Merge branch 'release/v4.0beta'

Makefile.am

@@ -4,12 +4,13 @@
 ACLOCAL_AMFLAGS = -I m4
 
 AM_CPPFLAGS = -Wall -I$(srcdir)/include
-AM_CXXFLAGS = $(EXTRA_CXXFLAGS)
+AM_CXXFLAGS = -std=c++11 $(EXTRA_CXXFLAGS)
 AM_LDFLAGS = -lpthread
 
 # Pre-declare all used variables.
 bin_PROGRAMS =
 bin_SCRIPTS =
+pkglibexec_PROGRAMS =
 noinst_SCRIPTS =
 noinst_HEADERS =
 EXTRA_DIST =
@@ -21,6 +22,9 @@ TESTS =
 TEST_EXTENSIONS =
 BUILT_SOURCES =
 
+# Where to install
+script_libdir = $(pkglibdir)
+
 # Special cleaning rules. Like CLEANFILES and DISTCLEANFILES, but for
 # directories.
 CLEANDIRS =
@@ -82,7 +86,8 @@ noinst_HEADERS += include/mummer/48bit_index.hpp		\
 noinst_HEADERS += include/mummer/dset.hpp		\
                   include/mummer/openmp_qsort.hpp	\
                   include/mt_skip_list/common.hpp	\
-                  include/mt_skip_list/set.hpp
+                  include/mt_skip_list/set.hpp		\
+                  include/mummer/redirect_to_pager.hpp
 
 ###########
 # essaMEM #
@@ -93,9 +98,10 @@ mummer_SOURCES = src/essaMEM/fasta.cpp src/essaMEM/mummer.cpp
 ########
 # tigr #
 ########
-bin_PROGRAMS += mgaps postnuc show-coords show-aligns show-snps	\
-                show-tiling show-diff repeat-match annotate	\
-                combineMUMs delta-filter prepro postpro
+bin_PROGRAMS += show-coords show-aligns show-snps show-tiling	\
+                show-diff repeat-match annotate combineMUMs	\
+                delta-filter
+pkglibexec_PROGRAMS += mgaps postnuc prepro postpro
 mgaps_SOURCES = src/tigr/mgaps_main.cc
 postnuc_SOURCES = src/tigr/postnuc_main.cc
 show_coords_SOURCES = src/tigr/show-coords.cc src/tigr/delta.cc
@@ -121,7 +127,7 @@ EXTRA_DIST += src/tigr/gaps.cc
 # what LIBTOOLS does.
 
 # List of scripts to install
-perl_scripts = mummerplot dnadiff
+perl_scripts = mummerplot dnadiff promer
 shell_scripts = exact-tandems
 all_scripts = $(perl_scripts) $(shell_scripts)
 
@@ -139,10 +145,13 @@ CLEANFILES += $(libs_scripts) $(all_scripts)
 # Rules to generate the scripts, in .libs and in build directory.
 script_inst_subst  = sed -e 's,[@]PERL[@],$(PERL),g' \
                        -e 's,[@]BIN_DIR[@],$(bindir),g' \
-                       -e 's,[@]LIB_DIR[@],$(script_libdir),g'
+                       -e 's,[@]LIB_DIR[@],$(script_libdir),g' \
+	               -e 's,[@]LIBEXEC_DIR[@],$(pkglibexecdir),g'
 script_local_subst = sed -e 's,[@]PERL[@],$(PERL),g' \
                        -e 's,[@]BIN_DIR[@],$(abs_builddir),g' \
-                       -e 's,[@]LIB_DIR[@],$(abs_srcdir)/scripts,g'
+                       -e 's,[@]LIB_DIR[@],$(abs_srcdir)/scripts,g' \
+	               -e 's,[@]LIBEXEC_DIR[@],$(abs_builddir),g'
+
 .libs/%: scripts/%.pl
 	@mkdir -p $(dir $@) && $(script_inst_subst) < $< > $@
 %: scripts/%.pl
@@ -154,7 +163,6 @@ script_local_subst = sed -e 's,[@]PERL[@],$(PERL),g' \
 
