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BasicReferenceOrderedDatum.java
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Framework for ROD walkers -- totally experiment and not working right now
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2009-09-12 19:13:15 +00:00 |
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BrokenRODSimulator.java
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Little class that can be used to simulate the results returned by the old ROD system. This is needed to keep couple of tests from breaking. All the code that uses this class must be changed urgently to accomodate the data as returned by new ROD system, and the corresponding tests (MD5 sums) have to be modified as well since some data as seen through the new ROD system is indeed different.
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2009-09-21 16:58:56 +00:00 |
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CleanedOutSNPROD.java
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Allow this ROD to consist of just the positions
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2009-09-01 12:43:18 +00:00 |
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Genotype.java
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more cleanup, depecaited the old genotype, corrected SNPCallsFromGenotypes' imports and two other classes that depend on it.
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2009-10-06 19:09:27 +00:00 |
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GenotypeList.java
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a trivial wrapper interface for the objects capable of holding 'full' genotype, i.e. both point (as in ref/snp) and indel variants at the same reference position
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2009-05-22 17:12:01 +00:00 |
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HapMapAlleleFrequenciesROD.java
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Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.
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2009-09-30 20:37:59 +00:00 |
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HapMapGenotypeROD.java
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Added ROD for parsing hapmap3 genotype files.
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2009-07-05 16:28:24 +00:00 |
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IntervalRod.java
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major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.
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2009-06-05 23:34:37 +00:00 |
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IntervalRodIterator.java
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Removed unused imports
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2009-09-21 16:45:22 +00:00 |
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PointIndelROD.java
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Add an indel rod which represents the initial point of the indel only
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2009-09-02 19:32:29 +00:00 |
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PooledEMSNPROD.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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RODRecordIterator.java
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Starting an update of ROD system. These basic classes will completely replace old ones, but with this update they are not linked to anything, so this checkpoint should be safe.
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2009-09-18 15:58:37 +00:00 |
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RODRecordList.java
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Minor performance improvements to VariantEval -- now all of the CPU time is spent dealing with the ROD system...
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2009-10-06 23:40:30 +00:00 |
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RefMetaDataTracker.java
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Minor performance improvements to VariantEval -- now all of the CPU time is spent dealing with the ROD system...
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2009-10-06 23:40:30 +00:00 |
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ReferenceOrderedData.java
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changes to add VCF to the rod system, fix VCF output in VariantsToVCF, and some other minor changes
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2009-09-24 15:16:11 +00:00 |
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ReferenceOrderedDatum.java
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Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files
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2009-05-14 23:20:11 +00:00 |
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RodGLF.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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RodGeliText.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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RodGenotypeChipAsGFF.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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RodVCF.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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SAMPileupRecord.java
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-add basic indel metrics to variant eval
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2009-07-28 03:25:03 +00:00 |
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SNPCallFromGenotypes.java
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more cleanup, depecaited the old genotype, corrected SNPCallsFromGenotypes' imports and two other classes that depend on it.
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2009-10-06 19:09:27 +00:00 |
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SangerSNPROD.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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SeekableRODIterator.java
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Starting an update of ROD system. These basic classes will completely replace old ones, but with this update they are not linked to anything, so this checkpoint should be safe.
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2009-09-18 15:58:37 +00:00 |
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SequenomROD.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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SimpleIndelROD.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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TabularROD.java
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Allow RODs to specify that incomplete records are okay (i.e. that they allow optional fields)
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2009-08-18 15:26:10 +00:00 |
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Transcript.java
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Transcript is now simply an interface
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2009-09-23 18:13:31 +00:00 |
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VariationRod.java
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adding an interface so that the current @Requires with ROD annotations work in walkers like VariantEval
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2009-09-23 18:24:05 +00:00 |
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package.html
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More package-level documentation.
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2009-06-17 16:28:45 +00:00 |
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rodDbSNP.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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rodGELI.java
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depricate this ROD yet again
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2009-07-15 13:33:03 +00:00 |
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rodRefSeq.java
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Added method: isCodingExon(). Returns true if position is simultaneously within an exon AND within coding interval of any single transcript from the list. The old method of detecting coding positions as isExon() && isCoding() is buggy, as the position could be in the UTR part of one transcript (isExon() is true), and within coding region bounds (but not in the exon) of another transcript (isCoding() is true). As a result UTR positions would be erroneously annotated as coding.
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2009-10-22 14:55:07 +00:00 |
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rodSAMPileup.java
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Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.
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2009-06-22 14:39:41 +00:00 |
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