ChangeLog

+biobambam2 (2.0.129-1) unstable; urgency=medium
+
+  * rename fastaexplode to fastaexplod
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 08 Aug 2019 09:29:48 +0200
+
 biobambam2 (2.0.128-1) unstable; urgency=medium
 
   * remove manual page for removed kmerprob

autom4te.cache/output.0

 @%:@! /bin/sh
 @%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.127.
+@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.128.
 @%:@
 @%:@ Report bugs to <tischler@mpi-cbg.de>.
 @%:@ 
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='biobambam2'
 PACKAGE_TARNAME='biobambam2'
-PACKAGE_VERSION='2.0.127'
-PACKAGE_STRING='biobambam2 2.0.127'
+PACKAGE_VERSION='2.0.128'
+PACKAGE_STRING='biobambam2 2.0.128'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='http://www.sanger.ac.uk'
@@ -1400,7 +1400,7 @@ 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 biobambam2 2.0.127 to adapt to many kinds of systems.
+\`configure' configures biobambam2 2.0.128 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1472,7 +1472,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of biobambam2 2.0.127:";;
+     short | recursive ) echo "Configuration of biobambam2 2.0.128:";;
    esac
   cat <<\_ACEOF
@@ -1631,7 +1631,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-biobambam2 configure 2.0.127
+biobambam2 configure 2.0.128
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2072,7 +2072,7 @@ 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 biobambam2 $as_me 2.0.127, which was
+It was created by biobambam2 $as_me 2.0.128, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -11972,7 +11972,7 @@ fi
 # Define the identity of the package.
  PACKAGE='biobambam2'
- VERSION='2.0.127'
+ VERSION='2.0.128'
 cat >>confdefs.h <<_ACEOF
@@ -18584,7 +18584,7 @@ cat >>$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 biobambam2 $as_me 2.0.127, which was
+This file was extended by biobambam2 $as_me 2.0.128, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -18651,7 +18651,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-biobambam2 config.status 2.0.127
+biobambam2 config.status 2.0.128
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"

