[med-svn] [Git][med-team/trnascan-se][upstream] New upstream version 2.0.5

Steffen Möller gitlab at salsa.debian.org
Sat Jan 18 22:38:07 GMT 2020



Steffen Möller pushed to branch upstream at Debian Med / trnascan-se


Commits:
95f46e94 by Steffen Moeller at 2020-01-18T23:32:50+01:00
New upstream version 2.0.5
- - - - -


11 changed files:

- − Makefile.in
- README
- − aclocal.m4
- − configure
- − depcomp
- − install-sh
- lib/tRNAscanSE/CM.pm
- lib/tRNAscanSE/Options.pm
- lib/tRNAscanSE/Sequence.pm
- − missing
- tRNAscan-SE.src


Changes:

=====================================
Makefile.in deleted
=====================================
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=====================================
README
=====================================
@@ -5,7 +5,7 @@ Patricia Chan, Brian Lin, and Todd Lowe
 
 School of Engineering, University of California, Santa Cruz, CA
 --------------------------------------------------------------
-Current release: 2.0 (December 2017)
+Current release: 2.0.4 (September 2019)
 
 tRNAscan-SE was written in the PERL (version 5) script language.
 Input consists of DNA or RNA sequences in FASTA format. tRNA


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-    am__tar_='tar chf - "$tardir"'
-    am__untar='tar xf -'
-    ;;
-  pax)
-    am__tar='pax -L -x $1 -w "$$tardir"'
-    am__tar_='pax -L -x $1 -w "$tardir"'
-    am__untar='pax -r'
-    ;;
-  cpio)
-    am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
-    am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
-    am__untar='cpio -i -H $1 -d'
-    ;;
-  none)
-    am__tar=false
-    am__tar_=false
-    am__untar=false
-    ;;
-  esac
-
-  # If the value was cached, stop now.  We just wanted to have am__tar
-  # and am__untar set.
-  test -n "${am_cv_prog_tar_$1}" && break
-
-  # tar/untar a dummy directory, and stop if the command works
-  rm -rf conftest.dir
-  mkdir conftest.dir
-  echo GrepMe > conftest.dir/file
-  AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
-  rm -rf conftest.dir
-  if test -s conftest.tar; then
-    AM_RUN_LOG([$am__untar <conftest.tar])
-    grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
-  fi
-done
-rm -rf conftest.dir
-
-AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
-AC_MSG_RESULT([$am_cv_prog_tar_$1])])
-AC_SUBST([am__tar])
-AC_SUBST([am__untar])
-]) # _AM_PROG_TAR
-


=====================================
configure deleted
=====================================
The diff for this file was not included because it is too large.

