Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/ChangeLog
+++ b/ChangeLog
--- a/Makefile.in
+++ b/Makefile.in
@@ -184,7 +184,7 @@ am__DIST_COMMON = $(srcdir)/Makefile.in $(top_srcdir)/config/compile \
 	$(top_srcdir)/config/config.sub \
 	$(top_srcdir)/config/install-sh $(top_srcdir)/config/ltmain.sh \
 	$(top_srcdir)/config/missing AUTHORS COPYING ChangeLog INSTALL \
-	NEWS README config/compile config/config.guess \
+	NEWS README TODO config/compile config/config.guess \
 	config/config.sub config/install-sh config/ltmain.sh \
 	config/missing
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
@@ -259,6 +259,7 @@ EXEEXT = @EXEEXT@
 FGREP = @FGREP@
 GMAPDB = @GMAPDB@
 GREP = @GREP@
+HAVE_INLINE = @HAVE_INLINE@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@

--- a/TODO
+++ b/TODO
+
+Add flag that allows for splitting afterwards.
+
--- a/VERSION
+++ b/VERSION
-2017-11-15
\ No newline at end of file
+2018-07-04
\ No newline at end of file
--- a/configure
+++ b/configure
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for gmap 2017-11-15.
+# Generated by GNU Autoconf 2.69 for gmap 2018-07-04.
 #
 # Report bugs to <Thomas Wu <twu@gene.com>>.
 #
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='gmap'
 PACKAGE_TARNAME='gmap'
-PACKAGE_VERSION='2017-11-15'
-PACKAGE_STRING='gmap 2017-11-15'
+PACKAGE_VERSION='2018-07-04'
+PACKAGE_STRING='gmap 2018-07-04'
 PACKAGE_BUGREPORT='Thomas Wu <twu@gene.com>'
 PACKAGE_URL=''
  
@@ -660,6 +660,7 @@ SIMD_SSSE3_CFLAGS
 SIMD_SSE2_CFLAGS
 POPCNT_CFLAGS
 ALLOCA
+HAVE_INLINE
 PTHREAD_CFLAGS
 PTHREAD_LIBS
 PTHREAD_CC
@@ -689,6 +690,8 @@ SED
 LIBTOOL
 PERL
 BINDIR
+MAKE_LIB_FALSE
+MAKE_LIB_TRUE
 MAINTAINER_FALSE
 MAINTAINER_TRUE
 FULLDIST_FALSE
@@ -800,6 +803,7 @@ enable_silent_rules
 enable_maintainer_mode
 enable_fulldist
 enable_maintainer
+enable_lib
 enable_shared
 enable_static
 with_pic
@@ -1369,7 +1373,7 @@ if test "$ac_init_help" = "long"; then
  # Omit some internal or obsolete options to make the list less imposing.
  # This message is too long to be a string in the A/UX 3.1 sh.
  cat <<_ACEOF
-\`configure' configures gmap 2017-11-15 to adapt to many kinds of systems.
+\`configure' configures gmap 2018-07-04 to adapt to many kinds of systems.
  
 Usage: $0 [OPTION]... [VAR=VALUE]...
  
@@ -1440,7 +1444,7 @@ fi
  
 if test -n "$ac_init_help"; then
  case $ac_init_help in
-     short | recursive ) echo "Configuration of gmap 2017-11-15:";;
+     short | recursive ) echo "Configuration of gmap 2018-07-04:";;
   esac
  cat <<\_ACEOF
  
@@ -1460,6 +1464,9 @@ Optional Features:
                          sometimes confusing) to the casual installer
  --enable-fulldist       For use by program maintainer
  --enable-maintainer     For use by program maintainer
+  --enable-lib            Build and install a GMAP library (Warning: will put
+                          headers into include subdirectory)
+                          (default=disable-lib)
  --enable-shared[=PKGS]  build shared libraries [default=yes]
  --enable-static[=PKGS]  build static libraries [default=yes]
  --enable-fast-install[=PKGS]
@@ -1469,8 +1476,9 @@ Optional Features:
                          (default=yes). Note: Use only if you have a parallel
                          I/O file system, like Lustre
  --enable-pthreads       Enable pthreads (default=yes)
-  --enable-alloca         Enable alloca (default=yes) for stack-based memory
-                          allocation.
+  --enable-alloca         Enable alloca (default=no) for stack-based memory
+                          allocation. Warning: Can cause GMAP to crash on long
+                          sequences.
  --enable-mmap           Enable mmap (default=yes). Recommend that you do not
                          disable this unless absolutely necessary.
  --enable-simd           Enable simd commands in general if they compile and
@@ -1577,7 +1585,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
  cat <<\_ACEOF
-gmap configure 2017-11-15
+gmap configure 2018-07-04
 generated by GNU Autoconf 2.69
  