autom4te.cache/output.1

 @%:@! /bin/sh
 @%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.128.
+@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.129.
 @%:@
 @%:@ Report bugs to <tischler@mpi-cbg.de>.
 @%:@ 
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='biobambam2'
 PACKAGE_TARNAME='biobambam2'
-PACKAGE_VERSION='2.0.128'
-PACKAGE_STRING='biobambam2 2.0.128'
+PACKAGE_VERSION='2.0.129'
+PACKAGE_STRING='biobambam2 2.0.129'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='http://www.sanger.ac.uk'
@@ -1400,7 +1400,7 @@ 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 biobambam2 2.0.128 to adapt to many kinds of systems.
+\`configure' configures biobambam2 2.0.129 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1472,7 +1472,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of biobambam2 2.0.128:";;
+     short | recursive ) echo "Configuration of biobambam2 2.0.129:";;
    esac
   cat <<\_ACEOF
@@ -1631,7 +1631,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-biobambam2 configure 2.0.128
+biobambam2 configure 2.0.129
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2072,7 +2072,7 @@ 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 biobambam2 $as_me 2.0.128, which was
+It was created by biobambam2 $as_me 2.0.129, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -11972,7 +11972,7 @@ fi
 # Define the identity of the package.
  PACKAGE='biobambam2'
- VERSION='2.0.128'
+ VERSION='2.0.129'
 cat >>confdefs.h <<_ACEOF
@@ -16979,12 +16979,12 @@ if test -n "$libmaus2_CFLAGS"; then
     pkg_cv_libmaus2_CFLAGS="$libmaus2_CFLAGS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -16996,12 +16996,12 @@ if test -n "$libmaus2_LIBS"; then
     pkg_cv_libmaus2_LIBS="$libmaus2_LIBS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17022,14 +17022,14 @@ else
         _pkg_short_errors_supported=no
 fi
         if test $_pkg_short_errors_supported = yes; then
-	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.653" 2>&1`
         else 
-	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.653" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2 >= 2.0.650) were not met:
+	as_fn_error $? "Package requirements (libmaus2 >= 2.0.653) were not met:
 $libmaus2_PKG_ERRORS
@@ -17070,12 +17070,12 @@ if test -n "$libmaus2digests_CFLAGS"; then
     pkg_cv_libmaus2digests_CFLAGS="$libmaus2digests_CFLAGS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17087,12 +17087,12 @@ if test -n "$libmaus2digests_LIBS"; then
     pkg_cv_libmaus2digests_LIBS="$libmaus2digests_LIBS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17113,14 +17113,14 @@ else
         _pkg_short_errors_supported=no
 fi
         if test $_pkg_short_errors_supported = yes; then
-	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.653" 2>&1`
         else 
-	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.653" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2digests_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.650) were not met:
+	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.653) were not met:
 $libmaus2digests_PKG_ERRORS
@@ -17161,12 +17161,12 @@ if test -n "$libmaus2seqchksumsfactory_CFLAGS"; then
     pkg_cv_libmaus2seqchksumsfactory_CFLAGS="$libmaus2seqchksumsfactory_CFLAGS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17178,12 +17178,12 @@ if test -n "$libmaus2seqchksumsfactory_LIBS"; then
     pkg_cv_libmaus2seqchksumsfactory_LIBS="$libmaus2seqchksumsfactory_LIBS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17204,14 +17204,14 @@ else
         _pkg_short_errors_supported=no
 fi
         if test $_pkg_short_errors_supported = yes; then
-	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>&1`
         else 
-	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2seqchksumsfactory_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.650) were not met:
+	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.653) were not met:
 $libmaus2seqchksumsfactory_PKG_ERRORS
@@ -17486,12 +17486,12 @@ if test -n "$libmaus2irods_CFLAGS"; then
     pkg_cv_libmaus2irods_CFLAGS="$libmaus2irods_CFLAGS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17503,12 +17503,12 @@ if test -n "$libmaus2irods_LIBS"; then
     pkg_cv_libmaus2irods_LIBS="$libmaus2irods_LIBS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17529,14 +17529,14 @@ else
         _pkg_short_errors_supported=no
 fi
         if test $_pkg_short_errors_supported = yes; then
-	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.653" 2>&1`
         else 
-	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.653" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2irods_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.650) were not met:
+	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.653) were not met:
 $libmaus2irods_PKG_ERRORS
@@ -18571,7 +18571,7 @@ cat >>$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 biobambam2 $as_me 2.0.128, which was
+This file was extended by biobambam2 $as_me 2.0.129, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -18638,7 +18638,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-biobambam2 config.status 2.0.128
+biobambam2 config.status 2.0.129
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"

