ebanks 2838629724 -VCF writer now checks whether the allele frequency has been set before trying to write it out. ... -Renamed methods to be more consistent. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2214 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-02 16:25:32 +00:00
..
bed	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
cmdLine	adding error log reporting to the GATK, and a stream based output method for the argument collection	2009-10-28 19:56:05 +00:00
duplicates	Restructuring and interface change to ReadBackedPileup. We now lower support the Pileup interface, the BasicPileup static methods, and the ReadBackedPileup class. Now everything is a ReadBackedPileup and all methods to manipulate pileups are off of it. Also provides the recommended iterable() interface of pileup elements so you can use the syntax for (PileupElement p : pileup) and access directly from p.getBase() and p.getQual() and p.getSecondBase(). Only a few straggler walkers use the old style interface -- but those walkers will be retired soon. Documentation coming in the AM. Please everyone use the new syntax, it's safer, and will be more efficient as soon as the LocusIteratorByState directly emits the ReadBackedPileup for the Alignment context, as opposed to the current interface. In the process of the change over, discovered several bugs in the second-best base code due to things getting out of sync, but these changes were resolved manually. All other integrationtests passed without modification.	2009-11-25 03:51:41 +00:00
fasta	fix for bug GSA-234: fasta index files couldn't handle anything but letters, numbers, or spaces in the contig name	2009-11-24 19:19:47 +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	-VCF writer now checks whether the allele frequency has been set before trying to write it out.	2009-12-02 16:25:32 +00:00
pileup	fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview	2009-12-02 15:41:35 +00:00
sam	Completing the optimization started by Matt: we now wrap SAMRecords and SAMReadGroupRecords with our own versions which cache oft-used variables (e.g. platform, readString, strand flag). All walkers automagically get this speedup since the wrapping occurs in the engine.	2009-11-30 17:39:29 +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	read.getReadString().charAt(offset) --> read.getReadBases()[offset]	2009-11-24 04:25:19 +00:00
BaseUtils.java	fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview	2009-12-02 15:41:35 +00:00
BasicPileup.java	ReadBackedPileup in all its glory. Documented, aligned with the output of LocusIteratorByState, and caching common outputs for performance	2009-11-25 20:54:44 +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	Validates intervals against sequence dictionary header bounds.	2009-10-22 19:31:15 +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	Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.	2009-09-29 22:23:19 +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	Stage 1 of the VariantFiltration refactoring is now complete. There now exists a parallel tool called VariantAnnotator which simply takes variant calls and annotates them with the same type of data that we used to use for filtering (e.g. DoC, allele balance). The output is a VCF with the INFO field appropriately annotated.	2009-11-16 02:41:20 +00:00
MergingIterator.java	General purpose merging iterator implementation	2009-09-12 19:06:15 +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	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
QualityUtils.java	Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5)	2009-08-28 14:14:21 +00:00
SWPairwiseAlignment.java	-set indel cleaning walkers to be in core package	2009-07-24 05:23:29 +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
Utils.java	minor code cleanup	2009-11-30 20:57:20 +00:00
WilcoxonRankSum.java	An unfinished implementation of the Wilcoxon rank sum test and a variant annotation that uses it. I need to merge and update this code with Tim's implementation somehow - but that won't happen until later this week, so I'm committing this before I accidentally blow it away.	2009-12-01 04:56:17 +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