a8f8077d7a
Simple optimizations for cases where there is no data or RODs at sites, such as with the FastaStats walker. private static immutable Lists and Maps in underlying data structures that have no associated data. Also, avoiding a double map.get() in the low-level genome loc parser. RefMetaDataTracker is now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5664 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-20 10:52:16 +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
49550e257f
Fix for JamesP's issue. This issue appeared because of a design flaw in the
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interface between SAMDataSource and IntervalSharder that needs to stay around
until the original BAM sharder is retired. Will add a JIRA to fix design
flaw.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5661 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-19 00:52:13 +00:00
541c9109b3
V1 of GATK Resource Bundling system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5659 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-18 19:23:45 +00:00
673772a522
Catch samtools exceptions and make them 'BAM Exceptions' asking the user to run Picard's validator and re-index the file before posting anything to the forum. Let's see whether this helps or not.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5658 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-18 03:52:43 +00:00
e97a5ca161
Rename 'verbose' argument to 'debug_file'.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5657 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-18 03:17:13 +00:00
e28fc21642
Spurious associations can develop from including ambiguous reads in these tests. Perhaps MQ0 reads shouldn't be used for anything except MQ0, but the best way to do that is to restructure the code, so for now I'll put it off.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5656 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-17 23:17:03 +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
e5ef8388fc
BatchMerge - AlleleVCF --> AllelesVCF, this (combined with Eric's fix) will solve James P.'s forum issue.
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After viewing results on real case/control data from RAW -- it's really working quite well. ReadIndels, however, needs to use a T-test rather than a U-test, especially in deep coverage (at indel sites, the reads with indels will have mostly the same number of CIGAR indel elements -- one -- which doesn't really play nicely with the UTest when sample sets are large). Modified ReadsLargeInsertSize to be a two-way test (e.g. ReadsLarge and ReadsSmall). BaseQualityScore also suffers from the same issue as read indels, so switching over to a T-test in that case as well.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5653 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-15 22:03:16 +00:00
1c32deb108
For some reason I wasn't allowing expressions to be used with the -all argument.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5652 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-15 20:59:10 +00:00
2cf6a06503
Throwing an error if INFO fields arguments contain whitespace.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5651 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-15 20:52:55 +00:00
fce6d25075
Moved the reference ID to a meta data field for validity declaration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5650 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-15 20:28:56 +00:00
59215dab48
Now writes results to a minimal vcf with annotations included in the INFO field. Must be run with -NO_HEADER to totally remove header for the most bare bones vcf; otherwise also includes command line meta data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5649 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-15 20:14:02 +00:00
fe26954ac6
Minimal support for reading in VCF4.1 files. Added TODOs that need to be fixed or cleaned up to truly support this version. VCF constants updated. Lower-case bases permitted. Please let's make sure to refactor once we're ready to support it for good.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5648 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-15 18:59:37 +00:00
7e9051ea25
The solution to James's bug was just to clean up the code and simplify it. What happened was that functionality that got put into UGCalcLikelihoods was then generalized into the UG engine but then never removed from UGCalcLikelihoods. This knowingly breaks the batch merger, but Chris said he'll take care of it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5647 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-15 18:05:10 +00:00
0d7cca169e
Sigh.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5645 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-15 14:37:24 +00:00
0965020804
Screwed up the doc string.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5644 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-15 14:30:20 +00:00
be3bad1f61
Low-memory sharding is now enabled by default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5643 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-15 14:22:07 +00:00
2830dc70b7
UG can still return null in certain nasty cases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5642 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-14 20:11:17 +00:00
8e0f5bc5a5
Prevent NullPointerException in cases where SNP is filtered
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5641 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-14 19:59:59 +00:00
ee94af3539
Oops, left out of earlier commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5640 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-14 18:21:16 +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
b3cd14d10a
Since GCcontentIntervalWalker no longer uses any ROD, turn it into a LocusWalker that traverses by REFERENCE
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5635 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-14 03:15:09 +00:00
2089c3bdef
removing; should of gone to the CGA repo
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5633 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-13 22:17:45 +00:00
da6f2d3c9d
adding the capseg tools to the new walker repo
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5632 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-13 22:11:08 +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
91d308fc6d
temporary patch until Picard (hopefully) fixes the NM calculation to deal with reads that align off the end of the contig
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5630 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-13 19:18:18 +00:00
fa6468d167
Remove the adaptor sequence clipping read filter because it is dangerous (it breaks LocusIteratorByState). We'll bring it back to life when ReadTransformers are created. Instead, have the utility code return a new clipped SAMRecord (necessary so that we don't break SNP calling in UG when the indel caller tries to hard-clip the reads).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5629 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-13 18:47:47 +00:00
5849e112e1
Fix exception in block weighting minus function.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5628 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-13 17:07:04 +00:00
a36adf0c6b
Request from the cancer team -- guarantee via javadoc that the returned
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read metrics are actually a clone, which they can do with as they wish.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5626 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-13 15:10:46 +00:00
06b1497902
Corrected bad merge.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5625 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-13 15:02:09 +00:00
9134bf3129
Long-forgotten change I neglected to commit a while back: add ability for SelectVariants to extracts either SNPs or Indels from combined vcf file. Not the ideal place to do it but it's important to at least have something to split vcfs now that we call snp's and indels combined.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5624 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-13 14:58:44 +00:00
8e0d191a70
Added a walker to help sort out which samples in a region are giving signal. Lots of reused code that shouldn't be. Will refactor later.