autom4te.cache/output.2

 @%:@! /bin/sh
 @%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.128.
+@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.129.
 @%:@
 @%:@ Report bugs to <tischler@mpi-cbg.de>.
 @%:@ 
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='biobambam2'
 PACKAGE_TARNAME='biobambam2'
-PACKAGE_VERSION='2.0.128'
-PACKAGE_STRING='biobambam2 2.0.128'
+PACKAGE_VERSION='2.0.129'
+PACKAGE_STRING='biobambam2 2.0.129'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='http://www.sanger.ac.uk'
@@ -1400,7 +1400,7 @@ 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 biobambam2 2.0.128 to adapt to many kinds of systems.
+\`configure' configures biobambam2 2.0.129 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1472,7 +1472,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of biobambam2 2.0.128:";;
+     short | recursive ) echo "Configuration of biobambam2 2.0.129:";;
    esac
   cat <<\_ACEOF
@@ -1631,7 +1631,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-biobambam2 configure 2.0.128
+biobambam2 configure 2.0.129
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2072,7 +2072,7 @@ 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 biobambam2 $as_me 2.0.128, which was
+It was created by biobambam2 $as_me 2.0.129, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -11972,7 +11972,7 @@ fi
 # Define the identity of the package.
  PACKAGE='biobambam2'
- VERSION='2.0.128'
+ VERSION='2.0.129'
 cat >>confdefs.h <<_ACEOF
@@ -16979,12 +16979,12 @@ if test -n "$libmaus2_CFLAGS"; then
     pkg_cv_libmaus2_CFLAGS="$libmaus2_CFLAGS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -16996,12 +16996,12 @@ if test -n "$libmaus2_LIBS"; then
     pkg_cv_libmaus2_LIBS="$libmaus2_LIBS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17022,14 +17022,14 @@ else
         _pkg_short_errors_supported=no
 fi
         if test $_pkg_short_errors_supported = yes; then
-	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.653" 2>&1`
         else 
-	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.653" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2 >= 2.0.650) were not met:
+	as_fn_error $? "Package requirements (libmaus2 >= 2.0.653) were not met:
 $libmaus2_PKG_ERRORS
@@ -17070,12 +17070,12 @@ if test -n "$libmaus2digests_CFLAGS"; then
     pkg_cv_libmaus2digests_CFLAGS="$libmaus2digests_CFLAGS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17087,12 +17087,12 @@ if test -n "$libmaus2digests_LIBS"; then
     pkg_cv_libmaus2digests_LIBS="$libmaus2digests_LIBS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17113,14 +17113,14 @@ else
         _pkg_short_errors_supported=no
 fi
         if test $_pkg_short_errors_supported = yes; then
-	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.653" 2>&1`
         else 
-	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.653" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2digests_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.650) were not met:
+	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.653) were not met:
 $libmaus2digests_PKG_ERRORS
@@ -17161,12 +17161,12 @@ if test -n "$libmaus2seqchksumsfactory_CFLAGS"; then
     pkg_cv_libmaus2seqchksumsfactory_CFLAGS="$libmaus2seqchksumsfactory_CFLAGS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17178,12 +17178,12 @@ if test -n "$libmaus2seqchksumsfactory_LIBS"; then
     pkg_cv_libmaus2seqchksumsfactory_LIBS="$libmaus2seqchksumsfactory_LIBS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17204,14 +17204,14 @@ else
         _pkg_short_errors_supported=no
 fi
         if test $_pkg_short_errors_supported = yes; then
-	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>&1`
         else 
-	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2seqchksumsfactory_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.650) were not met:
+	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.653) were not met:
 $libmaus2seqchksumsfactory_PKG_ERRORS
@@ -17486,12 +17486,12 @@ if test -n "$libmaus2irods_CFLAGS"; then
     pkg_cv_libmaus2irods_CFLAGS="$libmaus2irods_CFLAGS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17503,12 +17503,12 @@ if test -n "$libmaus2irods_LIBS"; then
     pkg_cv_libmaus2irods_LIBS="$libmaus2irods_LIBS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17529,14 +17529,14 @@ else
         _pkg_short_errors_supported=no
 fi
         if test $_pkg_short_errors_supported = yes; then
-	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.653" 2>&1`
         else 
-	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.653" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2irods_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.650) were not met:
+	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.653) were not met:
 $libmaus2irods_PKG_ERRORS
@@ -18571,7 +18571,7 @@ cat >>$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 biobambam2 $as_me 2.0.128, which was
+This file was extended by biobambam2 $as_me 2.0.129, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -18638,7 +18638,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-biobambam2 config.status 2.0.128
+biobambam2 config.status 2.0.129
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"

