.gitignore

@@ -55,3 +55,12 @@ pull.sh
 test/bamcmp
 test/bamtosam
 src/filtersam
+numproc.sh
+src/fastqtobam2
+bumprun.sh
+src/vcffilterinfo
+src/vcfpatchcontigprepend
+src/populaterefcache
+src/vcfconcat
+src/vcfsort
+removespace.sh

ChangeLog

+biobambam2 (2.0.128-1) unstable; urgency=medium
+
+  * remove manual page for removed kmerprob
+  * remove bamrefdepth and bamrefdepthpeaks
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 31 Jul 2019 14:10:27 +0200
+
+biobambam2 (2.0.127-1) unstable; urgency=medium
+
+  * add bamdepthintersect program
+  * add bamdepth program
+  * add DepthInterval class
+  * remove hard coded Z_DEFAULT_COMPRESSION default and replace by DeflateDefaults::getDefaultLevel()
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 31 Jul 2019 12:53:58 +0200
+
+biobambam2 (2.0.126-1) unstable; urgency=medium
+
+  * allow output to standard output in bamnumericalindex
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 30 Jul 2019 11:11:47 +0200
+
+biobambam2 (2.0.125-1) unstable; urgency=medium
+
+  * add construction of numerical index from numerical indexes of input files in bamfastcat
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 26 Jul 2019 17:17:43 +0200
+
+biobambam2 (2.0.124-1) unstable; urgency=medium
+
+  * update numerical index in bamreplacechecksums
+  * update numerical index in bamreheader
+  * put header and data in separate blocks in ReadHeader
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 25 Jul 2019 15:29:48 +0200
+
+biobambam2 (2.0.123-1) unstable; urgency=medium
+
+  * avoid explicitely invoking BamDecoder class (use factory instead)
+  * use output factory to allow SAM/BAM/CRAM output in bam12auxmerge
+  * use input factories in bam12auxmerge to support SAM and CRAM input
+  * add manual page for bamclipXT
+  * remove filtersam and kmerprob
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 25 Jul 2019 11:10:33 +0200
+
+biobambam2 (2.0.122-1) unstable; urgency=medium
+
+  * add bamnumericalindexstats
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 24 Jul 2019 15:01:14 +0200
+
+biobambam2 (2.0.121-1) unstable; urgency=medium
+
+  * add numerical indexing in bamsormadup
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 24 Jul 2019 14:34:22 +0200
+
+biobambam2 (2.0.120-1) unstable; urgency=medium
+
+  * add vcfsort program
+  * remove bamclipextract
+  * simplify bamdisthist
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 24 Jul 2019 11:02:17 +0200
+
+biobambam2 (2.0.119-1) unstable; urgency=medium
+
+  * add manual page for bambisect
+  * fix manual page for bamchecksort
+  * update help message in bamauxmerge2
+  * remove bamcheckalignments
+  * add manual page for bamauxmerge2
+  * add manual page for bamauxmerge
+  * clean up bamauxmerge
+  * change input order in bamalignfrac
+  * add documentation for regex option in manual page for bamalignfrac
+  * remove bamalignmentoffsets program
+  * add manual page for bamalignfrac
+  * rewrite bamalignfrac to produce more useful output
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 23 Jul 2019 21:55:28 +0200
+
+biobambam2 (2.0.118-1) unstable; urgency=medium
+
+  * avoid writing empty BGZF blocks in ReadHeader
+  * remove bamlastfilter
+  * remove deprecated bamcollate program
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Mon, 22 Jul 2019 09:36:51 +0200
+
+biobambam2 (2.0.117-1) unstable; urgency=medium
+
+  * fix breakages after libmaus2 cleanup
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 19 Jul 2019 13:09:16 +0200
+
+biobambam2 (2.0.116-1) unstable; urgency=medium
+
+  * avoid copying inline EOF blocks in bamfastcat
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 19 Jul 2019 12:27:19 +0200
+
+biobambam2 (2.0.115-1) unstable; urgency=medium
+
+  * add bamfiltereofblocks
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 19 Jul 2019 11:23:28 +0200
+
+biobambam2 (2.0.114-1) unstable; urgency=medium
+
+  * bump libmaus2 version
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 18 Jul 2019 10:55:18 +0200
+
+biobambam2 (2.0.113-1) unstable; urgency=medium
+
+  * add bamfastsplit
+  * add multi threaded processing in bamseqchksum
+  * add building numerical index in bamrecompress
+  * add vcfconcat
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 17 Jul 2019 16:19:52 +0200
+
+biobambam2 (2.0.112-1) unstable; urgency=medium
+
+  * fix bamrecompress for case of BAM input with inline empty BGZF blocks
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 16 Jul 2019 13:57:00 +0200
+
+biobambam2 (2.0.111-1) unstable; urgency=medium
+
+  * use readFileAsStream to read text header file in bamfastcat/bamreheader/bamreplacechecksums
+  * add tryoq flag in bamseqchksum
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 16 Jul 2019 11:13:33 +0200
+
+biobambam2 (2.0.110-1) unstable; urgency=medium
+
+  * add headerchecksums option in bamseqchecksum
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Mon, 15 Jul 2019 15:59:56 +0200
+
+biobambam2 (2.0.109-1) unstable; urgency=medium
+
+  * refactor bamreheader/bamfastcat and add bamreplacechecksums
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Mon, 15 Jul 2019 13:52:29 +0200
+
+biobambam2 (2.0.108-1) unstable; urgency=medium
+
+  * add include and exclude options in normalisefasta
+  * make sure we write an EOF block in bamfastexploderef even for "empty" output files
+  * add bisect tool
+  * add bamfastnumextract
+  * add low recompression bam input/output variant of exploderef functionality
+  * add populaterefcache program
+  * add bamexploderef
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 12 Jul 2019 16:34:24 +0200
+
+biobambam2 (2.0.107-1) unstable; urgency=medium
+
+  * add OQ tags in fastqtobam2
+  * add bamfastcat
+  * allow multi threading input and output in bamsplit
+  * replace usage of PosixRegex by std::regex
+  * fixes after changes in libmaus2
+  * remove lasToBAM
+  * added gzip output in vcffilterinfo
+  * added program vcfpatchcontigprepend (prepend string to all seq ids in a VCF file)
+  * add vcffilterinfo program (filter out all INFO fields not in a given filter list from a VCF file)
+  * add append option in bamreheader
+  * add bamreheader
+  * try to avoid stalling on blocked write queue in bamauxmerge2
+  * refactor Reference class out of bamauxmerge2 and add cigar string rewriting in bamauxmerge2
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 03 Jul 2019 21:04:34 +0200
+
+biobambam2 (2.0.106-1) unstable; urgency=medium
+
+  * fix email address in version bumping script
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 14 Jun 2019 12:39:35 +0200
+
+biobambam2 (2.0.105-1) unstable; urgency=medium
+
+  * no change version bump after fixing bumping script
+
+ -- German Tischler <germant@miltenyibiotec.de>  Fri, 14 Jun 2019 12:11:44 +0200
+
+biobambam2 (2.0.104-1) unstable; urgency=medium
+
+  * version bumping script test
+
+ -- German Tischler <germant@miltenyibiotec.de>  Fri, 14 Jun 2019 12:08:38 +0200
+
+biobambam2 (2.0.103-1) unstable; urgency=low
+
+  * bump libmaus2 version
+  * remove bamparsort
+  * fixes after libmaus2 changes
+  * do not replace cigar string for unmapped reads in bamauxmerge2
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 14 Jun 2019 12:00:00 +0000

