@@ -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: 1.5.13

+Version: 1.5.14

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

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

         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4),

@@ -17,7 +17,8 @@ setClass("BamTallyParam",

                         min_depth = "integer",

                         variant_strand = "integer",

                         ignore_query_Ns = "logical",

-                        indels = "logical"))

+                        indels = "logical",

+                        include_soft_clips = "integer"))

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

 ### Constructor

@@ -38,7 +39,7 @@ BamTallyParam <- function(genome, which = GRanges(),

                           primary_only = FALSE, ignore_duplicates = FALSE,

                           min_depth = 0L, variant_strand = 0L,

                           ignore_query_Ns = FALSE,

-                          indels = FALSE)

+                          indels = FALSE, include_soft_clips = 0L)

 {

   if (!is.null(desired_read_group) && !isSingleString(desired_read_group))

     stop("'desired_read_group' must be NULL or a single, non-NA string")

@@ -60,11 +61,14 @@ BamTallyParam <- function(genome, which = GRanges(),

     stop("ignore_query_Ns must be TRUE or FALSE")

   if (!isTRUEorFALSE(indels))

     stop("indels must be TRUE or FALSE")

+  if (include_soft_clips < 0)

+    stop("include_soft_clips must be non-negative")

   args <- names(formals(sys.function()))

   params <- mget(args, environment())

   params$genome <- as(genome, "GmapGenome")

   params$which <- normArgWhich(which, params$genome)

-  integer_params <- c("minimum_mapq", "min_depth", "variant_strand")

+  integer_params <- c("minimum_mapq", "min_depth", "variant_strand",

+                      "include_soft_clips")

   params[integer_params] <- lapply(params[integer_params], as.integer)

   do.call(new, c("BamTallyParam", params))  

 }

@@ -184,7 +184,8 @@ normArgTRUEorFALSE <- function(x) {

                          min_depth = 0L, variant_strand = 0L,

                          ignore_query_Ns = FALSE,

                          indels = FALSE,

-                         blocksize = 1000L, verbosep = FALSE)

+                         blocksize = 1000L, verbosep = FALSE,

+                         include_soft_clips = 0L)

 {

   if (!is(bamreader, "GmapBamReader"))

     stop("'bamreader' must be a GmapBamReader")

@@ -221,7 +222,8 @@ normArgTRUEorFALSE <- function(x) {

         normArgTRUEorFALSE(ignore_query_Ns),

         normArgTRUEorFALSE(indels),

         normArgSingleInteger(blocksize),

-        normArgTRUEorFALSE(verbosep))

+        normArgTRUEorFALSE(verbosep),

+        normArgSingleInteger(include_soft_clips))

 }

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

@@ -21,7 +21,7 @@

                 primary_only = FALSE, ignore_duplicates = FALSE,

                 min_depth = 0L, variant_strand = 0L,

                 ignore_query_Ns = FALSE,

-                indels = FALSE)

+                indels = FALSE, include_soft_clips = 0L)

 }

 \arguments{

   \item{genome}{A \code{GmapGenome} object, or something coercible to one.}

@@ -57,6 +57,13 @@

     always spans the sequence in \code{ref}; so e.g. a deletion extends

     one nt upstream of the actual deleted sequence.

   }

+  \item{include_soft_clips}{Maximum length of soft clips that are

+    considered for counting. Soft-clipping is often useful (for GSNAP at

+    least) during alignment, and it should be preserved in the

+    output. However, soft clipping can preferentially occur in regions

+    of discordance with the reference, and if those clipped regions are

+    ignored during counting, the allele fraction is misestimated.

