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tracks
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Bamboo isn't picking up commits for some reason; updating a copyright to see if it'll get this commit.
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2010-03-17 17:56:48 +00:00 |
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utils
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adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come.
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2010-03-03 15:56:44 +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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BeagleROD.java
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simple Beagle input ROD
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2010-02-09 01:21:04 +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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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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PlinkRod.java
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Support for validationRate calculation in variant eval 2; better error messages for failed genome loc parsing; tolerance to odd whitespace in plinkrod, and fix for monomorphic sites in vcf2variantcontext.
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2010-03-10 16:25:16 +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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Not nearly as badass as it looks. The problem I mentioned yesterday with "bleeding in" of samples comes from VCFUtils and SampleUtils looking for all VCF-class RODs in the tracker, and stealing the name from them. I have introduced a new HapmapVCF - type rod for use
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2010-01-29 15:19:50 +00:00 |
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RODRecordListImpl.java
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RODs for reads phase 2: modified RODRecordList to implement List<ReferenceOrderedDatum> so I could stub it out for testing, added a FlashBackIterator which is needed to prevent the ResourcePool from opening infinity+1 iterators, and some other interfaces to make unit testing much smoother.
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2010-02-25 22:48:55 +00:00 |
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ReadMetaDataTracker.java
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adding methods to get RODs by name or type in read traversals, performance improvements to RODs for Reads in general, and some more Tribble infrastructure.
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2010-03-11 21:13:39 +00:00 |
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RefMetaDataTracker.java
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RODs for reads phase 2: modified RODRecordList to implement List<ReferenceOrderedDatum> so I could stub it out for testing, added a FlashBackIterator which is needed to prevent the ResourcePool from opening infinity+1 iterators, and some other interfaces to make unit testing much smoother.
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2010-02-25 22:48:55 +00:00 |
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ReferenceOrderedData.java
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adding methods to get RODs by name or type in read traversals, performance improvements to RODs for Reads in general, and some more Tribble infrastructure.
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2010-03-11 21:13:39 +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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Geli to variant context.
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2010-03-23 06:45:29 +00:00 |
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RodGenotypeChipAsGFF.java
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1. To make indel calls, we need to get rid of the SNP-centricity of our code. First step is to have the reference be a String, not a char in the Genotype. Note that this is just a temporary patch until the genotype code is ported over to use VariantContext.
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2010-03-02 20:26:40 +00:00 |
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RodVCF.java
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Fixing/cleaning up the vcf merge util
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2010-03-19 15:13:32 +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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adding methods to get RODs by name or type in read traversals, performance improvements to RODs for Reads in general, and some more Tribble infrastructure.
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2010-03-11 21:13:39 +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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Will now work with simplest tabular format - genotype string ("+ACTT") does not have to be followed by ':'
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2010-02-01 15:40:01 +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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Transcript is now simply an interface
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2009-09-23 18:13:31 +00:00 |
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VariantContextAdaptors.java
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Geli to variant context.
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2010-03-23 06:45:29 +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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RODs for reads phase 2: modified RODRecordList to implement List<ReferenceOrderedDatum> so I could stub it out for testing, added a FlashBackIterator which is needed to prevent the ResourcePool from opening infinity+1 iterators, and some other interfaces to make unit testing much smoother.
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2010-02-25 22:48:55 +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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RODs for reads phase 2: modified RODRecordList to implement List<ReferenceOrderedDatum> so I could stub it out for testing, added a FlashBackIterator which is needed to prevent the ResourcePool from opening infinity+1 iterators, and some other interfaces to make unit testing much smoother.
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2010-02-25 22:48:55 +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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