=====================================
depcomp deleted
=====================================
@@ -1,630 +0,0 @@
-#! /bin/sh
-# depcomp - compile a program generating dependencies as side-effects
-
-scriptversion=2009-04-28.21; # UTC
-
-# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 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 outputing dependencies.
-  libtool     Whether libtool is used (yes/no).
-
-Report bugs to <bug-automake at gnu.org>.
-EOF
-    exit $?
-    ;;
-  -v | --v*)
-    echo "depcomp $scriptversion"
-    exit $?
-    ;;
-esac
-
-if test -z "$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"
-
-# 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 "$depmode" = msvcmsys; then
-   # This is just like msvisualcpp but w/o cygpath translation.
-   # Just convert the backslash-escaped backslashes to single forward
-   # slashes to satisfy depend.m4
-   cygpath_u="sed s,\\\\\\\\,/,g"
-   depmode=msvisualcpp
-fi
-
-case "$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 $stat -eq 0; then :
-  else
-    rm -f "$tmpdepfile"
-    exit $stat
-  fi
-  mv "$tmpdepfile" "$depfile"
-  ;;
-
-gcc)
-## There are various ways to get dependency output from gcc.  Here's
-## why we pick this rather obscure method:
-## - Don't want to use -MD because we'd like the dependencies to end
-##   up in a subdir.  Having to rename by hand is ugly.
-##   (We might end up doing this anyway to support other compilers.)
-## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
-##   -MM, not -M (despite what the docs say).
-## - Using -M directly means running the compiler twice (even worse
-##   than renaming).
-  if test -z "$gccflag"; then
-    gccflag=-MD,
-  fi
-  "$@" -Wp,"$gccflag$tmpdepfile"
-  stat=$?
-  if test $stat -eq 0; then :
-  else
-    rm -f "$tmpdepfile"
-    exit $stat
-  fi
-  rm -f "$depfile"
-  echo "$object : \\" > "$depfile"
-  alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
-## The second -e expression handles DOS-style file names with drive letters.
-  sed -e 's/^[^:]*: / /' \
-      -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
-## This next piece of magic avoids the `deleted header file' problem.
-## The problem is that when a header file which appears in a .P file
-## is deleted, the dependency causes make to die (because there is
-## typically no way to rebuild the header).  We avoid this by adding
-## dummy dependencies for each header file.  Too bad gcc doesn't do
-## this for us directly.
-  tr ' ' '
-' < "$tmpdepfile" |
-## 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.
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly.  Breaking it into two sed invocations is a workaround.
-    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/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 $stat -eq 0; then :
-  else
-    rm -f "$tmpdepfile"
-    exit $stat
-  fi
-  rm -f "$depfile"
-
-  if test -f "$tmpdepfile"; then  # yes, the sourcefile depend on other files
-    echo "$object : \\" > "$depfile"
-
-    # Clip off the initial element (the dependent).  Don't try to be
-    # clever and replace this with sed code, as IRIX sed won't handle
-    # lines with more than a fixed number of characters (4096 in
-    # IRIX 6.2 sed, 8192 in IRIX 6.5).  We also remove comment lines;
-    # the IRIX cc adds comments like `#:fec' to the end of the
-    # dependency line.
-    tr ' ' '
-' < "$tmpdepfile" \
-    | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
-    tr '
-' ' ' >> "$depfile"
-    echo >> "$depfile"
-
-    # The second pass generates a dummy entry for each header file.
-    tr ' ' '
-' < "$tmpdepfile" \
-   | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
-   >> "$depfile"
-  else
-    # The sourcefile does not contain any dependencies, so just
-    # store a dummy comment line, to avoid errors with the Makefile
-    # "include basename.Plo" scheme.
-    echo "#dummy" > "$depfile"
-  fi
-  rm -f "$tmpdepfile"
-  ;;
-
-aix)
-  # The C for AIX Compiler uses -M and outputs the dependencies
-  # in a .u file.  In older versions, this file always lives in the
-  # current directory.  Also, the AIX compiler puts `$object:' at the
-  # start of each line; $object doesn't have directory information.
-  # Version 6 uses the directory in both cases.
-  dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
-  test "x$dir" = "x$object" && dir=
-  base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
-  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 $stat -eq 0; then :
-  else
-    rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
-    exit $stat
-  fi
-
-  for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
-  do
-    test -f "$tmpdepfile" && break
-  done
-  if test -f "$tmpdepfile"; then
-    # Each line is of the form `foo.o: dependent.h'.
-    # Do two passes, one to just change these to
-    # `$object: dependent.h' and one to simply `dependent.h:'.
-    sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
-    # That's a tab and a space in the [].
-    sed -e 's,^.*\.[a-z]*:[	 ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
-  else
-    # The sourcefile does not contain any dependencies, so just
