Initial test to see how Bamboo will respond. More detailed email to follow.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4609 348d0f76-0448-11de-a6fe-93d51630548a
Unrelated change: in the sorted-target mode (when we read sorted target intervals one by on from a file), one can now specify multiple semicolon-separated interval files (all must be sorted). Not hugely useful probably, but makes --targetIntervals always process its values in exactly the same way, so we are consistent (it has been already taking ;-separated args in unsorted mode)
NwayIntervalMergingIterator: reads in multiple sorted GenomeLoc input streams (iterators) and presents them as a single sorted and merged stream
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4602 348d0f76-0448-11de-a6fe-93d51630548a
a) Sites were numerically well behaved now, but another hard fact of life is that the AF iteration is defined in linear Pr space, not in log likelihood space, and the math doesn't work out in log space. So, we need to convert back and forth from lin to log space.
b) As a consequence of a), the code got a major slowdown, and calling the 629 samples was about 15 times slower than before (sic).
c) To solve b), log10 of integers are now cached at init, and numerical approximations are now made. Most importantly, I'm using the approximation that log(exp(a) + exp(b)) ~= max(a,b) which seems almost inconsequential in practical performance but reduces computation time to what it was before. More detailes analyses are forthcoming. This approximation can be refined further on to avoid expensive log-exp conversions if further profiling and analysis deems it necessary.
Also, two other issues were solved:
a) Strand bias computation was actually wrong in the case where the optimal AC was bigger than max(forward reads,reverse reads). Now the code is exactly as buggy as the grid search model (all bugs are equal, but some are more equal than others)
b) Genotype likelihoods are now computed in a better way and if a likelihood < 0 we don't just cap to 0 but do something a bit smarter.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4600 348d0f76-0448-11de-a6fe-93d51630548a
interaction with Tribble. In Tribble, keeping these references in memory until
the shard is flushed means keeping one 512K character buffer per object in
memory. Fixed by purging the reference to the object at the end of the
shard traversal.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4599 348d0f76-0448-11de-a6fe-93d51630548a
of traversal to avoid holding a reference to the microscheduler, which holds a reference to
the engine, which in turn holds a reference to the walker, which itself holds a reference to
all the data aggregated during the course of the traversal.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4594 348d0f76-0448-11de-a6fe-93d51630548a
Updated a call to swapExt to specify the directory.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4586 348d0f76-0448-11de-a6fe-93d51630548a
parsing engine. Hugely lowers our memory footprint in integrationtests, but not yet enough to
run Mark's new parallelized VariantEvalIntegrationTests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4585 348d0f76-0448-11de-a6fe-93d51630548a
- Forcing user to set the temp directory via -Djava.io.tmpdir to avoid filling up /tmp.
- By default deleting job outputs tagged as intermediate.
- Defaulting pipeline to scatter count 1 (no reads deleted).
- Cleaning up temp classes even when scripting fails.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4573 348d0f76-0448-11de-a6fe-93d51630548a
When the cleaner interval scatter count is set to one explicitly setting the intrevals to Nil.
TODO: Need to add an option that lets the user choose from the command line to scatter all contigs or just those in the intervals list. For now can get relatively the same behavior by setting the interval scatter count equal to the number of contigs+1, assuming the random contigs come at the end of the sequence dictionary.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4565 348d0f76-0448-11de-a6fe-93d51630548a
Added a brute force -retry <count> option to Queue for transient errors.
Waiting up to 2 minutes for the LSF logs to appear before trying to display the errors from the logs.
Updates to the local job runner error logging when a job fails.
Refactored QGraph's settings as duplicate code was getting out of control.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4563 348d0f76-0448-11de-a6fe-93d51630548a
hanna
asivache
fromer
depristo
delangel
ebanks
kshakir
kiran
corin
rpoplin