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

 Basic Installation

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

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

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

+   Briefly, the shell commands `./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

@@ -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

@@ -2,7 +2,7 @@

 # Configuration validation subroutine script.

 #   Copyright 1992-2013 Free Software Foundation, Inc.

-timestamp='2013-08-10'

+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

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

 	| avr | avr32 \

 	| be32 | be64 \

 	| bfin \

-	| c4x | c8051 | clipper \

+	| c4x | clipper \

 	| d10v | d30v | dlx | dsp16xx \

 	| epiphany \

 	| fido | fr30 | frv \

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

 	| be32-* | be64-* \

 	| bfin-* | bs2000-* \

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

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

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

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

 	| elxsi-* \

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

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

 		os=-mingw64

 		;;

 	mingw32)

-		basic_machine=i686-pc

+		basic_machine=i386-pc

 		os=-mingw32

 		;;

 	mingw32ce)

@@ -830,7 +830,7 @@ case $basic_machine in

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

 		;;

 	msys)

-		basic_machine=i686-pc

+		basic_machine=i386-pc

 		os=-msys

 		;;

 	mvs)

@@ -1546,9 +1546,6 @@ case $basic_machine in

 	c4x-* | tic4x-*)

 		os=-coff

 		;;

-	c8051-*)

-		os=-elf

-		;;

 	hexagon-*)

 		os=-elf

 		;;

@@ -1312,7 +1312,7 @@ ia64-*-hpux*)

   rm -rf conftest*

   ;;

-x86_64-*kfreebsd*-gnu|x86_64-*linux*|powerpc*-*linux*| \

+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \

 s390*-*linux*|s390*-*tpf*|sparc*-*linux*)

   # Find out which ABI we are using.

   echo 'int i;' > conftest.$ac_ext

@@ -1324,19 +1324,9 @@ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)

 	    LD="${LD-ld} -m elf_i386_fbsd"

 	    ;;

 	  x86_64-*linux*)

-	    case `/usr/bin/file conftest.o` in

-	      *x86-64*)

-		LD="${LD-ld} -m elf32_x86_64"

-		;;

-	      *)

-		LD="${LD-ld} -m elf_i386"

-		;;

-	    esac

-	    ;;

-	  powerpc64le-*)

-	    LD="${LD-ld} -m elf32lppclinux"

+	    LD="${LD-ld} -m elf_i386"

 	    ;;

-	  powerpc64-*)

+	  ppc64-*linux*|powerpc64-*linux*)

 	    LD="${LD-ld} -m elf32ppclinux"

 	    ;;

 	  s390x-*linux*)

@@ -1355,10 +1345,7 @@ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)

 	  x86_64-*linux*)

 	    LD="${LD-ld} -m elf_x86_64"

 	    ;;

-	  powerpcle-*)

-	    LD="${LD-ld} -m elf64lppc"

-	    ;;

-	  powerpc-*)

+	  ppc*-*linux*|powerpc*-*linux*)

 	    LD="${LD-ld} -m elf64ppc"

 	    ;;

 	  s390*-*linux*|s390*-*tpf*)

@@ -1701,8 +1688,7 @@ AC_CACHE_VAL([lt_cv_sys_max_cmd_len], [dnl

     ;;

   *)

     lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null`

-    if test -n "$lt_cv_sys_max_cmd_len" && \

-	test undefined != "$lt_cv_sys_max_cmd_len"; then

+    if test -n "$lt_cv_sys_max_cmd_len"; then

       lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`

       lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`

     else

@@ -2526,6 +2512,17 @@ freebsd* | dragonfly*)

   esac

   ;;

+gnu*)

+  version_type=linux # correct to gnu/linux during the next big refactor

+  need_lib_prefix=no

+  need_version=no

+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'

+  soname_spec='${libname}${release}${shared_ext}$major'

