################################################################################
##
## 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
##
################################################################################

ifeq (,$($($(dataset)_SPLICE_SHORTNAME_R$(read))_squashed_rule_defined))
$($(dataset)_SPLICE_SHORTNAME_R$(read))_squashed_rule_defined:=yes

.SECONDARY: $(AUTOSQUASH_SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/.finished

$(AUTOSQUASH_SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/.finished : dataset := $(dataset)
$(AUTOSQUASH_SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/.finished : read := $(read)
$(AUTOSQUASH_SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/.finished : \
  $(SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/$(RNASS_AUTO) \
  $(AUTOSQUASH_SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/.sentinel
	$(RM) $(foreach ext, $(SQUASHED_GENOME_EXTENSIONS), $(dir $@)*$(ext)); \
    $(CMDPREFIX) $(SG) \
      --chrom-name-source=fileName \
      --validate-names=off \
      --allow-many-contigs=yes \
      $($(dataset)_SQUASH_GENOME_PARAMS) \
      $(dir $@) $(SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/$(RNASS_AUTO) \
    $(AND) $(TOUCH) $(UNPROTECTED_TARGET)


annotation_file_name:=$(notdir $($(dataset)_ELAND_RNA_GENOME_ANNOTATION))

$(SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/$(RNASS_AUTO): dataset:=$(dataset)
$(SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/$(RNASS_AUTO): read:=$(read)

ifeq ($($(dataset)_FLAT_TXT_GZ_SUFFIX),$(annotation_file_name:%$($(dataset)_FLAT_TXT_GZ_SUFFIX)=$($(dataset)_FLAT_TXT_GZ_SUFFIX)))

.SECONDARY: $(SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/$(RNASS_AUTO) 

$(SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/$(RNASS_AUTO): \
  $($(dataset)_ELAND_RNA_GENOME_ANNOTATION) \
  $($(dataset)_ELAND_GENOME_ORIG) \
  $(SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/.sentinel
	$(CMDPREFIX) $(GUNZIP) -c $< | $(SPLCSTS) \
	--leftFlank=$$(( $($(dataset)_READ_LENGTH$(read)) - 1 )) \
	--refSequences='$($(dataset)_ELAND_GENOME)' \
	--maskRefSeqFiles='$($(dataset)_ELAND_GENOME_MASK)' \
	--chromNameSource='$($(dataset)_CHROM_NAME_SOURCE)' \
	$($(dataset)_SPLCSTS_PARAMS) \
	>$(SAFEPIPETARGET)
endif

ifeq ($($(dataset)_GENE_MD_GZ_SUFFIX),$(annotation_file_name:%$($(dataset)_GENE_MD_GZ_SUFFIX)=$($(dataset)_GENE_MD_GZ_SUFFIX)))

.SECONDARY: $(SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/$(RNASS_AUTO) 

$(SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/$(RNASS_AUTO): \
  $($(dataset)_ELAND_RNA_GENOME_ANNOTATION) \
  $($(dataset)_ELAND_GENOME_ORIG) \
  $(SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/.sentinel
	$(CMDPREFIX) $(GUNZIP) -c $< \
	|$(SEQGENEMD2REFFLAT) \
	  --input-file - \
	  --group-label '$($(dataset)_ELAND_RNA_GENE_MD_GROUP_LABEL)' \
	  $($(dataset)_SEQGENEMD2REFFLAT_PARAMS) \
	|$(SPLCSTS) \
	  --leftFlank=$$(( $($(dataset)_READ_LENGTH$(read)) - 1 )) \
	  --refSequences='$($(dataset)_ELAND_GENOME)' \
	  --maskRefSeqFiles='$($(dataset)_ELAND_GENOME_MASK)' \
	  --chromNameSource='$($(dataset)_CHROM_NAME_SOURCE)' \
	  $($(dataset)_SPLCSTS_PARAMS) \
	>$(SAFEPIPETARGET)
endif

endif

$(dataset)_ELAND_GENOME_SQUASHED_R$(read):=$(AUTOSQUASH_SPLICE_DIR)/$($(dataset)_SPLICE_SHORTNAME_R$(read))/.finished