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gatk-3.8/java/src/org/broadinstitute/sting/gatk/refdata
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aaron af440943a4 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(). 
Changed peek() to element() to be consistant with the Java standards of the Queue and Stack classes (element() throws an exception if a record isn't available).  

Also updated some of the ROD iterator next() methods to throw NoSuchElementException if next() is called when a record isn't available.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2372 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-12-15 23:04:40 +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
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 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
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 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
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 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
SAMPileupRecord.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
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 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
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-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 -dbSNP rod should not implement VariantBackedByGenotype since dbsnp records have no genotype data 2009-12-04 14:56:48 +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 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