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set(QUASI_INDEX_CMD_PH ${CMAKE_BINARY_DIR}/rapmap quasiindex --perfectHash -t transcripts.fasta -i sample_quasi_index_ph)
execute_process(COMMAND ${QUASI_INDEX_CMD_PH}
WORKING_DIRECTORY ${TOPLEVEL_DIR}/sample_data
RESULT_VARIABLE QUASI_INDEX_RESULT_PH
)
if (QUASI_INDEX_RESULT_PH)
message(FATAL_ERROR "Error running ${QUASI_INDEX_COMMAND_PH}")
endif()
set(MAP_COMMAND_PH ${CMAKE_BINARY_DIR}/rapmap quasimap -t 2 -i sample_quasi_index_ph -1 reads_1.fastq -2 reads_2.fastq -o sample_quasi_map_ph.sam)
execute_process(COMMAND ${MAP_COMMAND_PH}
WORKING_DIRECTORY ${TOPLEVEL_DIR}/sample_data
RESULT_VARIABLE QUASI_MAP_RESULT_PH
)
if (QUASI_MAP_RESULT_PH)
message(FATAL_ERROR "Error running ${QUASI_MAP_RESULT_PH}")
endif()
if (EXISTS ${TOPLEVEL_DIR}/sample_data/sample_quasi_map_ph.sam)
message("RapMap (quasi, perfect-hash) ran successfully")
else()
message(FATAL_ERROR "RapMap (quasi-index & map) failed to produce output")
endif()
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