45d54f6258
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-07 16:49:49 -04:00
9604fb2ba3
Necessary but not sufficient step to fix GenotypeGivenAlleles mode in UG which is now busted
2011-09-07 16:49:16 -04:00
2ded027762
Removed dysfunctional tranches support from VariantEval
2011-09-07 16:09:24 -04:00
aa9e32f2f1
Reverting Mark's previous commit as per the open discussion. Now the eval modules check isPolymorphic() before accruing stats when appropriate. Fixed the IndelLengthHistogram module not to error out if the indel isn't simple (that would have been bad). Only integration test that needed to be updated was the tranches one based on a separate commit from Mark.
2011-09-07 15:48:06 -04:00
3a04955a30
We already had isPolymorphic and isMonomorphic in the VariantContext, but the implementation was incorrect for many edge cases (e.g. sites-only files, sites with samples who were no-called). Fixing. Moving on to VE now.
2011-09-07 14:01:42 -04:00
743bf7784c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-07 13:21:26 -04:00
5f22ef9a8c
Added missing javadoc info to Beagle arguments
2011-09-07 13:21:11 -04:00
3bcbfa6e06
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-07 13:13:17 -04:00
430da23446
At least 2 minutes must pass before a status message is printed, further stabilizing time estimates
2011-09-07 13:13:07 -04:00
6857d0324e
Merge branch 'master' into rr
2011-09-07 12:59:08 -04:00
7e9e20fed0
Forgot to delete previous call
2011-09-07 12:54:52 -04:00
d23d620494
Pushing traversal engine timer start to as close to actual start as possible
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-- Should make initial timings more accurate
2011-09-07 12:52:33 -04:00
6ff432e1f2
BugFix for TF argument to VariantEval, actually making it work properly
2011-09-07 12:50:17 -04:00
131cb7effd
Bringing Reduce Reads bug fixes to the main repository
2011-09-07 12:25:53 -04:00
a1920397e8
Major bugfix for per sample VariantEval
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-- per sample stratification was not being calculated correctly. The alt allele was always remaining, even if the genotype of the sample was hom-ref. Although conceptually fine, this breaks the assumptions of all of the eval modules, so per sample stratifications actually included all variants for everything. Eric is going to fix the system in general, so this commit may break the build.
2011-09-07 12:18:11 -04:00
a02636a1ac
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/ebanks/Sting_rodrefactor into rodrewrite
2011-09-07 10:50:00 -04:00
d5641cfac5
Merge branch 'variantEvalST'
2011-09-07 10:44:23 -04:00
2f4cf82e3b
VariantEval cleanup. Added VariantType Stratification
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-- ArrayList are List where possible
-- states refactored into VariantStratifier base class (reduces many lines of duplicate code)
-- Added VariantType stratification that partitions report by VariantContext.Type
2011-09-07 10:43:53 -04:00
436f6eb52b
Reverting Eric's change and pushing in some command-line-option documentation.
2011-09-07 08:53:30 -04:00
1ef8a1750a
I asked nicely and got nothing. Then I threatened and still got nothing. So I am carrying through on my threats. Guillermo, you have a short reprieve because you were away on vacation, but let's get yours done tomorrow afternoon.
2011-09-06 21:07:49 -04:00
da9c8ab386
Revving the Tribble jar where the DbsnpCodec class was renamed to OldDbsnpCodec. Updating GATK code accordingly.
2011-09-06 20:39:42 -04:00
3db7ecb920
ReducedRead flag cached in GATKSAMRecord. 20% performance improvement
2011-09-06 15:11:38 -04:00
47607a7eff
Fixed bug where deletions messed up interval clipping
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- Instead of using readLength, the ReadUtil function are used to get a proper read coordinate
- Added debug info in interval clipping ( with -dl)
NOTE: method might not be safe for production and checks need to be added to the ClippingOp code
2011-09-06 14:25:57 -04:00
0adb388dee
Fixed bug in SelectVariants that was annotating sample_file / exclude_sample_file as @Argument instead of @Input meaning they weren't tracked in Queue.
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Updates for HybridSelectionPipeline:
- Use VQSR on SNPs for projects using bait set whole_exome_agilent_1 and applying cut at 98.5.
- If a whole_exome_agilent_1 project has less than 50 samples also mixing in 1000G samples to reach VQSR thresholds.
- Updated SNP hard filters based on analysis done with ebanks to approximate VQSR results on small target batches.
- Removed GSA_PRODUCTION_ONLY flag from indel caller.
- Updated indel hard filters based on delangel's analysis.
- Updated HybridSelectionPipelineTest to use HARD SNP filters only, for now.
2011-09-06 12:41:46 -04:00
d471617c65
GATK binary VCF (gvcf) prototype format for efficiency testing
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-- Very minimal working version that can read / write binary VCFs with genotypes
-- Already 10x faster for sites, 5x for fully parsed genotypes, and 1000x for skipping genotypes when reading
2011-09-02 21:15:19 -04:00
048202d18e
Bugfix for cached quals
2011-09-02 21:13:28 -04:00
03aa04e37c
Simple refactoring to make formating functions public
2011-09-02 21:13:08 -04:00
124ef6c483
MISSING_VALUE now gets defaultValue in getAttribute functions
2011-09-02 21:12:28 -04:00
82f2131777
Simplied getAttributeAsX interfaces
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-- Removed versions getAttribriteAsX(key) that except on not having the value.
-- Removed version that getAttributeAsXNoException(key)
-- The only available assessors are now getAttributeAsX(key, default).
