################################################################################
##
## 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 ScoreFiles.mk
##
## brief Partial makefile to build the score files for a single dataset.
##
## - $(dataset)_PAS_PARAMS: the target-specific variable with additional command-
##   line arguments for produceAlignmentStats
##
## author Come Raczy
##
################################################################################

PAS_PARAMS:=

$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)$(TILES_SUFFIX): tiles:=$($(project)_$(sample)_$(lane)_PADDED_TILES)
$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)$(TILES_SUFFIX): lane:=$(lane)
$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)$(TILES_SUFFIX): $($(dataset)_STATS_DIR)/$(barcode)/.sentinel
	$(CMDPREFIX) $(ECHO) $(foreach tile, $(tiles), s_$(lane)_$(tile)) > $(SAFEPIPETARGET)

$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)%$(RESCORE_XML) \
$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)%$(SCORE_XML): lane:=$(lane)
$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)%$(RESCORE_XML) \
$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)%$(SCORE_XML): sample:=$(sample)
$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)%$(RESCORE_XML) \
$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)%$(SCORE_XML): barcode:=$(barcode)
$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)%$(RESCORE_XML) \
$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)%$(SCORE_XML): dataset:=$(dataset)
$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)%$(RESCORE_XML) \
$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)%$(SCORE_XML): tiles:=$($(project)_$(sample)_$(lane)_TILES)

# Note: The order of input files is very importat for produceAlignmentStats. Files must be sorted by set
# number. Files of the same set number must be ordered by read number.
$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)%$(RESCORE_XML) \
$($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)%$(SCORE_XML): \
  $($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)$(TILES_SUFFIX) \
  $(foreach set, $($(dataset)_ELAND_SETS), $(foreach r, $($(dataset)_READS), $($(dataset)_DESTINATION_PREFIX)_R$(r)_$(set)$(EXPORT_SUFFIX)))
	$(CMDPREFIX) $(PAS) \
	    --sample '$(sample)' \
	    --barcode '$(barcode)' \
	    --output_dir '$($(dataset)_STATS_DIR)/$(barcode)' \
	    --stats_prefix 's_$(lane)_' \
	    -T '$<' \
	    $($(dataset)_PAS_PARAMS) \
	    $(foreach r, $($(dataset)_READS), --read '$(r)') \
	    --export_input $(foreach set, $($(dataset)_ELAND_SETS), $(foreach r, $($(dataset)_READS), $($(dataset)_DESTINATION_PREFIX)_R$(r)_$(set)$(EXPORT_SUFFIX)))

# pre-aggregate each lane to reduce the whole project summary generation command line length in case of high plexity.
$(project)_$(lane)_SCORE_FILES:=$($(project)_$(lane)_SCORE_FILES) $($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)_$(SCORE_XML)
$(project)_$(lane)_RESCORE_FILES:=$($(project)_$(lane)_RESCORE_FILES) $($(dataset)_STATS_DIR)/$(barcode)/s_$(lane)_$(RESCORE_XML)