################################################################################
##
## 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 Alignment.mk
##
## brief Rules for alignment validation 
##
## author Roman Petrovski
##
################################################################################

ifeq (,$(UNALIGNED_ROOT))
  $(error "UNALIGNED_ROOT is required for Alignment to run")
endif

ifeq (,$(ALIGNMENT_CONFIG_TXT))
  $(error "ALIGNMENT_CONFIG_TXT is required for Alignment to run")
endif

ifneq (,$(ALIGNMENT_CONFIG_MK))
include $(ALIGNMENT_CONFIG_MK)
endif


Alignment.configured: SHELL=$(SHELL_LOG)
Alignment.configured:
	$(CMDPREFIX) \
	$(CONFIGURE_ALIGNMENT) $(ALIGNMENT_CONFIG_TXT) \
	  --EXPT_DIR=$(UNALIGNED_ROOT) \
	  --OUT_DIR=$(CURDIR)/Aligned \
	  --make \
	  --skip-variable-metadata \
	  $(CONFIGURE_ALIGNMENT_PARAMS) \
	$(AND) $(TOUCH) $@ \
	$(AND) ($(LOG_INFO) 'Configure alignment [OK]')

# make sure cat is used instead of copy for config.txt to get the default permission
# bits as opposite to inheriting the source ones which are often read-only
Aligned/$(notdir $(ALIGNMENT_CONFIG_TXT)): Alignment.configured Aligned/.sentinel
	$(CAT) $(ALIGNMENT_CONFIG_TXT) >$(SAFEPIPETARGET)

# make sure cat is used instead of copy for config.txt to get the default permission
# bits as opposite to inheriting the source ones which are often read-only
Aligned/$(notdir $(ALIGNMENT_CONFIG_MK)): Alignment.configured Aligned/.sentinel
	$(CAT) $(ALIGNMENT_CONFIG_MK) >$(SAFEPIPETARGET)

# make sure the submake uses our MAKEFILES_DIR regardless of what it has defined internally.
# this is useful when chaning the top level makefile during debugging
Alignment.finished: SHELL=$(SHELL_LOG_OLD)
Alignment.finished: Alignment.configured Aligned/$(notdir $(ALIGNMENT_CONFIG_TXT)) Aligned/$(notdir $(ALIGNMENT_CONFIG_MK))
	$(MAKE) -C Aligned POST_RUN_COMMAND:='$(TOUCH) ../$@' MAKEFILES_DIR:=$(MAKEFILES_DIR) $(EXECUTE_ALIGNMENT_PARAMS)