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2183,7 +2191,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
  
-It was created by gmap $as_me 2017-11-15, which was
+It was created by gmap $as_me 2018-07-04, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
  
  $ $0 $@
@@ -2533,8 +2541,8 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
  
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking package version" >&5
 $as_echo_n "checking package version... " >&6; }
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: 2017-11-15" >&5
-$as_echo "2017-11-15" >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: 2018-07-04" >&5
+$as_echo "2018-07-04" >&6; }
  
  
 ### Read defaults
@@ -4401,7 +4409,7 @@ fi
  
 # Define the identity of the package.
 PACKAGE='gmap'
- VERSION='2017-11-15'
+ VERSION='2018-07-04'
  
  
 cat >>confdefs.h <<_ACEOF
@@ -4679,6 +4687,22 @@ else
 fi
  
  
+ if test "x$enable_library" = xyes; then
+  MAKE_LIB_TRUE=
+  MAKE_LIB_FALSE='#'
+else
+  MAKE_LIB_TRUE='#'
+  MAKE_LIB_FALSE=
+fi
+
+# Check whether --enable-lib was given.
+if test "${enable_lib+set}" = set; then :
+  enableval=$enable_lib; enable_library="yes"
+else
+  enable_library="no"
+fi
+
+
 # For Perl scripts, because otherwise configure inserts
 # @bindir@ => "${exec_prefix}/bin";
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking bindir" >&5
@@ -14502,6 +14526,55 @@ done
  
  
 # Checks for typedefs, structures, and compiler characteristics.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for inline" >&5
+$as_echo_n "checking for inline... " >&6; }
+if ${ac_cv_c_inline+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_cv_c_inline=no
+for ac_kw in inline __inline__ __inline; do
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#ifndef __cplusplus
+typedef int foo_t;
+static $ac_kw foo_t static_foo () {return 0; }
+$ac_kw foo_t foo () {return 0; }
+#endif
+
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+  ac_cv_c_inline=$ac_kw
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  test "$ac_cv_c_inline" != no && break
+done
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_inline" >&5
+$as_echo "$ac_cv_c_inline" >&6; }
+
+case $ac_cv_c_inline in
+  inline | yes) ;;
+  *)
+    case $ac_cv_c_inline in
+      no) ac_val=;;
+      *) ac_val=$ac_cv_c_inline;;
+    esac
+    cat >>confdefs.h <<_ACEOF
+#ifndef __cplusplus
+#define inline $ac_val
+#endif
+_ACEOF
+    ;;
+esac
+
+if test "$ac_cv_c_line" != no; then
+
+$as_echo "#define HAVE_INLINE 1" >>confdefs.h
+
+
+fi
+
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether byte ordering is bigendian" >&5
 $as_echo_n "checking whether byte ordering is bigendian... " >&6; }
 if ${ac_cv_c_bigendian+:} false; then :
@@ -15258,194 +15331,8 @@ $as_echo "disabled" >&6; }
     ;;
  