 # Supporting modules
 script_lib_SCRIPTS = scripts/Foundation.pm scripts/tandem-repeat.awk
-script_libdir = $(libdir)/mummer
 EXTRA_DIST += $(script_lib_SCRIPTS)
 
 #######

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([MUMmer], [3.9.4alpha], [gmarcais@umd.edu])
+AC_INIT([MUMmer], [4.0.0beta], [gmarcais@umd.edu])
 AC_CANONICAL_HOST
 AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE([subdir-objects foreign parallel-tests color-tests])
@@ -17,7 +17,7 @@ AC_PATH_PROG(ENV_PROG, [env])
 # Add -std=c++0x always. Add -DNDEBUG only if CXXFLAGS is not given on command line
 CXXFLAGS="-std=c++0x $CXXFLAGS"
 AS_IF([test x$cxxflags_given = xno], [CXXFLAGS="-DNDEBUG $CXXFLAGS"])
-EXTRA_CXXFLAGS="-std=c++0x"
+EXTRA_CXXFLAGS=
 AC_SUBST([EXTRA_CXXFLAGS])
 
 # Check for openmp
@@ -54,7 +54,7 @@ AS_IF([test x$try_nano_sleep = xyes],
       [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include <thread>]],
                                          [[std::this_thread::sleep_for(std::chrono::seconds(1))]])],
                          [AC_MSG_RESULT([yes])]
-                         [EXTRA_CXXFLAGS="-D_GLIBCXX_USE_NANOSLEEP $CXXFLAGS"],
+                         [EXTRA_CXXFLAGS="-D_GLIBCXX_USE_NANOSLEEP $EXTRA_CXXFLAGS"],
                          [AC_MSG_RESULT([no])]
                          [AC_MSG_FAILURE([Compiler does not support std::this_thread::sleep_for])])]
       [CXXFLAGS="$save_cxxflags"])

include/mummer/nucmer.hpp

@@ -15,7 +15,27 @@
 #include <jellyfish/whole_sequence_parser.hpp>
 #include <mt_skip_list/set.hpp>
 
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
 namespace mummer {
+
+// Limit number of threads to use
+inline void set_num_threads(int nb) {
+#ifdef _OPENMP
+  omp_set_num_threads(nb);
+#endif
+}
+
+inline int get_num_threads() {
+#ifdef _OPENMP
+  return omp_get_num_threads();
+#else
+  return 1;
+#endif
+}
+
 namespace nucmer {
 void reverse_complement(std::string& s);
 

include/mummer/openmp_qsort.hpp

@@ -37,6 +37,7 @@ namespace openmp_qsort_imp {
 template<typename Iterator, class Compare>
 void openmp_qsort_(Iterator begin, Iterator end, const size_t sz, Compare Comp) {
   typedef typename std::iterator_traits<Iterator>::value_type Type;
+  assert((size_t)(end - begin) == sz);
   auto pivot = begin + sz/2;
   auto const pivot_v = *pivot;
 
@@ -45,16 +46,21 @@ void openmp_qsort_(Iterator begin, Iterator end, const size_t sz, Compare Comp)
   std::swap(*p, *(end - 1));
 
   auto const sz1 = p - begin, sz2 = end - p - 1;
+  assert(sz1 >= 0);
+  assert(sz2 >= 0);
+  assert((size_t)sz2 <= sz);
+  assert((size_t)sz1 <= sz);
+  assert((size_t)sz1 + (size_t)sz2 + 1 == sz);
   if(sz1 > 1024) {
-#pragma omp task
+#pragma omp task firstprivate(p, sz1)
     openmp_qsort_(begin, p, sz1, Comp);
     if(sz2 > 1024)
       openmp_qsort_(p + 1, end, sz2, Comp);
     else
       std::sort(p + 1, end, Comp);
   } else {
     if(sz2 > 1024)
-#pragma omp task
+#pragma omp task firstprivate(p, sz2)
       openmp_qsort_(p + 1, end, sz2, Comp);
     else
       std::sort(p + 1, end, Comp);