Makefile.in

-# Makefile.in generated by automake 1.15.1 from Makefile.am.
+# Makefile.in generated by automake 1.15 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2017 Free Software Foundation, Inc.
+# Copyright (C) 1994-2014 Free Software Foundation, Inc.
 
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -215,13 +215,9 @@ AUTOCONF = @AUTOCONF@
 AUTOHEADER = @AUTOHEADER@
 AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
-BAMALIGNMENTOFFSETSINSTEXP = @BAMALIGNMENTOFFSETSINSTEXP@
-BAMALIGNMENTOFFSETSNOINSTEXP = @BAMALIGNMENTOFFSETSNOINSTEXP@
 BAMBAM_CFLAGS = @BAMBAM_CFLAGS@
 BAMBAM_LDFLAGS = @BAMBAM_LDFLAGS@
 BAMBAM_LIBS = @BAMBAM_LIBS@
-BAMPARSORTINSTEXP = @BAMPARSORTINSTEXP@
-BAMPARSORTNOINSTEXP = @BAMPARSORTNOINSTEXP@
 BAMREFDEPTHPEAKS = @BAMREFDEPTHPEAKS@
 BASE64PROG = @BASE64PROG@
 BASHPROG = @BASHPROG@
@@ -611,7 +607,7 @@ distdir: $(DISTFILES)
 	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
 	|| chmod -R a+r "$(distdir)"
 dist-gzip: distdir
-	tardir=$(distdir) && $(am__tar) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).tar.gz
+	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
 	$(am__post_remove_distdir)
 
 dist-bzip2: distdir
@@ -637,7 +633,7 @@ dist-shar: distdir
 	@echo WARNING: "Support for shar distribution archives is" \
 	               "deprecated." >&2
 	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
-	shar $(distdir) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).shar.gz
+	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
 	$(am__post_remove_distdir)
 
 dist-zip: distdir
@@ -655,7 +651,7 @@ dist dist-all:
 distcheck: dist
 	case '$(DIST_ARCHIVES)' in \
 	*.tar.gz*) \
-	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\
+	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
 	*.tar.bz2*) \
 	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
 	*.tar.lz*) \
@@ -665,7 +661,7 @@ distcheck: dist
 	*.tar.Z*) \
 	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
 	*.shar.gz*) \
-	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\
+	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
 	*.zip*) \
 	  unzip $(distdir).zip ;;\
 	esac

aclocal.m4

-# generated automatically by aclocal 1.15.1 -*- Autoconf -*-
+# generated automatically by aclocal 1.15 -*- Autoconf -*-
 
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
 
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -296,7 +296,7 @@ AS_VAR_COPY([$1], [pkg_cv_][$1])
 AS_VAR_IF([$1], [""], [$5], [$4])dnl
 ])dnl PKG_CHECK_VAR
 
-# Copyright (C) 2002-2017 Free Software Foundation, Inc.
+# Copyright (C) 2002-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -311,7 +311,7 @@ AC_DEFUN([AM_AUTOMAKE_VERSION],
 [am__api_version='1.15'
 dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
 dnl require some minimum version.  Point them to the right macro.
-m4_if([$1], [1.15.1], [],
+m4_if([$1], [1.15], [],
       [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
 ])
 
@@ -327,14 +327,14 @@ m4_define([_AM_AUTOCONF_VERSION], [])
 # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
 # This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
 AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.15.1])dnl
+[AM_AUTOMAKE_VERSION([1.15])dnl
 m4_ifndef([AC_AUTOCONF_VERSION],
   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
 _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
 
 # AM_AUX_DIR_EXPAND                                         -*- Autoconf -*-
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -386,7 +386,7 @@ am_aux_dir=`cd "$ac_aux_dir" && pwd`
 
 # AM_CONDITIONAL                                            -*- Autoconf -*-
 
-# Copyright (C) 1997-2017 Free Software Foundation, Inc.
+# Copyright (C) 1997-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -417,7 +417,7 @@ AC_CONFIG_COMMANDS_PRE(
 Usually this means the macro was only invoked conditionally.]])
 fi])])
 
-# Copyright (C) 1999-2017 Free Software Foundation, Inc.
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -608,7 +608,7 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl
 
