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bed
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Looks bigger than it is:
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2010-01-15 00:14:35 +00:00 |
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cmdLine
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Update our error messages to point to getsatisfaction.com/gsa.
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2010-01-27 19:16:28 +00:00 |
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duplicates
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Removed used routines in duputils; duplicatequals to archive; docs for new duplicate traversal code; general code cleanup; bug fixes for combineduplicates; integration tests for combine duplicates walker
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2009-12-29 19:46:29 +00:00 |
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fasta
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Put a major.minor version into the GATK Javadoc for reading. Also,
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2010-01-15 21:48:30 +00:00 |
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fastq
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Improvements to make this work with uncompressed fastq files. Pulled the fastq parser out into it's own SAMFileReader-like entity.
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2009-09-03 17:20:16 +00:00 |
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genotype
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And now the UnifiedGenotyper can officially annotate genotype (FORMAT) fields too.
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2010-03-19 04:58:37 +00:00 |
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help
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Basic support for very simple index-driven locus traversals. Interface has been changed to
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2010-01-29 03:14:26 +00:00 |
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pileup
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new method to filter out overlapping PE reads
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2010-03-15 15:40:09 +00:00 |
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sam
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Let's make artificial reads that actually adhere to the specs...
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2010-03-17 16:51:42 +00:00 |
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threading
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Put a major.minor version into the GATK Javadoc for reading. Also,
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2010-01-15 21:48:30 +00:00 |
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AlignmentUtils.java
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refactored to provide a sum of mismatch quality scores capability as well (used by Cancer)
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2010-03-02 16:40:03 +00:00 |
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BaseUtils.java
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Unit tests for -XL arguments; expt. annotation calculating the GC content within 100 bp of the current SNP
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2010-03-14 21:08:14 +00:00 |
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CircularArray.java
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More archiving (with permission from Andrey) plus a move to core.
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2009-12-03 15:40:27 +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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Now uses expanding array list for coverage histograms. No hard limit on maximum depth now
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2009-09-16 23:27:25 +00:00 |
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GATKErrorReport.java
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Looks bigger than it is:
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2010-01-15 00:14:35 +00:00 |
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GenomeLoc.java
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code cleanup and containsStartPosition function
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2009-10-27 21:53:40 +00:00 |
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GenomeLocParser.java
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Remove some of the restrictions on getStart() and getStop(); getStart() and getStop()
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2010-03-17 19:39:30 +00:00 |
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GenomeLocSortedSet.java
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Unit tests for -XL arguments; expt. annotation calculating the GC content within 100 bp of the current SNP
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2010-03-14 21:08:14 +00:00 |
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JVMUtils.java
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Refactor the code I gave Eric yesterday to output command line arguments.
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2009-12-10 18:57:54 +00:00 |
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ListUtils.java
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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.
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2009-09-28 18:12:32 +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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Added - new tests (Hapmap was re-added)
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2009-12-14 21:57:20 +00:00 |
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MergingIterator.java
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some rods-for-reads cleaning and performance improvements.
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2010-03-10 22:54:58 +00:00 |
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NestedHashMap.java
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Optimization - Added method to Covariates: void getValues( SAMRecord read, Comparable[] comparable ) which takes an array of size (at least) read.getReadLength() and fills it with covariate values for all positions in the given read. Made CovariateCounterWalker and TableRecalibrationWalker use this method instead of calling getValue(..) for each covariate and each offset.
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2010-02-22 17:35:25 +00:00 |
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PackageUtils.java
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Some significant changes to the annotator:
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2010-03-18 05:38:32 +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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PluginManager.java
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a start to some of the infrastructure for Tribble, including dynamic detection of new RMD; not nearly wired in or complete yet.
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2010-02-18 18:43:52 +00:00 |
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PrimitivePair.java
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added PrimitivePair.Long and a few shortcut utility methods to PrimitivePairs: add(pair), subtract(pair), assignFrom(pair)
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2009-12-14 00:15:44 +00:00 |
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QualityUtils.java
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Variant optimizer now outputs VCF files via ApplyVariantClustersWalker. Documentation to be added to the wiki. It is ready to be used by other people but only with great caution.
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2010-03-17 20:41:42 +00:00 |
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SWPairwiseAlignment.java
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- Change sortOnDisk option to sortInMemory
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2010-02-17 20:52:57 +00:00 |
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SampleUtils.java
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Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system.
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2010-03-09 03:41:07 +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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TextFormattingUtils.java
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Better handling of enums by the command-line argument system.
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2010-01-20 21:36:46 +00:00 |
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Utils.java
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VariantContext to VCF converter. BeagleROD, and phasing of VCF calls. Integration tests galore :-)
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2010-02-09 19:02:25 +00:00 |
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WilcoxonRankSum.java
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Get rid of characters in the docs that aren't universally compatible with
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2009-12-07 21:41:07 +00:00 |
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package-info.java
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Put a major.minor version into the GATK Javadoc for reading. Also,
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2010-01-15 21:48:30 +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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