+  }

 }

 \seealso{

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

 static const R_CallMethodDef callMethods[] = {

   /* bamtally.c */

-  CALLMETHOD_DEF(R_Bamtally_iit, 19),

+  CALLMETHOD_DEF(R_Bamtally_iit, 20),

   CALLMETHOD_DEF(R_tally_iit_parse, 5),

   /* bamreader.c */

@@ -23,7 +23,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

                 SEXP ignore_query_Ns_p_R,

                 SEXP print_indels_p_R,

                 SEXP blocksize_R, 

-                SEXP verbosep_R)

+                SEXP verbosep_R, SEXP max_softclip_R)

 {

   Bamreader_T bamreader = (Bamreader_T) R_ExternalPtrAddr(bamreader_R);

   const char *genome_dir =

@@ -46,6 +46,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

   bool print_indels_p = asLogical(print_indels_p_R);

   int blocksize = asInteger(blocksize_R);

   int verbosep = asLogical(verbosep_R);

+  int max_softclip = asInteger(max_softclip_R);

   Genome_T genome = createGenome(genome_dir, db);

   IIT_T chromosome_iit = readChromosomeIIT(genome_dir, db);

@@ -71,7 +72,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

                                  ignore_duplicates_p,

                                  min_depth, variant_strands, ignore_query_Ns_p,

                                  print_indels_p, blocksize, verbosep,

-                                 /*readlevel_p*/false);

+                                 /*readlevel_p*/false, max_softclip);

   IIT_free(&chromosome_iit);

   Genome_free(&genome);

@@ -20,7 +20,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

                 SEXP ignore_query_Ns_p,

                 SEXP print_indels_p_R,

                 SEXP blocksize_R, 

-                SEXP verbosep_R);

+                SEXP verbosep_R, SEXP max_softclip_R);

 SEXP

 R_tally_iit_parse(SEXP tally_iit_R, SEXP cycle_breaks_R,

@@ -12,8 +12,8 @@ without warranty of any kind.

 Basic Installation

 ==================

-   Briefly, the shell commands `./configure; make; make install' should

-configure, build, and install this package.  The following

+   Briefly, the shell command `./configure && make && make install'

+should configure, build, and install this package.  The following

 more-detailed instructions are generic; see the `README' file for

 instructions specific to this package.  Some packages provide this

 `INSTALL' file but do not implement all of the features documented

@@ -1,4 +1,4 @@

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

+# Makefile.in generated by automake 1.14.1 from Makefile.am.

 # @configure_input@

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

@@ -79,13 +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

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

 LIPO = @LIPO@

 LN_S = @LN_S@

 LTLIBOBJS = @LTLIBOBJS@

-MAINT = @MAINT@

 MAKEINFO = @MAKEINFO@

 MANIFEST_TOOL = @MANIFEST_TOOL@

 MKDIR_P = @MKDIR_P@

@@ -357,7 +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*) \

@@ -384,9 +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

@@ -642,9 +641,10 @@ distcheck: dist

 	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \

 	  && am__cwd=`pwd` \

 	  && $(am__cd) $(distdir)/_build \

-	  && ../configure --srcdir=.. --prefix="$$dc_install_base" \

+	  && ../configure \

 	    $(AM_DISTCHECK_CONFIGURE_FLAGS) \

 	    $(DISTCHECK_CONFIGURE_FLAGS) \

+	    --srcdir=.. --prefix="$$dc_install_base" \

 	  && $(MAKE) $(AM_MAKEFLAGS) \

 	  && $(MAKE) $(AM_MAKEFLAGS) dvi \

 	  && $(MAKE) $(AM_MAKEFLAGS) check \

@@ -1,4 +1,4 @@

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

+# generated automatically by aclocal 1.14.1 -*- Autoconf -*-

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

@@ -35,7 +35,7 @@ AC_DEFUN([AM_AUTOMAKE_VERSION],

 [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], [1.14], [],

+m4_if([$1], [1.14.1], [],

       [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([1.14])dnl

+[AM_AUTOMAKE_VERSION([1.14.1])dnl

 m4_ifndef([AC_AUTOCONF_VERSION],

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

 _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])

@@ -642,42 +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.

