################################################################################
##
## 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_rna.mk
##
## brief Top level makefile for the "eland_rna" analysis.
##
## For RNA, ELAND is used for three different alignments: the genome alignment,
## the alignment to the splice junctions and the alignment to the contaminants.
##
## author Roman Petrovski
##
################################################################################

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


# Complete workflow
# Saving the initial values of the variables controlling ELAND rules
$(dataset)_ELAND_RESULT_EXTENDED_ORIG:=$(ELAND_RESULT_EXTENDED)
$(dataset)_GENOMESIZE_SUFFIX_ORIG:=$(GENOMESIZE_SUFFIX)
$(dataset)_EXPORT_SUFFIX_ORIG:=$(EXPORT_SUFFIX)
# Alignment for the splice junctions
ELAND_RESULT_EXTENDED:=$(ELAND_RESULT_SPLICE)

read := $(word 1, $($(dataset)_READS))
include $(MAKEFILES_DIR)/SquashSplice.mk
ifneq (1,$(words $($(dataset)_READS)))
read := $(word 2, $($(dataset)_READS))
include $(MAKEFILES_DIR)/SquashSplice.mk

endif

include $(MAKEFILES_DIR)/ElandExtended.mk

# Alignment for the contaminants
ifeq (,$($(dataset)_ELAND_RNA_GENOME_CONTAM))
$(error "eland_rna analysis requested, but $(dataset)_ELAND_RNA_GENOME_CONTAM is undefined")
endif

GENOMESIZE_SUFFIX:=$(CONTAM_GENOMESIZE_SUFFIX)
EXPORT_SUFFIX:=$(CONTAM_EXPORT_SUFFIX)
ELAND_RESULT_EXTENDED:=$(ELAND_RESULT_CONTAM)
include $(MAKEFILES_DIR)/SquashContam.mk
include $(MAKEFILES_DIR)/ElandExtended.mk
include $(MAKEFILES_DIR)/GenomeSize.mk
include $(MAKEFILES_DIR)/Single.mk

# Alignment for the genome
GENOMESIZE_SUFFIX:=$($(dataset)_GENOMESIZE_SUFFIX_ORIG)
EXPORT_SUFFIX:=$($(dataset)_EXPORT_SUFFIX_ORIG)
ELAND_RESULT_EXTENDED:=$($(dataset)_ELAND_RESULT_EXTENDED_ORIG)
include $(MAKEFILES_DIR)/SquashGenome.mk
include $(MAKEFILES_DIR)/ElandExtended.mk
include $(MAKEFILES_DIR)/GenomeSize.mk
include $(MAKEFILES_DIR)/Rna.mk
include $(MAKEFILES_DIR)/ScoreFiles.mk
include $(MAKEFILES_DIR)/ErrorGraphs.mk

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