ChangeLog

+Stacks 2.2 - Aug 22, 2018
+--------------------------
+    Feature: Added the --bestrad flag to process_radtags. When used it will look for reads that need transposed
+             before they are processed.
+    Feature: gstacks: New option --max-debrujin-reads to control the construction of the de Bruijn graph; replaces 
+             --min-kmer-freq which is now deprecated
+    Bugfix: Added run number to output FASTQ headers in process_radtags to make sure read IDs are always unique.
+
+Stacks 2.1 - June 25, 2018
+--------------------------
+    Bugfix: Fixed a performance regression in sstacks. Recent changes in sstacks made it more likely to
+            invoke the gapped algorithm to match to the catalog. In some cases, matches to the catalog
+            would be marked as ambiguous alignments and dropped from the next stages of analysis due to 
+            differences in CIGAR strings from the gapped alignment. 
+    Feature: ustacks Changed --high_cov_thres default value from 2.0 to 3.0.
+    Feature: gstacks: Changed --min-kmer-freq default value from 0.05 to 0.01.
+    Feature: Added further checks on zlib calls.
+
+Stacks 2.0 - Apr 23, 2018
+-------------------------
+    Feature: modified cstacks and ustacks gapped alignment algorithms to always align the two stacks/alleles
+             with the most k-mers in common, removed the previous minimum k-mer limit.
+    Feature: modified cstacks so that when a sample locus matches two or more catalog loci, those catalog
+             loci are combined, or rolled-up, reducing undermerged loci that generate excess homozygote calls.
+    Feature: modified tsv2bam so that when two loci from the same sample match the same catalog locus, those
+             loci are combined.
+    Bugfix: corrected BbvCI restriction enzyme to add the missing negative strand sequence.
+    Bugfix: corrected the catalog writing routines for unzipped output files to include missing column.
+    Bugfix: populations: Fixed the filtering of monomorphic loci.
+    Bugfix: populations: Now preserving sample ordering in all outputs.
+    Bugfix: Fixed ICPC compilation.
+
+    2.0b - May 1, 2018
+    Feature: gstacks: Removed the assertion that the first basepair of each locus should
+             be part of a cutsite (now a warning).
+    Feature: gstacks: The reported effective coverage is now a more realistic weighted mean.
+    Bugfix: populations: Fixed STRUCTURE output being corrupted for some unordereds population maps.
+
+Stacks 2.0 Beta 10 - Apr 10, 2018
+---------------------------------
+    Feature: Improved gapped alignment for secondary reads in ustacks.
+    Feature: Improved populations performance.
+    Feature: Added enzymes Cac8I, MslI.
+    Feature: Made population maps more tolerant to spurious extra spaces and lines.
+    Feature: populations: VCF output: changed the format of the catalog locus field and made the column 1-based.
+    Feature: gstacks: increased haplotyping rates by adding a filtering of spurious SNPs step.
+    Bugfix:  Fixed populations dramatric slow-down on datasets with more than several hundred samples.
+    Bugfix:  Restored the NS/locus distribution in populations's distributions log.
+    Bugfix:  Fixed the populations --radpainter export.
+    Bugfix:  stacks-dist-extract: Fixed OSX compatibility.
+    Bugfix:  Fixed breaking bug in populations --in-vcf mode filtering statistics.
+
 Stacks 2.0 Beta 9 - Mar 12, 2018
 --------------------------------
     Feature: Cleaned up tags/snps/alleles/matches files. We removed the batch ID from ustacks and cstacks

Makefile.am

@@ -85,7 +85,7 @@ populations_LDADD        = $(LDADD) libpop.a
 
 dist_bin_SCRIPTS = scripts/denovo_map.pl scripts/ref_map.pl \
 	scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py \
-	scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb
+	scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb # scripts/denovo_map.py
 
 dist_noinst_SCRIPTS = autogen.sh scripts/extract_interpop_chars.pl scripts/convert_stacks.pl
 
@@ -109,7 +109,7 @@ EXTRA_DIST = $(nobase_pkgdata_DATA) LICENSE INSTALL README ChangeLog $(TESTS)
 pkglocalstatedir = $(localstatedir)/$(PACKAGE)
 
 debug:
-	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -std=gnu++11"
+	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -O0"
 
 install-data-hook:
 	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.pl > $(DESTDIR)$(bindir)/denovo_map.pl.subst
@@ -128,6 +128,9 @@ install-data-hook:
 	chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments
 	chmod +x $(DESTDIR)$(bindir)/stacks-dist-extract
 	chmod +x $(DESTDIR)$(bindir)/stacks-gdb
+	##sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(DESTDIR)$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.py > $(DESTDIR)$(bindir)/denovo_map.py.subst
+	##mv $(DESTDIR)$(bindir)/denovo_map.py.subst $(DESTDIR)$(bindir)/denovo_map.py
+	##chmod +x $(DESTDIR)$(bindir)/denovo_map.py
 
 uninstall-hook:
 	rm -rf $(DESTDIR)$(pkglocalstatedir)

config.h.in

@@ -89,9 +89,6 @@
 /* Define to 1 if the system has the type `_Bool'. */
 #undef HAVE__BOOL
 
