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......@@ -37,7 +37,7 @@ src/kmerprob
src/fastqtobam
src/normalisefasta
src/fastabgzfextract
src/fastaexplode
src/fastaexplod
test/*.log
test/*.trs
src/*/.deps
......
ChangeLog
View file @ c9fb903f
biobambam2 (2.0.134-1) unstable; urgency=medium
* bump libmaus2 version
* be more verbose in bamrecalculatecigar when the input is not suitably sorted
*add fragmergepar option in bamsormadup to allow (some) control concerning the number of simultaneously open files used in duplicate marking
-- German Tischler-Höhle <germant@miltenyibiotec.de> Mon, 19 Aug 2019 15:18:51 +0200
biobambam2 (2.0.133-1) unstable; urgency=medium
* update libmaus2 version
-- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 16 Aug 2019 13:32:26 +0200
biobambam2 (2.0.132-1) unstable; urgency=medium
* use heaviest path per connected component as representative in bamconsensus
-- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 16 Aug 2019 13:14:32 +0200
biobambam2 (2.0.131-1) unstable; urgency=medium
* update help message in bamfilterk
* add bamfilterk
-- German Tischler-Höhle <germant@miltenyibiotec.de> Tue, 13 Aug 2019 09:36:30 +0200
biobambam2 (2.0.130-1) unstable; urgency=medium
* support numerical indexing in fastqtobam2
-- German Tischler-Höhle <germant@miltenyibiotec.de> Thu, 08 Aug 2019 11:13:12 +0200
biobambam2 (2.0.129-1) unstable; urgency=medium
* rename fastaexplode to fastaexplod
......
autom4te.cache/output.0
View file @ c9fb903f
@%:@! /bin/sh
@%:@ Guess values for system-dependent variables and create Makefiles.
@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.128.
@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.133.
@%:@
@%:@ Report bugs to <tischler@mpi-cbg.de>.
@%:@
......@@ -590,8 +590,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='biobambam2'
PACKAGE_TARNAME='biobambam2'
PACKAGE_VERSION='2.0.128'
PACKAGE_STRING='biobambam2 2.0.128'
PACKAGE_VERSION='2.0.133'
PACKAGE_STRING='biobambam2 2.0.133'
PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
PACKAGE_URL='http://www.sanger.ac.uk'
 
......@@ -1400,7 +1400,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
\`configure' configures biobambam2 2.0.128 to adapt to many kinds of systems.
\`configure' configures biobambam2 2.0.133 to adapt to many kinds of systems.
 
Usage: $0 [OPTION]... [VAR=VALUE]...
 
......@@ -1472,7 +1472,7 @@ fi
 
if test -n "$ac_init_help"; then
case $ac_init_help in
short | recursive ) echo "Configuration of biobambam2 2.0.128:";;
short | recursive ) echo "Configuration of biobambam2 2.0.133:";;
esac
cat <<\_ACEOF
 
......@@ -1631,7 +1631,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
biobambam2 configure 2.0.128
biobambam2 configure 2.0.133
generated by GNU Autoconf 2.69
 
Copyright (C) 2012 Free Software Foundation, Inc.
......@@ -2072,7 +2072,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
 
It was created by biobambam2 $as_me 2.0.128, which was
It was created by biobambam2 $as_me 2.0.133, which was
generated by GNU Autoconf 2.69. Invocation command line was
 
$ $0 $@
......@@ -11972,7 +11972,7 @@ fi
 
# Define the identity of the package.
PACKAGE='biobambam2'
VERSION='2.0.128'
VERSION='2.0.133'
 
 
cat >>confdefs.h <<_ACEOF
......@@ -16979,12 +16979,12 @@ if test -n "$libmaus2_CFLAGS"; then
pkg_cv_libmaus2_CFLAGS="$libmaus2_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.656\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.656") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.650" 2>/dev/null`
pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -16996,12 +16996,12 @@ if test -n "$libmaus2_LIBS"; then
pkg_cv_libmaus2_LIBS="$libmaus2_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.650\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.650") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.656\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.656") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.650" 2>/dev/null`
pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17022,14 +17022,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.656" 2>&1`
else
libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.650" 2>&1`
libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.656" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2 >= 2.0.650) were not met:
as_fn_error $? "Package requirements (libmaus2 >= 2.0.656) were not met:
 
$libmaus2_PKG_ERRORS
 
......@@ -17070,12 +17070,12 @@ if test -n "$libmaus2digests_CFLAGS"; then
pkg_cv_libmaus2digests_CFLAGS="$libmaus2digests_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.656\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.656") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.650" 2>/dev/null`
pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17087,12 +17087,12 @@ if test -n "$libmaus2digests_LIBS"; then
pkg_cv_libmaus2digests_LIBS="$libmaus2digests_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.650\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.650") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.656\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.656") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.650" 2>/dev/null`
pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17113,14 +17113,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.656" 2>&1`
else
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.650" 2>&1`
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.656" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2digests_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2digests >= 2.0.650) were not met:
as_fn_error $? "Package requirements (libmaus2digests >= 2.0.656) were not met:
 
$libmaus2digests_PKG_ERRORS
 
......@@ -17161,12 +17161,12 @@ if test -n "$libmaus2seqchksumsfactory_CFLAGS"; then
pkg_cv_libmaus2seqchksumsfactory_CFLAGS="$libmaus2seqchksumsfactory_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.656\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.656") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17178,12 +17178,12 @@ if test -n "$libmaus2seqchksumsfactory_LIBS"; then
pkg_cv_libmaus2seqchksumsfactory_LIBS="$libmaus2seqchksumsfactory_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.650\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.650") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.656\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.656") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17204,14 +17204,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.656" 2>&1`
else
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.650" 2>&1`
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.656" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2seqchksumsfactory_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.650) were not met:
as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.656) were not met:
 
$libmaus2seqchksumsfactory_PKG_ERRORS
 
......@@ -17486,12 +17486,12 @@ if test -n "$libmaus2irods_CFLAGS"; then
pkg_cv_libmaus2irods_CFLAGS="$libmaus2irods_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.656\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.656") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.650" 2>/dev/null`
pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17503,12 +17503,12 @@ if test -n "$libmaus2irods_LIBS"; then
pkg_cv_libmaus2irods_LIBS="$libmaus2irods_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.650\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.650") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.656\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.656") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.650" 2>/dev/null`
pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17529,14 +17529,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.656" 2>&1`
else
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.650" 2>&1`
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.656" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2irods_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2irods >= 2.0.650) were not met:
as_fn_error $? "Package requirements (libmaus2irods >= 2.0.656) were not met:
 
$libmaus2irods_PKG_ERRORS
 
......@@ -18584,7 +18584,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by biobambam2 $as_me 2.0.128, which was
This file was extended by biobambam2 $as_me 2.0.133, which was
generated by GNU Autoconf 2.69. Invocation command line was
 
CONFIG_FILES = $CONFIG_FILES
......@@ -18651,7 +18651,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
biobambam2 config.status 2.0.128
biobambam2 config.status 2.0.133
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
 
......
autom4te.cache/output.1
View file @ c9fb903f
@%:@! /bin/sh
@%:@ Guess values for system-dependent variables and create Makefiles.
@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.129.
@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.134.
@%:@
@%:@ Report bugs to <tischler@mpi-cbg.de>.
@%:@
......@@ -590,8 +590,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='biobambam2'
PACKAGE_TARNAME='biobambam2'
PACKAGE_VERSION='2.0.129'
PACKAGE_STRING='biobambam2 2.0.129'
PACKAGE_VERSION='2.0.134'
PACKAGE_STRING='biobambam2 2.0.134'
PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
PACKAGE_URL='http://www.sanger.ac.uk'
 
......@@ -1400,7 +1400,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
\`configure' configures biobambam2 2.0.129 to adapt to many kinds of systems.
\`configure' configures biobambam2 2.0.134 to adapt to many kinds of systems.
 
