78a00d2ddc
Updating UG integration tests (needed updating only because the -mbq default is different from the old -mmq one).
2011-11-02 21:13:44 -04:00
e1edd6bd12
Removing the min mapping quality argument since it wasn't being used in the normal processing of the pileups in UG - only for indel pileups. Instead, we apply the min base quality to the reads in the pileup for indels and define it to be the min 'confidence' of the base. Docs are updated but I didn't rename the argument as I don't want people to complain.
2011-11-02 20:32:58 -04:00
4501dce58d
Fixing merge conflict
2011-11-02 12:50:32 -04:00
54331b44e9
New way of looking at the size of a pileup: there's a physical number of elements in the data structure and there's a representative depth of coverage (since a reduced read represents depth >= 1). The size() method has been removed because its meaning is ambiguous. Updated several annotations and the UG engine to make use of the representative depths.
2011-11-02 12:47:30 -04:00
b004489c6d
Moving ReduceRead TAG to GATKSAMRecord
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ReduceReads are now a feature of a GATKSAMRecord, so the tag and the special methods needed to use it will now be housed by the GATKSAMRecord.
2011-11-01 17:12:09 -04:00
0ca7428e76
Allow processing of empty intervals, but warn user when this case is encountered.
2011-10-28 12:12:14 -04:00
649dfe98f0
Add VCF header for any expressions that are requested
2011-10-28 10:22:19 -04:00
8b1a62da27
Adding unit test to cover overlapping intervals from the same source with the intersection rule.
2011-10-28 09:59:43 -04:00
6ba08a103d
Empty ROD files should generate an exception when used for creating intervals. Moved some now obsolete files to the archive as the realigner will now read all target intervals into memory.
2011-10-28 09:23:25 -04:00
19e27d4568
Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.
2011-10-27 23:55:11 -04:00
ccfd853b34
Added further integration tests for rod-based intervals that deal with more complex cases. Good call by Mark to test the empty VCF example because we were failing on it; fixed.
2011-10-27 20:43:50 -04:00
b80d407dc7
No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
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Other minor cleanup.
2011-10-27 14:17:07 -04:00
8c4dbce6d8
Don't serialize the GATKArgumentCollection for the GATKRunReports (which would have meant dealing with the new IntervalBindings). Also, forgot to remove a test that's no longer relevant to BED parsing.
2011-10-27 13:58:19 -04:00
4a7e6fee3f
Remove support for BED file interval parsing in the GATK; it should all go through Tribble now. IndelRealigner no longer supports unordered interval input (which shouldn't have been used anyways). Temporarily commenting out serialization of arguments so that tests pass; this whole piece will be deleted soon anyways.
2011-10-27 13:38:08 -04:00
44f905b5e5
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-26 23:31:11 -04:00
034a997d07
Generalized Reads -> Fragment calculation
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-- Supports ReadBackedPileup -> FragmentCollection as before
-- Added support for List<SAMRecord> -> FragmentCollection for Ryan's haplotype caller
-- General cleanup, renaming, move to separate package, more extensive unit tests, etc.
-- Added toFragment() function to ReadBackedPileup interface
2011-10-26 15:54:38 -04:00
b39fcb1bea
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-26 15:44:25 -04:00
3273c20c98
Added integration tests for Tribble-based intervals and fixed up some of the other tests based on some method changes.
2011-10-26 15:29:18 -04:00
7fa943aef1
Renamed FragmentPileup to FragmentUtils
2011-10-26 14:01:45 -04:00
1b722c21cf
merge master
2011-10-25 16:08:39 -04:00
2794e5c1d4
Modified the VCFJarClassLoadingUnitTest to play nice with the packaged-jar test targets.
2011-10-25 14:47:15 -04:00
fac9932938
Embedding gsalib source and queueJobReport R scripts in the dist and package jars.
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Moved gsalib and queueJobReport.R to embeddable namespaced locations.
Updated packager dependencies/dir to add an @includes which filters the embedded fileset.
RScriptExecutor can now JIT compiles the gsalib.
RScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG.
Refactored ProcessController and IOUtils from Queue to Sting Utils.
Added more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count.
Replaced uses of some IOUtils with Apache Commons IO.
ShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown.
Better QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().
2011-10-24 15:58:34 -04:00
89a581a66f
Added ability to specify arguments in files via -args/--arg_file
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Pushing back downsample and read filter args so they show up in getApproximateCommandLineArgs()
2011-10-24 15:58:34 -04:00
502592671d
Cleanup FragmentPileup before main repo commit
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-- removed intermiate functions. Now only original version and best optimized new version remain
-- Moved general artificial read backed pileup creation code into ArtificialSamUtils
2011-10-24 14:40:05 -04:00
166174a551
Google caliper example execution script
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-- FragmentPileup with final performance testing
2011-10-24 14:04:53 -04:00
42bf9adede
Initial version of "fast" FragmentPileup code
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-- Uses mayOverlapRoutine in ReadUtils
-- Attempts to be smart when doing overlap calculation, to avoid unnecessary allocations
-- PileupElement now comparable (sorts on offset than on start)
-- Caliper microbenchmark to assess performance
2011-10-22 21:36:37 -04:00
f4b409fa0d
CombineVariants bug fix: when merging records with disparate alleles we were leaving AC,AF fields intact. This had as a consequence that we could end up with a record with 3 alt alleles but only 2 values in AC,AF fields. Now, if alleles in combined vc are different from original, and if AC,AF fields can't be recomputed from genotypes, we remove attributes from vc map since they'll be invalid anyway. Integration test md5 changed since there were several badly merged records in result
2011-10-21 14:07:20 -04:00
b863390cb1
Moving reduced read functionality into GATKSAMRecord
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-- More functions take / produce GATKSAMRecords instead of SAMRecord
2011-10-21 13:28:05 -04:00
110e13bc1e
Merge branch 'master' into SamRecordFactory
2011-10-21 09:43:52 -04:00
3227143a1c
Systematic test code for FragmentPileup
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-- Creates all combinatinos of overlapping and non-overlapping read pair pileups in all orientations and first/second pairings to validate fragment detection.
