893c9c85fa
Added previous optimization to diploid (non-pool) model and shaved off 20% of runtime from it. Moved out some common functionality to joint estimate parent class.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2453 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 21:20:48 +00:00
92e3682991
Moved NHashMap to sting/utils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2452 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 20:57:32 +00:00
562db45fa5
Sites that were marked NO_DINUC no longer get dinuc-corrected but are still recalibrated using the other available covariates. Solid cycle is now the same as Illumina cycle pending an analysis that looks at the effect of PrimerRoundCovariate. Solid color space methods cleaned up to reduce number of calls to read.getAttribute(). Polished NHashMap sort method in preparation for move to core/utils. Added additional plots in AnalyzeCovariates to look at reported quality as a function of the covariate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2451 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 20:19:37 +00:00
2a704e83df
Reads now have new traversal flag: generateExtendedEvents(). Support added to GenomeAnalysisEngine and Walker. This is a silent and transparent framework change that no existing code is going to see. The actual code that makes use of the new flag (which is false by default) will be committed separately...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2450 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 19:52:44 +00:00
c8d0e6e004
Optimization to pooled calculation model: stop calculating P(D|AF) if we are beyond the max likelihood such that subsequent likelihoods won't factor into the confidence score. Also, use new Pileup interface.
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Pooled calling now takes less than half the time it used to.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2449 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 18:39:55 +00:00
b1ac4b81d5
Optimization: look up diploid genotypes from a static matrix instead of creating them on the fly (with String.format); bases no longer need to be ordered appropriately
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2448 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 17:28:51 +00:00
57516582c2
Converter from HapMap chip genotype data to VCF added; HapMapGenotypeROD adjusted to not convert from Hg18 to b36 formatting of contigs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2447 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 01:36:08 +00:00
d2770f380c
Writing calls to standard out now works again (it got broken when we introduced parallelization)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2446 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-27 04:36:45 +00:00
12990c5e7a
Added qual-by-depth annotation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2445 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-25 02:30:30 +00:00
0571d9dcb9
Point MAX_QUAL_SCORE to SAMUtils.MAX_PHRED_SCORE.
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Also, array size for caches should be max score + 1.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2444 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-24 20:47:32 +00:00
438d21842a
The new recalibrator had been mimicking the behavior of the old one in that if there was no dinuc available (following a no-call base or at either end of a read), it didn't try to recalibrate. Now that Ryan has modularized the system, we no longer need to skip the base completely (we just need to skip the dinuc value)... which is good because the Picard people complained after realizing that cycle #1 never got recalibrated.
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The major effects of this commit are as follows:
1. We no longer skip any good bases (of course, this change alone breaks every single integration test).
2. The dinuc covariate returns a "no dinuc" value for the first base of a read (but not for the last base anymore, since there is a valid dinuc) or if the previous base is a bad base (e.g. 'N').
I've done a bunch of testing on real data and everything looks right; however, let's wait until the recalibrator guru gets back from vacation next week and can double-check everything before shipping this out in another early access release.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2443 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-24 20:41:29 +00:00
aaf674d9db
Cleaned up this annotation.
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Still experimental. As of now, it's not useful. More analysis is needed to determine how to handle cases where UG is unsure whether a sample is het or hom.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2442 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-24 03:06:46 +00:00
6df40876a3
Un-reverted Matt's previous changes and fixed integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2441 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-24 02:47:00 +00:00
2bd0b1bbf7
After further review, it's unclear that my patch in RecalDataManager was the right choice. Reverting.
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Also updating other IntervalCleanerIntegrationTest failures that were masked by my first patch.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2440 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-24 00:32:33 +00:00
98c268483e
Fixed issues with the integration tests:
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1) sam-jdk apparently no longer supports custom tags with type int[] values.
2) BAM output for indel cleaner integration test changed in a way that's so subtle it can't be seen after converting the output to .sam.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2439 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 23:12:22 +00:00
d1d6b79673
Update picard public and private to match new SAM update.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2438 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 22:34:12 +00:00
b134e0052f
added changes to the code to allow different types of interval merging,
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1: all overlapping and abutting intervals merged (ALL),
2: just overlapping, not abutting intervals (OVERLAPPING_ONLY),
3: no merging (NONE). This option is not currently allowed, it will throw an exception. Once we're more certain that unmerged lists are going to work in all cases in the GATK, we'll enable that.
The command line option is --interval_merging or -im
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2437 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 21:59:14 +00:00
159778416c
In TableRecalibrationWalker, update UQ tag if it was present in the original SAMRecord. This required a new sam.jar, which caused some other files to need to be changed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2435 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 21:42:36 +00:00
87ff2b15d4
First step in introducing a patch to Picard: create our ideal interface into the BAM file for sharding.
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This commit can iterate over the BAM file, pulling out information about the blocks in the file without actually loading
or decompressing the reads.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2434 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 21:35:08 +00:00
770093a40e
Oops - forgot to check this one in.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2433 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 19:53:28 +00:00
dc96879861
2 separate changes which both affect lots of UG integration md5s, so I'm committing them together:
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1. allele balance annotation is now weighted by genotype quality (so we don't get misled by borderline het calls)
2. Updates to the Unified Genotyper for parallelization:
a. verbose writing now works again; arg was moved from UAC to UG
b. UG checks for command that don't work with parallelization
c. some cleanup
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2432 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 19:03:56 +00:00
872a9d1c7b
I'm making this change now (as opposed to waiting until Monday) to honor Tim's request.
