e73720c2db
Updating VQSLOD annotation description
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5735 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 19:01:08 +00:00
d4cbd8691c
Make the default that we only output SNPs (so that when I make another release we don't get flooded with questions about why the UG is all of a sudden so slow)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5729 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 16:38:55 +00:00
3224bbe750
New visualization output for VQSR. It creates the R script file on the fly and then runs Rscript on it. Adding 1000G Project consensus code. First pass of having VQSR work with missing data by marginalizing over the missing dimension for that data point (thanks Chris and Bob for ideas). Updated math functions to use apache math commons instead of approximations from wikipedia. New parameters available for the priors based on further reading in Bishop and looking at the new visualizations. Updated integration test to use more modern files. Updated MDCP to use new best practices w.r.t. annotations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5723 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 19:14:42 +00:00
deed7c47a1
Continuing the epic fail, some of our existing integration tests were wrong because of the lazy loading failure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5712 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 17:54:41 +00:00
ab9ffb1a74
Epic failure on the lazy loading of genotypes: if the input VCF had its samples unsorted and we used a walker that didn't require genotypes, then we would sort the samples but not load genotypes (and therefore the genotypes wouldn't match the samples anymore). Added simple integration test to cover this case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5711 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 16:03:45 +00:00
b7334dcc1e
Rank sum test annotations are the Z-scores from the test instead of the p-value.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5707 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-28 14:35:00 +00:00
45081c32d7
continuing from last night, the integration tests weren't covering the right behavior either
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5706 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-28 13:30:57 +00:00
d650efd40a
Fix for bug GSA-449: Intervals that are not in GATK format are not validated
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to the same standard as GATK format intervals. Full validation against contig
bounds is now performed for all intervals, regardless of their source. Also
fixed a few tests for validation exclusions that were backwards.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5698 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 18:12:10 +00:00
7afeb1ab17
Removing broken imports (boo)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5692 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-26 18:55:25 +00:00
bc3fd70b0a
Removing the old association walker, switching test to just validate that MannWhitneyU is doing the right thing. Unit tests still pass.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5690 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-26 18:05:19 +00:00
f619dd3ca7
Refactored IntervalUtils used to parse and scatter intervals for Queue.
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Scattering non-contig interval lists by number of loci in the intervals instead of just number of intervals.
Queue caches the list of locs and how to split them up instead of reloading them from disk repeatedly.
TODO: general purpose function to divide data evenly.
Skip over comments when parsing picard analysis files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5687 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-26 00:06:00 +00:00
a56a2dfdb7
Nothing to see here. Move along.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5681 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 15:01:02 +00:00
600617a63c
Enabled code to deal with hard-clipping adaptor sequence when processing reads in pileup in indel caller. Proven now that changes are minimal (4 less calls in NA12878 chr20, quals slightly different), minor changes in vcf fields in integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5679 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 14:10:33 +00:00
7428ae338a
A fix for Marian Thieme's NPE in the new sharding system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5675 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-21 19:47:14 +00:00
8619f49d20
Added a utility method to retrieve the contig lengths for WG chunking.
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Added a rudimentary GATKReportParser for parsing VE3 results.
Re-enabled the FCPTest using VE3, the GATKRP, and the PicardAggregationUtils.
The tag type for .rod files is DBSNP, not ROD.
More explicit return types on implicit methods.
