ad90af94ed
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-13 15:10:10 -05:00
0920a1921e
Minor fixes to splitting multi-allelic records (as regards printing indel alleles correctly); minor code refactoring; adding integration tests to cover +/- splitting multi-allelics.
2012-02-13 15:09:53 -05:00
14981bed10
Cleaning up VariantsToTable: added docs for supported fields; removed one-off hidden arguments for multi-allelics; default behavior is now to include multi-allelics in one record; added option to split multi-allelics into separate records.
2012-02-13 14:32:03 -05:00
e9338e2c20
Context covariate needs to look in the reverse direction for negative stranded reads.
2012-02-13 13:40:41 -05:00
41ffd08d53
On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live.
2012-02-13 12:35:09 -05:00
3caa1b83bb
Updating HC integration tests
2012-02-11 11:48:32 -05:00
9b8fd4c2ff
Updating the half of the code that makes use of the recalibration information to work with the new refactoring of the bqsr. Reverting the covariate interface change in the original bqsr because the error model enum was moved to a different class and didn't make sense any more.
2012-02-11 10:57:20 -05:00
f52f1f659f
Multiallelic implementation of the TDT should be a pairwise list of values as per Mark Daly. Integration tests change because the count in the header is now A instead of 1.
2012-02-10 14:15:59 -05:00
1fb19a0f98
Moving the covariates and shared functionality to public
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so Ryan can work on the recalibration on the fly without breaking the build. Supposedly all the secret sauce is in the BQSR walker, which sits in private.
2012-02-10 11:44:01 -05:00
5e18020a5f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-10 11:08:33 -05:00
f53cd3de1b
Based on Ryan's suggestion, there's a new contract for genotyping multiple alleles. Now the requester submits alleles in any arbitrary order - rankings aren't needed. If the Exact model decides that it needs to subset the alleles because too many were requested, it does so based on PL mass (in other words, I moved this code from the SNPGenotypeLikelihoodsCalculationModel to the Exact model). Now subsetting alleles is consistent.
2012-02-10 11:07:32 -05:00
5af373a3a1
BQSR with indels integrated!
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* added support to base before deletion in the pileup
* refactored covariates to operate on mismatches, insertions and deletions at the same time
* all code is in private so original BQSR is still working as usual in public
* outputs a molten CSV with mismatches, insertions and deletions, time to play!
* barely tested, passes my very simple tests... haven't tested edge cases.
2012-02-09 18:46:45 -05:00
7a937dd1eb
Several bug fixes to new genotyping strategy. Update integration tests for multi-allelic indels accordingly.
2012-02-09 16:14:22 -05:00
0f728a0604
The Exact model now subsets the VC to the first N alleles when the VC contains more than the maximum number of alleles (instead of throwing it out completely as it did previously). [Perhaps the culling should be done by the UG engine? But theoretically the Exact model can be called outside of the UG and we'd still want the context subsetted.]
2012-02-09 14:02:34 -05:00
aa097a83d5
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-09 11:26:48 -05:00
b57d4250bf
Documentation request by Eric. At each stage of the GATK where filtering occurs, added documentation suggesting the goal of the filtering along with examples of suggested inputs and outputs.
2012-02-09 11:24:52 -05:00
d561914d4f
Revert "First implementation of GATKReportGatherer"
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premature push from my part. Roger is still working on the new format and we need to update the other tools to operate correctly with the new GATKReport.
This reverts commit aea0de314220810c2666055dc75f04f9010436ad.
2012-02-08 23:28:55 -05:00
2f800b078c
Changes to default behavior of UG: multi-allelic mode is always on; max number of alternate alleles to genotype is 3; alleles in the SNP model are ranked by their likelihood sum (Guillermo will do this for indels); SB is computed again.
2012-02-08 15:27:16 -05:00
51ac87b28c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-08 08:43:55 -05:00
5b58fe741a
Retiring Picard customizations for async I/O and cleaning up parts of the code to use common Picard utilities I recently discovered.
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Also embedded bug fix for issues reading sparse shards and did some cleanup based on comments during BAM reading code transition meetings.
2012-02-08 08:34:37 -05:00
337819e791
disabling the test while we fix it
2012-02-07 19:22:32 -05:00
c0c676590b
First implementation of GATKReportGatherer
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- Added the GATKReportGatherer
- Added private methods in GATKReport to combine Tables and Reports
- It is very conservative and it will only gather if the table columns, match.
- At the column level it uses the (redundant) row ids to add new rows. It will throw an exception if it is overwriting data.
