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
59dd79faab
One more optimization: don't use Math.round(), but do my own rouding/casting. UG now about 40% faster calling indels, 30-35% faster calling snp's+indels simultaneously.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5667 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-20 19:15:58 +00:00
246d8190b5
Round one of "easy" zero-effort optimizations to UG's indel caller. Mostly inline functions, avoid repeated computation and try to optimize SoftMaxPair() which is by far the bigest runtime hog. More to come...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5666 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-20 18:57:34 +00:00
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
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
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
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
74755cfd1c
Adding a ReadFilter to hard-clip out bases from adaptor sequences. This is actually slightly more correct than having it be part of LocusIteratorByState because it allows us to remove reads that are complete garbage (and there are definitely some) based on the insert sizes. However, although conceptually this is great, it doesn't actually work. 'Why?' you may ask. Because when we hard-clip reads it often changes their start positions... which means that reads are no longer passed to LocusIteratorByState in coordinate order... which makes it (understandably) barf all over the place (and makes for some really fascinating SNP calls). This took me forever to find. I'm going to bed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5598 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 03:15:58 +00:00
fece2167b3
Prototype implementation of protoshard merging when protoshard n and protoshard
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n+1 completely overlap. Gives a small but consistent performance increase in
non-intervaled whole exome traversals (2.79min original, 2.69min revised).
Needs a more in depth analysis of optimal shard sizing to determine a true
optimum.
Also renamed a variable because Khalid disapproved of my naming choices.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5595 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 02:09:14 +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
cb3e8aec5e
Modified the buildfile and help extractor doclet so that help text is only
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extracted from source files that have been modified since the help resource
file was last generated. This significantly speeds up builds where only a few
source files have been modified, at the expense of making clean builds take
slightly longer. Here's some performance data gathered by testing the old and
new versions of extracthelp in isolation and averaging across 10 runs:
old extracthelp, 1 modified source file: 20.1 seconds
new extracthelp, 1 modified source file: 7.2 seconds <-- woohoo! :)
old extracthelp, clean build: 17.8 seconds
new extracthelp, clean build: 20.5 seconds
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5590 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-07 18:40:53 +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
89bb21d024
typo in the argument description
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5587 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 19:45:32 +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
1aa4083352
Fortunately this code isn't used by anyone right now, but it needs to be fixed before someone unwitingly does: flags were wrong according to the SAM spec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5584 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 17:16:41 +00:00
b231a40da5
Augment PrintLocusContextWalker with extended event info.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5583 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 13:42:48 +00:00
ab5c4064ed
quick bug fix for variant context utils: only calculate the max AC if we're using the mergeInfoWithMaxAC flag, and if so deal with sites that have multiple alternate alleles correctly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5582 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 05:36:52 +00:00
cc713f2769
fixing exception text
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5581 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 00:29:13 +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
77ca4eef31
IntelliJ complains that @Override is not allowed when implementing interface methods. Whatever.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5578 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-05 16:57:59 +00:00
f4c06bb4ce
Traversal now says 'done with mapped reads' instead of 'done' so we don't confuse users when there are a lot of unmapped reads left to process.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5577 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-05 15:11:28 +00:00
5eccc7e528
Added annotation of INCORRECT SNP-based aa annotations in case of MNPdependentAA:true
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5576 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-05 02:46:45 +00:00
a0d096c993
Forgot an import statement
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5574 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-04 22:55:00 +00:00
b52c3e7e30
Make the window and slide-by values command-line accessible, and standardize for every context. Move the test classes (which are abstract association context modules) into the proper directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5573 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-04 22:37:12 +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
b722ebf244
quick help/comments updates to match the wikipage.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5569 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-04 12:55:55 +00:00
96f0f0d706
Fixing use of String != String
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5568 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-04 01:12:00 +00:00
b2a0331e2d
Pushing hard coded arguments into VariantRecalibratorArgumentCollection
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5566 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-03 19:55:09 +00:00
79c43845ad
Changing Uniform approximation to Normal approximation in rank sum test. n factorial was overflowing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5565 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-03 18:18:39 +00:00
b316c9a590
Renamed StratifyAlignmentContext to AlignmentContextUtils, and StatiefyContextType to ReadOrientation. Also, went through the system and deleted all references to second bases. That ship passed long ago. This was the actual commit, the last was an intellij error
