9053406798LocusReferenceView: If the locus a view is requested for spans beyond the reference contig ends, create the actual window bounded by contig ends (so that the locus will not be fully contained in the window!!).
asivache
2010-03-22 15:59:15 +0000
439c34ed38clean-up before annotating VariantEval2 for output.
aaron
2010-03-22 07:39:20 +0000
076d21d394Minor bug workaround in GenotypeConcordance module (see todo). General platform read filter. You can say -rl Platform illumina to remove all SLX reads
depristo
2010-03-22 02:47:09 +0000
6cd97b78abAn additional safety check to ensure that we only walk over coordinate-sorted data when doing locus traversals.
hanna
2010-03-21 23:31:45 +0000
b4b4e8d672For Sarah Calvo: initial implementation of read pair traversal, for BAM files sorted by read name.
hanna
2010-03-21 23:22:25 +0000
169d0c6e8fUp the svn revision number in an attempt to force an update, again due to an artifact of the way we build picard-private-parts.
hanna
2010-03-19 22:39:56 +0000
c0eb5c27eaLower memory support for merged sharding. Merged sharding is still not available. WARNING: If you update frequently, you might have to rm -rf ~/.ant/cache -- this is an unfortunate side effect of the way we distribute picard-private.jar.
hanna
2010-03-19 22:03:47 +0000
4d4db7fe63Renaming for consistency
ebanks
2010-03-19 18:45:01 +0000
4c4d048f14Moving VariantFiltration over to use VariantContext.
ebanks
2010-03-19 18:35:23 +0000
c88a2a3027Fixing/cleaning up the vcf merge util
ebanks
2010-03-19 15:13:32 +0000
cdec84aa8fBug fix for variant optimizer. Remember to close the PrintStreams it uses to output the cluster files.
rpoplin
2010-03-19 15:07:32 +0000
bb7e0c27fdupdating the package
ebanks
2010-03-19 13:42:31 +0000
d8ff552311Support for EXPERIMENT sampling-based genotype likelihoods
depristo
2010-03-19 13:19:40 +0000
7b17bcd0afRefactoring a few useful routines for detecting mendelian violations
depristo
2010-03-19 13:19:01 +0000
56092a0fc2Slight cleanup for mathutils
depristo
2010-03-19 13:18:08 +0000
b221ce94ceStill being tested trio-aware genotyper that calculates P(de novo)
depristo
2010-03-19 13:11:39 +0000
08d9ae403dbetter farm commands, and simple utility to convert ucsc repeat masks to interval lists
depristo
2010-03-19 13:11:06 +0000
03480c955cAnd now the UnifiedGenotyper can officially annotate genotype (FORMAT) fields too.
ebanks
2010-03-19 04:58:37 +0000
e757f6f078Missing value for arbitrary format entries is empty string (need to revisit at some point, but it will require updating the VCF spec).
ebanks
2010-03-19 03:56:27 +0000
0311980668The VariantAnnotator can now officially annotate genotype (FORMAT) fields.
ebanks
2010-03-19 03:30:14 +0000
9b61d95d9cKhalid found an out-of-memory condition with the new sharding system when merging lots of BAMs, and the fix is taking longer than I thought. Disable experimental sharding when merging until the fix is ready.
hanna
2010-03-19 02:43:46 +0000
b8e8852b4fBetter interface for the Annotator in how it interacts with VariantContext. Also, added a proof of concept genotype-level annotation (not working yet, almost there).
ebanks
2010-03-18 20:41:57 +0000
96662d8d1bMoving from GATK dependencies on isolated classes checked into the GATK codebase to a dependency on a jar file compiled from my private picard branch.
hanna
2010-03-18 17:43:42 +0000
f455412ea8adding a dependency that I forgot.
aaron
2010-03-18 13:32:37 +0000
8a5f0b746esome cleanup for the output system.
aaron
2010-03-18 12:54:39 +0000
c78fc23ec5Minor updates to output of variant optimizer.
