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

         methods 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: 1.7.6

+Version: 1.7.7

 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),

         GenomicRanges (>= 1.17.12)

 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),

@@ -47,11 +47,12 @@ normArgWhich <- function(x, genome) {

 setGeneric("normArgCdsIIT", function(exon_iit, genome, ...) standardGeneric("normArgCdsIIT"))

 setMethod("normArgCdsIIT", "ANY", function(exon_iit, genome, BPPARAM) {

-    if(!is(exon_iit, "character") || length(exon_iit) > 1)

-        stop("Invalid exon_iit value. Accepted values types are: single character value (file location), GRangesList of exons, a TxDb object (use the exons in the TxDb), or a GmapGenome (use the genome gene map iit)")

-    if(nchar(exon_iit) && !file.exists(exon_iit))

+    if(!is.null(exon_iit) && (!is(exon_iit, "character") || length(exon_iit) > 1))

+        stop("Invalid exon_iit value. Accepted values types are: single character value (file location), GRangesList of exons, a TxDb object (use the exons in the TxDb),  a GmapGenome (use the genome gene map iit), or NULL")

+    if(!is.null(exon_iit) && (nchar(exon_iit) && !file.exists(exon_iit)))

         stop("exon_iit is non-empty and does not point to an existing file")

     exon_iit

+

 })

 setMethod("normArgCdsIIT", "TxDb", function(exon_iit, genome, BPPARAM) {

@@ -45,13 +45,12 @@ $(SUBDIRS): %: %/Makefile

 gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools 

 	cd $(dir $@); \

-	CFLAGS="-g -O0" ./configure --enable-static --disable-shared \

+	CFLAGS="-g" ./configure --enable-static --disable-shared \

 	            --prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \

 	            --libdir=${PREFIX}/${LIBnn} \

 	            --with-samtools-lib=${R_SRC_DIR}/samtools \

                     --disable-binaries  \

-# --disable-maintainer-mode \

-		     #\ added by gabe 5/14/14

+                    --disable-maintainer-mode \

 ## does not appear to be a true dependency yet

 ##	            --with-gmap=${PREFIX}/bin

@@ -79,11 +79,11 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

                                  print_indels_p, blocksize, verbosep,

                                  /*readlevel_p*/false, max_softclip,

 				 /* print_xs_scores_p ??? */ false,

-//				 /* print_noncovered_p ??? */ false);

-				 /* print_noncovered_p ??? */ true);

+				 /* print_noncovered_p ??? */ false);

   IIT_free(&chromosome_iit);

   Genome_free(&genome);

-  IIT_free(&map_iit);

+  if(map_iit != NULL)

+    IIT_free(&map_iit);

   if (tally_iit == NULL) {

     error("Could not create tally\n");

   }

@@ -139,6 +139,7 @@ LIBTOOL = @LIBTOOL@

 LIPO = @LIPO@

 LN_S = @LN_S@

 LTLIBOBJS = @LTLIBOBJS@

+MAINT = @MAINT@

 MAKEINFO = @MAKEINFO@

 MKDIR_P = @MKDIR_P@

 NM = @NM@

@@ -235,7 +236,7 @@ all: all-recursive

 .SUFFIXES:

 am--refresh:

 	@:

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

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

 	@for dep in $?; do \

 	  case '$(am__configure_deps)' in \

 	    *$$dep*) \

@@ -262,9 +263,9 @@ 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:  $(am__configure_deps)

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

 	cd $(srcdir) && $(AUTOCONF)

-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)

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

 	cd $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)

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

 	cd $(top_builddir) && $(SHELL) ./config.status $@

@@ -531,6 +531,35 @@ 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, 1998, 2000, 2001, 2002, 2003, 2004, 2005

+# 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.

+

+# serial 4

+

+AC_DEFUN([AM_MAINTAINER_MODE],

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

+  dnl maintainer-mode is disabled by default

+  AC_ARG_ENABLE(maintainer-mode,

+[  --enable-maintainer-mode  enable make rules and dependencies not useful

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

+      USE_MAINTAINER_MODE=$enableval,

+      USE_MAINTAINER_MODE=no)

+  AC_MSG_RESULT([$USE_MAINTAINER_MODE])

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

+  MAINT=$MAINTAINER_MODE_TRUE

+  AC_SUBST(MAINT)dnl

+]

+)

+

+AU_DEFUN([jm_MAINTAINER_MODE], [AM_MAINTAINER_MODE])

+

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

 # Copyright (C) 2001, 2002, 2003, 2005  Free Software Foundation, Inc.

@@ -888,6 +888,9 @@ build

 LIBGSTRUCT_API_VERSION

 LIBGSTRUCT_SO_VERSION

 CFLAGS

+MAINT

+MAINTAINER_MODE_FALSE

+MAINTAINER_MODE_TRUE

 target_alias

 host_alias

 build_alias

@@ -928,6 +931,7 @@ SHELL'

 ac_subst_files=''

 ac_user_opts='

 enable_option_checking

+enable_maintainer_mode

 enable_largefile

 enable_dependency_tracking

 enable_fulldist

@@ -1591,6 +1595,8 @@ Optional Features:

   --disable-option-checking  ignore unrecognized --enable/--with options

   --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)

   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]

+  --enable-maintainer-mode  enable make rules and dependencies not useful

+			  (and sometimes confusing) to the casual installer

   --disable-largefile     omit support for large files

   --disable-dependency-tracking  speeds up one-time build

   --enable-dependency-tracking   do not reject slow dependency extractors

@@ -2091,6 +2097,33 @@ $as_echo_n "checking package version... " >&6; }

 { $as_echo "$as_me:$LINENO: result: 2014-08-05" >&5

 $as_echo "2014-08-05" >&6; }

+## Added by gabe to enable "--disable-maintainer-mode" configure argument

+## for bioc build machines

+{ $as_echo "$as_me:$LINENO: checking whether to enable maintainer-specific portions of Makefiles" >&5

+$as_echo_n "checking whether to enable maintainer-specific portions of Makefiles... " >&6; }

+    # Check whether --enable-maintainer-mode was given.

+if test "${enable_maintainer_mode+set}" = set; then

+  enableval=$enable_maintainer_mode; USE_MAINTAINER_MODE=$enableval

+else

+  USE_MAINTAINER_MODE=no

+fi

+

+  { $as_echo "$as_me:$LINENO: result: $USE_MAINTAINER_MODE" >&5

+$as_echo "$USE_MAINTAINER_MODE" >&6; }

+   if test $USE_MAINTAINER_MODE = yes; then

+  MAINTAINER_MODE_TRUE=

+  MAINTAINER_MODE_FALSE='#'

+else

+  MAINTAINER_MODE_TRUE='#'

+  MAINTAINER_MODE_FALSE=

+fi

+

+  MAINT=$MAINTAINER_MODE_TRUE

+

+

+

+

+

 ### Read defaults

 { $as_echo "$as_me:$LINENO: checking CONFIG_SITE" >&5

 $as_echo_n "checking CONFIG_SITE... " >&6; }

@@ -5819,13 +5852,13 @@ if test "${lt_cv_nm_interface+set}" = set; then

 else

   lt_cv_nm_interface="BSD nm"

   echo "int some_variable = 0;" > conftest.$ac_ext

-  (eval echo "\"\$as_me:5822: $ac_compile\"" >&5)

+  (eval echo "\"\$as_me:5855: $ac_compile\"" >&5)

   (eval "$ac_compile" 2>conftest.err)

   cat conftest.err >&5

-  (eval echo "\"\$as_me:5825: $NM \\\"conftest.$ac_objext\\\"\"" >&5)

+  (eval echo "\"\$as_me:5858: $NM \\\"conftest.$ac_objext\\\"\"" >&5)

   (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out)

   cat conftest.err >&5

-  (eval echo "\"\$as_me:5828: output\"" >&5)

+  (eval echo "\"\$as_me:5861: output\"" >&5)

   cat conftest.out >&5

   if $GREP 'External.*some_variable' conftest.out > /dev/null; then

     lt_cv_nm_interface="MS dumpbin"

@@ -7030,7 +7063,7 @@ ia64-*-hpux*)

   ;;

 *-*-irix6*)

   # Find out which ABI we are using.

-  echo '#line 7033 "configure"' > conftest.$ac_ext

+  echo '#line 7066 "configure"' > conftest.$ac_ext

   if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5

   (eval $ac_compile) 2>&5

   ac_status=$?

@@ -8887,11 +8920,11 @@ else

    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \

    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \

    -e 's:$: $lt_compiler_flag:'`

-   (eval echo "\"\$as_me:8890: $lt_compile\"" >&5)

+   (eval echo "\"\$as_me:8923: $lt_compile\"" >&5)

    (eval "$lt_compile" 2>conftest.err)

    ac_status=$?

    cat conftest.err >&5

-   echo "$as_me:8894: \$? = $ac_status" >&5

+   echo "$as_me:8927: \$? = $ac_status" >&5

    if (exit $ac_status) && test -s "$ac_outfile"; then

      # The compiler can only warn and ignore the option if not recognized

      # So say no if there are warnings other than the usual output.

@@ -9226,11 +9259,11 @@ else

    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \

    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \

    -e 's:$: $lt_compiler_flag:'`

-   (eval echo "\"\$as_me:9229: $lt_compile\"" >&5)

+   (eval echo "\"\$as_me:9262: $lt_compile\"" >&5)

    (eval "$lt_compile" 2>conftest.err)

    ac_status=$?