 # Generate code to set up dependency tracking.              -*- Autoconf -*-
 
-# Copyright (C) 1999-2017 Free Software Foundation, Inc.
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -684,7 +684,7 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
 
 # Do all the work for Automake.                             -*- Autoconf -*-
 
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -881,7 +881,7 @@ for _am_header in $config_headers :; do
 done
 echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -902,7 +902,7 @@ if test x"${install_sh+set}" != xset; then
 fi
 AC_SUBST([install_sh])])
 
-# Copyright (C) 2003-2017 Free Software Foundation, Inc.
+# Copyright (C) 2003-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -923,7 +923,7 @@ AC_SUBST([am__leading_dot])])
 
 # Check to see how 'make' treats includes.	            -*- Autoconf -*-
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -973,7 +973,7 @@ rm -f confinc confmf
 
 # Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-
 
-# Copyright (C) 1997-2017 Free Software Foundation, Inc.
+# Copyright (C) 1997-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1014,7 +1014,7 @@ fi
 # Obsolete and "removed" macros, that must however still report explicit
 # error messages when used, to smooth transition.
 #
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1041,7 +1041,7 @@ AU_DEFUN([fp_C_PROTOTYPES], [AM_C_PROTOTYPES])
 
 # Helper functions for option handling.                     -*- Autoconf -*-
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1070,7 +1070,7 @@ AC_DEFUN([_AM_SET_OPTIONS],
 AC_DEFUN([_AM_IF_OPTION],
 [m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
 
-# Copyright (C) 1999-2017 Free Software Foundation, Inc.
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1117,7 +1117,7 @@ AC_LANG_POP([C])])
 # For backward compatibility.
 AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1136,7 +1136,7 @@ AC_DEFUN([AM_RUN_LOG],
 
 # Check to make sure that the build environment is sane.    -*- Autoconf -*-
 
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1217,7 +1217,7 @@ AC_CONFIG_COMMANDS_PRE(
 rm -f conftest.file
 ])
 
-# Copyright (C) 2009-2017 Free Software Foundation, Inc.
+# Copyright (C) 2009-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1277,7 +1277,7 @@ AC_SUBST([AM_BACKSLASH])dnl
 _AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
 ])
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1305,7 +1305,7 @@ fi
 INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
 AC_SUBST([INSTALL_STRIP_PROGRAM])])
 
-# Copyright (C) 2006-2017 Free Software Foundation, Inc.
+# Copyright (C) 2006-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1324,7 +1324,7 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
 
 # Check how to create a tarball.                            -*- Autoconf -*-
 
-# Copyright (C) 2004-2017 Free Software Foundation, Inc.
+# Copyright (C) 2004-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,

