[med-svn] [vsearch] 01/01: Imported Upstream version 1.11.1
Andreas Tille
tille at debian.org
Thu May 19 10:57:33 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch upstream
in repository vsearch.
commit f83c1ffa4b7196148daae671e01de0279879a68f
Author: Andreas Tille <tille at debian.org>
Date: Thu May 19 12:41:30 2016 +0200
Imported Upstream version 1.11.1
---
.gitignore | 8 +
Makefile.in | 775 ------
README.md | 29 +-
aclocal.m4 | 1152 ---------
compile | 347 ---
config.h.in | 213 --
configure | 7292 -----------------------------------------------------
configure.ac | 2 +-
depcomp | 791 ------
install-sh | 501 ----
man/Makefile.in | 523 ----
man/vsearch.1 | 34 +-
missing | 215 --
src/Makefile.in | 854 -------
src/align_simd.cc | 22 +
src/derep.cc | 13 +-
src/fasta.cc | 74 +-
src/fasta.h | 13 +
src/fastq.cc | 2 +-
src/fastqops.cc | 34 +-
src/fastx.cc | 2 +-
src/mergepairs.cc | 19 +-
src/results.cc | 2 +-
23 files changed, 194 insertions(+), 12723 deletions(-)
diff --git a/.gitignore b/.gitignore
index e0a35e9..f4875a3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,3 +11,11 @@
/config.status
/stamp-h1
Makefile
+aclocal.m4
+config.h.in
+configure
+compile
+depcomp
+install-sh
+missing
+Makefile.in
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diff --git a/README.md b/README.md
index 946a85e..b9e539e 100644
--- a/README.md
+++ b/README.md
@@ -32,44 +32,46 @@ In the example below, VSEARCH will identify sequences in the file database.fsa t
## Download and install
-**Source distribution** To download the source distribution from a [release](https://github.com/torognes/vsearch/releases) and build the executable and the documentation using Autotools, use the following commands (replace x.y.z with the current version):
+**Source distribution** To download the source distribution from a [release](https://github.com/torognes/vsearch/releases) and build the executable and the documentation, use the following commands:
```
-wget https://github.com/torognes/vsearch/archive/vx.y.z.tar.gz
-tar xzf vx.y.z.tar.gz
-cd vsearch-x.y.z
+wget https://github.com/torognes/vsearch/archive/v1.11.1.tar.gz
+tar xzf v1.11.1.tar.gz
+cd vsearch-1.11.1
+./autogen.sh
./configure
make
make install # as root or sudo make install
```
-You may customize the installation directory using the `--prefix=DIR` option to `configure`. If the compression libraries [zlib](http://www.zlib.net) and/or [bzip2](http://www.bzip.org) are installed on the system, they will be detected automatically and support for compressed files will be included in vsearch. Support for compressed files may be disabled using the `--disable-zlib` and `--disable-bzip2` options to `configure`. A PDF version of the manual will be created from the `vsearch [...]
+You may customize the installation directory using the `--prefix=DIR` option to `configure`. If the compression libraries [zlib](http://www.zlib.net) and/or [bzip2](http://www.bzip.org) are installed on the system, they will be detected automatically and support for compressed files will be included in vsearch. Support for compressed files may be disabled using the `--disable-zlib` and `--disable-bzip2` options to `configure`. A PDF version of the manual will be created from the `vsearch [...]
**Cloning the repo** Instead of downloading the source distribution as a compressed archive, you could clone the repo and build it as shown below. The options to `configure` as described above are still valid.
```
git clone https://github.com/torognes/vsearch.git
cd vsearch
+./autogen.sh
./configure
make
make install # as root or sudo make install
```
-**Binary distribution** Starting with version 1.4.0, binary distribution files (.tar.gz) for GNU/Linux on x86-64 and Apple Mac OS X on x86-64 containing pre-compiled binaries as well as the documentation (man and pdf files) will be made available as part of each [release](https://github.com/torognes/vsearch/releases). The included executables include support for input files compressed by zlib and bzip2 (with files usually ending in `.gz` or `.bz2`). Download the appropriate executable fo [...]
+**Binary distribution** Starting with version 1.4.0, binary distribution files (.tar.gz) for GNU/Linux on x86-64 and Apple Mac OS X on x86-64 containing pre-compiled binaries as well as the documentation (man and pdf files) will be made available as part of each [release](https://github.com/torognes/vsearch/releases). The included executables include support for input files compressed by zlib and bzip2 (with files usually ending in `.gz` or `.bz2`). Download the appropriate executable fo [...]
```sh
-wget https://github.com/torognes/vsearch/releases/download/vx.y.z/vsearch-x.y.z-linux-x86_64.tar.gz
-tar xzf vsearch-x.y.z-linux-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v1.11.1/vsearch-1.11.1-linux-x86_64.tar.gz
+tar xzf vsearch-1.11.1-linux-x86_64.tar.gz
```
Or these commands if you are using a Mac:
```sh
-wget https://github.com/torognes/vsearch/releases/download/vx.y.z/vsearch-x.y.z-osx-x86_64.tar.gz
-tar xzf vsearch-x.y.z-osx-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v1.11.1/vsearch-1.11.1-osx-x86_64.tar.gz
+tar xzf vsearch-1.11.1-osx-x86_64.tar.gz
```
-You will now have the binary distribution in a folder called something like `vsearch-x.y.z-linux-x86_64` in which you will find three subfolders `bin`, `man` and `doc`. We recommend making a copy or a symbolic link to the vsearch binary `bin/vsearch` in a folder included in your `$PATH`, and a copy or a symbolic link to the vsearch man page `man/vsearch.1` in a folder included in your `$MANPATH`. The PDF version of the manual is available in `doc/vsearch_manual.pdf`.
+You will now have the binary distribution in a folder called something like `vsearch-1.11.1-linux-x86_64` in which you will find three subfolders `bin`, `man` and `doc`. We recommend making a copy or a symbolic link to the vsearch binary `bin/vsearch` in a folder included in your `$PATH`, and a copy or a symbolic link to the vsearch man page `man/vsearch.1` in a folder included in your `$MANPATH`. The PDF version of the manual is available in `doc/vsearch_manual.pdf`.
**Old binaries** Older VSEARCH binaries (until version 1.1.3) are available [here](https://github.com/torognes/vsearch/releases) for [GNU/Linux on x86-64 systems](https://github.com/torognes/vsearch/blob/master/bin/vsearch-1.1.3-linux-x86_64) and [Apple Mac OS X on x86-64 systems](https://github.com/torognes/vsearch/blob/master/bin/vsearch-1.1.3-osx-x86_64). These executables include support for input files compressed by zlib and bzip2 (with files usually ending in `.gz` or `.bz2`). Down [...]
@@ -83,12 +85,11 @@ chmod a+x vsearch-1.1.3-linux-x86_64
ln -s vsearch-1.1.3-linux-x86_64 vsearch
```
-
**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/doc/vsearch.1). A pdf version (vsearch_manual.pdf) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form (vsearch_manual.pd [...]
**Galaxy wrapper** Thanks to the work of the [Intergalactic Utilities Commission](https://wiki.galaxyproject.org/IUC) members, vsearch is now part of the [Galaxy ToolShed](https://toolshed.g2.bx.psu.edu/view/iuc/vsearch/).
-**Debian package** Thanks to the [Debian Med](https://www.debian.org/devel/debian-med/) team, there is now a [vsearch](https://packages.debian.org/sid/vsearch) package in [Debian](https://www.debian.org/). The `example/test` data is available in a separate [vsearch-data](https://packages.debian.org/sid/science/vsearch-data) package.
+**Debian package** Thanks to the [Debian Med](https://www.debian.org/devel/debian-med/) team, there is now a [vsearch](https://packages.debian.org/sid/vsearch) package in [Debian](https://www.debian.org/).
**Homebrew package** Thanks to [Torsten Seeman](https://github.com/tseemann), a vsearch package for [Homebrew](http://brew.sh/) [has been made](https://github.com/Homebrew/homebrew-science/pull/2409).
@@ -130,7 +131,7 @@ For the accuracy assessment searches in Rfam 11.0 with 100 replicates of the que
**Clustering:** The clustering commands `--cluster_smallmem` and `--cluster_fast` have been implemented. These commands support multiple threads. The only difference between `--cluster_smallmem` and `--cluster_fast` is that `--cluster_fast` will sort the sequences by length before clustering, while `--cluster_smallmem` require the sequences to be in length-sorted order unless the `--usersort` option is specified. An additional clustering command called `--cluster_size` has been added tha [...]
-The speed of clustering with VSEARCH relative to USEARCH depends on how many threads are used. Running with a single thread VSEARCH currently seems to be 2-4 times slower than with USEARCH, depending on parameters. Clustering has been parallelized with threads in VSEARCH, but clustering does not seem to be parallelized in USEARCH (despite what the name and documentation for `--cluster_fast` seems to indicate). Clustering with VSEARCH using 4-8 threads is often faster than USEARCH. The sp [...]
+The speed of clustering with VSEARCH relative to USEARCH depends on how many threads are used. Running with a single thread VSEARCH currently seems to be 2-4 times slower than with USEARCH, depending on parameters. Clustering has been parallelized with threads in VSEARCH, but clustering does not seem to be parallelized in USEARCH (despite what the name and documentation for `--cluster_fast` seems to indicate). Clustering with VSEARCH using 4-8 threads is often faster than USEARCH. The sp [...]
**Chimera detection:** Chimera detection using the algorithm described by Edgar *et al.* (2011) has been implemented in VSEARCH. Both the `--uchime_ref` and `--uchime_denovo` commands and all their options are supported.
diff --git a/aclocal.m4 b/aclocal.m4
deleted file mode 100644
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index a85b723..0000000
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-
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-right script to run: please start by reading the file 'INSTALL'.
-
-Report bugs to <bug-automake at gnu.org>.
-EOF
- exit $?
- ;;
- -v | --v*)
- echo "compile $scriptversion"
- exit $?
- ;;
- cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
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- ;;
-esac
-
-ofile=
-cfile=
-
-for arg
-do
- if test -n "$eat"; then
- eat=
- else
- case $1 in
- -o)
- # configure might choose to run compile as 'compile cc -o foo foo.c'.
- # So we strip '-o arg' only if arg is an object.
- eat=1
- case $2 in
- *.o | *.obj)
- ofile=$2
- ;;
- *)
- set x "$@" -o "$2"
- shift
- ;;
- esac
- ;;
- *.c)
- cfile=$1
- set x "$@" "$1"
- shift
- ;;
- *)
- set x "$@" "$1"
- shift
- ;;
- esac
- fi
- shift
-done
-
-if test -z "$ofile" || test -z "$cfile"; then
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- # pattern rule where we don't need one. That is ok -- this is a
- # normal compilation that the losing compiler can handle. If no
- # '.c' file was seen then we are probably linking. That is also
- # ok.
- exec "$@"
-fi
-
-# Name of file we expect compiler to create.
-cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
-
-# Create the lock directory.
-# Note: use '[/\\:.-]' here to ensure that we don't use the same name
-# that we are using for the .o file. Also, base the name on the expected
-# object file name, since that is what matters with a parallel build.
-lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
-while true; do
- if mkdir "$lockdir" >/dev/null 2>&1; then
- break
- fi
- sleep 1
-done
-# FIXME: race condition here if user kills between mkdir and trap.
-trap "rmdir '$lockdir'; exit 1" 1 2 15
-
-# Run the compile.
-"$@"
-ret=$?
