Merge branch 'release/v2.2.9'

gmarcais · Mar 7, 2018 · 8bd8e23 · 8bd8e23
2 parents 0adb7ea + 5e1f9b5
commit 8bd8e23
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Showing 3 changed files with 33 additions and 8 deletions.
diff --git a/configure.ac b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([jellyfish], [2.2.8], [gmarcais@umd.edu])
+AC_INIT([jellyfish], [2.2.9], [gmarcais@umd.edu])
 AC_CANONICAL_HOST
 AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE([subdir-objects foreign parallel-tests color-tests])

diff --git a/jellyfish/fastq2sam.cc b/jellyfish/fastq2sam.cc
@@ -25,7 +25,7 @@ int main(int argc, char* argv[]) {
     //    os << "@PG\tID:fastq2sam\tPN:fastq2sam\n";
 
     std::string name, seq, quals;
-    char c = is.get();
+    int c = is.get();
     while(c == '@') {
       std::getline(is, name);
       std::getline(is, seq);

diff --git a/m4/m4-ax_ext.m4 b/m4/m4-ax_ext.m4
@@ -1,5 +1,5 @@
 # ===========================================================================
-#          http://www.gnu.org/software/autoconf-archive/ax_ext.html
+#          https://www.gnu.org/software/autoconf-archive/ax_ext.html
 # ===========================================================================
 #
 # SYNOPSIS
@@ -31,19 +31,20 @@
 #     HAVE_SHA / HAVE_AES / HAVE_AVX / HAVE_FMA3 / HAVE_FMA4 / HAVE_XOP
 #     HAVE_AVX2 / HAVE_AVX512_F / HAVE_AVX512_CD / HAVE_AVX512_PF
 #     HAVE_AVX512_ER / HAVE_AVX512_VL / HAVE_AVX512_BW / HAVE_AVX512_DQ
-#     HAVE_AVX512_IFMA / HAVE_AVX512_VBMI
+#     HAVE_AVX512_IFMA / HAVE_AVX512_VBMI / HAVE_ALTIVEC / HAVE_VSX
 #
 # LICENSE
 #
 #   Copyright (c) 2007 Christophe Tournayre <turn3r@users.sourceforge.net>
 #   Copyright (c) 2013,2015 Michael Petch <mpetch@capp-sysware.com>
+#   Copyright (c) 2017 Rafael de Lucena Valle <rafaeldelucena@gmail.com>
 #
 #   Copying and distribution of this file, with or without modification, are
 #   permitted in any medium without royalty provided the copyright notice
 #   and this notice are preserved. This file is offered as-is, without any
 #   warranty.
 
-#serial 15
+#serial 17
 
 AC_DEFUN([AX_EXT],
 [
@@ -55,19 +56,43 @@ AC_DEFUN([AX_EXT],
 
   case $host_cpu in
     powerpc*)
-      AC_CACHE_CHECK([whether altivec is supported], [ax_cv_have_altivec_ext],
+      AC_CACHE_CHECK([whether altivec is supported for old distros], [ax_cv_have_altivec_old_ext],
           [
             if test `/usr/sbin/sysctl -a 2>/dev/null| grep -c hw.optional.altivec` != 0; then
                 if test `/usr/sbin/sysctl -n hw.optional.altivec` = 1; then
-                  ax_cv_have_altivec_ext=yes
+                  ax_cv_have_altivec_old_ext=yes
                 fi
             fi
           ])
 
-          if test "$ax_cv_have_altivec_ext" = yes; then
+          if test "$ax_cv_have_altivec_old_ext" = yes; then
             AC_DEFINE(HAVE_ALTIVEC,,[Support Altivec instructions])
             AX_CHECK_COMPILE_FLAG(-faltivec, SIMD_FLAGS="$SIMD_FLAGS -faltivec", [])
           fi
+
+      AC_CACHE_CHECK([whether altivec is supported], [ax_cv_have_altivec_ext],
+          [
+            if test `LD_SHOW_AUXV=1 /bin/true 2>/dev/null|grep -c altivec` != 0; then
+              ax_cv_have_altivec_ext=yes
+            fi
+          ])
+
+          if test "$ax_cv_have_altivec_ext" = yes; then
+            AC_DEFINE(HAVE_ALTIVEC,,[Support Altivec instructions])
+            AX_CHECK_COMPILE_FLAG(-maltivec, SIMD_FLAGS="$SIMD_FLAGS -maltivec", [])
+          fi
+
+      AC_CACHE_CHECK([whether vsx is supported], [ax_cv_have_vsx_ext],
+          [
+            if test `LD_SHOW_AUXV=1 /bin/true 2>/dev/null|grep -c vsx` != 0; then
+                ax_cv_have_vsx_ext=yes
+            fi
+          ])
+
+          if test "$ax_cv_have_vsx_ext" = yes; then
+            AC_DEFINE(HAVE_VSX,,[Support VSX instructions])
+            AX_CHECK_COMPILE_FLAG(-mvsx, SIMD_FLAGS="$SIMD_FLAGS -mvsx", [])
+          fi
     ;;
 
     i[[3456]]86*|x86_64*|amd64*)