Usage: $0 [OPTION]... [VAR=VALUE]...
 
......@@ -1472,7 +1472,7 @@ fi
 
if test -n "$ac_init_help"; then
case $ac_init_help in
short | recursive ) echo "Configuration of biobambam2 2.0.129:";;
short | recursive ) echo "Configuration of biobambam2 2.0.134:";;
esac
cat <<\_ACEOF
 
......@@ -1631,7 +1631,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
biobambam2 configure 2.0.129
biobambam2 configure 2.0.134
generated by GNU Autoconf 2.69
 
Copyright (C) 2012 Free Software Foundation, Inc.
......@@ -2072,7 +2072,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
 
It was created by biobambam2 $as_me 2.0.129, which was
It was created by biobambam2 $as_me 2.0.134, which was
generated by GNU Autoconf 2.69. Invocation command line was
 
$ $0 $@
......@@ -11972,7 +11972,7 @@ fi
 
# Define the identity of the package.
PACKAGE='biobambam2'
VERSION='2.0.129'
VERSION='2.0.134'
 
 
cat >>confdefs.h <<_ACEOF
......@@ -16979,12 +16979,12 @@ if test -n "$libmaus2_CFLAGS"; then
pkg_cv_libmaus2_CFLAGS="$libmaus2_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -16996,12 +16996,12 @@ if test -n "$libmaus2_LIBS"; then
pkg_cv_libmaus2_LIBS="$libmaus2_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17022,14 +17022,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.653" 2>&1`
libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.657" 2>&1`
else
libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.653" 2>&1`
libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.657" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2 >= 2.0.653) were not met:
as_fn_error $? "Package requirements (libmaus2 >= 2.0.657) were not met:
 
$libmaus2_PKG_ERRORS
 
......@@ -17070,12 +17070,12 @@ if test -n "$libmaus2digests_CFLAGS"; then
pkg_cv_libmaus2digests_CFLAGS="$libmaus2digests_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17087,12 +17087,12 @@ if test -n "$libmaus2digests_LIBS"; then
pkg_cv_libmaus2digests_LIBS="$libmaus2digests_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17113,14 +17113,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.653" 2>&1`
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.657" 2>&1`
else
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.653" 2>&1`
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.657" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2digests_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2digests >= 2.0.653) were not met:
as_fn_error $? "Package requirements (libmaus2digests >= 2.0.657) were not met:
 
$libmaus2digests_PKG_ERRORS
 
......@@ -17161,12 +17161,12 @@ if test -n "$libmaus2seqchksumsfactory_CFLAGS"; then
pkg_cv_libmaus2seqchksumsfactory_CFLAGS="$libmaus2seqchksumsfactory_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17178,12 +17178,12 @@ if test -n "$libmaus2seqchksumsfactory_LIBS"; then
pkg_cv_libmaus2seqchksumsfactory_LIBS="$libmaus2seqchksumsfactory_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17204,14 +17204,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>&1`
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.657" 2>&1`
else
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>&1`
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.657" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2seqchksumsfactory_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.653) were not met:
as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.657) were not met:
 
$libmaus2seqchksumsfactory_PKG_ERRORS
 
......@@ -17486,12 +17486,12 @@ if test -n "$libmaus2irods_CFLAGS"; then
pkg_cv_libmaus2irods_CFLAGS="$libmaus2irods_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17503,12 +17503,12 @@ if test -n "$libmaus2irods_LIBS"; then
pkg_cv_libmaus2irods_LIBS="$libmaus2irods_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17529,14 +17529,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.653" 2>&1`
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.657" 2>&1`
else
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.653" 2>&1`
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.657" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2irods_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2irods >= 2.0.653) were not met:
as_fn_error $? "Package requirements (libmaus2irods >= 2.0.657) were not met:
 
$libmaus2irods_PKG_ERRORS
 
......@@ -18571,7 +18571,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by biobambam2 $as_me 2.0.129, which was
This file was extended by biobambam2 $as_me 2.0.134, which was
generated by GNU Autoconf 2.69. Invocation command line was
 
CONFIG_FILES = $CONFIG_FILES
......@@ -18638,7 +18638,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
biobambam2 config.status 2.0.129
biobambam2 config.status 2.0.134
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
 
......
autom4te.cache/output.2
View file @ c9fb903f
@%:@! /bin/sh
@%:@ Guess values for system-dependent variables and create Makefiles.
@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.129.
@%:@ Generated by GNU Autoconf 2.69 for biobambam2 2.0.134.
@%:@
@%:@ Report bugs to <tischler@mpi-cbg.de>.
@%:@
......@@ -590,8 +590,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='biobambam2'
PACKAGE_TARNAME='biobambam2'
PACKAGE_VERSION='2.0.129'
PACKAGE_STRING='biobambam2 2.0.129'
PACKAGE_VERSION='2.0.134'
PACKAGE_STRING='biobambam2 2.0.134'
PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
PACKAGE_URL='http://www.sanger.ac.uk'
 
......@@ -1400,7 +1400,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
\`configure' configures biobambam2 2.0.129 to adapt to many kinds of systems.
\`configure' configures biobambam2 2.0.134 to adapt to many kinds of systems.
 
Usage: $0 [OPTION]... [VAR=VALUE]...
 
......@@ -1472,7 +1472,7 @@ fi
 
if test -n "$ac_init_help"; then
case $ac_init_help in
short | recursive ) echo "Configuration of biobambam2 2.0.129:";;
short | recursive ) echo "Configuration of biobambam2 2.0.134:";;
esac
cat <<\_ACEOF
 
......@@ -1631,7 +1631,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
biobambam2 configure 2.0.129
biobambam2 configure 2.0.134
generated by GNU Autoconf 2.69
 
Copyright (C) 2012 Free Software Foundation, Inc.
......@@ -2072,7 +2072,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
 
It was created by biobambam2 $as_me 2.0.129, which was
It was created by biobambam2 $as_me 2.0.134, which was
generated by GNU Autoconf 2.69. Invocation command line was
 
$ $0 $@
......@@ -11972,7 +11972,7 @@ fi
 
# Define the identity of the package.
PACKAGE='biobambam2'
VERSION='2.0.129'
VERSION='2.0.134'
 
 
cat >>confdefs.h <<_ACEOF
......@@ -16979,12 +16979,12 @@ if test -n "$libmaus2_CFLAGS"; then
pkg_cv_libmaus2_CFLAGS="$libmaus2_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -16996,12 +16996,12 @@ if test -n "$libmaus2_LIBS"; then
pkg_cv_libmaus2_LIBS="$libmaus2_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17022,14 +17022,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.653" 2>&1`
libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.657" 2>&1`
else
libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.653" 2>&1`
libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.657" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2 >= 2.0.653) were not met:
as_fn_error $? "Package requirements (libmaus2 >= 2.0.657) were not met:
 
$libmaus2_PKG_ERRORS
 
......@@ -17070,12 +17070,12 @@ if test -n "$libmaus2digests_CFLAGS"; then
pkg_cv_libmaus2digests_CFLAGS="$libmaus2digests_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17087,12 +17087,12 @@ if test -n "$libmaus2digests_LIBS"; then
pkg_cv_libmaus2digests_LIBS="$libmaus2digests_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17113,14 +17113,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.653" 2>&1`
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.657" 2>&1`
else
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.653" 2>&1`
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.657" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2digests_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2digests >= 2.0.653) were not met:
as_fn_error $? "Package requirements (libmaus2digests >= 2.0.657) were not met:
 
