From 5e5541df9e1658965d29f8837d5e5f7a8329f414 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Mon, 18 Dec 2023 15:10:51 -0800
Subject: [PATCH] configure.ac and Makefile.am: fixing inconsistencies in the
 short optimizations cli parameters for configure

---
 Makefile.am  | 4 ++--
 configure.ac | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index d81c8dc..caa4fae 100644
--- a/Makefile.am
+++ b/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
diff --git a/configure.ac b/configure.ac
index 3e477d4..860725e 100644
--- a/configure.ac
+++ b/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([