rpoplin
2010-03-18 12:46:47 +0000
0247548400Fixed one test and (temporarily) punted on another
ebanks
2010-03-18 06:22:48 +0000
ee0e833616Some significant changes to the annotator: 1. Annotations can now be "decorated" with any arbitrary interface description - not just standard or experimental. 2. Users can now not only specify specific annotations to use, but also the interface names from #1. Any number of them can be specified, e.g. -G Standard -G Experimental -A RankSumTest. 3. These same arguments can be used with the Unified Genotyper for when it calls into the Annotator. 4. There are now two types of annotations: those that are applied to the INFO field and those that are applied to specific genotypes (the FORMAT field) in the VCF (however, I haven't implemented any of these latter annotations just yet; coming soon).
ebanks
2010-03-18 05:38:32 +0000
58a31bab6aVariant optimizer now outputs VCF files via ApplyVariantClustersWalker. Documentation to be added to the wiki. It is ready to be used by other people but only with great caution.
rpoplin
2010-03-17 20:41:42 +0000
d9398dc347Remove some of the restrictions on getStart() and getStop(); getStart() and getStop() now do the minimum validation rather than the more rigorous only-within-the-contig-bounds header validation.
hanna
2010-03-17 19:39:30 +0000
4965d6b26aPassing just the single alternate allele to the converted maf on the recommendation of mike lawrence and kiran.
kshakir
2010-03-17 19:08:37 +0000
182f1061ffBamboo isn't picking up commits for some reason; updating a copyright to see if it'll get this commit.
aaron
2010-03-17 17:56:48 +0000
5e29d0c219Be smarter about dealing with infinite quals for ref calls
ebanks
2010-03-17 17:35:23 +0000
1bb4394aa9Adding a skeleton for the second step of the variant optimization process.
rpoplin
2010-03-17 17:03:40 +0000
ded4ba8966Let's make artificial reads that actually adhere to the specs...
ebanks
2010-03-17 16:51:42 +0000
5b34bb9ab0Adding three minor new features:
bthomas
2010-03-17 16:24:10 +0000
4340601c26-Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically -Better integration test
ebanks
2010-03-17 16:00:10 +0000
76d14d17dcoops, need to update class names too
ebanks
2010-03-17 14:01:31 +0000
85a030069drenaming for consistency
ebanks
2010-03-17 14:00:28 +0000
af5fd99444Added filter for bad cigars (based on consecutive indels) - and cleaned up bad mates filter.
ebanks
2010-03-17 13:53:42 +0000
2cc040aa1cNew sharding system is live. Disable with -ds.
hanna
2010-03-17 03:32:45 +0000
1fd909cdafFix for Kiran: -1 is a valid value for genotype qualities in VCF, so VariantContext shouldn't die. Cleaned up the relevant VCF code while I was in there.
ebanks
2010-03-17 00:20:15 +0000
849bd1f451Set the eagerDecode flag in such a way that the binary data block in the BAM will always be considered dirty.
hanna
2010-03-16 22:01:23 +0000
933823c8bcRemoved the StingException when mkdir fails for Sendu in AnalyzeCovariates. Incremental updates to VariantOptimizer.
rpoplin
2010-03-16 19:45:02 +0000
2525ecaa43Oops. Commented out some tests to improve performance and then checked in the commented out tests. Reverted.
hanna
2010-03-16 16:34:50 +0000
59045ccb28Filter,merge performs much better than merge,filter. Many thanks to Eric for checking in an integration test that so compellingly demonstrates this.
hanna
2010-03-16 16:23:37 +0000
6dd5f192e7Performance improvements for RODs in conjunction with new sharding system.
hanna
2010-03-16 14:54:12 +0000
f20f78d77fDon't crash if the tracker is null. Reset the alternate alleles based on the alts present in the subset of samples.
kiran
2010-03-16 04:00:04 +0000
10e76abbbcadding some VE2 report infrastructure; work-in-progress.
