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Allele.java
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1. Removing an old version of the Genotype interface which is no longer being used. Needed to do this now so that the naming conflicts would cease.
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2010-01-07 05:51:10 +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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1. Removing an old version of the Genotype interface which is no longer being used. Needed to do this now so that the naming conflicts would cease.
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2010-01-07 05:51:10 +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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Converter from HapMap chip genotype data to VCF added; HapMapGenotypeROD adjusted to not convert from Hg18 to b36 formatting of contigs
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2009-12-28 01:36:08 +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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Fixing a bug that Steven uncovered; we had an abigous contract for peek() in PushbackIterator, and SeekableRODIterator wasn't checking to see if it's PushbackIterator hasNext() was true before calling peek().
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2009-12-15 23:04:40 +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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The recalibrator now uses all input RODs when looking for known polymorphic sites not just the one named dbsnp. Added an integration test which uses both dbsnp and an input vcf file and skips over the union of the two.
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2010-01-12 18:50:39 +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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Changed the GLF record to store it's contig name and position in each record instead of in the Reader. Integration tests all stay the same.
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2009-12-18 22:54:56 +00:00 |
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RodGeliText.java
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-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).
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2009-11-01 05:35:47 +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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Convenience methods for getting the VCFReader and VCFRecord
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2010-01-16 20:22:31 +00:00 |
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SAMPileupRecord.java
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1. Removing an old version of the Genotype interface which is no longer being used. Needed to do this now so that the naming conflicts would cease.
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2010-01-07 05:51:10 +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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added: peekNextLocation(); it's quite hard (and probably unnecessary, ever) to make seekable iterator a peekable one, but it is quite easy and useful to be able to peek just the next location the iterator will jump to after next call to next()
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2010-01-14 17:38:19 +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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SequenomRodWithGenomeLoc.java
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First pass at a sequenom ROD. Nothing uses it; currently undergoing testing.
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2010-01-19 17:09:36 +00:00 |
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SimpleIndelROD.java
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1. Removing an old version of the Genotype interface which is no longer being used. Needed to do this now so that the naming conflicts would cease.
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2010-01-07 05:51:10 +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-info.java
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Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file
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2009-12-04 20:08:41 +00:00 |
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rodDbSNP.java
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two fixes in the new cached DbSNP code:
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2010-01-13 00:27:34 +00:00 |
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rodGELI.java
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Fixing a bug that Steven uncovered; we had an abigous contract for peek() in PushbackIterator, and SeekableRODIterator wasn't checking to see if it's PushbackIterator hasNext() was true before calling peek().
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2009-12-15 23:04:40 +00:00 |
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rodPicardDbSNP.java
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Fixing a bug that Steven uncovered; we had an abigous contract for peek() in PushbackIterator, and SeekableRODIterator wasn't checking to see if it's PushbackIterator hasNext() was true before calling peek().
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2009-12-15 23:04:40 +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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1. Removing an old version of the Genotype interface which is no longer being used. Needed to do this now so that the naming conflicts would cease.
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2010-01-07 05:51:10 +00:00 |
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