autom4te.cache/output.0

 @%:@! /bin/sh
 @%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.89.
+@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.127.
 @%:@
 @%:@ Report bugs to <tischler@mpi-cbg.de>.
 @%:@ 
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='biobambam2'
 PACKAGE_TARNAME='biobambam2'
-PACKAGE_VERSION='2.0.89'
-PACKAGE_STRING='biobambam2 2.0.89'
+PACKAGE_VERSION='2.0.127'
+PACKAGE_STRING='biobambam2 2.0.127'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='http://www.sanger.ac.uk'
@@ -646,10 +646,6 @@ BIOBAMBAM_HAVE_XERCES_C
 TESTDIR
 BLASTXMLTOBAMNOINSTEXP
 BLASTXMLTOBAMINSTEXP
-BAMALIGNMENTOFFSETSNOINSTEXP
-BAMALIGNMENTOFFSETSINSTEXP
-BAMPARSORTNOINSTEXP
-BAMPARSORTINSTEXP
 BAMREFDEPTHPEAKS
 LIFTINGWAVELETTRANSFORMDEFINE
 LIBMAUS2IRODSDEFINE
@@ -819,6 +815,7 @@ enable_debug
 enable_profile
 enable_fast
 enable_install_experimental
+enable_asan
 with_libmaus2
 with_liftingwavelettransform
 with_xerces_c
@@ -1403,7 +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 2.0.89 to adapt to many kinds of systems.
+\`configure' configures biobambam2 2.0.127 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1475,7 +1472,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of biobambam2 2.0.89:";;
+     short | recursive ) echo "Configuration of biobambam2 2.0.127:";;
    esac
   cat <<\_ACEOF
@@ -1500,6 +1497,7 @@ Optional Features:
   --enable-fast           disable evaluation of assertions (default no)
   --enable-install-experimental 
                           install experimental programs (default no)
+  --enable-asan           enable address sanitizer in debug mode (default no)
 Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
@@ -1633,7 +1631,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-biobambam2 configure 2.0.89
+biobambam2 configure 2.0.127
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2074,7 +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 2.0.89, which was
+It was created by biobambam2 $as_me 2.0.127, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -11974,7 +11972,7 @@ fi
 # Define the identity of the package.
  PACKAGE='biobambam2'
- VERSION='2.0.89'
+ VERSION='2.0.127'
 cat >>confdefs.h <<_ACEOF
@@ -12248,16 +12246,16 @@ else
   install_experimental=no
 fi
-
-if test "${install_experimental}" = "yes" ; then
-	BAMPARSORTINSTEXP=bamparsort
-	BAMALIGNMENTOFFSETSINSTEXP=bamalignmentoffsets
+@%:@ Check whether --enable-asan was given.
+if test "${enable_asan+set}" = set; then :
+  enableval=$enable_asan; enableasan=${enableval}
 else
-	BAMPARSORTNOINSTEXP=bamparsort
-	BAMALIGNMENTOFFSETSNOINSTEXP=bamalignmentoffsets
+  enableasan=no
 fi
+
+
 # check for C compiler
 CFLAGS_SAVE="${CFLAGS}"
 CFLAGS=""
@@ -16589,6 +16587,48 @@ fi
 CXXFLAGS="${CXXFLAGS_SAVE}"
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+CXXFLAGS_SAVE="${CXXFLAGS}"
+CXXFLAGS="-fsanitize=address"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C++ compiler supports the -fsanitize=address flag" >&5
+$as_echo_n "checking whether the C++ compiler supports the -fsanitize=address flag... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+  sanitizeaddress=yes
+else
+  sanitizeaddress=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: ${sanitizeaddress}" >&5
+$as_echo "${sanitizeaddress}" >&6; }
+CXXFLAGS="${CXXFLAGS_SAVE}"
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+if test \( "${sanitizeaddress}" = "yes" \) -a \( "${enableasan}" = "yes" \) ; then
+	CXXFLAGS="${CXXFLAGS} -fsanitize=address"
+	CFLAGS="${CFLAGS} -fsanitize=address"
+fi
+
 if test "${debug}" = "yes" ; then
 	CXXDEBUGFLAGS="-g -O0"
 	CDEBUGFLAGS="-g -O0"
@@ -16939,12 +16979,12 @@ if test -n "$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 >= 2.0.489\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.489") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.489" 2>/dev/null`
+  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -16956,12 +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 >= 2.0.489\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.489") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.489" 2>/dev/null`
+  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -16982,14 +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 >= 2.0.489" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
         else 
-	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.489" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2 >= 2.0.489) were not met:
+	as_fn_error $? "Package requirements (libmaus2 >= 2.0.650) were not met:
 $libmaus2_PKG_ERRORS
@@ -17030,12 +17070,12 @@ if test -n "$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 >= 2.0.489\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.489") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.489" 2>/dev/null`
+  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17047,12 +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 >= 2.0.489\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.489") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.489" 2>/dev/null`
+  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17073,14 +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 >= 2.0.489" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
         else 
-	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.489" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2digests_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.489) were not met:
+	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.650) were not met:
 $libmaus2digests_PKG_ERRORS
@@ -17121,12 +17161,12 @@ if test -n "$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 >= 2.0.489\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.489") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.489" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17138,12 +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 >= 2.0.489\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.489") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.489" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17164,14 +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 >= 2.0.489" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
         else 
-	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.489" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2seqchksumsfactory_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.489) were not met:
+	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.650) were not met:
 $libmaus2seqchksumsfactory_PKG_ERRORS
@@ -17446,12 +17486,12 @@ if test -n "$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 >= 2.0.489\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.489") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.489" 2>/dev/null`
+  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17463,12 +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 >= 2.0.489\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.489") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.489" 2>/dev/null`
+  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17489,14 +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 >= 2.0.489" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
         else 
-	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.489" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2irods_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.489) were not met:
+	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.650) were not met:
 $libmaus2irods_PKG_ERRORS
@@ -17997,10 +18037,6 @@ PACKAGE_VERSION=${VERSION}
-
-
-
-
 #
@@ -18548,7 +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 2.0.89, which was
+This file was extended by biobambam2 $as_me 2.0.127, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -18615,7 +18651,7 @@ _ACEOF
 cat >>$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 2.0.89
+biobambam2 config.status 2.0.127
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
@@ -19742,6 +19778,7 @@ $as_echo "$as_me: executing $ac_file commands" >&6;}
     cat <<_LT_EOF >> "$cfgfile"
 #! $SHELL
 # Generated automatically by $as_me ($PACKAGE) $VERSION
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
 # NOTE: Changes made to this file will be lost: look at ltmain.sh.
 # Provide generalized library-building support services.