-    # store a dummy comment line, to avoid errors with the Makefile
-    # "include basename.Plo" scheme.
-    echo "#dummy" > "$depfile"
-  fi
-  rm -f "$tmpdepfile"
-  ;;
-
-icc)
-  # Intel's C compiler understands `-MD -MF file'.  However on
-  #    icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
-  # ICC 7.0 will fill foo.d with something like
-  #    foo.o: sub/foo.c
-  #    foo.o: sub/foo.h
-  # which is wrong.  We want:
-  #    sub/foo.o: sub/foo.c
-  #    sub/foo.o: sub/foo.h
-  #    sub/foo.c:
-  #    sub/foo.h:
-  # ICC 7.1 will output
-  #    foo.o: sub/foo.c sub/foo.h
-  # and will wrap long lines using \ :
-  #    foo.o: sub/foo.c ... \
-  #     sub/foo.h ... \
-  #     ...
-
-  "$@" -MD -MF "$tmpdepfile"
-  stat=$?
-  if test $stat -eq 0; then :
-  else
-    rm -f "$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.
-  dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
-  test "x$dir" = "x$object" && dir=
-  base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
-  if test "$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 $stat -eq 0; then :
-  else
-     rm -f "$tmpdepfile1" "$tmpdepfile2"
-     exit $stat
-  fi
-
-  for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"
-  do
-    test -f "$tmpdepfile" && break
-  done
-  if test -f "$tmpdepfile"; then
-    sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
-    # Add `dependent.h:' lines.
-    sed -ne '2,${
-	       s/^ *//
-	       s/ \\*$//
-	       s/$/:/
-	       p
-	     }' "$tmpdepfile" >> "$depfile"
-  else
-    echo "#dummy" > "$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.
-   dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
-   test "x$dir" = "x$object" && dir=
-   base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
-
-   if test "$libtool" = yes; then
-      # With Tru64 cc, shared objects can also be used to make a
-      # static library.  This mechanism is used in libtool 1.4 series to
-      # handle both shared and static libraries in a single compilation.
-      # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
-      #
-      # With libtool 1.5 this exception was removed, and libtool now
-      # 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=$dir.libs/$base.lo.d   # libtool 1.4
-      tmpdepfile2=$dir$base.o.d          # libtool 1.5
-      tmpdepfile3=$dir.libs/$base.o.d    # libtool 1.5
-      tmpdepfile4=$dir.libs/$base.d      # Compaq CCC V6.2-504
-      "$@" -Wc,-MD
-   else
-      tmpdepfile1=$dir$base.o.d
-      tmpdepfile2=$dir$base.d
-      tmpdepfile3=$dir$base.d
-      tmpdepfile4=$dir$base.d
-      "$@" -MD
-   fi
-
-   stat=$?
-   if test $stat -eq 0; then :
-   else
-      rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
-      exit $stat
-   fi
-
-   for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
-   do
-     test -f "$tmpdepfile" && break
-   done
-   if test -f "$tmpdepfile"; then
-      sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
-      # That's a tab and a space in the [].
-      sed -e 's,^.*\.[a-z]*:[	 ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
-   else
-      echo "#dummy" > "$depfile"
-   fi
-   rm -f "$tmpdepfile"
-   ;;
-
-#nosideeffect)
-  # This comment above is used by automake to tell side-effect
-  # dependency tracking mechanisms from slower ones.
-
-dashmstdout)
-  # Important note: in order to support this mode, a compiler *must*
-  # always write the preprocessed file to stdout, regardless of -o.
-  "$@" || 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.
-  "$@" $dashmflag |
-    sed 's:^[  ]*[^: ][^:][^:]*\:[    ]*:'"$object"'\: :' > "$tmpdepfile"
-  rm -f "$depfile"
-  cat < "$tmpdepfile" > "$depfile"
-  tr ' ' '
-' < "$tmpdepfile" | \
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly.  Breaking it into two sed invocations is a workaround.
-    sed -e 's/^\\$//' -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 "$depfile"
-  cat < "$tmpdepfile" > "$depfile"
-  sed '1,2d' "$tmpdepfile" | tr ' ' '
-' | \
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly.  Breaking it into two sed invocations is a workaround.
-    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$1" != 'X--mode=compile'; do
-      shift
-    done
-    shift
-  fi
-
-  IFS=" "
-  for arg
-  do
-    case "$arg" in
-    -o)
-      shift
-      ;;
-    $object)
-      shift
-      ;;
-    "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
-	set fnord "$@"
-	shift
-	shift
-	;;
-    *)
-	set fnord "$@" "$arg"
-	shift
-	shift
-	;;
-    esac
-  done
-  "$@" -E 2>/dev/null |
-  sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
-  rm -f "$depfile"
-  echo "$object : \\" > "$depfile"
-  sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::	\1 \\:p' >> "$depfile"
-  echo "	" >> "$depfile"
-  sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
-  rm -f "$tmpdepfile"
-  ;;
-
-msvcmsys)
-  # This case exists only to let depend.m4 do its work.  It works by
-  # looking at the text of this script.  This case will never be run,
-  # since it is checked for above.
-  exit 1
-  ;;
-
-none)
-  exec "$@"
-  ;;
-
-*)
-  echo "Unknown depmode $depmode" 1>&2
-  exit 1
-  ;;
-esac
-
-exit 0
-
-# 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:


=====================================
install-sh deleted
=====================================
@@ -1,520 +0,0 @@
-#!/bin/sh
-# install - install a program, script, or datafile
-
-scriptversion=2009-04-28.21; # 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.
-
-nl='
-'
-IFS=" ""	$nl"
-
-# set DOITPROG to echo to test this script
-
-# Don't use :- since 4.3BSD and earlier shells don't like it.
-doit=${DOITPROG-}
-if test -z "$doit"; then
-  doit_exec=exec
-else
-  doit_exec=$doit
-fi
-
-# 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=${STRIPPROG-strip}
-
-posix_glob='?'
-initialize_posix_glob='
-  test "$posix_glob" != "?" || {
-    if (set -f) 2>/dev/null; then
-      posix_glob=
-    else
-      posix_glob=:
-    fi
-  }
-'
-
-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
-no_target_directory=
-
-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
-	  *' '* | *'	'* | *'
-'*	  | *'*'* | *'?'* | *'['*)
-	    echo "$0: invalid mode: $mode" >&2
-	    exit 1;;
-	esac
-	shift;;
-
-    -o) chowncmd="$chownprog $2"
-	shift;;
-
-    -s) stripcmd=$stripprog;;
-
-    -t) dst_arg=$2
-	shift;;
-
-    -T) no_target_directory=true;;
-
-    --version) echo "$0 $scriptversion"; exit $?;;
-
-    --)	shift
-	break;;
-
-    -*)	echo "$0: invalid option: $1" >&2
-	exit 1;;
-
-    *)  break;;
-  esac
-  shift
-done
-
-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
-  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
-  trap '(exit $?); exit' 1 2 13 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 starting with `-'.
-  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
-    # Protect names starting with `-'.
-    case $dst in
-      -*) dst=./$dst;;
-    esac
-
-    # If destination is a directory, append the input filename; won't work
-    # if double slashes aren't ignored.
-    if test -d "$dst"; then
-      if test -n "$no_target_directory"; then
-	echo "$0: $dst_arg: Is a directory" >&2
-	exit 1
-      fi
-      dstdir=$dst
-      dst=$dstdir/`basename "$src"`
-      dstdir_status=0
-    else
-      # Prefer dirname, but fall back on a substitute if dirname fails.
-      dstdir=`
-	(dirname "$dst") 2>/dev/null ||
-	expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-	     X"$dst" : 'X\(//\)[^/]' \| \
-	     X"$dst" : 'X\(//\)$' \| \
-	     X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
-	echo X"$dst" |
-	    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
-		   s//\1/
-		   q
-		 }
-		 /^X\(\/\/\)[^/].*/{
-		   s//\1/
-		   q
-		 }
-		 /^X\(\/\/\)$/{
-		   s//\1/
-		   q
-		 }
-		 /^X\(\/\).*/{
-		   s//\1/
-		   q
-		 }
-		 s/.*/./; q'
-      `
-
-      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
-		   # other-writeable bit of parent directory when it shouldn't.
-		   # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
-		   ls_ld_tmpdir=`ls -ld "$tmpdir"`
-		   case $ls_ld_tmpdir in
-		     d????-?r-*) different_mode=700;;
-		     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
-
-      eval "$initialize_posix_glob"
-
-      oIFS=$IFS
-      IFS=/
-      $posix_glob set -f
-      set fnord $dstdir
-      shift
-      $posix_glob set +f
-      IFS=$oIFS
-
-      prefixes=
-
-      for d
-      do
-	test -z "$d" && 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 "$dsttmp"	2>/dev/null` &&
-
-       eval "$initialize_posix_glob" &&
-       $posix_glob set -f &&
-       set X $old && old=:$2:$4:$5:$6 &&
-       set X $new && new=:$2:$4:$5:$6 &&
-       $posix_glob set +f &&
-
-       test "$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:


=====================================
lib/tRNAscanSE/CM.pm
=====================================
@@ -110,6 +110,13 @@ sub cm_cutoff
     return $self->{cm_cutoff};
 }
 
+sub organelle_cm_cutoff
+{
+    my $self = shift;
+    if (@_) { $self->{organelle_cm_cutoff} = shift; }
+    return $self->{organelle_cm_cutoff};
+}
+
 sub infernal_fp_cutoff
 {
     my $self = shift;
@@ -1200,6 +1207,12 @@ sub decode_tRNA_properties
         }
         
         $trna->isotype($gc->get_tRNA_type($self, $trna->anticodon(), $cur_cm_file, $trna->model(), $self->cove_mode()));
+        
+        if ($anticodon ne "TCA" and $trna->isotype() eq "SeC")
+        {
+            $trna->anticodon($gc->undef_anticodon());
+            $trna->isotype($gc->undef_isotype());
+        }
     }
     
     # Write current tRNA to temp file for re-analysis with other models
@@ -1231,26 +1244,30 @@ sub fix_fMet
         {
 			if (substr($trna->ss(), 0, 1) ne ".")
             {
-                $trna->seq(substr($trna->upstream(), length($trna->upstream())-1) . $trna->seq());
-                $trna->upstream(substr($trna->upstream(), 0, length($trna->upstream())-1));
-                $trna->ss(".".$trna->ss());
-                if ($trna->strand() eq "+")
-                {
-					$trna->start($trna->start() - 1);
-				}
-				else
+                if (($trna->strand() eq "+" and $trna->start() > 1) or
+                    ($trna->strand() eq "-" and $trna->end() < $trna->src_seqlen()))
                 {
-                    $trna->end($trna->end() + 1);
+                    $trna->seq(substr($trna->upstream(), length($trna->upstream())-1) . $trna->seq());
+                    $trna->upstream(substr($trna->upstream(), 0, length($trna->upstream())-1));
+                    $trna->ss(".".$trna->ss());
+                    if ($trna->strand() eq "+")
+                    {
+                        $trna->start($trna->start() - 1);
+                    }
+                    else
+                    {
+                        $trna->end($trna->end() + 1);
+                    }
+                    my @ar_ac_pos = $trna->ar_ac_pos();
+                    if (scalar(@ar_ac_pos) > 0)
+                    {
+                        $ar_ac_pos[0]->{rel_start} += 1;
+                        $ar_ac_pos[0]->{rel_end} += 1;
+                        $trna->ar_ac_pos(@ar_ac_pos);
+                    }
+                    
+                    $rescore = 1;
                 }
-                my @ar_ac_pos = $trna->ar_ac_pos();
-                if (scalar(@ar_ac_pos) > 0)
-                {
-					$ar_ac_pos[0]->{rel_start} += 1;
-                    $ar_ac_pos[0]->{rel_end} += 1;
-                    $trna->ar_ac_pos(@ar_ac_pos);
-				}
-				
-                $rescore = 1;
             }
             elsif (substr($trna->ss(), 0, 4) eq ".>.>" and substr($trna->seq(), 0, 2) eq "CG")
             {
@@ -2418,14 +2435,14 @@ sub run_cmsearch
         }
     }
     
-    if ($opts->mito_mode())
-    {
-		$score_cutoff = $self->{organelle_cm_cutoff};
-	}
-	else
-    {
+#    if ($opts->mito_mode())
+#    {
+#		$score_cutoff = $self->{organelle_cm_cutoff};
+#	}
+#	else
+#   {
         $score_cutoff = $self->{cm_cutoff};
-    }
+#   }
     
     foreach my $cur_cm (sort keys %{$self->{main_cm_file_path}})
     {
@@ -3286,7 +3303,7 @@ sub analyze_mito
             $cm_tRNA->start($cm_tRNA->start() + $prescan_tRNA->start() - 1);
             $cm_tRNA->end($cm_tRNA->end() + $prescan_tRNA->start() - 1);
 
-            if ($cm_tRNA->score() < $self->{organelle_cm_cutoff})
+            if ($cm_tRNA->score() < $self->{cm_cutoff})
             {
                 $log->broadcast("Low cmsearch score for ".$prescan_tRNA->tRNAscan_id().".$cms_hit_count: ".$cm_tRNA->score());
                 $trnaDesc .= "(CMSearch Hit#$cms_hit_count: ".$cm_tRNA->start()."-".$cm_tRNA->end().",".


=====================================
lib/tRNAscanSE/Options.pm
=====================================
@@ -813,10 +813,20 @@ sub display_run_options
         }
     }
 
-    if ($cm->cm_cutoff() != $global_constants->get("cm_cutoff"))
-    {
-        print $FHAND "tRNA covariance model search       \n"."    cutoff score:                  ".$cm->cm_cutoff()."\n";
-    }
+#    if ($self->mito_mode())
+#    {
+#        if ($cm->organelle_cm_cutoff() != $global_constants->get("organelle_cm_cutoff"))
+#        {
+#            print $FHAND "tRNA covariance model search       \n"."    cutoff score:                  ".$cm->organelle_cm_cutoff()."\n";
+#        }        
+#    }
+#    else
+#    {
+        if ($cm->cm_cutoff() != $global_constants->get("cm_cutoff"))
+        {
+            print $FHAND "tRNA covariance model search       \n"."    cutoff score:                  ".$cm->cm_cutoff()."\n";
+        }
+#    }
 
     if ($self->{use_prev_ts_run})
     {


=====================================
lib/tRNAscanSE/Sequence.pm
=====================================
@@ -335,7 +335,10 @@ sub read_fasta
             ## Remove long runs of N's from consideration by pre-scanners
             ## By doing this, pre-scanner false-pos rate is normal, even
             ## when scanning unfinished genomes with long N insert "placeholders"
-            $self->{sequence} =~ s/NNNNNNNNNN/CCCCCCCCCC/g; 
+            if ($opts->tscan_mode() or $opts->eufind_mode())
+            {
+                $self->{sequence} =~ s/NNNNNNNNNN/CCCCCCCCCC/g;
+            }
 
             return 1;
         }
@@ -524,6 +527,7 @@ sub read_fasta_subseq_slow
 sub read_more_fasta
 {    
     my $self = shift;
+    my $opts = shift;
     my $fh = $self->{FILE_H};
     