$libmaus2digests_PKG_ERRORS
 
......@@ -17161,12 +17161,12 @@ if test -n "$libmaus2seqchksumsfactory_CFLAGS"; then
pkg_cv_libmaus2seqchksumsfactory_CFLAGS="$libmaus2seqchksumsfactory_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17178,12 +17178,12 @@ if test -n "$libmaus2seqchksumsfactory_LIBS"; then
pkg_cv_libmaus2seqchksumsfactory_LIBS="$libmaus2seqchksumsfactory_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17204,14 +17204,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>&1`
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.657" 2>&1`
else
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>&1`
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.657" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2seqchksumsfactory_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.653) were not met:
as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.657) were not met:
 
$libmaus2seqchksumsfactory_PKG_ERRORS
 
......@@ -17486,12 +17486,12 @@ if test -n "$libmaus2irods_CFLAGS"; then
pkg_cv_libmaus2irods_CFLAGS="$libmaus2irods_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17503,12 +17503,12 @@ if test -n "$libmaus2irods_LIBS"; then
pkg_cv_libmaus2irods_LIBS="$libmaus2irods_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17529,14 +17529,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.653" 2>&1`
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.657" 2>&1`
else
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.653" 2>&1`
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.657" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2irods_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2irods >= 2.0.653) were not met:
as_fn_error $? "Package requirements (libmaus2irods >= 2.0.657) were not met:
 
$libmaus2irods_PKG_ERRORS
 
......@@ -18571,7 +18571,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by biobambam2 $as_me 2.0.129, which was
This file was extended by biobambam2 $as_me 2.0.134, which was
generated by GNU Autoconf 2.69. Invocation command line was
 
CONFIG_FILES = $CONFIG_FILES
......@@ -18638,7 +18638,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
biobambam2 config.status 2.0.129
biobambam2 config.status 2.0.134
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
 
