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gatk-3.8/java/src/org/broadinstitute/sting/gatk/walkers
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depristo 40f8e7644c Better, multi-haplotype aware haplotype scores. Looking very good now, seems to be vastly better at dealing with incorrect calls in deep and low pass data. Almost ready for use 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3099 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-03-30 23:57:36 +00:00
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annotator Better, multi-haplotype aware haplotype scores. Looking very good now, seems to be vastly better at dealing with incorrect calls in deep and low pass data. Almost ready for use 2010-03-30 23:57:36 +00:00
concordance Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system. 2010-03-09 03:41:07 +00:00
coverage Let's *not* import classes that no longer exist. How my own ant test compiled is beyond me. 2010-03-29 13:59:01 +00:00
fasta Renaming and moving relevant tools into a sequenom directory 2010-03-10 02:31:10 +00:00
filters Now checks if the i-th element of the FiltrationContext[] is null before trying to access it. This seems to happen occassionally at the very end of a VCF file... the array will be 6 elements long, but the last element will actually be null. 2010-03-30 22:40:17 +00:00
genotyper Deleting incorrect sampling genotype likelihoods from the codebase 2010-03-30 23:56:35 +00:00
indels Rods for reads hooked up into the cleaner 2010-03-24 18:17:56 +00:00
qc adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 2010-03-03 15:56:44 +00:00
recalibration -Push the --use_original_qualities argument into the engine. 2010-03-16 02:06:11 +00:00
sequenom misc improvements 2010-03-10 03:00:28 +00:00
varianteval Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system. 2010-03-09 03:41:07 +00:00
Allows.java @Required / @Allows flags for main arguments. 2009-05-19 23:26:17 +00:00
By.java Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along 2009-05-15 21:02:12 +00:00
ClipReadsWalker.java -Push the --use_original_qualities argument into the engine. 2010-03-16 02:06:11 +00:00
DataSource.java Framework for ROD walkers -- totally experiment and not working right now 2009-09-12 19:13:15 +00:00
DuplicateWalker.java Removed used routines in duputils; duplicatequals to archive; docs for new duplicate traversal code; general code cleanup; bug fixes for combineduplicates; integration tests for combine duplicates walker 2009-12-29 19:46:29 +00:00
FixBAMSortOrderTag.java adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 2010-03-03 15:56:44 +00:00
FlagStatWalker.java adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 2010-03-03 15:56:44 +00:00
LocusWalker.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
PileupWalker.java Refactoring and migration of new allele/variantcontext/genotype code into oneoffprojects. NOT FOR USE. PlinkRod commented out due to dependence on this new, rapidly changing interface. 2010-01-26 13:53:29 +00:00
PrintRODsWalker.java More documentation for walkers that I'm familiar with in the collection of core walkers. 2009-12-11 18:02:33 +00:00
PrintReadsWalker.java adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 2010-03-03 15:56:44 +00:00
RMD.java Windowed access to the reference. 2009-08-05 16:29:15 +00:00
ReadFilters.java Better support for specifying read filters to apply directly from the walkers. 2009-07-09 23:59:53 +00:00
ReadPairWalker.java For Sarah Calvo: initial implementation of read pair traversal, for BAM files 2010-03-21 23:22:25 +00:00
ReadWalker.java adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 2010-03-03 15:56:44 +00:00
RefWalker.java Added REFERENCE_BASES required annotation for performance 2009-06-18 21:03:57 +00:00
Reference.java Windowed access to the reference. 2009-08-05 16:29:15 +00:00
Requires.java @Required / @Allows flags for main arguments. 2009-05-19 23:26:17 +00:00
RodWalker.java Framework for ROD walkers -- totally experiment and not working right now 2009-09-12 19:13:15 +00:00
SplitSamFileWalker.java adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 2010-03-03 15:56:44 +00:00
TreeReducible.java N-way parallelism. Works for small test cases. Untested for large test cases. 2009-05-01 19:34:09 +00:00
VariantsToVCF.java Moving VariantsToVCF to core. 2010-03-26 18:55:12 +00:00
Walker.java Rework the way the MicroScheduler handles locus shards to handle intervals that span shards 2010-03-11 18:40:31 +00:00
WalkerName.java Make command-line arguments available in walker constructor, provide back door from 2009-03-26 20:45:27 +00:00
Window.java Windowed access to the reference. 2009-08-05 16:29:15 +00:00
package-info.java Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file 2009-12-04 20:08:41 +00:00