################################################################################
##
## 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 Pair.mk
##
## brief Partial makefile to pick the best pair alignments.
##
## Also used for the custom calibration workflow.
##
## author Come Raczy
##
################################################################################

ifeq (,$(currentSetList))
$(error $(dataset): empty list of sets)
endif

currentSetName := $(word 1, $(currentSetList))
currentSet := $($(dataset)_ELAND_SET_$(currentSetName))

ifeq (1,$(words $(currentSetList)))
currentSetList :=
else
currentSetList := $(wordlist 2, $(words $(currentSetList)), $(currentSetList))
endif


$(dataset)_$(currentSetName)_orphan_aligner_eland_extended_prereqs:=\
  $(foreach r, $($(dataset)_READS), \
      $($(dataset)_DESTINATION_PREFIX)_R$(r)_$(currentSetName)$(ELAND_RESULT_EXTENDED).finished)

# Collecting all OA prereqs of a dataset into one variable creates unnecessary 
# dependencies between orphan aligners and all aligners in dataset. 
# Due to various limitations of qmake (unability to protect variables of pattern rules, 
# improper resolution of pattern rule dependencies that are pater rules themselves, 
# inability to merge explicit and pattern target dependencies), 
# the alternative approaches are:
#  a) Use the '.finished' files.
#  b) combine orphan aligner and kagu recipes into one
$(dataset)_ORPHAN_ALIGNER_ALL_ELAND_EXTENDED_PREREQS += \
  $($(dataset)_$(currentSetName)_orphan_aligner_eland_extended_prereqs)

$(dataset)_PAIR_XML_FILES += $($(dataset)_DESTINATION_PREFIX)_$(currentSetName)$(PAIR_SUFFIX)
$(project)_$(sample)_DATASET_SOURCE_PAIR_XML_FILES += $($(dataset)_PAIR_XML_FILES)