......
autom4te.cache/requests
View file @ c9fb903f
This diff is collapsed.
autom4te.cache/traces.0
View file @ c9fb903f
......@@ -2905,36 +2905,36 @@ m4trace:configure.ac:139: -1- m4_pattern_allow([^PKG_CONFIG_PATH$])
m4trace:configure.ac:139: -1- m4_pattern_allow([^PKG_CONFIG_LIBDIR$])
m4trace:configure.ac:139: -1- m4_pattern_allow([^PKG_CONFIG$])
m4trace:configure.ac:147: -1- m4_pattern_allow([^STDC_HEADERS$])
m4trace:configure.ac:168: -1- PKG_CHECK_MODULES([libmaus2], [libmaus2 >= 2.0.650])
m4trace:configure.ac:168: -1- PKG_CHECK_MODULES([libmaus2], [libmaus2 >= 2.0.656])
m4trace:configure.ac:168: -1- m4_pattern_allow([^libmaus2_CFLAGS$])
m4trace:configure.ac:168: -1- m4_pattern_allow([^libmaus2_LIBS$])
m4trace:configure.ac:168: -1- PKG_CHECK_EXISTS([libmaus2 >= 2.0.650], [pkg_cv_[]libmaus2_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2 >= 2.0.650" 2>/dev/null`
m4trace:configure.ac:168: -1- PKG_CHECK_EXISTS([libmaus2 >= 2.0.656], [pkg_cv_[]libmaus2_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2 >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:168: -1- PKG_CHECK_EXISTS([libmaus2 >= 2.0.650], [pkg_cv_[]libmaus2_LIBS=`$PKG_CONFIG --[]libs "libmaus2 >= 2.0.650" 2>/dev/null`
m4trace:configure.ac:168: -1- PKG_CHECK_EXISTS([libmaus2 >= 2.0.656], [pkg_cv_[]libmaus2_LIBS=`$PKG_CONFIG --[]libs "libmaus2 >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:168: -1- _PKG_SHORT_ERRORS_SUPPORTED
m4trace:configure.ac:169: -1- PKG_CHECK_MODULES([libmaus2digests], [libmaus2digests >= 2.0.650])
m4trace:configure.ac:169: -1- PKG_CHECK_MODULES([libmaus2digests], [libmaus2digests >= 2.0.656])
m4trace:configure.ac:169: -1- m4_pattern_allow([^libmaus2digests_CFLAGS$])
m4trace:configure.ac:169: -1- m4_pattern_allow([^libmaus2digests_LIBS$])
m4trace:configure.ac:169: -1- PKG_CHECK_EXISTS([libmaus2digests >= 2.0.650], [pkg_cv_[]libmaus2digests_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2digests >= 2.0.650" 2>/dev/null`
m4trace:configure.ac:169: -1- PKG_CHECK_EXISTS([libmaus2digests >= 2.0.656], [pkg_cv_[]libmaus2digests_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2digests >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:169: -1- PKG_CHECK_EXISTS([libmaus2digests >= 2.0.650], [pkg_cv_[]libmaus2digests_LIBS=`$PKG_CONFIG --[]libs "libmaus2digests >= 2.0.650" 2>/dev/null`
m4trace:configure.ac:169: -1- PKG_CHECK_EXISTS([libmaus2digests >= 2.0.656], [pkg_cv_[]libmaus2digests_LIBS=`$PKG_CONFIG --[]libs "libmaus2digests >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:169: -1- _PKG_SHORT_ERRORS_SUPPORTED
m4trace:configure.ac:170: -1- PKG_CHECK_MODULES([libmaus2seqchksumsfactory], [libmaus2seqchksumsfactory >= 2.0.650])
m4trace:configure.ac:170: -1- PKG_CHECK_MODULES([libmaus2seqchksumsfactory], [libmaus2seqchksumsfactory >= 2.0.656])
m4trace:configure.ac:170: -1- m4_pattern_allow([^libmaus2seqchksumsfactory_CFLAGS$])
m4trace:configure.ac:170: -1- m4_pattern_allow([^libmaus2seqchksumsfactory_LIBS$])
m4trace:configure.ac:170: -1- PKG_CHECK_EXISTS([libmaus2seqchksumsfactory >= 2.0.650], [pkg_cv_[]libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
m4trace:configure.ac:170: -1- PKG_CHECK_EXISTS([libmaus2seqchksumsfactory >= 2.0.656], [pkg_cv_[]libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2seqchksumsfactory >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:170: -1- PKG_CHECK_EXISTS([libmaus2seqchksumsfactory >= 2.0.650], [pkg_cv_[]libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --[]libs "libmaus2seqchksumsfactory >= 2.0.650" 2>/dev/null`
m4trace:configure.ac:170: -1- PKG_CHECK_EXISTS([libmaus2seqchksumsfactory >= 2.0.656], [pkg_cv_[]libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --[]libs "libmaus2seqchksumsfactory >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:170: -1- _PKG_SHORT_ERRORS_SUPPORTED
m4trace:configure.ac:305: -1- PKG_CHECK_MODULES([libmaus2irods], [libmaus2irods >= 2.0.650])
m4trace:configure.ac:305: -1- PKG_CHECK_MODULES([libmaus2irods], [libmaus2irods >= 2.0.656])
m4trace:configure.ac:305: -1- m4_pattern_allow([^libmaus2irods_CFLAGS$])
m4trace:configure.ac:305: -1- m4_pattern_allow([^libmaus2irods_LIBS$])
m4trace:configure.ac:305: -1- PKG_CHECK_EXISTS([libmaus2irods >= 2.0.650], [pkg_cv_[]libmaus2irods_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2irods >= 2.0.650" 2>/dev/null`
m4trace:configure.ac:305: -1- PKG_CHECK_EXISTS([libmaus2irods >= 2.0.656], [pkg_cv_[]libmaus2irods_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2irods >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:305: -1- PKG_CHECK_EXISTS([libmaus2irods >= 2.0.650], [pkg_cv_[]libmaus2irods_LIBS=`$PKG_CONFIG --[]libs "libmaus2irods >= 2.0.650" 2>/dev/null`
m4trace:configure.ac:305: -1- PKG_CHECK_EXISTS([libmaus2irods >= 2.0.656], [pkg_cv_[]libmaus2irods_LIBS=`$PKG_CONFIG --[]libs "libmaus2irods >= 2.0.656" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:305: -1- _PKG_SHORT_ERRORS_SUPPORTED
m4trace:configure.ac:343: -1- PKG_CHECK_MODULES([liftingwavelettransform], [liftingwavelettransform >= 0.0.0])
......
autom4te.cache/traces.1
View file @ c9fb903f
......@@ -3,7 +3,7 @@ m4trace:aclocal.m4:1459: -1- m4_include([m4/ltoptions.m4])
m4trace:aclocal.m4:1460: -1- m4_include([m4/ltsugar.m4])
m4trace:aclocal.m4:1461: -1- m4_include([m4/ltversion.m4])
m4trace:aclocal.m4:1462: -1- m4_include([m4/lt~obsolete.m4])
m4trace:configure.ac:1: -1- AC_INIT([biobambam2], [2.0.129], [tischler@mpi-cbg.de], [biobambam2], [http://www.sanger.ac.uk])
m4trace:configure.ac:1: -1- AC_INIT([biobambam2], [2.0.134], [tischler@mpi-cbg.de], [biobambam2], [http://www.sanger.ac.uk])
m4trace:configure.ac:1: -1- m4_pattern_forbid([^_?A[CHUM]_])
m4trace:configure.ac:1: -1- m4_pattern_forbid([_AC_])
m4trace:configure.ac:1: -1- m4_pattern_forbid([^LIBOBJS$], [do not use LIBOBJS directly, use AC_LIBOBJ (see section `AC_LIBOBJ vs LIBOBJS'])
......
autom4te.cache/traces.2
View file @ c9fb903f
......@@ -2905,36 +2905,36 @@ m4trace:configure.ac:139: -1- m4_pattern_allow([^PKG_CONFIG_PATH$])
m4trace:configure.ac:139: -1- m4_pattern_allow([^PKG_CONFIG_LIBDIR$])
m4trace:configure.ac:139: -1- m4_pattern_allow([^PKG_CONFIG$])
m4trace:configure.ac:147: -1- m4_pattern_allow([^STDC_HEADERS$])
m4trace:configure.ac:168: -1- PKG_CHECK_MODULES([libmaus2], [libmaus2 >= 2.0.653])
m4trace:configure.ac:168: -1- PKG_CHECK_MODULES([libmaus2], [libmaus2 >= 2.0.657])
m4trace:configure.ac:168: -1- m4_pattern_allow([^libmaus2_CFLAGS$])
m4trace:configure.ac:168: -1- m4_pattern_allow([^libmaus2_LIBS$])
m4trace:configure.ac:168: -1- PKG_CHECK_EXISTS([libmaus2 >= 2.0.653], [pkg_cv_[]libmaus2_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2 >= 2.0.653" 2>/dev/null`
m4trace:configure.ac:168: -1- PKG_CHECK_EXISTS([libmaus2 >= 2.0.657], [pkg_cv_[]libmaus2_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2 >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:168: -1- PKG_CHECK_EXISTS([libmaus2 >= 2.0.653], [pkg_cv_[]libmaus2_LIBS=`$PKG_CONFIG --[]libs "libmaus2 >= 2.0.653" 2>/dev/null`
m4trace:configure.ac:168: -1- PKG_CHECK_EXISTS([libmaus2 >= 2.0.657], [pkg_cv_[]libmaus2_LIBS=`$PKG_CONFIG --[]libs "libmaus2 >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:168: -1- _PKG_SHORT_ERRORS_SUPPORTED
m4trace:configure.ac:169: -1- PKG_CHECK_MODULES([libmaus2digests], [libmaus2digests >= 2.0.653])
m4trace:configure.ac:169: -1- PKG_CHECK_MODULES([libmaus2digests], [libmaus2digests >= 2.0.657])
m4trace:configure.ac:169: -1- m4_pattern_allow([^libmaus2digests_CFLAGS$])
m4trace:configure.ac:169: -1- m4_pattern_allow([^libmaus2digests_LIBS$])
m4trace:configure.ac:169: -1- PKG_CHECK_EXISTS([libmaus2digests >= 2.0.653], [pkg_cv_[]libmaus2digests_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2digests >= 2.0.653" 2>/dev/null`
m4trace:configure.ac:169: -1- PKG_CHECK_EXISTS([libmaus2digests >= 2.0.657], [pkg_cv_[]libmaus2digests_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2digests >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:169: -1- PKG_CHECK_EXISTS([libmaus2digests >= 2.0.653], [pkg_cv_[]libmaus2digests_LIBS=`$PKG_CONFIG --[]libs "libmaus2digests >= 2.0.653" 2>/dev/null`
m4trace:configure.ac:169: -1- PKG_CHECK_EXISTS([libmaus2digests >= 2.0.657], [pkg_cv_[]libmaus2digests_LIBS=`$PKG_CONFIG --[]libs "libmaus2digests >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:169: -1- _PKG_SHORT_ERRORS_SUPPORTED
m4trace:configure.ac:170: -1- PKG_CHECK_MODULES([libmaus2seqchksumsfactory], [libmaus2seqchksumsfactory >= 2.0.653])
m4trace:configure.ac:170: -1- PKG_CHECK_MODULES([libmaus2seqchksumsfactory], [libmaus2seqchksumsfactory >= 2.0.657])
m4trace:configure.ac:170: -1- m4_pattern_allow([^libmaus2seqchksumsfactory_CFLAGS$])
m4trace:configure.ac:170: -1- m4_pattern_allow([^libmaus2seqchksumsfactory_LIBS$])
m4trace:configure.ac:170: -1- PKG_CHECK_EXISTS([libmaus2seqchksumsfactory >= 2.0.653], [pkg_cv_[]libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
m4trace:configure.ac:170: -1- PKG_CHECK_EXISTS([libmaus2seqchksumsfactory >= 2.0.657], [pkg_cv_[]libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2seqchksumsfactory >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:170: -1- PKG_CHECK_EXISTS([libmaus2seqchksumsfactory >= 2.0.653], [pkg_cv_[]libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --[]libs "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
m4trace:configure.ac:170: -1- PKG_CHECK_EXISTS([libmaus2seqchksumsfactory >= 2.0.657], [pkg_cv_[]libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --[]libs "libmaus2seqchksumsfactory >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:170: -1- _PKG_SHORT_ERRORS_SUPPORTED
m4trace:configure.ac:305: -1- PKG_CHECK_MODULES([libmaus2irods], [libmaus2irods >= 2.0.653])
m4trace:configure.ac:305: -1- PKG_CHECK_MODULES([libmaus2irods], [libmaus2irods >= 2.0.657])
m4trace:configure.ac:305: -1- m4_pattern_allow([^libmaus2irods_CFLAGS$])
m4trace:configure.ac:305: -1- m4_pattern_allow([^libmaus2irods_LIBS$])
m4trace:configure.ac:305: -1- PKG_CHECK_EXISTS([libmaus2irods >= 2.0.653], [pkg_cv_[]libmaus2irods_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2irods >= 2.0.653" 2>/dev/null`
m4trace:configure.ac:305: -1- PKG_CHECK_EXISTS([libmaus2irods >= 2.0.657], [pkg_cv_[]libmaus2irods_CFLAGS=`$PKG_CONFIG --[]cflags "libmaus2irods >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:305: -1- PKG_CHECK_EXISTS([libmaus2irods >= 2.0.653], [pkg_cv_[]libmaus2irods_LIBS=`$PKG_CONFIG --[]libs "libmaus2irods >= 2.0.653" 2>/dev/null`
m4trace:configure.ac:305: -1- PKG_CHECK_EXISTS([libmaus2irods >= 2.0.657], [pkg_cv_[]libmaus2irods_LIBS=`$PKG_CONFIG --[]libs "libmaus2irods >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes])
m4trace:configure.ac:305: -1- _PKG_SHORT_ERRORS_SUPPORTED
m4trace:configure.ac:343: -1- PKG_CHECK_MODULES([liftingwavelettransform], [liftingwavelettransform >= 0.0.0])
......
configure
View file @ c9fb903f
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for biobambam2 2.0.129.
# Generated by GNU Autoconf 2.69 for biobambam2 2.0.134.
#
# Report bugs to <tischler@mpi-cbg.de>.
#
......@@ -590,8 +590,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='biobambam2'
PACKAGE_TARNAME='biobambam2'
PACKAGE_VERSION='2.0.129'
PACKAGE_STRING='biobambam2 2.0.129'
PACKAGE_VERSION='2.0.134'
PACKAGE_STRING='biobambam2 2.0.134'
PACKAGE_BUGREPORT='tischler@mpi-cbg.de'
PACKAGE_URL='http://www.sanger.ac.uk'
 
......@@ -1400,7 +1400,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
\`configure' configures biobambam2 2.0.129 to adapt to many kinds of systems.
\`configure' configures biobambam2 2.0.134 to adapt to many kinds of systems.
 