     x)
-     { $as_echo "$as_me:${as_lineno-$LINENO}: result: not specified so enabled by default" >&5
-$as_echo "not specified so enabled by default" >&6; }
-     # The Ultrix 4.2 mips builtin alloca declared by alloca.h only works
-# for constant arguments.  Useless!
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for working alloca.h" >&5
-$as_echo_n "checking for working alloca.h... " >&6; }
-if ${ac_cv_working_alloca_h+:} false; then :
-  $as_echo_n "(cached) " >&6
-else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-#include <alloca.h>
-int
-main ()
-{
-char *p = (char *) alloca (2 * sizeof (int));
-			  if (p) return 0;
-  ;
-  return 0;
-}
-_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
-  ac_cv_working_alloca_h=yes
-else
-  ac_cv_working_alloca_h=no
-fi
-rm -f core conftest.err conftest.$ac_objext \
-    conftest$ac_exeext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_working_alloca_h" >&5
-$as_echo "$ac_cv_working_alloca_h" >&6; }
-if test $ac_cv_working_alloca_h = yes; then
-
-$as_echo "#define HAVE_ALLOCA_H 1" >>confdefs.h
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for alloca" >&5
-$as_echo_n "checking for alloca... " >&6; }
-if ${ac_cv_func_alloca_works+:} false; then :
-  $as_echo_n "(cached) " >&6
-else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-#ifdef __GNUC__
-# define alloca __builtin_alloca
-#else
-# ifdef _MSC_VER
-#  include <malloc.h>
-#  define alloca _alloca
-# else
-#  ifdef HAVE_ALLOCA_H
-#   include <alloca.h>
-#  else
-#   ifdef _AIX
- #pragma alloca
-#   else
-#    ifndef alloca /* predefined by HP cc +Olibcalls */
-void *alloca (size_t);
-#    endif
-#   endif
-#  endif
-# endif
-#endif
-
-int
-main ()
-{
-char *p = (char *) alloca (1);
-				    if (p) return 0;
-  ;
-  return 0;
-}
-_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
-  ac_cv_func_alloca_works=yes
-else
-  ac_cv_func_alloca_works=no
-fi
-rm -f core conftest.err conftest.$ac_objext \
-    conftest$ac_exeext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_alloca_works" >&5
-$as_echo "$ac_cv_func_alloca_works" >&6; }
-
-if test $ac_cv_func_alloca_works = yes; then
-
-$as_echo "#define HAVE_ALLOCA 1" >>confdefs.h
-
-else
-  # The SVR3 libPW and SVR4 libucb both contain incompatible functions
-# that cause trouble.  Some versions do not even contain alloca or
-# contain a buggy version.  If you still want to use their alloca,
-# use ar to extract alloca.o from them instead of compiling alloca.c.
-
-ALLOCA=\${LIBOBJDIR}alloca.$ac_objext
-
-$as_echo "#define C_ALLOCA 1" >>confdefs.h
-
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether \`alloca.c' needs Cray hooks" >&5
-$as_echo_n "checking whether \`alloca.c' needs Cray hooks... " >&6; }
-if ${ac_cv_os_cray+:} false; then :
-  $as_echo_n "(cached) " >&6
-else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-#if defined CRAY && ! defined CRAY2
-webecray
-#else
-wenotbecray
-#endif
-
-_ACEOF
-if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
-  $EGREP "webecray" >/dev/null 2>&1; then :
-  ac_cv_os_cray=yes
-else
-  ac_cv_os_cray=no
-fi
-rm -f conftest*
-
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_os_cray" >&5
-$as_echo "$ac_cv_os_cray" >&6; }
-if test $ac_cv_os_cray = yes; then
-  for ac_func in _getb67 GETB67 getb67; do
-    as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
-ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
-if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
-
-cat >>confdefs.h <<_ACEOF
-#define CRAY_STACKSEG_END $ac_func
-_ACEOF
-
-    break
-fi
-
-  done
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking stack direction for C alloca" >&5
-$as_echo_n "checking stack direction for C alloca... " >&6; }
-if ${ac_cv_c_stack_direction+:} false; then :
-  $as_echo_n "(cached) " >&6
-else
-  if test "$cross_compiling" = yes; then :
-  ac_cv_c_stack_direction=0
-else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-$ac_includes_default
-int
-find_stack_direction (int *addr, int depth)
-{
-  int dir, dummy = 0;
-  if (! addr)
-    addr = &dummy;
-  *addr = addr < &dummy ? 1 : addr == &dummy ? 0 : -1;
-  dir = depth ? find_stack_direction (addr, depth - 1) : 0;
-  return dir + dummy;
-}
-
-int
-main (int argc, char **argv)
-{
-  return find_stack_direction (0, argc + !argv + 20) < 0;
-}
-_ACEOF
-if ac_fn_c_try_run "$LINENO"; then :
-  ac_cv_c_stack_direction=1
-else
-  ac_cv_c_stack_direction=-1
-fi
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
-  conftest.$ac_objext conftest.beam conftest.$ac_ext
-fi
-
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_stack_direction" >&5
-$as_echo "$ac_cv_c_stack_direction" >&6; }
-cat >>confdefs.h <<_ACEOF
-#define STACK_DIRECTION $ac_cv_c_stack_direction
-_ACEOF
-
-
-fi
-
+     { $as_echo "$as_me:${as_lineno-$LINENO}: result: not specified so disabled by default" >&5
+$as_echo "not specified so disabled by default" >&6; }
     ;;
 esac
  
@@ -19400,6 +19287,8 @@ ac_config_files="$ac_config_files util/gvf_iit.pl"
  
 ac_config_files="$ac_config_files util/vcf_iit.pl"
  