include/mummer/redirect_to_pager.hpp

@@ -0,0 +1,61 @@
+#ifndef __REDIRECT_TO_PAGER_H__
+#define __REDIRECT_TO_PAGER_H__
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <signal.h>
+
+
+// Class that will redirect stdout to a pager if: (1) stdout is a tty
+// and (2) it can launch a pager. The pager is the content of the
+// PAGER environment variables or "more" if not set. This works with
+// stdio.
+struct stdio_launch_pager {
+  static constexpr const char* dflt_pager = "less -R";
+  FILE* pager_handle;
+
+  static void clean_exit(int) { exit(0); }
+
+  stdio_launch_pager(bool no_pager = false)
+    : pager_handle(NULL)
+  {
+    if(!isatty(1) || no_pager) return;
+    // Open a pager
+    const char* pager      = getenv("PAGER");
+    if(pager)
+      pager_handle = start_pager(pager);
+    if(!pager_handle) {
+      pager_handle = start_pager(dflt_pager);
+      if(!pager_handle)
+        return;
+    }
+
+    // Close stdout and put pager in its place
+    if(fileno(pager_handle) == 1)
+      return; // Done already!
+    if(dup2(fileno(pager_handle), 1) == -1)
+      stop_pager();
+
+    // Upon SIGPIPE, quit without error
+    struct sigaction act;
+    memset(&act, '\0', sizeof(act));
+    act.sa_handler = clean_exit;
+    sigaction(SIGPIPE, &act, NULL);
+  }
+
+  ~stdio_launch_pager() { stop_pager(); }
+
+  FILE* start_pager(const char* cmd) {
+    return popen(cmd, "w");
+  }
+
+  void stop_pager() {
+    if(pager_handle) {
+      pclose(pager_handle);
+      pager_handle = NULL;
+    }
+  }
+};
+
+#endif /* __REDIRECT_TO_PAGER_H__ */

include/mummer/translate.hh

@@ -7,7 +7,7 @@
 #include <cstring>
 
 long int Translate_DNA
-(char * A, char * tA, int Frame);
+(const char * A, int dnaseq_len, char * tA, int Frame);
 
      // function to translate dna sequence to aminoacid sequence
      // uses esttrans' headers and algo
@@ -17,6 +17,12 @@ long int Translate_DNA
      // returns new (strlen(A+1)) or -1 on error
      // See end of file for source.
 
+inline long int Translate_DNA
+(const char * A, char * tA, int Frame) {
+  return Translate_DNA(A, (int)strlen(A + 1), tA, Frame);
+}
+
+
 #define BAD_PEP_CHAR	-1
 #define SKIP_PEP_CHAR	-2
 #define NUM_DNA_SYMBOLS	16

scripts/mummerplot.pl

@@ -1189,7 +1189,7 @@ ($$)
             $xrange += $rref->{$xlabel}[1];
             $tic = $rref->{$xlabel}[0] + 1;
             $dir = ($rref->{$xlabel}[2] == 1) ? "" : "*";
-            print GFILE " \"$dir$xlabel\" $tic, \\\n";
+            print GFILE " \"$dir$xlabel\" $tic.0, \\\n";
         }
         print GFILE " \"\" $xrange \\\n\)\n";
         $xlabel = "REF";
@@ -1212,7 +1212,7 @@ ($$)
             $yrange += $qref->{$ylabel}[1];
             $tic = $qref->{$ylabel}[0] + 1;
             $dir = ($qref->{$ylabel}[2] == 1) ? "" : "*";
-            print GFILE " \"$dir$ylabel\" $tic, \\\n";
+            print GFILE " \"$dir$ylabel\" $tic.0, \\\n";
         }
         print GFILE " \"\" $yrange \\\n\)\n";
         $ylabel = "QRY";