@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

     to work with GMAP and GSNAP from within R. In addition, it provides 

     methods to tally alignment results on a per-nucleotide basis using 

     the bam_tally tool.

-Version: 1.5.3

+Version: 1.5.4

 Depends: R (>= 2.15.0), methods, GenomicRanges

 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),

          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,

@@ -70,7 +70,8 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

                                  need_unique_p, need_primary_p,

                                  ignore_duplicates_p,

                                  min_depth, variant_strands, ignore_query_Ns_p,

-                                 print_indels_p, blocksize, verbosep);

+                                 print_indels_p, blocksize, verbosep,

+                                 /*readlevel_p*/false);

   IIT_free(&chromosome_iit);

   Genome_free(&genome);

@@ -1,7 +1,7 @@

 Installation Instructions

 *************************

-Copyright (C) 1994-1996, 1999-2002, 2004-2012 Free Software Foundation,

+Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,

 Inc.

    Copying and distribution of this file, with or without modification,

@@ -1,7 +1,7 @@

-# Makefile.in generated by automake 1.13.1 from Makefile.am.

+# Makefile.in generated by automake 1.14 from Makefile.am.

 # @configure_input@

-# Copyright (C) 1994-2012 Free Software Foundation, Inc.

+# Copyright (C) 1994-2013 Free Software Foundation, Inc.

 # This Makefile.in is free software; the Free Software Foundation

 # gives unlimited permission to copy and/or distribute it,

@@ -14,23 +14,51 @@

 @SET_MAKE@

 VPATH = @srcdir@

-am__make_dryrun = \

-  { \

-    am__dry=no; \

+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'

+am__make_running_with_option = \

+  case $${target_option-} in \

+      ?) ;; \

+      *) echo "am__make_running_with_option: internal error: invalid" \

+              "target option '$${target_option-}' specified" >&2; \

+         exit 1;; \

+  esac; \

+  has_opt=no; \

+  sane_makeflags=$$MAKEFLAGS; \

+  if $(am__is_gnu_make); then \

+    sane_makeflags=$$MFLAGS; \

+  else \

     case $$MAKEFLAGS in \

       *\\[\ \	]*) \

-        echo 'am--echo: ; @echo "AM"  OK' | $(MAKE) -f - 2>/dev/null \

-          | grep '^AM OK$$' >/dev/null || am__dry=yes;; \

-      *) \

-        for am__flg in $$MAKEFLAGS; do \

-          case $$am__flg in \

-            *=*|--*) ;; \

-            *n*) am__dry=yes; break;; \

-          esac; \

-        done;; \

+        bs=\\; \

+        sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \

+          | sed "s/$$bs$$bs[$$bs $$bs	]*//g"`;; \

+    esac; \

+  fi; \

+  skip_next=no; \

+  strip_trailopt () \

+  { \

+    flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \

+  }; \

+  for flg in $$sane_makeflags; do \

+    test $$skip_next = yes && { skip_next=no; continue; }; \

+    case $$flg in \

+      *=*|--*) continue;; \

+        -*I) strip_trailopt 'I'; skip_next=yes;; \

+      -*I?*) strip_trailopt 'I';; \

+        -*O) strip_trailopt 'O'; skip_next=yes;; \

+      -*O?*) strip_trailopt 'O';; \

+        -*l) strip_trailopt 'l'; skip_next=yes;; \

+      -*l?*) strip_trailopt 'l';; \

+      -[dEDm]) skip_next=yes;; \

+      -[JT]) skip_next=yes;; \

     esac; \

-    test $$am__dry = yes; \

-  }

+    case $$flg in \

+      *$$target_option*) has_opt=yes; break;; \

+    esac; \

+  done; \

+  test $$has_opt = yes

+am__make_dryrun = (target_option=n; $(am__make_running_with_option))

+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))

 pkgdatadir = $(datadir)/@PACKAGE@

 pkgincludedir = $(includedir)/@PACKAGE@

 pkglibdir = $(libdir)/@PACKAGE@

@@ -51,13 +79,13 @@ build_triplet = @build@

 host_triplet = @host@

 target_triplet = @target@

 subdir = .

