.gitignore

@@ -64,3 +64,4 @@ src/populaterefcache
 src/vcfconcat
 src/vcfsort
 removespace.sh
+src/filtergtf
\ No newline at end of file

ChangeLog

+biobambam2 (2.0.137-1) unstable; urgency=medium
+
+  * add manual page for bamfeaturecount
+  * add manual page for filtergtf
+  * add filtergtf program
+  * implement simplified transcript level analysis in bamfeaturecount
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 28 Aug 2019 10:04:09 +0200
+
+biobambam2 (2.0.136-1) unstable; urgency=medium
+
+  * add bamfixpairinfo program
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 22 Aug 2019 14:44:39 +0200
+
+biobambam2 (2.0.135-1) unstable; urgency=medium
+
+  * add UniqueInterval class in bamfeaturecount
+  * add readgroup and program header lines in bamconsensus
+  * fix border check in bamrecalculatecigar
+  * fix computation of MD/NM fields in bamconsensus
+  * make exclude flags user settable in bamconsensus
+  * change default verbose setting in bamfillquery
+  * update synopsis in bamconsensus help message
+  * make bamconsensus output BAM file containing alignments of consensus with the reference instead of just the consensus as FastA
+  * construct fasta index in bamrecalculatecigar if needed
+  * add unmapped option for bamfilterlength
+  * add bamconsensus to list of installed programs and add documentation
+  * improve scaling in bamconsensus
+  * make running dot optional in bamconsensus
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 22 Aug 2019 10:47:00 +0200
+
 biobambam2 (2.0.134-1) unstable; urgency=medium
 
   * bump libmaus2 version

INSTALL

-Installation Instructions
-*************************
-
-Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,
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-==================
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compile

-#! /bin/sh
-# Wrapper for compilers which do not understand '-c -o'.
-
-scriptversion=2012-10-14.11; # UTC
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-# <automake-patches@gnu.org>.
-
-nl='
-'
-
-# We need space, tab and new line, in precisely that order.  Quoting is
-# there to prevent tools from complaining about whitespace usage.
-IFS=" ""	$nl"
-
-file_conv=
-
-# func_file_conv build_file lazy
-# Convert a $build file to $host form and store it in $file
-# Currently only supports Windows hosts. If the determined conversion
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-func_file_conv ()
-{
-  file=$1
-  case $file in
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-      if test -z "$file_conv"; then
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-	case `uname -s` in
-	  MINGW*)
-	    file_conv=mingw
-	    ;;
-	  CYGWIN*)
-	    file_conv=cygwin
-	    ;;
-	  *)
-	    file_conv=wine
-	    ;;
-	esac
-      fi
-      case $file_conv/,$2, in
-	*,$file_conv,*)
-	  ;;
-	mingw/*)
-	  file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
-	  ;;
-	cygwin/*)
-	  file=`cygpath -m "$file" || echo "$file"`
-	  ;;
-	wine/*)
-	  file=`winepath -w "$file" || echo "$file"`
-	  ;;
-      esac
-      ;;
-  esac
-}
-
-# func_cl_dashL linkdir
-# Make cl look for libraries in LINKDIR
-func_cl_dashL ()
-{
-  func_file_conv "$1"
-  if test -z "$lib_path"; then
-    lib_path=$file
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-    lib_path="$lib_path;$file"
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-  linker_opts="$linker_opts -LIBPATH:$file"
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-# func_cl_dashl library
-# Do a library search-path lookup for cl
-func_cl_dashl ()
-{
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-      lib=$dir/$lib.dll.lib
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-      found=yes
-      lib=$dir/$lib.lib
-      break
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-      lib=$dir/lib$lib.a
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-  IFS=$save_IFS
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-  if test "$found" != yes; then
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-	  # configure might choose to run compile as 'compile cc -o foo foo.c'.
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-	      func_file_conv "$2"
-	      set x "$@" -Fo"$file"
-	      shift
-	      ;;
-	    *)
-	      func_file_conv "$2"
-	      set x "$@" -Fe"$file"
-	      shift
-	      ;;
-	  esac
-	  ;;
-	-I)
-	  eat=1
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-	  set x "$@" -I"$file"
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-	  func_file_conv "$1" mingw
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-	eat=1
-	case $2 in
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-	    ofile=$2
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-	  *)
-	    set x "$@" -o "$2"
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-	cfile=$1
-	set x "$@" "$1"
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-if test -z "$ofile" || test -z "$cfile"; then
-  # If no '-o' option was seen then we might have been invoked from a
-  # pattern rule where we don't need one.  That is ok -- this is a
-  # normal compilation that the losing compiler can handle.  If no
-  # '.c' file was seen then we are probably linking.  That is also
-  # ok.
-  exec "$@"
-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:

configure.ac

-AC_INIT(biobambam2,2.0.134,[tischler@mpi-cbg.de],[biobambam2],[http://www.sanger.ac.uk])
+AC_INIT(biobambam2,2.0.137,[tischler@mpi-cbg.de],[biobambam2],[http://www.sanger.ac.uk])
 AC_CANONICAL_SYSTEM
 AC_PROG_LIBTOOL
 
