kshakir 92045ecaa6 Finally figured out what data in the LSF C API call lsb_readjobinfo is causing JNA to SIGSEGV with a strlen error: ... - 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		2011-03-07 04:29:06 +00:00
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qscript	Due to a problem in the way that dynamic type selection works, I've added an explicit (temporary) ability to restrict VE to specific variant types (SNPs, INDELs, etc), so that calculations will work when a site has a SNP in dbSNP but is called as an indel, causing the SNP site to mysteriously disappear from the comp track, a huge problem for validation report. VEU updated to allow both dynamic type (old) and just returning everything in the track.	2011-03-06 19:31:12 +00:00
src/org/broadinstitute/sting	Finally figured out what data in the LSF C API call lsb_readjobinfo is causing JNA to SIGSEGV with a strlen error:	2011-03-07 04:29:06 +00:00
test/org/broadinstitute/sting/queue	While generating YAML now warning and skipping TSV rows that don't have all values.	2011-02-25 20:50:03 +00:00