-DIST_COMMON = INSTALL NEWS README AUTHORS ChangeLog \

+DIST_COMMON = INSTALL NEWS README AUTHORS ChangeLog COPYING \

 	$(srcdir)/Makefile.in $(srcdir)/Makefile.am \

 	$(top_srcdir)/configure $(am__configure_deps) \

-	$(top_srcdir)/lib/gstruct.pc.in COPYING config/compile \

-	config/config.guess config/config.sub config/depcomp \

-	config/install-sh config/missing config/ltmain.sh \

-	$(top_srcdir)/config/compile $(top_srcdir)/config/config.guess \

+	$(top_srcdir)/lib/gstruct.pc.in config/compile \

+	config/config.guess config/config.sub config/install-sh \

+	config/missing config/ltmain.sh $(top_srcdir)/config/compile \

+	$(top_srcdir)/config/config.guess \

 	$(top_srcdir)/config/config.sub \

 	$(top_srcdir)/config/install-sh $(top_srcdir)/config/ltmain.sh \

 	$(top_srcdir)/config/missing

@@ -231,7 +259,6 @@ LIBTOOL = @LIBTOOL@

 LIPO = @LIPO@

 LN_S = @LN_S@

 LTLIBOBJS = @LTLIBOBJS@

-MAINT = @MAINT@

 MAKEINFO = @MAKEINFO@

 MANIFEST_TOOL = @MANIFEST_TOOL@

 MKDIR_P = @MKDIR_P@

@@ -329,7 +356,7 @@ all: all-recursive

 .SUFFIXES:

 am--refresh: Makefile

 	@:

-$(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am  $(am__configure_deps)

+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)

 	@for dep in $?; do \

 	  case '$(am__configure_deps)' in \

 	    *$$dep*) \

@@ -356,9 +383,9 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status

 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)

 	$(SHELL) ./config.status --recheck

-$(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)

+$(top_srcdir)/configure:  $(am__configure_deps)

 	$(am__cd) $(srcdir) && $(AUTOCONF)

-$(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)

+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)

 	$(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)

 $(am__aclocal_m4_deps):

 lib/gstruct-${LIBGSTRUCT_API_VERSION}.pc: $(top_builddir)/config.status $(top_srcdir)/lib/gstruct.pc.in

@@ -380,13 +407,12 @@ distclean-libtool:

 #     (which will cause the Makefiles to be regenerated when you run 'make');

 # (2) otherwise, pass the desired values on the 'make' command line.

 $(am__recursive_targets):

-	@fail= failcom='exit 1'; \

-	for f in x $$MAKEFLAGS; do \

-	  case $$f in \

-	    *=* | --[!k]*);; \

-	    *k*) failcom='fail=yes';; \

-	  esac; \

-	done; \

+	@fail=; \

+	if $(am__make_keepgoing); then \

+	  failcom='fail=yes'; \

+	else \

+	  failcom='exit 1'; \

+	fi; \

 	dot_seen=no; \

 	target=`echo $@ | sed s/-recursive//`; \

 	case "$@" in \

@@ -564,10 +590,16 @@ dist-xz: distdir

 	$(am__post_remove_distdir)

 dist-tarZ: distdir

+	@echo WARNING: "Support for shar distribution archives is" \

+	               "deprecated." >&2

+	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2

 	tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z

 	$(am__post_remove_distdir)

 dist-shar: distdir

+	@echo WARNING: "Support for distribution archives compressed with" \

+		       "legacy program 'compress' is deprecated." >&2

+	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2

 	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz

 	$(am__post_remove_distdir)

@@ -1 +1 @@

-2013-09-12

\ No newline at end of file

+2013-11-15

\ No newline at end of file

@@ -1,6 +1,6 @@

-# generated automatically by aclocal 1.13.1 -*- Autoconf -*-

+# generated automatically by aclocal 1.14 -*- Autoconf -*-

-# Copyright (C) 1996-2012 Free Software Foundation, Inc.

+# Copyright (C) 1996-2013 Free Software Foundation, Inc.