-- This single accessors properly handle their argument types, so if the value is a double it is returned directly for getAttributeAsDouble(), or if it's a string it's converted to a double. If the key isn't found, default is returned.
2011-09-02 12:27:11 -04:00
08ae6c0c61
ReadClipper is now handling unmapped reads
2011-09-02 11:32:30 -04:00
c57198a1b9
Optimizations in VCFCodec
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-- Don't create an empty LinkedHashSet() for PASS fields. Just return Collections.emptySet() instead.
-- For filter fields with actual values, returns an unmodifiableSet instead of one that can be changed
2011-09-02 08:46:17 -04:00
c3ea96d856
Removing many unused functions of unquestionable purpose
2011-09-02 08:42:01 -04:00
d241f0e903
Adding docs for the pcr error rate argument.
2011-09-01 21:57:02 -04:00
827fe6130c
Adding hidden printing option. Also, always run UG in mode GENOTYPE_GIVEN_ALLELES given that we don't actually test for the correct alleles (otherwise UG may choose a different allele and we may falsely validate the wrong one).
2011-09-01 11:40:35 -04:00
ac49b8d26b
Conditional support for PerformanceTrackingQuerySource to measure Tribble / GATK bridge performance
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-- Removed DEBUG option, instead use MEASURE_TRIBBLE_QUERY_PERFORMANCE in RMDTrackerBuilder
2011-09-01 10:41:55 -04:00
4b5a7046c5
Making ReadLengthDistribution Public
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Found this neat little walker Kiran wrote stashed in the private tree. Very useful. Generalized it a bit, added GATKDocs and moved it to public. I might include it as a QC step on the pacbio processing pipeline.
* generalize it so it works with non pair ended reads.
* generalize it to work with no read group information
2011-08-31 15:52:28 -04:00
7d79de91c5
Merge branch 'master' into rr
2011-08-30 02:50:19 -04:00
0cd9438ac2
fixed soft unclipped calculation
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* getRefCoordSoftUnclippedEnd was not resetting the shift when hitting insertions. Fixed.
* getReadCoordinateForReferenceCoordinateBeforeAlignmentEnd was returning the wrong read coordinate position. Fixed.
2011-08-30 02:45:29 -04:00
fd540592ab
Added RMS calculation for consensus MQ
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Consensus MQ is now the average of the RMS of the mapping qualities of the reads making each site.
2011-08-30 02:45:20 -04:00
6f9264d2b3
Hard Clipping no longer leaves indels on the tails
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The clipper could leave an insertion or deletion as the start or end of a read after hardclipping a read if the element adjacent to the clipping point was an indel. Fixed.
2011-08-30 02:44:58 -04:00
943876c6eb
Added QUAL/MINVAR parameters to the walker
2011-08-30 02:44:46 -04:00
7532be7f5a
Allowing to clip after AlignmentEnd if end is soft clipped.
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Read clipper now identifies and clips even if the requested coordinate is outside the alignment but the read contains soft clipped bases in that region.
2011-08-30 02:44:46 -04:00
90a1f5e15c
Several bug fixes
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* When hard clipping a read that had insertions in it, the insertion was being added to the cigar string's hard clip element. This way, the old UnclippedStart() was being modified and so was the calculation of the new AlignmentStart(). Fixed it by subtracting the number of insertions clipped from the total number of hard clipped bases.
* Walker was sending read instead of filtered read when deleting a read that contains only Q2 bases
* Sliding the window was causing reads that started on the new start position to be entirely clipped.
2011-08-30 02:44:19 -04:00
66a8b36cf5
Fixed most indexing bugs
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* added bases and quals to consensus
* fixed consensus read cigar generation.
2011-08-30 02:43:41 -04:00
1e5001b447
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-29 17:04:21 -04:00
3b09d42ed6
Now only prints 1 warning message about duplicate headers in simpleMerge
2011-08-29 14:41:29 -04:00
c2f0db969b
Don't use the default deletion value from UG if not asking to have it set
2011-08-29 13:48:10 -04:00
bb7a37e8f2
We need to allow reference calls in the input VCF for the GenotypeAndValidate walker when using the BAM as truth so that we can test supposed monomorphic calls against the truth.
2011-08-29 13:19:35 -04:00
bc252a0d62
misc minor bug fixes in assembly. Increasing the minimum number of bad variants to be used in negative model training in the VQSR
2011-08-29 08:11:31 -04:00
a5c65fc133
Debugging information to print out the Query tracks
2011-08-28 18:54:49 -04:00
7bf006278d
Moved ResolveHostname to general utils as a static function
2011-08-28 12:04:16 -04:00
ccec0b4d73
AnalyzeCovariates uses the general RScript system now
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-- Convenience constructor for collection for testing
-- callRScript() now accepts Objects not Strings, for convenience
2011-08-27 12:54:13 -04:00
1ceb020fae
UnitTests for RScript
2011-08-27 10:50:05 -04:00
e37a638e09
Fix for disallowed characters in GATKReportTable
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-- Illegal characters are automatically replaced with _
2011-08-26 13:24:06 -04:00
eef1ac415a
Merge branch 'master' into rodTesting
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Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
2011-08-26 00:35:41 -04:00
9b7512fd94
Just because there's a ref base doesn't mean the VC needs to be padded
2011-08-25 22:42:14 -04:00
e01273ca7c
Queue now writes out queueJobReport.pdf
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-- General purpose RScript executor in java (please use when invoking RScripts)
-- Removed groupName. This is now analysisName
-- Explicitly added capability to enable/disable individual QFunction
2011-08-25 16:57:11 -04:00
09a729da3a
Removing incorrect comment
2011-08-25 15:42:52 -04:00
8bbef79fc2
Create clipped alleles during allele parsing instead of creating a full VC, clipping alleles, and regenerating the VC from scratch.