+ac_config_files="$ac_config_files util/sam-exons.pl"
+
 ac_config_files="$ac_config_files tests/Makefile"
  
 ac_config_files="$ac_config_files tests/align.test"
@@ -19556,6 +19445,10 @@ if test -z "${MAINTAINER_TRUE}" && test -z "${MAINTAINER_FALSE}"; then
  as_fn_error $? "conditional \"MAINTAINER\" was never defined.
 Usually this means the macro was only invoked conditionally." "$LINENO" 5
 fi
+if test -z "${MAKE_LIB_TRUE}" && test -z "${MAKE_LIB_FALSE}"; then
+  as_fn_error $? "conditional \"MAKE_LIB\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
  
 if test -z "${MAKE_AVX512_TRUE}" && test -z "${MAKE_AVX512_FALSE}"; then
  as_fn_error $? "conditional \"MAKE_AVX512\" was never defined.
@@ -19978,7 +19871,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by gmap $as_me 2017-11-15, which was
+This file was extended by gmap $as_me 2018-07-04, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
  
  CONFIG_FILES    = $CONFIG_FILES
@@ -20044,7 +19937,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-gmap config.status 2017-11-15
+gmap config.status 2018-07-04
 configured by $0, generated by GNU Autoconf 2.69,
  with options \\"\$ac_cs_config\\"
  
@@ -20483,6 +20376,7 @@ do
    "util/dbsnp_iit.pl") CONFIG_FILES="$CONFIG_FILES util/dbsnp_iit.pl" ;;
    "util/gvf_iit.pl") CONFIG_FILES="$CONFIG_FILES util/gvf_iit.pl" ;;
    "util/vcf_iit.pl") CONFIG_FILES="$CONFIG_FILES util/vcf_iit.pl" ;;
+    "util/sam-exons.pl") CONFIG_FILES="$CONFIG_FILES util/sam-exons.pl" ;;
    "tests/Makefile") CONFIG_FILES="$CONFIG_FILES tests/Makefile" ;;
    "tests/align.test") CONFIG_FILES="$CONFIG_FILES tests/align.test" ;;
    "tests/coords1.test") CONFIG_FILES="$CONFIG_FILES tests/coords1.test" ;;

--- a/configure.ac
+++ b/configure.ac
@@ -131,6 +131,13 @@ AC_ARG_ENABLE([maintainer],
 	      [enable_maintainer="yes"],
              [enable_maintainer="no"])

+AM_CONDITIONAL(MAKE_LIB,test "x$enable_library" = xyes)
+AC_ARG_ENABLE([lib],
+	       AC_HELP_STRING([--enable-lib],
+                              [Build and install a GMAP library (Warning: will put headers into include subdirectory) (default=disable-lib)]),
+	      [enable_library="yes"],
+              [enable_library="no"])
+
 # For Perl scripts, because otherwise configure inserts 
 # @bindir@ => "${exec_prefix}/bin";
 AC_MSG_CHECKING(bindir)
@@ -223,6 +230,12 @@ AC_HEADER_DIRENT
 AC_CHECK_HEADERS([fcntl.h limits.h stddef.h stdlib.h string.h strings.h unistd.h sys/types.h])

 # Checks for typedefs, structures, and compiler characteristics.
+AC_C_INLINE
+if test "$ac_cv_c_line" != no; then
+  AC_DEFINE(HAVE_INLINE,1,[Define to 1 if compiler supports extern inline])
+  AC_SUBST(HAVE_INLINE)
+fi
+
 AC_C_BIGENDIAN
 AC_C_CONST
 AC_C_VOLATILE
@@ -247,7 +260,7 @@ AC_FUNC_FSEEKO
 AC_MSG_CHECKING(whether alloca is enabled)
 AC_ARG_ENABLE([alloca],
 	      AC_HELP_STRING([--enable-alloca],
-                             [Enable alloca (default=yes) for stack-based memory allocation.]),
+                             [Enable alloca (default=no) for stack-based memory allocation.  Warning: Can cause GMAP to crash on long sequences.]),
              [answer="$enableval"],
              [answer=""])
 case x"$answer" in
@@ -261,8 +274,7 @@ case x"$answer" in
     ;;

     x)
-     AC_MSG_RESULT([not specified so enabled by default])
-     AC_FUNC_ALLOCA
+     AC_MSG_RESULT([not specified so disabled by default])
     ;;
 esac	

@@ -586,6 +598,7 @@ AC_CONFIG_FILES([util/gff3_genes.pl])
 AC_CONFIG_FILES([util/dbsnp_iit.pl])
 AC_CONFIG_FILES([util/gvf_iit.pl])
 AC_CONFIG_FILES([util/vcf_iit.pl])
+AC_CONFIG_FILES([util/sam-exons.pl])
 AC_CONFIG_FILES([tests/Makefile])
 AC_CONFIG_FILES([tests/align.test],[chmod +x tests/align.test])
 AC_CONFIG_FILES([tests/coords1.test],[chmod +x tests/coords1.test])

--- a/debian/changelog
+++ b/debian/changelog
+gmap (2018-07-04-1) UNRELEASED; urgency=medium
+
+  * Cleanup d/rules
+  * New upstream version
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.5
+  * libgmap1-dev Depends: gmap, libgmap1 (instead of alternative)
+    Closes: #903793
+
+ -- Andreas Tille <tille@debian.org>  Tue, 17 Jul 2018 07:24:19 +0200
+
 gmap (2017-11-15-1) unstable; urgency=medium

  * New upstream version 2017-11-15

--- a/debian/compat
+++ b/debian/compat
-10
+11
--- a/debian/control
+++ b/debian/control
@@ -6,19 +6,21 @@ Uploaders: Shaun Jackman <sjackman@debian.org>,
 Section: non-free/science
 XS-Autobuild: no
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
               dh-exec,
               help2man,
               libbz2-dev,
               zlib1g-dev
-Standards-Version: 4.1.2
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/gmap.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/gmap.git
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/gmap
+Vcs-Git: https://salsa.debian.org/med-team/gmap.git
 Homepage: http://research-pub.gene.com/gmap

 Package: gmap
 Architecture: any
-Depends: ${misc:Depends}, ${perl:Depends}, ${shlibs:Depends}
+Depends: ${misc:Depends},
+         ${perl:Depends},
+         ${shlibs:Depends}
 Description: spliced and SNP-tolerant alignment for mRNA and short reads
 This package contains the programs GMAP and GSNAP as well as
 utilities to manage genome databases in GMAP/GSNAP format.
@@ -34,7 +36,8 @@ Description: spliced and SNP-tolerant alignment for mRNA and short reads
 Package: libgmap1
 Architecture: any
 Section: non-free/libs
-Depends: ${misc:Depends}, ${shlibs:Depends}
+Depends: ${misc:Depends},
+         ${shlibs:Depends}
 Description: library for gmap tool
 This package contains library for gmap tool.
 GMAP (Genomic Mapping and Alignment Program) is a tool for aligning
@@ -49,8 +52,9 @@ Description: library for gmap tool
 Package: libgmap1-dev
 Architecture: any
 Section: non-free/libdevel
-Depends: gmap (= ${binary:Version}) | libgmap1 (= ${binary:Version}),
-         ${misc:Depends},
+Depends: gmap (= ${binary:Version}),
+         libgmap1 (= ${binary:Version}),
+         ${misc:Depends}
 Description: development files for gmap
 This package contains header files for gmap.
 GMAP (Genomic Mapping and Alignment Program) is a tool for aligning

--- a/debian/rules
+++ b/debian/rules
@@ -2,8 +2,7 @@

 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 include /usr/share/dpkg/default.mk
-pkg 	:= gmap
-mandir  := $(CURDIR)/debian/$(pkg)/usr/share/man/man1
+mandir  := $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1
 utildir := $(CURDIR)/util
 bindir  := $(CURDIR)/src

@@ -34,11 +33,11 @@ override_dh_auto_install:

 override_dh_install:
 	dh_install
-	mkdir -p debian/$(pkg)/usr/bin
+	mkdir -p debian/$(DEB_SOURCE)/usr/bin
 	for bin in `echo gmap gsnap gmap_build gmapl gsnapl; \
-		cd $(CURDIR)/debian/tmp/usr/lib/$(pkg)/; \
+		cd $(CURDIR)/debian/tmp/usr/lib/$(DEB_SOURCE)/; \
 		ls -1 gmap*.* gsnap*.* `; do \
-		ln -s /usr/lib/gmap/$$bin debian/$(pkg)/usr/bin/$$bin; \
+		ln -s /usr/lib/gmap/$$bin debian/$(DEB_SOURCE)/usr/bin/$$bin; \
 	done

 override_dh_auto_test:

--- a/src/ChangeLog
+++ b/src/ChangeLog
--- a/src/Makefile.am
+++ b/src/Makefile.am
--- a/src/Makefile.in
+++ b/src/Makefile.in
--- a/src/access.c
+++ b/src/access.c
-static char rcsid[] = "$Id: access.c 198277 2016-09-24 00:46:18Z twu $";
+static char rcsid[] = "$Id: access.c 213998 2018-03-03 04:59:34Z twu $";
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
@@ -54,6 +54,9 @@ static char rcsid[] = "$Id: access.c 198277 2016-09-24 00:46:18Z twu $";
 #endif


