nvbio_module(bqsr)

addsources(
bam_loader.cu
bam_loader.h
baq.cu
baq.h
#baq-cpu.cu
#baq-cpu.h
bqsr.cu
bqsr_context.h
bqsr_context.cu
bqsr_types.h
cigar.h
cigar.cu
covariates.h
covariates_bit_packing.h
covariates_table.h
covariates_table.cu
covariates.cu
filters.h
filters.cu
reference.cu
reference.h
util.cu
util.h
variants.cu
variants.h
)

cuda_add_executable(bqsr ${bqsr_srcs})
target_link_libraries(bqsr nvbio zlibstatic crcstatic ${SYSTEM_LINK_LIBRARIES})


nvbio_module(bqsr)

addsources(
bam_loader.cu
bam_loader.h
baq.cu
baq.h
#baq-cpu.cu
#baq-cpu.h
bqsr.cu
bqsr_context.h
bqsr_context.cu
bqsr_types.h
cigar.h
cigar.cu
covariates.h
covariates_bit_packing.h
covariates_table.h
covariates_table.cu
covariates.cu
filters.h
filters.cu
reference.cu
reference.h
util.cu
util.h
variants.cu
variants.h
)

cuda_add_executable(bqsr ${bqsr_srcs})
target_link_libraries(bqsr nvbio zlibstatic crcstatic ${gamgee_LIB} ${SYSTEM_LINK_LIBRARIES})
add_dependencies(bqsr gamgee)


Add Boost and Gamgee to the build
Add Boost and Gamgee to the build

Build Boost and Gamgee as external projects, syncing from a local
NVIDIA mirror. Mark bqsr as depending on Gamgee and link the bqsr
binary with the Gamgee library.

Change-Id: Ie5cf47d529832e428309aeebd6c10dd15f3c5b03

[git-p4: depot-paths = "//sw/gpgpu/nvbio/bqsr/": change = 18886560]