2011-08-25 15:37:26 -04:00
29c7b10f7b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-24 15:18:58 -04:00
e5008aba00
Output the top two haplotypes as a variant call by running smith-waterman alignment against the reference and calling any difference as variation. This is the first verion that runs end-to-end by taking in reads as bam file and writing out variant calls in VCF.
2011-08-24 15:18:44 -04:00
e618cb1e79
a) Renamed/expanded SelectVariants arguments that choose particular kinds of variants and particular allelic types, now instead of -Indels or -SNPs we can specify for example -selectType [MIXED|INDEL|SNP|MNP|SYMBOLIC]. To select biallelic, multiallelic variants, use -restrictAllelesTo [BIALLELIC|MULTIALLELIC]. Corresponding gatkdocs changes.
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b) More useful AC,AF logging in VariantsToTable with multiallelic sites: instead of logging comma-separated values, log max value by default. Hidden, experimental argument -logACSum to log sum of ACs instead. This is due to extreme slowness of R in parsing strings to tokens and computing max/sum itself (~100x slower than gatk).
c) Added integrationtest for new SelectVariants commands
2011-08-24 12:25:50 -04:00
28ee6dac41
Fixed spelling mistake
2011-08-24 10:14:45 -04:00
569e1a1089
Walker.isDone() aborts execution early
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-- Useful if you want to have a parameter like MAX_RECORDS that wants the walker to stop after some number of map calls without having to resort to the old System.exit() call directly.
2011-08-23 16:53:06 -04:00
a1a1fac9e4
Likelihood engine now gives non-zero likelihoods. Using HMM function that can handle context specific gap open and gap continuation penalties
2011-08-23 13:43:07 -04:00
6e2552a9ef
Merge fix
2011-08-23 12:40:43 -04:00
8b7a0b3b62
Two new arguments to SelectVariants to exclude either multiallelic or biallelic sites from input vcf
2011-08-23 12:40:01 -04:00
ac36271457
Fixed extra reads showing up in Variable Sites
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Reads that were not hard clipped for the variable site no longer show up in output file
Walker now uses unclippedStart of Read to determine position in the sliding Window
2011-08-23 11:26:00 -04:00
6d6feb5540
Better error message when you cannot determine a ROD type because the file doesn't exist or cannot be read
2011-08-23 10:56:37 -04:00
feeab6075f
Merging ReduceReads development with unstable repo
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It is time to bring the ReadClipper class to the main repo. Read Clipper has tested functionality for soft and hard clipping reads. I will prepare thorough documentation for it as it will be very useful for the assembler and the GATK in general.
2011-08-22 23:03:03 -04:00
ee68713267
Further Bug fixes to CountVariants: stratifications were wrong in case genotypes had no-calls, for example if we stratified by sample and a sample had a no-call, this no-call was considered a true variant and counts were incorrectly increased
2011-08-22 20:42:47 -04:00
c270384b2e
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-22 20:39:32 -04:00
8ae24912f4
a) Misc fixes in Phase1 indel vqsr script,
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b) More R-friendly VariantsToTable printing of AC in case of multiple alt alleles
c) Rename FixPLOrderingWalker to FixGenotypesWalker and rewrote: no longer need older code, replaced with code to replace genotypes with all-zero PL's with a no-call.
2011-08-22 20:39:06 -04:00
85c5a6f890
Merge branch 'rodTesting'
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Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/performance/ProfileRodSystem.java
2011-08-22 17:43:47 -04:00
1eab9be35d
Now with accurate javadoc
2011-08-22 17:25:15 -04:00
3612a3501d
info, not warn, about dynamic type determination
2011-08-22 17:24:51 -04:00
dc42571dd9
Only create the genotype map when necessary
2011-08-22 15:40:36 -04:00
c4c90c8826
Updates to JobRunners from the Queue developer community and from running the WholeGenomePipeline:
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- Ability to pass a different resident memory reservation and limits. Useful for large pileups of low pass genome data that sometimes need high -Xmx6g but usually don't exceed 2-3g in actual heap size.
- Fixed jobPriority to work for all job runners. Now must be a integer between 0 and 100- even for GridEngine- and will be mapped to the correct values.
- Passing parallel environment and job resource requests to LSF and GridEngine. Useful for passing tokens like iodine_io=1 and -pe pe_slots 8
- Refactored GridEngine JobRunner to also provide basic support for other job dispatchers with DRMAA implementations such as Torque/PBS. Should work for basic running but advanced users must pass their own jobNativeArgs from the command line or in customized QScripts until someone maps properties like jobQueue, jobPriority, residentRequest, etc. into a Torque/PBS/etc. dispatcher.
2011-08-22 15:13:27 -04:00
2c24b68a96
Working implementation of DecodeLoc for VCF parsing. Makes indexing 3x faster.
2011-08-22 15:11:21 -04:00
518b3dd291
Don't let the genotypes map be null
2011-08-22 15:10:30 -04:00
f93a554b01
updating exome specific parameters in MDCP
2011-08-21 10:25:36 -04:00
dbff84c54e
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-21 10:09:19 -04:00
22ca44c015
Fixed Queue's tagging of RodBindings.