-/* Define to 1 if your C compiler doesn't accept -c and -o together. */
-#undef NO_MINUS_C_MINUS_O
-
 /* Name of package */
 #undef PACKAGE
 
@@ -107,6 +104,9 @@
 /* Define to the one symbol short name of this package. */
 #undef PACKAGE_TARNAME
 
+/* Define to the home page for this package. */
+#undef PACKAGE_URL
+
 /* Define to the version of this package. */
 #undef PACKAGE_VERSION
 

config/ar-lib

+#! /bin/sh
+# Wrapper for Microsoft lib.exe
+
+me=ar-lib
+scriptversion=2012-03-01.08; # UTC
+
+# Copyright (C) 2010-2014 Free Software Foundation, Inc.
+# Written by Peter Rosin <peda@lysator.liu.se>.
+#
+# 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.
+
+# This file is maintained in Automake, please report
+# bugs to <bug-automake@gnu.org> or send patches to
+# <automake-patches@gnu.org>.
+
+
+# func_error message
+func_error ()
+{
+  echo "$me: $1" 1>&2
+  exit 1
+}
+
+file_conv=
+
+# func_file_conv build_file
+# Convert a $build file to $host form and store it in $file
+# Currently only supports Windows hosts.
+func_file_conv ()
+{
+  file=$1
+  case $file in
+    / | /[!/]*) # absolute file, and not a UNC file
+      if test -z "$file_conv"; then
+	# lazily determine how to convert abs files
+	case `uname -s` in
+	  MINGW*)
+	    file_conv=mingw
+	    ;;
+	  CYGWIN*)
+	    file_conv=cygwin
+	    ;;
+	  *)
+	    file_conv=wine
+	    ;;
+	esac
+      fi
+      case $file_conv in
+	mingw)
+	  file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
+	  ;;
+	cygwin)
+	  file=`cygpath -m "$file" || echo "$file"`
+	  ;;
+	wine)
+	  file=`winepath -w "$file" || echo "$file"`
+	  ;;
+      esac
+      ;;
+  esac
+}
+
+# func_at_file at_file operation archive
+# Iterate over all members in AT_FILE performing OPERATION on ARCHIVE
+# for each of them.
+# When interpreting the content of the @FILE, do NOT use func_file_conv,
+# since the user would need to supply preconverted file names to
+# binutils ar, at least for MinGW.
+func_at_file ()
+{
+  operation=$2
+  archive=$3
+  at_file_contents=`cat "$1"`
+  eval set x "$at_file_contents"
+  shift
+
+  for member
+  do
+    $AR -NOLOGO $operation:"$member" "$archive" || exit $?
+  done
+}
+
+case $1 in
+  '')
+     func_error "no command.  Try '$0 --help' for more information."
+     ;;
+  -h | --h*)
+    cat <<EOF
+Usage: $me [--help] [--version] PROGRAM ACTION ARCHIVE [MEMBER...]
+
+Members may be specified in a file named with @FILE.
+EOF
+    exit $?
+    ;;
+  -v | --v*)
+    echo "$me, version $scriptversion"
+    exit $?
+    ;;
+esac
+
+if test $# -lt 3; then
+  func_error "you must specify a program, an action and an archive"
+fi
+
+AR=$1
+shift
+while :
+do
+  if test $# -lt 2; then
+    func_error "you must specify a program, an action and an archive"
+  fi
+  case $1 in
+    -lib | -LIB \
+    | -ltcg | -LTCG \
+    | -machine* | -MACHINE* \
+    | -subsystem* | -SUBSYSTEM* \
+    | -verbose | -VERBOSE \
+    | -wx* | -WX* )
+      AR="$AR $1"
+      shift
+      ;;
+    *)
+      action=$1
+      shift
+      break
+      ;;
+  esac
+done
+orig_archive=$1
+shift
+func_file_conv "$orig_archive"
+archive=$file
+
+# strip leading dash in $action
+action=${action#-}
+
+delete=
+extract=
+list=
+quick=
+replace=
+index=
+create=
+
+while test -n "$action"
+do
+  case $action in
+    d*) delete=yes  ;;
+    x*) extract=yes ;;
+    t*) list=yes    ;;
+    q*) quick=yes   ;;
+    r*) replace=yes ;;
+    s*) index=yes   ;;
+    S*)             ;; # the index is always updated implicitly
+    c*) create=yes  ;;
+    u*)             ;; # TODO: don't ignore the update modifier
+    v*)             ;; # TODO: don't ignore the verbose modifier
+    *)
+      func_error "unknown action specified"
+      ;;
+  esac
+  action=${action#?}
+done
+
+case $delete$extract$list$quick$replace,$index in
+  yes,* | ,yes)
+    ;;
+  yesyes*)
+    func_error "more than one action specified"
+    ;;
+  *)
+    func_error "no action specified"
+    ;;
+esac
+
+if test -n "$delete"; then
+  if test ! -f "$orig_archive"; then
+    func_error "archive not found"
+  fi
+  for member
+  do
+    case $1 in
+      @*)
+        func_at_file "${1#@}" -REMOVE "$archive"
+        ;;
+      *)
+        func_file_conv "$1"
+        $AR -NOLOGO -REMOVE:"$file" "$archive" || exit $?
+        ;;
+    esac
+  done
+
+elif test -n "$extract"; then
+  if test ! -f "$orig_archive"; then
+    func_error "archive not found"
+  fi
+  if test $# -gt 0; then
+    for member
+    do
+      case $1 in
+        @*)
+          func_at_file "${1#@}" -EXTRACT "$archive"
+          ;;
+        *)
+          func_file_conv "$1"
+          $AR -NOLOGO -EXTRACT:"$file" "$archive" || exit $?
+          ;;
+      esac
+    done
+  else
+    $AR -NOLOGO -LIST "$archive" | sed -e 's/\\/\\\\/g' | while read member
+    do
+      $AR -NOLOGO -EXTRACT:"$member" "$archive" || exit $?
+    done
+  fi
+
+elif test -n "$quick$replace"; then
+  if test ! -f "$orig_archive"; then
+    if test -z "$create"; then
+      echo "$me: creating $orig_archive"
+    fi
+    orig_archive=
+  else
+    orig_archive=$archive
+  fi
+
+  for member
+  do
+    case $1 in
+    @*)
+      func_file_conv "${1#@}"
+      set x "$@" "@$file"
+      ;;
+    *)
+      func_file_conv "$1"
+      set x "$@" "$file"
+      ;;
+    esac
+    shift
+    shift
+  done
+
+  if test -n "$orig_archive"; then
+    $AR -NOLOGO -OUT:"$archive" "$orig_archive" "$@" || exit $?
+  else
+    $AR -NOLOGO -OUT:"$archive" "$@" || exit $?
+  fi
+
+elif test -n "$list"; then
+  if test ! -f "$orig_archive"; then
+    func_error "archive not found"
+  fi
+  $AR -NOLOGO -LIST "$archive" || exit $?
+fi

