8377424089
Basic error checking to ensure incoming arguments are provided correctly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5831 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-21 13:43:48 +00:00
e234589240
Contracts for GenomeLocParser and GenomeLoc are now fully implemented.
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GenomeLocs can officially have any start/stop values from -Inf - +Inf. Bounds w.r.t. the reference are enforced, optionally, by GenomeLocParser. General code cleanup throughout the subsystem.
All validation code for GLs is now centralized, and all I/O systems now validate their inputs. Because of this, the Picard interval processing code has been changed to examine whether an interval is valid, and only keep the valid intervals. Note that the scatter/gather test was changed, because the original hg18 chr20 interval files as actually malformed (all records for some reason where on chr20).
Many interval processing routines were moved to IntervalUtils, as this is their natural home.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5830 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-21 02:01:59 +00:00
3aa56037af
If asked, filters out triple-het situations too (which cannot be simply phased by transmission).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5829 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-20 18:48:19 +00:00
e16bc2cbd9
Contracts for Java now write for GenomeLoc and GenomeLocParser. The semantics of GenomeLoc are now much clearer. It is no longer allowed to create invalid GenomeLocs -- you can only create them with well formed start, end, and contigs, with respect to the mater dictionary. Where one previously created an invalid GenomeLoc, and asked is this valid, you must now provide the raw arguments to helper functions to assess this. Providing bad arguments to GenomeLoc generates UserExceptions now. Added utilty functions contigIsInDictionary and indexIsInDictionary to help with this.
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Refactored several Interval utilties from GenomeLocParser to IntervalUtils, as one might expect they go
Removed GenomeLoc.clone() method, as this was not correctly implemented, and actually unnecessary, as GenomeLocs are immutable. Several iterator classes have changed to remove their use of clone()
Removed misc. unnecessary imports
Disabled, temporarily, the validating pileup integration test, as it uses reads mapped to an different reference sequence for ecoli, and this now does not satisfy the contracts for GenomeLoc
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5827 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-20 15:43:27 +00:00
d896a4a9d3
Given genotypes for a trio, phases child by transmission. Computes probability that the determined phase is correct given that the genotypes for mom and dad are correct (useful if you want to use this to compare phasing accuracy, but want to break that comparison down by phasing confidence in the truth set). Optionally filters out sites where the phasing is indeterminate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5824 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-19 21:27:37 +00:00
fe4b40ac2c
Adding new InbreedingCoeff and PercentNBases annotations for Guillermo to use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5823 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-19 19:50:39 +00:00
bc98ac1e74
Adding a TODO for future consideration
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5821 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-19 15:02:23 +00:00
0bb6b9a91a
Locus iterators were implemented in a peekable style, which meant that a locus
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and its three or four nearest neighbors could be in memory at once. Tweaking
the iterators to ensure that previous AlignmentContexts don't have strong
references which means that the garbage collector can work effectively to
help us trundle through these regions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5820 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-18 21:40:40 +00:00
a38b2be329
Fix for old, broken invariant where unmapped reads are represented by null rather than an empty BAMFileSpan.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5819 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-18 20:57:38 +00:00
ebcd333ed8
Quick small updates:
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SelectVariants: typo
MethodsDevelopmentPipeline: Added CEU Trio WGS dataset
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5818 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-18 20:08:39 +00:00
4b00fd2688
Adding User Exception to VQSR for the case of trying to cluster with an annotation that doesn't exist in the input VCF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5816 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-18 19:47:51 +00:00
d698c87bbf
More UserExceptions and warnings in VQSR.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5813 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-16 19:03:21 +00:00
541b5f7a80
Somehow checked in a version that was building extensions for everything ("") instead of selected packages. Fixed.
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Also added more logging when extension generation fails.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5812 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-16 16:58:37 +00:00
a27e8b1dc6
Bug fix - use correct variable to retrieve from map.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5811 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-16 15:32:58 +00:00
d925f76edc
Cutting down on the number of info lines in VQSR so that I can read the warning messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5810 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-16 13:35:51 +00:00
5a7444e186
First step in refactoring UG way of storing indel likelihoods - main motive is that rank sum annotations require per-read quality or likelihood information, and even the question "what allele of a variant is present in a read" which is trivial for SNPs may not be that straightforward for indels.
