AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch

Replace deprecate NUCMER flag -maxmatch with --maxmatch (from MUMmer 4.0.0rc)
see https://github.com/sanger-pathogens/circlator/issues/121 and https://github.com/mummer4/mummer/issues/49
diff -ru amos-3.1.0.orig/src/Pipeline/minimus2.acf amos-3.1.0/src/Pipeline/minimus2.acf
--- amos-3.1.0.orig/src/Pipeline/minimus2.acf	2011-07-25 01:27:26.000000000 +0200
+++ amos-3.1.0/src/Pipeline/minimus2.acf	2024-03-13 17:03:35.981707768 +0100
@@ -54,7 +54,7 @@
 13: $(BINDIR)/dumpreads $(BANK) -m $(REFCOUNT) > $(QRYSEQ)
 
 ## Getting overlaps 
-20: $(NUCMER) -maxmatch -c $(OVERLAP) $(REFSEQ) $(QRYSEQ) -p $(PREFIX)
+20: $(NUCMER) --maxmatch -c $(OVERLAP) $(REFSEQ) $(QRYSEQ) -p $(PREFIX)
 21: $(SHOWCOORDS) -H -c -l -o -r -I $(MINID) $(ALIGN) | $(BINDIR)/nucmerAnnotate | egrep 'BEGIN|END|CONTAIN|IDENTITY' > $(COORDS) 
 22: $(BINDIR)/nucmer2ovl -ignore $(MAXTRIM) -tab $(COORDS) | $(BINDIR)/sort2 > $(OVLTAB)