921d4f4e95
RemapAlignments is a standalone picard-level tool that does not use gatk engine; moved to 'tools'
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1396 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 15:41:07 +00:00
02f1af0743
Don't die when a readgroup is absent from the covariates table - it could
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happen when all reads are unmapped (or have MQ0); instead, just don't alter
the quals.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1394 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 03:10:33 +00:00
089dab00e2
Was discordance rate, now concordance rate
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1393 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 19:37:52 +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
20baa80751
Updated polarized reference priors, need DiploidGenotypePriors class that is directly used by the NewHotness genotypelikelihoods, more bug fixes and refactoring, etc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1391 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 19:01:04 +00:00
a864c2f025
Updated polarized reference priors, need DiploidGenotypePriors class that is directly used by the NewHotness genotypelikelihoods, more bug fixes and refactoring, etc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1390 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 19:00:06 +00:00
db250f8d3e
Don't print if not in learning mode
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1389 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 06:08:02 +00:00
4c1fa52ddf
-Added mapping quality zero filter
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-Set some reasonable defaults (based on pilot2)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1388 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 03:18:02 +00:00
bbd7bec5db
Continuing cleanup of SSG. GenotypeLikelihoods now have extensive testing routines. DiploidGenotype supports het, homref, etc calculations. SSG has been cleaned up to remove old garbage functionality. Also now supports output to standard output by simply omitting varout
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1387 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 22:25:30 +00:00
d60d5aa516
Fixed bug: previously reset likelihoods after each region/exon.
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Better comments/documentation added
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1386 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 18:44:46 +00:00
0d47798721
made booster distance a parameter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1385 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 18:29:21 +00:00
3b74b3ba74
print out ref/alt ratio, not major/minor
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1384 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 16:36:25 +00:00
48713e154c
Windowed access to the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1383 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 16:29:15 +00:00
65e9dcf5b7
Fully operational version of the new genotype likelihoods class. (1) Much cleaner interface. Now explicitly stores likelihoods, priors, and posteriors in separate arrays indexed by an enum, (2) no longer can be used to make calls, it relies on SSGGenotypeCall to order the likelihoods, calculate best to ref, etc, this is just for calculating genotype likelihoods now; (3) Now performs extensive error checking with validate() to ensure the system is behaving properly. (4) fixed incorrect treatment of N bases, which we being counted against everyone (5) likely found a stats bug in which heterozyosity was being applied incorrectly to the genotype priors
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1382 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 01:00:55 +00:00
4dc23f2763
Trivial formatting changes as I moved more legacy code into this system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1381 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 00:54:26 +00:00
34af669dbb
Explicit ENUM representation of the diploid genotypes. Please use this from now on to represent strings like AA or AT
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1380 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 00:53:43 +00:00
5487ab0ee6
Added several useful routines to MathUtils for summing and bounds checking of doubles
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1379 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 00:41:31 +00:00
68309408e4
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1378 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 21:23:01 +00:00
45ab212f22
Post-presentation update
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1377 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 21:21:12 +00:00
21d1eba502
Cleaned division of responsibilities between arguments to map function. Reference has been changed
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from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 21:01:37 +00:00
a5a7d7dab8
added "booster" metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1375 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 20:53:45 +00:00
3a8d923785
minor output changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1374 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 20:12:16 +00:00
939b19e715
Committing the first version of the homopolymer filter. Removes SNPs that occur at the edges of homopolymer runs and whose nonref allele matches the repeated base in the homopolymer.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1373 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 14:35:51 +00:00
20ff603339
New hotness and old and Busted genotype likelihood objects are now in the code base as I work towards a bug-free SSG along with a cleaner interface to the genotype likelihood object
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1372 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 23:07:53 +00:00
4986b2abd6
Fixing bug in SSG -- genotyping and discovery were mixed up by name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1371 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 22:13:35 +00:00
3485397483
Reorganization of the genotyping system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1370 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 20:55:31 +00:00
9f1d3aed26
-Output single filtration stats file with input from all filters
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-move out isHet test to GenotypeUtils so all can use it
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1369 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 20:44:21 +00:00
880a01cb5d
Slight reorganization of genotype interface
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1367 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 19:18:41 +00:00
d840a47b11
Slight reorganization of genotype interface
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1366 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 19:17:15 +00:00
20986a03de
cleanup before moving files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1365 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 19:08:24 +00:00
e3b08f245f
Pull out RMS calculation into MathUtils for all to use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1364 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 17:00:20 +00:00
e495b836d3
- added mapping quality filter
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- make the filters brainless in that they strictly have thresholds and filter based on them; require user to calculate and input these thresholds.
- update filters in preparation for migration to new output format
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1363 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 16:46:51 +00:00
ba07f057ac
finish the math for RMS
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1362 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 16:18:09 +00:00
8bc925a216
Commit on the behalf of Mark: cleaning up some old and busted code in GenotypeLikelihood and associated objects.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1361 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 21:18:30 +00:00
9dfee7a75c
the "-genotype" option now acts correctly as a discovery mode caller in SSG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1359 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 18:31:45 +00:00
c2c80dd946
cleanup and moving some things around to more logical locations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1358 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 16:28:39 +00:00
9dada95ec3
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1357 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 16:21:16 +00:00
9a0761cd8f
accidentally committed some debug code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1356 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 15:25:22 +00:00
2f2c8576a5
GLF output is now well validated, and some changes for new Genotypes interface code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1355 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 15:21:28 +00:00
8eeb87af2a
Tests for downsampling related utilities in ListUtils class that didn't get checked in earlier
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1352 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 00:09:35 +00:00
678c2533ca
Removed custom output stream for file and replaced with the standard out PrintStream
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1350 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 22:36:42 +00:00
2a7dfce9ae
fix the header string mismatch that Andrew found
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1349 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 22:26:34 +00:00
44673b2dce
Removed a debugging println that was accidentally checked in
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1348 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 22:23:27 +00:00
845488ff94
VariantEval now decides whether a variant is not confidently called using BestVsNetxBest if genotypes are being evaluated and BestVsRef if not (variant discovery only). Also, the absolute value of the BestVsRef LOD (getVariantionConfidence) is used so that confident reference calls (if the GELI has output them) will show up in the final table as reference calls rather than no calls.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1347 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 21:54:06 +00:00
fdc7cc555b
Removed extra column name from geliHeaderString that was mislabeling the 10 genotype likelihoods by shifting them over by onex
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1345 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 21:42:02 +00:00
0087234ed7
small code cleanup, a couple of little changes to SSGGenotypeCall
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1343 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 19:47:37 +00:00
fbc7d44bc7
don't allow users to input priors anymore; they should be using heterozygosity and having the SSG calculate priors.
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Note that nothing was changed for dnSNP/hapmap priors (not sure what we want to do with these yet - any thoughts?)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1342 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 19:10:33 +00:00
b282635b05
Complete reworking of Fisher's exact test for strand bias:
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- fixed math bug (pValue needs to be initialized to pCutoff, not 0)
- perform factorial calculations in log space so that huge numbers don't explode
- cache factorial calculations so that each value needs to be computed just once for any given instance of the filter
I've tested it against R and it has held up so far...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1341 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 18:52:13 +00:00
4033c718d2
moving some code around for better organizations, some fixes to the fields out of SSG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1340 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 15:09:43 +00:00
4366ce16e0
Made sure all RODs have a (good) toString() method - and use it in the Venn walker. (thanks, Mark)
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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
asivache
ebanks
depristo
sjia
kcibul
hanna
mmelgar
kiran
aaron
andrewk