+  shlibpath_var=LD_LIBRARY_PATH

+  shlibpath_overrides_runpath=no

+  hardcode_into_libs=yes

+  ;;

+

 haiku*)

   version_type=linux # correct to gnu/linux during the next big refactor

   need_lib_prefix=no

@@ -2642,7 +2639,7 @@ linux*oldld* | linux*aout* | linux*coff*)

   ;;

 # This must be glibc/ELF.

-linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)

+linux* | k*bsd*-gnu | kopensolaris*-gnu)

   version_type=linux # correct to gnu/linux during the next big refactor

   need_lib_prefix=no

   need_version=no

@@ -2687,18 +2684,6 @@ linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)

   dynamic_linker='GNU/Linux ld.so'

   ;;

-netbsdelf*-gnu)

-  version_type=linux

-  need_lib_prefix=no

-  need_version=no

-  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'

-  soname_spec='${libname}${release}${shared_ext}$major'

-  shlibpath_var=LD_LIBRARY_PATH

-  shlibpath_overrides_runpath=no

-  hardcode_into_libs=yes

-  dynamic_linker='NetBSD ld.elf_so'

-  ;;

-

 netbsd*)

   version_type=sunos

   need_lib_prefix=no

@@ -3258,6 +3243,10 @@ freebsd* | dragonfly*)

   fi

   ;;

+gnu*)

+  lt_cv_deplibs_check_method=pass_all

+  ;;

+

 haiku*)

   lt_cv_deplibs_check_method=pass_all

   ;;

@@ -3296,11 +3285,11 @@ irix5* | irix6* | nonstopux*)

   ;;

 # This must be glibc/ELF.

-linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)

+linux* | k*bsd*-gnu | kopensolaris*-gnu)

   lt_cv_deplibs_check_method=pass_all

   ;;

-netbsd* | netbsdelf*-gnu)

+netbsd*)

   if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then

     lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$'

   else

@@ -4048,7 +4037,7 @@ m4_if([$1], [CXX], [

 	    ;;

 	esac

 	;;

-      linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)

+      linux* | k*bsd*-gnu | kopensolaris*-gnu)

 	case $cc_basename in

 	  KCC*)

 	    # KAI C++ Compiler

@@ -4112,7 +4101,7 @@ m4_if([$1], [CXX], [

 	    ;;

 	esac

 	;;

-      netbsd* | netbsdelf*-gnu)

+      netbsd*)

 	;;

       *qnx* | *nto*)

         # QNX uses GNU C++, but need to define -shared option too, otherwise

@@ -4347,7 +4336,7 @@ m4_if([$1], [CXX], [

       _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'

       ;;

-    linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)

+    linux* | k*bsd*-gnu | kopensolaris*-gnu)

       case $cc_basename in

       # old Intel for x86_64 which still supported -KPIC.

       ecc*)

@@ -4589,9 +4578,6 @@ m4_if([$1], [CXX], [

       ;;

     esac

     ;;

-  linux* | k*bsd*-gnu | gnu*)

-    _LT_TAGVAR(link_all_deplibs, $1)=no

-    ;;

   *)

     _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'

     ;;

@@ -4654,9 +4640,6 @@ dnl Note also adjust exclude_expsyms for C++ above.

   openbsd*)

     with_gnu_ld=no

     ;;

-  linux* | k*bsd*-gnu | gnu*)

-    _LT_TAGVAR(link_all_deplibs, $1)=no

-    ;;

   esac

   _LT_TAGVAR(ld_shlibs, $1)=yes

@@ -4878,7 +4861,7 @@ _LT_EOF

       fi

       ;;

-    netbsd* | netbsdelf*-gnu)

