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--- config/amos.m4	2018-09-11 13:23:14.478444129 +0200
+++ config/amos.m4	2018-09-11 13:36:36.697612245 +0200
@@ -695,15 +695,15 @@
 else
 	jellyfish_unspecified=no
 fi
-if ! test -f "$jellyfish_dir/jellyfish/mer_counting.hpp"; then
+if ! test -f "$jellyfish_dir/jellyfish1/mer_counting.hpp"; then
 	if test $jellyfish_unspecified = no; then
-		AC_MSG_ERROR([Could not find the file "$jellyfish_dir/jellyfish/compacted_hash.hpp"])
+		AC_MSG_ERROR([Could not find the file "$jellyfish_dir/jellyfish1/compacted_hash.hpp"])
 	fi
 	JELLYFISH_LDADD=
 	JELLYFISH_CPPFLAGS=
 	AC_MSG_RESULT([not found])
 else
-	JELLYFISH_LDADD="-ljellyfish -lpthread"
+	JELLYFISH_LDADD="-ljellyfish-1.1 -lpthread"
 	JELLYFISH_CPPFLAGS="-I $jellyfish_dir"
 	AC_DEFINE([WITH_JELLYFISH], [1], [Define to 1 if using Jellyfish])
 	cppflags_save="$CPPFLAGS"
@@ -715,7 +715,7 @@
 	AC_LANG_PUSH([C++])
 	AC_LINK_IFELSE([
 		AC_LANG_PROGRAM([
-#include <jellyfish/mer_counting.hpp>
+#include <jellyfish1/mer_counting.hpp>
 #include <string>
 	], [
 std::string s;
--- src/Align/kmer-cov-plot.cc	2018-09-11 13:23:15.079443556 +0200
+++ src/Align/kmer-cov-plot.cc	2018-09-11 13:36:36.831612096 +0200
@@ -388,8 +388,8 @@
 
 #ifdef WITH_JELLYFISH
 
-#include <jellyfish/compacted_hash.hpp>
-#include <jellyfish/mer_counting.hpp>
+#include <jellyfish1/compacted_hash.hpp>
+#include <jellyfish1/mer_counting.hpp>
 
 // Assert that jellyfish is using the expected kmer representation
 static void jellyfish_check()