-
-if test -f "$cofile"; then
- test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
-elif test -f "${cofile}bj"; then
- test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
-fi
-
-rmdir "$lockdir"
-exit $ret
-
-# Local Variables:
-# mode: shell-script
-# sh-indentation: 2
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:
diff --git a/config.h.in b/config.h.in
deleted file mode 100644
index 6efc4a3..0000000
--- a/config.h.in
+++ /dev/null
@@ -1,213 +0,0 @@
-/* config.h.in. Generated from configure.ac by autoheader. */
-
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-
-/* Define to 1 if using `alloca.c'. */
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-
-/* Define to 1 if you have `alloca', as a function or macro. */
-#undef HAVE_ALLOCA
-
-/* Define to 1 if you have <alloca.h> and it should be used (not on Ultrix).
- */
-#undef HAVE_ALLOCA_H
-
-/* Define to 1 if you have the <bzlib.h> header file. */
-#undef HAVE_BZLIB_H
-
-/* Define to 1 if you have the <ctype.h> header file. */
-#undef HAVE_CTYPE_H
-
-/* Define to 1 if you have the <dlfcn.h> header file. */
-#undef HAVE_DLFCN_H
-
-/* Define to 1 if you have the <fcntl.h> header file. */
-#undef HAVE_FCNTL_H
-
-/* Define to 1 if you have the <float.h> header file. */
-#undef HAVE_FLOAT_H
-
-/* Define to 1 if you have the <getopt.h> header file. */
-#undef HAVE_GETOPT_H
-
-/* Define to 1 if you have the `gettimeofday' function. */
-#undef HAVE_GETTIMEOFDAY
-
-/* Define to 1 if you have the <inttypes.h> header file. */
-#undef HAVE_INTTYPES_H
-
-/* Define to 1 if you have the `dl' library (-ldl). */
-#undef HAVE_LIBDL
-
-/* Define to 1 if you have the `pthread' library (-lpthread). */
-#undef HAVE_LIBPTHREAD
-
-/* Define to 1 if you have the <limits.h> header file. */
-#undef HAVE_LIMITS_H
-
-/* Define to 1 if you have the <locale.h> header file. */
-#undef HAVE_LOCALE_H
-
-/* Define to 1 if you have the `localtime_r' function. */
-#undef HAVE_LOCALTIME_R
-
-/* Define to 1 if your system has a GNU libc compatible `malloc' function, and
- to 0 otherwise. */
-#undef HAVE_MALLOC
-
-/* Define to 1 if you have the `memchr' function. */
-#undef HAVE_MEMCHR
-
-/* Define to 1 if you have the `memcpy' function. */
-#undef HAVE_MEMCPY
-
-/* Define to 1 if you have the `memmove' function. */
-#undef HAVE_MEMMOVE
-
-/* Define to 1 if you have the <memory.h> header file. */
-#undef HAVE_MEMORY_H
-
-/* Define to 1 if you have the `memset' function. */
-#undef HAVE_MEMSET
-
-/* Define to 1 if you have the `posix_memalign' function. */
-#undef HAVE_POSIX_MEMALIGN
-
-/* Define to 1 if you have the `pow' function. */
-#undef HAVE_POW
-
-/* Define to 1 if you have the <pthread.h> header file. */
-#undef HAVE_PTHREAD_H
-
-/* Define to 1 if your system has a GNU libc compatible `realloc' function,
- and to 0 otherwise. */
-#undef HAVE_REALLOC
-
-/* Define to 1 if you have the `regcomp' function. */
-#undef HAVE_REGCOMP
-
-/* Define to 1 if you have the <regex.h> header file. */
-#undef HAVE_REGEX_H
-
-/* Define to 1 if you have the <stdint.h> header file. */
-#undef HAVE_STDINT_H
-
-/* Define to 1 if you have the <stdlib.h> header file. */
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-
-/* Define to 1 if you have the `strcasecmp' function. */
-#undef HAVE_STRCASECMP
-
-/* Define to 1 if you have the `strchr' function. */
-#undef HAVE_STRCHR
-
-/* Define to 1 if you have the `strcspn' function. */
-#undef HAVE_STRCSPN
-
-/* Define to 1 if you have the <strings.h> header file. */
-#undef HAVE_STRINGS_H
-
-/* Define to 1 if you have the <string.h> header file. */
-#undef HAVE_STRING_H
-
-/* Define to 1 if you have the `sysinfo' function. */
-#undef HAVE_SYSINFO
-
-/* Define to 1 if you have the <sys/stat.h> header file. */
-#undef HAVE_SYS_STAT_H
-
-/* Define to 1 if you have the <sys/time.h> header file. */
-#undef HAVE_SYS_TIME_H
-
-/* Define to 1 if you have the <sys/types.h> header file. */
-#undef HAVE_SYS_TYPES_H
-
-/* Define to 1 if you have the <unistd.h> header file. */
-#undef HAVE_UNISTD_H
-
-/* Define to 1 if you have the <zlib.h> header file. */
-#undef HAVE_ZLIB_H
-
-/* Name of package */
-#undef PACKAGE
-
-/* Define to the address where bug reports for this package should be sent. */
-#undef PACKAGE_BUGREPORT
-
-/* Define to the full name of this package. */
-#undef PACKAGE_NAME
-
-/* Define to the full name and version of this package. */
-#undef PACKAGE_STRING
-
-/* Define to the one symbol short name of this package. */
-#undef PACKAGE_TARNAME
-
-/* Define to the home page for this package. */
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-
-/* Define to the version of this package. */
-#undef PACKAGE_VERSION
-
-/* If using the C implementation of alloca, define if you know the
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- STACK_DIRECTION > 0 => grows toward higher addresses
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-#undef STACK_DIRECTION
-
-/* Define to 1 if you have the ANSI C header files. */
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-
-/* Version number of package */
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-
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- #define below would cause a syntax error. */
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-
-/* Define for Solaris 2.5.1 so the uint64_t typedef from <sys/synch.h>,
- <pthread.h>, or <semaphore.h> is not used. If the typedef were allowed, the
- #define below would cause a syntax error. */
-#undef _UINT64_T
-
-/* Define for Solaris 2.5.1 so the uint8_t typedef from <sys/synch.h>,
- <pthread.h>, or <semaphore.h> is not used. If the typedef were allowed, the
- #define below would cause a syntax error. */
-#undef _UINT8_T
-
-/* Define to `__inline__' or `__inline' if that's what the C compiler
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-#undef inline
-#endif
-
-/* Define to the type of a signed integer type of width exactly 64 bits if
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-
-/* Define to rpl_malloc if the replacement function should be used. */
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-
-/* Define to rpl_realloc if the replacement function should be used. */
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-
-/* Define to `unsigned int' if <sys/types.h> does not define. */
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-
-/* Define to the type of an unsigned integer type of width exactly 32 bits if
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-
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-
-/* Define to the type of an unsigned integer type of width exactly 8 bits if
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diff --git a/configure b/configure
deleted file mode 100755
index 6108c51..0000000
--- a/configure
+++ /dev/null
@@ -1,7292 +0,0 @@
-#! /bin/sh
-# Guess values for system-dependent variables and create Makefiles.
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-#
-# Report bugs to <torognes at ifi.uio.no>.
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-#
-# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
-#
-#
-# This configure script is free software; the Free Software Foundation
-# gives unlimited permission to copy, distribute and modify it.
-## -------------------- ##
-## M4sh Initialization. ##
-## -------------------- ##
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-
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-PS1='$ '
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-
-# CDPATH.
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-
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- cat conftest.er1 >&5
- mv -f conftest.er1 conftest.err
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- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
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-
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-
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-
-# ac_fn_cxx_check_header_mongrel LINENO HEADER VAR INCLUDES
-# ---------------------------------------------------------
-# Tests whether HEADER exists, giving a warning if it cannot be compiled using
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-ac_fn_cxx_check_header_mongrel ()
-{
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- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
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- # Is the header compilable?
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 usability" >&5
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-$4
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-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
- ac_header_compiler=yes
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- ac_header_compiler=no
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-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_compiler" >&5
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-
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-if ac_fn_cxx_try_cpp "$LINENO"; then :
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-{
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-{
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-{
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-
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-
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-{
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-{
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-{
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- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for int$2_t" >&5
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-{
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-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5
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-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5
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-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5
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-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5
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-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
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-
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-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5
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-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_strtod" >&5
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-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_pow" >&5
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-# for constant arguments. Useless!
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for working alloca.h" >&5
-$as_echo_n "checking for working alloca.h... " >&6; }
-if ${ac_cv_working_alloca_h+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include <alloca.h>
-int
-main ()
-{
-char *p = (char *) alloca (2 * sizeof (int));
- if (p) return 0;
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_cxx_try_link "$LINENO"; then :
- ac_cv_working_alloca_h=yes
-else
- ac_cv_working_alloca_h=no
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_working_alloca_h" >&5
-$as_echo "$ac_cv_working_alloca_h" >&6; }
-if test $ac_cv_working_alloca_h = yes; then
-
-$as_echo "#define HAVE_ALLOCA_H 1" >>confdefs.h
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for alloca" >&5
-$as_echo_n "checking for alloca... " >&6; }
-if ${ac_cv_func_alloca_works+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#ifdef __GNUC__
-# define alloca __builtin_alloca
-#else
-# ifdef _MSC_VER
-# include <malloc.h>
-# define alloca _alloca
-# else
-# ifdef HAVE_ALLOCA_H
-# include <alloca.h>
-# else
-# ifdef _AIX
- #pragma alloca
-# else
-# ifndef alloca /* predefined by HP cc +Olibcalls */
-void *alloca (size_t);
-# endif
-# endif
-# endif
-# endif
-#endif
-
-int
-main ()
-{
-char *p = (char *) alloca (1);
- if (p) return 0;
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_cxx_try_link "$LINENO"; then :
- ac_cv_func_alloca_works=yes
-else
- ac_cv_func_alloca_works=no
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_alloca_works" >&5
-$as_echo "$ac_cv_func_alloca_works" >&6; }
-
-if test $ac_cv_func_alloca_works = yes; then
-
-$as_echo "#define HAVE_ALLOCA 1" >>confdefs.h
-
-else
- # The SVR3 libPW and SVR4 libucb both contain incompatible functions
-# that cause trouble. Some versions do not even contain alloca or
-# contain a buggy version. If you still want to use their alloca,
-# use ar to extract alloca.o from them instead of compiling alloca.c.