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This step just changes storage of likelihoods so now we have, instead of an internal matrix, a class member which stores, as a hash table, a mapping from pileup element to an (allele, likelihood) pair. There's no functional change aside from internal data storage.
As a bonus, we get for free a 2-3x improvement in speed in calling because redundant likelihood computations are removed.
Next step will hook this up to, and redefine annotation engine interaction with UG for indel case.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5809 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-15 23:04:11 +00:00
3ccc08ace4
Now emits siteType = {SNP,INDEL}. Doesn't work (and may never actually work) for indels under current extended event system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5808 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-15 19:16:09 +00:00
75db4705ab
Added splitContextByReadGroup() and fixed bug in getPileupForReadGroup() that resulted in a NPE when no reads where present for a read group.
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Added doc string for getNBoundRodTracks()
Intermediate commit for CalibrateGenotypeLikelihoods and GenotypeConcordanceTable, so I have a record of my work. Not ready for public consumption. Really looking forward to making local commits so I can track my progress without needing to push incomplete functionality up to the server.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5807 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-15 17:36:07 +00:00
fa75efb6ac
Backing off - need to change pileup interface for rank sum tests before indels can be annotated with them
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5804 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-13 21:54:54 +00:00
befbcd274b
Computes additional stats we want to use later for filtering: median and mad for indel position with respect to starts and ends of all the reads that support it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5803 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-13 21:19:58 +00:00
5c889580c4
Change of logic: if "read" (sequence 2) sticks out beyond the boundary of the ref (sequence 1) it is aligned to, the extra bases on the left or on the right will be softclipped in the cigar generated for such an alignment, rather than added to the firts/last M block. This also affects alignment offset: if read starts before the ref (used to be represented by a negative offset), the cigar now will start with S, and the returned offset (alignment start) will be 0.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5802 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-13 21:12:54 +00:00
d4ca8d94fa
Trivial change to allow indels to be annotated by rank rum tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5801 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-13 20:24:08 +00:00
03452c15c0
Cleanup GATKBAMIndex unit test to allow a more efficient access pattern for
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FindLargeShards. Runtime of FindLargeShards on papuan dataset is now 75min.
GATK proper should benefit as well, although the benefits might be so small
as to not be measurable.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5798 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-12 21:50:33 +00:00
db1f9af679
Now supports multiple records in allele at sites that genotype as reference
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5796 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-12 17:36:27 +00:00
a22e98a2c4
Yikes. Fixing the build
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5794 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-12 01:52:35 +00:00
40797f9d45
Ensuring a minimum number of variants when clustering with bad variants. Better error message when Matrix library fails to calculate inverse.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5793 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-12 01:48:37 +00:00
a20d257773
Generating extensions for org.broadinstitute.sting.gatk.datasources.reads.utilities, including FindLargeShards.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5792 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-12 00:49:31 +00:00
fb1be2653c
A succint walker that reports GC content by interval. Taking down two old implementations of the same thing from oneoffs. Documentation added to the wiki.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5790 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-11 18:53:11 +00:00
9a1d0d7076
Simple bug fix to allow multiple records at same site when genotyping given alleles. Takes only the first record (respecting filters, SNP type, etc), and issues a warning if there is more than one valid record at a site
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5789 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-11 14:17:14 +00:00
dfdef2d29b
PLEASE READ ME! In order to prepare for the upcoming changes to VCF4, we felt it was best to split up the vcf3 and vcf4 codecs (vcf4 is not backwards compatible to vcf3 and certain changes are too complex to handle in both codecs). Using the 'VCF' rod type in the GATK will now throw a UserException for vcf3.2 or vcf3.3 files telling you to use the 'VCF3' type instead (and vice versa). Integration/unit tests have been updated. For programmers: note that there is currently a lot of code duplication in the two codecs (although I pulled out the easy stuff to a VCFCodecUtils class); however WE ARE FREEZING THE VCF3 CODEC AND WILL NO LONGER MAKE CHANGES TO IT. All updates/improvements will be targetted to the vcf4 codec only as vcf3 is there only to be able to read legacy files. People should really be using vcf4 files only.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5787 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-11 12:07:44 +00:00