+    netbsd*)

       if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then

 	_LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'

 	wlarc=

@@ -5055,7 +5038,6 @@ _LT_EOF

 	if test "$aix_use_runtimelinking" = yes; then

 	  shared_flag="$shared_flag "'${wl}-G'

 	fi

-	_LT_TAGVAR(link_all_deplibs, $1)=no

       else

 	# not using gcc

 	if test "$host_cpu" = ia64; then

@@ -5360,7 +5342,7 @@ _LT_EOF

       _LT_TAGVAR(link_all_deplibs, $1)=yes

       ;;

-    netbsd* | netbsdelf*-gnu)

+    netbsd*)

       if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then

 	_LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'  # a.out

       else

@@ -6240,6 +6222,9 @@ if test "$_lt_caught_CXX_error" != yes; then

         _LT_TAGVAR(ld_shlibs, $1)=yes

         ;;

+      gnu*)

+        ;;

+

       haiku*)

         _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'

         _LT_TAGVAR(link_all_deplibs, $1)=yes

@@ -6401,7 +6386,7 @@ if test "$_lt_caught_CXX_error" != yes; then

         _LT_TAGVAR(inherit_rpath, $1)=yes

         ;;

-      linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)

+      linux* | k*bsd*-gnu | kopensolaris*-gnu)

         case $cc_basename in

           KCC*)

 	    # Kuck and Associates, Inc. (KAI) C++ Compiler

@@ -70,7 +70,7 @@

 #         compiler:		$LTCC

 #         compiler flags:		$LTCFLAGS

 #         linker:		$LD (gnu? $with_gnu_ld)

-#         $progname:	(GNU libtool) 2.4.2 Debian-2.4.2-1.7ubuntu1

+#         $progname:	(GNU libtool) 2.4.2

 #         automake:	$automake_version

 #         autoconf:	$autoconf_version

 #

@@ -80,7 +80,7 @@

 PROGRAM=libtool

 PACKAGE=libtool

-VERSION="2.4.2 Debian-2.4.2-1.7ubuntu1"

+VERSION=2.4.2

 TIMESTAMP=""

 package_revision=1.3337

@@ -6124,10 +6124,7 @@ func_mode_link ()

 	case $pass in

 	dlopen) libs="$dlfiles" ;;

 	dlpreopen) libs="$dlprefiles" ;;

-	link)

-	  libs="$deplibs %DEPLIBS%"

-	  test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs"

-	  ;;

+	link) libs="$deplibs %DEPLIBS% $dependency_libs" ;;

 	esac

       fi

       if test "$linkmode,$pass" = "lib,dlpreopen"; then

@@ -6447,19 +6444,19 @@ func_mode_link ()

 	    # It is a libtool convenience library, so add in its objects.

 	    func_append convenience " $ladir/$objdir/$old_library"

 	    func_append old_convenience " $ladir/$objdir/$old_library"

-	    tmp_libs=

-	    for deplib in $dependency_libs; do

-	      deplibs="$deplib $deplibs"

-	      if $opt_preserve_dup_deps ; then

-		case "$tmp_libs " in

-		*" $deplib "*) func_append specialdeplibs " $deplib" ;;

-		esac

-	      fi

-	      func_append tmp_libs " $deplib"

-	    done

 	  elif test "$linkmode" != prog && test "$linkmode" != lib; then

 	    func_fatal_error "\`$lib' is not a convenience library"

 	  fi

+	  tmp_libs=

+	  for deplib in $dependency_libs; do

+	    deplibs="$deplib $deplibs"

+	    if $opt_preserve_dup_deps ; then

+	      case "$tmp_libs " in

+	      *" $deplib "*) func_append specialdeplibs " $deplib" ;;

+	      esac

+	    fi

+	    func_append tmp_libs " $deplib"

+	  done

 	  continue

 	fi # $pass = conv

@@ -7352,9 +7349,6 @@ func_mode_link ()

 	    revision="$number_minor"

 	    lt_irix_increment=no

 	    ;;

-	  *)

-	    func_fatal_configuration "$modename: unknown library version type \`$version_type'"

-	    ;;

 	  esac

 	  ;;

 	no)

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

 #! /bin/sh

 # Common wrapper for a few potentially missing GNU programs.

-scriptversion=2013-10-28.13; # UTC

+scriptversion=2012-06-26.16; # 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 'autom4te' program to be rebuilt."