autom4te.cache/traces.1

@@ -3,7 +3,7 @@ m4trace:aclocal.m4:1459: -1- m4_include([m4/ltoptions.m4])
 m4trace:aclocal.m4:1460: -1- m4_include([m4/ltsugar.m4])
 m4trace:aclocal.m4:1461: -1- m4_include([m4/ltversion.m4])
 m4trace:aclocal.m4:1462: -1- m4_include([m4/lt~obsolete.m4])
-m4trace:configure.ac:1: -1- AC_INIT([biobambam2], [2.0.128], [tischler@mpi-cbg.de], [biobambam2], [http://www.sanger.ac.uk])
+m4trace:configure.ac:1: -1- AC_INIT([biobambam2], [2.0.129], [tischler@mpi-cbg.de], [biobambam2], [http://www.sanger.ac.uk])
 m4trace:configure.ac:1: -1- m4_pattern_forbid([^_?A[CHUM]_])
 m4trace:configure.ac:1: -1- m4_pattern_forbid([_AC_])
 m4trace:configure.ac:1: -1- m4_pattern_forbid([^LIBOBJS$], [do not use LIBOBJS directly, use AC_LIBOBJ (see section `AC_LIBOBJ vs LIBOBJS'])

autom4te.cache/traces.2

@@ -2905,36 +2905,36 @@ m4trace:configure.ac:139: -1- m4_pattern_allow([^PKG_CONFIG_PATH$])
 m4trace:configure.ac:139: -1- m4_pattern_allow([^PKG_CONFIG_LIBDIR$])
 m4trace:configure.ac:139: -1- m4_pattern_allow([^PKG_CONFIG$])
 m4trace:configure.ac:147: -1- m4_pattern_allow([^STDC_HEADERS$])
-m4trace:configure.ac:168: -1- PKG_CHECK_MODULES([libmaus2], [libmaus2 >= 2.0.650])
+m4trace:configure.ac:168: -1- PKG_CHECK_MODULES([libmaus2], [libmaus2 >= 2.0.653])
 m4trace:configure.ac:168: -1- m4_pattern_allow([^libmaus2_CFLAGS$])
 m4trace:configure.ac:168: -1- m4_pattern_allow([^libmaus2_LIBS$])
-m4trace:configure.ac:168: -1- PKG_CHECK_EXISTS([libmaus2 >= 2.0.650], [pkg_cv_[]libmaus2_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2 >= 2.0.650" 2>/dev/null`
+m4trace:configure.ac:168: -1- PKG_CHECK_EXISTS([libmaus2 >= 2.0.653], [pkg_cv_[]libmaus2_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2 >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
-m4trace:configure.ac:168: -1- PKG_CHECK_EXISTS([libmaus2 >= 2.0.650], [pkg_cv_[]libmaus2_LIBS=`$PKG_CONFIG --[]libs "libmaus2 >= 2.0.650" 2>/dev/null`
+m4trace:configure.ac:168: -1- PKG_CHECK_EXISTS([libmaus2 >= 2.0.653], [pkg_cv_[]libmaus2_LIBS=`$PKG_CONFIG --[]libs "libmaus2 >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
 m4trace:configure.ac:168: -1- _PKG_SHORT_ERRORS_SUPPORTED
-m4trace:configure.ac:169: -1- PKG_CHECK_MODULES([libmaus2digests], [libmaus2digests >= 2.0.650])
+m4trace:configure.ac:169: -1- PKG_CHECK_MODULES([libmaus2digests], [libmaus2digests >= 2.0.653])
 m4trace:configure.ac:169: -1- m4_pattern_allow([^libmaus2digests_CFLAGS$])
 m4trace:configure.ac:169: -1- m4_pattern_allow([^libmaus2digests_LIBS$])
-m4trace:configure.ac:169: -1- PKG_CHECK_EXISTS([libmaus2digests >= 2.0.650], [pkg_cv_[]libmaus2digests_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2digests >= 2.0.650" 2>/dev/null`
+m4trace:configure.ac:169: -1- PKG_CHECK_EXISTS([libmaus2digests >= 2.0.653], [pkg_cv_[]libmaus2digests_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2digests >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
