masurca: build on arm. (#12416)

* remove -minline-all-stringops when target is arm.
* change int3 to raise(SIGTRAP) when target is arm.

var/spack/repos/builtin/packages/masurca/arm.patch

@@ -0,0 +1,46 @@
+diff -ru spack-src/global-1/PacBio/include/charb.hpp spack-src.new/global-1/PacBio/include/charb.hpp
+--- spack-src/global-1/PacBio/include/charb.hpp 2018-01-23 05:03:06.000000000 +0900
++++ spack-src.new/global-1/PacBio/include/charb.hpp     2019-08-14 10:32:47.741826823 +0900
+@@ -25,6 +25,7 @@
+ #include <stdexcept>
+ #include <string>
+ #include <cstring>
++#include <csignal>
+ #include <istream>
+ #include <assert.h>
+
+@@ -186,7 +187,11 @@
+     }
+     cptr      += char_read;
+     if(cptr == b.base_)
++#ifdef __x86_64
+       asm("int3;");
++#else
++      raise(SIGTRAP);
++#endif
+     if(cptr < b.end_ - 1 || *(cptr - 1) == '\n')
+       break;
+     size_t off  = cptr  - b.base_;
+diff -ru spack-src/global-1/SuperReads/include/charb.hpp spack-src.new/global-1/SuperReads/include/charb.hpp
+--- spack-src/global-1/SuperReads/include/charb.hpp     2018-12-15 01:57:56.000000000 +0900
++++ spack-src.new/global-1/SuperReads/include/charb.hpp 2019-08-14 10:34:10.501841240 +0900
+@@ -25,6 +25,7 @@
+ #include <stdexcept>
+ #include <string>
+ #include <cstring>
++#include <csignal>
+ #include <istream>
+ #include <assert.h>
+
+@@ -186,7 +187,11 @@
+     }
+     cptr      += char_read;
+     if(cptr == b.base_)
++#ifdef __x86_64
+       asm("int3;");
++#else
++      raise(SIGTRAP);
++#endif
+     if(cptr < b.end_ - 1 || *(cptr - 1) == '\n')
+       break;
+     size_t off  = cptr  - b.base_;

var/spack/repos/builtin/packages/masurca/package.py

@@ -20,6 +20,15 @@ class Masurca(Package):
     depends_on('perl', type=('build', 'run'))
     depends_on('boost')
     depends_on('zlib')
+    patch('arm.patch', when='target=aarch64')
+
+    def patch(self):
+        if self.spec.satisfies('target=aarch64'):
+            for makefile in 'Makefile.am', 'Makefile.in':
+                m = join_path('global-1', 'prepare', makefile)
+                filter_file('-minline-all-stringops', '', m)
+                m = join_path('global-1', makefile)
+                filter_file('-minline-all-stringops', '', m)
 
     def install(self, spec, prefix):
         installer = Executable('./install.sh')