     my ($seqlen, $filepos);
@@ -579,7 +583,10 @@ sub read_more_fasta
     ## Remove long runs of N's from consideration by pre-scanners
     ## By doing this, pre-scanner false-pos rate is normal, even
     ## when scanning unfinished genomes with long N insert "placeholders"
-    $self->{sequence} =~ s/NNNNNNNNNN/CCCCCCCCCC/g; 
+    if ($opts->tscan_mode() or $opts->eufind_mode())
+    {
+        $self->{sequence} =~ s/NNNNNNNNNN/CCCCCCCCCC/g;
+    }
     
     return 1;
 }
@@ -656,7 +663,7 @@ sub get_tRNA_sequence
         $self->seekpos(0);
         if (!$self->read_fasta_subseq_slow($opts, $trna->seqname(), $src_seqid, $fwd_start, $query_len))
         {
-            $log->warning("Could not find ".$trna->seqname()." in ".$opts->fastafile());
+            $log->warning("Could not find ".$trna->seqname()." in ".$opts->fasta_file());
             $log->broadcast("Skipping to next tRNA hit...");
             return 0;
         }


=====================================
missing deleted
=====================================
@@ -1,376 +0,0 @@
-#! /bin/sh
-# Common stub for a few missing GNU programs while installing.
-
-scriptversion=2009-04-28.21; # UTC
-
-# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
-# 2008, 2009 Free Software Foundation, Inc.
-# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
-
-# 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.
-
-if test $# -eq 0; then
-  echo 1>&2 "Try \`$0 --help' for more information"
-  exit 1
-fi
-
-run=:
-sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
-sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
-
-# In the cases where this matters, `missing' is being run in the
-# srcdir already.
-if test -f configure.ac; then
-  configure_ac=configure.ac
-else
-  configure_ac=configure.in
-fi
-
-msg="missing on your system"
-
-case $1 in
---run)
-  # Try to run requested program, and just exit if it succeeds.
-  run=
-  shift
-  "$@" && exit 0
-  # Exit code 63 means version mismatch.  This often happens
-  # when the user try to use an ancient version of a tool on
-  # a file that requires a minimum version.  In this case we
-  # we should proceed has if the program had been absent, or
-  # if --run hadn't been passed.
-  if test $? = 63; then
-    run=:
-    msg="probably too old"
-  fi
-  ;;
-
-  -h|--h|--he|--hel|--help)
-    echo "\
-$0 [OPTION]... PROGRAM [ARGUMENT]...
-
-Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
-error status if there is no known handling for PROGRAM.
-
-Options:
-  -h, --help      display this help and exit
-  -v, --version   output version information and exit
-  --run           try to run the given command, and emulate it if it fails
-
-Supported PROGRAM values:
-  aclocal      touch file \`aclocal.m4'
-  autoconf     touch file \`configure'
-  autoheader   touch file \`config.h.in'
-  autom4te     touch the output file, or create a stub one
-  automake     touch all \`Makefile.in' files
-  bison        create \`y.tab.[ch]', if possible, from existing .[ch]
-  flex         create \`lex.yy.c', if possible, from existing .c
-  help2man     touch the output file
-  lex          create \`lex.yy.c', if possible, from existing .c
-  makeinfo     touch the output file
-  tar          try tar, gnutar, gtar, then tar without non-portable flags
-  yacc         create \`y.tab.[ch]', if possible, from existing .[ch]
-
-Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
-\`g' are ignored when checking the name.
-
-Send bug reports to <bug-automake at gnu.org>."
-    exit $?
-    ;;
-
-  -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
-    echo "missing $scriptversion (GNU Automake)"
-    exit $?
-    ;;
-
-  -*)
-    echo 1>&2 "$0: Unknown \`$1' option"
-    echo 1>&2 "Try \`$0 --help' for more information"
-    exit 1
-    ;;
-
-esac
-
-# normalize program name to check for.
-program=`echo "$1" | sed '
-  s/^gnu-//; t
-  s/^gnu//; t
-  s/^g//; t'`
-
-# Now exit if we have it, but it failed.  Also exit now if we
-# don't have it and --version was passed (most likely to detect
-# the program).  This is about non-GNU programs, so use $1 not
-# $program.
-case $1 in
-  lex*|yacc*)
-    # Not GNU programs, they don't have --version.
-    ;;
-
-  tar*)
-    if test -n "$run"; then
-       echo 1>&2 "ERROR: \`tar' requires --run"
-       exit 1
-    elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
-       exit 1
-    fi
-    ;;
-
-  *)
-    if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
-       # We have it, but it failed.
-       exit 1
-    elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
-       # Could not run --version or --help.  This is probably someone
-       # running `$TOOL --version' or `$TOOL --help' to check whether
-       # $TOOL exists and not knowing $TOOL uses missing.
-       exit 1
-    fi
-    ;;
-esac
-
-# If it does not exist, or fails to run (possibly an outdated version),
-# try to emulate it.
-case $program in
-  aclocal*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-         you modified \`acinclude.m4' or \`${configure_ac}'.  You might want
-         to install the \`Automake' and \`Perl' packages.  Grab them from
-         any GNU archive site."
-    touch aclocal.m4
-    ;;
-
-  autoconf*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-         you modified \`${configure_ac}'.  You might want to install the
-         \`Autoconf' and \`GNU m4' packages.  Grab them from any GNU
-         archive site."
-    touch configure
-    ;;
-
-  autoheader*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-         you modified \`acconfig.h' or \`${configure_ac}'.  You might want
-         to install the \`Autoconf' and \`GNU m4' packages.  Grab them
-         from any GNU archive site."
-    files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