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

 #! /bin/sh

 # Attempt to guess a canonical system name.

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

+#   Copyright 1992-2014 Free Software Foundation, Inc.

-timestamp='2013-05-16'

+timestamp='2014-02-12'

 # 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

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

 GNU config.guess ($timestamp)

 Originally written by Per Bothner.

-Copyright 1992-2013 Free Software Foundation, Inc.

+Copyright 1992-2014 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."

@@ -149,7 +149,7 @@ Linux|GNU|GNU/*)

 	LIBC=gnu

 	#endif

 	EOF

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

+	eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC' | sed 's, ,,g'`

 	;;

 esac

@@ -995,6 +995,12 @@ EOF

     ppc:Linux:*:*)

 	echo powerpc-unknown-linux-${LIBC}

 	exit ;;

+    ppc64le:Linux:*:*)

+	echo powerpc64le-unknown-linux-${LIBC}

+	exit ;;

+    ppcle:Linux:*:*)

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

+	exit ;;

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

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

 	exit ;;

@@ -1014,7 +1020,18 @@ EOF

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

 	exit ;;

     x86_64:Linux:*:*)

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

+	eval $set_cc_for_build

+	X86_64_ABI=

+	# If there is a compiler, see if it is configured for 32-bit objects.

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

+	    if (echo '#ifdef __ILP32__'; echo IS_X32; echo '#endif') | \

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

+		grep IS_X32 >/dev/null

+	    then

+		X86_64_ABI=x32

+	    fi

+	fi

+	echo x86_64-unknown-linux-gnu${X86_64_ABI}

 	exit ;;

     xtensa*:Linux:*:*)

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

@@ -1254,16 +1271,26 @@ EOF

 	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

+	if test `echo "$UNAME_RELEASE" | sed -e 's/\..*//'` -le 10 ; then

+	    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

+	elif test "$UNAME_PROCESSOR" = i386 ; then

+	    # Avoid executing cc on OS X 10.9, as it ships with a stub

+	    # that puts up a graphical alert prompting to install

+	    # developer tools.  Any system running Mac OS X 10.7 or

+	    # later (Darwin 11 and later) is required to have a 64-bit

+	    # processor. This is not true of the ARM version of Darwin

+	    # that Apple uses in portable devices.

+	    UNAME_PROCESSOR=x86_64

 	fi

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

 	exit ;;

@@ -1355,154 +1382,6 @@ EOF

 	exit ;;

 esac

-eval $set_cc_for_build

-cat >$dummy.c <<EOF

-#ifdef _SEQUENT_

-# include <sys/types.h>

-# include <sys/utsname.h>

-#endif

-main ()

-{

-#if defined (sony)

-#if defined (MIPSEB)

-  /* BFD wants "bsd" instead of "newsos".  Perhaps BFD should be changed,

-     I don't know....  */

-  printf ("mips-sony-bsd\n"); exit (0);

-#else

-#include <sys/param.h>

-  printf ("m68k-sony-newsos%s\n",

-#ifdef NEWSOS4

-	"4"

-#else

-	""

-#endif

-	); exit (0);

-#endif

-#endif

-

-#if defined (__arm) && defined (__acorn) && defined (__unix)

-  printf ("arm-acorn-riscix\n"); exit (0);

-#endif

-

-#if defined (hp300) && !defined (hpux)

-  printf ("m68k-hp-bsd\n"); exit (0);

-#endif

-

-#if defined (NeXT)

-#if !defined (__ARCHITECTURE__)

-#define __ARCHITECTURE__ "m68k"

-#endif

-  int version;

-  version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;

-  if (version < 4)

-    printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);

-  else

-    printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);

-  exit (0);

-#endif

-

-#if defined (MULTIMAX) || defined (n16)

-#if defined (UMAXV)

-  printf ("ns32k-encore-sysv\n"); exit (0);

-#else

-#if defined (CMU)