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Fixed argument definition names.
2011-08-21 02:34:20 -04:00
a8cbced71b
Bug fix for Ryan: check for no context
2011-08-20 22:49:51 -04:00
0ccd173967
Fixing the recent SelectVariants fix
2011-08-20 21:30:08 -04:00
b008676878
fixing the previous fix
2011-08-20 21:21:55 -04:00
782453235a
Updated VariantEvalIntegrationTest since there's a new column separating nMixed and nComplex in CountVariants
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Misc updates to WholeGenomeIndelCalling.scala
Bug fix in VariantEval (may be temporary, need more investigation): if -disc option is used in sites-only vcf's then a null pointer exception is produced, caused by recent introduction of -xl_sf options.
2011-08-20 12:24:22 -04:00
539e157ecd
Fixing misc parameters in MDCP. The pipeline now does VariantEval of output by default. Fix for NaN vqslod values in VQSR
2011-08-20 11:28:48 -04:00
4939648fd4
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-20 08:50:43 -04:00
a96ecbab71
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-19 19:30:05 -04:00
ddb5045e14
Updating the methods development calling pipeline for the new rod binding syntax and the new best practices.
2011-08-19 19:29:51 -04:00
8b3cfb2f1c
Final documented version of GATKDoclet and associated classes
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-- Docs on everything.
-- Feature complete. At this point only minor improvements and bugfixes are anticipated
2011-08-19 16:52:17 -04:00
b08d63a6b8
Documentation and code cleanup for ClipReads, CallableLoci, and VariantsToTable
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-- Swapped -o [summary] and -ob [bam] for more standard -o [bam] and -os [summary] arguments.
-- @Advanced arguments
2011-08-19 15:06:37 -04:00
49e831a13b
Should have checked in
2011-08-19 14:35:16 -04:00
7b5fa4486d
GenotypeAndValidate - Added docs to the @Arguments
2011-08-19 13:35:11 -04:00
9f7d4beb89
Merge branch 'help'
2011-08-19 13:14:02 -04:00
4d1fd17a97
GATKDoclet cleanup and documentation
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-- Fixed bug in the way ArgumentCollections were handled that lead to failure in handling the dbsnp argument collection.
2011-08-19 13:13:41 -04:00
0f25167efd
minor fix in VariantEval docs
2011-08-19 11:01:04 -04:00
198955f752
GATKDoc descriptions for all standard codecs, or TODO for their owners
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-- Also added vcf.gz support in the VCF codec. This wasn't committed in the last round, because it was missed by the parallel documentation effort.
2011-08-19 09:57:21 -04:00
269ed1206c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-19 09:32:20 -04:00
40e67cff1b
I like the @Advanced annotation
2011-08-18 22:27:34 -04:00
2457c7b8f5
Merge branch 'master' into help
2011-08-18 22:20:43 -04:00
5fbdf968f7
ArgumentSource no longer comparable. Arguments sorted by GATKDoclet
2011-08-18 22:20:14 -04:00
77fa2c1546
Renaming read filters with a superfluous 'Read' in their names. Kept the ones that made sense to have it (e.g. MalformedReadFilter).
2011-08-18 22:01:33 -04:00
1d3799ddf7
Merge branch 'master' into help
2011-08-18 22:00:29 -04:00
d1892cd0d7
Bug fixes
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-- Sorting of ArgumentSources now done in GATKDoclet, not in the ParsingEngine, as the system depends on the LinkedTreeMap
-- Fixed broken exception throwing in the case where a file's type could not be determined
2011-08-18 21:58:36 -04:00
c5efb6f40e
Usability improvements to GATKDocs
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-- ArgumentSources are now sorted by case insensitive names, so arguments are shown in alphabetical order (Ryan)
-- @Advanced annotation can be used to indicate that an argument is an advanced option and should be visually deemphasized in the GATKs. There's now an advanced section. Mauricio or Ryan -- could you figure out how to make this section less prominent in the style.css?
2011-08-18 21:39:11 -04:00
d94da0b1cf
Moved CG and SOAP codecs to private
2011-08-18 21:20:26 -04:00
f7414e39bc
Improvements to GATKDocs
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-- Allowed values for RodBinding<T> are displayed in the GATKDocs
-- Longest name up to 30 characters is chosen for main argument list (suggested by Ryan/Mauricio)
-- Features are listed in alphabetical order
-- Moved useful getParameterizedType() function to JVMUtils
-- Tests of these features in the Documentation Test
2011-08-18 21:20:09 -04:00
09d099cada
Added GATKDocs to the UnifiedGenotyper.
2011-08-18 20:57:02 -04:00
6ef01e40b8
Complete rewrite of Hard Clipping (ReadClipper)
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Hard clipping is now completely independent from softclipping and plows through previously hard or soft clipped reads.
2011-08-18 18:35:45 -04:00
626cbf9411
Bug fixes and cleanups for IndelStatistics
2011-08-18 16:28:40 -04:00
58560a6d50
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 16:17:52 -04:00
3dfb60a46e
Fixing up and refactoring usage of indel categories. On a variant context, isInsertion() and isDeletion() are now removed because behavior before was wrong in case of multiallelic sites. Now, methods isSimpleInsertion() and isSimpleDeletion() will return true only if sites are biallelic. For multiallelic sites, isComplex() will return true in all cases.
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VariantEval module CountVariants is corrected and an additional column is added so that we log mixed events and complex indels separately (before they were being conflated).