config/compile

 #! /bin/sh
-# Wrapper for compilers which do not understand `-c -o'.
+# Wrapper for compilers which do not understand '-c -o'.
 
-scriptversion=2009-10-06.20; # UTC
+scriptversion=2012-10-14.11; # UTC
 
-# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2009  Free Software
-# Foundation, Inc.
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
 # Written by Tom Tromey <tromey@cygnus.com>.
 #
 # This program is free software; you can redistribute it and/or modify
@@ -29,21 +28,224 @@ scriptversion=2009-10-06.20; # UTC
 # bugs to <bug-automake@gnu.org> or send patches to
 # <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
+# type is listed in (the comma separated) LAZY, no conversion will
+# take place.
+func_file_conv ()
+{
+  file=$1
+  case $file in
+    / | /[!/]*) # absolute file, and not a UNC file
+      if test -z "$file_conv"; then
+	# lazily determine how to convert abs files
+	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=$file
+  else
+    lib_path="$lib_path;$file"
+  fi
+  linker_opts="$linker_opts -LIBPATH:$file"
+}
+
+# func_cl_dashl library
+# Do a library search-path lookup for cl
+func_cl_dashl ()
+{
+  lib=$1
+  found=no
+  save_IFS=$IFS
+  IFS=';'
+  for dir in $lib_path $LIB
+  do
+    IFS=$save_IFS
+    if $shared && test -f "$dir/$lib.dll.lib"; then
+      found=yes
+      lib=$dir/$lib.dll.lib
+      break
+    fi
+    if test -f "$dir/$lib.lib"; then
+      found=yes
+      lib=$dir/$lib.lib
+      break
+    fi
+    if test -f "$dir/lib$lib.a"; then
+      found=yes
+      lib=$dir/lib$lib.a
+      break
+    fi
+  done
+  IFS=$save_IFS
+
+  if test "$found" != yes; then
+    lib=$lib.lib
+  fi
+}
+
+# func_cl_wrapper cl arg...
+# Adjust compile command to suit cl
+func_cl_wrapper ()
+{
+  # Assume a capable shell
+  lib_path=
+  shared=:
+  linker_opts=
+  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'.
+	  eat=1
+	  case $2 in
+	    *.o | *.[oO][bB][jJ])
+	      func_file_conv "$2"
+	      set x "$@" -Fo"$file"
+	      shift
+	      ;;
+	    *)
+	      func_file_conv "$2"
+	      set x "$@" -Fe"$file"
+	      shift
+	      ;;
+	  esac
+	  ;;
+	-I)
+	  eat=1
+	  func_file_conv "$2" mingw
+	  set x "$@" -I"$file"
+	  shift
+	  ;;
+	-I*)
+	  func_file_conv "${1#-I}" mingw
+	  set x "$@" -I"$file"
+	  shift
+	  ;;
+	-l)
+	  eat=1
+	  func_cl_dashl "$2"
+	  set x "$@" "$lib"
+	  shift
+	  ;;
+	-l*)
+	  func_cl_dashl "${1#-l}"
+	  set x "$@" "$lib"
+	  shift
+	  ;;
+	-L)
+	  eat=1
+	  func_cl_dashL "$2"
+	  ;;
+	-L*)
+	  func_cl_dashL "${1#-L}"
+	  ;;
+	-static)
+	  shared=false
+	  ;;
+	-Wl,*)
+	  arg=${1#-Wl,}
+	  save_ifs="$IFS"; IFS=','
+	  for flag in $arg; do
+	    IFS="$save_ifs"
+	    linker_opts="$linker_opts $flag"
+	  done
+	  IFS="$save_ifs"
+	  ;;
+	-Xlinker)
+	  eat=1
+	  linker_opts="$linker_opts $2"
+	  ;;
+	-*)
+	  set x "$@" "$1"
+	  shift
+	  ;;
+	*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
+	  func_file_conv "$1"
+	  set x "$@" -Tp"$file"
+	  shift
+	  ;;
+	*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
+	  func_file_conv "$1" mingw
+	  set x "$@" "$file"
+	  shift
+	  ;;
+	*)
+	  set x "$@" "$1"
+	  shift
+	  ;;
+      esac
+    fi
+    shift
+  done
+  if test -n "$linker_opts"; then
+    linker_opts="-link$linker_opts"
+  fi
+  exec "$@" $linker_opts
+  exit 1
+}
+
+eat=
+
 case $1 in
   '')
-     echo "$0: No command.  Try \`$0 --help' for more information." 1>&2
+     echo "$0: No command.  Try '$0 --help' for more information." 1>&2
      exit 1;
      ;;
   -h | --h*)
     cat <<\EOF
 Usage: compile [--help] [--version] PROGRAM [ARGS]
 