-  printf ("ns32k-encore-mach\n"); exit (0);

-#else

-  printf ("ns32k-encore-bsd\n"); exit (0);

-#endif

-#endif

-#endif

-

-#if defined (__386BSD__)

-  printf ("i386-pc-bsd\n"); exit (0);

-#endif

-

-#if defined (sequent)

-#if defined (i386)

-  printf ("i386-sequent-dynix\n"); exit (0);

-#endif

-#if defined (ns32000)

-  printf ("ns32k-sequent-dynix\n"); exit (0);

-#endif

-#endif

-

-#if defined (_SEQUENT_)

-    struct utsname un;

-

-    uname(&un);

-

-    if (strncmp(un.version, "V2", 2) == 0) {

-	printf ("i386-sequent-ptx2\n"); exit (0);

-    }

-    if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */

-	printf ("i386-sequent-ptx1\n"); exit (0);

-    }

-    printf ("i386-sequent-ptx\n"); exit (0);

-

-#endif

-

-#if defined (vax)

-# if !defined (ultrix)

-#  include <sys/param.h>

-#  if defined (BSD)

-#   if BSD == 43

-      printf ("vax-dec-bsd4.3\n"); exit (0);

-#   else

-#    if BSD == 199006

-      printf ("vax-dec-bsd4.3reno\n"); exit (0);

-#    else

-      printf ("vax-dec-bsd\n"); exit (0);

-#    endif

-#   endif

-#  else

-    printf ("vax-dec-bsd\n"); exit (0);

-#  endif

-# else

-    printf ("vax-dec-ultrix\n"); exit (0);

-# endif

-#endif

-

-#if defined (alliant) && defined (i860)

-  printf ("i860-alliant-bsd\n"); exit (0);

-#endif

-

-  exit (1);

-}

-EOF

-

-$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` &&

-	{ echo "$SYSTEM_NAME"; exit; }

-

-# Apollos put the system type in the environment.

-

-test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; }

-

-# Convex versions that predate uname can use getsysinfo(1)

-

-if [ -x /usr/convex/getsysinfo ]

-then

-    case `getsysinfo -f cpu_type` in

-    c1*)

-	echo c1-convex-bsd

-	exit ;;

-    c2*)

-	if getsysinfo -f scalar_acc

-	then echo c32-convex-bsd

-	else echo c2-convex-bsd

-	fi

-	exit ;;

-    c34*)

-	echo c34-convex-bsd

-	exit ;;

-    c38*)

-	echo c38-convex-bsd

-	exit ;;

-    c4*)

-	echo c4-convex-bsd

-	exit ;;

-    esac

-fi

-

 cat >&2 <<EOF

 $0: unable to guess system type

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

 #! /bin/sh

 # Configuration validation subroutine script.

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

+#   Copyright 1992-2014 Free Software Foundation, Inc.

-timestamp='2013-04-24'

+timestamp='2014-01-01'

 # 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

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

 version="\

 GNU config.sub ($timestamp)

-Copyright 1992-2013 Free Software Foundation, Inc.

+Copyright 1992-2014 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."

@@ -257,7 +257,7 @@ case $basic_machine in

 	| avr | avr32 \

 	| be32 | be64 \

 	| bfin \

-	| c4x | clipper \

+	| c4x | c8051 | clipper \

 	| d10v | d30v | dlx | dsp16xx | dvp \

 	| epiphany \

 	| fido | fr30 | frv \

@@ -265,6 +265,7 @@ case $basic_machine in

 	| hexagon \

 	| i370 | i860 | i960 | ia64 \

 	| ip2k | iq2000 \

+	| k1om \

 	| le32 | le64 \

 	| lm32 \

 	| m32c | m32r | m32rle | m68000 | m68k | m88k \

@@ -324,7 +325,7 @@ case $basic_machine in

 	c6x)

 		basic_machine=tic6x-unknown

 		;;