-    test -z "$files" && files="config.h"
-    touch_files=
-    for f in $files; do
-      case $f in
-      *:*) touch_files="$touch_files "`echo "$f" |
-				       sed -e 's/^[^:]*://' -e 's/:.*//'`;;
-      *) touch_files="$touch_files $f.in";;
-      esac
-    done
-    touch $touch_files
-    ;;
-
-  automake*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-         you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
-         You might want to install the \`Automake' and \`Perl' packages.
-         Grab them from any GNU archive site."
-    find . -type f -name Makefile.am -print |
-	   sed 's/\.am$/.in/' |
-	   while read f; do touch "$f"; done
-    ;;
-
-  autom4te*)
-    echo 1>&2 "\
-WARNING: \`$1' is needed, but is $msg.
-         You might have modified some files without having the
-         proper tools for further handling them.
-         You can get \`$1' as part of \`Autoconf' from any GNU
-         archive site."
-
-    file=`echo "$*" | sed -n "$sed_output"`
-    test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
-    if test -f "$file"; then
-	touch $file
-    else
-	test -z "$file" || exec >$file
-	echo "#! /bin/sh"
-	echo "# Created by GNU Automake missing as a replacement of"
-	echo "#  $ $@"
-	echo "exit 0"
-	chmod +x $file
-	exit 1
-    fi
-    ;;
-
-  bison*|yacc*)
-    echo 1>&2 "\
-WARNING: \`$1' $msg.  You should only need it if
-         you modified a \`.y' file.  You may need the \`Bison' package
-         in order for those modifications to take effect.  You can get
-         \`Bison' from any GNU archive site."
-    rm -f y.tab.c y.tab.h
-    if test $# -ne 1; then
-        eval LASTARG="\${$#}"
-	case $LASTARG in
-	*.y)
-	    SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
-	    if test -f "$SRCFILE"; then
-	         cp "$SRCFILE" y.tab.c
-	    fi
-	    SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
-	    if test -f "$SRCFILE"; then
-	         cp "$SRCFILE" y.tab.h
-	    fi
-	  ;;
-	esac
-    fi
-    if test ! -f y.tab.h; then
-	echo >y.tab.h
-    fi
-    if test ! -f y.tab.c; then
-	echo 'main() { return 0; }' >y.tab.c
-    fi
-    ;;
-
-  lex*|flex*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-         you modified a \`.l' file.  You may need the \`Flex' package
-         in order for those modifications to take effect.  You can get
-         \`Flex' from any GNU archive site."
-    rm -f lex.yy.c
-    if test $# -ne 1; then
-        eval LASTARG="\${$#}"
-	case $LASTARG in
-	*.l)
-	    SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
-	    if test -f "$SRCFILE"; then
-	         cp "$SRCFILE" lex.yy.c
-	    fi
-	  ;;
-	esac
-    fi
-    if test ! -f lex.yy.c; then
-	echo 'main() { return 0; }' >lex.yy.c
-    fi
-    ;;
-
-  help2man*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-	 you modified a dependency of a manual page.  You may need the
-	 \`Help2man' package in order for those modifications to take
-	 effect.  You can get \`Help2man' from any GNU archive site."
-
-    file=`echo "$*" | sed -n "$sed_output"`
-    test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
-    if test -f "$file"; then
-	touch $file
-    else
-	test -z "$file" || exec >$file
-	echo ".ab help2man is required to generate this page"
-	exit $?
-    fi
-    ;;
-
-  makeinfo*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-         you modified a \`.texi' or \`.texinfo' file, or any other file
-         indirectly affecting the aspect of the manual.  The spurious
-         call might also be the consequence of using a buggy \`make' (AIX,
-         DU, IRIX).  You might want to install the \`Texinfo' package or
-         the \`GNU make' package.  Grab either from any GNU archive site."
-    # The file to touch is that specified with -o ...
-    file=`echo "$*" | sed -n "$sed_output"`
-    test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
-    if test -z "$file"; then
-      # ... or it is the one specified with @setfilename ...
-      infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
-      file=`sed -n '
-	/^@setfilename/{
-	  s/.* \([^ ]*\) *$/\1/
-	  p
-	  q
-	}' $infile`
-      # ... or it is derived from the source name (dir/f.texi becomes f.info)
-      test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
-    fi
-    # If the file does not exist, the user really needs makeinfo;
-    # let's fail without touching anything.
-    test -f $file || exit 1
-    touch $file
-    ;;
-
-  tar*)
-    shift
-
-    # We have already tried tar in the generic part.
-    # Look for gnutar/gtar before invocation to avoid ugly error
-    # messages.
-    if (gnutar --version > /dev/null 2>&1); then
-       gnutar "$@" && exit 0
-    fi
-    if (gtar --version > /dev/null 2>&1); then
-       gtar "$@" && exit 0
-    fi
-    firstarg="$1"
-    if shift; then
-	case $firstarg in
-	*o*)
-	    firstarg=`echo "$firstarg" | sed s/o//`
-	    tar "$firstarg" "$@" && exit 0
-	    ;;
-	esac
-	case $firstarg in
-	*h*)
-	    firstarg=`echo "$firstarg" | sed s/h//`
-	    tar "$firstarg" "$@" && exit 0
-	    ;;
-	esac
-    fi
-
-    echo 1>&2 "\
-WARNING: I can't seem to be able to run \`tar' with the given arguments.
-         You may want to install GNU tar or Free paxutils, or check the
-         command line arguments."
-    exit 1
-    ;;
-
-  *)
-    echo 1>&2 "\
-WARNING: \`$1' is needed, and is $msg.
-         You might have modified some files without having the
-         proper tools for further handling them.  Check the \`README' file,
-         it often tells you about the needed prerequisites for installing
-         this package.  You may also peek at any GNU archive site, in case
-         some other package would contain this missing \`$1' program."
-    exit 1
-    ;;
-esac
-
-exit 0
-
-# 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:


=====================================
tRNAscan-SE.src
=====================================
@@ -4,7 +4,7 @@
 # tRNAscan-SE: a program for improved detection of transfer RNA
 #              genes in genomic sequence
 #
-# Version 2.0.3
+# Version 2.0.5
 #
 # Copyright (C) 2019 Patricia Chan and Todd Lowe 
 #
@@ -39,8 +39,8 @@ use tRNAscanSE::IntResultFile;
 use tRNAscanSE::MultiResultFile;
 use tRNAscanSE::SS;
 
-our $version = "2.0.3"; 
-our $release_date = "April 2019";
+our $version = "2.0.5"; 
+our $release_date = "October 2019";
 our $program_id = "tRNAscan-SE-".$version;
 
 # modified by 'make'
@@ -260,7 +260,7 @@ sub first_pass_prescan
             if ($seq_file->seq_buf_overrun())
             {
                 $start_index = $seq_file->buffer_end_index() + 1;
-                if ($seq_file->read_more_fasta())
+                if ($seq_file->read_more_fasta($opts))
                 {
                     $sequence_scanned = 0;
                 }
@@ -1520,7 +1520,7 @@ sub set_options
     # do max scan 
     if ($opt_max != 0)
     {                       
-        if ($opt_eufind || $opt_tscan || $opt_cove || $opt_legacy || $opt_mid)
+        if ($opt_eufind || $opt_tscan || $opt_cove || $opt_legacy || ($opt_mid and $opt_mito != 0))
         {
             die "FATAL: Conflicting search options have been selected. --max, -t, -e, -C, and -L cannot be used simultaneously.\n";
         }
@@ -1531,6 +1531,10 @@ sub set_options
         {
             $opts->infernal_fp(0);
         }
+	elsif ($opt_mito)
+	{
+	    $opt_mid = 0;
+	}
     }
     
     # set hmm filter flag for infernal
@@ -1875,8 +1879,8 @@ sub set_options
         $cm->cm_cutoff($opt_score);
         if ($opt_score < $cm->infernal_fp_cutoff())
         {
-			$cm->infernal_fp_cutoff($opt_score);
-		}		
+		$cm->infernal_fp_cutoff($opt_score);
+	}
     }
     
     if ($opt_thread != 999)



View it on GitLab: https://salsa.debian.org/med-team/trnascan-se/commit/95f46e942b4f13a130d3e2cbcb0063ebe5099a64

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View it on GitLab: https://salsa.debian.org/med-team/trnascan-se/commit/95f46e942b4f13a130d3e2cbcb0063ebe5099a64
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