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gatk-3.8/java/src/org/broadinstitute/sting/gatk/refdata
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chartl d57a86ad41 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 
when you want to protect your VCF header from being infected by the samples in a bound hapmap VCF. Changes are as follows:

VCFRecord - minor change to adapt isNovel() to the case where the dbsnp ID field is empty, but the info field has DB=1

HapmapVCFRod - introduced for the reason at the top

RODRecordIterator - was: catch ( Exception e ) { throw new StingException("long ass message") }
                 is now: catch ( Exception e ) { throw new StingException("long ass message",e) }
                    to permit full stack ejaculation.

RodVCF - Now with more brackets!

ReferenceOrderedData - registering HapmapVCF as a bindable string

VariantAnnotator - There's an extra space on a line. And some new brackets.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2733 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-01-29 15:19:50 +00:00
..
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
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 Converter from HapMap chip genotype data to VCF added; HapMapGenotypeROD adjusted to not convert from Hg18 to b36 formatting of contigs 2009-12-28 01:36:08 +00:00
HapmapVCFROD.java 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 2010-01-29 15:19:50 +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 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(). 2009-12-15 23:04:40 +00:00
PlinkRod.java Refactoring and migration of new allele/variantcontext/genotype code into oneoffprojects. NOT FOR USE. PlinkRod commented out due to dependence on this new, rapidly changing interface. 2010-01-26 13:53:29 +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 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 2010-01-29 15:19:50 +00:00
RODRecordList.java -B 1kg_ceu,VFC,CEU.vcf -B 1kg_yri,VCF,YRI.vcf system supported to allow 1KG % (like dbSNP%) 2010-01-19 21:33:13 +00:00
RefMetaDataTracker.java -B 1kg_ceu,VFC,CEU.vcf -B 1kg_yri,VCF,YRI.vcf system supported to allow 1KG % (like dbSNP%) 2010-01-19 21:33:13 +00:00
ReferenceOrderedData.java 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 2010-01-29 15:19:50 +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 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. 2009-12-18 22:54:56 +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 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 2010-01-29 15:19:50 +00:00
SAMPileupRecord.java 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. 2010-01-07 05:51:10 +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 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() 2010-01-14 17:38:19 +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 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. 2010-01-07 05:51:10 +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-info.java Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file 2009-12-04 20:08:41 +00:00
rodDbSNP.java two fixes in the new cached DbSNP code: 2010-01-13 00:27:34 +00:00
rodGELI.java 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(). 2009-12-15 23:04:40 +00:00
rodPicardDbSNP.java 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(). 2009-12-15 23:04:40 +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 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. 2010-01-07 05:51:10 +00:00