 # This file is free software; the Free Software Foundation

 # gives unlimited permission to copy and/or distribute it,

@@ -32,10 +32,10 @@ To do so, use the procedure documented by the package, typically 'autoreconf'.])

 # generated from the m4 files accompanying Automake X.Y.

 # (This private macro should not be called outside this file.)

 AC_DEFUN([AM_AUTOMAKE_VERSION],

-[am__api_version='1.13'

+[am__api_version='1.14'

 dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to

 dnl require some minimum version.  Point them to the right macro.

-m4_if([$1], [1.13.1], [],

+m4_if([$1], [1.14], [],

       [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl

 ])

@@ -51,7 +51,7 @@ m4_define([_AM_AUTOCONF_VERSION], [])

 # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.

 # This function is AC_REQUIREd by AM_INIT_AUTOMAKE.

 AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],

-[AM_AUTOMAKE_VERSION([1.13.1])dnl

+[AM_AUTOMAKE_VERSION([1.14])dnl

 m4_ifndef([AC_AUTOCONF_VERSION],

   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl

 _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])

@@ -373,7 +373,7 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],

     DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`

     test -z "$DEPDIR" && continue

     am__include=`sed -n 's/^am__include = //p' < "$mf"`

-    test -z "am__include" && continue

+    test -z "$am__include" && continue

     am__quote=`sed -n 's/^am__quote = //p' < "$mf"`

     # Find all dependency output files, they are included files with

     # $(DEPDIR) in their names.  We invoke sed twice because it is the

@@ -418,6 +418,12 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],

 # This macro actually does too much.  Some checks are only needed if

 # your package does certain things.  But this isn't really a big deal.

+dnl Redefine AC_PROG_CC to automatically invoke _AM_PROG_CC_C_O.

+m4_define([AC_PROG_CC],

+m4_defn([AC_PROG_CC])

+[_AM_PROG_CC_C_O

+])

+

 # AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])

 # AM_INIT_AUTOMAKE([OPTIONS])

 # -----------------------------------------------

@@ -526,7 +532,48 @@ dnl macro is hooked onto _AC_COMPILER_EXEEXT early, see below.

 AC_CONFIG_COMMANDS_PRE(dnl

 [m4_provide_if([_AM_COMPILER_EXEEXT],

   [AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl

-])

+

+# POSIX will say in a future version that running "rm -f" with no argument

+# is OK; and we want to be able to make that assumption in our Makefile

+# recipes.  So use an aggressive probe to check that the usage we want is

+# actually supported "in the wild" to an acceptable degree.

+# See automake bug#10828.

+# To make any issue more visible, cause the running configure to be aborted

+# by default if the 'rm' program in use doesn't match our expectations; the

+# user can still override this though.

+if rm -f && rm -fr && rm -rf; then : OK; else

+  cat >&2 <<'END'

+Oops!

+

+Your 'rm' program seems unable to run without file operands specified

+on the command line, even when the '-f' option is present.  This is contrary

+to the behaviour of most rm programs out there, and not conforming with

+the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>

+

+Please tell bug-automake@gnu.org about your system, including the value

+of your $PATH and any error possibly output before this message.  This

+can help us improve future automake versions.

+

+END

+  if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then

+    echo 'Configuration will proceed anyway, since you have set the' >&2

+    echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2

+    echo >&2

+  else

+    cat >&2 <<'END'

+Aborting the configuration process, to ensure you take notice of the issue.

+

+You can download and install GNU coreutils to get an 'rm' implementation

+that behaves properly: <http://www.gnu.org/software/coreutils/>.

+

+If you want to complete the configuration process using your problematic

+'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM

+to "yes", and re-run configure.

+

+END

+    AC_MSG_ERROR([Your 'rm' program is bad, sorry.])