autom4te.cache/output.1

 @%:@! /bin/sh
 @%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.95.
+@%:@ 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='2.0.95'
-PACKAGE_STRING='biobambam2 2.0.95'
+PACKAGE_VERSION='2.0.128'
+PACKAGE_STRING='biobambam2 2.0.128'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='http://www.sanger.ac.uk'
@@ -646,10 +646,6 @@ BIOBAMBAM_HAVE_XERCES_C
 TESTDIR
 BLASTXMLTOBAMNOINSTEXP
 BLASTXMLTOBAMINSTEXP
-BAMALIGNMENTOFFSETSNOINSTEXP
-BAMALIGNMENTOFFSETSINSTEXP
-BAMPARSORTNOINSTEXP
-BAMPARSORTINSTEXP
 BAMREFDEPTHPEAKS
 LIFTINGWAVELETTRANSFORMDEFINE
 LIBMAUS2IRODSDEFINE
@@ -819,6 +815,7 @@ enable_debug
 enable_profile
 enable_fast
 enable_install_experimental
+enable_asan
 with_libmaus2
 with_liftingwavelettransform
 with_xerces_c
@@ -1403,7 +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 2.0.95 to adapt to many kinds of systems.
+\`configure' configures biobambam2 2.0.128 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1475,7 +1472,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of biobambam2 2.0.95:";;
+     short | recursive ) echo "Configuration of biobambam2 2.0.128:";;
    esac
   cat <<\_ACEOF
@@ -1500,6 +1497,7 @@ Optional Features:
   --enable-fast           disable evaluation of assertions (default no)
   --enable-install-experimental 
                           install experimental programs (default no)
+  --enable-asan           enable address sanitizer in debug mode (default no)
 Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
@@ -1633,7 +1631,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-biobambam2 configure 2.0.95
+biobambam2 configure 2.0.128
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2074,7 +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 2.0.95, 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 $@
@@ -11974,7 +11972,7 @@ fi
 # Define the identity of the package.
  PACKAGE='biobambam2'
- VERSION='2.0.95'
+ VERSION='2.0.128'
 cat >>confdefs.h <<_ACEOF
@@ -12248,16 +12246,16 @@ else
   install_experimental=no
 fi
-
-if test "${install_experimental}" = "yes" ; then
-	BAMPARSORTINSTEXP=bamparsort
-	BAMALIGNMENTOFFSETSINSTEXP=bamalignmentoffsets
+@%:@ Check whether --enable-asan was given.
+if test "${enable_asan+set}" = set; then :
+  enableval=$enable_asan; enableasan=${enableval}
 else
-	BAMPARSORTNOINSTEXP=bamparsort
-	BAMALIGNMENTOFFSETSNOINSTEXP=bamalignmentoffsets
+  enableasan=no
 fi
+
+
 # check for C compiler
 CFLAGS_SAVE="${CFLAGS}"
 CFLAGS=""
@@ -16589,6 +16587,48 @@ fi
 CXXFLAGS="${CXXFLAGS_SAVE}"
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+CXXFLAGS_SAVE="${CXXFLAGS}"
+CXXFLAGS="-fsanitize=address"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C++ compiler supports the -fsanitize=address flag" >&5
+$as_echo_n "checking whether the C++ compiler supports the -fsanitize=address flag... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+  sanitizeaddress=yes
+else
+  sanitizeaddress=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: ${sanitizeaddress}" >&5
+$as_echo "${sanitizeaddress}" >&6; }
+CXXFLAGS="${CXXFLAGS_SAVE}"
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+if test \( "${sanitizeaddress}" = "yes" \) -a \( "${enableasan}" = "yes" \) ; then
+	CXXFLAGS="${CXXFLAGS} -fsanitize=address"
+	CFLAGS="${CFLAGS} -fsanitize=address"
+fi
+
 if test "${debug}" = "yes" ; then
 	CXXDEBUGFLAGS="-g -O0"
 	CDEBUGFLAGS="-g -O0"
@@ -16939,12 +16979,12 @@ if test -n "$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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -16956,12 +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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -16982,14 +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 >= 2.0.606" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
         else 
-	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.606" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2 >= 2.0.606) were not met:
+	as_fn_error $? "Package requirements (libmaus2 >= 2.0.650) were not met:
 $libmaus2_PKG_ERRORS
@@ -17030,12 +17070,12 @@ if test -n "$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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17047,12 +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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17073,14 +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 >= 2.0.606" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
         else 
-	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.606" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2digests_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.606) were not met:
+	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.650) were not met:
 $libmaus2digests_PKG_ERRORS
@@ -17121,12 +17161,12 @@ if test -n "$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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17138,12 +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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17164,14 +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 >= 2.0.606" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
         else 
-	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.606" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2seqchksumsfactory_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.606) were not met:
+	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.650) were not met:
 $libmaus2seqchksumsfactory_PKG_ERRORS
@@ -17446,12 +17486,12 @@ if test -n "$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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17463,12 +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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17489,14 +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 >= 2.0.606" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
         else 
-	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.606" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2irods_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.606) were not met:
+	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.650) were not met:
 $libmaus2irods_PKG_ERRORS
@@ -17984,10 +18024,6 @@ PACKAGE_VERSION=${VERSION}
-
-
-
-
 #
@@ -18535,7 +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 2.0.95, 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    = $CONFIG_FILES
@@ -18602,7 +18638,7 @@ _ACEOF
 cat >>$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 2.0.95
+biobambam2 config.status 2.0.128
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
@@ -19729,6 +19765,7 @@ $as_echo "$as_me: executing $ac_file commands" >&6;}
     cat <<_LT_EOF >> "$cfgfile"
 #! $SHELL
 # Generated automatically by $as_me ($PACKAGE) $VERSION
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
 # NOTE: Changes made to this file will be lost: look at ltmain.sh.
 # Provide generalized library-building support services.