VariantEval module IndelStatistics is considerably simplified as the sample stratification was wrong and redundant, now it should work with the VE-generic Sample stratification. Several columns are renamed or removed since they're not really useful
2011-08-18 16:17:38 -04:00
6b256a8ac5
Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/chartl/dev/git
2011-08-18 15:29:24 -04:00
a8935c99fc
dding docs for DepthOfCoverage and ValidationAmplicons
2011-08-18 15:28:35 -04:00
f2f51e35e3
Merge branch 'master' into help
2011-08-18 14:05:33 -04:00
faa3f8b6f6
Only concrete classes are now documented
2011-08-18 14:04:47 -04:00
7c4ce6d969
Added GATKDocs for the VQSR walkers.
2011-08-18 14:00:39 -04:00
5772766dd5
Improvements to GATKDocs
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-- Now supports a static list of root classes / interfaces that should receive docs. A complementary approach to documenting features to the DocumentedGATKFeature annotation
-- Tribble codecs are now documented!
-- No longer displayed sub and super classes
2011-08-18 14:00:09 -04:00
e03db30ca0
New uses DocumentedGATKFeatureObject instead of annotation directly
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-- Step 1 on the way to creating a static list of additional classes that we want to document.
2011-08-18 12:31:04 -04:00
d4511807ed
Merge branch 'master' into help
2011-08-18 11:53:37 -04:00
c787fd0b70
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 11:52:45 -04:00
c797616c65
If you have one sample in your BAM, getToolkit().getSamples().size() == 2
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Also deleted double initializationm, where a line of code was duplicated in creating the GATK engine.
2011-08-18 11:51:53 -04:00
cbec69a130
Merge branch 'master' into help
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Conflicts:
public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
2011-08-18 11:33:27 -04:00
aa21fc7c9c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 11:30:59 -04:00
f5d7cabb20
Fix for reintroducing an already solved problem.
2011-08-18 11:20:12 -04:00
a45498150a
Remove non-ascii char
2011-08-18 11:18:29 -04:00
c08a9964d4
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 10:58:04 -04:00
bb79d3edae
Added GATKDocs for the BQSR walkers.
2011-08-18 10:57:48 -04:00
47bbddb724
Now provides type-specific user feedback
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For RodBinding<VariantContext> error messages now list only the Tribble types that produce VariantContexts
2011-08-18 10:47:16 -04:00
2d41ba15a4
Vastly better Tribble help message
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Here's a new example:
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.1-520-g76495cd):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Invalid command line: Failed to parse value /humgen/gsa-hpprojects/GATK/data/refGene_b37.filtered.sorted.txt for argument refSeqRodBinding. Message: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :TYPE listing the correct type from among the supported types:
##### ERROR Name FeatureType Documentation
##### ERROR BEAGLE BeagleFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_beagle_BeagleCodec.html
##### ERROR BED BEDFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broad_tribble_bed_BEDCodec.html
##### ERROR BEDTABLE TableFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_table_BedTableCodec.html
##### ERROR CGVAR VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_completegenomics_CGVarCodec.html
##### ERROR DBSNP DbSNPFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broad_tribble_dbsnp_DbSNPCodec.html
##### ERROR GELITEXT GeliTextFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broad_tribble_gelitext_GeliTextCodec.html
##### ERROR MAF MafFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_gatk_features_maf_MafCodec.html
##### ERROR MILLSDEVINE VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_MillsDevineCodec.html
##### ERROR RAWHAPMAP RawHapMapFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_hapmap_RawHapMapCodec.html
##### ERROR REFSEQ RefSeqFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_refseq_RefSeqCodec.html
##### ERROR SAMPILEUP SAMPileupFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_sampileup_SAMPileupCodec.html
##### ERROR SAMREAD SAMReadFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_samread_SAMReadCodec.html
##### ERROR SNPEFF SnpEffFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_snpEff_SnpEffCodec.html
##### ERROR SOAPSNP VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_soapsnp_SoapSNPCodec.html
##### ERROR TABLE TableFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_table_TableCodec.html
##### ERROR VCF VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_vcf_VCFCodec.html
##### ERROR VCF3 VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_vcf_VCF3Codec.html
##### ERROR ------------------------------------------------------------------------------------------
2011-08-18 10:31:32 -04:00
c2287c93d7
Cleanup of codec locations. No more dbSNPHelper
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-- refdata/features now in utils/codecs with the other codecs
-- Deleted dbsnpHelper. rsID function now in VCFutils. Remaining code either deleted or put into VariantContextAdaptors
-- Many associated import updates due to code move
2011-08-18 10:02:46 -04:00
9c17d54cb6
getFeatureClass() now returns Class<T> not Class to avoid yesterday's runtime error
2011-08-18 09:39:20 -04:00
c30e1db744
Better location for help utils
2011-08-18 09:38:51 -04:00
4da42d9f39
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 09:32:57 -04:00
c91a442be1
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 22:40:16 -04:00
a7b70e6bb4
Adding feature for Khalid: ability to exclude particular samples.
2011-08-17 22:28:22 -04:00
cc3df8f11a
Moving GAV walker to public
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Walker is updated to the new RodBinding system and has the new GATKDocs layout.
2011-08-17 21:55:17 -04:00
fa1db3913b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 21:49:25 -04:00
8e83b6646b
Bug fix for Chris: don't validate ref base for complex events.
