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120 Commits (0feee9cdfde4bf5c2c8de90d8fd7d0d506b63c40)

Author SHA1 Message Date
aaron 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. 
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
depristo 6e13a36059 Framework for ROD walkers -- totally experiment and not working right now 
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
depristo 3949b4ac72 commented out version of next() and hasNext() that appear to be correct but are causing testing problems 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1596 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:09:21 +00:00
depristo 58105636c8 getBoundRods() convenience method 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1595 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:07:57 +00:00
depristo 4e1eded389 Fixed bad compareTo operator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1594 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:07:10 +00:00
chartl d6a0b65ac9 Changes: 
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
chartl 0c54aba92a Changes: 
@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
ebanks 5dbba6711c Lots of changes: (I'll send email out in a sec) 
1) Moved various disparate concordance / set splitting functionalities to a new parent tool which works like VariantFiltration (i.e. people can write various modules that fit inside and can be run though it).
2) Fixed up argument parsing in VariantFiltration to use key=value format so we don't accidentally mox up values (like I had been doing).
3) Have indel rod print samples


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1540 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-07 01:12:09 +00:00
depristo 2b0d1c52b2 General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1538 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 19:13:37 +00:00
aaron 0cc634ed5d -Renamed rodVariants to RodGeliText 
-Remove KGenomesSNPROD
-Remove rodFLT
-Renamed rodGFF to RodGenotypeChipAsGFF
-Fixed a problem in SSGenotypeCall
-Added basic SSGenotype Test class
-Make VCFHeader constructors public

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1536 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 18:40:43 +00:00
ebanks 849dce799d This rod was all wrong for generating the alternate snp alleles (it returned null or even the wrong value); fixed. 
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
depristo a08c68362e Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1530 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 12:39:06 +00:00
ebanks 3dfc77dc89 Add an indel rod which represents the initial point of the indel only 
(useful for alternate reference making)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1507 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-02 19:32:29 +00:00
ebanks 54c0b6c430 Allow this ROD to consist of just the positions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1497 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-01 12:43:18 +00:00
ebanks 0addae967a IndelArtifact filter can now handle filtering false SNPs that occur within the span of an indel but after the first position 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1495 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-01 03:34:39 +00:00
ebanks 8e3c3324fa Added filter for SNPs cleaned out by the realigner. 
It uses the realigner output for filtering; in addition, dbsnp indels partially work; IndelGenotyper calls don't yet work.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1489 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-31 04:32:32 +00:00
depristo bde67428fd Better formatting of the code 
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
ebanks ed8c92a12a make isReference do the right thing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1439 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-19 20:32:29 +00:00
ebanks 53153fcd79 Allow RODs to specify that incomplete records are okay (i.e. that they allow optional fields) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1433 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-18 15:26:10 +00:00
ebanks b2a18a9d61 - first pass at a basic indel filter (for now, based on size and homopolymer runs) 
- fix simple indel rod printout


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1431 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-18 03:04:12 +00:00
jmaguire 92c63fb530 It's just "lod" not discovery_lod now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1427 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-17 18:44:09 +00:00
aaron d101c20b30 added the ability to pass in a csv file of ROD triplets (one triplet per line) to the -B option 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1412 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-11 22:10:20 +00:00
ebanks 2c3f56cb8d fix length calculation (it was including +/- char when it shouldn't) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1410 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-11 20:28:24 +00:00
asivache 2841e151d0 javadoc comments only 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1399 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-10 18:44:35 +00:00
depristo 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 
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
ebanks 4366ce16e0 Made sure all RODs have a (good) toString() method - and use it in the Venn walker. (thanks, Mark) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1339 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 14:53:27 +00:00
ebanks feb7238f10 Wasn't always returning the correct alt base 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1337 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 03:08:04 +00:00
ebanks 3c4410f104 -add basic indel metrics to variant eval 
-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
ebanks ee8ed534e0 print full genotype for alt allele 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1297 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-23 01:35:23 +00:00
depristo 9c12c02768 AlleleBalance and on/off primary base filters -- version 0.0.1 -- for experimental use only 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1294 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-22 17:54:44 +00:00
depristo 8588f75eb6 Better printing with toSimpleString() -- now prints out chip-genotype string 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1288 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 21:57:59 +00:00
kiran 436a196e2b Bug fixes to support hapmap genotyping concordance. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1285 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 16:20:10 +00:00
aaron f13a1e8591 adding a couple of small changes to support contract with VariantEval 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1283 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 03:49:15 +00:00
aaron b4adb5133a GLF rod as a AllelicVariant object. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1282 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 00:55:52 +00:00
ebanks 54fce98056 duh, don't print newline 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1280 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-20 03:04:27 +00:00
ebanks 1d2b545608 add FLT toString method (to be used in PrintRODs) and add it to ROD list 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1279 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-20 02:47:50 +00:00
ebanks 387316ebe1 added indel rod 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1276 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-17 16:05:51 +00:00
ebanks da4af3b620 print indels in the format required for 1KG submissions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1275 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-17 15:59:18 +00:00
ebanks d45c90b166 ROD to represent simple output from IndelGenotyper 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1274 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-17 14:36:12 +00:00
depristo 107f42a01e Hacks for getting GLFs support in the Rod system working 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1268 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-16 21:03:47 +00:00
ebanks 88ffb08af4 Need to return real values for some of the AllelicVariant methods 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1264 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-16 02:31:10 +00:00
ebanks ba349e8d52 add FLT ROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1257 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 19:40:50 +00:00
ebanks 800f7e6360 make AllelicVariant extend ReferenceOrderedDatum (not Comparable) since ROD itself is Comparable. Then we can generalize RMD tags. 
Blame Matt if this doesn't work - he said it wouldn't break anything.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1256 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 19:25:06 +00:00
ebanks 5be5e1d45f added conversion from iupac format and new rod to deal with FLT file format 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1254 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 18:34:41 +00:00
aaron d36e232ed3 adding GLF rods to the module list 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1252 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 15:42:34 +00:00
aaron 9ecb3e0015 adding GLFRods with tests and some other code changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1251 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 15:30:19 +00:00
ebanks 513d43b5f3 now implements AllelicVariant 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1246 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 14:06:25 +00:00
ebanks d369136bda depricate this ROD yet again 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1245 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 13:33:03 +00:00
ebanks efcbb16688 un-deprecate this ROD and make it implement Genotype 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1240 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-14 19:45:41 +00:00
depristo 84d407ff3f Fixing odd merge problem with VariantEval -- better cluster analysis (no cumsum), rodVariant is now an AllelicVariant 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1239 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-14 18:53:27 +00:00