+#define MAX_KILL_ATTEMPTS 5	/* Limits on attempts to kill unattached memory segments */
+
+
 #ifdef DEBUG
 #define debug(x) x
 #else
@@ -470,6 +473,45 @@ Access_deallocate (void *memory, int shmid, key_t key) {
 }


+/* Same as Access_deallocate, but without deleting semaphore */
+void
+Access_deallocate_wo_semaphore (void *memory, int shmid, key_t key) {
+  struct shmid_ds *buf = NULL;
+  short nattached;
+  int semid;
+
+  /* First, detach memory */
+  if (shmdt(memory) == -1) {
+#if 0      
+    /* Somehow, shmdt forks and prints the error message and continues with the rest of the code */
+    fprintf(stderr,"Error in Access_emergency_cleanup with shmdt on memory %p, shmid %d.  Error %d: %s\n",
+	    memory,shmid,errno,strerror(errno));
+#endif
+  }
+
+  /* Then, delete memory and semaphores, if applicable */
+  if ((semid = Semaphore_find(key)) != -1 && Semaphore_get_value(semid,SEMNO_KEEP) == SEMAPHORE_RESIDENT) {
+    fprintf(stderr,"Keeping memory for shmid %d resident, because it was pre-loaded.  To remove, run gsnap on this genome index with --unload-shared-memory\n",
+	    shmid);
+
+  } else if ((nattached = shmem_nattached(shmid)) > 0) {
+    fprintf(stderr,"Keeping memory for shmid %d resident, because it is being used by %d processes\n",
+	    shmid,nattached);
+
+  } else if (shmctl(shmid,IPC_RMID,buf) == -1) {
+    /* Somehow, shmctl forks and prints the error message and continues with the rest of the code */
+    /* fprintf(stderr,"Error in Access_deallocate with shmctl.  Error %d: %s\n",errno,strerror(errno)); */
+    /* Semaphore_delete(semid); */
+
+  } else {
+    fprintf(stderr,"Removed existing memory for shmid %d\n",shmid);
+    /* Semaphore_delete(semid); */
+  }
+
+  return;
+}
+
+

 #define FREAD_BATCH 100000000	/* 100 million elements at a time */

@@ -495,6 +537,17 @@ copy_memory_from_file (void *memory, char *filename, size_t filesize, size_t elt
      fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
    }

+  } else if (eltsize == 2) {
+    for (i = 0; i + FREAD_BATCH < filesize/eltsize; i += FREAD_BATCH) {
+      p = (void *) &(((UINT2 *) memory)[i]);
+      fread(p,sizeof(UINT2),FREAD_BATCH,fp);
+    }
+
+    if (i < filesize/eltsize) {
+      p = (void *) &(((UINT2 *) memory)[i]);
+      fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
+    }
+
  } else if (eltsize == 4) {
    for (i = 0; i + FREAD_BATCH < filesize/eltsize; i += FREAD_BATCH) {
      p = (void *) &(((UINT4 *) memory)[i]);
@@ -545,6 +598,14 @@ copy_limited_from_file (void *memory, char *filename, size_t filesize, size_t el
      fread(p,sizeof(unsigned char),filesize/eltsize,fp);
    }

+  } else if (eltsize == 2) {
+    p = (void *) &(((UINT2 *) memory)[0]);
+    if (FREAD_BATCH < filesize/eltsize) {
+      fread(p,sizeof(UINT2),FREAD_BATCH,fp);
+    } else {
+      fread(p,sizeof(UINT2),filesize/eltsize,fp);
+    }
+
  } else if (eltsize == 4) {
    p = (void *) &(((UINT4 *) memory)[0]);
    if (FREAD_BATCH < filesize/eltsize) {
@@ -570,11 +631,15 @@ copy_limited_from_file (void *memory, char *filename, size_t filesize, size_t el
  return;
 }

+
 static void *
 shmem_attach (int *shmid, key_t *key, char *filename, size_t filesize, size_t eltsize) {
  void *memory = NULL;
  int semid = -1;
  ushort values[NSEMAPHORES];
+  int nattached;
+  bool donep;
+  int niter;

  values[SEMNO_LOCK] = -1;
  /* For some reason, these values are not being set, so using Semaphore_set_value below */
@@ -615,41 +680,66 @@ shmem_attach (int *shmid, key_t *key, char *filename, size_t filesize, size_t el
     others wait.  They will be woken up when the semaphore is
     removed. */