Usage: $0 [OPTION]... [VAR=VALUE]...
 
......@@ -1472,7 +1472,7 @@ fi
 
if test -n "$ac_init_help"; then
case $ac_init_help in
short | recursive ) echo "Configuration of biobambam2 2.0.129:";;
short | recursive ) echo "Configuration of biobambam2 2.0.134:";;
esac
cat <<\_ACEOF
 
......@@ -1631,7 +1631,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
biobambam2 configure 2.0.129
biobambam2 configure 2.0.134
generated by GNU Autoconf 2.69
 
Copyright (C) 2012 Free Software Foundation, Inc.
......@@ -2072,7 +2072,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
 
It was created by biobambam2 $as_me 2.0.129, which was
It was created by biobambam2 $as_me 2.0.134, which was
generated by GNU Autoconf 2.69. Invocation command line was
 
$ $0 $@
......@@ -11972,7 +11972,7 @@ fi
 
# Define the identity of the package.
PACKAGE='biobambam2'
VERSION='2.0.129'
VERSION='2.0.134'
 
 
cat >>confdefs.h <<_ACEOF
......@@ -16979,12 +16979,12 @@ if test -n "$libmaus2_CFLAGS"; then
pkg_cv_libmaus2_CFLAGS="$libmaus2_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2_CFLAGS=`$PKG_CONFIG --cflags "libmaus2 >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -16996,12 +16996,12 @@ if test -n "$libmaus2_LIBS"; then
pkg_cv_libmaus2_LIBS="$libmaus2_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2 >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2 >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2_LIBS=`$PKG_CONFIG --libs "libmaus2 >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17022,14 +17022,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.653" 2>&1`
libmaus2_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2 >= 2.0.657" 2>&1`
else
libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.653" 2>&1`
libmaus2_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2 >= 2.0.657" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2 >= 2.0.653) were not met:
as_fn_error $? "Package requirements (libmaus2 >= 2.0.657) were not met:
 
$libmaus2_PKG_ERRORS
 
......@@ -17070,12 +17070,12 @@ if test -n "$libmaus2digests_CFLAGS"; then
pkg_cv_libmaus2digests_CFLAGS="$libmaus2digests_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2digests_CFLAGS=`$PKG_CONFIG --cflags "libmaus2digests >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17087,12 +17087,12 @@ if test -n "$libmaus2digests_LIBS"; then
pkg_cv_libmaus2digests_LIBS="$libmaus2digests_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2digests >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2digests >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2digests_LIBS=`$PKG_CONFIG --libs "libmaus2digests >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17113,14 +17113,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.653" 2>&1`
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2digests >= 2.0.657" 2>&1`
else
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.653" 2>&1`
libmaus2digests_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2digests >= 2.0.657" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2digests_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2digests >= 2.0.653) were not met:
as_fn_error $? "Package requirements (libmaus2digests >= 2.0.657) were not met:
 
$libmaus2digests_PKG_ERRORS
 
......@@ -17161,12 +17161,12 @@ if test -n "$libmaus2seqchksumsfactory_CFLAGS"; then
pkg_cv_libmaus2seqchksumsfactory_CFLAGS="$libmaus2seqchksumsfactory_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2seqchksumsfactory_CFLAGS=`$PKG_CONFIG --cflags "libmaus2seqchksumsfactory >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17178,12 +17178,12 @@ if test -n "$libmaus2seqchksumsfactory_LIBS"; then
pkg_cv_libmaus2seqchksumsfactory_LIBS="$libmaus2seqchksumsfactory_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2seqchksumsfactory >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2seqchksumsfactory >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2seqchksumsfactory_LIBS=`$PKG_CONFIG --libs "libmaus2seqchksumsfactory >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17204,14 +17204,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>&1`
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.657" 2>&1`
else
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.653" 2>&1`
libmaus2seqchksumsfactory_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2seqchksumsfactory >= 2.0.657" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2seqchksumsfactory_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.653) were not met:
as_fn_error $? "Package requirements (libmaus2seqchksumsfactory >= 2.0.657) were not met:
 
$libmaus2seqchksumsfactory_PKG_ERRORS
 
......@@ -17486,12 +17486,12 @@ if test -n "$libmaus2irods_CFLAGS"; then
pkg_cv_libmaus2irods_CFLAGS="$libmaus2irods_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2irods_CFLAGS=`$PKG_CONFIG --cflags "libmaus2irods >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17503,12 +17503,12 @@ if test -n "$libmaus2irods_LIBS"; then
pkg_cv_libmaus2irods_LIBS="$libmaus2irods_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.653\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.653") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libmaus2irods >= 2.0.657\""; } >&5
($PKG_CONFIG --exists --print-errors "libmaus2irods >= 2.0.657") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.653" 2>/dev/null`
pkg_cv_libmaus2irods_LIBS=`$PKG_CONFIG --libs "libmaus2irods >= 2.0.657" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -17529,14 +17529,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.653" 2>&1`
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libmaus2irods >= 2.0.657" 2>&1`
else
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.653" 2>&1`
libmaus2irods_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libmaus2irods >= 2.0.657" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$libmaus2irods_PKG_ERRORS" >&5
 
as_fn_error $? "Package requirements (libmaus2irods >= 2.0.653) were not met:
as_fn_error $? "Package requirements (libmaus2irods >= 2.0.657) were not met:
 
$libmaus2irods_PKG_ERRORS
 
......@@ -18571,7 +18571,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by biobambam2 $as_me 2.0.129, which was
This file was extended by biobambam2 $as_me 2.0.134, which was
generated by GNU Autoconf 2.69. Invocation command line was
 
CONFIG_FILES = $CONFIG_FILES
......@@ -18638,7 +18638,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
biobambam2 config.status 2.0.129
biobambam2 config.status 2.0.134
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
 
