################################################################################
##
## 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 PairAux1.mk
##
## brief Partial makefile to build the pair xml files for a single dataset.
##
## Calls PairAux.mk for each $(dataset)_ELAND_SETS
##
## author Roman Petrovski
##
################################################################################

$(dataset)_ORPHAN_ALIGNER_ALL_ELAND_EXTENDED_PREREQS:=

# Iterative generation of the partial temporary export files
currentSetList := $($(dataset)_ELAND_SETS)
include $(foreach set, $($(dataset)_ELAND_SETS), $(MAKEFILES_DIR)/PairAux.mk)

# make-3.78 is not able to construct the correct list of prerequisites for 
# intermediate and secondary targets. For this reason the multi-target pattern
# must be moved deepen in the makefiles, to a location where all the information
# is available for both the prerequisites and the action.

orphan_aligner_targets:=\
  $(foreach set, $($(dataset)_ELAND_SETS), \
    $(foreach r, $($(dataset)_READS), \
      $($(dataset)_TEMP_PREFIX)_R$(r)_$(set)$(ELAND_RESULT_EXTENDED)$($(dataset)_OA_SUFFIX)))
.SECONDARY: $(orphan_aligner_targets)

orphan_aligner_pattern_targets:=\
  $(foreach r, $($(dataset)_READS), \
      $($(dataset)_TEMP_PREFIX)_R$(r)_%$(ELAND_RESULT_EXTENDED)$($(dataset)_OA_SUFFIX))

# Notice the commented-out dependency on the squashed genome. Since it is a .SECONDARY target,
# it will break the pattern rule with qmake if uncommented. Luckily, we can avoid having it
# in the prerequisites list because the alignment rule for eland_extended.txt files will
# ensure it gets built anyways.
$(orphan_aligner_pattern_targets): \
  $($(dataset)_ORPHAN_ALIGNER_ALL_ELAND_EXTENDED_PREREQS)# $($(dataset)_ELAND_GENOME_SQUASHED_R$(word 1,$($(dataset)_READS)))
	$(CMDPREFIX) $(OA) \
	  $(foreach r, $($(dataset)_READS), $($(dataset)_TEMP_PREFIX)_R$(r)_$*$(ELAND_RESULT_EXTENDED)) \
      $(dir $($(dataset)_ELAND_GENOME_SQUASHED_R$(word 1,$($(dataset)_READS)))) \
      $($(dataset)_OA_SUFFIX).tmp \
	  $($(dataset)_ORPHAN_ALIGNER_PARAMS) \
	$(foreach ifile, \
	  $(foreach r, $($(dataset)_READS), $($(dataset)_TEMP_PREFIX)_R$(r)_$*$(ELAND_RESULT_EXTENDED)), \
      $(AND) $(MV) $(ifile)$($(dataset)_OA_SUFFIX).tmp $(ifile)$($(dataset)_OA_SUFFIX))


kagu_pattern_targets:=\
  $($(dataset)_DESTINATION_PREFIX)_%$(PAIR_SUFFIX) \
  $(foreach r, $($(dataset)_READS), $($(dataset)_DESTINATION_PREFIX)_R$(r)_%$(EXPORT_SUFFIX))

$(dataset)_kagu_oa_suffix := $(if $(call IS_BOOLEAN_TRUE, $($(dataset)_WITH_ORPHAN_ALIGNER)),$($(dataset)_OA_SUFFIX),'')
kagu_eland_extended_pattern_prereqs:=\
  $(foreach r, $($(dataset)_READS), \
      $($(dataset)_TEMP_PREFIX)_R$(r)_%$(ELAND_RESULT_EXTENDED)$($(dataset)_kagu_oa_suffix))


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

# NOTE: dependencies on fastq files require translation between % and fastq sets which is non-trivial
# with qmake. Also, external dependencies tend to cause sudden rebuilds of everything...
.PRECIOUS: $(kagu_pattern_targets)
$(kagu_pattern_targets): \
  $(kagu_eland_extended_pattern_prereqs) \
  $($(dataset)_DESTINATION_PREFIX)$(GENOMESIZE_SUFFIX)
	$(CMDPREFIX) $(PICK_BEST_ALIGNMENT) \
	  $(foreach r, $($(dataset)_READS), \
	    --ie$(r) "$($(dataset)_TEMP_PREFIX)_R$(r)_$*$(ELAND_RESULT_EXTENDED)$($(dataset)_kagu_oa_suffix)" \
	    --sl$(r) "$($(dataset)_ELAND_SEED_LENGTH$(r))" \
	    --ub$(r) "$($(dataset)_USE_BASES$(r))" \
	    --oe$(r) "$($(dataset)_DESTINATION_PREFIX)_R$(r)_$*$(EXPORT_SUFFIX).tmp" \
	    $(foreach fastq_set, $($(dataset)_ELAND_SET_$*), \
	       --if$(r) "$(EXPT_DIR)/$($(dataset)_SOURCE_PREFIX)_R$(r)_$(fastq_set).fastq.gz") \
	  ) \
	  --irs "$($(dataset)_DESTINATION_PREFIX)$(GENOMESIZE_SUFFIX)" \
	  --os $($(dataset)_DESTINATION_PREFIX)_$*$(PAIR_SUFFIX).tmp \
	  $($(dataset)_kagu_params) 1>&2 \
	$(AND) $(MV) $($(dataset)_DESTINATION_PREFIX)_$*$(PAIR_SUFFIX).tmp $($(dataset)_DESTINATION_PREFIX)_$*$(PAIR_SUFFIX) \
	$(foreach r, $($(dataset)_READS), \
	  $(AND) $(MV) "$($(dataset)_DESTINATION_PREFIX)_R$(r)_$*$(EXPORT_SUFFIX).tmp.gz" \
	               "$($(dataset)_DESTINATION_PREFIX)_R$(r)_$*$(EXPORT_SUFFIX)")