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

       program_details 'autom4te'

       ;;

     bison*|yacc*)

@@ -6164,8 +6164,7 @@ else

     ;;

   *)

     lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null`

-    if test -n "$lt_cv_sys_max_cmd_len" && \

-	test undefined != "$lt_cv_sys_max_cmd_len"; then

+    if test -n "$lt_cv_sys_max_cmd_len"; then

       lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`

       lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`

     else

@@ -6566,6 +6565,10 @@ freebsd* | dragonfly*)

   fi

   ;;

+gnu*)

+  lt_cv_deplibs_check_method=pass_all

+  ;;

+

 haiku*)

   lt_cv_deplibs_check_method=pass_all

   ;;

@@ -6604,11 +6607,11 @@ irix5* | irix6* | nonstopux*)

   ;;

 # This must be glibc/ELF.

-linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)

+linux* | k*bsd*-gnu | kopensolaris*-gnu)

   lt_cv_deplibs_check_method=pass_all

   ;;

-netbsd* | netbsdelf*-gnu)

+netbsd*)

   if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then

     lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$'

   else

@@ -7685,7 +7688,7 @@ ia64-*-hpux*)

   rm -rf conftest*

   ;;

-x86_64-*kfreebsd*-gnu|x86_64-*linux*|powerpc*-*linux*| \

+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \

 s390*-*linux*|s390*-*tpf*|sparc*-*linux*)

   # Find out which ABI we are using.

   echo 'int i;' > conftest.$ac_ext

@@ -7701,19 +7704,9 @@ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)

 	    LD="${LD-ld} -m elf_i386_fbsd"

 	    ;;

 	  x86_64-*linux*)

-	    case `/usr/bin/file conftest.o` in

-	      *x86-64*)

-		LD="${LD-ld} -m elf32_x86_64"

-		;;

-	      *)

-		LD="${LD-ld} -m elf_i386"

-		;;

-	    esac

-	    ;;

-	  powerpc64le-*)

-	    LD="${LD-ld} -m elf32lppclinux"

+	    LD="${LD-ld} -m elf_i386"

 	    ;;

-	  powerpc64-*)

+	  ppc64-*linux*|powerpc64-*linux*)

 	    LD="${LD-ld} -m elf32ppclinux"

 	    ;;

 	  s390x-*linux*)

@@ -7732,10 +7725,7 @@ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)

 	  x86_64-*linux*)

 	    LD="${LD-ld} -m elf_x86_64"

 	    ;;

-	  powerpcle-*)

-	    LD="${LD-ld} -m elf64lppc"

-	    ;;

-	  powerpc-*)

+	  ppc*-*linux*|powerpc*-*linux*)

 	    LD="${LD-ld} -m elf64ppc"

 	    ;;

 	  s390*-*linux*|s390*-*tpf*)

@@ -9543,7 +9533,7 @@ lt_prog_compiler_static=

       lt_prog_compiler_static='-non_shared'

       ;;

-    linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)

+    linux* | k*bsd*-gnu | kopensolaris*-gnu)

       case $cc_basename in

       # old Intel for x86_64 which still supported -KPIC.

       ecc*)

@@ -10021,9 +10011,6 @@ $as_echo_n "checking whether the $compiler linker ($LD) supports shared librarie

   openbsd*)

     with_gnu_ld=no

     ;;

-  linux* | k*bsd*-gnu | gnu*)

-    link_all_deplibs=no

-    ;;

   esac

   ld_shlibs=yes

@@ -10245,7 +10232,7 @@ _LT_EOF

       fi

       ;;

-    netbsd* | netbsdelf*-gnu)

