SimpleTimer	2011-11-06 22:22:49 -05:00
Utils.java	Algorithmically faster version of DiffEngine	2012-06-14 16:42:30 -04:00
package-info.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00