-
-ALLOCA=\${LIBOBJDIR}alloca.$ac_objext
-
-$as_echo "#define C_ALLOCA 1" >>confdefs.h
-
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether \`alloca.c' needs Cray hooks" >&5
-$as_echo_n "checking whether \`alloca.c' needs Cray hooks... " >&6; }
-if ${ac_cv_os_cray+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#if defined CRAY && ! defined CRAY2
-webecray
-#else
-wenotbecray
-#endif
-
-_ACEOF
-if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
- $EGREP "webecray" >/dev/null 2>&1; then :
- ac_cv_os_cray=yes
-else
- ac_cv_os_cray=no
-fi
-rm -f conftest*
-
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_os_cray" >&5
-$as_echo "$ac_cv_os_cray" >&6; }
-if test $ac_cv_os_cray = yes; then
- for ac_func in _getb67 GETB67 getb67; do
- as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
-ac_fn_cxx_check_func "$LINENO" "$ac_func" "$as_ac_var"
-if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
-
-cat >>confdefs.h <<_ACEOF
-#define CRAY_STACKSEG_END $ac_func
-_ACEOF
-
- break
-fi
-
- done
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking stack direction for C alloca" >&5
-$as_echo_n "checking stack direction for C alloca... " >&6; }
-if ${ac_cv_c_stack_direction+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- if test "$cross_compiling" = yes; then :
- ac_cv_c_stack_direction=0
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-$ac_includes_default
-int
-find_stack_direction (int *addr, int depth)
-{
- int dir, dummy = 0;
- if (! addr)
- addr = &dummy;
- *addr = addr < &dummy ? 1 : addr == &dummy ? 0 : -1;
- dir = depth ? find_stack_direction (addr, depth - 1) : 0;
- return dir + dummy;
-}
-
-int
-main (int argc, char **argv)
-{
- return find_stack_direction (0, argc + !argv + 20) < 0;
-}
-_ACEOF
-if ac_fn_cxx_try_run "$LINENO"; then :
- ac_cv_c_stack_direction=1
-else
- ac_cv_c_stack_direction=-1
-fi
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
- conftest.$ac_objext conftest.beam conftest.$ac_ext
-fi
-
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_stack_direction" >&5
-$as_echo "$ac_cv_c_stack_direction" >&6; }
-cat >>confdefs.h <<_ACEOF
-#define STACK_DIRECTION $ac_cv_c_stack_direction
-_ACEOF
-
-
-fi
-
-for ac_header in stdlib.h
-do :
- ac_fn_cxx_check_header_mongrel "$LINENO" "stdlib.h" "ac_cv_header_stdlib_h" "$ac_includes_default"
-if test "x$ac_cv_header_stdlib_h" = xyes; then :
- cat >>confdefs.h <<_ACEOF
-#define HAVE_STDLIB_H 1
-_ACEOF
-
-fi
-
-done
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU libc compatible realloc" >&5
-$as_echo_n "checking for GNU libc compatible realloc... " >&6; }
-if ${ac_cv_func_realloc_0_nonnull+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- if test "$cross_compiling" = yes; then :
- ac_cv_func_realloc_0_nonnull=no
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#if defined STDC_HEADERS || defined HAVE_STDLIB_H
-# include <stdlib.h>
-#else
-char *realloc ();
-#endif
-
-int
-main ()
-{
-return ! realloc (0, 0);
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_cxx_try_run "$LINENO"; then :
- ac_cv_func_realloc_0_nonnull=yes
-else
- ac_cv_func_realloc_0_nonnull=no
-fi
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
- conftest.$ac_objext conftest.beam conftest.$ac_ext
-fi
-
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_realloc_0_nonnull" >&5
-$as_echo "$ac_cv_func_realloc_0_nonnull" >&6; }
-if test $ac_cv_func_realloc_0_nonnull = yes; then :
-
-$as_echo "#define HAVE_REALLOC 1" >>confdefs.h
-
-else
- $as_echo "#define HAVE_REALLOC 0" >>confdefs.h
-
- case " $LIBOBJS " in
- *" realloc.$ac_objext "* ) ;;
- *) LIBOBJS="$LIBOBJS realloc.$ac_objext"
- ;;
-esac
-
-
-$as_echo "#define realloc rpl_realloc" >>confdefs.h
-
-fi
-
-
-for ac_func in memmove memcpy posix_memalign gettimeofday localtime_r memchr memset pow regcomp strcasecmp strchr strcspn sysinfo
-do :
- as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
-ac_fn_cxx_check_func "$LINENO" "$ac_func" "$as_ac_var"
-if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
- cat >>confdefs.h <<_ACEOF
-#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
-_ACEOF
-
-fi
-done
-
-
-have_pthreads=no
-have_bzip2=no
-have_zlib=no
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing pthread_create" >&5
-$as_echo_n "checking for library containing pthread_create... " >&6; }
-if ${ac_cv_search_pthread_create+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_func_search_save_LIBS=$LIBS
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char pthread_create ();
-int
-main ()
-{
-return pthread_create ();
- ;
- return 0;
-}
-_ACEOF
-for ac_lib in '' pthread; do
- if test -z "$ac_lib"; then
- ac_res="none required"
- else
- ac_res=-l$ac_lib
- LIBS="-l$ac_lib $ac_func_search_save_LIBS"
- fi
- if ac_fn_cxx_try_link "$LINENO"; then :
- ac_cv_search_pthread_create=$ac_res
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext
- if ${ac_cv_search_pthread_create+:} false; then :
- break
-fi
-done
-if ${ac_cv_search_pthread_create+:} false; then :
-
-else
- ac_cv_search_pthread_create=no
-fi
-rm conftest.$ac_ext
-LIBS=$ac_func_search_save_LIBS
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_pthread_create" >&5
-$as_echo "$ac_cv_search_pthread_create" >&6; }
-ac_res=$ac_cv_search_pthread_create
-if test "$ac_res" != no; then :
- test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
- have_pthreads=yes
-fi
-
-
-# Check whether --enable-bzip2 was given.
-if test "${enable_bzip2+set}" = set; then :
- enableval=$enable_bzip2;
-fi
-
-if test "x$enable_bzip2" != "xno"; then :
-
- have_bzip2=yes
-
-fi
-
-# Check whether --enable-zlib was given.
-if test "${enable_zlib+set}" = set; then :
- enableval=$enable_zlib;
-fi
-
-if test "x$enable_zlib" != "xno"; then :
-
- have_zlib=yes
-
-fi
-
-have_ps2pdf=no
-# Check whether --enable-pdfman was given.
-if test "${enable_pdfman+set}" = set; then :
- enableval=$enable_pdfman;
-fi
-
-if test "x$enable_pdfman" != "xno"; then :
-
- have_ps2pdf=yes
- # Extract the first word of "ps2pdf", so it can be a program name with args.
-set dummy ps2pdf; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_HAVE_PS2PDF+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- if test -n "$HAVE_PS2PDF"; then
- ac_cv_prog_HAVE_PS2PDF="$HAVE_PS2PDF" # Let the user override the test.
-else
-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_prog_HAVE_PS2PDF="yes"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
- done
-IFS=$as_save_IFS
-
- test -z "$ac_cv_prog_HAVE_PS2PDF" && ac_cv_prog_HAVE_PS2PDF="no"
-fi
-fi
-HAVE_PS2PDF=$ac_cv_prog_HAVE_PS2PDF
-if test -n "$HAVE_PS2PDF"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $HAVE_PS2PDF" >&5
-$as_echo "$HAVE_PS2PDF" >&6; }
-else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
-
- if test "x$HAVE_PS2PDF" = "xno"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: *** ps2pdf is required to build a PDF version of the manual" >&5
-$as_echo "$as_me: WARNING: *** ps2pdf is required to build a PDF version of the manual" >&2;}
- have_ps2pdf=no
- fi
-
-fi
-
-if test "x${have_pthreads}" = "xyes"; then
- for ac_header in pthread.h
-do :
- ac_fn_cxx_check_header_mongrel "$LINENO" "pthread.h" "ac_cv_header_pthread_h" "$ac_includes_default"
-if test "x$ac_cv_header_pthread_h" = xyes; then :
- cat >>confdefs.h <<_ACEOF
-#define HAVE_PTHREAD_H 1
-_ACEOF
-
-else
- have_pthreads=no
-fi
-
-done
-
-fi
-
-if test "x${have_bzip2}" = "xyes"; then
- for ac_header in bzlib.h
-do :
- ac_fn_cxx_check_header_mongrel "$LINENO" "bzlib.h" "ac_cv_header_bzlib_h" "$ac_includes_default"
-if test "x$ac_cv_header_bzlib_h" = xyes; then :
- cat >>confdefs.h <<_ACEOF
-#define HAVE_BZLIB_H 1
-_ACEOF
-
-else
- have_bzip2=no
-fi
-
-done
-
-fi
-
-if test "x${have_zlib}" = "xyes"; then
- for ac_header in zlib.h
-do :
- ac_fn_cxx_check_header_mongrel "$LINENO" "zlib.h" "ac_cv_header_zlib_h" "$ac_includes_default"
-if test "x$ac_cv_header_zlib_h" = xyes; then :
- cat >>confdefs.h <<_ACEOF
-#define HAVE_ZLIB_H 1
-_ACEOF
-
-else
- have_zlib=no
-fi
-
-done
-
-fi
-
- if test "x${have_bzip2}" = "xyes"; then
- HAVE_BZLIB_TRUE=
- HAVE_BZLIB_FALSE='#'
-else
- HAVE_BZLIB_TRUE='#'
- HAVE_BZLIB_FALSE=
-fi
-
- if test "x${have_zlib}" = "xyes"; then
- HAVE_ZLIB_TRUE=
- HAVE_ZLIB_FALSE='#'
-else
- HAVE_ZLIB_TRUE='#'
- HAVE_ZLIB_FALSE=
-fi
-
- if test "x${have_pthreads}" = "xyes"; then
- HAVE_PTHREADS_TRUE=
- HAVE_PTHREADS_FALSE='#'
-else
- HAVE_PTHREADS_TRUE='#'
- HAVE_PTHREADS_FALSE=
-fi
-
- if test "x${have_ps2pdf}" = "xyes"; then
- HAVE_PS2PDF_TRUE=
- HAVE_PS2PDF_FALSE='#'
-else
- HAVE_PS2PDF_TRUE='#'
- HAVE_PS2PDF_FALSE=
-fi
-
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-if test -n "$ac_tool_prefix"; then
- # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
-set dummy ${ac_tool_prefix}gcc; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_CC+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- if test -n "$CC"; then
- ac_cv_prog_CC="$CC" # Let the user override the test.
-else
-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_prog_CC="${ac_tool_prefix}gcc"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
- done
-IFS=$as_save_IFS
-
-fi
-fi
-CC=$ac_cv_prog_CC
-if test -n "$CC"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
-$as_echo "$CC" >&6; }
-else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
-
-fi
-if test -z "$ac_cv_prog_CC"; then
- ac_ct_CC=$CC
- # Extract the first word of "gcc", so it can be a program name with args.
-set dummy gcc; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_ac_ct_CC+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- if test -n "$ac_ct_CC"; then
- ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
-else
-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_prog_ac_ct_CC="gcc"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
- done
-IFS=$as_save_IFS
-
-fi
-fi
-ac_ct_CC=$ac_cv_prog_ac_ct_CC
-if test -n "$ac_ct_CC"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
-$as_echo "$ac_ct_CC" >&6; }
-else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
- if test "x$ac_ct_CC" = x; then
- CC=""
- else
- case $cross_compiling:$ac_tool_warned in
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-{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
-$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
-ac_tool_warned=yes ;;
-esac
- CC=$ac_ct_CC
- fi
-else
- CC="$ac_cv_prog_CC"
-fi
-
-if test -z "$CC"; then
- if test -n "$ac_tool_prefix"; then
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-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_CC+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- if test -n "$CC"; then
- ac_cv_prog_CC="$CC" # Let the user override the test.
-else
-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
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-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
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- ac_cv_prog_CC="${ac_tool_prefix}cc"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
- done
-IFS=$as_save_IFS
-
-fi
-fi
-CC=$ac_cv_prog_CC
-if test -n "$CC"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
-$as_echo "$CC" >&6; }
-else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
-
- fi
-fi
-if test -z "$CC"; then
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-set dummy cc; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_CC+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- if test -n "$CC"; then
- ac_cv_prog_CC="$CC" # Let the user override the test.
-else
- ac_prog_rejected=no
-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
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- ac_prog_rejected=yes
- continue
- fi
- ac_cv_prog_CC="cc"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
- done
-IFS=$as_save_IFS
-
-if test $ac_prog_rejected = yes; then
- # We found a bogon in the path, so make sure we never use it.
- set dummy $ac_cv_prog_CC
- shift
- if test $# != 0; then
- # We chose a different compiler from the bogus one.
- # However, it has the same basename, so the bogon will be chosen
- # first if we set CC to just the basename; use the full file name.
- shift
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-{
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-
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-
-
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-
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-{
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-{
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-{
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-
- print line
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-
-_ACAWK
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-
- case $ac_file$ac_mode in
- "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
- # Older Autoconf quotes --file arguments for eval, but not when files
- # are listed without --file. Let's play safe and only enable the eval
- # if we detect the quoting.