Added null checks for implicit string to/from file conversions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5668 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-20 19:22:21 +00:00
54660a8c25
Fix requested by Lee Lichtenstein: first check to see whether it's time for
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a progress message, then aggregate metrics. Makes the overhead of
printProgress in RealignerTargetCreator go from >20% to ~3%.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5663 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-20 03:22:48 +00:00
49ea07acce
My fixes to Tribble yesterday revealed that some of the test VCFs for integration tests were actually malformed. Also, Guillermo updated the b37 dbSNP VCF and that broke some tests. Should be good for now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5655 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-17 03:39:11 +00:00
8ed9c0f518
VariantsToTable now blows up by default if you ask for a field that isn't present in a record.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5636 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-14 14:42:43 +00:00
4bb573b1f5
Centralizing a bunch of Broad specific utility functions from code scattered in GSA-Firehose, PipelineTest, custom QScripts, etc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5631 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-13 21:29:02 +00:00
efe6c539ac
Re-enabling disabled test. Apparently T-tests are very picky about your using an unbiased variance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5622 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-13 03:05:50 +00:00
42bc003f46
Oops. I'll need to look at this, I think it was accidentally enabled. Disabling for now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5621 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-13 00:54:52 +00:00
22a11e41e1
Rewrite of GATKBAMIndex to avoid mmaps causing false reports of heavy memory
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usage.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5620 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-12 23:49:58 +00:00
30a19a00fe
Fix for when running with EMIT_ALL_SITES but not GENOTYPE_GIVEN_ALLELES. Still want to emit a site even when over the deletion fraction for example.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5617 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-12 20:07:06 +00:00
3b424fd74d
Enable new indel likelihood model by default, cleanup code, remove dead arguments, still more cleanups to follow. This isn't final version but at least it performs better in all cases than previous Dindel-based version, so no reason to keep old one around.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5615 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-12 17:54:46 +00:00
b6e7b5dace
Updating to reflect my recent Tribble fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5601 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 11:48:00 +00:00
53db7b8faa
Did some refactoring which broke some unit tests, and then failed to run
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the unit tests. Definitely not my best effort...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5599 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 03:31:52 +00:00
cd61ef7169
Re-enabling multi-threaded integration tests. To make this work, downsampling and annotations are disabled for this test so that we don't have randomization issues for it based on which shards get executed first.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5597 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 03:07:39 +00:00
32d502c122
Enable BAM OTF index writing by default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5594 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-07 23:44:25 +00:00
af09170167
As I threatened yesterday, I've moved the various and disparate randomization code out of the walkers. Now they all (except VQSRv1, whose days are numbered anyways) use a static generator available in the engine itself. Please use this from now on. The seed is reset before every individual integration test is run. I think there may still be an issue with the IndelRealigner but I need to confirm with the commit to see what testNG does. Integration tests are already broken anyways, so no big deal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5589 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-07 17:03:48 +00:00
45ebbf725c
Instead of always merging Picard interval files they are optionally merged by Sting Utils.
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Disabled the MFCP while the FCP gets an update.
Minor updates to email messages for upcoming scala 2.9.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5588 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 21:12:05 +00:00
3f3f35dea0
UnifiedGenotyper now BAQs via ADD_TAG to facilitate using BAQed quals for GL calculations but unBAQed quals for annotation calculations. UnifiedGenotyper now produces SNP and indel calls simultaneously. 40 base mismatch intrinsic filter removed from UG to greatly simplify the code. RankSumTests are now standard annotations but the integration tests are commented out pending changes that will allow random annotations to work.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5585 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 19:06:24 +00:00
4b451314b2
Only store a read in the mate hash if it could possibly be moved. This reduces memory consumption especially when dealing with a case of tons of unmapped reads at the end of the bam; however, it's only mildly helpful for chr1 of the Papuans (there's a truly massive pileup 120Mb into it; more thought needed at a later point). Integration tests changed only because some of the reads in the original bam were busted to begin with (it's an old pilot 1000G bam).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5580 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-05 22:20:09 +00:00
79b5fa6cc5
Structural refactoring in advance of dichotomization statistics; generalization of statistical test infrastructure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5579 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-05 18:52:32 +00:00
bb6a30611c
Forgot to modify the test too. What a bad commit. Sorry guys.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5575 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-05 02:11:08 +00:00
db9908ec02
Small correction to the unit test code from my last commit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5572 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-04 18:55:38 +00:00
a5acb0b7a6
Fix for bug GSA-314: Detect -XL and -L incompatibility. An ArgumentException is
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now thrown if the combination of -L and -XL intervals specified on the command
line results in an empty interval set after set subtraction.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5571 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-04 18:41:55 +00:00
095125152b
Updated to now longer include 2nd-best base output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5567 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-03 20:13:10 +00:00
0927b7c297
Fix for bug GSA-441: BAM file list with blank lines gives a confusing error
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message. Lines containing only whitespace in .list files are now ignored.
