..
BasicReferenceOrderedDatum.java
Framework for ROD walkers -- totally experiment and not working right now
2009-09-12 19:13:15 +00:00
BrokenRODSimulator.java
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.
2009-09-21 16:58:56 +00:00
CleanedOutSNPROD.java
Allow this ROD to consist of just the positions
2009-09-01 12:43:18 +00:00
Genotype.java
more cleanup, depecaited the old genotype, corrected SNPCallsFromGenotypes' imports and two other classes that depend on it.
2009-10-06 19:09:27 +00:00
GenotypeList.java
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
2009-05-22 17:12:01 +00:00
HapMapAlleleFrequenciesROD.java
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.
2009-09-30 20:37:59 +00:00
HapMapGenotypeROD.java
Added ROD for parsing hapmap3 genotype files.
2009-07-05 16:28:24 +00:00
IntervalRod.java
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.
2009-06-05 23:34:37 +00:00
IntervalRodIterator.java
Removed unused imports
2009-09-21 16:45:22 +00:00
PointIndelROD.java
Add an indel rod which represents the initial point of the indel only
2009-09-02 19:32:29 +00:00
PooledEMSNPROD.java
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.
2009-10-23 06:31:15 +00:00
RODRecordIterator.java
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.
2009-09-18 15:58:37 +00:00
RODRecordList.java
Minor performance improvements to VariantEval -- now all of the CPU time is spent dealing with the ROD system...
2009-10-06 23:40:30 +00:00
RefMetaDataTracker.java
Minor performance improvements to VariantEval -- now all of the CPU time is spent dealing with the ROD system...
2009-10-06 23:40:30 +00:00
ReferenceOrderedData.java
Add rodPicardDbSNP
2009-11-19 17:27:46 +00:00
ReferenceOrderedDatum.java
Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files
2009-05-14 23:20:11 +00:00
RodGLF.java
GenotypeLocusData now extends Variation.
2009-11-24 21:07:55 +00:00
RodGeliText.java
-Generalized the GenotypeConcordance module to deal with any number of individuals (although it will default to its old behavior if the -samples argument is left out).
2009-11-01 05:35:47 +00:00
RodGenotypeChipAsGFF.java
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.
2009-10-23 06:31:15 +00:00
RodVCF.java
Completing the optimization started by Matt: we now wrap SAMRecords and SAMReadGroupRecords with our own versions which cache oft-used variables (e.g. platform, readString, strand flag). All walkers automagically get this speedup since the wrapping occurs in the engine.
2009-11-30 17:39:29 +00:00
SAMPileupRecord.java
Restructuring and interface change to ReadBackedPileup. We now lower support the Pileup interface, the BasicPileup static methods, and the ReadBackedPileup class. Now everything is a ReadBackedPileup and all methods to manipulate pileups are off of it. Also provides the recommended iterable() interface of pileup elements so you can use the syntax for (PileupElement p : pileup) and access directly from p.getBase() and p.getQual() and p.getSecondBase(). Only a few straggler walkers use the old style interface -- but those walkers will be retired soon. Documentation coming in the AM. Please everyone use the new syntax, it's safer, and will be more efficient as soon as the LocusIteratorByState directly emits the ReadBackedPileup for the Alignment context, as opposed to the current interface. In the process of the change over, discovered several bugs in the second-best base code due to things getting out of sync, but these changes were resolved manually. All other integrationtests passed without modification.
2009-11-25 03:51:41 +00:00
SNPCallFromGenotypes.java
more cleanup, depecaited the old genotype, corrected SNPCallsFromGenotypes' imports and two other classes that depend on it.
2009-10-06 19:09:27 +00:00
SangerSNPROD.java
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.
2009-10-23 06:31:15 +00:00
SeekableRODIterator.java
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.
2009-09-18 15:58:37 +00:00
SequenomROD.java
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.
2009-10-23 06:31:15 +00:00
SimpleIndelROD.java
GenotypeLocusData now extends Variation.
2009-11-24 21:07:55 +00:00
TabularROD.java
Allow RODs to specify that incomplete records are okay (i.e. that they allow optional fields)
2009-08-18 15:26:10 +00:00
Transcript.java
Transcript is now simply an interface
2009-09-23 18:13:31 +00:00
VariationRod.java
adding an interface so that the current @Requires with ROD annotations work in walkers like VariantEval
2009-09-23 18:24:05 +00:00
package.html
More package-level documentation.
2009-06-17 16:28:45 +00:00
rodDbSNP.java
2 major changes:
2009-11-12 22:51:49 +00:00
rodGELI.java
depricate this ROD yet again
2009-07-15 13:33:03 +00:00
rodPicardDbSNP.java
GenotypeLocusData now extends Variation.
2009-11-24 21:07:55 +00:00
rodRefSeq.java
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.
2009-10-22 14:55:07 +00:00
rodSAMPileup.java
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.
2009-06-22 14:39:41 +00:00
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