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cmdLine
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Update gsadevelopers -> gsahelp.
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2009-09-20 23:36:54 +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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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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little fixes; also fixed a tyPo
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2009-09-18 22:38:51 +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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General-purpose management of output streams.
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2009-08-23 00:56:02 +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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the life in the magical kingdom of fully spec-conforming SAM files would be so... magical. For now, however, there are plenty of ways to end up with inconsistent SAM records. For instance, a SAM file with missing header will result in SAM records with ref. name set, but getReferenceIndex() returning null. This, in turn, was tripping isReadUnmapped(). The method is now fixed, so that it suffices to have *either* reference name *or* reference index set for the read to be considered mapped (the flag is still checked)
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2009-09-14 16:04:19 +00:00 |
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BaseUtils.java
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N reference base fix for SSG
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2009-09-09 21:19:36 +00:00 |
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BasicPileup.java
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-deal with offsets that can be -1
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2009-09-16 16:44:57 +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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GenomeLoc.java
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Easier to print GenomeLoc compareTo()
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2009-09-12 19:10:35 +00:00 |
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GenomeLocParser.java
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changes to make GenomeLoc string parsing 25% faster
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2009-09-21 22:37:47 +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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Changes to switch Variant Eval over to the new Variation system.
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2009-09-14 05:34:33 +00:00 |
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JVMUtils.java
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Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*
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2009-07-29 16:11:45 +00:00 |
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ListUtils.java
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@ListUtils - Bugfix in getQScoreOrderStatistic: method would attempt to access an empty list fed into it. Now it checks for null pointers and returns 0.
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2009-08-27 19:31:53 +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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@ListUtils - Bugfix in getQScoreOrderStatistic: method would attempt to access an empty list fed into it. Now it checks for null pointers and returns 0.
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2009-08-27 19:31:53 +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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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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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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ReadBackedPileup.java
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-deal with offsets that can be -1
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2009-09-16 16:44:57 +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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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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Utils.java
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bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa
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2009-09-09 15:36:12 +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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