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Also fixed an "issue" with InsertSizeDistribution -- apparently for mate pairs, the first mate (karyotypically) will have a POSITIVE insert size, and the second a NEGATIVE insert size -- thus the insert size distribution was being conflated with enrichment/depletion of first-in-pair or second-in-pair reads. Gah.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5623 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-13 13:53:31 +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
36d8f55286
Use the 'standard' arcsine transform
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5619 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-12 23:11:45 +00:00
8125b8b901
Old changes to the exome VQSR search.
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SGA updated to include new proportion-based insert size test.
Major fix for dichotomization test: MathUtils now optionally ignores NaN values for sums, averages, variances. In the future this feature can be pushed back into the AssociationContext object iself (e.g. no data? no entry), but it's kept like this for transparency for now.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5618 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-12 23:00:50 +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
488622041d
Further trivial cleanup: Renamed DindelGenotypeLikelihoodsCalculationModel to IndelGenotypeLikelihoodsCalculationModel
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5616 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-12 18:00:48 +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
9c36b0a39b
Refactored read clipping framework into a generic utilities class, independent of ClipReadsWalker, which now uses this framework. Some more cleanup is really needed, as some of the arguments to the classes are really only useful for ClipReads
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ReduceReadsWalker -- does consensus-based read compression, v2. Does all of the consensus calculations within the ConsensusReadCompressor per sample, and multi-sample case is handled by MultiSampleConsensusReadCompressor. For deeply covered data sets, this projects a significant reduction in the number of mapped reads. Impact on analysis call quality tbd. Expected to be relatively minor, as the system automatically detects regions without a strong consensus, and expands a window around these so that +/- 10bp of all reads are shown around the unclear sites. Not usable yet -- as it does not yet support streaming output, and actually holds all reads in memory at once.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5610 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-10 13:55:05 +00:00
13c5f3322d
Added argument to avoid writing 0 over all uncovered contigs, so you can just plot chrX, for example
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5609 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-10 13:50:21 +00:00
de4eaa455e
Squashing some bugs. Current implementation of AlignmentContextUtils.splitContextBySample() eliminates all sample meta data. Per Mark's request I'm working around this rather than fixing it -- the extender now maintains a mapping from sample id to sample object. Addition of a proportion test for large-insert-size reads, and slight refactoring of code to deal with bad window initialization of subclasses (e.g. chris forgot that constructors aren't inherited)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5608 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-09 21:07:52 +00:00
b4b52cc0fe
Reduce unnecessary repetitive accesses to the BAM index file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5607 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 19:28:14 +00:00
0a58d7aa1a
Marked boolean SAMFileWriterATD arguments as flags so scala generator maps them to Boolean instead of Option[Boolean].
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Using the VCFWriterATD isCompressed to check if the VCF index will be auto generated.
Tracking BAM and Tribble indexes as @Inputs and @Outputs in generated QFunctions.
Updates to the BamGatherFunction to disable the index during merge when disable_bam_indexing = true.
Made a shortcut for live-running pipelinetest, pipelinetestrun.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5606 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 18:44:32 +00:00
866f4fd569
Test version of consensus compressing strategy. Cannot be used, and is being rewritten right now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5605 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 18:37:03 +00:00
80d547ae71
Fix for bug GSA-445: Sequence dictionary validation can be very slow with
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large numbers of contigs. SequenceDictionaryUtils.getCommonContigsByName() was
running in O(n^2) time due to poor choice of data structure -- modified it to
run in O(n) time. Also removed an unnecessary O(n log n) step at another stage
in the sequence dictionary validation process. In tests with a 181,813-entry
sequence dictionary, runtime improved from an average of 21.4 minutes to 45.1
seconds.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5604 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 18:33:10 +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
4f17004590
Allow walkers to enforce the ordering in which ReadFilters are applied (so that they're now done in the order specified in the walker). Useful if you have a computationally expensive filter (like adaptor clipping) that should only be applied to reads passing all other filters.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5600 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 03:34:50 +00:00
depristo
hanna
ebanks
chartl
corin
fromer
aaron
kshakir
delangel
rpoplin
droazen