+  fi

+fi])

 dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion.  Do not

 dnl add the conditional right here, as _AC_COMPILER_EXEEXT may be further

@@ -534,7 +581,6 @@ dnl mangled by Autoconf and run in a shell conditional statement.

 m4_define([_AC_COMPILER_EXEEXT],

 m4_defn([_AC_COMPILER_EXEEXT])[m4_provide([_AM_COMPILER_EXEEXT])])

-

 # When config.status generates a header, we must update the stamp-h file.

 # This file resides in the same directory as the config header

 # that is generated.  The stamp files are numbered to have different names.

@@ -596,42 +642,6 @@ fi

 rmdir .tst 2>/dev/null

 AC_SUBST([am__leading_dot])])

-# Add --enable-maintainer-mode option to configure.         -*- Autoconf -*-

-# From Jim Meyering

-

-# Copyright (C) 1996-2013 Free Software Foundation, Inc.

-#

-# This file is free software; the Free Software Foundation

-# gives unlimited permission to copy and/or distribute it,

-# with or without modifications, as long as this notice is preserved.

-

-# AM_MAINTAINER_MODE([DEFAULT-MODE])

-# ----------------------------------

-# Control maintainer-specific portions of Makefiles.

-# Default is to disable them, unless 'enable' is passed literally.

-# For symmetry, 'disable' may be passed as well.  Anyway, the user

-# can override the default with the --enable/--disable switch.

-AC_DEFUN([AM_MAINTAINER_MODE],

-[m4_case(m4_default([$1], [disable]),

-       [enable], [m4_define([am_maintainer_other], [disable])],

-       [disable], [m4_define([am_maintainer_other], [enable])],

-       [m4_define([am_maintainer_other], [enable])

-        m4_warn([syntax], [unexpected argument to AM@&t@_MAINTAINER_MODE: $1])])

-AC_MSG_CHECKING([whether to enable maintainer-specific portions of Makefiles])

-  dnl maintainer-mode's default is 'disable' unless 'enable' is passed

-  AC_ARG_ENABLE([maintainer-mode],

-    [AS_HELP_STRING([--]am_maintainer_other[-maintainer-mode],

-      am_maintainer_other[ make rules and dependencies not useful

-      (and sometimes confusing) to the casual installer])],

-    [USE_MAINTAINER_MODE=$enableval],

-    [USE_MAINTAINER_MODE=]m4_if(am_maintainer_other, [enable], [no], [yes]))

-  AC_MSG_RESULT([$USE_MAINTAINER_MODE])

-  AM_CONDITIONAL([MAINTAINER_MODE], [test $USE_MAINTAINER_MODE = yes])

-  MAINT=$MAINTAINER_MODE_TRUE

-  AC_SUBST([MAINT])dnl

-]

-)

-

 # Check to see how 'make' treats includes.	            -*- Autoconf -*-

 # Copyright (C) 2001-2013 Free Software Foundation, Inc.

@@ -682,38 +692,6 @@ AC_MSG_RESULT([$_am_result])

 rm -f confinc confmf

 ])

-# Copyright (C) 1999-2013 Free Software Foundation, Inc.

-#

-# This file is free software; the Free Software Foundation

-# gives unlimited permission to copy and/or distribute it,

-# with or without modifications, as long as this notice is preserved.

-

-# AM_PROG_CC_C_O

-# --------------

-# Like AC_PROG_CC_C_O, but changed for automake.

-AC_DEFUN([AM_PROG_CC_C_O],

-[AC_REQUIRE([AC_PROG_CC_C_O])dnl

-AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl

-AC_REQUIRE_AUX_FILE([compile])dnl

-# FIXME: we rely on the cache variable name because

-# there is no other way.

-set dummy $CC

-am_cc=`echo $[2] | sed ['s/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/']`

-eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o

-if test "$am_t" != yes; then

-   # Losing compiler, so override with the script.

-   # FIXME: It is wrong to rewrite CC.

-   # But if we don't then we get into trouble of one sort or another.

-   # A longer-term fix would be to have automake use am__CC in this case,

-   # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"

-   CC="$am_aux_dir/compile $CC"

-fi

-dnl Make sure AC_PROG_CC is never called again, or it will override our

-dnl setting of CC.

-m4_define([AC_PROG_CC],

-          [m4_fatal([AC_PROG_CC cannot be called after AM_PROG_CC_C_O])])

-])

-

 # Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-

 # Copyright (C) 1997-2013 Free Software Foundation, Inc.

@@ -784,6 +762,70 @@ AC_DEFUN([_AM_SET_OPTIONS],

 AC_DEFUN([_AM_IF_OPTION],

 [m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])

+# Copyright (C) 1999-2013 Free Software Foundation, Inc.

