bfd6bf9ec5
PileupWalker just got a new option: --showIndelPileups. When this option is used, two lines are printed for every genomic location that has indels associated with it: first line is a conventional base pileup, the second line is an "extended event" (indel) pileup. The refence base in that second line is always set to "E" (for Extended), and the pileup string contains I,D,. symbols for insertion, deletion, noevent, respectively. Only this simple short format for indel pileups is implemented so far.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2472 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 20:16:34 +00:00
9652692019
Modified to enable locus traversals firing additional calls to walker's map() with alignment context filled with extended events (indels). Walker should override generateExtendedEvents() to return true, and it should make sure that it catches those additional indel pileups and processes them differently, as needed. If there are indels associated with a specific reference base, TWO map() calls will be issued in locus traversal at that location: first one will have a context filled with a regular base pileup, the second call will provide the context filled with indel pileup (pileup elements will have insertion, deletion, or noevent type associated with them and will also carry information about the full length of the event and inserted bases).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2471 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 20:13:25 +00:00
06eb576924
Can now be constructed with either base pileup or extended event (indel) pileup; has query methods checking what kind of pileup is served by the context, and getter methods return the appropriate pileup. TODO: while it is impossible right now to create a context that contains both types of pileups simultaneously, this restriction is only weakly enforced through the lack of appropriate constructor. Either we keep it this way, or some getters may become ambiguous and have to be fixed!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2470 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 20:07:29 +00:00
f445745c56
Pileup element and corresponding container class tweaked for representing pileups of extended events (indels) at a given locus. There's some redundancy with PileupElement and ReadBackedPileup (should we rename them to BasePileupElement and ReadBackedBasePileup?), so that abstracting a basic interface/abstract base from these classes can be considered in the future
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2469 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 20:03:39 +00:00
87e863b48d
Removed used routines in duputils; duplicatequals to archive; docs for new duplicate traversal code; general code cleanup; bug fixes for combineduplicates; integration tests for combine duplicates walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2468 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 19:46:29 +00:00
29f94119d1
Fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2466 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 18:08:41 +00:00
5fdf17fccb
Removed the VCF "NS" annotation (which wasn't working for pooled calls anyways) since it's ambiguous and not useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2465 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 17:30:47 +00:00
e32174fbc4
UnifiedGenotyper now works without -varout or -vf set.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2464 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 16:46:24 +00:00
b125571a98
Intermediate check in: transfer responsibility of wrapping the GenotypeWriter around the output stream to the output
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management code. Currently, will not work when neither -varout nor -vf are specified, but should work in all other
cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2463 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 16:11:11 +00:00
aeb34758e6
Adding a validation stringency to the VCF writers (which defaults to STRICT). If set to SILENT, it will not throw an exception for (reasonable) off-spec requests but will instead ignore such requests and silently move on.
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This change allows the pooled calculation model to work correctly with multiple threads. Boys, the Genotyper is now officially parallelized.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2462 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 15:33:53 +00:00
29a3d9b47a
AnalyzeCovariates also has to skip over NO_DINUC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2461 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 14:36:05 +00:00
a34c2442c0
moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2460 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 07:40:48 +00:00
9d263b2565
Integration tests for count duplicates walker validated on a TCGA hybrid capture lane.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2459 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 23:57:25 +00:00
fcc80e8632
Completely rewritten duplicate traversal, more free of bugs, with integration tests for count duplicates walker validated on a TCGA hybrid capture lane.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2458 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 23:56:49 +00:00
4617052b3c
For Alec, and others at the Broad who want to run our unit/integration tests off of gsa1/gsa2: put a ceiling on the amount of memory that integration tests can use. Reduce the memory footprint of the fasta reader test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2457 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 23:42:46 +00:00
b5e5e27225
New versions of picard-private, sam and picard jars for TileCovariate and regeneration of NM tag
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2456 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 22:18:55 +00:00
d4ee999ef9
Creates files supplemental to the reference sequence, consumed by BWA.
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ANN - Alternate form of the sequence dictionary. Should be created from a sequence dictionary with full contig names.
AMB - A map of 'holes' in the genome, aka runs of non-ACGTacgt bases. This skeletal implementation always reports no
holes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2455 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 21:40:44 +00:00
fcc52fbcd1
Fixed the build. Added missing import line.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2454 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 21:26:00 +00:00
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
asivache
depristo
ebanks
hanna
rpoplin
aaron
alecw
andrewk
kiran