-Wrapper for compilers which do not understand `-c -o'.
-Remove `-o dest.o' from ARGS, run PROGRAM with the remaining
+Wrapper for compilers which do not understand '-c -o'.
+Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
 arguments, and rename the output as expected.
 
 If you are trying to build a whole package this is not the
-right script to run: please start by reading the file `INSTALL'.
+right script to run: please start by reading the file 'INSTALL'.
 
 Report bugs to <bug-automake@gnu.org>.
 EOF
@@ -53,11 +255,13 @@ EOF
     echo "compile $scriptversion"
     exit $?
     ;;
+  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
+    func_cl_wrapper "$@"      # Doesn't return...
+    ;;
 esac
 
 ofile=
 cfile=
-eat=
 
 for arg
 do
@@ -66,8 +270,8 @@ do
   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.
+	# 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)
@@ -94,10 +298,10 @@ do
 done
 
 if test -z "$ofile" || test -z "$cfile"; then
-  # If no `-o' option was seen then we might have been invoked from a
+  # 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
+  # '.c' file was seen then we are probably linking.  That is also
   # ok.
   exec "$@"
 fi
@@ -106,7 +310,7 @@ fi
 cofile=`echo "$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
+# 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

config/install-sh

 #!/bin/sh
 # install - install a program, script, or datafile
 
-scriptversion=2009-04-28.21; # UTC
+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
@@ -35,25 +35,21 @@ scriptversion=2009-04-28.21; # UTC
 # 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
+# '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=" ""	$nl"
+IFS=" $tab$nl"
 
-# set DOITPROG to echo to test this script
+# 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=$doit
-fi
+doit_exec=${doit:-exec}
 
 # Put in absolute file names if you don't have them in your path;
 # or use environment vars.
@@ -68,17 +64,6 @@ 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.
@@ -97,7 +82,7 @@ dir_arg=
 dst_arg=
 
 copy_on_change=false
-no_target_directory=
+is_target_a_directory=possibly
 
 usage="\
 Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
@@ -143,8 +128,7 @@ while test $# -ne 0; do
 
     -m) mode=$2
         case $mode in
-	  *' '* | *'	'* | *'
-'*	  | *'*'* | *'?'* | *'['*)
+          *' '* | *"$tab"* | *"$nl"* | *'*'* | *'?'* | *'['*)
             echo "$0: invalid mode: $mode" >&2
             exit 1;;
         esac
@@ -155,10 +139,16 @@ while test $# -ne 0; do
 
     -s) stripcmd=$stripprog;;
 
-    -t) dst_arg=$2
+    -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) no_target_directory=true;;
+    -T) is_target_a_directory=never;;
 
     --version) echo "$0 $scriptversion"; exit $?;;
 