autom4te.cache/output.2

 @%:@! /bin/sh
 @%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.95.
+@%:@ 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='2.0.95'
-PACKAGE_STRING='biobambam2 2.0.95'
+PACKAGE_VERSION='2.0.128'
+PACKAGE_STRING='biobambam2 2.0.128'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='http://www.sanger.ac.uk'
@@ -646,10 +646,6 @@ BIOBAMBAM_HAVE_XERCES_C
 TESTDIR
 BLASTXMLTOBAMNOINSTEXP
 BLASTXMLTOBAMINSTEXP
-BAMALIGNMENTOFFSETSNOINSTEXP
-BAMALIGNMENTOFFSETSINSTEXP
-BAMPARSORTNOINSTEXP
-BAMPARSORTINSTEXP
 BAMREFDEPTHPEAKS
 LIFTINGWAVELETTRANSFORMDEFINE
 LIBMAUS2IRODSDEFINE
@@ -819,6 +815,7 @@ enable_debug
 enable_profile
 enable_fast
 enable_install_experimental
+enable_asan
 with_libmaus2
 with_liftingwavelettransform
 with_xerces_c
@@ -1403,7 +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 2.0.95 to adapt to many kinds of systems.
+\`configure' configures biobambam2 2.0.128 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1475,7 +1472,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of biobambam2 2.0.95:";;
+     short | recursive ) echo "Configuration of biobambam2 2.0.128:";;
    esac
   cat <<\_ACEOF
@@ -1500,6 +1497,7 @@ Optional Features:
   --enable-fast           disable evaluation of assertions (default no)
   --enable-install-experimental 
                           install experimental programs (default no)
+  --enable-asan           enable address sanitizer in debug mode (default no)
 Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
@@ -1633,7 +1631,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-biobambam2 configure 2.0.95
+biobambam2 configure 2.0.128
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2074,7 +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 2.0.95, 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 $@
@@ -11974,7 +11972,7 @@ fi
 # Define the identity of the package.
  PACKAGE='biobambam2'
- VERSION='2.0.95'
+ VERSION='2.0.128'
 cat >>confdefs.h <<_ACEOF
@@ -12248,16 +12246,16 @@ else
   install_experimental=no
 fi
-
-if test "${install_experimental}" = "yes" ; then
-	BAMPARSORTINSTEXP=bamparsort
-	BAMALIGNMENTOFFSETSINSTEXP=bamalignmentoffsets
+@%:@ Check whether --enable-asan was given.
+if test "${enable_asan+set}" = set; then :
+  enableval=$enable_asan; enableasan=${enableval}
 else
-	BAMPARSORTNOINSTEXP=bamparsort
-	BAMALIGNMENTOFFSETSNOINSTEXP=bamalignmentoffsets
+  enableasan=no
 fi
+
+
 # check for C compiler
 CFLAGS_SAVE="${CFLAGS}"
 CFLAGS=""
@@ -16589,6 +16587,48 @@ fi
 CXXFLAGS="${CXXFLAGS_SAVE}"
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+CXXFLAGS_SAVE="${CXXFLAGS}"
+CXXFLAGS="-fsanitize=address"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C++ compiler supports the -fsanitize=address flag" >&5
+$as_echo_n "checking whether the C++ compiler supports the -fsanitize=address flag... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+  sanitizeaddress=yes
+else
+  sanitizeaddress=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: ${sanitizeaddress}" >&5
+$as_echo "${sanitizeaddress}" >&6; }
+CXXFLAGS="${CXXFLAGS_SAVE}"
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+if test \( "${sanitizeaddress}" = "yes" \) -a \( "${enableasan}" = "yes" \) ; then
+	CXXFLAGS="${CXXFLAGS} -fsanitize=address"
+	CFLAGS="${CFLAGS} -fsanitize=address"
+fi
+
 if test "${debug}" = "yes" ; then
 	CXXDEBUGFLAGS="-g -O0"
 	CDEBUGFLAGS="-g -O0"
@@ -16939,12 +16979,12 @@ if test -n "$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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -16956,12 +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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -16982,14 +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 >= 2.0.606" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
         else 
-	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.606" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2 >= 2.0.606) were not met:
+	as_fn_error $? "Package requirements (libmaus2 >= 2.0.650) were not met:
 $libmaus2_PKG_ERRORS
@@ -17030,12 +17070,12 @@ if test -n "$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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17047,12 +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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17073,14 +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 >= 2.0.606" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
         else 
-	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.606" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2digests_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.606) were not met:
+	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.650) were not met:
 $libmaus2digests_PKG_ERRORS
@@ -17121,12 +17161,12 @@ if test -n "$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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17138,12 +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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17164,14 +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 >= 2.0.606" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
         else 
-	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.606" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2seqchksumsfactory_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.606) were not met:
+	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.650) were not met:
 $libmaus2seqchksumsfactory_PKG_ERRORS
@@ -17446,12 +17486,12 @@ if test -n "$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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17463,12 +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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes 
 else
   pkg_failed=yes
@@ -17489,14 +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 >= 2.0.606" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
         else 
-	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.606" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2irods_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.606) were not met:
+	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.650) were not met:
 $libmaus2irods_PKG_ERRORS
@@ -17984,10 +18024,6 @@ PACKAGE_VERSION=${VERSION}
-
-
-
-
 #
@@ -18535,7 +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 2.0.95, 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    = $CONFIG_FILES
@@ -18602,7 +18638,7 @@ _ACEOF
 cat >>$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 2.0.95
+biobambam2 config.status 2.0.128
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
@@ -19729,6 +19765,7 @@ $as_echo "$as_me: executing $ac_file commands" >&6;}
     cat <<_LT_EOF >> "$cfgfile"
 #! $SHELL
 # Generated automatically by $as_me ($PACKAGE) $VERSION
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
 # NOTE: Changes made to this file will be lost: look at ltmain.sh.
 # Provide generalized library-building support services.

bumplibmausversion.sh

@@ -13,10 +13,4 @@ git add configure.ac
 git commit -m "bump libmaus2 version"
 git push
 
-git checkout experimental-debian
-sed -i -e "s/libmaus2-dev (>= [0-9][0-9]*.[0-9][0-9]*.[0-9][0-9]*)/libmaus2-dev (>= ${LIBMAUS2VERSION})/" debian/control
-git add debian/control
-git commit -m "bump libmaus2 version"
-git push
-
 git checkout experimental

bumpversion.sh

@@ -4,6 +4,8 @@ FIRST=`echo $VERSION | awk -F'.' '{print $1}'`
 SECOND=`echo $VERSION | awk -F'.' '{print $2}'`
 THIRD=`echo $VERSION | awk -F'.' '{print $3}'`
 NEXTTHIRD=`expr ${THIRD} + 1`
+export DEBEMAIL=germant@miltenyibiotec.de
+export DEBFULLNAME="German Tischler-Höhle"
 
 function cleanup
 {
@@ -34,30 +36,14 @@ fi
 awk -v first=${FIRST} -v second=${SECOND} -v third=${THIRD} '/^AC_INIT/ {gsub(first"."second"."third,first"."second"."third+1);print} ; !/^AC_INIT/{print}' < configure.ac > configure.ac.tmp
 mv configure.ac.tmp configure.ac
 
-# commit file
-git add configure.ac
-git commit -F "${COMMITFILE}"
-git push
-
-# switch to experimental debian branch
-git checkout experimental-debian
-git pull
-git merge experimental
+# update change log
+CHANGELOG=ChangeLog dch --distribution unstable -v ${FIRST}.${SECOND}.${NEXTTHIRD}-1
 
-# create change log message
-pushd debian
-export DEBEMAIL=tischler@mpi-cbg.de
-export DEBFULLNAME="German Tischler"
-dch --distribution unstable -v ${FIRST}.${SECOND}.${NEXTTHIRD}
-dch --release
-popd
-git add debian/changelog
+# commit file
+git add configure.ac ChangeLog
 git commit -F "${COMMITFILE}"
 git push
 
