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AllelicVariant.java
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Changes:
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2009-09-11 16:23:01 +00:00 |
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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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-add basic indel metrics to variant eval
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2009-07-28 03:25:03 +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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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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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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Changes:
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2009-09-11 16:23:01 +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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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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RefMetaDataTracker.java
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Changing the carpet under your feet!! New incremental update to th eROD system has arrived.
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2009-09-21 16:55:22 +00:00 |
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ReferenceOrderedData.java
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Changing the carpet under your feet!! New incremental update to th eROD system has arrived.
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2009-09-21 16:55:22 +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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Adding the VCF ROD. Also changed the VCF objects to much more user friendly.
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2009-09-18 20:19:34 +00:00 |
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RodGeliText.java
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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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RodGenotypeChipAsGFF.java
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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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RodVCF.java
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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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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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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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SangerSNPROD.java
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Changes:
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2009-09-11 16:23:01 +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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SimpleIndelROD.java
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Changes:
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2009-09-11 16:23:01 +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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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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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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little fixes; also fixed a tyPo
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2009-09-18 22:38:51 +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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synchronyzing; debug statements commented out, so nothing changed really
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2009-07-10 16:38:33 +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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