......
configure.ac
View file @ c9fb903f
AC_INIT(biobambam2,2.0.129,[tischler@mpi-cbg.de],[biobambam2],[http://www.sanger.ac.uk])
AC_INIT(biobambam2,2.0.134,[tischler@mpi-cbg.de],[biobambam2],[http://www.sanger.ac.uk])
AC_CANONICAL_SYSTEM
AC_PROG_LIBTOOL
......@@ -165,9 +165,9 @@ if test ! -z "${with_libmaus2}" ; then
fi
fi
PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.653])
PKG_CHECK_MODULES([libmaus2digests],[libmaus2digests >= 2.0.653])
PKG_CHECK_MODULES([libmaus2seqchksumsfactory],[libmaus2seqchksumsfactory >= 2.0.653])
PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.657])
PKG_CHECK_MODULES([libmaus2digests],[libmaus2digests >= 2.0.657])
PKG_CHECK_MODULES([libmaus2seqchksumsfactory],[libmaus2seqchksumsfactory >= 2.0.657])
if test ! -z "${with_libmaus2}" ; then
if test ! -z "${PKGCONFIGPATHSAVE}" ; then
......@@ -302,7 +302,7 @@ if test "${have_libmaus2_irods}" = "yes" ; then
fi
fi
PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.653])
PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.657])
LIBMAUS2IRODSCPPFLAGS="${libmaus2irods_CFLAGS}"
LIBMAUS2IRODSLIBS="${libmaus2irods_LIBS}"
......
debian/changelog
View file @ c9fb903f
biobambam2 (2.0.134-1) UNRELEASED; urgency=medium
* New upstream version
* Versioned Build-Depends: libmaus2-dev (>= 2.0.657)
-- Andreas Tille <tille@debian.org> Mon, 19 Aug 2019 18:12:42 +0200
biobambam2 (2.0.129-1) unstable; urgency=medium
* New upstream version
......
debian/control
View file @ c9fb903f
......@@ -5,7 +5,7 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
pkg-config,
libmaus2-dev (>= 2.0.650)
libmaus2-dev (>= 2.0.657)
Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/biobambam2
Vcs-Git: https://salsa.debian.org/med-team/biobambam2.git
......
src/Makefile.am
View file @ c9fb903f
......@@ -114,6 +114,7 @@ bin_PROGRAMS = bamtofastq bammarkduplicates bamsort bammaskflags bamrecompress \
bamfiltereofblocks \
bamdepth \
bamdepthintersect \
bamfilterk \
@BLASTXMLTOBAMINSTEXP@
noinst_PROGRAMS = bamfilter bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname \
......@@ -153,7 +154,7 @@ bamconsensus_LDADD = ${LIBMAUS2LIBS}
bamconsensus_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
bamconsensus_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}
fastqtobam2_SOURCES = programs/fastqtobam2.cpp biobambam2/Licensing.cpp biobambam2/KmerPoisson.cpp
fastqtobam2_SOURCES = programs/fastqtobam2.cpp biobambam2/Licensing.cpp biobambam2/KmerPoisson.cpp biobambam2/RunEOFFilter.cpp
fastqtobam2_LDADD = ${LIBMAUS2LIBS}
fastqtobam2_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
fastqtobam2_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}
......@@ -587,3 +588,8 @@ bamfeaturecount_SOURCES = programs/bamfeaturecount.cpp biobambam2/Licensing.cpp
bamfeaturecount_LDADD = ${LIBMAUS2LIBS}
bamfeaturecount_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
bamfeaturecount_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}
bamfilterk_SOURCES = programs/bamfilterk.cpp biobambam2/Licensing.cpp biobambam2/DepthInterval.cpp biobambam2/RunEOFFilter.cpp
bamfilterk_LDADD = ${LIBMAUS2LIBS}
bamfilterk_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
bamfilterk_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}
src/Makefile.in
View file @ c9fb903f
This diff is collapsed.
src/programs/bamconsensus.cpp
View file @ c9fb903f
This diff is collapsed.
src/programs/bamfilterk.cpp 0 → 100644
View file @ c9fb903f
/**
bambam
Copyright (C) 2019 German Tischler
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
**/
#include <libmaus2/lz/BgzfInflateBase.hpp>
#include <libmaus2/bambam/BamHeader.hpp>
#include <libmaus2/bambam/SamDecoder.hpp>
#include <libmaus2/util/ArgInfo.hpp>
#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/LineBuffer.hpp>
#include <libmaus2/util/Concat.hpp>
#include <libmaus2/bambam/BamBlockWriterBaseFactory.hpp>
#include <libmaus2/bambam/BamNumericalIndexDecoder.hpp>
#include <libmaus2/bambam/BamNumericalIndexGenerator.hpp>
#include <libmaus2/fastx/StreamFastAReader.hpp>
#include <libmaus2/lz/BgzfDeflate.hpp>
#include <libmaus2/aio/InputOutputStreamInstance.hpp>
#include <libmaus2/util/GetFileSize.hpp>
#include <libmaus2/util/PrefixSums.hpp>
#include <libmaus2/aio/TempFileArray.hpp>
#include <libmaus2/parallel/NumCpus.hpp>
#include <libmaus2/clustering/KmerBase.hpp>
#include <libmaus2/fastx/SingleWordDNABitBuffer.hpp>
#include <libmaus2/hashing/hash.hpp>
#include <libmaus2/bambam/BamMultiAlignmentDecoderFactory.hpp>
#include <biobambam2/BamBamConfig.hpp>
#include <biobambam2/Licensing.hpp>
#include <biobambam2/ReadHeader.hpp>
#include <biobambam2/RunEOFFilter.hpp>
int getDefaultLevel()
{
return -1;
}
void printHelpMessage(libmaus2::util::ArgInfo const & arginfo)
{
std::cerr << ::biobambam2::Licensing::license();
std::cerr << std::endl;
std::cerr << "synopsis: " << arginfo.progname << " [thresval=3] [k=24] [threads=1] [level=6] <in.bam> <in.fasta> >out.bam" << std::endl;
std::cerr << std::endl;
std::cerr << "Key=Value pairs:" << std::endl;
std::cerr << std::endl;
std::vector< std::pair<std::string,std::string> > V;
V.push_back ( std::pair<std::string,std::string> ( "level=<["+::biobambam2::Licensing::formatNumber(getDefaultLevel())+"]>", libmaus2::bambam::BamBlockWriterBaseFactory::getBamOutputLevelHelpText() ) );
V.push_back ( std::pair<std::string,std::string> ( "threads=<["+::biobambam2::Licensing::formatNumber(1)+"]>", "number of threads used (default: 1)" ) );
V.push_back ( std::pair<std::string,std::string> ( "k=<["+::biobambam2::Licensing::formatNumber(24)+"]>", "k-mer size used (default: 24)" ) );
V.push_back ( std::pair<std::string,std::string> ( "thresval=<["+::biobambam2::Licensing::formatNumber(3)+"]>", "threshold for number of k-mers required to keep read (default: 3)" ) );
::biobambam2::Licensing::printMap(std::cerr,V);
std::cerr << std::endl;
}
std::vector<std::string> loadRef(std::string const & fn)
{
libmaus2::aio::InputStreamInstance ISI(fn);
libmaus2::fastx::StreamFastAReaderWrapper SFAR(ISI);
libmaus2::fastx::StreamFastAReader::pattern_type pattern;
std::vector<std::string> V;
while ( SFAR.getNextPatternUnlocked(pattern) )
{
std::string & s = pattern.spattern;
for ( uint64_t i = 0; i < s.size(); ++i )
s[i] = libmaus2::fastx::remapChar(libmaus2::fastx::mapChar(s[i]));
V.push_back(s);