-# back to experimental branch
-git checkout experimental
-
 TAG=biobambam2_experimental_${FIRST}_${SECOND}_${NEXTTHIRD}
 git tag -a ${TAG} -m "biobambam2 experimental version ${FIRST}_${SECOND}_${NEXTTHIRD}"
 git push origin ${TAG}

bundle.sh

+#!/bin/bash
+D=`date "+%Y_%m_%d"`
+P=`head -n 1 configure.ac | sed "s|AC_INIT(||;s|,.*||"`
+set -x
+git bundle create ../${P}_${D}.bundle --branches --tags

configure

 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for biobambam2 2.0.95.
+# 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='2.0.95'
-PACKAGE_STRING='biobambam2 2.0.95'
+PACKAGE_VERSION='2.0.128'
+PACKAGE_STRING='biobambam2 2.0.128'
 PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
 PACKAGE_URL='http://www.sanger.ac.uk'
@@ -646,10 +646,6 @@ BIOBAMBAM_HAVE_XERCES_C
 TESTDIR
 BLASTXMLTOBAMNOINSTEXP
 BLASTXMLTOBAMINSTEXP
-BAMALIGNMENTOFFSETSNOINSTEXP
-BAMALIGNMENTOFFSETSINSTEXP
-BAMPARSORTNOINSTEXP
-BAMPARSORTINSTEXP
 BAMREFDEPTHPEAKS
 LIFTINGWAVELETTRANSFORMDEFINE
 LIBMAUS2IRODSDEFINE
@@ -819,6 +815,7 @@ enable_debug
 enable_profile
 enable_fast
 enable_install_experimental
+enable_asan
 with_libmaus2
 with_liftingwavelettransform
 with_xerces_c
@@ -1403,7 +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 2.0.95 to adapt to many kinds of systems.
+\`configure' configures biobambam2 2.0.128 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1475,7 +1472,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of biobambam2 2.0.95:";;
+     short | recursive ) echo "Configuration of biobambam2 2.0.128:";;
    esac
   cat <<\_ACEOF
@@ -1500,6 +1497,7 @@ Optional Features:
   --enable-fast           disable evaluation of assertions (default no)
   --enable-install-experimental
                           install experimental programs (default no)
+  --enable-asan           enable address sanitizer in debug mode (default no)
 Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
@@ -1633,7 +1631,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-biobambam2 configure 2.0.95
+biobambam2 configure 2.0.128
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2074,7 +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 2.0.95, 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 $@
@@ -11974,7 +11972,7 @@ fi
 # Define the identity of the package.
  PACKAGE='biobambam2'
- VERSION='2.0.95'
+ VERSION='2.0.128'
 cat >>confdefs.h <<_ACEOF
@@ -12248,16 +12246,16 @@ else
   install_experimental=no
 fi
-
-if test "${install_experimental}" = "yes" ; then
-	BAMPARSORTINSTEXP=bamparsort
-	BAMALIGNMENTOFFSETSINSTEXP=bamalignmentoffsets
+# Check whether --enable-asan was given.
+if test "${enable_asan+set}" = set; then :
+  enableval=$enable_asan; enableasan=${enableval}
 else
-	BAMPARSORTNOINSTEXP=bamparsort
-	BAMALIGNMENTOFFSETSNOINSTEXP=bamalignmentoffsets
+  enableasan=no
 fi
+
+
 # check for C compiler
 CFLAGS_SAVE="${CFLAGS}"
 CFLAGS=""
@@ -16589,6 +16587,48 @@ fi
 CXXFLAGS="${CXXFLAGS_SAVE}"
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+CXXFLAGS_SAVE="${CXXFLAGS}"
+CXXFLAGS="-fsanitize=address"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C++ compiler supports the -fsanitize=address flag" >&5
+$as_echo_n "checking whether the C++ compiler supports the -fsanitize=address flag... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+  sanitizeaddress=yes
+else
+  sanitizeaddress=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: ${sanitizeaddress}" >&5
+$as_echo "${sanitizeaddress}" >&6; }
+CXXFLAGS="${CXXFLAGS_SAVE}"
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+if test \( "${sanitizeaddress}" = "yes" \) -a \( "${enableasan}" = "yes" \) ; then
+	CXXFLAGS="${CXXFLAGS} -fsanitize=address"
+	CFLAGS="${CFLAGS} -fsanitize=address"
+fi
+
 if test "${debug}" = "yes" ; then
 	CXXDEBUGFLAGS="-g -O0"
 	CDEBUGFLAGS="-g -O0"
@@ -16939,12 +16979,12 @@ if test -n "$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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -16956,12 +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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -16982,14 +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 >= 2.0.606" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
         else
-	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.606" 2>&1`
+	        libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2 >= 2.0.606) were not met:
+	as_fn_error $? "Package requirements (libmaus2 >= 2.0.650) were not met:
 $libmaus2_PKG_ERRORS
@@ -17030,12 +17070,12 @@ if test -n "$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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -17047,12 +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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -17073,14 +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 >= 2.0.606" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
         else
-	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.606" 2>&1`
+	        libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2digests_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.606) were not met:
+	as_fn_error $? "Package requirements (libmaus2digests >= 2.0.650) were not met:
 $libmaus2digests_PKG_ERRORS
@@ -17121,12 +17161,12 @@ if test -n "$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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -17138,12 +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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -17164,14 +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 >= 2.0.606" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
         else
-	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.606" 2>&1`
+	        libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2seqchksumsfactory_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.606) were not met:
+	as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.650) were not met:
 $libmaus2seqchksumsfactory_PKG_ERRORS
@@ -17446,12 +17486,12 @@ if test -n "$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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -17463,12 +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 >= 2.0.606\""; } >&5
-  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.606") 2>&5
+    { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
+  ($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
   ac_status=$?
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
-  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.606" 2>/dev/null`
+  pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.650" 2>/dev/null`
 		      test "x$?" != "x0" && pkg_failed=yes
 else
   pkg_failed=yes
@@ -17489,14 +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 >= 2.0.606" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
         else
-	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.606" 2>&1`
+	        libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
         fi
 	# Put the nasty error message in config.log where it belongs
 	echo "$libmaus2irods_PKG_ERRORS" >&5
-	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.606) were not met:
+	as_fn_error $? "Package requirements (libmaus2irods >= 2.0.650) were not met:
 $libmaus2irods_PKG_ERRORS
@@ -17984,10 +18024,6 @@ PACKAGE_VERSION=${VERSION}
-
-
-
-
 #
@@ -18535,7 +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 2.0.95, 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    = $CONFIG_FILES
@@ -18602,7 +18638,7 @@ _ACEOF
 cat >>$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 2.0.95
+biobambam2 config.status 2.0.128
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
@@ -19729,6 +19765,7 @@ $as_echo "$as_me: executing $ac_file commands" >&6;}
     cat <<_LT_EOF >> "$cfgfile"
 #! $SHELL
 # Generated automatically by $as_me ($PACKAGE) $VERSION
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
 # NOTE: Changes made to this file will be lost: look at ltmain.sh.
 # Provide generalized library-building support services.