- case $CONFIG_FILES in
- *\'*) eval set x "$CONFIG_FILES" ;;
- *) set x $CONFIG_FILES ;;
- esac
- shift
- for mf
- do
- # Strip MF so we end up with the name of the file.
- mf=`echo "$mf" | sed -e 's/:.*$//'`
- # Check whether this is an Automake generated Makefile or not.
- # We used to match only the files named 'Makefile.in', but
- # some people rename them; so instead we look at the file content.
- # Grep'ing the first line is not enough: some people post-process
- # each Makefile.in and add a new line on top of each file to say so.
- # Grep'ing the whole file is not good either: AIX grep has a line
- # limit of 2048, but all sed's we know have understand at least 4000.
- if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
- dirpart=`$as_dirname -- "$mf" ||
-$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
- X"$mf" : 'X\(//\)[^/]' \| \
- X"$mf" : 'X\(//\)$' \| \
- X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$mf" |
- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
- s//\1/
- q
- }
- /^X\(\/\/\)[^/].*/{
- s//\1/
- q
- }
- /^X\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'`
- else
- continue
- fi
- # Extract the definition of DEPDIR, am__include, and am__quote
- # from the Makefile without running 'make'.
- DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
- test -z "$DEPDIR" && continue
- am__include=`sed -n 's/^am__include = //p' < "$mf"`
- test -z "$am__include" && continue
- am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
- # Find all dependency output files, they are included files with
- # $(DEPDIR) in their names. We invoke sed twice because it is the
- # simplest approach to changing $(DEPDIR) to its actual value in the
- # expansion.
- for file in `sed -n "
- s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
- sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
- # Make sure the directory exists.
- test -f "$dirpart/$file" && continue
- fdir=`$as_dirname -- "$file" ||
-$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
- X"$file" : 'X\(//\)[^/]' \| \
- X"$file" : 'X\(//\)$' \| \
- X"$file" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$file" |
- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
- s//\1/
- q
- }
- /^X\(\/\/\)[^/].*/{
- s//\1/
- q
- }
- /^X\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'`
- as_dir=$dirpart/$fdir; as_fn_mkdir_p
- # echo "creating $dirpart/$file"
- echo '# dummy' > "$dirpart/$file"
- done
- done
-}
- ;;
-
- esac
-done # for ac_tag
-
-
-as_fn_exit 0
-_ACEOF
-ac_clean_files=$ac_clean_files_save
-
-test $ac_write_fail = 0 ||
- as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
-
-
-# configure is writing to config.log, and then calls config.status.
-# config.status does its own redirection, appending to config.log.
-# Unfortunately, on DOS this fails, as config.log is still kept open
-# by configure, so config.status won't be able to write to it; its
-# output is simply discarded. So we exec the FD to /dev/null,
-# effectively closing config.log, so it can be properly (re)opened and
-# appended to by config.status. When coming back to configure, we
-# need to make the FD available again.
-if test "$no_create" != yes; then
- ac_cs_success=:
- ac_config_status_args=
- test "$silent" = yes &&
- ac_config_status_args="$ac_config_status_args --quiet"
- exec 5>/dev/null
- $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
- exec 5>>config.log
- # Use ||, not &&, to avoid exiting from the if with $? = 1, which
- # would make configure fail if this is the last instruction.
- $ac_cs_success || as_fn_exit 1
-fi
-if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
-$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
-fi
-
diff --git a/configure.ac b/configure.ac
index 25e5088..79d3c5c 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], [1.10.1], [torognes at ifi.uio.no])
+AC_INIT([vsearch], [1.11.1], [torognes at ifi.uio.no])
AM_INIT_AUTOMAKE([subdir-objects])
AC_LANG([C++])
AC_CONFIG_SRCDIR([src/vsearch.cc])
diff --git a/depcomp b/depcomp
deleted file mode 100755
index fc98710..0000000
--- a/depcomp
+++ /dev/null
@@ -1,791 +0,0 @@
-#! /bin/sh
-# depcomp - compile a program generating dependencies as side-effects
-
-scriptversion=2013-05-30.07; # UTC
-
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
-
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-# Originally written by Alexandre Oliva <oliva at dcc.unicamp.br>.
-
-case $1 in
- '')
- echo "$0: No command. Try '$0 --help' for more information." 1>&2
- exit 1;
- ;;
- -h | --h*)
- cat <<\EOF
-Usage: depcomp [--help] [--version] PROGRAM [ARGS]
-
-Run PROGRAMS ARGS to compile a file, generating dependencies
-as side-effects.
-
-Environment variables:
- depmode Dependency tracking mode.
- source Source file read by 'PROGRAMS ARGS'.
- object Object file output by 'PROGRAMS ARGS'.
- DEPDIR directory where to store dependencies.
- depfile Dependency file to output.
- tmpdepfile Temporary file to use when outputting dependencies.
- libtool Whether libtool is used (yes/no).
-
-Report bugs to <bug-automake at gnu.org>.
-EOF
- exit $?
- ;;
- -v | --v*)
- echo "depcomp $scriptversion"
- exit $?
- ;;
-esac
-
-# Get the directory component of the given path, and save it in the
-# global variables '$dir'. Note that this directory component will
-# be either empty or ending with a '/' character. This is deliberate.
-set_dir_from ()
-{
- case $1 in
- */*) dir=`echo "$1" | sed -e 's|/[^/]*$|/|'`;;
- *) dir=;;
- esac
-}
-
-# Get the suffix-stripped basename of the given path, and save it the
-# global variable '$base'.
-set_base_from ()
-{
- base=`echo "$1" | sed -e 's|^.*/||' -e 's/\.[^.]*$//'`
-}
-
-# If no dependency file was actually created by the compiler invocation,
-# we still have to create a dummy depfile, to avoid errors with the
-# Makefile "include basename.Plo" scheme.
-make_dummy_depfile ()
-{
- echo "#dummy" > "$depfile"
-}
-
-# Factor out some common post-processing of the generated depfile.
-# Requires the auxiliary global variable '$tmpdepfile' to be set.
-aix_post_process_depfile ()
-{
- # If the compiler actually managed to produce a dependency file,
- # post-process it.
- if test -f "$tmpdepfile"; then
- # Each line is of the form 'foo.o: dependency.h'.
- # Do two passes, one to just change these to
- # $object: dependency.h
- # and one to simply output
- # dependency.h:
- # which is needed to avoid the deleted-header problem.
- { sed -e "s,^.*\.[$lower]*:,$object:," < "$tmpdepfile"
- sed -e "s,^.*\.[$lower]*:[$tab ]*,," -e 's,$,:,' < "$tmpdepfile"
- } > "$depfile"
- rm -f "$tmpdepfile"
- else
- make_dummy_depfile
- fi
-}
-
-# A tabulation character.
-tab=' '
-# A newline character.
-nl='
-'
-# Character ranges might be problematic outside the C locale.
-# These definitions help.
-upper=ABCDEFGHIJKLMNOPQRSTUVWXYZ
-lower=abcdefghijklmnopqrstuvwxyz
-digits=0123456789
-alpha=${upper}${lower}
-
-if test -z "$depmode" || test -z "$source" || test -z "$object"; then
- echo "depcomp: Variables source, object and depmode must be set" 1>&2
- exit 1
-fi
-
-# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
-depfile=${depfile-`echo "$object" |
- sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
-tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
-
-rm -f "$tmpdepfile"
-
-# Avoid interferences from the environment.
-gccflag= dashmflag=
-
-# Some modes work just like other modes, but use different flags. We
-# parameterize here, but still list the modes in the big case below,
-# to make depend.m4 easier to write. Note that we *cannot* use a case
-# here, because this file can only contain one case statement.
-if test "$depmode" = hp; then
- # HP compiler uses -M and no extra arg.
- gccflag=-M
- depmode=gcc
-fi
-
-if test "$depmode" = dashXmstdout; then
- # This is just like dashmstdout with a different argument.
- dashmflag=-xM
- depmode=dashmstdout
-fi
-
-cygpath_u="cygpath -u -f -"
-if test "$depmode" = msvcmsys; then
- # This is just like msvisualcpp but w/o cygpath translation.
- # Just convert the backslash-escaped backslashes to single forward
- # slashes to satisfy depend.m4
- cygpath_u='sed s,\\\\,/,g'
- depmode=msvisualcpp
-fi
-
-if test "$depmode" = msvc7msys; then
- # This is just like msvc7 but w/o cygpath translation.
- # Just convert the backslash-escaped backslashes to single forward
- # slashes to satisfy depend.m4
- cygpath_u='sed s,\\\\,/,g'
- depmode=msvc7
-fi
-
-if test "$depmode" = xlc; then
- # IBM C/C++ Compilers xlc/xlC can output gcc-like dependency information.
- gccflag=-qmakedep=gcc,-MF
- depmode=gcc
-fi
-
-case "$depmode" in
-gcc3)
-## gcc 3 implements dependency tracking that does exactly what
-## we want. Yay! Note: for some reason libtool 1.4 doesn't like
-## it if -MD -MP comes after the -MF stuff. Hmm.
-## Unfortunately, FreeBSD c89 acceptance of flags depends upon
-## the command line argument order; so add the flags where they
-## appear in depend2.am. Note that the slowdown incurred here
-## affects only configure: in makefiles, %FASTDEP% shortcuts this.
- for arg
- do
- case $arg in
- -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;
- *) set fnord "$@" "$arg" ;;
- esac
- shift # fnord
- shift # $arg
- done
- "$@"
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
- fi
- mv "$tmpdepfile" "$depfile"
- ;;
-
-gcc)
-## Note that this doesn't just cater to obsosete pre-3.x GCC compilers.
-## but also to in-use compilers like IMB xlc/xlC and the HP C compiler.
-## (see the conditional assignment to $gccflag above).
-## There are various ways to get dependency output from gcc. Here's
-## why we pick this rather obscure method:
-## - Don't want to use -MD because we'd like the dependencies to end
-## up in a subdir. Having to rename by hand is ugly.
-## (We might end up doing this anyway to support other compilers.)
-## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
-## -MM, not -M (despite what the docs say). Also, it might not be
-## supported by the other compilers which use the 'gcc' depmode.
-## - Using -M directly means running the compiler twice (even worse
-## than renaming).
- if test -z "$gccflag"; then
- gccflag=-MD,
- fi
- "$@" -Wp,"$gccflag$tmpdepfile"
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- # The second -e expression handles DOS-style file names with drive
- # letters.
- sed -e 's/^[^:]*: / /' \
- -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
-## This next piece of magic avoids the "deleted header file" problem.
-## The problem is that when a header file which appears in a .P file
-## is deleted, the dependency causes make to die (because there is
-## typically no way to rebuild the header). We avoid this by adding
-## dummy dependencies for each header file. Too bad gcc doesn't do
-## this for us directly.
-## Some versions of gcc put a space before the ':'. On the theory
-## that the space means something, we add a space to the output as
-## well. hp depmode also adds that space, but also prefixes the VPATH
-## to the object. Take care to not repeat it in the output.
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly. Breaking it into two sed invocations is a workaround.
- tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^\\$//' -e '/^$/d' -e "s|.*$object$||" -e '/:$/d' \
- | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-hp)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
- exit 1
- ;;
-
-sgi)
- if test "$libtool" = yes; then
- "$@" "-Wp,-MDupdate,$tmpdepfile"
- else
- "$@" -MDupdate "$tmpdepfile"
- fi
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
-
- if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
- echo "$object : \\" > "$depfile"
- # Clip off the initial element (the dependent). Don't try to be
- # clever and replace this with sed code, as IRIX sed won't handle
- # lines with more than a fixed number of characters (4096 in
- # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
- # the IRIX cc adds comments like '#:fec' to the end of the
- # dependency line.
- tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' \
- | tr "$nl" ' ' >> "$depfile"
- echo >> "$depfile"
- # The second pass generates a dummy entry for each header file.
- tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
- >> "$depfile"
- else
- make_dummy_depfile
- fi
- rm -f "$tmpdepfile"
- ;;
-
-xlc)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
- exit 1
- ;;
-
-aix)
- # The C for AIX Compiler uses -M and outputs the dependencies
- # in a .u file. In older versions, this file always lives in the
- # current directory. Also, the AIX compiler puts '$object:' at the
- # start of each line; $object doesn't have directory information.
- # Version 6 uses the directory in both cases.
- set_dir_from "$object"
- set_base_from "$object"
- if test "$libtool" = yes; then
- tmpdepfile1=$dir$base.u
- tmpdepfile2=$base.u
- tmpdepfile3=$dir.libs/$base.u
- "$@" -Wc,-M
- else
- tmpdepfile1=$dir$base.u
- tmpdepfile2=$dir$base.u
- tmpdepfile3=$dir$base.u
- "$@" -M
- fi
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
- exit $stat
- fi
-
- for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
- do
- test -f "$tmpdepfile" && break
- done
- aix_post_process_depfile
- ;;
-
-tcc)
- # tcc (Tiny C Compiler) understand '-MD -MF file' since version 0.9.26
- # FIXME: That version still under development at the moment of writing.
- # Make that this statement remains true also for stable, released
- # versions.
- # It will wrap lines (doesn't matter whether long or short) with a
- # trailing '\', as in:
- #
- # foo.o : \
- # foo.c \
- # foo.h \
- #
- # It will put a trailing '\' even on the last line, and will use leading
- # spaces rather than leading tabs (at least since its commit 0394caf7
- # "Emit spaces for -MD").
- "$@" -MD -MF "$tmpdepfile"
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- # Each non-empty line is of the form 'foo.o : \' or ' dep.h \'.
- # We have to change lines of the first kind to '$object: \'.
- sed -e "s|.*:|$object :|" < "$tmpdepfile" > "$depfile"
- # And for each line of the second kind, we have to emit a 'dep.h:'
- # dummy dependency, to avoid the deleted-header problem.
- sed -n -e 's|^ *\(.*\) *\\$|\1:|p' < "$tmpdepfile" >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-## The order of this option in the case statement is important, since the
-## shell code in configure will try each of these formats in the order
-## listed in this file. A plain '-MD' option would be understood by many
-## compilers, so we must ensure this comes after the gcc and icc options.
-pgcc)
- # Portland's C compiler understands '-MD'.
- # Will always output deps to 'file.d' where file is the root name of the
- # source file under compilation, even if file resides in a subdirectory.
- # The object file name does not affect the name of the '.d' file.
- # pgcc 10.2 will output
- # foo.o: sub/foo.c sub/foo.h
- # and will wrap long lines using '\' :
- # foo.o: sub/foo.c ... \
- # sub/foo.h ... \
- # ...
- set_dir_from "$object"
- # Use the source, not the object, to determine the base name, since
- # that's sadly what pgcc will do too.
- set_base_from "$source"
- tmpdepfile=$base.d
-
- # For projects that build the same source file twice into different object
- # files, the pgcc approach of using the *source* file root name can cause
- # problems in parallel builds. Use a locking strategy to avoid stomping on
- # the same $tmpdepfile.
- lockdir=$base.d-lock
- trap "
- echo '$0: caught signal, cleaning up...' >&2
- rmdir '$lockdir'
- exit 1
- " 1 2 13 15
- numtries=100
- i=$numtries
- while test $i -gt 0; do
- # mkdir is a portable test-and-set.
- if mkdir "$lockdir" 2>/dev/null; then
- # This process acquired the lock.
- "$@" -MD
- stat=$?
- # Release the lock.
- rmdir "$lockdir"
- break
- else
- # If the lock is being held by a different process, wait
- # until the winning process is done or we timeout.
- while test -d "$lockdir" && test $i -gt 0; do
- sleep 1
- i=`expr $i - 1`
- done
- fi
- i=`expr $i - 1`
- done
- trap - 1 2 13 15
- if test $i -le 0; then
- echo "$0: failed to acquire lock after $numtries attempts" >&2
- echo "$0: check lockdir '$lockdir'" >&2
- exit 1
- fi
-
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- # Each line is of the form `foo.o: dependent.h',
- # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
- # Do two passes, one to just change these to
- # `$object: dependent.h' and one to simply `dependent.h:'.
- sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
- # Some versions of the HPUX 10.20 sed can't process this invocation
- # correctly. Breaking it into two sed invocations is a workaround.
- sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" \
- | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-hp2)
- # The "hp" stanza above does not work with aCC (C++) and HP's ia64
- # compilers, which have integrated preprocessors. The correct option
- # to use with these is +Maked; it writes dependencies to a file named
- # 'foo.d', which lands next to the object file, wherever that
- # happens to be.
- # Much of this is similar to the tru64 case; see comments there.
- set_dir_from "$object"
- set_base_from "$object"
- if test "$libtool" = yes; then
- tmpdepfile1=$dir$base.d
- tmpdepfile2=$dir.libs/$base.d
- "$@" -Wc,+Maked
- else
- tmpdepfile1=$dir$base.d
- tmpdepfile2=$dir$base.d
- "$@" +Maked
- fi
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile1" "$tmpdepfile2"
- exit $stat
- fi
-
- for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"
- do
- test -f "$tmpdepfile" && break
- done
- if test -f "$tmpdepfile"; then
- sed -e "s,^.*\.[$lower]*:,$object:," "$tmpdepfile" > "$depfile"
- # Add 'dependent.h:' lines.
- sed -ne '2,${
- s/^ *//
- s/ \\*$//
- s/$/:/
- p
- }' "$tmpdepfile" >> "$depfile"
- else
- make_dummy_depfile
- fi
- rm -f "$tmpdepfile" "$tmpdepfile2"
- ;;
-
-tru64)
- # The Tru64 compiler uses -MD to generate dependencies as a side
- # effect. 'cc -MD -o foo.o ...' puts the dependencies into 'foo.o.d'.
- # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
- # dependencies in 'foo.d' instead, so we check for that too.
- # Subdirectories are respected.
- set_dir_from "$object"
- set_base_from "$object"
-
- if test "$libtool" = yes; then
- # Libtool generates 2 separate objects for the 2 libraries. These
- # two compilations output dependencies in $dir.libs/$base.o.d and
- # in $dir$base.o.d. We have to check for both files, because
- # one of the two compilations can be disabled. We should prefer
- # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
- # automatically cleaned when .libs/ is deleted, while ignoring
- # the former would cause a distcleancheck panic.
- tmpdepfile1=$dir$base.o.d # libtool 1.5
- tmpdepfile2=$dir.libs/$base.o.d # Likewise.
- tmpdepfile3=$dir.libs/$base.d # Compaq CCC V6.2-504
- "$@" -Wc,-MD
- else
- tmpdepfile1=$dir$base.d
- tmpdepfile2=$dir$base.d
- tmpdepfile3=$dir$base.d
- "$@" -MD
- fi
-
- stat=$?
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- rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
- exit $stat
- fi
-
- for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
- do
- test -f "$tmpdepfile" && break
- done
- # Same post-processing that is required for AIX mode.
- aix_post_process_depfile
- ;;
-
-msvc7)
- if test "$libtool" = yes; then
- showIncludes=-Wc,-showIncludes
- else
- showIncludes=-showIncludes
- fi
- "$@" $showIncludes > "$tmpdepfile"
- stat=$?
- grep -v '^Note: including file: ' "$tmpdepfile"
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- # The first sed program below extracts the file names and escapes
- # backslashes for cygpath. The second sed program outputs the file
- # name when reading, but also accumulates all include files in the
- # hold buffer in order to output them again at the end. This only
- # works with sed implementations that can handle large buffers.
- sed < "$tmpdepfile" -n '
-/^Note: including file: *\(.*\)/ {
- s//\1/
- s/\\/\\\\/g
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-}' | $cygpath_u | sort -u | sed -n '
-s/ /\\ /g
-s/\(.*\)/'"$tab"'\1 \\/p
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-H
-$ {
- s/.*/'"$tab"'/
- G
- p
-}' >> "$depfile"
- echo >> "$depfile" # make sure the fragment doesn't end with a backslash
- rm -f "$tmpdepfile"
- ;;
-
-msvc7msys)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
- exit 1
- ;;
-
-#nosideeffect)
- # This comment above is used by automake to tell side-effect
- # dependency tracking mechanisms from slower ones.
-
-dashmstdout)
- # Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout, regardless of -o.
- "$@" || exit $?
-
- # Remove the call to Libtool.
- if test "$libtool" = yes; then
- while test "X$1" != 'X--mode=compile'; do
- shift
- done
- shift
- fi
-
- # Remove '-o $object'.
- IFS=" "
- for arg
- do
- case $arg in
- -o)
- shift
- ;;
- $object)
- shift
- ;;
- *)
- set fnord "$@" "$arg"
- shift # fnord
- shift # $arg
- ;;
- esac
- done
-
- test -z "$dashmflag" && dashmflag=-M
- # Require at least two characters before searching for ':'
- # in the target name. This is to cope with DOS-style filenames:
- # a dependency such as 'c:/foo/bar' could be seen as target 'c' otherwise.
- "$@" $dashmflag |
- sed "s|^[$tab ]*[^:$tab ][^:][^:]*:[$tab ]*|$object: |" > "$tmpdepfile"
- rm -f "$depfile"
- cat < "$tmpdepfile" > "$depfile"
- # Some versions of the HPUX 10.20 sed can't process this sed invocation
- # correctly. Breaking it into two sed invocations is a workaround.
- tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
- | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-dashXmstdout)
- # This case only exists to satisfy depend.m4. It is never actually
- # run, as this mode is specially recognized in the preamble.
- exit 1
- ;;
-
-makedepend)
- "$@" || exit $?
- # Remove any Libtool call
- if test "$libtool" = yes; then
- while test "X$1" != 'X--mode=compile'; do
- shift
- done
- shift
- fi
- # X makedepend
- shift
- cleared=no eat=no
- for arg
- do
- case $cleared in
- no)
- set ""; shift
- cleared=yes ;;
- esac
- if test $eat = yes; then
- eat=no
- continue
- fi
- case "$arg" in
- -D*|-I*)
- set fnord "$@" "$arg"; shift ;;
- # Strip any option that makedepend may not understand. Remove
- # the object too, otherwise makedepend will parse it as a source file.
- -arch)
- eat=yes ;;
- -*|$object)
- ;;
- *)
- set fnord "$@" "$arg"; shift ;;
- esac
- done
- obj_suffix=`echo "$object" | sed 's/^.*\././'`
- touch "$tmpdepfile"
- ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
- rm -f "$depfile"
- # makedepend may prepend the VPATH from the source file name to the object.
- # No need to regex-escape $object, excess matching of '.' is harmless.
- sed "s|^.*\($object *:\)|\1|" "$tmpdepfile" > "$depfile"
- # Some versions of the HPUX 10.20 sed can't process the last invocation
- # correctly. Breaking it into two sed invocations is a workaround.
- sed '1,2d' "$tmpdepfile" \
- | tr ' ' "$nl" \
- | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
- | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile" "$tmpdepfile".bak
- ;;
-
-cpp)
- # Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout.
- "$@" || exit $?
-
- # Remove the call to Libtool.
- if test "$libtool" = yes; then
- while test "X$1" != 'X--mode=compile'; do
- shift
- done
- shift
- fi
-
- # Remove '-o $object'.