+#

+# This file is free software; the Free Software Foundation

+# gives unlimited permission to copy and/or distribute it,

+# with or without modifications, as long as this notice is preserved.

+

+# _AM_PROG_CC_C_O

+# ---------------

+# Like AC_PROG_CC_C_O, but changed for automake.  We rewrite AC_PROG_CC

+# to automatically call this.

+AC_DEFUN([_AM_PROG_CC_C_O],

+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl

+AC_REQUIRE_AUX_FILE([compile])dnl

+AC_LANG_PUSH([C])dnl

+AC_CACHE_CHECK(

+  [whether $CC understands -c and -o together],

+  [am_cv_prog_cc_c_o],

+  [AC_LANG_CONFTEST([AC_LANG_PROGRAM([])])

+  # Make sure it works both with $CC and with simple cc.

+  # Following AC_PROG_CC_C_O, we do the test twice because some

+  # compilers refuse to overwrite an existing .o file with -o,

+  # though they will create one.

+  am_cv_prog_cc_c_o=yes

+  for am_i in 1 2; do

+    if AM_RUN_LOG([$CC -c conftest.$ac_ext -o conftest2.$ac_objext]) \

+         && test -f conftest2.$ac_objext; then

+      : OK

+    else

+      am_cv_prog_cc_c_o=no

+      break

+    fi

+  done

+  rm -f core conftest*

+  unset am_i])

+if test "$am_cv_prog_cc_c_o" != yes; then

+   # Losing compiler, so override with the script.

+   # FIXME: It is wrong to rewrite CC.

+   # But if we don't then we get into trouble of one sort or another.

+   # A longer-term fix would be to have automake use am__CC in this case,

+   # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"

+   CC="$am_aux_dir/compile $CC"

+fi

+AC_LANG_POP([C])])

+

+# For backward compatibility.

+AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])

+

+# Copyright (C) 2001-2013 Free Software Foundation, Inc.

+#

+# This file is free software; the Free Software Foundation

+# gives unlimited permission to copy and/or distribute it,

+# with or without modifications, as long as this notice is preserved.

+

+# AM_RUN_LOG(COMMAND)

+# -------------------

+# Run COMMAND, save the exit status in ac_status, and log it.

+# (This has been adapted from Autoconf's _AC_RUN_LOG macro.)

+AC_DEFUN([AM_RUN_LOG],

+[{ echo "$as_me:$LINENO: $1" >&AS_MESSAGE_LOG_FD

+   ($1) >&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD

+   ac_status=$?

+   echo "$as_me:$LINENO: \$? = $ac_status" >&AS_MESSAGE_LOG_FD

+   (exit $ac_status); }])

+

 # Check to make sure that the build environment is sane.    -*- Autoconf -*-

 # Copyright (C) 1996-2013 Free Software Foundation, Inc.

@@ -993,76 +1035,114 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])

 # Substitute a variable $(am__untar) that extract such

 # a tarball read from stdin.

 #     $(am__untar) < result.tar

+#

 AC_DEFUN([_AM_PROG_TAR],

 [# Always define AMTAR for backward compatibility.  Yes, it's still used

 # in the wild :-(  We should find a proper way to deprecate it ...

 AC_SUBST([AMTAR], ['$${TAR-tar}'])

-m4_if([$1], [v7],

-     [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],

-     [m4_case([$1], [ustar],, [pax],,

-              [m4_fatal([Unknown tar format])])

-AC_MSG_CHECKING([how to create a $1 tar archive])

-# Loop over all known methods to create a tar archive until one works.

+

+# We'll loop over all known methods to create a tar archive until one works.

 _am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'

-_am_tools=${am_cv_prog_tar_$1-$_am_tools}

-# Do not fold the above two line into one, because Tru64 sh and

-# Solaris sh will not grok spaces in the rhs of '-'.

