VSEARCH 1.9.6: Fix for bug in aligned sequences with --fastapairs and…

… --userout

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for vsearch 1.9.5.
+# Generated by GNU Autoconf 2.69 for vsearch 1.9.6.
 #
 # Report bugs to <[email protected]>.
 #
@@ -580,8 +580,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='vsearch'
 PACKAGE_TARNAME='vsearch'
-PACKAGE_VERSION='1.9.5'
-PACKAGE_STRING='vsearch 1.9.5'
+PACKAGE_VERSION='1.9.6'
+PACKAGE_STRING='vsearch 1.9.6'
 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 1.9.5 to adapt to many kinds of systems.
+\`configure' configures vsearch 1.9.6 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 1.9.5:";;
+     short | recursive ) echo "Configuration of vsearch 1.9.6:";;
    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 1.9.5
+vsearch configure 1.9.6
 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 1.9.5, which was
+It was created by vsearch $as_me 1.9.6, 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='1.9.5'
+ VERSION='1.9.6'
 
 
 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 1.9.5, which was
+This file was extended by vsearch $as_me 1.9.6, 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 1.9.5
+vsearch config.status 1.9.6
 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], [1.9.5], [[email protected]])
+AC_INIT([vsearch], [1.9.6], [[email protected]])
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])
 AC_CONFIG_SRCDIR([src/vsearch.cc])

man/vsearch.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH vsearch 1 "December 3, 2015" "version 1.9.5" "USER COMMANDS"
+.TH vsearch 1 "January 8, 2016" "version 1.9.6" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em chimera detection, clustering, dereplication, FASTA/FASTQ
@@ -1996,7 +1996,7 @@ Source code and binaries are available at
 <https://github.com/torognes/vsearch>.
 .\" ============================================================================
 .SH COPYRIGHT
-Copyright (C) 2014-2015, Torbjørn Rognes, Frédéric Mahé and Tomás Flouri
+Copyright (C) 2014-2016, Torbjørn Rognes, Frédéric Mahé and Tomás Flouri
 .PP
 All rights reserved.
 .PP
@@ -2311,6 +2311,10 @@ Fixed incrementation of counter when relabeling dereplicated sequences.
 .TP
 .BR v1.9.5\~ "released December 3rd, 2015"
 Fixed bug resulting in inferior chimera detection performance.
+.TP
+.BR v1.9.6\~ "released January 8th, 2016"
+Fixed bug in aligned sequences produced with \-\-fastapairs and
+\-\-userout (qrow, trow) options.
 .RE
 .LP
 .\" ============================================================================

src/showalign.cc

@@ -2,7 +2,7 @@
 
   VSEARCH: a versatile open source tool for metagenomics
 
-  Copyright (C) 2014-2015, Torbjorn Rognes, Frederic Mahe and Tomas Flouri
+  Copyright (C) 2014-2016, Torbjorn Rognes, Frederic Mahe and Tomas Flouri
   All rights reserved.
 
   Contact: Torbjorn Rognes <[email protected]>,
@@ -267,6 +267,7 @@ char * align_getrow(char * seq, char * cigar, int alen, int origin)
         {
           strncpy(r, s, len);
           r += len;
+          s += len;
         }
       else
         {