+    netbsd*)

       if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then

 	archive_cmds='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'

 	wlarc=

@@ -10422,7 +10409,6 @@ _LT_EOF

 	if test "$aix_use_runtimelinking" = yes; then

 	  shared_flag="$shared_flag "'${wl}-G'

 	fi

-	link_all_deplibs=no

       else

 	# not using gcc

 	if test "$host_cpu" = ia64; then

@@ -10876,7 +10862,7 @@ $as_echo "$lt_cv_irix_exported_symbol" >&6; }

       link_all_deplibs=yes

       ;;

-    netbsd* | netbsdelf*-gnu)

+    netbsd*)

       if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then

 	archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'  # a.out

       else

@@ -11713,6 +11699,17 @@ freebsd* | dragonfly*)

   esac

   ;;

+gnu*)

+  version_type=linux # correct to gnu/linux during the next big refactor

+  need_lib_prefix=no

+  need_version=no

+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'

+  soname_spec='${libname}${release}${shared_ext}$major'

+  shlibpath_var=LD_LIBRARY_PATH

+  shlibpath_overrides_runpath=no

+  hardcode_into_libs=yes

+  ;;

+

 haiku*)

   version_type=linux # correct to gnu/linux during the next big refactor

   need_lib_prefix=no

@@ -11829,7 +11826,7 @@ linux*oldld* | linux*aout* | linux*coff*)

   ;;

 # This must be glibc/ELF.

-linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)

+linux* | k*bsd*-gnu | kopensolaris*-gnu)

   version_type=linux # correct to gnu/linux during the next big refactor

   need_lib_prefix=no

   need_version=no

@@ -11893,18 +11890,6 @@ fi

   dynamic_linker='GNU/Linux ld.so'

   ;;

-netbsdelf*-gnu)

-  version_type=linux

-  need_lib_prefix=no

-  need_version=no

-  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'

-  soname_spec='${libname}${release}${shared_ext}$major'

-  shlibpath_var=LD_LIBRARY_PATH

-  shlibpath_overrides_runpath=no

-  hardcode_into_libs=yes

-  dynamic_linker='NetBSD ld.elf_so'

-  ;;

-

 netbsd*)

   version_type=sunos

   need_lib_prefix=no

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

-static char rcsid[] = "$Id: bamread.c 160725 2015-03-11 16:45:17Z twu $";

+static char rcsid[] = "$Id: bamread.c 163197 2015-04-13 21:57:42Z twu $";

 #ifdef HAVE_CONFIG_H

 #include <config.h>

 #endif

@@ -1891,10 +1891,16 @@ Bamline_new (char *acc, unsigned int flag, int nhits, bool good_unique_p, int ma

   if (copy_aux_contents_p == true) {

     new->aux_length = aux_end - aux_start;

-    new->aux_contents = (uint8_t *) MALLOC(new->aux_length * sizeof(unsigned char));

-    memcpy(new->aux_contents,aux_start,new->aux_length);

-    new->aux_start = (unsigned char *) new->aux_contents;

-    new->aux_end = new->aux_start + new->aux_length;

+    if (new->aux_length == 0) {

+      new->aux_contents = (uint8_t *) NULL;

+      new->aux_start = (uint8_t *) NULL;

+      new->aux_end = (uint8_t *) NULL;

+    } else {

+      new->aux_contents = (uint8_t *) MALLOC(new->aux_length * sizeof(unsigned char));

+      memcpy(new->aux_contents,aux_start,new->aux_length);

+      new->aux_start = (unsigned char *) new->aux_contents;

+      new->aux_end = new->aux_start + new->aux_length;

+    }

   } else {

     /* Point to bam->data */

     new->aux_contents = (uint8_t *) NULL;

@@ -1,5 +1,4 @@

-#define DEBUG2 1

-static char rcsid[] = "$Id: bamtally.c 161991 2015-03-25 23:24:46Z twu $";

