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gatk-3.8/java/src/org/broadinstitute/sting/utils
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aaron de6ae51f7e Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar. 
A couple of notes:
-Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed).
-Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing).
-Added configurations items to the ivy xml file.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1956 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-11-02 06:02:41 +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
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 -Generalized the GenotypeConcordance module to deal with any number of individuals (although it will default to its old behavior if the -samples argument is left out). 2009-11-01 05:35:47 +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
GATKErrorReport.java 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
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 @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 Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar. 2009-11-02 06:02:41 +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