aaron
2010-03-16 03:57:42 +0000
202231141c-Push the --use_original_qualities argument into the engine. -Check that base and qual strings are the same lengths -Fix one more bug in the clipper.
ebanks
2010-03-16 02:06:11 +0000
035d4170aafix bug in read clipper: output bam can be null, so check for it.
ebanks
2010-03-15 18:49:26 +0000
411d25c8d1-Integration tests for walkers that use original quals. -framework for pushing -OQ into GATK (not done)
ebanks
2010-03-15 18:46:31 +0000
e365d308d4add a new JEXLContext that lazy-evaluates JEXL expressions given the VariantContext.
aaron
2010-03-15 16:00:55 +0000
9f519af06dnew method to filter out overlapping PE reads
kcibul
2010-03-15 15:40:09 +0000
4bdc3b2784automatic generation of individual and individual set import files
chartl
2010-03-15 10:36:33 +0000
d9b12b468fAdding default filter info
chartl
2010-03-15 10:05:46 +0000
45f70de6dfFixed bug that failed to reset an accumulator when crossing contig boundaries, meaning that in special cases of shallow coverage, an interval might get dropped.
hanna
2010-03-15 04:45:55 +0000
4dd7c5972cUnit tests for -XL arguments; expt. annotation calculating the GC content within 100 bp of the current SNP
depristo
2010-03-14 21:08:14 +0000
e367a50e9bAdded genotype concordance module. Not at all finished, but needed to give something to Aaron to look at for help in printing the output nicely. Also misc cleanup and fixes (e.g. perform evalulation even when no comp tracks are provided).
ebanks
2010-03-14 19:02:24 +0000
ecb59f5d0dremoved old tests and old code
aaron
2010-03-12 22:57:01 +0000
88a48821earemoved the dependence on removeRegion() in GenomeLocSortedSet
aaron
2010-03-12 22:35:49 +0000
196bca6819Script to split concordance files into their constituent sets and calculate summary stats from a concordance file - SNPs called and number in dbSNP
andrewk
2010-03-12 22:20:44 +0000
b39b5edca8Bug fix in variant eval 2. Preliminary (slow and buggy) support for -XL exclude lists.
depristo
2010-03-12 19:23:12 +0000
1eb5f97255fixed dropping single base intervals from deleteRegion, moving onto performance fixes.
aaron
2010-03-12 19:14:21 +0000
7aa7a5f9b8Bug fixes for edge cases and filtration in the earlier performance fixes.
hanna
2010-03-12 04:46:08 +0000
1e170369b9A quick module to load up text files more easily
kiran
2010-03-12 02:31:29 +0000
5e8654fcdcOops! Introduced a performance bug in read interval sharding, when the new sharding system is available. Track more state to avoid this problem in the future.
hanna
2010-03-11 23:19:42 +0000
740238b4faremoving a reference to the VCFValidator, which is gone.
aaron
2010-03-11 21:32:17 +0000
d804bdf210New option: --maxReadsInRam . When using ON_DISK sorting option, the tool may still run out of memory in the regions of pathologically deep coverage because of the generous memory usage limit set in the underlying samtools' sorting sam writers. With this option, the user can lower the number of reads the writer keeps in memory before spilling them on disk.
asivache
2010-03-11 21:15:03 +0000
661a043cefadding methods to get RODs by name or type in read traversals, performance improvements to RODs for Reads in general, and some more Tribble infrastructure.
aaron
2010-03-11 21:13:39 +0000
18ba9929f9notes for eric
depristo
2010-03-11 20:34:54 +0000
cbd529d544Better chopping up of data for ref walkers.
hanna
2010-03-11 20:13:26 +0000
a7ba88e649Rework the way the MicroScheduler handles locus shards to handle intervals that span shards with less memory consumption.
hanna
2010-03-11 18:40:31 +0000
4a05757a2aFixed strand bias calculation because of -Infinity issues.