Added the gatherer functions to CoverageByRG
Also added the scatterCount parameter in the Interval Coverage script
Made some more GATKReport methods public
The UnitTest included shows that the merging methods work
Added a getter for the PrimaryKeyName
Fixed bugs that prevented the gatherer form working
Working GATKReportGatherer
Has only the functional to addLines
The input file parser assumes that the first column is the primary key
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
2012-02-07 18:14:47 -05:00
e89887cd8e
laying groundwork to have insertions and deletions going through the system.
2012-02-07 18:11:53 -05:00
0d3ea0401c
BQSR Parameter cleanup
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* get rid of 320C argument that nobody uses.
* get rid of DEFAULT_READ_GROUP parameter and functionality (later to become an engine argument).
2012-02-07 14:42:11 -05:00
717cd4b912
Document -L unmapped
2012-02-07 13:30:54 -05:00
718da7757e
Fixes to ValidateVariants as per GS post: ref base of mixed alleles were sometimes wrong, error print out of bad ACs was throwing a RuntimeException, don't validate ACs if there are no genotypes.
2012-02-07 13:15:58 -05:00
9d1a19bbaa
Multi-allelic indels were not being printed out correctly in VariantsToTable; fixed.
2012-02-06 22:49:29 -05:00
5961868a7f
fixup for BQSR (HC integration tests)
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In the new BQSR implementation, covariates do depend on the RecalibrationArgumentCollection.
2012-02-06 22:47:27 -05:00
6e6f0f10e1
BaseQualityScoreRecalibration walker (bqsr v2) first commit includes
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* Adding the context covariate standard in both modes (including old CountCovariates) with parameters
* Updating all covariates and modules to use GATKSAMRecord throughout the code.
* BQSR now processes indels in the pileup (but doesn't do anything with them yet)
2012-02-06 17:38:29 -05:00
0717c79901
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-06 16:23:36 -05:00
91897f5fe7
Transpose rows/cols in AF table to make it molten (so I can plot easily in R)
2012-02-06 16:23:32 -05:00
fb5786385c
Merged bug fix from Stable into Unstable
2012-02-06 13:22:56 -05:00
6ec686b877
Complement to previous commit: make sure we also don't inherit filter from input VCF when genotyping at an empty site
2012-02-06 13:19:26 -05:00
93ffca1e3a
Merged bug fix from Stable into Unstable
2012-02-06 11:58:58 -05:00
827be878b4
Bug fix when running UG in GenotypeGivenAlleles mode: if an input site to genotype had no coverage, the output VCF had AC,AF and AN inherited from input VCF, which could have nothing to do with given BAM so numbers could be non-sensical. Now new vc has clear attributes instead of attributes inherited from input VCF.
2012-02-06 11:58:13 -05:00
fbbd04621d
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-06 11:53:31 -05:00
edb4edc08f
Commented out unused metrics for now
2012-02-06 11:53:15 -05:00
096c23a473
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-06 11:10:38 -05:00
dc05b71e39
Updating Covariate interface with Mauricio to include an errorModel parameter. On the fly recalibration of base insertion and base deletion quals is live for the HaplotypeCaller
2012-02-06 11:10:24 -05:00
1e11408f8b
Merged bug fix from Stable into Unstable
2012-02-06 10:34:26 -05:00
090d87b48b
Bug fix in ValidationSiteSelector: when input vcf had genotypes and was multiallelic, the parsing of the AF/AC fields was wrong. Better logic to unify parsing of field
2012-02-06 10:33:12 -05:00
9d94f310f1
Break AF histogram into max and min AFs
2012-02-06 09:01:19 -05:00
b7ffd144e8
Cleaning up the covariate classes and removing unused code from the bqsr optimizations in 2009.
2012-02-06 08:54:42 -05:00
cef550903e
Minor optimization
2012-02-06 00:48:00 -05:00
5343f8ba67
Initial version of on-the-fly, lazy loading base quality score recalibration. It isn't completely hooked up yet but I'm committing so Mauricio and Mark can see how I envision it will fit together. Look it over and give any feedback. With the exception of the Solid specific code we are very very close to being able to remove TableRecalibrationWalker from the code base and just replace it with PrintReads -BQSR recal.csv
2012-02-05 13:09:03 -05:00
f94d547e97
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-03 17:14:20 -05:00
894d3340be
Active Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup.
2012-02-03 17:13:52 -05:00
4a57add6d0
First implementation of DiagnoseTargets
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* calculates and interprets the coverage of a given interval track
* allows to expand intervals by specified number of bases
* classifies targets as CALLABLE, LOW_COVERAGE, EXCESSIVE_COVERAGE and POOR_QUALITY.
