Makefile

all: pdf

PDFS =	BCFv1_qref.pdf \
	BCFv2_qref.pdf \
	CRAMv2.1.pdf \
	CRAMv3.pdf \
	CSIv1.pdf \
	SAMv1.pdf \
	SAMtags.pdf \
	tabix.pdf \
	VCFv4.1.pdf \
	VCFv4.2.pdf \
	VCFv4.3.pdf

pdf: $(PDFS:%=new/%)

%.pdf: new/%.pdf
	cp $^ $@

new/CRAMv2.1.pdf: CRAMv2.1.tex new/CRAMv2.1.ver
new/CRAMv3.pdf: CRAMv3.tex new/CRAMv3.ver
new/SAMv1.pdf: SAMv1.tex new/SAMv1.ver
new/SAMtags.pdf: SAMtags.tex new/SAMtags.ver
new/VCFv4.1.pdf: VCFv4.1.tex new/VCFv4.1.ver
new/VCFv4.2.pdf: VCFv4.2.tex new/VCFv4.2.ver
new/VCFv4.3.pdf: VCFv4.3.tex new/VCFv4.3.ver

PDFLATEX = pdflatex

new/%.pdf: %.tex
	$(PDFLATEX) --output-directory new $<
	while grep -q 'Rerun to get [a-z-]* right' new/$*.log; do $(PDFLATEX) --output-directory new $< || exit; done

new/CRAMv2.1.ver new/CRAMv3.ver: img/CRAMFileFormat2-1-fig001.png img/CRAMFileFormat2-1-fig002.png img/CRAMFileFormat2-1-fig003.png img/CRAMFileFormat2-1-fig004.png img/CRAMFileFormat2-1-fig005.png img/CRAMFileFormat2-1-fig006.png img/CRAMFileFormat2-1-fig007.png

new/VCFv4.1.ver new/VCFv4.2.ver new/VCFv4.3.ver: img/all_orientations-400x296.png img/derivation-400x267.png img/erosion-400x211.png img/inserted_contig-400x247.png img/inserted_sequence-400x189.png img/inversion-400x95.png img/microhomology-400x248.png img/multiple_mates-400x280.png img/phasing-400x259.png img/reciprocal_rearrangement-400x192.png img/telomere-400x251.png

new/%.ver: %.tex
	./genversion.sh $^ > $@


mostlyclean:
	-cd new && rm -f *.aux *.idx *.log *.out *.toc *.ver

clean: mostlyclean
	-cd new && rm -f $(PDFS)
	-rm -rf _site


.PHONY: all pdf mostlyclean clean