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The cycle covariate is now first/second of pair aware. I'm taking it on faith from both Chris Hartl (waiting on slides from him) and Tim that this is the right thing to do. We'll have Ryan confirm it all next week.
The only change is that if a read is the second of a pair, we multiple the cycle by -1 (a simple way of separating its index from that of its mate).
Of course, this broke all integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2431 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 16:26:43 +00:00
e29e8e52b9
Multithreading support for the unified genotyper. Tests on a 10Mbase region on pilot 1 show a 6.8x improvement
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when running 8 ways parallel.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2430 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 00:48:06 +00:00
164a94a3d0
Modified the walker documentation so that the stray punctuation wouldn't cause the GATK to stop parsing the help documenation early (aka I changed one word).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2429 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-22 20:50:01 +00:00
4ee6a478e3
Creates a table of reference allele percentage and alternate allele percentage at Hapmap-chip sites in a BAM file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2428 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-22 20:43:44 +00:00
03bf75e335
Now implements TreeReducible
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2427 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-22 17:52:51 +00:00
66eeb4a552
Adding a package description for making a version of the GATK that only includes the FixBAMSortOrderTag walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2426 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-22 00:35:24 +00:00
0d890e1bf0
Rework Eric's output management code given that the behavior of the UG changes drastically
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depending on its output format. Current implementation is probably a bit overkill-ish and
we can whittle this down to what's absolutely necessary.
Writing VCFs to the 'out' protected printstream may not work at this moment.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2425 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-22 00:33:43 +00:00
f448a263e9
The cleaner now cleans duplicate reads (instead of ignoring them) - although it doesn't include them for scoring ref or alt consenses
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2424 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 21:01:55 +00:00
cf303810d3
VCF reader now creates the correct type of header line for each header type
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2423 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 20:39:06 +00:00
c0c9f6c8b6
Create package that contains just what Picard needs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2421 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 18:48:27 +00:00
e06dfe44c4
Check for null platform (even when the read group isn't null) and assign it the default platform if it is
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2420 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 07:01:41 +00:00
87e5a41964
Fixed a bug that accounted for a bunch of my remaining mis-cleaned indels.
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Also, slightly optimized the cleaner by using readBases (instead of readString) and caching cigar element lengths.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2419 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 05:46:16 +00:00
b780ffb34a
Add a getFormat() method to get the output format from the writer. The need for
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this call suggests that I may be thinking about the typing of the GenotypeWriter object the wrong way.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2418 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 01:46:26 +00:00
11cbfcec9c
Get rid of backlink from ArgumentDefinitions to ArgumentSources. This will help in the future with multiple
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source -> single definition mapping sets.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2417 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 00:39:36 +00:00
9e53c06328
First revision of command-line argument support for GenotypeWriter. Also, fixed the damn build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2416 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-20 19:19:23 +00:00
4ff61097cf
Trivial change: < -> <=
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2415 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-20 03:35:27 +00:00
566b556b50
Give user ability to turn off max allowed interval size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2414 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-20 03:20:22 +00:00
a5f75cbfd4
The previous commit broke the build, so this is a temporary patch to get it to compile. ConcordanceTruthTable should use enums (esp. now that all of the concordance variables need to be public), but VariantEval will need to be rewritten soon anyways so I'll just push it off until then.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2413 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-20 02:34:41 +00:00
ee8bcdc61d
PooledConcordance calculations have been reformatted and bugs fixed. Now properly handles monomorphic sites. Also works with -G option now, correctly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2412 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-19 23:22:36 +00:00
9bf2d12c64
Misc. improvements to the LMW code. Support for emitting all sites, regardless of genotype. Min and max quality scores.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2411 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-19 23:20:57 +00:00
7e0f69dab5
Changed the GLF record to store it's contig name and position in each record instead of in the Reader. Integration tests all stay the same.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2410 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 22:54:56 +00:00
80b3eb85fa
Fixed curiously epic failure in read-backed pileup: size() mismatched the numReads-numDeletions at that locus in the case where includeReadsWithDeletionsAtLoci == false, causing failures including bad output from pileup walker. Also fixed up ValidatingPileup to run with the new ReadBackedPileup instead of just compiling successfully.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2409 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 22:52:44 +00:00
fdf542c214
The CycleCovariate for 454 data is now the TACG flow cycle. That is, each flow grabs all the T's, A's, C's, and G's in order in a single cycle. This is changed from incrementing the cycle whenever there is a discontinuous nucleotide along the direction of the read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2408 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 22:39:51 +00:00
c39675d2c1
VCFTool.java got left off of the last commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2407 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 21:33:53 +00:00
4ea31fd949
Pushed header initialization out of the GenotypeWriter constructors and into a writeHeader method, in preparation for parallelization.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2406 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 19:16:41 +00:00
eeddf0d08e
Adding sample utils for convenience methods to pull out samples from e.g. SAMFileHeader or Genotype objects
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2405 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 18:51:21 +00:00
79b997f43d
Minor fix to getValue (thanks Ryan!)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2404 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 15:45:51 +00:00
9971a8da9a
adding a check to the RodVCF to ensure that records are in-order in the underlying VCF file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2403 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 15:24:45 +00:00
38563bbc2d
The values used to be integers (-1 for unpaired, 0 for unmapped, 1 for first, 2 for second); but i switched to strings before commit so it was more clear. Forgot to update the OTHER getValue method.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2402 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 15:05:14 +00:00
ebanks
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