asivache 8330058216 method added: getEventStringsWithCounts() ... Returns list of Pairs <String,Integer>, where each pair consists of a unique indel event observed at the site and the total number of observations of that event. String representation for insertions is verbose (e.g. +ACT), while deletions are represented as "5D" (since read backed pileup has no reference information, so we can not get actual sequence of deleted bases) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2479 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-29 22:41:58 +00:00
..
bed	added changes to the code to allow different types of interval merging,	2009-12-23 21:59:14 +00:00
cmdLine	UnifiedGenotyper now works without -varout or -vf set.	2009-12-29 16:46:24 +00:00
duplicates	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
fasta	A bit of cleanup in preparation for Picard patch.	2009-12-08 16:09:04 +00:00
fastq	Improvements to make this work with uncompressed fastq files. Pulled the fastq parser out into it's own SAMFileReader-like entity.	2009-09-03 17:20:16 +00:00
genotype	Removed the VCF "NS" annotation (which wasn't working for pooled calls anyways) since it's ambiguous and not useful.	2009-12-29 17:30:47 +00:00
help	Get rid of backlink from ArgumentDefinitions to ArgumentSources. This will help in the future with multiple	2009-12-21 00:39:36 +00:00
pileup	method added: getEventStringsWithCounts()	2009-12-29 22:41:58 +00:00
sam	In TableRecalibrationWalker, update UQ tag if it was present in the original SAMRecord. This required a new sam.jar, which caused some other files to need to be changed.	2009-12-23 21:42:36 +00:00
threading	Package level documentation -- helps new users get acclimated to the codebase more quickly.	2009-06-17 16:27:48 +00:00
AlignmentUtils.java	Optimizations:	2009-12-16 21:39:58 +00:00
BaseUtils.java	Updating the two solid_recal_mode options to also change the previous base since solid aligner prefers single color mismatch alignments over true SNP alignments. COUNT_AS_MISMATCH mode has been removed completely. The default mode is now SET_Q_ZERO.	2009-12-17 20:07:26 +00:00
CircularArray.java	More archiving (with permission from Andrey) plus a move to core.	2009-12-03 15:40:27 +00:00
ComparableSAMRecord.java	only compare pair position for paired end reads	2009-07-08 04:07:08 +00:00
ExpandingArrayList.java	Now uses expanding array list for coverage histograms. No hard limit on maximum depth now	2009-09-16 23:27:25 +00:00
GATKErrorReport.java	comments for eric	2009-11-13 14:19:31 +00:00
GenomeLoc.java	code cleanup and containsStartPosition function	2009-10-27 21:53:40 +00:00
GenomeLocParser.java	added changes to the code to allow different types of interval merging,	2009-12-23 21:59:14 +00:00
GenomeLocSortedSet.java	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
GenotypeUtils.java	intermediate commit for some changes in the Variation system, so Eric can go ahead with his changes. Everything is pretty set, but the Variation interface could use a convenience method that joins all the alternate alleles.	2009-10-23 06:31:15 +00:00
JVMUtils.java	Refactor the code I gave Eric yesterday to output command line arguments.	2009-12-10 18:57:54 +00:00
ListUtils.java	Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass.	2009-09-28 18:12:32 +00:00
MalformedGenomeLocException.java	A fix for the 'rod blows up when it hits a GenomeLoc outside the reference' issu	2009-06-02 18:14:46 +00:00
MathUtils.java	Added - new tests (Hapmap was re-added)	2009-12-14 21:57:20 +00:00
MergingIterator.java	General purpose merging iterator implementation	2009-09-12 19:06:15 +00:00
NHashMap.java	Moved NHashMap to sting/utils	2009-12-28 20:57:32 +00:00
NestedHashMap.java	Recalibrator now uses NestedHashMap instead of NHashMap. The keys are now nested hash maps instead of Lists of Comparables. These results in a big speed up (thanks Tim!). There is still a little bit of clean up to do, but everything works now.	2009-12-29 21:01:32 +00:00
PackageUtils.java	New PackageUtils interferes with the packaging utility. Revert until Aaron and	2009-11-02 19:14:14 +00:00
Pair.java	The building blocks for segmenting covariate counting data by read group.	2009-06-04 19:55:24 +00:00
PathUtils.java	Added a method to refresh an NFS mount point (necessary to prevent NFS flakiness when running on the LSF farm.	2009-05-21 19:31:54 +00:00
PluginManager.java	Allow users to directly specify filters from the command-line, applicable to	2009-11-10 18:40:16 +00:00
PrimitivePair.java	added PrimitivePair.Long and a few shortcut utility methods to PrimitivePairs: add(pair), subtract(pair), assignFrom(pair)	2009-12-14 00:15:44 +00:00
QualityUtils.java	Point MAX_QUAL_SCORE to SAMUtils.MAX_PHRED_SCORE.	2009-12-24 20:47:32 +00:00
SWPairwiseAlignment.java	-set indel cleaning walkers to be in core package	2009-07-24 05:23:29 +00:00
SampleUtils.java	Adding sample utils for convenience methods to pull out samples from e.g. SAMFileHeader or Genotype objects	2009-12-18 18:51:21 +00:00
StingException.java	Changed Sting exception from a base exception to a runtime exception. This makes it so you can throw it without the consumer having to check it, and hopefully people will be more inclined to use it.	2009-04-29 22:09:41 +00:00
TextFormattingUtils.java	Incorporated feedback from Kiran. Use the Javadoc first sentence extraction capability to just show the first sentence from each line of Javadoc. @help.description can still be used to produce exceptionally verbose descriptions.	2009-12-11 21:59:55 +00:00
Utils.java	minor code cleanup	2009-11-30 20:57:20 +00:00
WilcoxonRankSum.java	Get rid of characters in the docs that aren't universally compatible with	2009-12-07 21:41:07 +00:00
package.html	Package level documentation -- helps new users get acclimated to the codebase more quickly.	2009-06-17 16:27:48 +00:00
xReadLines.java	Documentation and cleanup of xReadLines.	2009-03-25 15:36:21 +00:00