- IFS=" "
- for arg
- do
- case $arg in
- -o)
- shift
- ;;
- $object)
- shift
- ;;
- *)
- set fnord "$@" "$arg"
- shift # fnord
- shift # $arg
- ;;
- esac
- done
-
- "$@" -E \
- | sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
- -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
- | sed '$ s: \\$::' > "$tmpdepfile"
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- cat < "$tmpdepfile" >> "$depfile"
- sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-msvisualcpp)
- # Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout.
- "$@" || exit $?
-
- # Remove the call to Libtool.
- if test "$libtool" = yes; then
- while test "X$1" != 'X--mode=compile'; do
- shift
- done
- shift
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-
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- -o)
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- set fnord "$@"
- shift
- shift
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- *)
- set fnord "$@" "$arg"
- shift
- shift
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- "$@" -E 2>/dev/null |
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- sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::'"$tab"'\1 \\:p' >> "$depfile"
- echo "$tab" >> "$depfile"
- sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-msvcmsys)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
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-
-none)
- exec "$@"
- ;;
-
-*)
- echo "Unknown depmode $depmode" 1>&2
- exit 1
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-esac
-
-exit 0
-
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-# time-stamp-end: "; # UTC"
-# End:
diff --git a/install-sh b/install-sh
deleted file mode 100755
index 0b0fdcb..0000000
--- a/install-sh
+++ /dev/null
@@ -1,501 +0,0 @@
-#!/bin/sh
-# install - install a program, script, or datafile
-
-scriptversion=2013-12-25.23; # UTC
-
-# This originates from X11R5 (mit/util/scripts/install.sh), which was
-# later released in X11R6 (xc/config/util/install.sh) with the
-# following copyright and license.
-#
-# Copyright (C) 1994 X Consortium
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to
-# deal in the Software without restriction, including without limitation the
-# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
-# sell copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
-# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
-# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-#
-# Except as contained in this notice, the name of the X Consortium shall not
-# be used in advertising or otherwise to promote the sale, use or other deal-
-# ings in this Software without prior written authorization from the X Consor-
-# tium.
-#
-#
-# FSF changes to this file are in the public domain.
-#
-# Calling this script install-sh is preferred over install.sh, to prevent
-# 'make' implicit rules from creating a file called install from it
-# when there is no Makefile.
-#
-# This script is compatible with the BSD install script, but was written
-# from scratch.
-
-tab=' '
-nl='
-'
-IFS=" $tab$nl"
-
-# Set DOITPROG to "echo" to test this script.
-
-doit=${DOITPROG-}
-doit_exec=${doit:-exec}
-
-# Put in absolute file names if you don't have them in your path;
-# or use environment vars.
-
-chgrpprog=${CHGRPPROG-chgrp}
-chmodprog=${CHMODPROG-chmod}
-chownprog=${CHOWNPROG-chown}
-cmpprog=${CMPPROG-cmp}
-cpprog=${CPPROG-cp}
-mkdirprog=${MKDIRPROG-mkdir}
-mvprog=${MVPROG-mv}
-rmprog=${RMPROG-rm}
-stripprog=${STRIPPROG-strip}
-
-posix_mkdir=
-
-# Desired mode of installed file.
-mode=0755
-
-chgrpcmd=
-chmodcmd=$chmodprog
-chowncmd=
-mvcmd=$mvprog
-rmcmd="$rmprog -f"
-stripcmd=
-
-src=
-dst=
-dir_arg=
-dst_arg=
-
-copy_on_change=false
-is_target_a_directory=possibly
-
-usage="\
-Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
- or: $0 [OPTION]... SRCFILES... DIRECTORY
- or: $0 [OPTION]... -t DIRECTORY SRCFILES...
- or: $0 [OPTION]... -d DIRECTORIES...
-
-In the 1st form, copy SRCFILE to DSTFILE.
-In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
-In the 4th, create DIRECTORIES.
-
-Options:
- --help display this help and exit.
- --version display version info and exit.
-
- -c (ignored)
- -C install only if different (preserve the last data modification time)
- -d create directories instead of installing files.
- -g GROUP $chgrpprog installed files to GROUP.
- -m MODE $chmodprog installed files to MODE.
- -o USER $chownprog installed files to USER.
- -s $stripprog installed files.
- -t DIRECTORY install into DIRECTORY.
- -T report an error if DSTFILE is a directory.
-
-Environment variables override the default commands:
- CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
- RMPROG STRIPPROG
-"
-
-while test $# -ne 0; do
- case $1 in
- -c) ;;
-
- -C) copy_on_change=true;;
-
- -d) dir_arg=true;;
-
- -g) chgrpcmd="$chgrpprog $2"
- shift;;
-
- --help) echo "$usage"; exit $?;;
-
- -m) mode=$2
- case $mode in
- *' '* | *"$tab"* | *"$nl"* | *'*'* | *'?'* | *'['*)
- echo "$0: invalid mode: $mode" >&2
- exit 1;;
- esac
- shift;;
-
- -o) chowncmd="$chownprog $2"
- shift;;
-
- -s) stripcmd=$stripprog;;
-
- -t)
- is_target_a_directory=always
- dst_arg=$2
- # Protect names problematic for 'test' and other utilities.
- case $dst_arg in
- -* | [=\(\)!]) dst_arg=./$dst_arg;;
- esac
- shift;;
-
- -T) is_target_a_directory=never;;
-
- --version) echo "$0 $scriptversion"; exit $?;;
-
- --) shift
- break;;
-
- -*) echo "$0: invalid option: $1" >&2
- exit 1;;
-
- *) break;;
- esac
- shift
-done
-
-# We allow the use of options -d and -T together, by making -d
-# take the precedence; this is for compatibility with GNU install.
-
-if test -n "$dir_arg"; then
- if test -n "$dst_arg"; then
- echo "$0: target directory not allowed when installing a directory." >&2
- exit 1
- fi
-fi
-
-if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
- # When -d is used, all remaining arguments are directories to create.
- # When -t is used, the destination is already specified.
- # Otherwise, the last argument is the destination. Remove it from $@.
- for arg
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- if test -n "$dst_arg"; then
- # $@ is not empty: it contains at least $arg.
- set fnord "$@" "$dst_arg"
- shift # fnord
- fi
- shift # arg
- dst_arg=$arg
- # Protect names problematic for 'test' and other utilities.
- case $dst_arg in
- -* | [=\(\)!]) dst_arg=./$dst_arg;;
- esac
- done
-fi
-
-if test $# -eq 0; then
- if test -z "$dir_arg"; then
- echo "$0: no input file specified." >&2
- exit 1
- fi
- # It's OK to call 'install-sh -d' without argument.
- # This can happen when creating conditional directories.
- exit 0
-fi
-
-if test -z "$dir_arg"; then
- if test $# -gt 1 || test "$is_target_a_directory" = always; then
- if test ! -d "$dst_arg"; then
- echo "$0: $dst_arg: Is not a directory." >&2
- exit 1
- fi
- fi
-fi
-
-if test -z "$dir_arg"; then
- do_exit='(exit $ret); exit $ret'
- trap "ret=129; $do_exit" 1
- trap "ret=130; $do_exit" 2
- trap "ret=141; $do_exit" 13
- trap "ret=143; $do_exit" 15
-
- # Set umask so as not to create temps with too-generous modes.
- # However, 'strip' requires both read and write access to temps.
- case $mode in
- # Optimize common cases.
- *644) cp_umask=133;;
- *755) cp_umask=22;;
-
- *[0-7])
- if test -z "$stripcmd"; then
- u_plus_rw=
- else
- u_plus_rw='% 200'
- fi
- cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
- *)
- if test -z "$stripcmd"; then
- u_plus_rw=
- else
- u_plus_rw=,u+rw
- fi
- cp_umask=$mode$u_plus_rw;;
- esac
-fi
-
-for src
-do
- # Protect names problematic for 'test' and other utilities.
- case $src in
- -* | [=\(\)!]) src=./$src;;
- esac
-
- if test -n "$dir_arg"; then
- dst=$src
- dstdir=$dst
- test -d "$dstdir"
- dstdir_status=$?
- else
-
- # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
- # might cause directories to be created, which would be especially bad
- # if $src (and thus $dsttmp) contains '*'.
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- echo "$0: $src does not exist." >&2
- exit 1
- fi
-
- if test -z "$dst_arg"; then
- echo "$0: no destination specified." >&2
- exit 1
- fi
- dst=$dst_arg
-
- # If destination is a directory, append the input filename; won't work
- # if double slashes aren't ignored.
- if test -d "$dst"; then
- if test "$is_target_a_directory" = never; then
- echo "$0: $dst_arg: Is a directory" >&2
- exit 1
- fi
- dstdir=$dst
- dst=$dstdir/`basename "$src"`
- dstdir_status=0
- else
- dstdir=`dirname "$dst"`
- test -d "$dstdir"
- dstdir_status=$?
- fi
- fi
-
- obsolete_mkdir_used=false
-
- if test $dstdir_status != 0; then
- case $posix_mkdir in
- '')
- # Create intermediate dirs using mode 755 as modified by the umask.
- # This is like FreeBSD 'install' as of 1997-10-28.
- umask=`umask`
- case $stripcmd.$umask in
- # Optimize common cases.
- *[2367][2367]) mkdir_umask=$umask;;
- .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
-
- *[0-7])
- mkdir_umask=`expr $umask + 22 \
- - $umask % 100 % 40 + $umask % 20 \
- - $umask % 10 % 4 + $umask % 2
- `;;
- *) mkdir_umask=$umask,go-w;;
- esac
-
- # With -d, create the new directory with the user-specified mode.
- # Otherwise, rely on $mkdir_umask.
- if test -n "$dir_arg"; then
- mkdir_mode=-m$mode
- else
- mkdir_mode=
- fi
-
- posix_mkdir=false
- case $umask in
- *[123567][0-7][0-7])
- # POSIX mkdir -p sets u+wx bits regardless of umask, which
- # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
- ;;
- *)
- tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
- trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
-
- if (umask $mkdir_umask &&
- exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
- then
- if test -z "$dir_arg" || {
- # Check for POSIX incompatibilities with -m.
- # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
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- # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
- ls_ld_tmpdir=`ls -ld "$tmpdir"`
- case $ls_ld_tmpdir in
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- d????-?--*) different_mode=755;;
- *) false;;
- esac &&
- $mkdirprog -m$different_mode -p -- "$tmpdir" && {
- ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
- test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
- }
- }
- then posix_mkdir=:
- fi
- rmdir "$tmpdir/d" "$tmpdir"
- else
- # Remove any dirs left behind by ancient mkdir implementations.
- rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
- fi
- trap '' 0;;
- esac;;
- esac
-
- if
- $posix_mkdir && (
- umask $mkdir_umask &&
- $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
- )
- then :
- else
-
- # The umask is ridiculous, or mkdir does not conform to POSIX,
- # or it failed possibly due to a race condition. Create the
- # directory the slow way, step by step, checking for races as we go.
-
- case $dstdir in
- /*) prefix='/';;
- [-=\(\)!]*) prefix='./';;
- *) prefix='';;
- esac
-
- oIFS=$IFS
- IFS=/
- set -f
- set fnord $dstdir
- shift
- set +f
- IFS=$oIFS
-
- prefixes=
-
- for d
- do
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-
- prefix=$prefix$d
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- prefixes=
- else
- if $posix_mkdir; then
- (umask=$mkdir_umask &&
- $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
- # Don't fail if two instances are running concurrently.
- test -d "$prefix" || exit 1
- else
- case $prefix in
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- *) qprefix=$prefix;;
- esac
- prefixes="$prefixes '$qprefix'"
- fi
- fi
- prefix=$prefix/
- done
-
- if test -n "$prefixes"; then
- # Don't fail if two instances are running concurrently.
