3a487dd64e
little fixes; also fixed a tyPo
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1662 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-18 22:38:51 +00:00
b6d7d6acc6
fix for the eval tests, and a change to the backedbygenotypes interface, more changes to come
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1661 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-18 22:25:16 +00:00
7b39aa4966
Adding the VCF ROD. Also changed the VCF objects to much more user friendly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1658 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-18 20:19:34 +00:00
b401929e41
incremental clean-up and changes for VariantEval, moved DiploidGenotype to a better home, and fixed a spelling error.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1624 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 04:48:42 +00:00
e03fccb223
Changes to switch Variant Eval over to the new Variation system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1611 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-14 05:34:33 +00:00
5b41ef5f70
rod DBSNP had a bug where the reference wasn't calculated correctly under certain conditions. Fixed getRefBasesFWD and getRefSnpFWD so that they were more in line with getAltBasesFWD and getAltSnpFWD. Also updated Variant Eval tests to reflect this change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1609 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-13 23:48:58 +00:00
6e13a36059
Framework for ROD walkers -- totally experiment and not working right now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1600 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-12 19:13:15 +00:00
d6a0b65ac9
Changes:
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Rollback of Variant-related changes of r1585, additional PGC code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1586 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-11 16:23:01 +00:00
0c54aba92a
Changes:
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@VariantEvalWalker - added a command line option to input a file path to a pooled call file for pooled genotype concordance checking. This string is to be passed to the PooledGenotypeConcordance object.
@AllelicVariant - added a method isPooled() to distinguish pooled AllelicVariants from unpooled ones.
@ all the rest - implemented isPooled(); for everything other than PooledEMSNProd it simply returns false, for PooledEMSNProd it returns true.
Added:
@PooledGenotypeConcordance - takes in a filepath to a pool file with the names of hapmap individuals for concordance checking with pooled calls
and does said concordance checking over all pools. Commented out as all the methods are as yet unwritten.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1585 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-11 15:01:50 +00:00
849dce799d
This rod was all wrong for generating the alternate snp alleles (it returned null or even the wrong value); fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1531 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 14:21:46 +00:00
bde67428fd
Better formatting of the code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1477 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-29 21:46:47 +00:00
6d3ef73868
Now includes statistics on the allele agreement with dbSNP -- counts concordant calls as dbSNP = A/C and we say A/C, vs. we say A/T
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1392 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 19:37:07 +00:00
3c4410f104
-add basic indel metrics to variant eval
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-variants need a length method (can't assume it's a SNP)!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1324 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-28 03:25:03 +00:00
bcb64d92e9
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 14:39:41 +00:00
678ddd914f
Stopgap fixes GFF, DbSNP being half-open rather than half-closed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@980 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 21:38:57 +00:00
7fa84ea157
10x speedup of recalibration walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@954 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 15:39:40 +00:00
6e60cddfed
A fix for the 'rod blows up when it hits a GenomeLoc outside the reference' issu
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e. Really a stopgap; error handling in the RODs needs to be addressed in a more comprehensive way. Right now, hasNext() isn't guaranteed to be correct.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@878 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 18:14:46 +00:00
5e8c08ee63
Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 20:13:01 +00:00
ce6a0f522b
First incarnation of the population-based SNP analysis tool. Also bug fixes throughout the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@845 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 22:02:24 +00:00
7a979859a9
Intermediate checking for evaluation -- now supports transition / transversion evaluation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@793 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:05:06 +00:00
8e9e2f4502
Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@716 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 21:06:28 +00:00
e95f427965
Added isReference() to AllelicVariant and updated rodDbSNP accordingly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@311 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 14:49:20 +00:00
551ce9130f
added isBiallelic() to the AllelicVariant interface and to rodDbSNP implementation. We probably don't really know how to deal with non-biallelic sites just as yet...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@294 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-04 21:31:16 +00:00
edc44807af
rod's now have names. Use getName() to access it. Next step is better interface to accessing rods
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@286 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 16:41:33 +00:00
4bc035d919
half-way through making rodDbSNP implement AllelicVariant interface; does not work yet
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@267 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 20:48:59 +00:00
63cd1fe201
Push core / playground lower into the tree.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-23 23:19:54 +00:00
aaron
depristo
chartl
ebanks
hanna
asivache