################################################################################
##
## 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 eland_extended.mk
##
## brief Top level makefile for the "eland_pair" analysis.
##
## Detailed description comes here.
##
## author Roman Petrovski
##
################################################################################

ifeq (0,$(words $($(dataset)_READS)))
$(error ERROR: Dataset $(dataset): ANALYSIS eland_pair: no read specified)
endif

ifneq (2,$(words $($(dataset)_READS)))
$(warning ***)
$(warning ERROR: Dataset $(dataset): ANALYSIS eland_pair: the number of reads must be 2, actual: $($(dataset)_READS))
$(error ***)
endif

# Get the list of fastq files from the file system
fastqFiles := $(wildcard $(EXPT_DIR)/$($(dataset)_SOURCE_PREFIX)_R$(word 1, $($(dataset)_READS))_*.fastq.gz)
$(dataset)_FASTQ_SETS := $(fastqFiles:$(EXPT_DIR)/$($(dataset)_SOURCE_PREFIX)_R$(word 1, $($(dataset)_READS))_%.fastq.gz=%)

# group the fastq into sets of the requested size
$(dataset)_ELAND_SETS :=
currentFastqSets := $($(dataset)_FASTQ_SETS)
setPrefix := 00
include $(MAKEFILES_DIR)/ElandSets.mk

include $(MAKEFILES_DIR)/SquashGenome.mk
include $(MAKEFILES_DIR)/ElandExtended.mk
include $(MAKEFILES_DIR)/GenomeSize.mk
include $(MAKEFILES_DIR)/ScoreFiles.mk
include $(MAKEFILES_DIR)/ErrorGraphs.mk

include $(MAKEFILES_DIR)/Pair.mk

$($(dataset)_TARGET): \
  $(foreach set, $($(dataset)_ELAND_SETS), \
    $(foreach r, $($(dataset)_READS), $($(dataset)_DESTINATION_PREFIX)_R$(r)_$(set)$(EXPORT_SUFFIX)))
	$(TOUCH) $@ ; echo $^