From a9a8841fc9ee66090d1b91a2eda73e5ace4ff260 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Torbj=C3=B8rn=20Rognes?= Date: Fri, 22 Jan 2016 13:09:21 +0100 Subject: [PATCH] VSEARCH 1.9.9: Adjusted default min word matches for improved performance --- configure | 20 ++++++++++---------- configure.ac | 2 +- man/Makefile.in | 4 ++-- man/vsearch.1 | 6 +++++- src/Makefile.in | 4 ++-- src/searchcore.h | 5 ++--- 6 files changed, 22 insertions(+), 19 deletions(-) diff --git a/configure b/configure index 6280dec7..60584c4b 100755 --- a/configure +++ b/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 . # @@ -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='torognes@ifi.uio.no' 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\\" diff --git a/configure.ac b/configure.ac index e040899d..991810af 100644 --- a/configure.ac +++ b/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], [torognes@ifi.uio.no]) +AC_INIT([vsearch], [1.9.9], [torognes@ifi.uio.no]) AM_INIT_AUTOMAKE([subdir-objects]) AC_LANG([C++]) AC_CONFIG_SRCDIR([src/vsearch.cc]) diff --git a/man/Makefile.in b/man/Makefile.in index 53d48a81..76b4093f 100644 --- a/man/Makefile.in +++ b/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*) \ diff --git a/man/vsearch.1 b/man/vsearch.1 index cba6bcc5..7c5a220e 100644 --- a/man/vsearch.1 +++ b/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 .\" ============================================================================ diff --git a/src/Makefile.in b/src/Makefile.in index 8151bd49..3e43e33a 100644 --- a/src/Makefile.in +++ b/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*) \ diff --git a/src/searchcore.h b/src/searchcore.h index e5fa6800..a8e08637 100644 --- a/src/searchcore.h +++ b/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 {