2011-08-17 21:49:14 -04:00
c104dd7a09
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 16:59:12 -04:00
81a792afeb
Reverting optimization disable in unstable.
2011-08-17 16:58:24 -04:00
2e35592295
GATKDocs for CallableLoci
2011-08-17 16:32:01 -04:00
c193f52e5d
Fixed up examples: pasting from wiki still had old rod syntax
2011-08-17 16:29:45 -04:00
2b2a4e0795
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-17 16:26:45 -04:00
297c9e513c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable into unstable
2011-08-17 16:24:02 -04:00
a210a62ab9
Merged bug fix from Stable into Unstable
2011-08-17 16:23:31 -04:00
d59e6ed274
Fix for RefSeqCodec bug and better error messages
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-- RefSeqCodec bug: getFeatureClass() returned RefSeqCodec.class, not RefSeqFeature.class. Really should change this in Tribble to require Class<T extends Feature> to get compile time type checking
-- Better error messages that actually list the available tribble types, when there's a type error
2011-08-17 16:22:07 -04:00
d170187896
Disable optimization that increases marginal speed of the GATK slightly but
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can produce data loss in a narrow corner case where the BGZF block(s) locations
and offsets in the last index bucket of contig n overlap exactly with the BGZF
block locations and offset in the last index bucket of contig n+1.
A proper fix that keeps the optimization has already been introduced into
unstable, but disabling the optimization is a low risk way to make sure that
users of stable experience no data loss.
2011-08-17 16:16:05 -04:00
53006da9a5
Improved descriptions for the SnpEff annotations in the VCF header
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(based on Eric's feedback).
2011-08-17 16:09:10 -04:00
784fb148b9
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 15:47:01 -04:00
671330950d
Updated Beagle walker for gatkdocs format. Pushed unsupported, undocumented arguments to @Hidden
2011-08-17 15:46:31 -04:00
0af68e052a
Merge branch 'master' of ssh://cga1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 15:17:47 -04:00
a423546cdd
fix: RefSeq contains records with zero coding length and the refsec codec/feature used to crash on those; now such records are ignored, with warning printed (once)
2011-08-17 15:17:31 -04:00
710d34633e
now the reads that are too long are truly ignored (fix of the fix)
2011-08-17 15:16:23 -04:00
2f19046f0c
Adding docs to the 2 beasts. Saved the worst for last.
2011-08-17 14:19:14 -04:00
069554efe5
somatic indel detector does not die on reads that are too long (likely contain a huge deletion) anymore; instead print a warning and ignore the read
2011-08-17 14:05:19 -04:00
c405a75f54
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 13:28:25 -04:00
575303ae6b
Renaming for consistency and bringing up to speed with new rod system
2011-08-17 13:28:19 -04:00
6d629c176c
Adding docs
2011-08-17 13:27:36 -04:00
a21e193a9e
Adding docs to 3 more walkers
2011-08-17 12:35:08 -04:00
98acb546a9
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 12:22:29 -04:00
d1bb302d12
Added GatkDocs documentation
2011-08-17 12:21:37 -04:00
3da71a9bb6
Clean up summary
2011-08-17 12:04:45 -04:00
c6fb215faf
GATKDocs for VariantsToTable
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-- Made a previously required argument optional, as this was a long-standing bug
2011-08-17 12:02:41 -04:00
5f794d16a7
Fixed bad character in documentation
2011-08-17 12:01:08 -04:00
9d1d5bd27a
Revert "Fixed bad character in documentation"
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This reverts commit a1f50c82d3cb25e5e83d36e9054d74cdee957d87.
2011-08-17 11:57:31 -04:00
78deb3f195
Fixed bad character in documentation
2011-08-17 11:57:00 -04:00
79dcfca25f
Fixed bad character in documentation
2011-08-17 11:56:51 -04:00
b3b5d608ca
Adding docs to yet more walkers
2011-08-17 09:57:19 -04:00
fadcbf68fd
Adding docs to QC walkers
2011-08-17 09:39:33 -04:00
5d6a6fab98
Renamed softUnclipped functions to refCoord*
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These functions return reference coordinates, so they should be named accordingly.
2011-08-16 18:56:28 -04:00
ed8f769dce
Fixed index for getSoftUnclippedEnd()
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Unclipped end can be calculated simply by looking at the last cigar element and adding it's length in case it's a soft clip.
2011-08-16 18:54:28 -04:00
5f3f46aad1
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-16 16:26:33 -04:00
946f5c53fe
Adding docs to more walkers
2011-08-16 16:26:26 -04:00
6e828260a0
Removed -B support. Now explodes with error if -B provided.
2011-08-16 16:13:47 -04:00
2d5bbecd9e
Merged bug fix from Stable into Unstable
2011-08-16 14:19:04 -04:00
07c1e113cd
Fixed interval traversal for previously hard clipped reads.
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If a read was hard clipped for being low quality and no does not overlap the interval anymore, this read will now be discarded instead of treated as an error by the GATK traversal engine.
2011-08-16 14:18:05 -04:00
9d4add3268
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-16 14:18:03 -04:00
170d1ff7b6
Fix in UG for trying to call indels at IUPAC code bases when in EMIT_ALL_SITES mode
2011-08-16 14:17:46 -04:00
b135565183
Added low quality clipping
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Clips both tails of a read if the tails are below a given quality threshold (default Q2).
*Added special treatment for reads that get completely clipped.
