projects/radseq/make/bwa.mk

   1 FQPATH := out
   2
   3 ALNARG:=aln -l 17 -q 10
   4 SAMPEARG:=sampe -a 800
   5 REF:=cat62
   6
   7 FQEXTS:=.fq.gz
   8 BWACMD:=bwa
   9
  10 FQS1 = $(foreach d,$(FQPATH),$(wildcard $(addprefix $(d)/*,.1$(FQEXTS))))
  11 FQS2 = $(foreach d,$(FQPATH),$(wildcard $(addprefix $(d)/*,.2$(FQEXTS))))
  12 ALLITEMS := $(FQS1:.1.fq.gz=.sam)
  13
  14 .PHONY: all clean
  15
  16 all: $(ALLITEMS)
  17         @echo all [$@] [$<] [${MAKEOPTS}]
  18
  19 %.sai: %.fq.gz
  20         @echo "1 $(BWACMD) $(ALNARG) $(REF) $< > $@ 2>$@.log"
  21         $(BWACMD) $(ALNARG) $(REF) $< > $@ 2>$@.log
  22
  23 %.sam: %.1.sai %.2.sai
  24         @echo "2 $(BWACMD) $(SAMPEARG) $(REF) $(@:.sam=).1.sai $(@:.sam=).2.sai $(@:.sam=).1.fq.gz $(@:.sam=).2.fq.gz 2>$@.log |gzip -9c >$@.gz"
  25         $(BWACMD) $(SAMPEARG) $(REF) $(@:.sam=).1.sai $(@:.sam=).2.sai $(@:.sam=).1.fq.gz $(@:.sam=).2.fq.gz 2>$@.log |gzip -9c >$@.gz
  26         touch $@
  27
  28