-	m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x | picochip)

+	m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x | nvptx | picochip)

 		basic_machine=$basic_machine-unknown

 		os=-none

 		;;

@@ -372,7 +373,7 @@ case $basic_machine in

 	| be32-* | be64-* \

 	| bfin-* | bs2000-* \

 	| c[123]* | c30-* | [cjt]90-* | c4x-* \

-	| clipper-* | craynv-* | cydra-* \

+	| c8051-* | clipper-* | craynv-* | cydra-* \

 	| d10v-* | d30v-* | dlx-* \

 	| elxsi-* \

 	| f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \

@@ -381,6 +382,7 @@ case $basic_machine in

 	| hexagon-* \

 	| i*86-* | i860-* | i960-* | ia64-* \

 	| ip2k-* | iq2000-* \

+	| k1om-* \

 	| le32-* | le64-* \

 	| lm32-* \

 	| m32c-* | m32r-* | m32rle-* \

@@ -794,7 +796,7 @@ case $basic_machine in

 		os=-mingw64

 		;;

 	mingw32)

-		basic_machine=i386-pc

+		basic_machine=i686-pc

 		os=-mingw32

 		;;

 	mingw32ce)

@@ -848,7 +850,7 @@ case $basic_machine in

 		basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`

 		;;

 	msys)

-		basic_machine=i386-pc

+		basic_machine=i686-pc

 		os=-msys

 		;;

 	mvs)

@@ -1564,6 +1566,9 @@ case $basic_machine in

 	c4x-* | tic4x-*)

 		os=-coff

 		;;

+	c8051-*)

+		os=-elf

+		;;

 	hexagon-*)

 		os=-elf

 		;;

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

 #! /bin/sh

 # Common wrapper for a few potentially missing GNU programs.

-scriptversion=2012-06-26.16; # UTC

+scriptversion=2013-10-28.13; # UTC

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

 # Originally written by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.

@@ -160,7 +160,7 @@ give_advice ()

       ;;

    autom4te*)

       echo "You might have modified some maintainer files that require"

-      echo "the 'automa4te' program to be rebuilt."

+      echo "the 'autom4te' program to be rebuilt."

       program_details 'autom4te'

       ;;

     bison*|yacc*)

@@ -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

@@ -1441,9 +1437,6 @@ Optional Features:

                           speeds up one-time build

   --enable-silent-rules   less verbose build output (undo: "make V=1")

   --disable-silent-rules  verbose build output (undo: "make V=0")

-  --disable-maintainer-mode

-                          disable make rules and dependencies not useful (and

-                          sometimes confusing) to the casual installer

   --enable-fulldist       For use by program maintainer

   --enable-maintainer     For use by program maintainer

   --enable-static-linking Link binaries statically (default=no)

@@ -4538,29 +4531,6 @@ END

   fi

 fi

-{ $as_echo "$as_me:${as_lineno-$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=yes

-fi

-

-  { $as_echo "$as_me:${as_lineno-$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

-

-

-

  if test "x$enable_fulldist" = xyes; then

   FULLDIST_TRUE=

   FULLDIST_FALSE='#'

@@ -15497,10 +15467,6 @@ else

   am__EXEEXT_FALSE=

 fi

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

-  as_fn_error $? "conditional \"MAINTAINER_MODE\" was never defined.

-Usually this means the macro was only invoked conditionally." "$LINENO" 5

-fi

 if test -z "${FULLDIST_TRUE}" && test -z "${FULLDIST_FALSE}"; then

   as_fn_error $? "conditional \"FULLDIST\" was never defined.

