VSEARCH 1.9.9: Adjusted default min word matches for improved perform…

…ance

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for vsearch 1.9.8.
+# Generated by GNU Autoconf 2.69 for vsearch 1.9.9.
 #
 # Report bugs to <[email protected]>.
 #
@@ -580,8 +580,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='vsearch'
 PACKAGE_TARNAME='vsearch'
-PACKAGE_VERSION='1.9.8'
-PACKAGE_STRING='vsearch 1.9.8'
+PACKAGE_VERSION='1.9.9'
+PACKAGE_STRING='vsearch 1.9.9'
 PACKAGE_BUGREPORT='[email protected]'
 PACKAGE_URL=''
 
@@ -1291,7 +1291,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures vsearch 1.9.8 to adapt to many kinds of systems.
+\`configure' configures vsearch 1.9.9 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1357,7 +1357,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of vsearch 1.9.8:";;
+     short | recursive ) echo "Configuration of vsearch 1.9.9:";;
    esac
   cat <<\_ACEOF
 
@@ -1453,7 +1453,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-vsearch configure 1.9.8
+vsearch configure 1.9.9
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2044,7 +2044,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by vsearch $as_me 1.9.8, which was
+It was created by vsearch $as_me 1.9.9, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2907,7 +2907,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='vsearch'
- VERSION='1.9.8'
+ VERSION='1.9.9'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -6364,7 +6364,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by vsearch $as_me 1.9.8, which was
+This file was extended by vsearch $as_me 1.9.9, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -6430,7 +6430,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-vsearch config.status 1.9.8
+vsearch config.status 1.9.9
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.63])
-AC_INIT([vsearch], [1.9.8], [[email protected]])
+AC_INIT([vsearch], [1.9.9], [[email protected]])
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])
 AC_CONFIG_SRCDIR([src/vsearch.cc])

man/Makefile.in

@@ -263,9 +263,9 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign man/Makefile'; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu man/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --foreign man/Makefile
+	  $(AUTOMAKE) --gnu man/Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
 	  *config.status*) \

man/vsearch.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH vsearch 1 "January 22, 2016" "version 1.9.8" "USER COMMANDS"
+.TH vsearch 1 "January 22, 2016" "version 1.9.9" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em chimera detection, clustering, dereplication, FASTA/FASTQ
@@ -2374,6 +2374,10 @@ input sequences unchanged when no masking is performed. Masking is now performed
 .BR v1.9.8\~ "released January 22nd, 2016"
 Fixed bug causing segfault when chimera detection is performed on
 extremely short sequences.
+.TP
+.BR v1.9.9\~ "released January 22nd, 2016"
+Adjusted default minimum number of word matches during searches for
+improved performance.
 .RE
 .LP
 .\" ============================================================================

src/Makefile.in

@@ -422,9 +422,9 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --foreign src/Makefile
+	  $(AUTOMAKE) --gnu src/Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
 	  *config.status*) \

src/searchcore.h

@@ -63,10 +63,9 @@
 /* the number of alignments that can be delayed */
 #define MAXDELAYED 8
 
-/* Default minimum number of word matches for word lengths 0-15 */
-/* Choosen for optimal F1 score on Rfam classification test */
+/* Default minimum number of word matches for word lengths 7-15 */
 const int minwordmatches_defaults[] =
-  { -1, -1, -1, -1, -1, -1, -1, 14, 10,  9,  8,  6,  5,  4,  3,  2 };
+  { -1, -1, -1, -1, -1, -1, -1, 14, 12, 11, 10,  9,  8,  7,  5,  3 };
 
 struct hit
 {