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bed
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GSA-182: Adding support for BED interval files.
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2009-10-06 02:45:31 +00:00 |
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cmdLine
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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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duplicates
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Move MSG - plus now obsolete classes which it depends on -- to oneoffprojects (with permission from Jared).
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2009-12-02 20:04:22 +00:00 |
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fasta
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A bit of cleanup in preparation for Picard patch.
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2009-12-08 16:09:04 +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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A few improvements to pooled concordance calcluations. Now will show you FN with the -V option. BasicGenotype now prints out a reasonable representaiton wiwth toString
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2009-12-10 23:09:10 +00:00 |
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help
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Move some files around to reflect our growing help infrastructure.
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2009-12-07 19:23:12 +00:00 |
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pileup
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Fixed deletion depth calculation plus mis-spelling in ReadBackedPileup method.
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2009-12-10 21:11:42 +00:00 |
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sam
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Completing the optimization started by Matt: we now wrap SAMRecords and SAMReadGroupRecords with our own versions which cache oft-used variables (e.g. platform, readString, strand flag). All walkers automagically get this speedup since the wrapping occurs in the engine.
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2009-11-30 17:39:29 +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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AlignmentUtils.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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BaseUtils.java
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Added --solid_recal_mode argument to experiment with different ways of dealing with solid reference bias. Currently the default option is DO_NOTHING which means use the same behavior as the old recalibrator. Eventually the new methods in RecalDataManager will be moved over to a SolidUtils class. Added transition and transversion methods to BaseUtils that work like simpleComplement, used with the color space in my solid methods. Also, initial check-in of HomopolymerCovariate.
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2009-12-07 14:26:27 +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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comments for eric
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2009-11-13 14:19:31 +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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Validates intervals against sequence dictionary header bounds.
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2009-10-22 19:31:15 +00:00 |
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GenomeLocSortedSet.java
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GSA-182: Adding support for BED interval files.
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2009-10-06 02:45:31 +00:00 |
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GenotypeUtils.java
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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.
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2009-10-23 06:31:15 +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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Stage 1 of the VariantFiltration refactoring is now complete. There now exists a parallel tool called VariantAnnotator which simply takes variant calls and annotates them with the same type of data that we used to use for filtering (e.g. DoC, allele balance). The output is a VCF with the INFO field appropriately annotated.
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2009-11-16 02:41:20 +00:00 |
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MergingIterator.java
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General purpose merging iterator implementation
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2009-09-12 19:06:15 +00:00 |
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PackageUtils.java
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New PackageUtils interferes with the packaging utility. Revert until Aaron and
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2009-11-02 19:14:14 +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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Allow users to directly specify filters from the command-line, applicable to
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2009-11-10 18:40:16 +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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Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5)
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2009-08-28 14:14:21 +00:00 |
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SWPairwiseAlignment.java
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-set indel cleaning walkers to be in core package
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2009-07-24 05:23:29 +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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Clean up some of the walker help output based on additional experience and
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2009-12-07 21:33:11 +00:00 |
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Utils.java
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minor code cleanup
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2009-11-30 20:57:20 +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.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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