################################################################################
##
## Copyright (c) 2007-2011 Illumina, Inc.
##
## This software is covered by the "Illumina Genome Analyzer Software
## License Agreement" and the "Illumina Source Code License Agreement",
## and certain third party copyright/licenses, and any user of this
## source file is bound by the terms therein (see accompanying files
## Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
## Illumina_Source_Code_License_Agreement.pdf and third party
## copyright/license notices).
##
## This file is part of the Consensus Assessment of Sequence And VAriation
## (CASAVA) software package.
##
## file GenomeSize.mk
##
## brief Partial makefile to build the genome file for a single lane.
##
## Detailed description comes here.
##
## author Come Raczy
##
################################################################################

# one read is fine. only splice sites are squashed per read
read := $(word 1, $($(dataset)_READS))

ifeq (,$($(dataset)_ELAND_GENOME_SQUASHED_R$(read)))
$(error GenomeSize.mk must be included after SquashGenome.mk is processed)
endif

# $(dataset)_ELAND_GENOME_SQUASHED must be protected for eland_rna to be able to
# fiddle with it

.PRECIOUS: \
$($(dataset)_DESTINATION_PREFIX)$(GENOMESIZE_SUFFIX)

$($(dataset)_DESTINATION_PREFIX)$(GENOMESIZE_SUFFIX): dataset:=$(dataset)
$($(dataset)_DESTINATION_PREFIX)$(GENOMESIZE_SUFFIX): squashedGenome := $($(dataset)_ELAND_GENOME_SQUASHED_R$(read))
$($(dataset)_DESTINATION_PREFIX)$(GENOMESIZE_SUFFIX): \
  $($(dataset)_DESTINATION)/.sentinel $($(dataset)_ELAND_GENOME_SQUASHED_R$(read))
	$(SG) $(dir $(squashedGenome)) > $(SAFEPIPETARGET)