@@ -173,6 +163,16 @@ while test $# -ne 0; do
   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.
@@ -186,6 +186,10 @@ if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
     fi
     shift # arg
     dst_arg=$arg
+    # Protect names problematic for 'test' and other utilities.
+    case $dst_arg in
+      -* | [=\(\)!]) dst_arg=./$dst_arg;;
+    esac
   done
 fi
 
@@ -194,13 +198,26 @@ if test $# -eq 0; then
     echo "$0: no input file specified." >&2
     exit 1
   fi
-  # It's OK to call `install-sh -d' without argument.
+  # 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
+  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.
@@ -228,9 +245,9 @@ fi
 
 for src
 do
-  # Protect names starting with `-'.
+  # Protect names problematic for 'test' and other utilities.
   case $src in
-    -*) src=./$src;;
+    -* | [=\(\)!]) src=./$src;;
   esac
 
   if test -n "$dir_arg"; then
@@ -252,17 +269,12 @@ do
       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
+      if test "$is_target_a_directory" = never; then
         echo "$0: $dst_arg: Is a directory" >&2
         exit 1
       fi
@@ -270,33 +282,7 @@ do
       dst=$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'
-      `
-
+      dstdir=`dirname "$dst"`
       test -d "$dstdir"
       dstdir_status=$?
     fi
@@ -338,34 +324,41 @@ do
             # 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/d" "$tmpdir" 2>/dev/null; exit $ret' 0
+            trap 'ret=$?; 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 &&
-		exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
+                $mkdirprog $mkdir_mode "$tmpdir" &&
+                exec $mkdirprog $mkdir_mode -p -- "$tmpdir/a/b") >/dev/null 2>&1
             then
               if test -z "$dir_arg" || {
                    # Check for POSIX incompatibilities with -m.
                    # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
-		   # other-writeable bit of parent directory when it shouldn't.
+                   # other-writable bit of parent directory when it shouldn't.
                    # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
-		   ls_ld_tmpdir=`ls -ld "$tmpdir"`
+                   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 -- "$tmpdir" && {
-		     ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
+                   $mkdirprog -m$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 "$tmpdir/d" "$tmpdir"
+              rmdir "$tmpdir/a/b" "$tmpdir/a" "$tmpdir"
             else
               # Remove any dirs left behind by ancient mkdir implementations.
-	      rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
+              rmdir ./$mkdir_mode ./-p ./-- "$tmpdir" 2>/dev/null
             fi
             trap '' 0;;
         esac;;
@@ -385,25 +378,23 @@ do
 
       case $dstdir in
         /*) prefix='/';;
-	-*) prefix='./';;
+        [-=\(\)!]*) prefix='./';;
         *)  prefix='';;
       esac
 
-      eval "$initialize_posix_glob"
-
       oIFS=$IFS
       IFS=/
-      $posix_glob set -f
+      set -f
       set fnord $dstdir
       shift
-      $posix_glob set +f
+      set +f
       IFS=$oIFS
 
       prefixes=
 
       for d
       do
-	test -z "$d" && continue
+        test X"$d" = X && continue
 
         prefix=$prefix$d
         if test -d "$prefix"; then
@@ -467,13 +458,10 @@ do
     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 -f &&
        set X $old && old=:$2:$4:$5:$6 &&
        set X $new && new=:$2:$4:$5:$6 &&
-       $posix_glob set +f &&
-
+       set +f &&
        test "$old" = "$new" &&
        $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
     then

config/missing

 #! /bin/sh
-# Common stub for a few missing GNU programs while installing.
+# Common wrapper for a few potentially missing GNU programs.
 
-scriptversion=2009-04-28.21; # UTC
+scriptversion=2013-10-28.13; # UTC
 
-# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
-# 2008, 2009 Free Software Foundation, Inc.
-# Originally by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Originally written by Fran,cois Pinard <pinard@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
@@ -26,69 +25,40 @@ scriptversion=2009-04-28.21; # UTC
 # 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"
+  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
+case $1 in
 
-msg="missing on your system"
+  --is-lightweight)
+    # Used by our autoconf macros to check whether the available missing
+    # script is modern enough.
+    exit 0
+    ;;
 
-case $1 in
   --run)
-  # Try to run requested program, and just exit if it succeeds.
-  run=
+    # Back-compat with the calling convention used by older automake.
     shift
-  "$@" && 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.
+Run 'PROGRAM [ARGUMENT]...', returning a proper advice when this fails due
+to PROGRAM being missing or too old.
 
 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]
+  aclocal   autoconf  autoheader   autom4te  automake  makeinfo
+  bison     yacc      flex         lex       help2man
 
-Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
-\`g' are ignored when checking the name.
+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@gnu.org>."
     exit $?
@@ -100,272 +70,141 @@ Send bug reports to <bug-automake@gnu.org>."
     ;;
 
   -*)
-    echo 1>&2 "$0: Unknown \`$1' option"
-    echo 1>&2 "Try \`$0 --help' for more information"
+    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 "$1" | sed '
-  s/^gnu-//; t
-  s/^gnu//; t
-  s/^g//; t'`
+# Run the given program, remember its exit status.
+"$@"; st=$?
 
