################################################################################
##
## 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 SingleAux.mk
##
## brief Partial makefile to pick the best alignments.
##
## author Roman Petrovski
##
################################################################################
ifeq (,$(currentSetList))
$(error $(dataset): empty list of sets)
endif

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

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

kagu_target:=$($(dataset)_DESTINATION_PREFIX)_R$(read)_$(currentSetName)$(EXPORT_SUFFIX)

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

$(dataset)_kagu_params:= $($(dataset)_KAGU_PARAMS)
ifeq (contigName,$($(dataset)_CHROM_NAME_SOURCE))
  $(dataset)_kagu_params += --ucn
endif


.PRECIOUS: $(kagu_target)
$(kagu_target): ELAND_RESULT_EXTENDED := $(ELAND_RESULT_EXTENDED)
$(kagu_target): EXPORT_SUFFIX := $(EXPORT_SUFFIX)
$(kagu_target): GENOMESIZE_SUFFIX := $(GENOMESIZE_SUFFIX)
$(kagu_target): read := $(read)
$(kagu_target): currentSetName :=  $(currentSetName)
$(kagu_target): currentSet :=  $(currentSet)
$(kagu_target): \
  $(kagu_eland_extended_prereqs)\
  $($(dataset)_DESTINATION_PREFIX)$(GENOMESIZE_SUFFIX)
	$(CMDPREFIX) $(PICK_BEST_ALIGNMENT) \
	  --ie1 "$($(dataset)_TEMP_PREFIX)_R$(read)_$(currentSetName)$(ELAND_RESULT_EXTENDED)" \
	  --sl1 "$($(dataset)_ELAND_SEED_LENGTH$(read))" \
	  --ub1 "$($(dataset)_USE_BASES$(read))" \
	  --oe1 "$($(dataset)_DESTINATION_PREFIX)_R$(read)_$(currentSetName)$(EXPORT_SUFFIX).tmp" \
	  $(foreach fastq_set, $(currentSet), \
	      --if1 "$(EXPT_DIR)/$($(dataset)_SOURCE_PREFIX)_R$(read)_$(fastq_set).fastq.gz") \
	  --irs "$($(dataset)_DESTINATION_PREFIX)$(GENOMESIZE_SUFFIX)" \
	  $($(dataset)_kagu_params) 1>&2 \
	$(AND) $(MV) "$($(dataset)_DESTINATION_PREFIX)_R$(read)_$(currentSetName)$(EXPORT_SUFFIX).tmp.gz" \
	               "$($(dataset)_DESTINATION_PREFIX)_R$(read)_$(currentSetName)$(EXPORT_SUFFIX)"