2011-08-16 13:51:25 -04:00
9f3328db53
fixing read group name collision: before writing the read into respective stream in nway-out mode we now retrieve the original rg, not the merged/modified one
2011-08-16 13:45:40 -04:00
ab0b56ed11
Minor doc fixes
2011-08-16 12:55:45 -04:00
125ad0bcfa
Added docs to RTC
2011-08-16 12:46:48 -04:00
ef9216011e
Added docs to IR
2011-08-16 12:24:53 -04:00
ab1e3d6a98
Use the right set of sample names
2011-08-16 01:03:05 -04:00
36c7f83208
Refactoring VE stratifications so that they don't pass around bulky data; instead just pull needed data from the VE parent. This allows us stop using deprecated features of the rod system.
2011-08-15 16:31:57 -04:00
1246b89049
Forgot to initialize variants on the merge
2011-08-15 16:00:43 -04:00
993ecb85da
Added Hard Clipping Tail Ends
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Added functionality to hard clip the low quality tail ends of reads (lowQual <= 2)
2011-08-15 15:22:54 -04:00
045e8a045e
Updating random walkers to new rod system; removing unused GenotypeAndValidateWalker
2011-08-15 14:05:23 -04:00
fc2c21433b
Updating random walkers to new rod system
2011-08-15 13:29:31 -04:00
3d56bbf087
Resolving merge conflicts
2011-08-15 12:28:05 -04:00
9ddbfdcb9f
Check filtered status before applying to alt reference
2011-08-15 12:25:23 -04:00
0d976d6211
Fixed second time clipping
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When a read is clipped once, and then in the second operation, because of indels, it doesn't reach the coordinate initially set for hard clipping, the indices were wrong. This should fix it.
2011-08-15 12:04:53 -04:00
489c15b99d
Fixed indexing issue in coordinate conversion
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When a read had been previously soft clipped, the UnclippedEnd could not be used directly as Reference Coordinate for clipping , because the read does not go that far.
2011-08-15 01:42:34 -04:00
c7b69a4574
Fixed integration tests
2011-08-14 16:38:20 -04:00
6ae3f9e322
Wrapped clipping op information
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The clipping op extra information being kept by this walker was specific to the walker, not to the read clipper. Created a wrapper ReadClipperWithData class that keeps the extra information and leaves the ReadClipper slim.
(this is a quick commit to unbreak the build, performing integration tests and will make further commits if necessary)
2011-08-14 15:44:48 -04:00
8a51732049
Fixes to ReadClipper and added Reference Coordinate clipping.
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* Added reference coordinate based hard clipping functions. This allows you to set a hard cut on where you need the read to be trimmed despite indels.
* soft clipping was messing up cigar string if there was already a hard clip at the beginning of the read. Fixed.
* hard clipping now works with previously hard clipped reads.
2011-08-14 14:54:33 -04:00
291d8c7596
Fixed HardClipping and Interval containment
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* Hard clipping was wrongfully hard clipping unmapped reads while soft clipping then hard clipping mapped reads. Now we throw exception if we try to hard/soft clip unmapped reads and use the soft->hard clip procedure fore every mapped read.
* Interval containment needed a <= and >= to make sure it caught the borders right.
2011-08-14 14:54:33 -04:00
0be1dacddb
Refactored interval clipping utility
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reads are clipped in map() and now we cover almost all cases. Left behind the case where the read stretches through two intervals. This will need special treatment later.
2011-08-14 14:54:33 -04:00
bb4ced3201
SnpEff-related fixes.
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-To correctly handle indels and MNPs, only consider features that start at the current locus,
rather than features that span the current locus, when selecting the most significant effect.
-Throw a UserException when a SnpEff rodbinding is not provided instead of simply not adding
any annotations and silently returning.
2011-08-12 15:26:24 -04:00
10e873d9c6
Merge branch 'repval'
2011-08-12 15:24:31 -04:00
31dc831531
Merged bug fix from Stable into Unstable
2011-08-12 13:26:41 -04:00
9121b8ed65
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 12:24:19 -04:00
7ed120361d
Fixed bug that required symbolic alleles to be padded with reference base and added integration test to test parsing and output of symbolic alleles
2011-08-12 12:23:44 -04:00
7ea9196321
Better error message for name/type clashes.
2011-08-12 11:18:14 -04:00
27f0748b33
Renaming the HapMap codec and feature to RawHapMap so that we don't get esoteric errors when trying to bind a rod with the name 'hapmap' (since it was also a feature).
2011-08-12 11:11:56 -04:00
c7ca33cbff
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 10:12:09 -04:00
41f3da75d7
Implementation in VE was confusing 'variant' status vs. 'polymorphic' status. This led to issues because we now match types of eval and comp; specifically, subsetting a VC to a monomorphic sample can't change the 'variant' status of the VC (it's still a variant site or otherwise we'll never match the comps, which breaks GenotypeConcordance). CountVariants really got this wrong. Fixed. VE now passes all integration tests.
2011-08-12 02:22:44 -04:00
eba316621d
Finish moving VE over to new rod system and fixing up the type inconsistency between eval and comp rods. Now the novel count is always 0 under the known stratification. :)
2011-08-12 00:40:08 -04:00
9de06560df
Update to new RodBinding system
2011-08-11 17:54:16 -04:00
90771b74b4
When matching eval to comps, try to choose the one with the same alt allele.
2011-08-11 13:55:01 -04:00
200f73b008
No reason to warn the user anymore because it's no longer possible for them to specify a dbsnp file on the command-line.
