zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
8,216 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

8216 Commits (6c2555885c271bf8a1c4ff97da5db3c18fecb242)

Author SHA1 Message Date
Mark DePristo 6c2555885c Caching getSimpleName() in VariantEval is a big performance improvement 
-- Removed the SimpleMetricsByAC table, as one should just use the AlleleCount Stratefication and the upcoming VariantSummary table
 2011-11-23 08:34:05 -05:00
Mark DePristo a3aef8fa53 Final performance optimization for GenotypesContext 2011-11-22 17:19:30 -05:00
Mark DePristo 990c02e4de Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-11-22 17:19:11 -05:00
Mauricio Carneiro 0fa50056eb Reorganizing package structure for compression tools (incl. Reduce Reads) 
ReduceReads is no longer the only compression tool. Reorganizing the package structure to reflect that.
 2011-11-22 15:03:31 -05:00
Mauricio Carneiro 1a50d54c03 A walker that generates the distribution of quality scores 
Outputs a GATKReportTable that will be used as input to the Quantization walker. Eventually this functionality may be merged into ReduceReads or CountCovariates to avoid another traversal.
 2011-11-22 14:49:28 -05:00
Mauricio Carneiro 1614ca1115 Force use of LinkedList 
Disambiguating which collection I need to use for mapped reads.
 2011-11-22 14:49:28 -05:00
Guillermo del Angel 38a90da92c Fixed merge conflict to Unstable 2011-11-22 14:39:45 -05:00
Guillermo del Angel 32a77a8a56 Prevent out of bound error in case read span > reference context + indel length. Can happen in RNAseq reads with long N CIGAR operators in the middle. 2011-11-22 13:57:24 -05:00
Eric Banks 5821c11fad For BAM and Reviewed errors we now check the error message to see if it's actually a 'too many open files' problem and, if so, we generate a User Error instead. 2011-11-22 10:50:22 -05:00
Eric Banks 5e7b9ae119 The NONE option is not supported yet (but the error message should mention this) 2011-11-22 10:48:38 -05:00
Mark DePristo 7087310373 Embarassing bug fixed 2011-11-22 10:16:36 -05:00
Mark DePristo e484625594 GenotypesContext now updates cached data for add, set, replace operations when possible 
-- Involved separately managing the sample -> offset and sample sorted list operations.  This should improve performance throughout the system
 2011-11-22 08:40:48 -05:00
Mark DePristo 29ca24694a UG now encoding NO_CALLs as ./. not ./.:.:4:0,0,0 
A few updated UGs integration tests
 2011-11-22 08:22:32 -05:00
Mark DePristo 4ea74c42de Including GENCODE BED argument, removing CAPTURE target 2011-11-21 19:18:43 -05:00
Mark DePristo 2b51c01df4 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-11-21 19:16:06 -05:00
Mark DePristo 5443d3634a Again, fixing the add call when we really mean replace 
-- Updating MD5s for UG to reflect that what was previously called ./.:.:10:0,0,0 is now just ./.  Eric will fix long-standing bug in QD observed from this change
-- VFW MD5s restored to their old correct values.  There was a bug in my implementation to caused the genotypes to not be parsed from the lazy output even through the header was incorrect.
 2011-11-21 19:15:56 -05:00
Mauricio Carneiro 8c7430e6ff Bugfix: isOriginalRead had the wrong check for WGS 
The original read has to be contained in the current interval and the first read in the list. In WGS all reads are 'original'.
 2011-11-21 17:12:11 -05:00
Mauricio Carneiro 756695ee3f Better Unit tests for Synthetic Reads 2011-11-21 17:12:11 -05:00
Mauricio Carneiro 5ad3dfcd62 BugFix: byte overflow in SyntheticRead compressed base counts 
* fixed and added unit test
 2011-11-21 17:11:50 -05:00
Mark DePristo 9ea7b70a02 Added decode method to LazyGenotypesContext 
-- AbstractVCFCodec calls this if the samples are not sorted.  Previously called getGenotypes() which didn't actually trigger the decode
 2011-11-21 16:21:23 -05:00
Mark DePristo ab2efe3bd3 Reverting bad exact model changes 2011-11-21 16:14:40 -05:00
Eric Banks 44554b2bfd Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-11-21 15:01:45 -05:00
Eric Banks 022832bd74 Very bad use of the == operator with Strings was ensuring that validating GenomeLocs was very inefficient. This fix resulted in a significant speedup for a simple RodWalker. 2011-11-21 14:49:47 -05:00
Mark DePristo 1561af22af Exact model code cleanup 
-- Fixed up code when fixing a bug detected by aggressive contracts in GenotypesContext.
 2011-11-21 14:35:15 -05:00
Mark DePristo 2c501364b8 GenotypesContext no longer have immutability in constructor 
-- additional bug fixes throughout VariantContext and GenotypesContext objects
 2011-11-21 14:34:31 -05:00
David Roazen 1296dd41be Removing the legacy -L "interval1;interval2" syntax 
This syntax predates the ability to have multiple -L arguments, is
inconsistent with the syntax of all other GATK arguments, requires
quoting to avoid interpretation by the shell, and was causing
problems in Queue.

