diff --git a/bin/abyss-pe b/bin/abyss-pe index 74bd5b4ea..f818eff3c 100755 --- a/bin/abyss-pe +++ b/bin/abyss-pe @@ -562,9 +562,17 @@ endif # Resolve repeats with short reads +ifdef B %-1-rr.fa %-1-rr.$g: %-1.fa %-1.$g $(gtime) abyss-rresolver-short $v -b$B -j$j -k$k $(RRESOLVER_OPTIONS) \ -h $*-1-rr --$g -c $*-1-rr.fa -g $*-1-rr.$g $^ $(in) $(se) +else +%-1-rr.fa: %-1.fa + ln -s $< $@ + +%-1-rr.$g: %-1.$g + ln -s $< $@ +endif # Remove shim contigs