 Usually this means the macro was only invoked conditionally." "$LINENO" 5

@@ -64,7 +64,6 @@ AC_ARG_PROGRAM

 #AM_INIT_AUTOMAKE([no-dependencies])

 AM_INIT_AUTOMAKE(AC_PACKAGE_NAME, AC_PACKAGE_VERSION)

-AM_MAINTAINER_MODE([enable])

 AM_CONDITIONAL(FULLDIST,test "x$enable_fulldist" = xyes)

 AC_ARG_ENABLE([fulldist],

@@ -1,4 +1,4 @@

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

+# Makefile.in generated by automake 1.14.1 from Makefile.am.

 # @configure_input@

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

@@ -388,7 +388,6 @@ LIBTOOL = @LIBTOOL@

 LIPO = @LIPO@

 LN_S = @LN_S@

 LTLIBOBJS = @LTLIBOBJS@

-MAINT = @MAINT@

 MAKEINFO = @MAKEINFO@

 MANIFEST_TOOL = @MANIFEST_TOOL@

 MKDIR_P = @MKDIR_P@

@@ -733,7 +732,7 @@ all: config.h

 .SUFFIXES:

 .SUFFIXES: .c .lo .o .obj

-$(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*) \

@@ -758,9 +757,9 @@ 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: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)

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

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

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

+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)

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

 $(am__aclocal_m4_deps):

@@ -771,7 +770,7 @@ 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: @MAINTAINER_MODE_TRUE@ $(am__configure_deps) 

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

 	($(am__cd) $(top_srcdir) && $(AUTOHEADER))

 	rm -f stamp-h1

 	touch $@

@@ -1,4 +1,4 @@

-static char rcsid[] = "$Id: bamread.c 114330 2013-11-07 19:55:05Z twu $";

+static char rcsid[] = "$Id: bamread.c 129099 2014-03-04 18:44:44Z twu $";

 #ifdef HAVE_CONFIG_H

 #include <config.h>

 #endif

@@ -370,7 +370,7 @@ static void

 parse_line (T this, char **acc, unsigned int *flag, int *mapq, char **chr, Genomicpos_T *chrpos,

 	    char **mate_chr, Genomicpos_T *mate_chrpos, int *insert_length,

 	    Intlist_T *cigartypes, Uintlist_T *cigarlengths, int *cigarlength,

-	    int *readlength, char **read, char **quality_string, char **read_group) {

+	    int *readlength, char **read, char **quality_string, char **read_group, bool *terminalp) {

   int type;

   int i;

   unsigned int length;

@@ -435,6 +435,15 @@ parse_line (T this, char **acc, unsigned int *flag, int *mapq, char **chr, Genom

     *read_group = bam_aux2Z(ptr);

   }

+  ptr = bam_aux_get(this->bam,"PG");

+  if (ptr == NULL) {

+    *terminalp = false;

+  } else if (strcmp((char *) ptr,"T")) {

+    *terminalp = false;

+  } else {

+    *terminalp = true;

+  }

+

   /* Cigar */

   *cigarlength = 0;

   *cigartypes = (Intlist_T) NULL;

@@ -475,7 +484,8 @@ int

 Bamread_next_line (T this, char **acc, unsigned int *flag, int *mapq, char **chr, Genomicpos_T *chrpos,

 		   char **mate_chr, Genomicpos_T *mate_chrpos,

 		   Intlist_T *cigartypes, Uintlist_T *cigarlengths, int *cigarlength,

-		   int *readlength, char **read, char **quality_string, char **read_group) {

+		   int *readlength, char **read, char **quality_string, char **read_group,

+		   bool *terminalp) {

   int insert_length;

 #ifndef HAVE_SAMTOOLS

@@ -488,7 +498,8 @@ Bamread_next_line (T this, char **acc, unsigned int *flag, int *mapq, char **chr

       parse_line(this,&(*acc),&(*flag),&(*mapq),&(*chr),&(*chrpos),

 		 &(*mate_chr),&(*mate_chrpos),&insert_length,

 		 &(*cigartypes),&(*cigarlengths),&(*cigarlength),

-		 &(*readlength),&(*read),&(*quality_string),&(*read_group));