-for _am_tool in $_am_tools

-do

-  case $_am_tool in

-  gnutar)

-    for _am_tar in tar gnutar gtar;

-    do

-      AM_RUN_LOG([$_am_tar --version]) && break

-    done

-    am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'

-    am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'

-    am__untar="$_am_tar -xf -"

-    ;;

-  plaintar)

-    # Must skip GNU tar: if it does not support --format= it doesn't create

-    # ustar tarball either.

-    (tar --version) >/dev/null 2>&1 && continue

-    am__tar='tar chf - "$$tardir"'

-    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

+m4_if([$1], [v7],

+  [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],

+

+  [m4_case([$1],

+    [ustar],

+     [# The POSIX 1988 'ustar' format is defined with fixed-size fields.

+      # There is notably a 21 bits limit for the UID and the GID.  In fact,

+      # the 'pax' utility can hang on bigger UID/GID (see automake bug#8343

+      # and bug#13588).

+      am_max_uid=2097151 # 2^21 - 1

+      am_max_gid=$am_max_uid

+      # The $UID and $GID variables are not portable, so we need to resort

+      # to the POSIX-mandated id(1) utility.  Errors in the 'id' calls

+      # below are definitely unexpected, so allow the users to see them

+      # (that is, avoid stderr redirection).

+      am_uid=`id -u || echo unknown`

+      am_gid=`id -g || echo unknown`

+      AC_MSG_CHECKING([whether UID '$am_uid' is supported by ustar format])

+      if test $am_uid -le $am_max_uid; then

+         AC_MSG_RESULT([yes])

+      else

+         AC_MSG_RESULT([no])

+         _am_tools=none

+      fi

+      AC_MSG_CHECKING([whether GID '$am_gid' is supported by ustar format])

+      if test $am_gid -le $am_max_gid; then

+         AC_MSG_RESULT([yes])

+      else

+        AC_MSG_RESULT([no])

+        _am_tools=none

+      fi],

+

+  [pax],

+    [],

+

+  [m4_fatal([Unknown tar format])])

+

+  AC_MSG_CHECKING([how to create a $1 tar archive])

+

+  # Go ahead even if we have the value already cached.  We do so because we

+  # need to set the values for the 'am__tar' and 'am__untar' variables.

+  _am_tools=${am_cv_prog_tar_$1-$_am_tools}

+

+  for _am_tool in $_am_tools; do

+    case $_am_tool in

+    gnutar)

+      for _am_tar in tar gnutar gtar; do

+        AM_RUN_LOG([$_am_tar --version]) && break

+      done

+      am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'

+      am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'

+      am__untar="$_am_tar -xf -"

+      ;;

+    plaintar)

+      # Must skip GNU tar: if it does not support --format= it doesn't create

+      # ustar tarball either.

+      (tar --version) >/dev/null 2>&1 && continue

+      am__tar='tar chf - "$$tardir"'

+      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

-  # 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])

+    # 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])

+      AM_RUN_LOG([cat conftest.dir/file])

+      grep GrepMe conftest.dir/file >/dev/null 2>&1 && break

+    fi

+  done

   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_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

@@ -1,10 +1,8 @@

 #! /bin/sh

 # Attempt to guess a canonical system name.

-#   Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,

-#   2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,

-#   2011, 2012, 2013 Free Software Foundation, Inc.

+#   Copyright 1992-2013 Free Software Foundation, Inc.

-timestamp='2012-12-30'

+timestamp='2013-05-16'

 # This file is free software; you can redistribute it and/or modify it

 # under the terms of the GNU General Public License as published by

@@ -52,9 +50,7 @@ version="\

 GNU config.guess ($timestamp)

 Originally written by Per Bothner.

-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000,

-2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011,

-2012, 2013 Free Software Foundation, Inc.

+Copyright 1992-2013 Free Software Foundation, Inc.

 This is free software; see the source for copying conditions.  There is NO

 warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."

@@ -137,22 +133,20 @@ UNAME_SYSTEM=`(uname -s) 2>/dev/null`  || UNAME_SYSTEM=unknown

 UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown

 case "${UNAME_SYSTEM}" in

-Linux|GNU/*)

+Linux|GNU|GNU/*)

+	# If the system lacks a compiler, then just pick glibc.

