a) Forgot to convert from phred to log-prob when computing gap penalties from recal table.
b) Forgot to uncomment code to correctly deal with hard-clipped bases in a read. But because of this, had to do a short term workaround to at least temporarily return class from hardClipAdaptorSequence to GATKSAMRecord. Otherwise, I get exceptions when casting because somehow some reads in HiSeq get to be SAMRecord (which GATKSAMRecord inherits from) but some reads get to be BAMRecords (which can't be cast into GATKSAMRecord), not sure why.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5771 348d0f76-0448-11de-a6fe-93d51630548a
Minor updates to the FCPTest to match the changes due to using the old indel caller.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5766 348d0f76-0448-11de-a6fe-93d51630548a
to extend from org.broadinstitute.sting.gatk.filters.ReadFilter rather than
directly from net.sf.picard.filter.SamRecordFilter, which allows us to add
an initialize(GATKEngine) method so that filters can do any initialization
they'd like based on CL arguments, SAM headers, etc.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5760 348d0f76-0448-11de-a6fe-93d51630548a
- Added sensitivity and Specificity to the report.
- With the changes in genotype likelihoods, the indel analysis only happens if the BAM file also has an extended event. Not great, but at least it's not broken.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5759 348d0f76-0448-11de-a6fe-93d51630548a
each base both in bytes and as a percentage of the used heap size.
May be a bit buggy at this point; there are a lot of metrics around the Java
heap and I'm not completely sure that the metrics I'm outputting are exactly
the ones that I'm looking for.
Also fixed a documentation bug in my Sizeof class.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5730 348d0f76-0448-11de-a6fe-93d51630548a
checked in immediately following the build breaking code passes integration
tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5727 348d0f76-0448-11de-a6fe-93d51630548a
normal use case, but they cut startup times and memory allocation noise in
the profiler, making my profiling time more productive.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5726 348d0f76-0448-11de-a6fe-93d51630548a
through an option!
set -ndrs if you want the GATK to be really random (non-deterministic). Engine option, available to every walker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5715 348d0f76-0448-11de-a6fe-93d51630548a
temporarily). Unfortunately this does not completely fix the IndelRealigner
exception that Ryan is seeing, but it helps things quite a bit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5710 348d0f76-0448-11de-a6fe-93d51630548a
intervals -- altered the validation methods to not throw an error for
unmapped intervals.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5700 348d0f76-0448-11de-a6fe-93d51630548a
to the same standard as GATK format intervals. Full validation against contig
bounds is now performed for all intervals, regardless of their source. Also
fixed a few tests for validation exclusions that were backwards.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5698 348d0f76-0448-11de-a6fe-93d51630548a
ByteBuffer.allocateDirect() behaves like Java NIO MappedByteBuffers in that
it consumes address space, which counts against our virtual memory allocation;
but cannot be destroyed or otherwise freed. This was definitely contributing
to the LSF failures that I was seeing, but I'm not yet convinced that it's the
sole source of these virtual memory 'leaks'. More tomorrow as the results of
my whole exome tests start to roll in.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5693 348d0f76-0448-11de-a6fe-93d51630548a
delangel
kshakir
carneiro
hanna
rpoplin
ebanks
depristo
droazen
chartl