2011-10-19 17:50:27 -04:00
d8d73fe4f2
Treat ./X genotypes as MIXED so that isHet, isHom, etc. still return the expected and correct values. Added docs to these accessors with contracts explicitly mentioned. Fixed case where NPE could be thrown.
2011-10-19 15:11:13 -04:00
5a6468c11e
Allowing ./X genotypes and adding a unit test to ensure that this case is covered from now on (especially given that we may want to revert in the future). Reverting this change is really easy and entails uncommenting a few lines of code. But for now, despite Mark's objections, this case is allowed in the VCF spec and we are wrong not to allow it.
2011-10-19 11:52:05 -04:00
88d6b8bc1f
Merged bug fix from Stable into Unstable
2011-10-14 20:13:38 -04:00
bd8bb93811
Split RScriptExecutorUnitTest into public and private test classes.
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We can't have a public test that depends on both public and private
code/data -- the new release system needs to do public-only tests,
and will catch this sort of thing.
2011-10-14 20:04:42 -04:00
4f01a742cb
Merged bug fix from Stable into Unstable
2011-10-13 21:39:52 -04:00
edfd6f8a06
Removing a public -> private dependency from the test suite.
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The public integration test VariantContextIntegrationTest was dependent on the
private walker TestVariantContextWalker. Moved this walker to public/java/test
(NOT public/java/src, since this walker is only used by the test suite) to avoid
errors during public-only tests.
2011-10-13 21:32:52 -04:00
404ef741f1
Merged bug fix from Stable into Unstable
2011-10-13 18:02:06 -04:00
2ebdff074c
Update MD5s for SOLiD recalibration
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-- MD5 db had spelling error; fixed
-- Bug in AlignmentUtils resulted in some bases not being color space corrected. The integration test caught the change, and it's clear that the new version is correct, as the prev. version was not considering the last the N qualities for reads with a ND operation.
2011-10-13 18:01:51 -04:00
9aecd50473
Adding ability to exclude annotations from the VA and UG lists. As described in the docs, this argument trumps all others (including -all) so that we can get around the SnpEff issue brought up by Menachem. Added integration test for it.
2011-10-12 15:44:54 -04:00
cfd0ac8410
Merged bug fix from Stable into Unstable
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Conflicts:
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
2011-10-11 12:03:51 -04:00
24b72334b3
UnifiedGenotyper now correctly initializes the VariantAnnotator engine.
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This allows the annotation classes to perform any necessary initialization/validation.
For example, it allows the SnpEff annotator to (among other things) validate its rod binding.
This will prevent a NullPointerException when SnpEff annotation is requested but no rod binding
is present.
Added an integration test to cover this case so that it doesn't break again.
2011-10-11 12:02:05 -04:00
fb72bcf732
DiffObjects no longer prints out the file name in the status so MD5 are stable
2011-10-10 15:10:57 -04:00
e3ff4f4266
Failing MD5 because output now contains absolute path
2011-10-10 11:05:02 -04:00
3e6c16d961
CombineVariants preserves allele order
2011-10-10 11:04:38 -04:00
a4bb842958
RankSum tests have lightly different MD5 results based on allele order
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-- UG GENOTYPE_GIVEN_ALLELES now uses the order of alleles in the VCF, so this changes the MD5
2011-10-10 11:04:07 -04:00
46e7370128
this.allele, getAlleles(), and getAltAlleles() now return List not set
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-- Changes associated code throughout the codebase
-- Updated necessary (but minimal) UnitTests to reflect new behavior
-- Much better makealleles() function in VC.java that enforces a lot of key constraints in VC
2011-10-09 11:45:55 -07:00
822654b119
UnitTests for allele getting functions in VC in prep for move from set to list
2011-10-09 10:36:14 -07:00
c67f6c076b
simpleMerge now preserves allele order
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-- UnitTests for dangerous PL merging cases in the multi-allelic case. The new behavior is correct
2011-10-08 17:39:53 -07:00
e94e6ba101
A UnitTest to ensure that the order of alleles is maintained
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-> A, C, T and A, T, C are different and must be maintained. The constructors were doing this appropriately, so nothing needed to be changed
2011-10-08 08:47:58 -07:00
6fbd41724a
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-07 11:20:00 -04:00
Eric Banks
Mauricio Carneiro
Khalid Shakir
Mark DePristo
David Roazen
Guillermo del Angel
Matt Hanna