2011-08-11 13:44:07 -04:00
e93538cdf7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 13:39:36 -04:00
265c3d744b
Fixing VariantEval logic and having it use the new rod system.
2011-08-11 13:39:34 -04:00
b705d9cf15
Oops, these VariantAnnotator input bindings aren't needed during the UG
2011-08-11 13:17:16 -04:00
7fade88070
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 11:02:47 -04:00
c7b9a9ef0a
Updating UnifiedGenotyper to use the new rod binding system.
2011-08-11 11:02:11 -04:00
418a4d541f
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 11:01:38 -04:00
e71255d3c2
GATKDocsExample walker
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-- Shows the best practice for documentating a walker with the GATKdocs
-- See http://www.broadinstitute.org/gsa/wiki/index.php/GATKdocs#Writing_GATKdocs_for_your_walkers for a brief discussion
2011-08-11 11:01:21 -04:00
79c86e211f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 09:59:20 -04:00
ea42ee4a95
Updating BQSR for the new rod binding system.
2011-08-11 09:58:42 -04:00
8cdc0cbd9c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 08:58:49 -04:00
40e06f9afb
Fixed broken RodBinding defaults.
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-- Verified now to be correct at runtime
-- UnitTest covers this
-- createTypeDefault now takes a Type, not a Class, so that parameterized classes can have their parameter fetched in the defaults.
2011-08-11 08:58:30 -04:00
dd5fe8291d
Fixing up some comments in the BQSR
2011-08-11 08:36:00 -04:00
f1b09db39e
Fixes for rod bindings
2011-08-10 23:08:47 -04:00
75985c2fa0
Resolving merge conflicts
2011-08-10 22:45:11 -04:00
bdb1da30fd
Better interface for getting RodBindings to the VariantAnnotatorEngine and its annotations: pass around an AnnotatorCompatibleWalker (interface) object. Updating VA to use the new rod system.
2011-08-10 22:43:08 -04:00
0086e27741
makeUnbound now package protected
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-- Removed references to it in the codebase
-- Fixed documentation I saw that had the summary + body style
2011-08-10 22:29:32 -04:00
cb6cf25bb0
Updating SelectVariants documentation to reflect best practice
2011-08-10 22:24:18 -04:00
00b4d6ec57
Updated the best practice on documenting a field
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-- Best practice is now to skip the summary, as this is the @annotation doc value.
2011-08-10 22:21:12 -04:00
2007d2fcad
Better documentation for default value fields
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-- DocString function for types that create default outputs "stdout"
-- RodBinding now creates a makeUnbound default value automatically for you if your RodBinding isn't required
-- Removed warning about sparse help from TextFormattingUtils
2011-08-10 22:16:22 -04:00
bb557266ca
Merge branches to get new RodBinding framework
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Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/replication_validation/ReplicationValidationWalker.java
2011-08-10 18:23:01 -04:00
8325cb8c26
Fixing up apparent source control/merge snafu: fix to correctly output PL ordering in multi-allelic sites by UG was only half-committed and hence not working. This completes fix
2011-08-10 15:31:49 -04:00
07ad8c78a9
More tools moved over. Fixed the VariantContextIntegrationTest which was not useful because the md5s were all removed. In the future, instead of removing md5s (putting it in 'parameterization' mode), you should instead use @Test{enabled=false} since it's easier to track.
2011-08-10 14:24:40 -04:00
8d14d32a62
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-10 13:42:37 -04:00
749c8bfbcd
Moving more tools over to the new rod system
2011-08-10 13:42:35 -04:00
0497170bc9
SnpEffCodec now implements SelfScopingFeatureCodec so that we no longer have to specify the codec name on the command line for SnpEff files.
2011-08-10 13:12:09 -04:00
577f861f69
Pass the rodBindings into the VariantAnnotator engine, and from there to the
...
annotation classes themselves.
2011-08-10 13:11:57 -04:00
480e7a7984
Correctly initialize the optional SnpEff rod binding in VariantAnnotator using
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RodBinding.makeUnbound()
2011-08-10 12:25:26 -04:00
a42f90db11
Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.
2011-08-10 12:20:18 -04:00
c884b6bf1f
Fixed comment
2011-08-10 12:07:43 -04:00
06cdc4d5f9
Added a StandardVariantContextInputArgumentCollection that is now used for consistency by many of the core tools.
2011-08-10 12:00:56 -04:00
bc125f104a
TrainingSets class is obsolete now.
2011-08-10 10:23:33 -04:00
c60cf52f73
Updating VQSR for new RodBinding syntax. Cleaning up indel specific parts of VQSR.
2011-08-10 10:20:37 -04:00
1ea5ec276b
Minor cleanup
2011-08-09 23:28:59 -04:00
bc2d4f554d
Bringing Indel Realigner up to speed with the new rod binding syntax; now use -known to specify the known indels track.
2011-08-09 23:21:17 -04:00
b8f572b571
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-09 23:19:51 -04:00
08631546c8
Partial commit for David so he can see what I want to do with the VariantAnnotator. Added a DbsnpArgumentCollection that people can use in their walkers to ensure that we have a standard syntax whenever allowing dbsnp rods. Added it to UG, but didn't hook it up. Maybe we should do the same for the 'variant' rod?
2011-08-09 23:19:40 -04:00
Guillermo del Angel
Mark DePristo
Eric Banks
Mauricio Carneiro
Christopher Hartl
Roger Zurawicki
Khalid Shakir
Ryan Poplin
Matt Hanna
David Roazen
Andrey Sivachenko
Menachem Fromer