-# 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.
-    ;;
+# If it succeeded, we are done.
+test $st -eq 0 && exit 0
 
-  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
-    ;;
+# Also exit now if we it failed (or wasn't found), and '--version' was
+# passed; such an option is passed most likely to detect whether the
+# program is present and works.
+case $2 in --version|--help) exit $st;; esac
 
-  *)
-    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
+# Exit code 63 means version mismatch.  This often happens when the user
+# tries to use an ancient version of a tool on a file that requires a
+# minimum version.
+if test $st -eq 63; then
+  msg="probably too old"
+elif test $st -eq 127; then
+  # Program was missing.
+  msg="missing on your system"
+else
+  # Program was found and executed, but failed.  Give up.
+  exit $st
 fi
+
+perl_URL=http://www.perl.org/
+flex_URL=http://flex.sourceforge.net/
+gnu_software_URL=http://www.gnu.org/software
+
+program_details ()
+{
+  case $1 in
+    aclocal|automake)
+      echo "The '$1' program is part of the GNU Automake package:"
+      echo "<$gnu_software_URL/automake>"
+      echo "It also requires GNU Autoconf, GNU m4 and Perl in order to run:"
+      echo "<$gnu_software_URL/autoconf>"
+      echo "<$gnu_software_URL/m4/>"
+      echo "<$perl_URL>"
+      ;;
+    autoconf|autom4te|autoheader)
+      echo "The '$1' program is part of the GNU Autoconf package:"
+      echo "<$gnu_software_URL/autoconf/>"
+      echo "It also requires GNU m4 and Perl in order to run:"
+      echo "<$gnu_software_URL/m4/>"
+      echo "<$perl_URL>"
       ;;
   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
-    ;;
+give_advice ()
+{
+  # Normalize program name to check for.
+  normalized_program=`echo "$1" | sed '
+    s/^gnu-//; t
+    s/^gnu//; t
+    s/^g//; t'`
+
+  printf '%s\n' "'$1' is $msg."
 
+  configure_deps="'configure.ac' or m4 files included by 'configure.ac'"
+  case $normalized_program in
     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
+      echo "You should only need it if you modified 'configure.ac',"
+      echo "or m4 files included by it."
+      program_details 'autoconf'
       ;;
-
     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 $touch_files
+      echo "You should only need it if you modified 'acconfig.h' or"
+      echo "$configure_deps."
+      program_details 'autoheader'
       ;;
-
     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
+      echo "You should only need it if you modified 'Makefile.am' or"
+      echo "$configure_deps."
+      program_details 'automake'
+      ;;
+    aclocal*)
+      echo "You should only need it if you modified 'acinclude.m4' or"
+      echo "$configure_deps."
+      program_details 'aclocal'
       ;;
-
    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
+      echo "You might have modified some maintainer files that require"
+      echo "the 'autom4te' program to be rebuilt."
+      program_details 'autom4te'
       ;;
-
     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 "$SRCFILE" y.tab.h
-	    fi
-	  ;;
-	esac
-    fi
-    if test ! -f y.tab.h; then
-	echo >y.tab.h
-    fi
-    if test ! -f y.tab.c; then
-	echo 'main() { return 0; }' >y.tab.c
-    fi
+      echo "You should only need it if you modified a '.y' file."
+      echo "You may want to install the GNU Bison package:"
+      echo "<$gnu_software_URL/bison/>"
       ;;
-
     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 "$SRCFILE" lex.yy.c
-	    fi
-	  ;;
-	esac
-    fi
-    if test ! -f lex.yy.c; then
-	echo 'main() { return 0; }' >lex.yy.c
-    fi
+      echo "You should only need it if you modified a '.l' file."
+      echo "You may want to install the Fast Lexical Analyzer package:"
+      echo "<$flex_URL>"
       ;;
-
     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 $?
-    fi
+      echo "You should only need it if you modified a dependency" \
+           "of a man page."
+      echo "You may want to install the GNU Help2man package:"
+      echo "<$gnu_software_URL/help2man/>"
     ;;
-
     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 "You should only need it if you modified a '.texi' file, or"
+      echo "any other file indirectly affecting the aspect of the manual."
+      echo "You might want to install the Texinfo package:"
+      echo "<$gnu_software_URL/texinfo/>"
+      echo "The spurious makeinfo call might also be the consequence of"
+      echo "using a buggy 'make' (AIX, DU, IRIX), in which case you might"
+      echo "want to install GNU make:"
+      echo "<$gnu_software_URL/make/>"
       ;;
-
     *)
-    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
+      echo "You might have modified some files without having the proper"
+      echo "tools for further handling them.  Check the 'README' file, it"
+      echo "often tells you about the needed prerequisites for installing"
+      echo "this package.  You may also peek at any GNU archive site, in"
+      echo "case some other package contains this missing '$1' program."
       ;;
   esac
+}
 
