################################################################################
##
## 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 SquashGenome.mk
##
## brief Partial makefile to squash the genome file for a single lane.
##
## Detailed description comes here.
##
## author Roman Petrovski
##
################################################################################

#  $($(dataset)_ELAND_RNA_GENOME_CONTAM)/$($(dataset)_ELAND_RNA_GENOME_CONTAM_MASK) \

# Warning! there must be no dependency on reference fasta files. If such dependency
# exists, theny any update to the reference sequences (which are usually shared
# and sometimes updated in an organization), will trigger cascade rebuild of everything

# Note: the dataset CONTAM_SHORTNAMEs are made unique for a combination of reference
# and squash params. This is done to avoid repeated squashing of exactly the same 
# reference for each dataset 

ifeq (,$($($(dataset)_CONTAM_SHORTNAME)_rule_defined))
$($(dataset)_CONTAM_SHORTNAME)_rule_defined:=yes

.SECONDARY: $(AUTOSQUASH_CONTAM_DIR)/$($(dataset)_CONTAM_SHORTNAME)/.finished

$(AUTOSQUASH_CONTAM_DIR)/$($(dataset)_CONTAM_SHORTNAME)/.finished : dataset := $(dataset)
$(AUTOSQUASH_CONTAM_DIR)/$($(dataset)_CONTAM_SHORTNAME)/.finished : \
  $(AUTOSQUASH_CONTAM_DIR)/$($(dataset)_CONTAM_SHORTNAME)/.sentinel
	$(RM) $(foreach ext, $(SQUASHED_GENOME_EXTENSIONS), $(dir $@)*$(ext)); \
    $(CMDPREFIX) $(SG) \
      --chrom-name-source=fileName \
      --validate-names=off \
      --allow-many-contigs=no \
      $($(dataset)_SQUASH_GENOME_PARAMS) \
      $(dir $@) $($(dataset)_ELAND_RNA_GENOME_CONTAM)/$($(dataset)_ELAND_RNA_GENOME_CONTAM_MASK) \
    $(AND) $(TOUCH) $(UNPROTECTED_TARGET)
endif

$(dataset)_ELAND_GENOME_SQUASHED_R$(word 1, $($(dataset)_READS)):=$(AUTOSQUASH_CONTAM_DIR)/$($(dataset)_CONTAM_SHORTNAME)/.finished
$(dataset)_ELAND_GENOME_SQUASHED_R$(word 2, $($(dataset)_READS)):=$(AUTOSQUASH_CONTAM_DIR)/$($(dataset)_CONTAM_SHORTNAME)/.finished