+static char rcsid[] = "$Id: bamtally.c 172388 2015-08-21 20:10:50Z twu $";

 #ifdef HAVE_CONFIG_H

 #include <config.h>

 #endif

@@ -1584,7 +1583,7 @@ static Ucharlist_T

 push_string (int *nbytes, Ucharlist_T list, char *string) {

   int length, i;

-  debug2(printf("%d: Pushing char %s\n",*nbytes,string));

+  debug2(printf("%d: Pushing string %s\n",*nbytes,string));

   length = strlen(string);

   for (i = 0; i < length; i++) {

     list = Ucharlist_push(list,string[i]);

@@ -2287,7 +2286,7 @@ process_codons_plus (Ucharlist_T bytes, int *nbytes, Tally_T tally0, Tally_T tal

 	    Codon_free(&(array[i]));

 	  }

-

+	  

 	  FREE(array);

 	  List_free(&alt_codons);

 	}

@@ -2330,10 +2329,10 @@ process_codons_plus (Ucharlist_T bytes, int *nbytes, Tally_T tally0, Tally_T tal

 	    }

 	    Codon_free(&(array[i]));

 	  }

-	}

-	FREE(array);

-	List_free(&alt_codons);

+	  FREE(array);

+	  List_free(&alt_codons);

+	}

       }

     }

   }

@@ -2577,10 +2576,10 @@ process_codons_minus (Ucharlist_T bytes, int *nbytes, Tally_T tally0, Tally_T ta

 	    }

 	    Codon_free(&(array[i]));

 	  }

-	}

-	FREE(array);

-	List_free(&alt_codons);

+	  FREE(array);

+	  List_free(&alt_codons);

+	}

       }

     }

   }

@@ -4366,10 +4365,13 @@ iit_block (List_T *intervallist, List_T *labellist, List_T *datalist,

 	for (i = 0; i < ndeletions; i++) {

 	  del0 = del_array_byshift[i];

 	  /* Counts and segment for deletion i */

+	  debug2(printf("plus and minus counts for deletion\n"));

 	  bytes = push_int(&nbytes,bytes,del0->count_plus);

 	  bytes = push_int(&nbytes,bytes,del0->count_minus);

+	  debug2(printf("plus and minus counts for reference\n"));

 	  bytes = push_int(&nbytes,bytes,this->n_fromleft_plus); /* ref count */

 	  bytes = push_int(&nbytes,bytes,this->n_fromleft_minus); /* ref count */

+	  debug2(printf("Deletion string:\n"));

 	  bytes = push_string(&nbytes,bytes,del0->segment);

 	  /* Cycles for deletion i */

@@ -5766,12 +5768,11 @@ best_mapping_p (Tableuint_T resolve_low_table, Tableuint_T resolve_high_table, c

 static void

-get_passing_counts (__m128i *counts, int readlength, Bamline_T *bamlines, int nreps, int minimum_quality_score) {

+get_passing_counts (__m128i *counts, int ncounts, int readlength, Bamline_T *bamlines, int nreps, int minimum_quality_score) {

   int i, r, b;

   char *quality_string, buffer[16];

   int x;

-

   __m128i block, cmp16, cmp8, threshold, ones;

   __m128i foo;

@@ -5792,23 +5793,35 @@ get_passing_counts (__m128i *counts, int readlength, Bamline_T *bamlines, int nr

       counts[b] = _mm_set1_epi16(0);

     }

   }

+  if (b > ncounts) {

+    fprintf(stderr,"Allocated only %d vectors, but need %d\n",ncounts,b);

+    abort();

+  }

   for (i = 0; i < nreps; i++) {

     quality_string = Bamline_quality_string(bamlines[0]);

     /* printf("quality string: %s\n",quality_string); */

     b = 0; r = 0;

     while (r + 16 < readlength) {

-      block = _mm_loadu_si128((__m128i *) &(quality_string[r]));

+      block = _mm_loadu_si128((__m128i *) &(quality_string[r])); /* Put 16 bytes of quality string into block */

+

+      /* Count bytes where (threshold > quality).  "true": 0xFF => 0.