@@ -165,9 +165,9 @@ if test ! -z "${with_libmaus2}" ; then
 	fi
 fi
 
-PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.657])
-PKG_CHECK_MODULES([libmaus2digests],[libmaus2digests >= 2.0.657])
-PKG_CHECK_MODULES([libmaus2seqchksumsfactory],[libmaus2seqchksumsfactory >= 2.0.657])
+PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.663])
+PKG_CHECK_MODULES([libmaus2digests],[libmaus2digests >= 2.0.663])
+PKG_CHECK_MODULES([libmaus2seqchksumsfactory],[libmaus2seqchksumsfactory >= 2.0.663])
 
 if test ! -z "${with_libmaus2}" ; then
 	if test ! -z "${PKGCONFIGPATHSAVE}" ; then
@@ -302,7 +302,7 @@ if test "${have_libmaus2_irods}" = "yes" ; then
 		fi
 	fi
 
-	PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.657])
+	PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.663])
 
 	LIBMAUS2IRODSCPPFLAGS="${libmaus2irods_CFLAGS}"
 	LIBMAUS2IRODSLIBS="${libmaus2irods_LIBS}"

install-sh

-#!/bin/sh
-# install - install a program, script, or datafile
-
-scriptversion=2014-09-12.12; # 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 $@.
-  for arg
-  do
-    if test -n "$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 $dsttmp) contains '*'.
-    if test ! -f "$src" && test ! -d "$src"; then
-      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.
-            ;;
-          *)
-            # $RANDOM is not portable (e.g. dash);  use it when possible to
-            # lower collision chance
-            tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
-            trap 'ret=$?; rmdir "$tmpdir/a/b" "$tmpdir/a" "$tmpdir" 2>/dev/null; exit $ret' 0
-
-            # As "mkdir -p" follows symlinks and we work in /tmp possibly;  so
-            # create the $tmpdir first (and fail if unsuccessful) to make sure
-            # that nobody tries to guess the $tmpdir name.
-            if (umask $mkdir_umask &&
-                $mkdirprog $mkdir_mode "$tmpdir" &&
-                exec $mkdirprog $mkdir_mode -p -- "$tmpdir/a/b") >/dev/null 2>&1
-            then
-              if test -z "$dir_arg" || {
-                   # Check for POSIX incompatibilities with -m.
-                   # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
-                   # other-writable bit of parent directory when it shouldn't.
-                   # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
-                   test_tmpdir="$tmpdir/a"
-                   ls_ld_tmpdir=`ls -ld "$test_tmpdir"`
-                   case $ls_ld_tmpdir in
-                     d????-?r-*) different_mode=700;;
-                     d????-?--*) different_mode=755;;
-                     *) false;;
-                   esac &&
-                   $mkdirprog -m$different_mode -p -- "$test_tmpdir" && {
-                     ls_ld_tmpdir_1=`ls -ld "$test_tmpdir"`
-                     test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
-                   }
-                 }
-              then posix_mkdir=:
-              fi
-              rmdir "$tmpdir/a/b" "$tmpdir/a" "$tmpdir"
-            else
-              # Remove any dirs left behind by ancient mkdir implementations.
-              rmdir ./$mkdir_mode ./-p ./-- "$tmpdir" 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
-        test X"$d" = X && continue
-
-        prefix=$prefix$d
-        if test -d "$prefix"; then
-          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 $prefix in
-              *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
-              *) 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" "$dst" 2>/dev/null ||
-
-      # The rename failed, perhaps because mv can't rename something else
-      # to itself, or perhaps because mv is so ancient that it does not
-      # support -f.
-      {
-        # Now remove or move aside any old file at destination location.
-        # We try this two ways since rm can't unlink itself on some
-        # systems and the destination file might be busy for other
-        # reasons.  In this case, the final cleanup might fail but the new
-        # file should still install successfully.
-        {
-          test ! -f "$dst" ||
-          $doit $rmcmd -f "$dst" 2>/dev/null ||
-          { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
-            { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
-          } ||
-          { echo "$0: cannot unlink or rename $dst" >&2
-            (exit 1); exit 1
-          }
-        } &&
-
-        # Now rename the file to the real destination.
-        $doit $mvcmd "$dsttmp" "$dst"
-      }
-    fi || exit 1
-
-    trap '' 0
-  fi
-done
-
-# Local variables:
-# 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: