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
e24c8d00d5
So, the VCF spec allows for an optional meta field in the header representing the date. However, using this field means that integration tests run on the vcf file will fail the MD5 test (which is what happened to the VariantFiltration test this morning after working just fine yesterday).
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After consulting our resident expert (Aaron), we're going to (temporarily) remove the date from the vcf output until we can come up with a better solution. However, this shouldn't cause any short-term problems because the data truly is optional.
VF test's MD5s are updated.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1580 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 14:28:43 +00:00
5a64a80ab5
changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1577 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 04:31:33 +00:00
1362a56227
Added fasta tests and small fix to cleaner test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1575 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 03:13:11 +00:00
8ca89279aa
Added a test for VariantFiltration and the VECs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1574 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 02:21:14 +00:00
bed646e4f6
Adding cleaner test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1561 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 16:05:56 +00:00
d9588e6083
bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1558 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:36:12 +00:00
0df6a9da5c
-Seperating out normal (unit) tests and integration tests. From now on if your test are more of an integration test (i.e. you're testing a walker and all the subunits it relies on) please name the test "______IntegrationTest.java" instead of "______Test.java".
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-Bamboo will now run the integration tests once a day, and the normal units tests on each check-in.
-Also added a bunch of unit tests for VariantEval walker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1555 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:01:40 +00:00
eeb9b6eb13
GenotypeLikelhoods now support a cache per subclass, avoiding genotyping clashes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1554 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 10:39:14 +00:00
0cc219c0df
-Added unit test for walkers dealing with intervals for cleaning
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-I also uncovered a corner case in the cleaner that for some reason was commented out but shouldn't have been. Hooray for unit tests!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1553 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 02:35:17 +00:00
ec0f6f23c7
LocusIterationByState is now the system deafult. Fixed Aaron's build problem
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1552 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 01:28:05 +00:00
1c3d67f0f3
Improvements to the CountCovariates and TableRecablirator, as well as regression tests for SLX and 454 data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1539 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 22:26:57 +00:00
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
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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
0cc634ed5d
-Renamed rodVariants to RodGeliText
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-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
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!
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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
49a7babb2c
Better organization of Genotype likelihood calculations. NewHotness is now just GenotypeLikelihoods. There are 1, 3, and empirical base error models available as subclasses, along with a simple way to make this (see the factory).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1481 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-30 19:16:30 +00:00
8e129d76fd
Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1474 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 14:14:21 +00:00
37a9b84276
corresponding test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1470 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 00:17:42 +00:00
ccdb4a0313
General-purpose management of output streams.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1454 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-23 00:56:02 +00:00
d101c20b30
added the ability to pass in a csv file of ROD triplets (one triplet per line) to the -B option
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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
d69ae60b69
fixed two tests affected by my previous commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1408 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 17:57:50 +00:00
dd228880ed
Partially implemented NewHotnessGenotypeLikelihoodsTest caused the tests to fail.
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Ouch! So hot it burned me.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1403 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 20:45:44 +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
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
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
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
bca894ebce
Adding the intial changes for the new Genotyping interface. The bullet points are:
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- SSG is much simpler now
- GeliText has been added as a GenotypeWriter
- AlleleFrequencyWalker will be deleted when I untangle the AlleleMetric's dependance on it
- GenotypeLikelihoods now implements GenotypeGenerator, but could still use cleanup
There is still a lot more work to do, but this is a good initial check-in.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1335 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 19:43:59 +00:00
7a13647c35
Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*
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rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1332 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 16:11:45 +00:00
2db86b7829
Move the cleaned read injector test from playground to core. Remove CovariateCounterTest's dependency on the CleanedReadInjector. Start doing a bit of cleanup on the CLP's FieldParsers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1312 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 19:44:04 +00:00
0b16253db3
an iterator to fix the problem where read-based interval traversals are getting duplicate reads because reads span the two intervals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1305 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 23:59:48 +00:00
b4adb5133a
GLF rod as a AllelicVariant object.
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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
9ecb3e0015
adding GLFRods with tests and some other code changes
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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
d86717db93
Refactoring of the traversal engine base class, I removed a lot of old code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1209 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 21:57:00 +00:00
da4d26b1ea
Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1199 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 20:26:16 +00:00
433ad1f060
Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1196 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 18:49:08 +00:00
d8fbb2b62c
Refactoring; make a better home for the MalformedReadFilteringIterator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1194 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 16:54:20 +00:00
f6a273a537
other fixes for some broken unit tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1181 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 05:53:13 +00:00
033bafe7a1
fixed sam by reads test for the new filtering code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1180 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 05:45:50 +00:00
b9d533042e
Two-tailed HardyWeinberg test implemented. VariantEval now separate violations from summary outputs for clarity; Fixing problems with CovariateCounterTest and TabularRodTest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1177 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 22:02:04 +00:00
bc17ff567a
When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1156 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:15:50 +00:00
9b182e3063
Prep for documenting command-line arguments: delete some arguments that don't make sense any more given
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the state of the traversals and GATK input requirements: all_loci (replaced by walker annotation), max
OTF sorts (bam files must be sorted and indexed), threaded io (replaced by data sharding framework).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1144 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 18:23:35 +00:00
03f8177a53
When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1121 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 20:51:55 +00:00
1dcababad1
a fix to make the test run
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1120 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 20:24:32 +00:00
5289230eb8
Version 0.2.1 (released) of the TableRecalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:50:55 +00:00
ad3a3aa350
First pass at passing lists of files / lists of interval arguments work. Note that the interval
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ROD system will throw up its hands and not deal with intervals at all if multiple interval files
are passed in (see JIRA GSA-95).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1105 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:44:23 +00:00
0a16519aa2
a couple of additions to the tests, plus a change to the artificial resource pool to support the queryContained flag
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1099 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 18:30:32 +00:00
5b1c23a7f2
changes to fix and test the interval based traversals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1095 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 17:54:15 +00:00
ef546868bf
Pooling of unmapped reads -- improves runtime of files with tons of unmapped reads by an order of magnitude.
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Desperately needs cleanup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1080 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 23:48:06 +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
8ac40e8e2d
Updated version of the recalibration tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 17:45:47 +00:00
depristo
ebanks
aaron
hanna