+		 &(*readlength),&(*read),&(*quality_string),&(*read_group),

+		 &(*terminalp));

       return 1;

     }

   } else {

@@ -498,7 +509,8 @@ Bamread_next_line (T this, char **acc, unsigned int *flag, int *mapq, char **chr

       parse_line(this,&(*acc),&(*flag),&(*mapq),&(*chr),&(*chrpos),

 		 &(*mate_chr),&(*mate_chrpos),&insert_length,

 		 &(*cigartypes),&(*cigarlengths),&(*cigarlength),

-		 &(*readlength),&(*read),&(*quality_string),&(*read_group));

+		 &(*readlength),&(*read),&(*quality_string),&(*read_group),

+		 &(*terminalp));

       return 1;

     }

   }

@@ -525,6 +537,7 @@ struct Bamline_T {

   int readlength;

   char *read;

   char *quality_string;

+  bool terminalp;

   unsigned char *aux_start;

   unsigned char *aux_end;

 };

@@ -707,6 +720,11 @@ Bamline_quality_string (Bamline_T this) {

   return this->quality_string;

 }

+bool

+Bamline_terminalp (Bamline_T this) {

+  return this->terminalp;

+}

+

 static void

 aux_print (FILE *fp, unsigned char *s, unsigned char *aux_end) {

@@ -1211,7 +1229,8 @@ Bamline_new (char *acc, unsigned int flag, int nhits, bool good_unique_p, int ma

 	     char splice_strand, char *chr, Genomicpos_T chrpos_low,

 	     char *mate_chr, Genomicpos_T mate_chrpos_low, int insert_length,

 	     Intlist_T cigar_types, Uintlist_T cigar_npositions, int cigar_querylength, int readlength,

-	     char *read, char *quality_string, unsigned char *aux_start, unsigned char *aux_end) {

+	     char *read, char *quality_string, bool terminalp,

+	     unsigned char *aux_start, unsigned char *aux_end) {

   Bamline_T new = (Bamline_T) MALLOC(sizeof(*new));

   new->acc = (char *) CALLOC(strlen(acc)+1,sizeof(char));

@@ -1258,6 +1277,8 @@ Bamline_new (char *acc, unsigned int flag, int nhits, bool good_unique_p, int ma

     strncpy(new->quality_string,quality_string,readlength);

   }

+  new->terminalp = terminalp;

+

   new->aux_start = aux_start;

   new->aux_end = aux_end;

@@ -1282,6 +1303,7 @@ Bamread_next_bamline (T this, char *desired_read_group, int minimum_mapq, int go

   char *read;

   char *quality_string;

   char *read_group;

+  bool terminalp;

 #ifndef HAVE_SAMTOOLS

   return (Bamline_T) NULL;

@@ -1293,7 +1315,8 @@ Bamread_next_bamline (T this, char *desired_read_group, int minimum_mapq, int go

       parse_line(this,&acc,&flag,&mapq,&chr,&chrpos_low,

 		 &mate_chr,&mate_chrpos_low,&insert_length,

 		 &cigar_types,&cigarlengths,&cigar_querylength,

-		 &readlength,&read,&quality_string,&read_group);

+		 &readlength,&read,&quality_string,&read_group,

+		 &terminalp);

       if (desired_read_group != NULL && (read_group == NULL || strcmp(desired_read_group,read_group))) {

 	debug1(fprintf(stderr,"Fails because doesn't have desired read group %s\n",desired_read_group));

 	Intlist_free(&cigar_types);

@@ -1336,7 +1359,7 @@ Bamread_next_bamline (T this, char *desired_read_group, int minimum_mapq, int go

 	return Bamline_new(acc,flag,nhits,good_unique_p,mapq,splice_strand,chr,chrpos_low,

 			   mate_chr,mate_chrpos_low,insert_length,

 			   cigar_types,cigarlengths,cigar_querylength,

-			   readlength,read,quality_string,