A UserException is now thrown if someone tries to use this syntax.
 2011-11-21 13:18:53 -05:00
Mark DePristo e467b8e1ae More contracts on LazyGenotypesContext 2011-11-21 09:34:57 -05:00
Mark DePristo 2e9ecf639e Generalized interface to LazyGenotypesContext 
-- Now you provide a LazyParsing object
-- LazyGenotypesContext now knows nothing about the VCF parser itself.  The parser holds all of the necessary data to parse the VCF genotypes when necessarily, and the LGC only has a pointer to this object
-- Using new interface added LazyGenotypesContext to unit tests with a simple lazy version
-- Deleted VCFParser interface, as it was no longer necessary
 2011-11-21 09:30:40 -05:00
Mark DePristo f0ac588d32 Extensive unit test for GenotypeContextUnitTest 
-- Currently only tests base class.  Adding subclass testing in a bit
 2011-11-20 18:28:01 -05:00
Mark DePristo bc44f6fd9e Utility function Collection<Genotype> -> Collection<String> 2011-11-20 18:26:56 -05:00
Mark DePristo 9445326c6c Genotype is Comparable via sampleName 2011-11-20 18:26:27 -05:00
Mark DePristo f9e25081ab Completed documented LazyGenotypesContext 2011-11-20 08:35:52 -05:00
Mark DePristo 9cb3fe3a59 Vastly better way of doing on-demand genotyping loading 
-- With our GenotypesContext class we can naturally create a LazyGenotypesContext subclass that does the on-demand loading.
-- This new class was replaced all of the old, complex functionality
-- Better still, there were many cases were the genotypes were being loaded unnecessarily, resulting in efficiency.  This was detected because some of the integration tests changed as the genotypes were no longer being parsing unnecessarily
-- Misc. bug fixes throughout the system
-- Bug fixes for PhaseByTransmission with new GenotypesContext
 2011-11-20 08:23:09 -05:00
Mark DePristo f392d330c3 Proper use of builder. Previous conversion attempt was flawed 2011-11-19 22:09:56 -05:00
Mark DePristo 7d09c0064b Bug fixes and code cleanup throughout 
-- chromosomeCounts now takes builder as well, cleaning up a lot of code throughout the codebase.
 2011-11-19 18:40:15 -05:00
Mark DePristo 707bd30b3f Should have been @BeforeMethod 2011-11-19 16:10:09 -05:00
Mark DePristo 8f7eebbaaf Bugfix for pError not being checked correctly in CommonInfo 
-- UnitTests to ensure correct behavior
-- UnitTests to ensure correct behavior for pass filters vs. failed filters vs. unfiltered
 2011-11-19 15:58:59 -05:00
Mark DePristo b7b57ef39a Updating MD5 to reflect canonical ordering of calculation 
-- We should no longer have md5s changing because of hashmaps changing their sort order on us
-- Added GenotypeLikelihoodsUnitTests
-- Refactored ExactAFCaclculation to put the PL -> QUAL calculation in the GenotypeLikelihoods class to avoid the code copy.
 2011-11-19 15:57:33 -05:00
Mark DePristo 73119c8e3c Merge with master 
-- A few bug fixes
 2011-11-19 09:56:06 -05:00
Mark DePristo f685fff79b Killing the final versions of old new VariantContext interface 2011-11-18 21:32:43 -05:00
Mark DePristo 6cf315e17b Change interface to getNegLog10PError to getLog10PError 2011-11-18 21:07:30 -05:00
Mark DePristo c7f2d5c7c7 Final minor fix to contract 2011-11-18 19:40:05 -05:00
Mauricio Carneiro b5de182014 isEmpty now checks if mReadBases is null 
Since newly created reads have mReadBases == null. This is an effort to centralize the place to check for empty GATKSAMRecords.
 2011-11-18 18:34:05 -05:00
Mauricio Carneiro 8ab3ee9c65 Merge remote-tracking branch 'unstable/master' into rr 2011-11-18 16:50:25 -05:00
Mauricio Carneiro 333e5de812 returning read instead of GATKSAMRecord 
Do not create new GATKSAMRecord when read has been fully clipped, because it is essentially the same as returning the currently fully clipped read.
 2011-11-18 16:49:59 -05:00
Mauricio Carneiro 3f141d3c32 slightly clearer context to finalizeAndAdd() 
now it can handle "both" synthetic and running consensus at once. This should avoid forgetting to close one or the other in the future.
 2011-11-18 16:35:14 -05:00
Mauricio Carneiro e08b070a6a Bug fix: Variant region starting after synthetic read didn't close it properly 
If a synthetic read preceded a variant region, the variant region was not closing the synthetic read before moving the sliding window. Fixed.
 2011-11-18 16:35:14 -05:00
Mauricio Carneiro 74eeb32d74 adapting reduce reads script to do WGS 2011-11-18 16:35:14 -05:00
Matt Hanna 8bb4d4dca3 First pass of the asynchronous block loader. 
Block loads are only triggered on queue empty at this point.  Disabled by
default (enable with nt:io=?).
 2011-11-18 15:02:59 -05:00
Mark DePristo a2e79fbe8a Fixes to contracts 2011-11-18 14:18:53 -05:00