ebanks
2010-03-11 16:05:51 +0000
dde9fd8a15some rods-for-reads cleaning and performance improvements.
aaron
2010-03-10 22:54:58 +0000
4f4555c80fPPV and Sensitivity added to validation tool output; support for arbitrary -sample arguments to subset variant contexts by sample
depristo
2010-03-10 22:28:31 +0000
40d305bc7eAdded test of Nway cleaning for Matt; thanks to Aaron for the help.
ebanks
2010-03-10 21:00:41 +0000
486bef9318Support for validationRate calculation in variant eval 2; better error messages for failed genome loc parsing; tolerance to odd whitespace in plinkrod, and fix for monomorphic sites in vcf2variantcontext.
depristo
2010-03-10 16:25:16 +0000
c85ed1ce90Plumbing is now in place to emit indel calls from the UnifiedGenotyper.
ebanks
2010-03-10 04:30:12 +0000
5c35be39efNow that extended events work for reference traversals, turn it off in the genotyper for non-indel models (thereby fixing busted integration tests).
ebanks
2010-03-10 03:14:06 +0000
7ddd45d059Hmm. I thought I removed this already.
ebanks
2010-03-10 03:09:13 +0000
6e855809e1Renaming and moving relevant tools into a sequenom directory
ebanks
2010-03-10 02:31:10 +0000
c638c29eeaIn reference traversals, this view did not expect a possibility of TWO alignment contexts (base pileup followed by extended event pileup) associated with the same location. As the result, extended event pileups were silently skipped even when enabled in the traversal engine. Fixed.
asivache
2010-03-09 22:18:44 +0000
bc3761dc16allow clipper to use original quals if requested
ebanks
2010-03-09 21:50:31 +0000
ee68e38e02Eliminate the shell items, as FH will be calling this with /broad/tools/apps/R-2.72/bin/Rscript
chartl
2010-03-09 20:15:21 +0000
f096a958d6Initial commit for Andrey of plumbing for indels. Not finished - need to track down bug with him.
ebanks
2010-03-09 19:13:01 +0000
0a49dffa8fRow/Column names are now R-friendly
chartl
2010-03-09 19:01:03 +0000
0e360ea8afAlleles now hash correctly. Special thanks to Matt & Aaron.
ebanks
2010-03-09 18:09:44 +0000
5a20bf0e643 changes to UG which break integration tests: 1. emit AA,AB,BB likelihoods in the FORMAT field for Mark 2. remove constraint that genotype alleles (in the GT field) need to be lexigraphically sorted. 3. Add bam file(s) used by genotyper to header for Kiran
ebanks
2010-03-09 17:16:47 +0000
aa7191353aPlotDepthOfCoverage now produces a set of useful QC plots. Currently a first-draft, and it is unclear how the visualization will scale with increasing sample size and/or depth.
chartl
2010-03-09 16:42:35 +0000
cdce639baePartially reclaim performance lost during integration test fixes.
hanna
2010-03-09 12:36:11 +0000
9f3b99c11bMoving UnifiedGenotyper and VariantAnnotator over to VariantContext system. Removing obsolete genotyping classes. First stage of removing dependence on old Genotype class. More changes to come.
ebanks
2010-03-09 03:41:07 +0000
02f48b6457Fix bug that's been in the GATK for a very long time: update nReads (as well as nRecords), so that INFO logging doesn't say 'skipped 0 of 0 reads'. While I'm in there, update TraversalStatistics to store longs.
hanna
2010-03-08 22:44:54 +0000
81ffb8243dWaypoint commit of plotting R script for Depth Of Coverage/Coverage Statistics
chartl
2010-03-08 21:42:51 +0000
bca9bdcc68Add integration test for quartiles overflowing on interval reduce
chartl
2010-03-08 16:18:45 +0000
asivache
aaron
depristo
hanna
ebanks
rpoplin
kshakir
bthomas
kiran
kcibul
chartl
andrewk