-exit 0
+give_advice "$1" | sed -e '1s/^/WARNING: /' \
+                       -e '2,$s/^/         /' >&2
+
+# Propagate the correct exit status (expected to be 127 for a program
+# not found, 63 for a program that failed due to version mismatch).
+exit $st
 
 # Local variables:
 # eval: (add-hook 'write-file-hooks 'time-stamp)

config/test-driver

+#! /bin/sh
+# test-driver - basic testsuite driver script.
+
+scriptversion=2013-07-13.22; # UTC
+
+# Copyright (C) 2011-2014 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.
+
+# This file is maintained in Automake, please report
+# bugs to <bug-automake@gnu.org> or send patches to
+# <automake-patches@gnu.org>.
+
+# Make unconditional expansion of undefined variables an error.  This
+# helps a lot in preventing typo-related bugs.
+set -u
+
+usage_error ()
+{
+  echo "$0: $*" >&2
+  print_usage >&2
+  exit 2
+}
+
+print_usage ()
+{
+  cat <<END
+Usage:
+  test-driver --test-name=NAME --log-file=PATH --trs-file=PATH
+              [--expect-failure={yes|no}] [--color-tests={yes|no}]
+              [--enable-hard-errors={yes|no}] [--]
+              TEST-SCRIPT [TEST-SCRIPT-ARGUMENTS]
+The '--test-name', '--log-file' and '--trs-file' options are mandatory.
+END
+}
+
+test_name= # Used for reporting.
+log_file=  # Where to save the output of the test script.
+trs_file=  # Where to save the metadata of the test run.
+expect_failure=no
+color_tests=no
+enable_hard_errors=yes
+while test $# -gt 0; do
+  case $1 in
+  --help) print_usage; exit $?;;
+  --version) echo "test-driver $scriptversion"; exit $?;;
+  --test-name) test_name=$2; shift;;
+  --log-file) log_file=$2; shift;;
+  --trs-file) trs_file=$2; shift;;
+  --color-tests) color_tests=$2; shift;;
+  --expect-failure) expect_failure=$2; shift;;
+  --enable-hard-errors) enable_hard_errors=$2; shift;;
+  --) shift; break;;
+  -*) usage_error "invalid option: '$1'";;
+   *) break;;
+  esac
+  shift
+done
+
+missing_opts=
+test x"$test_name" = x && missing_opts="$missing_opts --test-name"
+test x"$log_file"  = x && missing_opts="$missing_opts --log-file"
+test x"$trs_file"  = x && missing_opts="$missing_opts --trs-file"
+if test x"$missing_opts" != x; then
+  usage_error "the following mandatory options are missing:$missing_opts"
+fi
+
+if test $# -eq 0; then
+  usage_error "missing argument"
+fi
+
+if test $color_tests = yes; then
+  # Keep this in sync with 'lib/am/check.am:$(am__tty_colors)'.
+  red='' # Red.
+  grn='' # Green.
+  lgn='' # Light green.
+  blu='' # Blue.
+  mgn='' # Magenta.
+  std=''     # No color.
+else
+  red= grn= lgn= blu= mgn= std=
+fi
+
+do_exit='rm -f $log_file $trs_file; (exit $st); exit $st'
+trap "st=129; $do_exit" 1
+trap "st=130; $do_exit" 2
+trap "st=141; $do_exit" 13
+trap "st=143; $do_exit" 15
+
+# Test script is run here.
+"$@" >$log_file 2>&1
+estatus=$?
+
+if test $enable_hard_errors = no && test $estatus -eq 99; then
+  tweaked_estatus=1
+else
+  tweaked_estatus=$estatus
+fi
+
+case $tweaked_estatus:$expect_failure in
+  0:yes) col=$red res=XPASS recheck=yes gcopy=yes;;
+  0:*)   col=$grn res=PASS  recheck=no  gcopy=no;;
+  77:*)  col=$blu res=SKIP  recheck=no  gcopy=yes;;
+  99:*)  col=$mgn res=ERROR recheck=yes gcopy=yes;;
+  *:yes) col=$lgn res=XFAIL recheck=no  gcopy=yes;;
+  *:*)   col=$red res=FAIL  recheck=yes gcopy=yes;;
+esac
+
+# Report the test outcome and exit status in the logs, so that one can
+# know whether the test passed or failed simply by looking at the '.log'
+# file, without the need of also peaking into the corresponding '.trs'
+# file (automake bug#11814).
+echo "$res $test_name (exit status: $estatus)" >>$log_file
+
+# Report outcome to console.
+echo "${col}${res}${std}: $test_name"
+
+# Register the test result, and other relevant metadata.
+echo ":test-result: $res" > $trs_file
+echo ":global-test-result: $res" >> $trs_file
+echo ":recheck: $recheck" >> $trs_file
+echo ":copy-in-global-log: $gcopy" >> $trs_file
+
+# 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