Also added support for comments in .list files: lines whose first
non-whitespace character is '#' are now also ignored.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5550 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-01 15:04:35 +00:00
7b452ea2b9
Fix for bug GSA-430: Can't specify same BAM file twice on the command line. An ArgumentException with an appropriate error message and a list of the duplicate BAMs is now thrown in this case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5542 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-30 22:23:24 +00:00
deab9f0aa5
Initial work on proto-shard merger:
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- create size() method that returns an approximation of the uncompressed size in bytes of BAM span.
I'll use this method as a protoshard weighting function until we determine how to normalize the
weights across the different data access mechanisms (reads, reference, RODs).
- Implementations of basic union/intersection/subtraction mechanisms for BAM spans; should be enough
to get an accurate weight for two proto-shards put together.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5541 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-30 22:03:43 +00:00
328f89f66a
Minor changes to MannWhitneyU:
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- Comment fixes to better explain why two-sided test wants to use the LOWER (not higher) value for U
- Much more direct testing of MWU functions
- Uniform approximation was always using the < cumulant (sometimes the > cumulant should be used instead)
- Uniform approximation currently not used (regime in which it was being used was not the right one -- not necessarily bad, but not an improvement over normal)
+ this particular approximation is for major imbalances of the form m >> n. Code may be altered in the future to use this method for this particular regime, if the method's not too slow.
- Hook into one-sided test.
RegionalAssociationRecalibrator: NaNs were being caused by presence of Infinity and -Infinity values out of the walker. Currently I'm just re-setting them to arbitrary post-whitened values, but the walker will be changed to prevent output of these values, and the "fix" will undone.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5539 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-30 17:03:02 +00:00
5ddc0e464a
Under guidance from Matt added ability to use key-value tags with ROD binding command line arguments, so now one can say -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmap.vcf and get the tags in a walker. Look at ContrastiveRecalibrator for an example of how to use the new ReferenceOrderedDataSource.getTags(). Removed references to FDR in tranches since we are only using truth sensitivity. Finally fixed long standing bug where tranche filters weren't set appropriately.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5536 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-29 21:04:09 +00:00
f6dfdc7f3b
Single-tailed hypothesis testing in MWU
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5533 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-29 15:53:40 +00:00
cd8321cdc9
Removed the completely unused generic but extremely expensive infrastructure for dynamic LocusIteratorFilters. Now the one, and probably only useful one, is called directly in the LocusIteratorByState itself to filter adaptor bases from reads. This shaves 10% off the runtime of all walkers, apparently. Has the additional benefit of eliminating a lot of complex infrastructure that resulted ultimately in only a single function call.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5525 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-27 20:48:24 +00:00
3bcd4c5d75
--simplifyBAM is now in the SAMFileWriterArgumentTypeDescriptor, as suggested by map. PrintReads has an integrationtest now that writes out a 1 MB bit of HiSeq normally, with compress 0, and with simplifyBAM on.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5521 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-26 14:57:18 +00:00
7272fcf539
Now uses the NO_HEADER option to avoid breaking MD5s due to changes in GATKArgumentCollection
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5518 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-26 12:00:37 +00:00
fc8acd503e
Enabled the parameterize option for debugging PipelineTest MD5s.
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Fixed escaping expressions that have more than one space between arguments.
Updated example to match the wiki.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5516 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-26 00:41:47 +00:00
69646ff840
... and the corresponding integration test update
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2011-03-23 01:58:07 +00:00
5a79f16ea4
Fixed an edge case where an exception was thrown if either of the sets was empty for the MWU test. Also altered the output format so U itself is not printed (which though interesting, isn't so useful for recalibration), but rather a value I call V (really the deviation of U from its expectation).
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2011-03-22 16:28:44 +00:00
1c95208e26
Finally found the bug that everyone is reporting on GS. Iterators on PriorityQueues aren't guaranteed to return elements in sorted order (a pretty stupid contract) - so we were passing items to the constrained writer out of order. Just do a Collections.sort instead (1 line of code). Happy father's day!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5476 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 21:28:19 +00:00
rpoplin
ebanks
droazen
chartl
kshakir
delangel
hanna
depristo