- Repeat Expansions
- Novel sequence
And for indels of size <=2 we get a per-mononuc. or dinuc. breakdown of novels and expansions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4828 348d0f76-0448-11de-a6fe-93d51630548a
VariantEvalWalker's logger is made public, so that variant eval modules can access it through the parent object.
DesignFileGenerator comment lists how best to bind things to it, and the feature accessor is better refined to grab the genome loc. (old change)
scala changes:
convenience addAll( List[CommandLineFunction] ) added to QScript class (and thus removed from the fCPV2)
useful command line functions added to a new library package for command line functions (these are fast simple VCF command lines)
bug fixed in ProjectManagement for the class where there's only one batch to be batch-merged (not really part of the use-case, but an edge-condition that came up during pipeline testing)
first draft of a private mutations pipeline which will be elaborated in future
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4823 348d0f76-0448-11de-a6fe-93d51630548a
Minor refactoring to add more of the CLibrary including setenv().
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4819 348d0f76-0448-11de-a6fe-93d51630548a
- bsub command line is no longer fully printed out.
- extraBsubArgs hack is now a callback function updateJobRun.
Updated FullCallingPipelineTest to reflect latest changes to fullCallingPipeline.q.
Added a pipeline that tests the UGv2 runtimes at different bam counts and memory limits.
Updated VE packages that live in oneoffs to compile to oneoffs.
Added a hack to replace the deprecated symbol environ in Mac OS X 10.5+ which is needed by LSF7 on Mac.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4816 348d0f76-0448-11de-a6fe-93d51630548a
subjected to and passes cursory testing on one dataset (and all integration tests pass).
However, there's a small library of validation checks, and unit and integration tests
that must be added.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4813 348d0f76-0448-11de-a6fe-93d51630548a
BAQ has generally useful improvements. Refactor code to make it easier for BAQUnitTest to run. minBaseQuality enforced on output, as well as input now. Added BAQUnitTest that checks that the BAQ calculation is performing as expected. Still needs to be expanded significantly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4804 348d0f76-0448-11de-a6fe-93d51630548a
a) Really fix this time strand bias computation for indels, previous version was a partial fix only.
b) Change way in which we deal with bad bases at the edge of reads. Even if a base is soft clipped in CIGAR string, there may still be dangling bases with Q=2 that may throw off QUAL computation in some sites. So, we're stricter and we also trim off those bases off read edges even if they are not soft-clipped officially.
c) First feeble-minded attempt at runtime optimization - don't compute log and 10^base_qual every time. Rather, cache 10^-k/10 and log(1-10^-k/10) for all k <=60. This speeds up code about 4x.
d) Further optimization: don't compute log(10^x+10^y) but rather use softMax function recently put into ExactAFCalculationModel.
e) Skip bad reads where all Q=2 (sic)
f) Avoid log to lin and back to log conversions of genotype likelihoods - this was legacy code from back when exact model did stuff in linear domain. This improves precision overall.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4802 348d0f76-0448-11de-a6fe-93d51630548a
SAMFileWriterStub now supports BAQ writing as an internal feature. Several walkers have the @BAQMode applied to this, with parameters that I think are reasonable. Please look if you own these walkers, though
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4798 348d0f76-0448-11de-a6fe-93d51630548a
2. Update to UGCalcLikelihoods for Chris: require a vcf bound to 'allele' to be provided so that we know exactly which alternate allele we should be calculating GLs for at each site. The user is warned when the VC is not biallelic or there are multiple records at a site.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4780 348d0f76-0448-11de-a6fe-93d51630548a
a) Avoid complete crash of caller that broke due to a recent refactoring by someone who must not be named <cough>EB<cough>... an integration test to avoid this in the future coming soon.
b) Fixed up strand bias computation for indels
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4779 348d0f76-0448-11de-a6fe-93d51630548a
IndelRealigner now uses this functionality to correctly un-mangle read group id's in --nWayOut mode (i.e. when we need to write reads into separate output bams with headers matching the original inputs).
Some hidden changes to IndelRealigner: purely testing and development, transparent to the users (hidden option added)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4775 348d0f76-0448-11de-a6fe-93d51630548a
Minor fixes to avoid crashes vs CG indel files:
- Add count for complex events, not just insertions and deletions
- Handle correctly cases of large indels falling out of bounds of histogram array: added a count of indels ouf of bounds and avoid exceptions.
2) Cosmetic fix for R script assessing UG calling performance: draw red y=x line on top of Simulated vs Estimated AC to get a better view of under/over-estimation of AC.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4758 348d0f76-0448-11de-a6fe-93d51630548a
Set the -bigMemQueue in the FullCallingPipelineTest to GSA to avoid waiting for the week queue when it is busy.
Fixed the package definition of PipelineTest so that scalac won't recompile it every time.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4755 348d0f76-0448-11de-a6fe-93d51630548a
specify -B:dbsnp,vcf <filename> if the filename passed if the --DBSNP argument
value contains 'vcf'. We'll replace this functionality once dbSNP 132 starts
playing nicely with the tagging system.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4749 348d0f76-0448-11de-a6fe-93d51630548a
1. Fix: VCs were padded before the merge, but they were never unpadded afterwards. This leaves us with a VC that doesn't meet our spec.
2. Update: instead of running the merged VC through every standard annotation (which seems really wrong, since this isn't the annotator tool), just update the chromosome count annotations (AC,AF,AN) through VCUtils.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4734 348d0f76-0448-11de-a6fe-93d51630548a
Added an initial test for genotyping chr20 on ten 1000G bams.
Since tribble needs logging support too, for now setting the logging level and appending the console logger to the root logger, not just to "org.broadinstitute.sting".
Updated IntervalUtilsUnitTest to output to a temp directory and not the SVN controlled testdata directory.
Added refseq tables and dbsnps to validation data in BaseTest.
Now waiting up to two minutes for gather parts to propagate over NFS before attempting to merge the files.
Setting scatter/gather directories relative to the -run directory instead of the current directory that queue is running.
Fixed a bug where escaping test expressions didn't handle delimiters at the beginning or end of the String.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4717 348d0f76-0448-11de-a6fe-93d51630548a
rather than a UserException when an the input argument is specified without
an argument value.
The magnitude of code required to fix this points to a need to give the
command-line argument system a good spring cleaning.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4714 348d0f76-0448-11de-a6fe-93d51630548a
Updated the package of ValidationGenotyper to match the file location.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4710 348d0f76-0448-11de-a6fe-93d51630548a
When a QGraph is empty displaying a warning instead of crashing with an JGraph internal assertion error.
Cleaned up code using the Log4J root logger and explicitly talking to a logger for Sting.
When integration tests are run detecting that the logger has already been setup so that messages aren't logged twice.
Updated from Ivy 2.2.0-rc1 to 2.2.0.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4707 348d0f76-0448-11de-a6fe-93d51630548a
of a sequence dictionary and related info. This will hopefully eliminate the cases in
which the refseq track depends a sequence dictionary / contig parser that hasn't been
specified.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4700 348d0f76-0448-11de-a6fe-93d51630548a
- Number of insertions
- Number of deletions
- Length distribution for indels.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4694 348d0f76-0448-11de-a6fe-93d51630548a
Added a @Hidden experimental argument -validate to VariantEval that allows external JEXL assertions that must evaluate to true will throw an exception.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4692 348d0f76-0448-11de-a6fe-93d51630548a
dependent on the contents of the integrationtest directory. Will figure
out how to better manage the integrationtest directory at some point in
the future.
- Up the max heap size for tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4691 348d0f76-0448-11de-a6fe-93d51630548a
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