-m4trace:configure.ac:169: -1- PKG_CHECK_EXISTS([libmaus2digests >= 2.0.650], [pkg_cv_[]libmaus2digests_LIBS=`$PKG_CONFIG --[]libs "libmaus2digests >= 2.0.650" 2>/dev/null`
+m4trace:configure.ac:169: -1- PKG_CHECK_EXISTS([libmaus2digests >= 2.0.653], [pkg_cv_[]libmaus2digests_LIBS=`$PKG_CONFIG --[]libs "libmaus2digests >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
 m4trace:configure.ac:169: -1- _PKG_SHORT_ERRORS_SUPPORTED
-m4trace:configure.ac:170: -1- PKG_CHECK_MODULES([libmaus2seqchksumsfactory], [libmaus2seqchksumsfactory >= 2.0.650])
+m4trace:configure.ac:170: -1- PKG_CHECK_MODULES([libmaus2seqchksumsfactory], [libmaus2seqchksumsfactory >= 2.0.653])
 m4trace:configure.ac:170: -1- m4_pattern_allow([^libmaus2seqchksumsfactory_CFLAGS$])
 m4trace:configure.ac:170: -1- m4_pattern_allow([^libmaus2seqchksumsfactory_LIBS$])
-m4trace:configure.ac:170: -1- PKG_CHECK_EXISTS([libmaus2seqchksumsfactory >= 2.0.650], [pkg_cv_[]libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
+m4trace:configure.ac:170: -1- PKG_CHECK_EXISTS([libmaus2seqchksumsfactory >= 2.0.653], [pkg_cv_[]libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
-m4trace:configure.ac:170: -1- PKG_CHECK_EXISTS([libmaus2seqchksumsfactory >= 2.0.650], [pkg_cv_[]libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --[]libs "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
+m4trace:configure.ac:170: -1- PKG_CHECK_EXISTS([libmaus2seqchksumsfactory >= 2.0.653], [pkg_cv_[]libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --[]libs "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
 m4trace:configure.ac:170: -1- _PKG_SHORT_ERRORS_SUPPORTED
-m4trace:configure.ac:305: -1- PKG_CHECK_MODULES([libmaus2irods], [libmaus2irods >= 2.0.650])
+m4trace:configure.ac:305: -1- PKG_CHECK_MODULES([libmaus2irods], [libmaus2irods >= 2.0.653])
 m4trace:configure.ac:305: -1- m4_pattern_allow([^libmaus2irods_CFLAGS$])
 m4trace:configure.ac:305: -1- m4_pattern_allow([^libmaus2irods_LIBS$])
-m4trace:configure.ac:305: -1- PKG_CHECK_EXISTS([libmaus2irods >= 2.0.650], [pkg_cv_[]libmaus2irods_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2irods >= 2.0.650" 2>/dev/null`
+m4trace:configure.ac:305: -1- PKG_CHECK_EXISTS([libmaus2irods >= 2.0.653], [pkg_cv_[]libmaus2irods_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2irods >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
-m4trace:configure.ac:305: -1- PKG_CHECK_EXISTS([libmaus2irods >= 2.0.650], [pkg_cv_[]libmaus2irods_LIBS=`$PKG_CONFIG --[]libs "libmaus2irods >= 2.0.650" 2>/dev/null`
+m4trace:configure.ac:305: -1- PKG_CHECK_EXISTS([libmaus2irods >= 2.0.653], [pkg_cv_[]libmaus2irods_LIBS=`$PKG_CONFIG --[]libs "libmaus2irods >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
 m4trace:configure.ac:305: -1- _PKG_SHORT_ERRORS_SUPPORTED
 m4trace:configure.ac:343: -1- PKG_CHECK_MODULES([liftingwavelettransform], [liftingwavelettransform >= 0.0.0])