* outputs text file for now (testing purposes only), soon to be VCF.
* filters are overly aggressive for now.
2012-02-03 17:12:43 -05:00
3dd6a1f962
Adding some generic sum and average functions to MathUtils
2012-02-03 17:12:43 -05:00
e1d69e4060
make the size of a GenomeLoc int instead of long
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it will never be bigger than an int and it's actually useful to be an int so we can use it as parameters to array/list/hash size creation.
2012-02-03 17:12:42 -05:00
0e44430e47
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-03 13:45:11 -05:00
aa3638ecb3
Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-03 13:42:09 -05:00
3abfbcbcf2
Generalized the TDT for multi-allelic events
2012-02-03 12:23:21 -05:00
601e53d633
Fix when specifying preset active regions with -AR argument
2012-02-02 16:34:26 -05:00
0111505ea9
Terrible. Swapping the paternal and sample ids.
2012-02-02 11:41:16 -05:00
1f50f6970b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-02 10:17:13 -05:00
4ed06801a7
Updating HaplotypeCaller's HMM calc to use GOP as a function of the read instead of a function of the haplotype in preparation for IQSR
2012-02-02 10:17:04 -05:00
8adfc79123
Merged bug fix from Stable into Unstable
2012-02-01 16:07:41 -05:00
30b937d2af
Fix bug discovered in FGTP branch in which BlockInputStream returns -1 in cases where some data could be read,
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but not all the data requested by the caller.
2012-02-01 16:06:22 -05:00
45da892ecc
Better exceptions to catch malformed reads
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* throw exceptions in LocusIteratorByState when hitting reads starting or ending with deletions
2012-02-01 11:56:19 -05:00
810996cfca
Introducing: VariantsToPed, the world's most annoying walker! And also a busted QScript to run it that I need Khalid's help debugging ( frownie face ). Note that VariantsToPed and PlinkSeq generate the same binary file (up to strand flips...thanks PlinkSeq), so I know it's working properly. Hooray!
2012-02-01 10:39:03 -05:00
25d943f706
Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-01 10:32:11 -05:00
056b24ccd6
Resolving merge conflicts with LocusIteratorByState
2012-01-31 16:13:32 -05:00
febc634557
Changing PileupElement's isSoftClipped to isNextToSoftClip since soft clipped bases aren't actually added to pileups, oops. Removing the intrinsic clustered variants filter from the HaplotypeCaller
2012-01-31 16:06:14 -05:00
7f70612beb
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-31 11:59:25 -05:00
a630db1703
Oops...HierarchicalMicroScheduler was transforming any exception from the walker level into a ReviewedStingException.
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Thanks to Ryan for pointing this out.
2012-01-31 11:58:21 -05:00
faba3dd530
Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-31 10:25:29 -05:00
17dbe9a95d
A few cleanups in the LocusIteratorByState
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* No more N's in the extended event pileups
* Only add to the pileup MQ0 counter if the read actually goes into the pileup
2012-01-31 09:40:51 -05:00
f9162ea705
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-30 19:45:19 -05:00
abb91cf26b
Increasing the size of the active regions that are produced by the active probability integrator, more context is needed to call more complex events
2012-01-30 15:36:12 -05:00
d5d4fa8a88
Fixed discordance bug reported by Brad Chapman
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discordance now reports discordance between genotypes as well (just like concordance)
2012-01-30 09:50:45 -05:00
3164c8dee5
S3 upload now directly creates the XML report in memory and puts that in S3
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-- This is a partial fix for the problem with uploading S3 logs reported by Mauricio. There the problem is that the java.io.tmpdir is not accessible (network just hangs). Because of that the s3 upload fails because the underlying system uses tmpdir for caching, etc. As far as I can tell there's no way around this bug -- you cannot overload the java.io.tmpdir programmatically and even if I could what value would we use? The only solution seems to me is to detect that tmpdir is hanging (how?!) and fail with a meaningful error.
2012-01-29 15:14:58 -05:00
0e17cbbce9
Merged bug fix from Stable into Unstable
2012-01-27 16:03:16 -05:00
a9671b73ca
Fix to permit proper handling of mapping qualities between 128 to 255 (which get converted to byte values of -128 to -1)
2012-01-27 16:01:30 -05:00
f7ac1f4a69
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-27 15:12:55 -05:00
fc08235ff3
Bug fix in active region traversal, locusView.getNext() skips over pileups with zero coverage but still need to count them in the active probability integrator
2012-01-27 15:12:37 -05:00
0f2e8400b5
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-27 10:12:50 -05:00
ec9920b04f
Updating the SAM TAG for Original Alignment Start to "OP"
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per Mark's recommendation to reuse the Indel Realigner tag that made it to the SAM spec. The Alignment end tag is still "OE" as there is no official tag to reuse.