}
return V;
}
template<unsigned int kl>
struct KMerBlockTemplate
{
uint64_t kmer;
uint64_t hash;
uint64_t from;
uint64_t to;
static uint64_t getHashSize()
{
return 1ull << kl;
}
static uint64_t getHash(uint64_t const kmer)
{
return libmaus2::hashing::EvaHash::hash642(&kmer,1) & (getHashSize()-1);
}
KMerBlockTemplate() : kmer(0), hash(0), from(0), to(0) {}
KMerBlockTemplate(uint64_t const rkmer)
: kmer(rkmer), hash(getHash(kmer)), from(0), to(0) {}
KMerBlockTemplate(uint64_t const rkmer, uint64_t const rfrom, uint64_t const rto)
: kmer(rkmer), hash(getHash(kmer)), from(rfrom), to(rto) {}
bool operator<(KMerBlockTemplate<kl> const & K) const
{
if ( hash != K.hash )
return hash < K.hash;
else
return kmer < K.kmer;
}
};
struct HashBlock
{
uint64_t from;
uint64_t to;
HashBlock() : from(0), to(0) {}
HashBlock(uint64_t const rfrom, uint64_t const rto)
: from(rfrom), to(rto) {}
};
static unsigned int const kl = 16;
typedef KMerBlockTemplate<kl> KMerBlock;
static libmaus2::bambam::BamHeader::unique_ptr_type readBamHeader(libmaus2::util::ArgInfo const & arginfo, std::string const & bamfn)
{
libmaus2::util::ArgInfo arginfoCopy = arginfo;
arginfoCopy.replaceKey("I",bamfn);
libmaus2::bambam::BamAlignmentDecoderWrapper::unique_ptr_type bamdecwrapper(
libmaus2::bambam::BamMultiAlignmentDecoderFactory::construct(arginfoCopy)
);
libmaus2::bambam::BamHeader::unique_ptr_type ubamheader(bamdecwrapper->getDecoder().getHeader().uclone());
return ubamheader;
}
struct Match
{
uint64_t seqid;
uint64_t strand;
uint64_t pos;
uint64_t readpos;
Match()
{}
Match(uint64_t const rseqid, uint64_t const rstrand, uint64_t const rpos, uint64_t const rreadpos)
: seqid(rseqid), strand(rstrand), pos(rpos), readpos(rreadpos) {}
bool operator<(Match const & M) const
{
if ( seqid != M.seqid )
return seqid < M.seqid;
else if ( strand != M.strand )
return strand < M.strand;
else
return pos < M.pos;
}
};
struct KMer
{
uint64_t kmer;
uint64_t seqid;
uint64_t pos;
uint64_t strand;
KMer()
{
}
KMer(
uint64_t rkmer,
uint64_t rseqid,
uint64_t rpos,
uint64_t rstrand
) : kmer(rkmer), seqid(rseqid), pos(rpos), strand(rstrand)
{
}
std::string toString(uint64_t const k) const
{
libmaus2::fastx::SingleWordDNABitBuffer forw(k);
forw.buffer = kmer;
std::ostringstream ostr;
ostr << "KMer(" << forw << "," << seqid << "," << pos << "," << strand << ")";
return ostr.str();
}
};
struct KMerKSorter
{
bool operator()(KMer const & A, KMer const & B) const
{
return A.kmer < B.kmer;
}
};
struct MatchCallback
{
uint64_t AMo;
libmaus2::autoarray::AutoArray<HashBlock> const & KH;
libmaus2::autoarray::AutoArray< KMerBlock > const & AKB;
libmaus2::autoarray::AutoArray<KMer> const & AK;
libmaus2::autoarray::AutoArray<Match> & AM;
MatchCallback(
libmaus2::autoarray::AutoArray<HashBlock> const & rKH,
libmaus2::autoarray::AutoArray< KMerBlock > const & rAKB,
libmaus2::autoarray::AutoArray<KMer> const & rAK,
libmaus2::autoarray::AutoArray<Match> & rAM
) : AMo(0), KH(rKH), AKB(rAKB), AK(rAK), AM(rAM)
{
}
void operator()(uint64_t const kmer, uint64_t const rpos)
{
uint64_t const hash = KMerBlock::getHash(kmer);
assert ( hash < KH.size() );
HashBlock const & HB = KH[hash];
if ( HB.from < HB.to )
{
for ( uint64_t h = HB.from; h < HB.to; ++h )
{
KMerBlock const & KB = AKB[h];
assert ( KB.hash == hash );
if ( KB.kmer == kmer )
{
uint64_t const kfrom = KB.from;
uint64_t const kto = KB.to;
for ( uint64_t z = kfrom; z < kto; ++z )
{
assert ( AK[z].kmer == kmer );
AM.push(AMo,Match(AK[z].seqid,AK[z].strand,AK[z].pos,rpos));
}
}
}
}
}
bool thres(uint64_t const rthres)
{
std::sort(AM.begin(),AM.begin()+AMo);
uint64_t ilow = 0;
bool found = false;
while ( ilow < AMo )
{
uint64_t ihigh = ilow+1;
// look for same seqid and strand
while (
ihigh < AMo
&&
AM[ihigh].seqid == AM[ilow].seqid
&&
AM[ihigh].strand == AM[ilow].strand
)
++ihigh;
// std::cerr << AM[ilow].seqid << "," << AM[ilow].strand << "=" << ihigh-ilow << std::endl;
uint64_t c = 1;
for ( uint64_t z = ilow+1; z < ihigh; ++z )
if ( AM[z-1].pos != AM[z].pos )
++c;
if ( c >= rthres )
found = true;
ilow = ihigh;
}
return found;
}
};
struct Filter
{
libmaus2::autoarray::AutoArray<HashBlock> const & KH;
libmaus2::autoarray::AutoArray< KMerBlock > const & AKB;
libmaus2::autoarray::AutoArray<KMer> const & AK;
libmaus2::clustering::KmerBase const & KB;
unsigned int const k;
uint64_t const thresval;
Filter(
libmaus2::autoarray::AutoArray<HashBlock> const & rKH,
libmaus2::autoarray::AutoArray< KMerBlock > const & rAKB,
libmaus2::autoarray::AutoArray<KMer> const & rAK,
libmaus2::clustering::KmerBase const & rKB,
unsigned int const rk,
uint64_t const rthresval
) : KH(rKH), AKB(rAKB), AK(rAK), KB(rKB), k(rk), thresval(rthresval)
{
}
bool checkFilter(
std::pair<
std::pair<uint8_t const *,uint64_t>,
libmaus2::bambam::BamRawDecoderBase::RawInterval
> const & P,
libmaus2::autoarray::AutoArray<char> & A,
libmaus2::fastx::SingleWordDNABitBuffer & forw,
libmaus2::autoarray::AutoArray<Match> & AM
) const
{
uint64_t const lseq = libmaus2::bambam::BamAlignmentDecoderBase::decodeRead(P.first.first,A);
#if 0
for ( uint64_t z = 0; z < lseq; ++z )
A[z] = libmaus2::fastx::mapChar(A[z]);
#endif
// std::cerr << "j=" << j << " lseq=" << lseq << " [" << low << "," << high << ")" << std::endl;
MatchCallback CB(KH,AKB,AK,AM);
KB.kmerCallbackPosForwardOnly(
A.begin(),
lseq,
CB,
forw,
k
);
bool const thres = CB.thres(thresval);
return thres;
}
};
static void putAlignment(
std::pair<
std::pair<uint8_t const *,uint64_t>,
libmaus2::bambam::BamRawDecoderBase::RawInterval
> const & P,
libmaus2::lz::BgzfDeflate<std::ostream> & BOS
)
{
// write block size
::libmaus2::bambam::EncoderBase::putLE<libmaus2::lz::BgzfDeflate<std::ostream>,uint32_t>(BOS,P.first.second);
BOS.write(
reinterpret_cast<char const *>(P.first.first),
P.first.second
);
}
int bamfilterk(libmaus2::util::ArgInfo const & arginfo)
{
uint64_t const numrest = arginfo.getNumRestArgs();
int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue("level",getDefaultLevel()));
unsigned int numthreads = arginfo.getValue<unsigned int>("threads",1);
unsigned int const k = arginfo.getValue<unsigned int>("k",24);
uint64_t const thresval = arginfo.getValue<unsigned int>("thresval",3);
assert ( k );
if ( ! numthreads )
numthreads = libmaus2::parallel::NumCpus::getNumLogicalProcessors();
