GenotypeAndValidate: now annotates the validations with callStatus.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5425 348d0f76-0448-11de-a6fe-93d51630548a
b) Add an experimental annotation to log indel type string inside the INFO field, just for debugging/temp analysis purposes (will consider making it standard if it proves useful).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5424 348d0f76-0448-11de-a6fe-93d51630548a
Added a property to allow generating Queue extensions around an external version of the GATK.
Updated argument order in -help.
Restored the ability to use QScript trait imported annotations in constructors.
Removing line feeds from email password files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5416 348d0f76-0448-11de-a6fe-93d51630548a
Deleting files from intermediate jobs as soon as all the dependent jobs are done.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5413 348d0f76-0448-11de-a6fe-93d51630548a
given an annotated VCF and a BAM file, it genotypes (using the reads in the BAM) each variant in the VCF (for snp or indel) and validates (or not) the 'known' annotation. Outputs a truth table with the PPV and NPV values, and optionally a vcf file with the variants that had enough coverage to be validated. You can optionally provide a minimum depth of coverage and only do the analysis conditional on that. (will write a wiki for this walker, as it might be useful for future validation essays).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5409 348d0f76-0448-11de-a6fe-93d51630548a
- Don't know how I got the wiggle header so utterly wrong. Fixed.
- Q-values now have a static maximum of 2000 so IGV averaging won't make everything look spikey and ugly.
- Changing windows to size 100 for (hopefully) better resolution.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5406 348d0f76-0448-11de-a6fe-93d51630548a
- Basic
- Multiple technology
- Test minIndelCnt parameter
Added also 2 disabled tests:
- Parallelization: issue w/code right now is that if -nt > 1, filter field shows "PASS" instead to ".", cause TBD
- Genotype given alleles mode: code not working yet.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5404 348d0f76-0448-11de-a6fe-93d51630548a
Added an empty wrapper for a GridEngine job runner which is only activated when SGE_ROOT is detected.
Refactored a bit more common code into CommandLineJobRunner / JobRunner / FunctionEdge.
Status for analyisNames now includes the number of functions in state.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5399 348d0f76-0448-11de-a6fe-93d51630548a
GAV: First version of the walker that validates reads from a BAM file based on an annotated VCF with TP/FP annotations.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5396 348d0f76-0448-11de-a6fe-93d51630548a
same shards as the previous sharder, so that I can directly compare filespans
to see where some performance bugs lie.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5395 348d0f76-0448-11de-a6fe-93d51630548a
-disc (--discordance) parameter together with a ROD track will output a VCF with the variants in the ROD track that are not present in the 'variants' VCF. Useful tool to list the variants from hapmap (for example) that weren't called in a dataset.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5392 348d0f76-0448-11de-a6fe-93d51630548a
Model is disabled by default and we're still using the old Dindel model until I'm more confident that new model is a definitive improvement, so right now this is enabled by hidden command line arguments, and it's not to be used yet.
In detail:
a) Several refactorings to share softMax() available to other modules, so its now part of MathUtils.
b) Refactored a couple of read utilities and moved from BAQ to ReadUtils.
c) New PairHMMIndelErrorModel class implementing new likelihood model
d) Several new hidden debug arguments in UAC.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5389 348d0f76-0448-11de-a6fe-93d51630548a
- LSF recycles memory for C arrays, but sets a separate variable setting the size of the array to zero.
- JNA only sees the non-NULL pointer and starts to auto-access it, sometimes causing a SIGSEGV.
- In the short term neutered the jobInfoEnt structure so that this bad array is not autoRead().
QGraph updates:
- Job status is now checked in bulk every 30 seconds instead of one job at a time, even in the middle of dispatching jobs.
- If there is a hiccup (unexpected but not fatal error) during status check then the the error is ignored and status is checked again 30 seconds later.
- Jobs prefer to dispatch depth vs. breadth first.
More refactoring of SG framework separating the reusable code from the implementations.
The DistributedScatterFunction is still a work in progress and is not enabled yet. Still need to think through how Queue handles when a job dies.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5387 348d0f76-0448-11de-a6fe-93d51630548a
Also, created a standard Queue script that calculates a suite of standard indel and SNP assessment results. Will be the basis for a general evaluation Queue script with standardized data files for SNPs and Indels.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5385 348d0f76-0448-11de-a6fe-93d51630548a
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