configure.ac and Makefile.am: fixing inconsistencies in the short opt…

…imizations cli parameters for configure

Makefile.am

@@ -38,8 +38,8 @@ install installdirs: SUBDIRS := $(filter-out src/smithlab_cpp, $(SUBDIRS))
 AM_CPPFLAGS = -I $(top_srcdir)/src/smithlab_cpp -I $(top_srcdir)/src/bamxx
 
 AM_CXXFLAGS = $(OPENMP_CXXFLAGS)
-if ENABLE_VERY_SHORT
-AM_CXXFLAGS += -DENABLE_VERY_SHORT
+if ENABLE_SHORT
+AM_CXXFLAGS += -DENABLE_SHORT
 endif
 
 CXXFLAGS = -O3 # default has optimization on

configure.ac

@@ -60,10 +60,10 @@ dnl making the index. When abismal loads the index, it compares the
 dnl value with a constant so abismalidx and abismal must both be
 dnl compiled this way to work together.
 AC_ARG_ENABLE([short],
-  [AS_HELP_STRING([--enable-very-short],
+  [AS_HELP_STRING([--enable-short],
                   [optimize for very short reads @<:@no@:>@])],
-  [enable_very_short=yes], [enable_very_short=no])
-AM_CONDITIONAL([ENABLE_VERY_SHORT], [test "x$enable_very_short" = "xyes"])
+  [enable_short=yes], [enable_short=no])
+AM_CONDITIONAL([ENABLE_SHORT], [test "x$enable_short" = "xyes"])
 
 
 AC_CONFIG_FILES([