2012-01-27 08:51:39 -05:00
13d1626f51
Minor improvements in ref QC walker. Unfortunately this doesn't actually catch Chris's error
2012-01-27 08:24:22 -05:00
2a565ebf90
embarrassing fix-up, thanks Khalid.
2012-01-26 19:58:42 -05:00
246e085ec9
Unit tests for GATKSAMRecord class
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* new unit tests for the alignment shift properties of reduce reads
* moved unit tests from ReadUtils that were actually testing GATKSAMRecord, not any of the ReadUtils to it.
* cleaned up ReadUtilsUnitTest
2012-01-26 17:06:36 -05:00
0d4027104f
Reduced reads are now aware of their original alignments
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* Added annotations for reads that had been soft clipped prior to being reduced so that we can later recuperate their original alignments (start and end).
* Tags keep the alignment shifts, not real alignment, for better compression
* Tags are defined in the GATKSAMRecord
* GATKSAMRecord has new functionality to retrieve original alignment start of all reads (trimmed or not) -- getOriginalAlignmentStart() and getOriginalAligmentEnd()
* Updated ReduceReads MD5s accordingly
2012-01-26 17:06:36 -05:00
07f72516ae
Unsupported platform should be a user error
2012-01-26 16:14:25 -05:00
cdff23269d
HaplotypeCaller now uses insertions and softclipped bases as possible triggers. LocusIteratorByState tags pileup elements with the required info to make this calculation efficient. The days of the extended event pileup are coming to a close.
2012-01-26 15:56:33 -05:00
673ceadd11
While this fix worked for the evaluator module, it could potentially have bad effects in the phasing walkers. Special-case nocalls in the PhasingEvaluator and return AllelePair to previous state.
2012-01-26 13:06:36 -05:00
9c6fda7e15
Yup. I was right.
2012-01-26 12:54:11 -05:00
7d059540a4
Allow segments of genome to be excluded in generating a reference panel. Occasionally targets would contain no variation (typically, in the middle of the centromere), which beagle doesn't particularly like, and errors out rather than producing empty output files. The best way to deal with these is to just exclude the regions on a second-pass, and the remaining bits will be gathered with no additional work.
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AllelePair is being mean and not telling me what genotype it sees when it finds a non-diploid genotype, but i suspect it's a no-call (".") rather than a no call ("./.").
2012-01-26 12:43:52 -05:00
25532bdc37
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-26 11:43:32 -05:00
390d493049
Updating ActiveRegionWalker interface to output a probability of active status instead of a boolean. Integrator runs a band-pass filter over this probability to produce actual active regions. First version of HaplotypeCaller which decides for itself where to trigger and assembles those regions.
2012-01-26 11:37:08 -05:00
859dd882c9
Don't make it standard for now
2012-01-26 00:38:16 -05:00
c5e81be978
Adding pairwise AF table. Not polished at all, but usable none-the-less.
2012-01-26 00:37:06 -05:00
702a2d768f
Initial version of multi-allelic summary module in VariantEval
2012-01-25 19:42:55 -05:00
9a60887567
Lost an import in the merge
2012-01-25 19:41:41 -05:00
cba5f1a8b1
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-25 19:19:03 -05:00
ddaf51a50f
Updated one integration test for indels
2012-01-25 19:18:51 -05:00
add6918f32
Cleaner, more efficient way of determining the last dependent set in the queue.
2012-01-25 16:21:10 -05:00
db645a94ca
Added options to make the batch-merger more all-inclusive: keep all indels, SNPs (even filtered ones) but maintain their annotations. Also, VariantContextUtils.simpleMerge can now merge variants of all types using the Hidden non-default enum MultipleAllelesMergeType=MIX_TYPES
2012-01-25 16:10:59 -05:00
ef335a5812
Better implementation of the fix; PL index is now traversed in order.
2012-01-25 15:15:42 -05:00
8e2d372ab0
Use remove instead of setting the value to null
2012-01-25 14:41:34 -05:00
05816955aa
It was possible that we'd clean up a matrix column too early when a dependent column aborted early (with not enough probability mass) because we weren't being smart about the order in which we created dependencies. Fixed.
2012-01-25 14:28:21 -05:00
Eric Banks
Ryan Poplin
Mauricio Carneiro
Matt Hanna
Roger Zurawicki
Guillermo del Angel
Christopher Hartl
Mark DePristo
Menachem Fromer