################################################################################
##
## 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 ValidateAlignment.mk
##
## brief Rules that perform comparison of alignment data 
##
## author Roman Petrovski
##
################################################################################

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

Alignment.list.ori: ALIGNED_ROOT:=$(ALIGNED_ROOT)
Alignment.list.ori: Alignment.finished $(TEMP_DIR)/.sentinel
	( $(CD) $(ALIGNED_ROOT) && $(FIND) ./ -type f  \
	    $(foreach ign, $(ALIGNMENT_VALIDATE_IGNORE_FILES), -not -name '$(ign)') \
	    $(foreach nos, $(ALIGNMENT_VALIDATE_NOSIZE_FILES), -not -name '$(nos)') -printf '%p %s\n' \
	    $(foreach nos, $(ALIGNMENT_VALIDATE_NOSIZE_FILES), -name '$(nos)') -printf '%p\n') \
	    | $(SORT) | $(INTERSPERSE) >$(SAFEPIPETARGET)

Alignment.list.local: Alignment.finished $(TEMP_DIR)/.sentinel
	( $(CD) Aligned && $(FIND) ./ -type f \
	    $(foreach ign, $(ALIGNMENT_VALIDATE_IGNORE_FILES), -not -name '$(ign)') \
	    $(foreach nos, $(ALIGNMENT_VALIDATE_NOSIZE_FILES), -not -name '$(nos)') -printf '%p %s\n' \
	    $(foreach nos, $(ALIGNMENT_VALIDATE_NOSIZE_FILES), -name '$(nos)') -printf '%p\n') \
	    | $(SORT) | $(INTERSPERSE) >$(SAFEPIPETARGET)

Alignment.diff: ALIGNED_ROOT:=$(ALIGNED_ROOT)
Alignment.diff: Alignment.list.local Alignment.list.ori
	( $(DIFF) Alignment.list.local Alignment.list.ori || ([[ 1 == $$? ]] && $(EXIT) 0)) \
	  |( $(GREP) -E '^<|^>' \
	    |$(GREP) -vE '^<\s*$$|^>\s*$$' || ([[ 1 == $$? ]] && $(EXIT) 0) ) \
	  |$(SED) 's/^<\s\(.*$$\)/< $(subst /,\/,$(CURDIR))\/Aligned\/\1/' \
	  |$(SED) 's/^>\s\(.*$$\)/> $(subst /,\/,$(ALIGNED_ROOT))\/\1/' \
	>$(SAFEPIPETARGET)