################################################################################
##
## 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 ElandExtendedAux1.mk
##
## brief Partial makefile to build the eland extended files for a set of tiles.
##
## This partial makefile encapsulates the mechanisms to split each lane into a
## number of subsets of tiles before processing by ELAND. The size of the sets
## is defined as a number of tiles, controlled by ELAND_FASTQ_FILES_PER_PROCESS
## (customisable on the make command line).
##
## The processing is recursive. The end condition is the emptyness of the
## current list of tiles (the variable currentTileList).
##
## author Come Raczy
##
################################################################################

ifeq (,$(currentSetList))
$(error $(lane): empty set list)
endif

currentSetName := $(word 1, $(currentSetList))
currentSet := $($(dataset)_ELAND_SET_$(currentSetName))

ifeq (1,$(words $(currentSetList)))
currentSetList :=
else
currentSetList := $(wordlist 2, $(words $(currentSetList)), $(currentSetList))
endif

r$(read)_eland_extended := $(r$(read)_eland_extended) $($(dataset)_TEMP_PREFIX)_R$(read)_$(currentSetName)$(ELAND_RESULT_EXTENDED)

.SECONDARY: $($(dataset)_TEMP_PREFIX)_R$(read)_$(currentSetName)$(ELAND_RESULT_EXTENDED)

$($(dataset)_TEMP_PREFIX)_R$(read)_$(currentSetName)$(ELAND_RESULT_EXTENDED): dataset := $(dataset)
$($(dataset)_TEMP_PREFIX)_R$(read)_$(currentSetName)$(ELAND_RESULT_EXTENDED): currentSet := $(currentSet)
$($(dataset)_TEMP_PREFIX)_R$(read)_$(currentSetName)$(ELAND_RESULT_EXTENDED): sample := $(sample)
$($(dataset)_TEMP_PREFIX)_R$(read)_$(currentSetName)$(ELAND_RESULT_EXTENDED): barcode := $(barcode)
$($(dataset)_TEMP_PREFIX)_R$(read)_$(currentSetName)$(ELAND_RESULT_EXTENDED): lane := $(lane)
$($(dataset)_TEMP_PREFIX)_R$(read)_$(currentSetName)$(ELAND_RESULT_EXTENDED): read := $(read)
$($(dataset)_TEMP_PREFIX)_R$(read)_$(currentSetName)$(ELAND_RESULT_EXTENDED): $(dataset)_ELAND_GENOME_SQUASHED_R$(read) := $($(dataset)_ELAND_GENOME_SQUASHED_R$(read))
$($(dataset)_TEMP_PREFIX)_R$(read)_$(currentSetName)$(ELAND_RESULT_EXTENDED): $($(dataset)_ELAND_GENOME_SQUASHED_R$(read)) \
    $(foreach fastq, $(currentSet), $(EXPT_DIR)/$($(dataset)_SOURCE_PREFIX)_R$(read)_$(fastq).fastq.gz) \
    $($(dataset)_TEMP_DIR)/.sentinel
	$(CMDPREFIX) $(ELAND_EXEC) \
	  --oligo-length=$($(dataset)_ELAND_SEED_LENGTH$(read)) \
	  --data-format "fastq" \
	  --lane "$(lane)" \
	  --read "$(read)" \
	  --qseq-mask "$($(dataset)_USE_BASES$(read))" \
	  --cluster-sets "$(currentSet)" \
	  --sample "$(sample)" \
	  --barcode "$(barcode)" \
	  --base-calls-dir "$(EXPT_DIR)/$($(dataset)_SOURCE)" \
	  --genome-directory "$(dir $<)" \
	  --output-file "$@.tmp" \
	  --tmp-file-prefix "$@" \
	  --multi$(if $($(dataset)_ELAND_MAX_MATCHES),$($(dataset)_ELAND_MAX_MATCHES:%==%)) \
	  $($(dataset)_SINGLESEED) $($(dataset)_UNGAPPED) $($(dataset)_INCREASED_SENSITIVITY) \
	  $(if $($(dataset)_ELAND_REPEAT), $($(dataset)_ELAND_REPEAT:%=--repeat-file=%)) \
	  $($(dataset)_ELAND_PARAMS) 1>&2 \
	  && $(MV) $@.tmp $@

# Proxy rule. Required for all Temp/ based artifacts that are dependencies of pattern rules
# Otherwise pattern rules get broken when their direct dependencies are listed as .SECONDARY with qmake
$($(dataset)_DESTINATION_PREFIX)_R$(read)_$(currentSetName)$(ELAND_RESULT_EXTENDED).finished: \
  $($(dataset)_DESTINATION)/.sentinel \
  $($(dataset)_TEMP_PREFIX)_R$(read)_$(currentSetName)$(ELAND_RESULT_EXTENDED)
	$(TOUCH) $@