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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Mark DePristo ad04fdb233 PerReadAlleleLikelihoodMap getMostLikelyAllele returns an MostLikelyAllele objects now 
-- This new functionality allows the client to make decisions about how to handle non-informative reads, rather than having a single enforced constant that isn't really appropriate for all users.  The previous functionality is maintained now and used by all of the updated pieces of code, except the BAM writers, which now emit reads to display to their best allele, regardless of whether this is particularly informative or not.  That way you can see all of your data realigned to the new HC structure, rather than just those that are specifically informative.
-- This all makes me concerned that the informative thresholding isn't appropriately used in the annotations themselves.  There are many cases where nearby variation makes specific reads non-informative about one event, due to not being informative about the second.  For example, suppose you have two SNPs A/B and C/D that are in the same active region but separated by more than the read length of the reads.   All reads would be non-informative as no read provides information about the full combination of 4 haplotypes, as they reads only span a single event.  In this case our annotations will all fall apart, returning their default values.  Added a JIRA to address this (should be discussed in group meeting)
 		2013-03-26 14:27:13 -04:00
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R R issue in Queue fixed. 2013-01-28 14:42:20 -05:00
activeregion Changing CALLED_IN_DB_UNKNOWN_STATUS to count as TRUE_POSITIVEs in the simplified stats for AssessNA12878. 2013-03-14 14:44:18 -04:00
analysis Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
baq Fixing BQSR/BAQ bug: 2013-01-31 11:03:17 -05:00
classloader Added verbose error message to the PluginManager 2013-02-19 16:00:35 -05:00
clipping Fixed reported bug in BQSR for RNA seq alignments with Ns. 2013-03-14 11:26:52 -04:00
codecs Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
collections Replace uses of NestedHashMap with NestedIntegerArray. 2013-02-27 14:03:39 -05:00
crypt Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
duplicates Cleanup and unit tests for QualityUtils 2013-02-16 07:31:37 -08:00
exceptions Created new DeprecatedToolChecks class 2013-03-20 06:46:02 -04:00
fasta Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00
file Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
fragments New GATKSAMRecord concept of a strandless read, update to FS 2013-03-13 11:16:36 -04:00
genotyper PerReadAlleleLikelihoodMap getMostLikelyAllele returns an MostLikelyAllele objects now 2013-03-26 14:27:13 -04:00
haplotypeBAMWriter PerReadAlleleLikelihoodMap getMostLikelyAllele returns an MostLikelyAllele objects now 2013-03-26 14:27:13 -04:00
help Created ListAnnotations utility (extends CommandLineProgram) 2013-03-20 06:15:27 -04:00
instrumentation Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
interval Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
io Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs 2013-01-30 16:42:23 -05:00
locusiterator Vast improvements to AssessNA12878 code and functionality 2013-02-21 20:43:12 -05:00
nanoScheduler Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
pairhmm Merged bug fix from Stable into Unstable 2013-03-18 12:36:21 -04:00
pileup Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
progressmeter Resolves Genome Sequence Analysis GSA-750 Don't print an endless series of starting messages from the ProgressMeter 2013-02-04 15:47:30 -05:00
recalibration The Bayesian calculation of Qemp in the BQSR is now hierarchical. This fixes issues in which the covariate bins were very sparse and the prior estimate being used was the original quality score. This resulted in large correction factors for each covariate which breaks the equation. There is also now a new option, qlobalQScorePrior, which can be used to ignore the given (very high) quality scores and instead use this value as the prior. 2013-01-28 15:56:33 -05:00
runtime Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
sam AlignmentUtils.calcNumDifferentBases computes the number of bases that differ between a reference and read sequence given a cigar between the two. 2013-03-20 22:54:35 -04:00
text Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
threading Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variant AssessNA12878 bugfixes 2013-03-18 15:48:08 -04:00
wiggle Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
AutoFormattingTime.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
BaseUtils.java - Added more comprehensive tests for consensus creation to RR. Still need to add tests for I/D ops. 2013-02-01 15:37:19 -05:00
BitSetUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ContigComparator.java Generalize and fixup ContigComparator 2013-02-09 09:52:13 -05:00
DeprecatedToolChecks.java Created new DeprecatedToolChecks class 2013-03-20 06:46:02 -04:00
GenomeLoc.java Added distance across contigs calculation to GenomeLocs 2013-02-07 16:31:41 -05:00
GenomeLocParser.java Refactoring and unit testing GenomeLocParser 2013-01-30 09:47:47 -05:00
GenomeLocSortedSet.java Fixed the add functionality of GenomeLocSortedSet. 2013-02-28 23:31:00 -05:00
Haplotype.java HaplotypeCaller now has the ability to only consider the best N haplotypes for genotyping 2013-03-20 22:54:36 -04:00
HasGenomeLocation.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
HeapSizeMonitor.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
IndelUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
LRUCache.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MRUCachingSAMSequenceDictionary.java Refactoring and unit testing GenomeLocParser 2013-01-30 09:47:47 -05:00
MannWhitneyU.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
MathUtils.java Final edge case bug fixes to QualityUtil routines 2013-02-16 07:31:38 -08:00
Median.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MendelianViolation.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MultiThreadedErrorTracker.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
NGSPlatform.java Expand NGSPlatform to meet SAM 1.4 spec, with full unit tests 2013-02-09 11:16:21 -05:00
PathUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
QualityUtils.java Relax bounds checking in QualityUtils.boundQual 2013-02-22 08:46:59 -05:00
SWPairwiseAlignment.java Expanded functionality for writing BAMs from HaplotypeCaller 2013-03-03 12:07:29 -05:00
SWPairwiseAlignmentMain.java Expanded functionality for writing BAMs from HaplotypeCaller 2013-03-03 12:07:29 -05:00
SampleUtils.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
SequenceDictionaryUtils.java Sequence dictionary validation: detect problematic contig indexing differences 2013-02-25 11:14:22 -05:00
SimpleTimer.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
UnvalidatingGenomeLoc.java Refactoring the SimpleGenomeLoc into the now public utility UnvalidatingGenomeLoc and the RR-specific FinishedGenomeLoc. 2013-01-30 10:45:29 -05:00
Utils.java HaplotypeCaller now uses SeqGraph instead of kmer graph to build haplotypes. 2013-03-20 22:54:36 -04:00
package-info.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00