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bed
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added changes to the code to allow different types of interval merging,
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2009-12-23 21:59:14 +00:00 |
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cmdLine
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UnifiedGenotyper now works without -varout or -vf set.
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2009-12-29 16:46:24 +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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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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We emit genotype data in the VCF record if the format string instructs us to (regardless of whether or not genotypes are provided - this was the wrong test).
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2010-01-13 15:40:27 +00:00 |
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help
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Get rid of backlink from ArgumentDefinitions to ArgumentSources. This will help in the future with multiple
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2009-12-21 00:39:36 +00:00 |
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pileup
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reverting last changes. no cacheing
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2010-01-06 18:59:37 +00:00 |
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sam
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A rogue QualityUtils.MAX_REASONABLE_Q_SCORE managed to get through my previous bug fix. It should instead check the command line -maxQ argument.
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2010-01-07 21:17:39 +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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Support throughout for S and N cigar elements.
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2010-01-14 03:45:42 +00:00 |
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BaseUtils.java
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isNBase method
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2010-01-06 15:01:51 +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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added changes to the code to allow different types of interval merging,
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2009-12-23 21:59:14 +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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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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MergingIterator completely re-done. Now it is not a generic class (sorry guys), but rather it is tailored for merging ROD tracks. This implementation peeks the locations of next ROD annotations in each track, but does not actually read these RODs from underlying streams until the location is reached and it is time to actually return the object. Now underlying ROD track iterators (registered in the resource pool!) are not advanced prematurely past the current position and all the way to the next ROD record wherever it is, so that the sharding system can reuse them.
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2010-01-14 17:43:36 +00:00 |
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NestedHashMap.java
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Misc clean up in the recalibrator related to the nested hash map implementation. CountCovariates no longer creates the full flattened set of keys and iterates over them. The output csv file is in sorted order by default now but there is a new option -unsorted which can be used to save a little bit of run time.
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2009-12-30 16:58:04 +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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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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Modifications:
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2010-01-06 19:18:07 +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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SampleUtils.java
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Added a walker to the vcf tools compilation: one that combines vcf records. Both merges and unions are supported (see documentation... when it gets written this week).
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2010-01-10 06:45:11 +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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Incorporated feedback from Kiran. Use the Javadoc first sentence extraction capability to just show the first sentence from each line of Javadoc. @help.description can still be used to produce exceptionally verbose descriptions.
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2009-12-11 21:59:55 +00:00 |
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Utils.java
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-Fixed VCF header line bug
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2010-01-07 17:51:41 +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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