- (umask $mkdir_umask &&
- eval "\$doit_exec \$mkdirprog $prefixes") ||
- test -d "$dstdir" || exit 1
- obsolete_mkdir_used=true
- fi
- fi
- fi
-
- if test -n "$dir_arg"; then
- { test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
- { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
- { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
- test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
- else
-
- # Make a couple of temp file names in the proper directory.
- dsttmp=$dstdir/_inst.$$_
- rmtmp=$dstdir/_rm.$$_
-
- # Trap to clean up those temp files at exit.
- trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
-
- # Copy the file name to the temp name.
- (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
-
- # and set any options; do chmod last to preserve setuid bits.
- #
- # If any of these fail, we abort the whole thing. If we want to
- # ignore errors from any of these, just make sure not to ignore
- # errors from the above "$doit $cpprog $src $dsttmp" command.
- #
- { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
- { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
- { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
- { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
-
- # If -C, don't bother to copy if it wouldn't change the file.
- if $copy_on_change &&
- old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
- new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
- set -f &&
- set X $old && old=:$2:$4:$5:$6 &&
- set X $new && new=:$2:$4:$5:$6 &&
- set +f &&
- test "$old" = "$new" &&
- $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
- then
- rm -f "$dsttmp"
- else
- # Rename the file to the real destination.
- $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
-
- # The rename failed, perhaps because mv can't rename something else
- # to itself, or perhaps because mv is so ancient that it does not
- # support -f.
- {
- # Now remove or move aside any old file at destination location.
- # We try this two ways since rm can't unlink itself on some
- # systems and the destination file might be busy for other
- # reasons. In this case, the final cleanup might fail but the new
- # file should still install successfully.
- {
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diff --git a/man/vsearch.1 b/man/vsearch.1
index 5fd7c2f..4572afb 100644
--- a/man/vsearch.1
+++ b/man/vsearch.1
@@ -1,5 +1,5 @@
.\" ============================================================================
-.TH vsearch 1 "February 23, 2016" "version 1.10.1" "USER COMMANDS"
+.TH vsearch 1 "April 13, 2016" "version 1.11.1" "USER COMMANDS"
.\" ============================================================================
.SH NAME
vsearch \(em chimera detection, clustering, dereplication and
@@ -727,8 +727,9 @@ complement sequences.
.PP
.TP 9
.B \-\-eeout
-When using \-\-fastq_filter, and when writing FASTQ file output,
-include the number of expected errors in the sequence header.
+For \-\-fastq_filter or \-\-fastq_mergepairs, include the
+number of expected errors (ee) in the sequence header of FASTQ and FASTA
+files. This option is a synonym of the \-\-fastq_eeout option.
.TP
.BI \-\-eetabbedout \0filename
When specified with the \-\-fastq_mergepairs command, write statistics
@@ -803,8 +804,9 @@ mimimum and maximum output quality scores may be limited using the
specified with the \-\-fastqout option.
.TP
.B \-\-fastq_eeout
-When writing FASTQ file output, include the number of expected errors
-in the sequence header. Used with \-\-fastq_mergepairs.
+For \-\-fastq_filter or \-\-fastq_mergepairs, include the
+number of expected errors (ee) in the sequence header of FASTQ and FASTA
+files. This option is a synonym of the \-\-eeout option.
.TP
.BI \-\-fastq_eestats \0filename
Analyse a FASTQ file and report statistics on the sequence lengths,
@@ -856,7 +858,7 @@ With the \-\-fastq_filter command, discard sequences with more than
the specified number of expected errors per base.
.TP
.BI \-\-fastq_maxmergelen\~ "positive integer"
-Specifity the maximum length of the merged sequence with the
+Specify the maximum length of the merged sequence with the
\-\-fastq_mergepairs command. By default there is no limit.
.TP
.BI \-\-fastq_maxns\~ "positive integer"
@@ -973,8 +975,8 @@ specified FASTQ file.
.BI \-\-fastx_revcomp \0filename
Reverse-complement the sequences in the given FASTA or FASTQ file to a
files specified with the \-\-fastaout and/or \-\-fastqout options. If
-the input file is in FASTA format, the output can not be written top a
-FASTQ file due to missing base quality scores.
+the input file is in FASTA format, the output can not be written back
+to a FASTQ file due to missing base quality scores.
.TP
.BI \-\-label_suffix\~ string
Label to add as a suffix to the header in the output from
@@ -1703,7 +1705,6 @@ Write abundance information to the output file.
.TP
.B \-\-xsize
Strip abundance information from the headers when writing the output file.
-.TP
.RE
.PP
.\" ----------------------------------------------------------------------------
@@ -2436,6 +2437,21 @@ typos. Added relabelling to files produced with \-\-consout and
Fixed a bug affecting the fastq_mergepairs command causing FASTQ
headers to be truncated at first space. Full headers are now included
in the output (no matter if --notrunclabels is in effect or not).
+.TP
+.BR v1.10.2\~ "released March 18, 2016"
+Fixed a bug causing a segmentation fault when running usearch_global
+with an empty query sequence. Also fixed a bug causing imperfect
+alignments to be reported with an alignment string of "=" in uc output
+files. Fixed typos in man file. Fixed fasta/fastq processing code
+regarding presence or absence of compression library header files.
+.TP
+.BR v1.11.1\~ "released April 13, 2016"
+Added strand information in UC file for derep_fulllength and
+derep_prefix. Added expected errors (ee) to header of FASTA files
+specified with \-\-fastaout and \-\-fastaout_discarded when \-\-eeout
+or \-\-fastq_eeout option is in effect for fastq_filter and
+fastq_mergepairs. The options \-\-eeout and \-\-fastq_eeout are now
+equivalent.
.RE
.LP
.\" ============================================================================
diff --git a/missing b/missing
deleted file mode 100755
index f62bbae..0000000
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- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libcpu_ssse3_a_CXXFLAGS) $(CXXFLAGS) -c -o libcpu_ssse3_a-cpu.obj `if test -f 'cpu.cc'; then $(CYGPATH_W) 'cpu.cc'; else $(CYGPATH_W) '$(srcdir)/cpu.cc'; fi`
-
-ID: $(am__tagged_files)
- $(am__define_uniq_tagged_files); mkid -fID $$unique
-tags: tags-am
-TAGS: tags
-
-tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
- set x; \
- here=`pwd`; \
- $(am__define_uniq_tagged_files); \
- shift; \
- if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
- test -n "$$unique" || unique=$$empty_fix; \
- if test $$# -gt 0; then \
- $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
- "$$@" $$unique; \
- else \
- $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
- $$unique; \
- fi; \
- fi
-ctags: ctags-am
-
-CTAGS: ctags
-ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
- $(am__define_uniq_tagged_files); \
- test -z "$(CTAGS_ARGS)$$unique" \
- || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
- $$unique
-
-GTAGS:
- here=`$(am__cd) $(top_builddir) && pwd` \
- && $(am__cd) $(top_srcdir) \
- && gtags -i $(GTAGS_ARGS) "$$here"
-cscopelist: cscopelist-am
-
-cscopelist-am: $(am__tagged_files)
- list='$(am__tagged_files)'; \
- case "$(srcdir)" in \
- [\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
- *) sdir=$(subdir)/$(srcdir) ;; \
- esac; \
- for i in $$list; do \
- if test -f "$$i"; then \
- echo "$(subdir)/$$i"; \
- else \
- echo "$$sdir/$$i"; \
- fi; \
- done >> $(top_builddir)/cscope.files
-
-distclean-tags:
- -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
-distdir: $(DISTFILES)
- @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
- topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
- list='$(DISTFILES)'; \
- dist_files=`for file in $$list; do echo $$file; done | \
- sed -e "s|^$$srcdirstrip/||;t" \
- -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
- case $$dist_files in \
- */*) $(MKDIR_P) `echo "$$dist_files" | \
- sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
- sort -u` ;; \
- esac; \
- for file in $$dist_files; do \
- if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
- if test -d $$d/$$file; then \
- dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
- if test -d "$(distdir)/$$file"; then \
- find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
- fi; \
- if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
- cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
- find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
- fi; \
- cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
- else \
- test -f "$(distdir)/$$file" \
- || cp -p $$d/$$file "$(distdir)/$$file" \
- || exit 1; \
- fi; \
- done
-check-am: all-am
-check: check-am
-all-am: Makefile $(LIBRARIES) $(PROGRAMS)
-installdirs:
- for dir in "$(DESTDIR)$(bindir)"; do \
- test -z "$$dir" || $(MKDIR_P) "$$dir"; \
- done
-install: install-am
-install-exec: install-exec-am
-install-data: install-data-am
-uninstall: uninstall-am
-
-install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-am
-install-strip:
- if test -z '$(STRIP)'; then \
- $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
- install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
- install; \
- else \
- $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
- install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
- "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
- fi
-mostlyclean-generic:
-
-clean-generic:
-
-distclean-generic:
- -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
- -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
- -test -z "$(top_builddir)/bin/$(am__dirstamp)" || rm -f $(top_builddir)/bin/$(am__dirstamp)
-
-maintainer-clean-generic:
- @echo "This command is intended for maintainers to use"
- @echo "it deletes files that may require special tools to rebuild."