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.59)
-AC_INIT([Stacks], [2.0Beta9])
+AC_INIT([Stacks], [2.2])
 AC_CONFIG_AUX_DIR([config])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])
 AC_CONFIG_SRCDIR([src/ustacks.cc])

debian/changelog

+stacks (2.2+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Fix path for Perl interpreter
+
+ -- Andreas Tille <tille@debian.org>  Thu, 13 Sep 2018 09:51:56 +0200
+
 stacks (2.0Beta9+dfsg-1) unstable; urgency=medium
 
   * New upstream Beta release

debian/control

@@ -11,9 +11,9 @@ Build-Depends: debhelper (>= 11~),
                libsparsehash-dev (>= 2.0),
                samtools,
                libhts-dev
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/stacks.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/stacks.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/stacks
+Vcs-Git: https://salsa.debian.org/med-team/stacks.git
 Homepage: http://creskolab.uoregon.edu/stacks/
 
 Package: stacks

debian/patches/script-exe-paths

@@ -10,7 +10,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 --- a/Makefile.am
 +++ b/Makefile.am
 @@ -112,13 +112,13 @@ debug:
- 	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -std=gnu++11"
+ 	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -O0"
  
  install-data-hook:
 -	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.pl > $(DESTDIR)$(bindir)/denovo_map.pl.subst

debian/rules

@@ -25,6 +25,7 @@ override_dh_install:
 	! cd debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin || \
 	  for f in *.pl ; do \
 	    ln -s "$$f" "`basename $$f .pl`" ; \
+	    sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' $$f ; \
 	  done
 	# Skip this bit if not building stacks-web
 	# Note - directory perms will be set in postinst

scripts/denovo_map.pl

@@ -227,8 +227,8 @@ sub execute_stacks {
     }
 
     $cmd = $exe_path . "tsv2bam -P $out_path $file_paths " . join(" ", @_tsv2bam);
-    print STDERR  "  $cmd\n";
-    print $log_fh "$cmd\n";
+    print STDERR  "  $cmd\n\n";
+    print $log_fh "$cmd\n\n";
 
     if (!$dry_run) {
         open($pipe_fh, "$time $cmd 2>&1 |");
@@ -292,8 +292,12 @@ sub parse_population_map {
         next if ($line =~ /^\s*#/);
 
         @parts = split(/\t/, $line);
-        if (scalar(@parts) > 3) {
-            die("Unable to parse population map, '$popmap_path' (map should contain no more than three columns).\n");
+        if (scalar(@parts) != 2 and scalar(@parts) != 3) {
+            die("Unable to parse population map, '$popmap_path' (expected 2 or 3 columns, found " . scalar(@parts) . "); at line:\n$line\n");
+        }
+
+        foreach my $part (@parts) {
+            $part =~ s/^\s*|\s*$//g;
         }
 
         push(@{$sample_list}, $parts[0]);
@@ -615,7 +619,7 @@ denovo_map.pl --samples dir --popmap path -o dir [--paired] (assembly options) [
 
   Stack assembly options:
     M: number of mismatches allowed between stacks within individuals (for ustacks).
-    n: number of mismatches allowed between stacks between individuals (for cstacks).
+    n: number of mismatches allowed between stacks between individuals (for cstacks; default 1; suggested: set to ustacks -M).
 
   SNP model options:
     --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05).

scripts/ref_map.pl

@@ -165,9 +165,12 @@ sub parse_population_map {
         next if ($line =~ /^\s*#/);
 
         @parts = split(/\t/, $line);
+        if (scalar(@parts) != 2 and scalar(@parts) != 3) {
+            die("Unable to parse population map, '$popmap_path' (expected 2 or 3 columns, found " . scalar(@parts) . "); at line:\n$line\n");
+        }
 
-        if (scalar(@parts) > 3) {
-            die("Unable to parse population map, '$popmap_path' (map should contain no more than three columns).\n");
+        foreach my $part (@parts) {
+            $part =~ s/^\s*|\s*$//g;
         }
 
         push(@{$sample_list}, $parts[0]);

scripts/stacks-dist-extract

-#!/bin/bash
+#!/usr/bin/env bash
 
 usage="\
 Usage:
@@ -23,7 +23,7 @@ if [[ "$2" ]] ;then
         echo "Error: Couldn't find section '$section' in '$dist_f'." >&1
         exit 1
     fi
-    sed -n "/^END $section\\b/ q; /^BEGIN $section\\b/,$ p" "$dist_f" | sed 1d
+    sed -nE "/^END $section($| )/ q; /^BEGIN $section($| )/,$ p" "$dist_f" | sed 1d
 else
     grep ^BEGIN "$dist_f" | cut -c7-
 fi