852e555c00
Fix broken functionality from previous commit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5786 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-10 18:38:25 +00:00
8d47d2e813
Fix for Tim. It was possible for the constrained mate fixer to dump its cache in them middle of a given realignment (so the IndelRealigner was playing by the rules). No longer possible.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5785 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-10 16:48:24 +00:00
3c364279f4
Add simple ability to create "X out of N" combined files: if a site is present in at least X input rods, it gets output, otherwise it's skipped, controlled with argument -minN.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5783 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-10 15:27:18 +00:00
f275be6968
A 'fat shard' finder. Cranks through the indices of a BAM file or list of
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BAM files looking for outliers (outliers right now are defined naively as
shards whose sizes are more than 5 stddevs away from the mean). Runs in
13 minutes per chromosome on 707 low pass whole genome BAMs -- not great, but
much faster than running UG on the same region to discover anomalies.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5782 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-10 12:56:47 +00:00
7d21350a17
Fixed import.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5780 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-09 18:07:40 +00:00
0861451726
Print on multiple rows in standalone command line mode when the sequences are too long
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5779 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-09 13:51:00 +00:00
bf40351094
Minor update
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5778 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-08 03:48:37 +00:00
15c7bd82a5
Fix for IndelRealigner memory problem. Now the Constrained mate fixing writer is told whether a read has been modified and, if it wasn't, can dump it when the cache needs to get flushed at places with tons of coverage.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5777 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-06 19:34:41 +00:00
d8a761bbbd
Warn the user if trying to train with too few variants
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5776 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-06 17:47:58 +00:00
c2e8c460cb
Factor out all testing dependencies into a separate test configuration and
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only download that test configuration when running unit/integration tests.
This means that the build will (hopefully) never break because it can't
fetch a file that isn't required for the GATK to run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5775 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-05 22:42:11 +00:00
b94d8dae17
Removing requirement of providing known track in VQSR for the non-humans. Updating placement of legend on tranche plot.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5773 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-05 20:24:06 +00:00
7d7ce6cf00
Two embarassing bug fixes:
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a) Forgot to convert from phred to log-prob when computing gap penalties from recal table.
b) Forgot to uncomment code to correctly deal with hard-clipped bases in a read. But because of this, had to do a short term workaround to at least temporarily return class from hardClipAdaptorSequence to GATKSAMRecord. Otherwise, I get exceptions when casting because somehow some reads in HiSeq get to be SAMRecord (which GATKSAMRecord inherits from) but some reads get to be BAMRecords (which can't be cast into GATKSAMRecord), not sure why.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5771 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-05 17:08:34 +00:00
28b897d5de
Fixed O(N^2) operation when scattering interval files.
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Cleaned up intervals contig count function.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5768 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-05 03:32:35 +00:00
3882d1b9c0
fixing the build \o/
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5767 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-05 00:57:49 +00:00
8ad547e6c2
Fixed another interval bug where dividing up N intervals into N parts wasn't working.
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Minor updates to the FCPTest to match the changes due to using the old indel caller.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5766 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 20:49:35 +00:00
5c6965575e
Some refactoring that Mauricio and I worked through together. Changed filters
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to extend from org.broadinstitute.sting.gatk.filters.ReadFilter rather than
directly from net.sf.picard.filter.SamRecordFilter, which allows us to add
an initialize(GATKEngine) method so that filters can do any initialization
they'd like based on CL arguments, SAM headers, etc.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5760 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 19:29:08 +00:00
b66c6dced1
- No longer prints out non confident calls (they were leading to tables that don't add up and confusing some Pacbio folk).
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- Added sensitivity and Specificity to the report.