configure

 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for biobambam2 2.0.128.
+# Generated by GNU Autoconf 2.69 for biobambam2 2.0.129.
 #
 # Report bugs to <tischler@mpi-cbg.de>.
 #
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='biobambam2'
 PACKAGE_TARNAME='biobambam2'
-PACKAGE_VERSION='2.0.128'
-PACKAGE_STRING='biobambam2 2.0.128'
+PACKAGE_VERSION='2.0.129'
+PACKAGE_STRING='biobambam2 2.0.129'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='http://www.sanger.ac.uk'
@@ -1400,7 +1400,7 @@ 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 biobambam2 2.0.128 to adapt to many kinds of systems.
+\`configure' configures biobambam2 2.0.129 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1472,7 +1472,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of biobambam2 2.0.128:";;
+     short | recursive ) echo "Configuration of biobambam2 2.0.129:";;
    esac
   cat <<\_ACEOF
@@ -1631,7 +1631,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-biobambam2 configure 2.0.128
+biobambam2 configure 2.0.129
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2072,7 +2072,7 @@ 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 biobambam2 $as_me 2.0.128, which was
+It was created by biobambam2 $as_me 2.0.129, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -11972,7 +11972,7 @@ fi
 # Define the identity of the package.
  PACKAGE='biobambam2'
- VERSION='2.0.128'
+ VERSION='2.0.129'
 cat >>confdefs.h <<_ACEOF
@@ -16979,12 +16979,12 @@ if test -n "$libmaus2_CFLAGS"; then
     pkg_cv_libmaus2_CFLAGS="$libmaus2_CFLAGS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -16996,12 +16996,12 @@ if test -n "$libmaus2_LIBS"; then
     pkg_cv_libmaus2_LIBS="$libmaus2_LIBS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -17022,14 +17022,14 @@ else
         _pkg_short_errors_supported=no
 fi
         if test $_pkg_short_errors_supported = yes; then
-	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.653" 2>&1`
         else
-	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.653" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2 >= 2.0.650) were not met:
+	as_fn_error $? "Package requirements (libmaus2 >= 2.0.653) were not met:
 $libmaus2_PKG_ERRORS
@@ -17070,12 +17070,12 @@ if test -n "$libmaus2digests_CFLAGS"; then
     pkg_cv_libmaus2digests_CFLAGS="$libmaus2digests_CFLAGS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -17087,12 +17087,12 @@ if test -n "$libmaus2digests_LIBS"; then
     pkg_cv_libmaus2digests_LIBS="$libmaus2digests_LIBS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -17113,14 +17113,14 @@ else
         _pkg_short_errors_supported=no
 fi
         if test $_pkg_short_errors_supported = yes; then
-	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.653" 2>&1`
         else
-	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.653" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2digests_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.650) were not met:
+	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.653) were not met:
 $libmaus2digests_PKG_ERRORS
@@ -17161,12 +17161,12 @@ if test -n "$libmaus2seqchksumsfactory_CFLAGS"; then
     pkg_cv_libmaus2seqchksumsfactory_CFLAGS="$libmaus2seqchksumsfactory_CFLAGS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -17178,12 +17178,12 @@ if test -n "$libmaus2seqchksumsfactory_LIBS"; then
     pkg_cv_libmaus2seqchksumsfactory_LIBS="$libmaus2seqchksumsfactory_LIBS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -17204,14 +17204,14 @@ else
         _pkg_short_errors_supported=no
 fi
         if test $_pkg_short_errors_supported = yes; then
-	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>&1`
         else
-	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2seqchksumsfactory_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.650) were not met:
+	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.653) were not met:
 $libmaus2seqchksumsfactory_PKG_ERRORS
@@ -17486,12 +17486,12 @@ if test -n "$libmaus2irods_CFLAGS"; then
     pkg_cv_libmaus2irods_CFLAGS="$libmaus2irods_CFLAGS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -17503,12 +17503,12 @@ if test -n "$libmaus2irods_LIBS"; then
     pkg_cv_libmaus2irods_LIBS="$libmaus2irods_LIBS"
  elif test -n "$PKG_CONFIG"; then
     if test -n "$PKG_CONFIG" && \
-    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.653\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.653") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.650" 2>/dev/null`
+  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.653" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -17529,14 +17529,14 @@ else
         _pkg_short_errors_supported=no
 fi
         if test $_pkg_short_errors_supported = yes; then
-	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.653" 2>&1`
         else
-	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.653" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2irods_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.650) were not met:
+	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.653) were not met:
 $libmaus2irods_PKG_ERRORS
@@ -18571,7 +18571,7 @@ cat >>$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 biobambam2 $as_me 2.0.128, which was
+This file was extended by biobambam2 $as_me 2.0.129, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -18638,7 +18638,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-biobambam2 config.status 2.0.128
+biobambam2 config.status 2.0.129
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"