+	# We could probably try harder.

+	LIBC=gnu

+

 	eval $set_cc_for_build

 	cat <<-EOF > $dummy.c

 	#include <features.h>

-	#ifdef __UCLIBC__

-	# ifdef __UCLIBC_CONFIG_VERSION__

-	LIBC=uclibc __UCLIBC_CONFIG_VERSION__

-	# else

+	#if defined(__UCLIBC__)

 	LIBC=uclibc

-	# endif

-	#else

-	# ifdef __dietlibc__

+	#elif defined(__dietlibc__)

 	LIBC=dietlibc

-	# else

+	#else

 	LIBC=gnu

-	# endif

 	#endif

 	EOF

 	eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'`

@@ -910,6 +904,9 @@ EOF

 	if test "$?" = 0 ; then LIBC="gnulibc1" ; fi

 	echo ${UNAME_MACHINE}-unknown-linux-${LIBC}

 	exit ;;

+    arc:Linux:*:* | arceb:Linux:*:*)

+	echo ${UNAME_MACHINE}-unknown-linux-${LIBC}

+	exit ;;

     arm*:Linux:*:*)

 	eval $set_cc_for_build

 	if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \

@@ -972,6 +969,9 @@ EOF

 	eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`

 	test x"${CPU}" != x && { echo "${CPU}-unknown-linux-${LIBC}"; exit; }

 	;;

+    or1k:Linux:*:*)

+	echo ${UNAME_MACHINE}-unknown-linux-${LIBC}

+	exit ;;

     or32:Linux:*:*)

 	echo ${UNAME_MACHINE}-unknown-linux-${LIBC}

 	exit ;;

@@ -996,7 +996,7 @@ EOF

 	echo powerpc-unknown-linux-${LIBC}

 	exit ;;

     s390:Linux:*:* | s390x:Linux:*:*)

-	echo ${UNAME_MACHINE}-ibm-linux

+	echo ${UNAME_MACHINE}-ibm-linux-${LIBC}

 	exit ;;

     sh64*:Linux:*:*)

 	echo ${UNAME_MACHINE}-unknown-linux-${LIBC}

@@ -1250,19 +1250,21 @@ EOF

 	exit ;;

     *:Darwin:*:*)

 	UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown

-	case $UNAME_PROCESSOR in

-	    i386)

-		eval $set_cc_for_build

-		if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then

-		  if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \

-		      (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \

-		      grep IS_64BIT_ARCH >/dev/null

-		  then

-		      UNAME_PROCESSOR="x86_64"

-		  fi

-		fi ;;

-	    unknown) UNAME_PROCESSOR=powerpc ;;

-	esac

+	eval $set_cc_for_build

+	if test "$UNAME_PROCESSOR" = unknown ; then

+	    UNAME_PROCESSOR=powerpc

+	fi

+	if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then

+	    if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \

+		(CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \

+		grep IS_64BIT_ARCH >/dev/null

+	    then

+		case $UNAME_PROCESSOR in

+		    i386) UNAME_PROCESSOR=x86_64 ;;

+		    powerpc) UNAME_PROCESSOR=powerpc64 ;;

+		esac

+	    fi

+	fi

 	echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}

 	exit ;;

     *:procnto*:*:* | *:QNX:[0123456789]*:*)

@@ -1,10 +1,8 @@

 #! /bin/sh

 # Configuration validation subroutine script.

-#   Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,

-#   2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,

-#   2011, 2012, 2013 Free Software Foundation, Inc.

+#   Copyright 1992-2013 Free Software Foundation, Inc.

-timestamp='2013-01-11'

+timestamp='2013-04-24'

 # This file is free software; you can redistribute it and/or modify it

 # under the terms of the GNU General Public License as published by

@@ -70,9 +68,7 @@ Report bugs and patches to <config-patches@gnu.org>."

 version="\

 GNU config.sub ($timestamp)

-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000,

-2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011,

-2012, 2013 Free Software Foundation, Inc.

+Copyright 1992-2013 Free Software Foundation, Inc.

 This is free software; see the source for copying conditions.  There is NO

 warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."

