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cmdLine
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Better formatting of available walkers, and only output them along with help. Cleanup JVMUtils.
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2009-07-21 22:23:28 +00:00 |
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containers
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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.
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2009-06-24 15:39:47 +00:00 |
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duplicates
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Cleanup emergency fixes for out-of-bounds issues in reference retrieval. Fix spelling mistakes.
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2009-07-06 15:41:30 +00:00 |
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fasta
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Better handling of fasta files with non-standard extensions.x
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2009-07-09 18:18:48 +00:00 |
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genotype
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GLF rod as a AllelicVariant object.
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2009-07-21 00:55:52 +00:00 |
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io
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Package level documentation -- helps new users get acclimated to the codebase more quickly.
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2009-06-17 16:27:48 +00:00 |
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sam
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Fix minor bug introduced in filtration, and cleaned up the artificial sam records so that they use SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX and SAMRecord.NO_ALIGNMENT_START rather than hardcoded -1's.
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2009-07-22 22:37:41 +00:00 |
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threading
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Package level documentation -- helps new users get acclimated to the codebase more quickly.
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2009-06-17 16:27:48 +00:00 |
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windowmaker
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template for windowmaker utility -- total non-functional
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2009-05-07 18:13:03 +00:00 |
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BaseUtils.java
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AlleleBalance and on/off primary base filters -- version 0.0.1 -- for experimental use only
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2009-07-22 17:54:44 +00:00 |
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BasicPileup.java
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AlleleBalance and on/off primary base filters -- version 0.0.1 -- for experimental use only
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2009-07-22 17:54:44 +00:00 |
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ComparableSAMRecord.java
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only compare pair position for paired end reads
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2009-07-08 04:07:08 +00:00 |
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ExpandingArrayList.java
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Updated version of the recalibration tool
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2009-06-19 17:45:47 +00:00 |
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FileProgressTracker.java
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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.
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2009-03-27 14:02:55 +00:00 |
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GenomeLoc.java
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Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.
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2009-06-30 19:17:24 +00:00 |
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GenomeLocParser.java
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performance improvement to GenomeLocParser -- moved regex pattern compile out of local field
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2009-07-17 02:56:25 +00:00 |
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GenomeLocSortedSet.java
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added a big speed-up for interval list input processing. With large interval sets this was taking way too long...
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2009-07-13 22:00:00 +00:00 |
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GenotypeUtils.java
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minor changes
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2009-05-26 21:03:06 +00:00 |
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JVMUtils.java
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Better formatting of available walkers, and only output them along with help. Cleanup JVMUtils.
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2009-07-21 22:23:28 +00:00 |
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ListUtils.java
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Added unit tests for function in ListUtils to randomly sample lists with replacement, updated AlleleFrequencyEstimate to provide a callType of HomRef, HetSNP, HomSNP, update indices in CoverageEval.py, and made a lot of changes to CoverageWalker biggest one being that it directly calls SingleSampleGenotyper instead of implementing some parts of SSG itself.
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2009-07-08 02:05:40 +00:00 |
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LogisticRegressor.java
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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.
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2009-04-28 00:37:48 +00:00 |
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MalformedGenomeLocException.java
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A fix for the 'rod blows up when it hits a GenomeLoc outside the reference' issu
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2009-06-02 18:14:46 +00:00 |
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MathUtils.java
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major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.
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2009-06-05 23:34:37 +00:00 |
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PackageUtils.java
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Switched to Reflections (http://code.google.com/p/reflections/) project for
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2009-07-21 18:32:22 +00:00 |
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Pair.java
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The building blocks for segmenting covariate counting data by read group.
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2009-06-04 19:55:24 +00:00 |
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PathUtils.java
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Added a method to refresh an NFS mount point (necessary to prevent NFS flakiness when running on the LSF farm.
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2009-05-21 19:31:54 +00:00 |
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Pileup.java
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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.
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2009-04-14 22:13:10 +00:00 |
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Predicate.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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PrimitivePair.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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QualityUtils.java
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Version 0.2.1 (released) of the TableRecalibrator
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2009-06-25 22:50:55 +00:00 |
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ReadBackedPileup.java
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Behold MultiSampleCaller!
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2009-06-16 20:03:24 +00:00 |
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RefHanger.java
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Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.
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2009-06-30 19:17:24 +00:00 |
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StingException.java
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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.
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2009-04-29 22:09:41 +00:00 |
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Utils.java
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Fix for GSA-90: System isn't failing with an error when you use the wrong reference.
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2009-07-13 20:42:12 +00:00 |
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package.html
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Package level documentation -- helps new users get acclimated to the codebase more quickly.
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2009-06-17 16:27:48 +00:00 |
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xReadLines.java
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Documentation and cleanup of xReadLines.
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2009-03-25 15:36:21 +00:00 |
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