+	 "false": 0x00 => 1.  Equivalently, cmp8 contains a 1 whenever

+	 quality >= threshold. */

       cmp8 = _mm_add_epi8(_mm_cmpgt_epi8(threshold,block),ones);

+

+      /* Tally the lower 8 bytes */

       cmp16 = _mm_cvtepi8_epi16(cmp8);

       counts[b] = _mm_add_epi16(counts[b],cmp16); b++;

+      /* Tally the upper 8 bytes */

       cmp16 = _mm_cvtepi8_epi16(_mm_srli_si128(cmp8,8));

       counts[b] = _mm_add_epi16(counts[b],cmp16); b++;

       r += 16;

     }

     if (r < readlength) {

+      /* Handle the last 8 bytes */

       strncpy(buffer,&(quality_string[r]),readlength-r);

       block = _mm_loadu_si128((__m128i *) buffer);

       cmp8 = _mm_add_epi8(_mm_cmpgt_epi8(threshold,block),ones);

@@ -5898,7 +5911,8 @@ Bamtally_run (long int **tally_matches, long int **tally_mismatches,

   unsigned int linei = 0, linei_start, linei_end;

   int nlines;

   int nreps;

-  __m128i counts[50], foo;

+  __m128i *counts, foo;

+  int ncounts;

   int i;

@@ -6013,13 +6027,16 @@ Bamtally_run (long int **tally_matches, long int **tally_mismatches,

 			genome,chroffset,ignore_query_Ns_p,print_indels_p,readlevel_p,

 			max_softclip,linei+linei_start,/*counts*/NULL,nreps);

 	  } else {

-	    get_passing_counts(counts,readlength,&(bamlines[linei_start]),nreps,minimum_quality_score);

+	    ncounts = (readlength + 7)/8;

+	    counts = (__m128i *) _mm_malloc(ncounts * sizeof(__m128i),16);

+	    get_passing_counts(counts,ncounts,readlength,&(bamlines[linei_start]),nreps,minimum_quality_score);

 	    revise_read(alloc_tallies,chrstart,chrend,chrpos_low,Bamline_flag(bamline_rep),

 			Bamline_cigar_types(bamline_rep),Bamline_cigar_npositions(bamline_rep),

 			Bamline_cigar_querylength(bamline_rep),rsequence,Bamline_nm(bamline_rep),

 			Bamline_splice_strand(bamline_rep),Bamline_terminalp(bamline_rep),alloc_low,

 			genome,chroffset,ignore_query_Ns_p,print_indels_p,readlevel_p,

 			max_softclip,linei+linei_start,counts,nreps);

+	    _mm_free(counts);

 	  }

 	  goodp = true;

 	}

@@ -6167,7 +6184,9 @@ Bamtally_run (long int **tally_matches, long int **tally_mismatches,

 			max_softclip,linei + linei_start,/*counts*/NULL,nreps);

 	  } else {

 	    readlength = Bamline_readlength(bamline_rep);

-	    get_passing_counts(counts,readlength,&(bamlines[linei_start]),nreps,minimum_quality_score);

+	    ncounts = (readlength + 7)/8;

+	    counts = (__m128i *) _mm_malloc(ncounts * sizeof(__m128i),16);

+	    get_passing_counts(counts,ncounts,readlength,&(bamlines[linei_start]),nreps,minimum_quality_score);

 	    revise_read(alloc_tallies,chrstart,chrend,chrpos_low,Bamline_flag(bamline_rep),

 			Bamline_cigar_types(bamline_rep),Bamline_cigar_npositions(bamline_rep),

 			Bamline_cigar_querylength(bamline_rep),Bamline_read(bamline_rep),