@@ -256,7 +252,7 @@ case $basic_machine in

 	| alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \

 	| alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \

 	| am33_2.0 \

-	| arc \

+	| arc | arceb \

 	| arm | arm[bl]e | arme[lb] | armv[2-8] | armv[3-8][lb] | armv7[arm] \

 	| avr | avr32 \

 	| be32 | be64 \

@@ -297,10 +293,10 @@ case $basic_machine in

 	| mt \

 	| msp430 \

 	| nds32 | nds32le | nds32be \

-	| nios | nios2 \

+	| nios | nios2 | nios2eb | nios2el \

 	| ns16k | ns32k \

 	| open8 \

-	| or32 \

+	| or1k | or32 \

 	| pdp10 | pdp11 | pj | pjl \

 	| powerpc | powerpc64 | powerpc64le | powerpcle \

 	| pyramid \

@@ -370,7 +366,7 @@ case $basic_machine in

 	| aarch64-* | aarch64_be-* \

 	| alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \

 	| alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \

-	| alphapca5[67]-* | alpha64pca5[67]-* | arc-* \

+	| alphapca5[67]-* | alpha64pca5[67]-* | arc-* | arceb-* \

 	| arm-*  | armbe-* | armle-* | armeb-* | armv*-* \

 	| avr-* | avr32-* \

 	| be32-* | be64-* \

@@ -414,7 +410,7 @@ case $basic_machine in

 	| mt-* \

 	| msp430-* \

 	| nds32-* | nds32le-* | nds32be-* \

-	| nios-* | nios2-* \

+	| nios-* | nios2-* | nios2eb-* | nios2el-* \

 	| none-* | np1-* | ns16k-* | ns32k-* \

 	| open8-* \

 	| orion-* \

@@ -1611,6 +1607,9 @@ case $basic_machine in

 	mips*-*)

 		os=-elf

 		;;

+	or1k-*)

+		os=-elf

+		;;

 	or32-*)

 		os=-coff

 		;;

@@ -1,7 +1,7 @@

 #! /bin/sh

 # depcomp - compile a program generating dependencies as side-effects

-scriptversion=2012-10-18.11; # UTC

+scriptversion=2013-05-30.07; # UTC

 # Copyright (C) 1999-2013 Free Software Foundation, Inc.

@@ -552,6 +552,7 @@ $ {

   G

   p

 }' >> "$depfile"

+  echo >> "$depfile" # make sure the fragment doesn't end with a backslash

   rm -f "$tmpdepfile"

   ;;

@@ -1,6 +1,6 @@

 #! /bin/sh

 # Guess values for system-dependent variables and create Makefiles.

-# Generated by GNU Autoconf 2.69 for gstruct 2013-09-12.

+# Generated by GNU Autoconf 2.69 for gstruct 2013-11-15.

 #

 # Report bugs to <Thomas Wu <twu@gene.com>>.

 #

@@ -590,8 +590,8 @@ MAKEFLAGS=

 # Identity of this package.

 PACKAGE_NAME='gstruct'

 PACKAGE_TARNAME='gstruct'

-PACKAGE_VERSION='2013-09-12'

-PACKAGE_STRING='gstruct 2013-09-12'

+PACKAGE_VERSION='2013-11-15'

+PACKAGE_STRING='gstruct 2013-11-15'

 PACKAGE_BUGREPORT='Thomas Wu <twu@gene.com>'

 PACKAGE_URL=''

@@ -684,9 +684,6 @@ MAINTAINER_FALSE

 MAINTAINER_TRUE

 FULLDIST_FALSE

 FULLDIST_TRUE

-MAINT

-MAINTAINER_MODE_FALSE

-MAINTAINER_MODE_TRUE

 AM_BACKSLASH

 AM_DEFAULT_VERBOSITY

 AM_DEFAULT_V

@@ -789,7 +786,6 @@ enable_option_checking

 enable_largefile

 enable_dependency_tracking

 enable_silent_rules

-enable_maintainer_mode

 enable_fulldist

 enable_maintainer

 enable_static_linking

@@ -1355,7 +1351,7 @@ if test "$ac_init_help" = "long"; then