depristo be333da9c0 charSeq2byteSeq -- convert a char[] to a byte[] for convenience ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1917 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-27 21:52:23 +00:00
..
bed	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
cmdLine	Improved error messages -- now easier to read, points to the GATK Error Messages wiki, and avoids double printing of stack traces	2009-10-15 12:07:44 +00:00
containers	Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.	2009-10-20 12:23:36 +00:00
duplicates	Cleanup emergency fixes for out-of-bounds issues in reference retrieval. Fix spelling mistakes.	2009-07-06 15:41:30 +00:00
fasta	Bumping version of Picard for firehose compatibility.	2009-10-16 19:38:56 +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	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
io	Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.	2009-10-20 12:23:36 +00:00
sam	General-purpose management of output streams.	2009-08-23 00:56:02 +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	the life in the magical kingdom of fully spec-conforming SAM files would be so... magical. For now, however, there are plenty of ways to end up with inconsistent SAM records. For instance, a SAM file with missing header will result in SAM records with ref. name set, but getReferenceIndex() returning null. This, in turn, was tripping isReadUnmapped(). The method is now fixed, so that it suffices to have *either* reference name *or* reference index set for the read to be considered mapped (the flag is still checked)	2009-09-14 16:04:19 +00:00
BaseUtils.java	charSeq2byteSeq -- convert a char[] to a byte[] for convenience	2009-10-27 21:52:23 +00:00
BasicPileup.java	@BasicPileup - made the counts public so they can be used	2009-10-16 21:56:56 +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
GenomeLoc.java	Easier to print GenomeLoc compareTo()	2009-09-12 19:10:35 +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	@ListUtils - Bugfix in getQScoreOrderStatistic: method would attempt to access an empty list fed into it. Now it checks for null pointers and returns 0.	2009-08-27 19:31:53 +00:00
MergingIterator.java	General purpose merging iterator implementation	2009-09-12 19:06:15 +00:00
PackageUtils.java	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +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
Pileup.java	General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.	2009-04-14 22:13:10 +00:00
Predicate.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +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
ReadBackedPileup.java	Major code refactoring:	2009-10-20 14:58:04 +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	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
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