configure.ac

-AC_INIT(biobambam2,2.0.128,[tischler@mpi-cbg.de],[biobambam2],[http://www.sanger.ac.uk])
+AC_INIT(biobambam2,2.0.129,[tischler@mpi-cbg.de],[biobambam2],[http://www.sanger.ac.uk])
 AC_CANONICAL_SYSTEM
 AC_PROG_LIBTOOL
 
@@ -165,9 +165,9 @@ if test ! -z "${with_libmaus2}" ; then
 	fi
 fi
 
-PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.650])
-PKG_CHECK_MODULES([libmaus2digests],[libmaus2digests >= 2.0.650])
-PKG_CHECK_MODULES([libmaus2seqchksumsfactory],[libmaus2seqchksumsfactory >= 2.0.650])
+PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.653])
+PKG_CHECK_MODULES([libmaus2digests],[libmaus2digests >= 2.0.653])
+PKG_CHECK_MODULES([libmaus2seqchksumsfactory],[libmaus2seqchksumsfactory >= 2.0.653])
 
 if test ! -z "${with_libmaus2}" ; then
 	if test ! -z "${PKGCONFIGPATHSAVE}" ; then
@@ -302,7 +302,7 @@ if test "${have_libmaus2_irods}" = "yes" ; then
 		fi
 	fi
 
-	PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.650])
+	PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.653])
 
 	LIBMAUS2IRODSCPPFLAGS="${libmaus2irods_CFLAGS}"
 	LIBMAUS2IRODSLIBS="${libmaus2irods_LIBS}"

debian/changelog

+biobambam2 (2.0.129-1) unstable; urgency=medium
+
+  * New upstream version
+  * Upstream has renamed fastaexplode to fastaexplod
+    Closes: #933937
+
+ -- Andreas Tille <tille@debian.org>  Thu, 08 Aug 2019 10:38:37 +0200
+
 biobambam2 (2.0.128-1) unstable; urgency=medium
 
   * New upstream version

src/Makefile.am

@@ -29,7 +29,7 @@ MANPAGES = programs/bamtofastq.1 programs/bamsort.1 programs/bammarkduplicates.1
 	programs/bamseqchksum.1 programs/bamvalidate.1 \
 	programs/bamflagsplit.1 programs/bamintervalcomment.1 \
 	programs/bamstreamingmarkduplicates.1 \
-	programs/bamsormadup.1 programs/fastaexplode.1 \
+	programs/bamsormadup.1 programs/fastaexplod.1 \
 	programs/bamrecalculatecigar.1 programs/bamfiltermc.1 \
 	programs/bamfillquery.1 programs/bamalignfrac.1 programs/bamauxmerge.1 programs/bamauxmerge2.1 \
 	programs/bambisect.1 programs/bamclipXT.1
@@ -87,7 +87,7 @@ bin_PROGRAMS = bamtofastq bammarkduplicates bamsort bammaskflags bamrecompress \
     	fastqtobampar \
 	bamranksort \
 	bamtagconversion \
-	fastaexplode \
+	fastaexplod \
 	bamrecalculatecigar \
 	bamfiltermc \
 	bamnumericalindex \
@@ -119,7 +119,7 @@ bin_PROGRAMS = bamtofastq bammarkduplicates bamsort bammaskflags bamrecompress \
 noinst_PROGRAMS = bamfilter bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname \
 	bamdisthist fastabgzfextract @BAMREFDEPTHPEAKS@ \
 	bamheap bamfrontback bamconsensus \
-	@BLASTXMLTOBAMNOINSTEXP@ bamrandomtag
+	@BLASTXMLTOBAMNOINSTEXP@ bamrandomtag bamfeaturecount
 	