-clean: clean-am
-
-clean-am: clean-binPROGRAMS clean-generic clean-noinstLIBRARIES \
- mostlyclean-am
-
-distclean: distclean-am
- -rm -rf ./$(DEPDIR)
- -rm -f Makefile
-distclean-am: clean-am distclean-compile distclean-generic \
- distclean-tags
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
-
-html-am:
-
-info: info-am
-
-info-am:
-
-install-data-am:
-
-install-dvi: install-dvi-am
-
-install-dvi-am:
-
-install-exec-am: install-binPROGRAMS
-
-install-html: install-html-am
-
-install-html-am:
-
-install-info: install-info-am
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-am
-
-install-pdf-am:
-
-install-ps: install-ps-am
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-am
- -rm -rf ./$(DEPDIR)
- -rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-compile mostlyclean-generic
-
-pdf: pdf-am
-
-pdf-am:
-
-ps: ps-am
-
-ps-am:
-
-uninstall-am: uninstall-binPROGRAMS
-
-.MAKE: install-am install-strip
-
-.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
- clean-binPROGRAMS clean-generic clean-noinstLIBRARIES \
- cscopelist-am ctags ctags-am distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
- uninstall-am uninstall-binPROGRAMS
-
-.PRECIOUS: Makefile
-
-
-export MACOSX_DEPLOYMENT_TARGET
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/src/align_simd.cc b/src/align_simd.cc
index 778e490..498236a 100644
--- a/src/align_simd.cc
+++ b/src/align_simd.cc
@@ -824,6 +824,28 @@ void search16(s16info_s * s,
CELL * hearray = (CELL*) s->hearray;
unsigned long qlen = s->qlen;
+ if (qlen == 0)
+ {
+ for (unsigned int cand_id = 0; cand_id < sequences; cand_id++)
+ {
+ unsigned int seqno = seqnos[cand_id];
+ long length = db_getsequencelen(seqno);
+ pscores[cand_id] = 0;
+ paligned[cand_id] = 0;
+ pmatches[cand_id] = 0;
+ pmismatches[cand_id] = length;
+ pgaps[cand_id] = length;
+
+ char * cigar = 0;
+ int ret = asprintf(&cigar, "%ldI", length);
+ pcigar[cand_id] = cigar;
+
+ if ((ret < 2) || !cigar)
+ fatal("Unable to allocate enough memory.");
+ }
+ return;
+ }
+
/* find longest target sequence and reallocate direction buffer */
unsigned long maxdlen = 0;
for(long i = 0; i < sequences; i++)
diff --git a/src/derep.cc b/src/derep.cc
index 1e4b6df..336d3d6 100644
--- a/src/derep.cc
+++ b/src/derep.cc
@@ -200,6 +200,9 @@ void derep_fulllength()
unsigned int * nextseqtab = (unsigned int*) xmalloc(sizeof(unsigned int) * dbsequencecount);
memset(nextseqtab, 0, sizeof(unsigned int) * dbsequencecount);
+ char * match_strand = (char *) xmalloc(dbsequencecount);
+ memset(match_strand, 0, dbsequencecount);
+
char * seq_up = (char*) xmalloc(db_getlongestsequence() + 1);
char * rc_seq_up = (char*) xmalloc(db_getlongestsequence() + 1);
@@ -283,6 +286,7 @@ void derep_fulllength()
{
bp = rc_bp;
j = k;
+ match_strand[i] = 1;
}
}
@@ -418,8 +422,10 @@ void derep_fulllength()
next;
next = nextseqtab[next])
fprintf(fp_uc,
- "H\t%ld\t%ld\t%.1f\t*\t0\t0\t*\t%s\t%s\n",
- i, len, 100.0, db_getheader(next), h);
+ "H\t%ld\t%ld\t%.1f\t%s\t0\t0\t*\t%s\t%s\n",
+ i, len, 100.0,
+ (match_strand[next] ? "-" : "+"),
+ db_getheader(next), h);
progress_update(i);
}
@@ -454,6 +460,7 @@ void derep_fulllength()
100.0 * (clusters - selected) / clusters);
}
+ free(match_strand);
free(nextseqtab);
free(hashtable);
db_free();
@@ -760,7 +767,7 @@ void derep_prefix()
next;
next = nextseqtab[next])
fprintf(fp_uc,
- "H\t%ld\t%lu\t%.1f\t*\t0\t0\t*\t%s\t%s\n",
+ "H\t%ld\t%lu\t%.1f\t+\t0\t0\t*\t%s\t%s\n",
i, db_getsequencelen(next), 100.0, db_getheader(next), h);
progress_update(i);
diff --git a/src/fasta.cc b/src/fasta.cc
index 09af9c0..6a80abf 100644
--- a/src/fasta.cc
+++ b/src/fasta.cc
@@ -142,7 +142,7 @@ fasta_handle fasta_open(const char * filename)
if (h->format == FORMAT_BZIP)
{
/* BZIP2: Keep original file open, then open as bzipped file as well */
-#ifdef HAVE_ZLIB_H
+#ifdef HAVE_BZLIB_H
if (!bz2_lib)
fatal("Files compressed with bzip2 are not supported");
int bzError;
@@ -593,17 +593,25 @@ void fasta_print(FILE * fp, const char * hdr,
fasta_print_sequence(fp, seq, len, opt_fasta_width);
}
+void fasta_print_ee(FILE * fp, const char * hdr,
+ char * seq, unsigned long len,
+ double ee)
+{
+ fprintf(fp, ">%s;%6.4lf;\n", hdr, ee);
+ fasta_print_sequence(fp, seq, len, opt_fasta_width);
+}
-void fasta_print_relabel_cluster(FILE * fp,
- char * seq,
- int len,
- char * header,
- int header_len,
- int abundance,
- int ordinal,
- int clustersize,
- bool showclusterid,
- int clusterid)
+void fasta_print_general(FILE * fp,
+ char * seq,
+ int len,
+ char * header,
+ int header_len,
+ int abundance,
+ int ordinal,
+ int clustersize,
+ bool showclusterid,
+ int clusterid,
+ double ee)
{
fprintf(fp, ">");
@@ -630,7 +638,7 @@ void fasta_print_relabel_cluster(FILE * fp,
fprintf(fp, "%s", header);
}
- if ((clustersize > 0) || opt_sizeout || showclusterid)
+ if ((clustersize > 0) || opt_sizeout || showclusterid || (ee >= 0.0))
fprintf(fp, ";");
if (clustersize > 0)
@@ -642,6 +650,9 @@ void fasta_print_relabel_cluster(FILE * fp,
if (showclusterid)
fprintf(fp, "clusterid=%d;", clusterid);
+ if (ee >= 0.0)
+ fprintf(fp, "ee=%6.4lf;", ee);
+
if (opt_relabel_keep &&
((opt_relabel || opt_relabel_sha1 || opt_relabel_md5)))
fprintf(fp, " %s", header);
@@ -653,6 +664,38 @@ void fasta_print_relabel_cluster(FILE * fp,
}
+void fasta_print_relabel_cluster(FILE * fp,
+ char * seq,
+ int len,
+ char * header,
+ int header_len,
+ int abundance,
+ int ordinal,
+ int clustersize,
+ bool showclusterid,
+ int clusterid)
+{
+ fasta_print_general(fp, seq, len, header, header_len,
+ abundance, ordinal,
+ clustersize, showclusterid, clusterid,
+ -1.0);
+}
+
+void fasta_print_relabel_ee(FILE * fp,
+ char * seq,
+ int len,
+ char * header,
+ int header_len,
+ int abundance,
+ int ordinal,
+ double ee)
+{
+ fasta_print_general(fp, seq, len, header, header_len,
+ abundance, ordinal,
+ 0, 0, 0,
+ ee);
+}
+
void fasta_print_relabel(FILE * fp,
char * seq,
int len,
@@ -661,9 +704,10 @@ void fasta_print_relabel(FILE * fp,
int abundance,
int ordinal)
{
- fasta_print_relabel_cluster(fp, seq, len, header, header_len,
- abundance, ordinal,
- 0, 0, 0);
+ fasta_print_general(fp, seq, len, header, header_len,
+ abundance, ordinal,
+ 0, 0, 0,
+ -1.0);
}
void fasta_print_db_relabel(FILE * fp,
diff --git a/src/fasta.h b/src/fasta.h
index bf3edf8..0c1d5a9 100644
--- a/src/fasta.h
+++ b/src/fasta.h
@@ -124,6 +124,10 @@ void fasta_print_sequence(FILE * fp, char * seq,
void fasta_print(FILE * fp, const char * hdr,
char * seq, unsigned long len);
+void fasta_print_ee(FILE * fp, const char * hdr,
+ char * seq, unsigned long len,
+ double ee);
+
void fasta_print_relabel_cluster(FILE * fp,
char * seq,
int len,
@@ -135,6 +139,15 @@ void fasta_print_relabel_cluster(FILE * fp,
bool showclusterid,
int clusterid);
+void fasta_print_relabel_ee(FILE * fp,
+ char * seq,
+ int len,
+ char * header,
+ int header_len,
+ int abundance,
+ int ordinal,
+ double ee);
+
void fasta_print_relabel(FILE * fp,
char * seq,
int len,
diff --git a/src/fastq.cc b/src/fastq.cc
index 33a3ad8..894d4ea 100644
--- a/src/fastq.cc
+++ b/src/fastq.cc
@@ -192,7 +192,7 @@ fastq_handle fastq_open(const char * filename)
if (h->format == FORMAT_BZIP)
{
/* BZIP2: Keep original file open, then open as bzipped file as well */
-#ifdef HAVE_ZLIB_H
+#ifdef HAVE_BZLIB_H
if (!bz2_lib)
fatal("Files compressed with bzip2 are not supported");
int bzError;
diff --git a/src/fastqops.cc b/src/fastqops.cc
index d9330a8..2281e31 100644
--- a/src/fastqops.cc
+++ b/src/fastqops.cc
@@ -217,10 +217,17 @@ void fastq_filter()
if (opt_fastaout)
{
- fasta_print_relabel(fp_fastaout,
- p, length,
- d, fastq_get_header_length(h),
- 1, kept);
+ if (opt_eeout || opt_fastq_eeout)
+ fasta_print_relabel_ee(fp_fastaout,
+ p, length,
+ d, fastq_get_header_length(h),
+ 1, kept,
+ ee);
+ else
+ fasta_print_relabel(fp_fastaout,
+ p, length,
+ d, fastq_get_header_length(h),
+ 1, kept);
}
if (opt_fastqout)
{
@@ -241,7 +248,7 @@ void fastq_filter()
d = hex_sha1;
}
- if (opt_eeout)
+ if (opt_eeout || opt_fastq_eeout)
fastq_print_with_ee(fp_fastqout, d, p, q, ee);
else
fastq_print(fp_fastqout, d, p, q);
@@ -258,10 +265,17 @@ void fastq_filter()
if (opt_fastaout_discarded)
{
- fasta_print_relabel(fp_fastaout_discarded,
- p, length,
- d, fastq_get_header_length(h),
- 1, discarded);
+ if (opt_eeout || opt_fastq_eeout)
+ fasta_print_relabel_ee(fp_fastaout_discarded,
+ p, length,
+ d, fastq_get_header_length(h),
+ 1, discarded,
+ ee);
+ else
+ fasta_print_relabel(fp_fastaout_discarded,
+ p, length,
+ d, fastq_get_header_length(h),
+ 1, discarded);
}
if (opt_fastqout_discarded)
@@ -282,7 +296,7 @@ void fastq_filter()
d = hex_sha1;
}
- if (opt_eeout)
+ if (opt_eeout || opt_fastq_eeout)
fastq_print_with_ee(fp_fastqout_discarded, d, p, q, ee);
else
fastq_print(fp_fastqout_discarded, d, p, q);
diff --git a/src/fastx.cc b/src/fastx.cc
index 5f7b123..7953d69 100644
--- a/src/fastx.cc
+++ b/src/fastx.cc
@@ -131,7 +131,7 @@ int fastx_detect(const char * filename)
if (format == FORMAT_BZIP)
{
/* BZIP2: Keep original file open, then open as bzipped file as well */
-#ifdef HAVE_ZLIB_H
+#ifdef HAVE_BZLIB_H
if (!bz2_lib)
fatal("Files compressed with bzip2 are not supported");
int bzError;
diff --git a/src/mergepairs.cc b/src/mergepairs.cc
index 01bfb4f..33d478c 100644
--- a/src/mergepairs.cc
+++ b/src/mergepairs.cc
@@ -273,7 +273,7 @@ void keep(merge_data_t * ip)
if (opt_fastqout)
{
- if (opt_fastq_eeout)
+ if (opt_fastq_eeout || opt_eeout)
fastq_print_with_ee(fp_fastqout,
ip->merged_header,
ip->merged_sequence,
@@ -287,10 +287,19 @@ void keep(merge_data_t * ip)
}
if (opt_fastaout)
- fasta_print(fp_fastaout,
- ip->merged_header,
- ip->merged_sequence,
- strlen(ip->merged_sequence));
+ {
+ if (opt_fastq_eeout || opt_eeout)
+ fasta_print_ee(fp_fastaout,
+ ip->merged_header,
+ ip->merged_sequence,
+ strlen(ip->merged_sequence),
+ ip->ee_merged);
+ else
+ fasta_print(fp_fastaout,
+ ip->merged_header,
+ ip->merged_sequence,
+ strlen(ip->merged_sequence));
+ }
if (opt_eetabbedout)
fprintf(fp_eetabbedout, "%.2lf\t%.2lf\t%ld\t%ld\n",
diff --git a/src/results.cc b/src/results.cc
index 4a0a630..342c2a4 100644
--- a/src/results.cc
+++ b/src/results.cc
@@ -188,7 +188,7 @@ void results_show_uc_one(FILE * fp,
if (hp)
{
bool perfect = (hp->matches == qseqlen) &&
- (qseqlen = db_getsequencelen(hp->target));
+ ((unsigned long)(qseqlen) == db_getsequencelen(hp->target));
fprintf(fp,
"H\t%d\t%ld\t%.1f\t%c\t0\t0\t%s\t%s\t%s\n",
--
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