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5564 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-03 15:36:17 +00:00
5cca100aea
Eliminated the redundant StratifiedAlignmentContext, which previously just held a ReadBackedPileup, and made all of the class methods here just static functions. Far more logical organization, and avoided O(N) endless copying of data for the COMPLETE context. Many tools have been trivially reorganized to take an alignment context now. Everything passes integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5562 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-03 14:20:43 +00:00
98798eb276
Adding ReadPos rank sum test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5560 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-02 22:28:41 +00:00
09e89c8c97
Adding ReadPos rank sum test. Transitioned rank sum tests over to using Chris's implementation in order to harmonize the codebase. There isn't any reason to have competing implementations of rank sum. Thanks to Chris for adding the necessary hypothesis testing options. WilcoxonRankSum.java will be deleted soon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5559 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-02 22:26:35 +00:00
11822da578
Stand alone, GATK dependent tool that Reads a list of BAM files and slices all of them into a single merged BAM file containing reads in overlapping chr:start-stop interval. Highly efficient when working with thousands of BAM files. Can merge 1MB of sequence of 1600 4x BAMs in 4g in only 2 hours.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5558 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-02 13:41:29 +00:00
27bfec785e
Some walkers for printing FASTA of reference for bed ROD, and "inverting" a bed file (finding regions not covered in bed)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5554 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-01 21:13:51 +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
4f8411f4b5
Revved Picard to access new flag to disable mmap for bam indices. Only added a 3% speed boost but the mmap was added to the heap count, making it harder to specify/restrict the total resident memory size in LSF. Specifying -Xmx4g will now stay much closer to 4g resident memory usage versus bumping up to 9g when accessing 900 x ~8Mb bai's.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5549 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-01 01:40:41 +00:00
df53351b0f
Get rid of score cutoff at 0 in the alignment matrix (i.e. score[cell] = max(0, score[from_parent_cells]). Use the computed score as is. Technically, it's pretty much NW now, not SW.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5548 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-01 00:11:04 +00:00
0a772688fe
implementation of the Gatherer class for CountCovariates, which makes it now scatter/gatherable. Kudos to the @Gather annotation Khalid just introduced!
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QuickCCTest is my test script for the gatherer.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5547 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-31 21:15:21 +00:00
dac1309dbd
Added two modes for selecting variants at random (random sampling).
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-number N -- generates a VCF with exactly N randomly chosen variants with equal probability.
-fraction F -- generates a VCF with approximately F (between 0-1) randomly chosen variants with equal probability. (Similar behavior to RandomlySplitVariants walker).
The reason for two modes is that the first one may need a lot of memory if your sample size is too large. The wiki is being updated with this information now.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5545 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-31 21:12:40 +00:00
8a3b7d88aa
It was returning 1 when it should return 0
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5544 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-31 20:50:38 +00:00
c7445a6fbd
Now that logging is so standard, only prints messages about logging to DEBUG. Also, found a way to silence the mime.types warning, that doesn't matter at all to us.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5543 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-31 16:49:39 +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
fff11a3279
No more pesky NaNs for norms ( HINT::: ((double) x) == Double.NaN is NOT (somehow) the same as Double.compare(x,Double.NaN) == 0). Effectively reverse sorting by changing (rank/size) to ((size-rank)/size).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5538 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-29 22:43:24 +00:00
5d26c66769
Count Covariates is almost scatter-gatherable now!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5537 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-29 22:25:33 +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
0f4ace0902
fixed a bug when the concordance track doesn't have the sample in the variant track.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5535 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-29 18:24:19 +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
8ae14793f2
Small standalone utility to aggregate BGZF block statistics in a BAM file.
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Works in the same coordinate space as BAM chunks, so this will be used to
calibrate chunk weighting.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5531 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-28 22:25:45 +00:00
f3e4c24f63
Framework works properly now, but whitening still has a kink which is that the covariance matrix gets re-sorted automatically by the eigendecomposition, so somehow the association between eigenvalue and dimension (e.g. association track) needs to be maintained throughout.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5530 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-28 22:22:37 +00:00
4c04c5a47a
Addition of a BedTableCodec to allow for parsing of Bed-formatted tables (e.g. bedGraphs). Fixes for the recalibrator. Implementation of the data whitening input. Some TODOs in the RAW.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5529 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-28 21:35:09 +00:00
f2d84bf746
Changes the validity declaration from a true to false to a five point scale
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5527 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-28 18:31:53 +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
kshakir
delangel
depristo
hanna
ebanks
chartl
corin
fromer
aaron
rpoplin
droazen
carneiro
asivache