    cat conftest.err >&5

-   echo "$as_me:9233: \$? = $ac_status" >&5

+   echo "$as_me:9266: \$? = $ac_status" >&5

    if (exit $ac_status) && test -s "$ac_outfile"; then

      # The compiler can only warn and ignore the option if not recognized

      # So say no if there are warnings other than the usual output.

@@ -9331,11 +9364,11 @@ else

    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \

    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \

    -e 's:$: $lt_compiler_flag:'`

-   (eval echo "\"\$as_me:9334: $lt_compile\"" >&5)

+   (eval echo "\"\$as_me:9367: $lt_compile\"" >&5)

    (eval "$lt_compile" 2>out/conftest.err)

    ac_status=$?

    cat out/conftest.err >&5

-   echo "$as_me:9338: \$? = $ac_status" >&5

+   echo "$as_me:9371: \$? = $ac_status" >&5

    if (exit $ac_status) && test -s out/conftest2.$ac_objext

    then

      # The compiler can only warn and ignore the option if not recognized

@@ -9386,11 +9419,11 @@ else

    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \

    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \

    -e 's:$: $lt_compiler_flag:'`

-   (eval echo "\"\$as_me:9389: $lt_compile\"" >&5)

+   (eval echo "\"\$as_me:9422: $lt_compile\"" >&5)

    (eval "$lt_compile" 2>out/conftest.err)

    ac_status=$?

    cat out/conftest.err >&5

-   echo "$as_me:9393: \$? = $ac_status" >&5

+   echo "$as_me:9426: \$? = $ac_status" >&5

    if (exit $ac_status) && test -s out/conftest2.$ac_objext

    then

      # The compiler can only warn and ignore the option if not recognized

@@ -12186,7 +12219,7 @@ else

   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2

   lt_status=$lt_dlunknown

   cat > conftest.$ac_ext <<_LT_EOF

-#line 12189 "configure"

+#line 12222 "configure"

 #include "confdefs.h"

 #if HAVE_DLFCN_H

@@ -12282,7 +12315,7 @@ else

   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2

   lt_status=$lt_dlunknown

   cat > conftest.$ac_ext <<_LT_EOF

-#line 12285 "configure"

+#line 12318 "configure"

 #include "confdefs.h"

 #if HAVE_DLFCN_H

@@ -21234,6 +21267,13 @@ LIBOBJS=$ac_libobjs

 LTLIBOBJS=$ac_ltlibobjs

+if test -z "${MAINTAINER_MODE_TRUE}" && test -z "${MAINTAINER_MODE_FALSE}"; then

+  { { $as_echo "$as_me:$LINENO: error: conditional \"MAINTAINER_MODE\" was never defined.

+Usually this means the macro was only invoked conditionally." >&5

+$as_echo "$as_me: error: conditional \"MAINTAINER_MODE\" was never defined.

+Usually this means the macro was only invoked conditionally." >&2;}

+   { (exit 1); exit 1; }; }

+fi

 if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then

   { { $as_echo "$as_me:$LINENO: error: conditional \"AMDEP\" was never defined.

 Usually this means the macro was only invoked conditionally." >&5

@@ -20,6 +20,12 @@ AC_INIT([gstruct],PKG_VERSION,[Thomas Wu <twu@gene.com>])

 AC_MSG_CHECKING(package version)

 AC_MSG_RESULT(PKG_VERSION)

+## Added by gabe to enable "--disable-maintainer-mode" configure argument 

+## for bioc build machines

+AM_MAINTAINER_MODE([enable]) 

+

+

+

 ### Read defaults

 AC_MSG_CHECKING(CONFIG_SITE)

 if test -z "$CONFIG_SITE"; then

@@ -250,6 +250,7 @@ LIBTOOL = @LIBTOOL@

 LIPO = @LIPO@

 LN_S = @LN_S@

 LTLIBOBJS = @LTLIBOBJS@

+MAINT = @MAINT@

 MAKEINFO = @MAKEINFO@

 MKDIR_P = @MKDIR_P@

 NM = @NM@

@@ -411,7 +412,7 @@ all: config.h

 .SUFFIXES:

 .SUFFIXES: .c .lo .o .obj

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

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

 	@for dep in $?; do \

 	  case '$(am__configure_deps)' in \

 	    *$$dep*) \

@@ -436,9 +437,9 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status

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

 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh

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

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

 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh

-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)

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

 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh

 config.h: stamp-h1

@@ -450,7 +451,7 @@ config.h: stamp-h1

 stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status

 	@rm -f stamp-h1

 	cd $(top_builddir) && $(SHELL) ./config.status src/config.h

-$(srcdir)/config.h.in:  $(am__configure_deps) 

+$(srcdir)/config.h.in: @MAINTAINER_MODE_TRUE@ $(am__configure_deps) 

 	cd $(top_srcdir) && $(AUTOHEADER)

 	rm -f stamp-h1

 	touch $@