configure.ac

-AC_INIT(biobambam2,2.0.95,[tischler@mpi-cbg.de],[biobambam2],[http://www.sanger.ac.uk])
+AC_INIT(biobambam2,2.0.128,[tischler@mpi-cbg.de],[biobambam2],[http://www.sanger.ac.uk])
 AC_CANONICAL_SYSTEM
 AC_PROG_LIBTOOL
 
@@ -32,14 +32,13 @@ AC_ARG_ENABLE(fast,
 AC_ARG_ENABLE(install-experimental,
         AS_HELP_STRING([--enable-install-experimental],[install experimental programs (default no)]),
         [install_experimental=${enableval}],[install_experimental=no])
+AC_ARG_ENABLE(asan,
+        AS_HELP_STRING([--enable-asan],[enable address sanitizer in  debug mode (default no)]),
+        [enableasan=${enableval}],[enableasan=no])
 
-if test "${install_experimental}" = "yes" ; then
-	BAMPARSORTINSTEXP=bamparsort
-	BAMALIGNMENTOFFSETSINSTEXP=bamalignmentoffsets
-else
-	BAMPARSORTNOINSTEXP=bamparsort
-	BAMALIGNMENTOFFSETSNOINSTEXP=bamalignmentoffsets
-fi
+dnl if test "${install_experimental}" = "yes" ; then
+dnl else
+dnl fi
 
 
 # check for C compiler
@@ -62,6 +61,20 @@ CXXFLAGS=""
 AC_PROG_CXX
 CXXFLAGS="${CXXFLAGS_SAVE}"
 
+AC_LANG_PUSH([C++])
+CXXFLAGS_SAVE="${CXXFLAGS}"
+CXXFLAGS="-fsanitize=address"
+AC_MSG_CHECKING([whether the C++ compiler supports the -fsanitize=address flag])
+AC_TRY_COMPILE([],[],[sanitizeaddress=yes],[sanitizeaddress=no])
+AC_MSG_RESULT([${sanitizeaddress}])
+CXXFLAGS="${CXXFLAGS_SAVE}"
+AC_LANG_POP
+
+if test \( "${sanitizeaddress}" = "yes" \) -a \( "${enableasan}" = "yes" \) ; then
+	CXXFLAGS="${CXXFLAGS} -fsanitize=address"
+	CFLAGS="${CFLAGS} -fsanitize=address"
+fi
+
 if test "${debug}" = "yes" ; then
 	CXXDEBUGFLAGS="-g -O0"
 	CDEBUGFLAGS="-g -O0"
@@ -152,9 +165,9 @@ if test ! -z "${with_libmaus2}" ; then
 	fi
 fi
 
-PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.606])
-PKG_CHECK_MODULES([libmaus2digests],[libmaus2digests >= 2.0.606])
-PKG_CHECK_MODULES([libmaus2seqchksumsfactory],[libmaus2seqchksumsfactory >= 2.0.606])
+PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.650])
+PKG_CHECK_MODULES([libmaus2digests],[libmaus2digests >= 2.0.650])
+PKG_CHECK_MODULES([libmaus2seqchksumsfactory],[libmaus2seqchksumsfactory >= 2.0.650])
 
 if test ! -z "${with_libmaus2}" ; then
 	if test ! -z "${PKGCONFIGPATHSAVE}" ; then
@@ -289,7 +302,7 @@ if test "${have_libmaus2_irods}" = "yes" ; then
 		fi
 	fi
 
-	PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.606])
+	PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.650])
 
 	LIBMAUS2IRODSCPPFLAGS="${libmaus2irods_CFLAGS}"
 	LIBMAUS2IRODSLIBS="${libmaus2irods_LIBS}"
@@ -469,10 +482,6 @@ AC_SUBST([LIBMAUS2IRODSDEFINE])
 AC_SUBST([LIFTINGWAVELETTRANSFORMDEFINE])
 AC_SUBST([BAMREFDEPTHPEAKS])
 #
-AC_SUBST([BAMPARSORTINSTEXP])
-AC_SUBST([BAMPARSORTNOINSTEXP])
-AC_SUBST([BAMALIGNMENTOFFSETSINSTEXP])
-AC_SUBST([BAMALIGNMENTOFFSETSNOINSTEXP])
 AC_SUBST([BLASTXMLTOBAMINSTEXP])
 AC_SUBST([BLASTXMLTOBAMNOINSTEXP])
 AC_SUBST([TESTDIR])

debian/changelog

+biobambam2 (2.0.128-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Versioned Build-Depends: libmaus2-dev (>= 2.0.650)
+
+ -- Andreas Tille <tille@debian.org>  Wed, 07 Aug 2019 11:28:02 +0200
+
 biobambam2 (2.0.95-1) unstable; urgency=medium
 
   * Initial release (Closes: #926978)