- With the changes in genotype likelihoods, the indel analysis only happens if the BAM file also has an extended event. Not great, but at least it's not broken.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5759 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 19:26:55 +00:00
7ed8b4ddb0
Making sure CalculateLikelihoodsAndGenotypes returns an empty variant context when 'EMIT_ALL_SITES' and 'GENOTYPE_GIVEN_ALLELES' are being used, now for indels too!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5756 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 18:04:56 +00:00
6c7a0adc76
Updating VariantGaussianMixtureModelUnitTest to use truth sensitivity cutting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5750 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 13:56:01 +00:00
a19389528d
Bring back from the dead the old likelihoods model for indels, which has worse performance but is about 4x faster. Enabled with argument -GSA_PRODUCTION_ONLY in UG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5748 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 22:38:33 +00:00
e5cc0f4eec
Added 'specificity' to variant eval's Validation Report evaluator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5742 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 20:48:30 +00:00
b88dec387c
clean up from VQSR movement
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5741 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 20:35:30 +00:00
23cd3a7a5d
Moving VQSR v2 to core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5740 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 20:20:06 +00:00
44a717f63a
Good bye VQSR v1. This commit will break the build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5739 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 20:09:52 +00:00
2dacf1b2b2
Better header support when running R's read.table(...,header=T).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5738 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 19:56:20 +00:00
ad8c786b2d
Now more easily R-parseable.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5737 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 19:30:50 +00:00
5bade81c6d
Adding tranche plot generation back to VQSR
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5736 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 19:26:26 +00:00
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
11052918d9
Better exception text for common error in VQSR.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5734 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 18:37:25 +00:00
4bbce42861
Renaming ContrastiveRecalibrator --> VariantRecalibrator in preparation for move to core
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5733 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 18:12:47 +00:00
6323fb8673
misc cleanup in VQSR
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5732 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 18:00:22 +00:00
f3bd11a02e
Dress up some formatting issues.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5731 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 17:35:18 +00:00
9c809ed68e
A walker to analyze the memory consumption of reference, reads, and RODs at
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each base both in bytes and as a percentage of the used heap size.
May be a bit buggy at this point; there are a lot of metrics around the Java
heap and I'm not completely sure that the metrics I'm outputting are exactly
the ones that I'm looking for.
Also fixed a documentation bug in my Sizeof class.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5730 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 17:08:15 +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
70f8ab6f89
Adding AF bin stratification for VariantEval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5728 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 15:22:50 +00:00
870e65a685
Fixing a build failure because I want to be completely sure that the code I
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checked in immediately following the build breaking code passes integration
tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5727 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 02:09:53 +00:00
411980a50a
Performance enhancements in GATKBAMIndex. Not sure these will assist in a
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normal use case, but they cut startup times and memory allocation noise in
the profiler, making my profiling time more productive.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5726 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 20:48:16 +00:00
422d4ceeea
removed useless file - no need for tableRecalibration, right now everything is done in PairHMMIndelErrorModel
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5725 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 20:35:44 +00:00
2a80ffa2ee
Totally experimental, barely useable not to be used yet implementation of an "Indel Quality Recalibrator" Idea is that any indel that's not in input dbsnp is treated as an artifact, and then a csv is built with # of indels and # of observations as a function of each input covariate (initially, only cycle, read group and homopolymer run are useful). Then, when computing likelihoods of indels based on input haplotypes we compute gap penalties based on value of covariates at read. Feature is disabled by default with hidden arguments. TBD if usefulness of feature is worth the extra time and pain.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5724 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 20:31:43 +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
fcf8cff64a
We didn't actually support all of these extensions. Updated to be accurate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5722 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 19:03:46 +00:00
34092fd32f
minor update...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5716 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 21:29:01 +00:00
36ac8beee1
Making the GATK unpredictably random...