-  if ((*shmid = shmget(*key,filesize,IPC_CREAT | IPC_EXCL |
+  donep = false;
+  niter = 0;
+  while (donep == false) {
+    if ((*shmid = shmget(*key,filesize,IPC_CREAT | IPC_EXCL |
 #ifdef HAVE_SHM_NORESERVE
-		       SHM_NORESERVE | 
-#endif
-		       0666)) != -1) {
-    /* Created new shared memory */
-    if ((memory = shmat(*shmid,NULL,0)) == (void *) -1) {
-      fprintf(stderr,"Error with shmat.  Error %d: %s\n",errno,strerror(errno));
-    } else if (unload_shared_memory_p == true) {
-      semaphore_ids = Intlist_push(semaphore_ids,semid);
-      shmem_memory = List_push(shmem_memory,memory);
-      shmem_ids = Intlist_push(shmem_ids,*shmid);
-      copy_limited_from_file(memory,filename,filesize,eltsize);
-    } else {
-      semaphore_ids = Intlist_push(semaphore_ids,semid);
-      shmem_memory = List_push(shmem_memory,memory);
-      shmem_ids = Intlist_push(shmem_ids,*shmid);
-      copy_memory_from_file(memory,filename,filesize,eltsize);
-      fprintf(stderr,"Attached new memory for %s...",filename);
-    }
+			 SHM_NORESERVE | 
+#endif
+			 0666)) != -1) {
+      /* Created new shared memory */
+      if ((memory = shmat(*shmid,NULL,0)) == (void *) -1) {
+	fprintf(stderr,"Error with shmat.  Error %d: %s\n",errno,strerror(errno));
+      } else if (unload_shared_memory_p == true) {
+	semaphore_ids = Intlist_push(semaphore_ids,semid);
+	shmem_memory = List_push(shmem_memory,memory);
+	shmem_ids = Intlist_push(shmem_ids,*shmid);
+	copy_limited_from_file(memory,filename,filesize,eltsize);
+	donep = true;
+      } else {
+	semaphore_ids = Intlist_push(semaphore_ids,semid);
+	shmem_memory = List_push(shmem_memory,memory);
+	shmem_ids = Intlist_push(shmem_ids,*shmid);
+	copy_memory_from_file(memory,filename,filesize,eltsize);
+	fprintf(stderr,"Attached new memory for %s...",filename);
+	donep = true;
+      }
+
+    } else if ((*shmid = shmget(*key,0,0)) != -1) {
+      /* Found existing shared memory */
+      if ((memory = shmat(*shmid,NULL,0)) == (void *) -1) {
+	fprintf(stderr,"Error with shmat.  Error %d: %s\n",errno,strerror(errno));
+	
+      } else if ((nattached = shmem_nattached(*shmid)) > 1) {
+	/* Existing memory is indeed valid: attached (by a process other than this one) */
+	semaphore_ids = Intlist_push(semaphore_ids,semid);
+	shmem_memory = List_push(shmem_memory,memory);
+	shmem_ids = Intlist_push(shmem_ids,*shmid);
+	fprintf(stderr,"Attached existing memory (%d attached) for %s...",nattached,filename);
+	donep = true;
+
+      } else if (niter > MAX_KILL_ATTEMPTS) {
+	/* Existing memory is not attached by any other process, but unable to kill.  Could be corrupted */
+	fprintf(stderr,"Abandoned shared memory found, but could not be removed after %d attempts.  Using malloc instead of shared memory\n",niter);
+	memory = (void *) NULL;
+	donep = true;

-  } else if ((*shmid = shmget(*key,0,0)) != -1) {
-    /* Found existing shared memory */
-    if ((memory = shmat(*shmid,NULL,0)) == (void *) -1) {
-      fprintf(stderr,"Error with shmat.  Error %d: %s\n",errno,strerror(errno));
+      } else {
+	/* Existing memory is not attached by any other process.  Could be corrupted. */
+	fprintf(stderr,"Clearing existing shared memory for %s...\n",filename);
+	Access_deallocate_wo_semaphore(memory,*shmid,*key);
+	
+	/* Now loop above to try again */
+      }
+    
    } else {
-      semaphore_ids = Intlist_push(semaphore_ids,semid);
-      shmem_memory = List_push(shmem_memory,memory);
-      shmem_ids = Intlist_push(shmem_ids,*shmid);
-      fprintf(stderr,"Attached existing memory for %s...",filename);
+      fprintf(stderr,"Using malloc instead of shmget for file %s\n",filename);
+      memory = (void *) NULL;
+      donep = true;
    }
-    
-  } else {
-    fprintf(stderr,"Using malloc instead of shmget for file %s\n",filename);
-    memory = (void *) NULL;
+
+    niter++;
  }

