GATK classes accessing package protected htsjdk classes changed to new package names.
POMs updated to support merging of sam/tribble/variant -> htsjdk and changes to picard artifact.
RodSystemValidation outputs changed due to variant codec packages changes, requiring test md5 updates.
Second of four commits for picard/htsjdk package rename.
The JNI treats shared memory as critical memory and doesn't allow any
parallel reads or writes to it until the native code finishes. This is
not a problem *per se* it is the right thing to do, but we need to
enable **-nct** when running the haplotype caller and with it have
multiple native PairHMM running for each map call.
Move to a copy based memory sharing where the JNI simply copies the
memory over to C++ and then has no blocked critical memory when running,
allowing -nct to work.
This version is slightly (almost unnoticeably) slower with -nct 1, but
scales better with -nct 2-4 (we haven't tested anything beyond that
because we know the GATK falls apart with higher levels of parallelism
* Make VECTOR_LOGLESS_CACHING the default implementation for PairHMM.
* Changed version number in pom.xml under public/VectorPairHMM
* VectorPairHMM can now be compiled using gcc 4.8.x
* Modified define-* to get rid of gcc warnings for extra tokens after #undefs
* Added a Linux kernel version check for AVX - gcc's __builtin_cpu_supports function does not check whether the kernel supports AVX or not.
* Updated PairHMM profiling code to update and print numbers only in single-thread mode
* Edited README.md, pom.xml and Makefile for users to pass path to gcc 4.8.x if necessary
* Moved all cpuid inline assembly to single function Changed info message to clog from cinfo
* Modified version in pom.xml in VectorPairHMM from 3.1 to 3.2
* Deleted some unnecessary code
* Modified C++ sandbox to print per interval timing
New properties to disable regenerating example resources artifact when each parallel test runs under packagetest.
Moved collection of packagetest parameters from shell scripts into maven profiles.
Fixed necessity of test-utils jar by removing incorrect dependenciesToScan element during packagetests.
When building picard libraries, run clean first.
Fixed tools jar dependency in picard pom.
Integration tests properly use the ant-bridge.sh test.debug.port variable, like unit tests.
Khalid Shakir
Karthik Gururaj
David Roazen