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through an option!
set -ndrs if you want the GATK to be really random (non-deterministic). Engine option, available to every walker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5715 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 19:29:08 +00:00
f97e7d2fb4
Walker that calculates the percentage of bases that are covered to at least 20x. Very useful! In oneoffs until someone else thinks it's as useful as I think it is ;)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5714 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 19:19:39 +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
96571b55be
Disable caching of ReadShards by the GenomeLocProcessingTracker (at least
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temporarily). Unfortunately this does not completely fix the IndelRealigner
exception that Ryan is seeing, but it helps things quite a bit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5710 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 13:59:34 +00:00
a5b96e0e04
I have to remember that this is Java, not C.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5709 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-28 17:40:14 +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
f34e6d5b8c
Somewhere along the way someone broke this tool and failed to update the documentation to boot. Fixing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5705 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-28 03:16:20 +00:00
ae8f3f2cde
Check for bad reference bases before creating simple/'empty' VCs. Updated the code in the indel GL model to be consistent and to use the existing utility in the Allele class.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5704 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 23:55:20 +00:00
6cce3e00f3
A test walker that does consensus compression of deep read data sets.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5702 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 22:00:48 +00:00
3907377f37
When genotyping given alleles, for multiallelic sites we go back to the reads and use the alternate base with the highest sum of quality scores instead of taking the first alternate allele from the vcf file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5701 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 21:31:09 +00:00
6e9e766a71
The tighter interval validation wasn't interacting well with unmapped
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intervals -- altered the validation methods to not throw an error for
unmapped intervals.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5700 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 20:56:46 +00:00
6d5e45b5c6
Revbump Picard dependencies at Tim/Kathleen's request. Exclude anonymous
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classes from PluginManager.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5699 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 20:38:05 +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
df35a143b2
Removed -debug/--debug_mode.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5697 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 10:56:39 +00:00
27495a0c64
Killed quiet mode. Should probably kill debugMode as well, but Queue's using
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it. Will check with Khalid tomorrow.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5695 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 04:17:36 +00:00
f3dacd3c40
Use ByteBuffer.allocateDirect() instead of ByteBuffer.allocate().
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ByteBuffer.allocateDirect() behaves like Java NIO MappedByteBuffers in that
it consumes address space, which counts against our virtual memory allocation;
but cannot be destroyed or otherwise freed. This was definitely contributing
to the LSF failures that I was seeing, but I'm not yet convinced that it's the
sole source of these virtual memory 'leaks'. More tomorrow as the results of
my whole exome tests start to roll in.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5693 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 02:01:11 +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
379f837e82
RankSum z-scores are looking quite good, so RIP Wilcoxon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5691 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-26 18:34:39 +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
57a4700299
Ported small BAM performance test suite to the Google Caliper microbenchmarking suite. Looks promising,
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but I'm still not sure that GC is a good long-term solution.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5683 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 22:09:17 +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
88735a8c9b
Adding in a delta to try and better measure effect size -- equivalent to looking at the lower end of the N^th percentile confidence interval. Kind of a hacky way to add it in, the infrastructure is about due for a streamlining rewrite.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5676 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 03:53:33 +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
5b9a8555cd
Queue graph time is currently of O(n^m) where n = num jobs, m = num unique base files. This script therefore was running in order 1200^16, which I don't think would finish before the heat death of the universe. For now, push down the number of files to 1 and gather them outside of Queue, once I've fixed up scatter-gather in core, outputs can be uncommented.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5674 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-21 12:56:25 +00:00
cbcdfc584d
Moving out of core and into playground
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5671 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-21 02:30:22 +00:00
cc78027bd3
Two optimizations. Even more aggressive printProgress meter optimization to only even consider doing work once every 1000 cycles through the engine. Second, GenomeLocParser now uses a single indirection around the contigInfo variable. This class uses a last used cache to retrieve efficiently contig information instead of always returning to the underlying SAMSequenceDictionary hashmap to make genome locs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5670 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-21 01:31:26 +00:00
29857f5ba6
Fix for instability in output of fasta alternative reference maker when snpmask and snp files are provided and have overlapping records. The order of the records changed due to optimization of the refmetadatatracker, and uncovered this non-determinanism. Now preferrentially masks out includes sites from snps before considering masking out sites in snpmask
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5669 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-20 21:54:09 +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
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
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
depristo
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