 #if 0
@@ -713,6 +803,8 @@ Access_allocate_private (Access_T *access, size_t *len, double *seconds, char *f

  if (eltsize == 1) {
    FREAD_CHARS(memory2,(*len)/eltsize,fp);
+  } else if (eltsize == 2) {
+    FREAD_USHORTS(memory2,(*len)/eltsize,fp);
  } else if (eltsize == 4) {
    FREAD_UINTS(memory2,(*len)/eltsize,fp);
  } else if (eltsize == 8) {
@@ -778,6 +870,8 @@ Access_allocate_shared (Access_T *access, int *shmid, key_t *key, int *fd, size_

  if (eltsize == 1) {
    FREAD_CHARS(memory2,(*len)/eltsize,fp);
+  } else if (eltsize == 2) {
+    FREAD_USHORTS(memory2,(*len)/eltsize,fp);
  } else if (eltsize == 4) {
    FREAD_UINTS(memory2,(*len)/eltsize,fp);
  } else if (eltsize == 8) {

--- a/src/atoi.c
+++ b/src/atoi.c
-static char rcsid[] = "$Id: atoi.c 195989 2016-08-08 21:42:24Z twu $";
+static char rcsid[] = "$Id: atoi.c 214305 2018-03-19 23:40:43Z twu $";
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
@@ -16435,3 +16435,18 @@ Atoi_reduce_ag (Oligospace_T oligo) {
  return reduced;
 }
  
+
+UINT2
+Atoi_reduce_tc_local (UINT2 oligo) {
+
+  /* Handles 16 bits, or k-mer up to 8 */
+  return convert_tc[oligo];
+}
+
+UINT2
+Atoi_reduce_ag_local (UINT2 oligo) {
+
+  /* Handles 16 bits, or k-mer up to 8 */
+  return convert_ag[oligo];
+}
+
--- a/src/atoi.h
+++ b/src/atoi.h
-/* $Id: atoi.h 180699 2015-12-10 19:10:10Z twu $ */
+/* $Id: atoi.h 214305 2018-03-19 23:40:43Z twu $ */
 #ifndef ATOI_INCLUDED
 #define ATOI_INCLUDED

@@ -8,6 +8,10 @@ extern Oligospace_T
 Atoi_reduce_ag (Oligospace_T oligo);
 extern Oligospace_T
 Atoi_reduce_tc (Oligospace_T oligo);
+extern UINT2
+Atoi_reduce_tc_local (UINT2 oligo);
+extern UINT2
+Atoi_reduce_ag_local (UINT2 oligo);

 #endif

--- a/src/atoiindex.c
+++ b/src/atoiindex.c
--- a/src/bitpack64-access.h
+++ b/src/bitpack64-access.h
+/* $Id: bitpack64-access.h 212659 2018-01-20 00:58:14Z twu $ */
 #ifndef BITPACK64_ACCESS_INCLUDED
 #define BITPACK64_ACCESS_INCLUDED
 #include "types.h"

--- a/src/bitpack64-incr.c
+++ b/src/bitpack64-incr.c
-static char rcsid[] = "$Id: bitpack64-incr.c 199469 2016-10-23 03:49:07Z twu $";
+static char rcsid[] = "$Id: bitpack64-incr.c 212659 2018-01-20 00:58:14Z twu $";
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
@@ -9537,7 +9537,7 @@ transfer_22_24 (UINT4 *out, const UINT4 *in) {
  value = ( CONVERT(*in) >>  18  )   % (1U << 22 ) ;
  in += WORD_INCR;
  value |= (CONVERT(*in) % (1U<< 8 ))<<( 22 - 8 );
-  *out |= (value << 8);	/* was 16 */
+  *out |= (value << 8);

  /* 12 */
  value = ( CONVERT(*in) >>  8  )   % (1U << 22 ) ;
@@ -9719,7 +9719,7 @@ transfer_26_28 (UINT4 *out, const UINT4 *in) {
  value |= (CONVERT(*in) % (1U<< 2 ))<<( 26 - 2 );
  *out |= (value << 16);
  out += WORD_INCR;
-  *out |= (value >> (28 - 12));	/* was (28 - 8) */
+  *out |= (value >> (28 - 12));

  /* 05 */
  value = ( CONVERT(*in) >>  2  )   % (1U << 26 ) ;

--- a/src/bitpack64-incr.h
+++ b/src/bitpack64-incr.h
+/* $Id: bitpack64-incr.h 212659 2018-01-20 00:58:14Z twu $ */
 #ifndef BITPACK64_INCR_INCLUDED
 #define BITPACK64_INCR_INCLUDED
 #include "types.h"