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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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adding error log reporting to the GATK, and a stream based output method for the argument collection
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2009-10-28 19:56:05 +00:00 |
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containers
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Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.
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2009-10-20 12:23:36 +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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Bumping version of Picard for firehose compatibility.
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2009-10-16 19:38:56 +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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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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io
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Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.
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2009-10-20 12:23:36 +00:00 |
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sam
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cleanup of the traversal output code
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2009-11-12 06:18:10 +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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charSeq2byteSeq -- convert a char[] to a byte[] for convenience
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2009-10-27 21:52:23 +00:00 |
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BasicPileup.java
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Ignoring deletions in the primary pileup by default was causing the primary pileup to become shorter than the secondary pileup when building up the secondary base pileup string. This fix makes sure to include the primary Ds within the pileup so that not only are the pileups guaranteed to be the same size, the same offsets will truly correspond with the same read.
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2009-11-17 17:20:13 +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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Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.
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2009-09-29 22:23:19 +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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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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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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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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Output changes for VCF and UG:
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2009-11-10 16:31:31 +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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a convenience method to join a map into a single string, which I need for some VCF work. Added some documentation to the join method as well.
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2009-11-17 16:50:01 +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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