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gatk-3.8/java/src/org/broadinstitute/sting/utils
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asivache 144b424933 Added : String reverse(String s) - reverses a string 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1416 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-08-12 20:16:22 +00:00
..
cmdLine Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very* 2009-07-29 16:11:45 +00:00
containers A priority-queue-like container that allows you to add a specified number of elements. When the limit has been reached, new additions replace the lower scoring elements. 2009-06-24 15:39:47 +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 Better handling of fasta files with non-standard extensions.x 2009-07-09 18:18:48 +00:00
genotype Continuing cleanup of SSG. GenotypeLikelihoods now have extensive testing routines. DiploidGenotype supports het, homref, etc calculations. SSG has been cleaned up to remove old garbage functionality. Also now supports output to standard output by simply omitting varout 2009-08-05 22:25:30 +00:00
io Package level documentation -- helps new users get acclimated to the codebase more quickly. 2009-06-17 16:27:48 +00:00
sam Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
threading Package level documentation -- helps new users get acclimated to the codebase more quickly. 2009-06-17 16:27:48 +00:00
windowmaker template for windowmaker utility -- total non-functional 2009-05-07 18:13:03 +00:00
AlignmentUtils.java -set indel cleaning walkers to be in core package 2009-07-24 05:23:29 +00:00
BaseUtils.java Added : String reverse(String s) - reverses a string 2009-08-12 20:16:22 +00:00
BasicPileup.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
ComparableSAMRecord.java only compare pair position for paired end reads 2009-07-08 04:07:08 +00:00
ExpandingArrayList.java Updated version of the recalibration tool 2009-06-19 17:45:47 +00:00
FileProgressTracker.java moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes. 2009-03-27 14:02:55 +00:00
GenomeLoc.java Windowed access to the reference. 2009-08-05 16:29:15 +00:00
GenomeLocParser.java performance improvement to GenomeLocParser -- moved regex pattern compile out of local field 2009-07-17 02:56:25 +00:00
GenomeLocSortedSet.java added a big speed-up for interval list input processing. With large interval sets this was taking way too long... 2009-07-13 22:00:00 +00:00
GenotypeUtils.java -Output single filtration stats file with input from all filters 2009-08-03 20:44:21 +00:00
JVMUtils.java Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very* 2009-07-29 16:11:45 +00:00
ListUtils.java Added ability to sample from a list *without* replacement. 2009-07-23 21:00:19 +00:00
LogisticRegressor.java Several changes to CovariateCounter walker to print more tables (called vs. observed Q scores), bug fixes to LogisticRecalibrationWalker and LogisticRegressor, and print string functionality added to Pair. 2009-04-28 00:37:48 +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 several useful routines to MathUtils for summing and bounds checking of doubles 2009-08-05 00:41:31 +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 Version 0.2.1 (released) of the TableRecalibrator 2009-06-25 22:50:55 +00:00
ReadBackedPileup.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
RefHanger.java Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser. 2009-06-30 19:17:24 +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 Major: allow genotyper to optionally output in 1KG format, including outputting the samples in which indels are found. 2009-07-23 19:53:51 +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