 EXTRA_PROGRAMS = blastnxmltobam
 
@@ -498,10 +498,10 @@ bamtagconversion_LDADD = ${LIBMAUS2LIBS}
 bamtagconversion_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
 bamtagconversion_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}
 
-fastaexplode_SOURCES = programs/fastaexplode.cpp biobambam2/Licensing.cpp
-fastaexplode_LDADD = ${LIBMAUS2LIBS}
-fastaexplode_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
-fastaexplode_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}
+fastaexplod_SOURCES = programs/fastaexplod.cpp biobambam2/Licensing.cpp
+fastaexplod_LDADD = ${LIBMAUS2LIBS}
+fastaexplod_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
+fastaexplod_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}
 
 bamrecalculatecigar_SOURCES = programs/bamrecalculatecigar.cpp biobambam2/Licensing.cpp
 bamrecalculatecigar_LDADD = ${LIBMAUS2LIBS}
@@ -582,3 +582,8 @@ bamfiltereofblocks_SOURCES = programs/bamfiltereofblocks.cpp biobambam2/Licensin
 bamfiltereofblocks_LDADD = ${LIBMAUS2LIBS}
 bamfiltereofblocks_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
 bamfiltereofblocks_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}
+
+bamfeaturecount_SOURCES = programs/bamfeaturecount.cpp biobambam2/Licensing.cpp
+bamfeaturecount_LDADD = ${LIBMAUS2LIBS}
+bamfeaturecount_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
+bamfeaturecount_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}

src/programs/fastaexplode.1 → src/programs/fastaexplod.1

-.TH FASTAEXPLODE 1 "January 2016" BIOBAMBAM2
+.TH FASTAEXPLOD 1 "January 2016" BIOBAMBAM2
 .SH NAME
-fastaexplode - split multi sequence FastA file into one file per sequence
+fastaexplod - split multi sequence FastA file into one file per sequence
 .SH SYNOPSIS
 .PP
-.B fastaexplode
+.B fastaexplod
 [options]
 .SH DESCRIPTION
-fastaexplode reads a FastA file from standard input and writes the contained sequences to a set
+fastaexplod reads a FastA file from standard input and writes the contained sequences to a set
 of files. It writes one sequence per output file. The file names used are
 fasta_<id>.fasta where id is a git digit running decimal number. The prefix
 (fasta_ by default) can be set using the -p switch. The .fasta suffix is

src/programs/fastaexplode.cpp → src/programs/fastaexplod.cpp

@@ -33,7 +33,7 @@ static uint64_t getDefaultLineLength()
 	return 80;
 }
 
-int fastaexplode(libmaus2::util::ArgParser const & arg)
+int fastaexplod(libmaus2::util::ArgParser const & arg)
 {
 	libmaus2::fastx::StreamFastAReaderWrapper SFA(std::cin);
 	libmaus2::fastx::StreamFastAReaderWrapper::pattern_type pattern;
@@ -115,7 +115,7 @@ int main(int argc, char * argv[])
 
 		}
 
-		return fastaexplode(arg);
+		return fastaexplod(arg);
 	}
 	catch(std::exception const & ex)
 	{