Run aclocal and autoheader if necessary

Run aclocal (or autoheader) if there are any AX_ (or AH_) macros used,
but not if there are explicit m4_include lines to provide the macros.

Also rewrite @HTSLIB@ on the new config.mk recipe line.

Also take htslib/samtools/bcftools from alongside rather than ../rel.

Author: jmarshall

Makefile

@@ -8,10 +8,10 @@ tar: htslib-$(HTSTAG)$(TAR) bcftools-$(TAG)$(TAR) samtools-$(TAG)$(TAR)
 	./addhtslib $@ $^ $(HTSTAG)
 
 htslib-$(HTSTAG)$(TAR):
-	./mktarball ../rel/htslib $(HTSTAG)
+	./mktarball ../htslib $(HTSTAG)
 
 %-$(TAG)-solo$(TAR):
-	./mktarball ../rel/$* $(TAG) -solo
+	./mktarball ../$* $(TAG) -solo
 
 .PRECIOUS: %-$(TAG)-solo$(TAR)
 

addhtslib

@@ -9,7 +9,7 @@ innertag=$4
 rm -rf $outerprojver
 tar xf $outer
 (cd $outerprojver && tar xf ../$inner &&
- sed -e "/^HTSDIR/s/=.*/= htslib-$innertag/" -i.bak Makefile; rm Makefile.bak)
+ sed -e "/^HTSDIR/s/=.*/= htslib-$innertag/;s,@HTSDIR@#[^#]*#,@HTSDIR@#htslib-$innertag#,g" -i '' Makefile)
 rm -f $dest
 tar cjf $dest $outerprojver
 rm -r $outerprojver

mktarball

@@ -15,8 +15,13 @@ rm -rf $projver
   done
 if test -f $projver/configure.ac
 then
-  (cd $projver && MAKEFLAGS= MAKELEVEL= MAKEOVERRIDES= autoconf --warnings=all)
-  rm -rf $projver/autom4te.cache
+  (cd $projver
+  touch config.mk
+  grep -q AX_ configure.ac && (grep -q m4_include configure.ac || aclocal)
+  grep -q AH_ configure.ac && autoheader
+  MAKEFLAGS= MAKELEVEL= MAKEOVERRIDES= autoconf --warnings=all
+  egrep '^[^#]*[[:<:]]A[A-Z]_[A-Z_]*' configure && exit 1
+  rm -rf autom4te.cache config.mk)
 fi
 rm -f $projver$tarsuffix.tar.bz2
 tar cjf $projver$tarsuffix.tar.bz2 $projver