std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
std::string const tmpfilenameout = tmpfilenamebase + "_bamfilterk";
if ( numrest < 2 )
{
printHelpMessage(arginfo);
libmaus2::exception::LibMausException lme;
lme.getStream() << "[E] insufficient number of arguments provided" << std::endl;
lme.finish();
throw lme;
}
std::string const bamfn = arginfo.getUnparsedRestArg(0);
std::string const kfn = arginfo.getUnparsedRestArg(1);
libmaus2::bambam::BamHeader::unique_ptr_type ubamheader(readBamHeader(arginfo,bamfn));
std::string bgzfhead;
{
std::ostringstream headerstr;
ubamheader->serialise(headerstr);
std::string const headerser = headerstr.str();
std::ostringstream defstr;
libmaus2::lz::BgzfDeflate<std::ostream> def(defstr,level);
def.write(headerser.c_str(),headerser.size());
def.flush();
bgzfhead = biobambam2::runEOFFilter(defstr.str());
}
std::string const indexfn = libmaus2::bambam::BamNumericalIndexBase::getIndexName(bamfn);
libmaus2::bambam::BamNumericalIndexGenerator::indexFileCheck(bamfn,1024,numthreads);
libmaus2::bambam::BamNumericalIndexDecoder indexdec(indexfn);
uint64_t const n = indexdec.getAlignmentCount();
uint64_t const packsperthread = 8;
uint64_t const tnumpacks = packsperthread*numthreads;
assert ( tnumpacks );
uint64_t packsize = (n + tnumpacks - 1)/tnumpacks;
if ( packsize % 2 )
packsize += 1;
assert ( packsize % 2 == 0 );
uint64_t const numpacks = packsize ? (n + packsize - 1)/packsize : 0;
std::vector<std::string> const Vref = loadRef(kfn);
libmaus2::clustering::KmerBase const KB;
libmaus2::autoarray::AutoArray<KMer> AK;
uint64_t o_AK = 0;
for ( uint64_t i = 0; i < Vref.size(); ++i )
{
libmaus2::fastx::SingleWordDNABitBuffer forw(k);
libmaus2::fastx::SingleWordDNABitBuffer reve(k);
struct Callback
{
uint64_t const seqid;
libmaus2::autoarray::AutoArray<KMer> & AK;
uint64_t o_AK;
Callback(uint64_t const rseqid, libmaus2::autoarray::AutoArray<KMer> & rAK, uint64_t ro_AK) : seqid(rseqid), AK(rAK), o_AK(ro_AK) {}
void operator()(uint64_t const kmer, uint64_t const pos, bool const z)
{
AK.push(o_AK,KMer(kmer,seqid,pos,z));
}
};
Callback CB(i,AK,o_AK);
KB.kmerCallbackPos(
Vref[i].c_str(),
Vref[i].size(),
CB,
forw,
reve,
k
);
o_AK = CB.o_AK;
}
std::sort(AK.begin(),AK.begin()+o_AK,KMerKSorter());
libmaus2::autoarray::AutoArray< KMerBlock > AKB;
uint64_t o_AKB = 0;
uint64_t ilow = 0;
while ( ilow < o_AK )
{
uint64_t const kmer = AK[ilow].kmer;
uint64_t ihigh = ilow+1;
while ( ihigh < o_AK && AK[ihigh].kmer == kmer )
++ihigh;
AKB.push(o_AKB,KMerBlock(kmer,ilow,ihigh));
ilow = ihigh;
}
std::sort(AKB.begin(),AKB.begin()+o_AKB);
libmaus2::autoarray::AutoArray<HashBlock> KH(KMerBlock::getHashSize());
ilow = 0;
while ( ilow < o_AKB )
{
uint64_t const hash = AKB[ilow].hash;
uint64_t ihigh = ilow+1;
while ( ihigh < o_AKB && AKB[ihigh].hash == hash )
++ihigh;
assert ( hash < KH.size() );
KH[hash] = HashBlock(ilow,ihigh);
// std::cerr << "H\t" << hash << "\t" << ihigh-ilow << std::endl;
ilow = ihigh;
}
std::vector<std::string> Vtmp(numpacks);
#if defined(_OPENMP)
#pragma omp parallel for num_threads(numthreads)
#endif
for ( uint64_t i = 0; i < numpacks; ++i )
{
std::ostringstream fnostr;
fnostr << tmpfilenameout << "_" << std::setw(6) << std::setfill('0') << i << std::setw(0);
Vtmp[i] = fnostr.str();
}
for ( uint64_t i = 0; i < numpacks; ++i )
libmaus2::util::TempFileRemovalContainer::addTempFile(Vtmp[i]);
std::atomic<uint64_t> packfinished(0);
std::atomic<uint64_t> written(0);
Filter const filter(KH,AKB,AK,KB,k,thresval);
#if defined(_OPENMP)
#pragma omp parallel for num_threads(numthreads)
#endif
for ( uint64_t i = 0; i < numpacks; ++i )
{
std::string const & tmpfn = Vtmp[i];
uint64_t const low = i * packsize;
uint64_t const high = std::min(low+packsize,n);
assert ( high > low );
assert ( low % 2 == 0 );
assert ( high % 2 == 0 );
uint64_t const nump = (high-low)/2;
// uint64_t const size = high-low;
libmaus2::aio::OutputStreamInstance::unique_ptr_type pOS(new libmaus2::aio::OutputStreamInstance(tmpfn));
libmaus2::lz::BgzfDeflate<std::ostream>::unique_ptr_type pBOS(new libmaus2::lz::BgzfDeflate<std::ostream>(*pOS,level));
std::pair<
std::pair<uint8_t const *,uint64_t>,
libmaus2::bambam::BamRawDecoderBase::RawInterval
> P[2];
libmaus2::bambam::BamRawDecoder::unique_ptr_type pdec(indexdec.getRawDecoderAt(bamfn,low));
libmaus2::autoarray::AutoArray<uint8_t> U0;
libmaus2::autoarray::AutoArray<uint8_t> U1;
libmaus2::autoarray::AutoArray<char> A;
libmaus2::fastx::SingleWordDNABitBuffer forw(k);
libmaus2::autoarray::AutoArray<Match> AM;
for ( uint64_t pindex = 0; pindex < nump; ++pindex )
{
P[0] = pdec->getPos();
assert ( P[0].first.first );
U0.ensureSize(P[0].first.second);
std::copy(P[0].first.first,P[0].first.first + P[0].first.second,U0.begin());
P[0].first.first = U0.begin();
P[1] = pdec->getPos();
assert ( P[1].first.first );
#if 0
U1.ensureSize(P[1].first.second);
std::copy(P[1].first.first,P[1].first.first + P[1].first.second,U1.begin());
P[1].first.first = U1.begin();
#endif
char const * c0 = libmaus2::bambam::BamAlignmentDecoderBase::getReadName(P[0].first.first);
char const * c1 = libmaus2::bambam::BamAlignmentDecoderBase::getReadName(P[1].first.first);
bool const samename = (strcmp(c0,c1) == 0);
assert ( samename );
bool const thres0 = filter.checkFilter(P[0],A,forw,AM);
bool const thres1 = filter.checkFilter(P[1],A,forw,AM);
if ( thres0 || thres1 )
{
putAlignment(P[0],*pBOS);
putAlignment(P[1],*pBOS);
written += 1;
}
}
pBOS->flush();
pBOS.reset();
pOS->flush();
pOS.reset();
uint64_t const lpackfinished = ++packfinished;
{
libmaus2::parallel::ScopeStdSpinLock slock(libmaus2::aio::StreamLock::cerrlock);
std::cerr << lpackfinished << "/" << numpacks << "\t" << written << std::endl;
}
}
std::cerr << "[V] wrote " << written << " pairs" << std::endl;
std::cout.write(bgzfhead.c_str(),bgzfhead.size());
for ( uint64_t i = 0; i < numpacks; ++i )
{
std::string const & tmpfn = Vtmp[i];
// std::cerr << tmpfn << "\t" << libmaus2::util::GetFileSize::getFileSize(tmpfn) << std::endl;
{
libmaus2::aio::InputStreamInstance ISI(tmpfn);
libmaus2::util::Concat::concat(ISI,std::cout);
}
libmaus2::aio::FileRemoval::removeFile(tmpfn);
}
std::string const eofblock = libmaus2::lz::BgzfDeflate<std::ostream>::getEOFBlock();
std::cout.write(eofblock.c_str(),eofblock.size());
std::cout.flush();
if ( ! std::cout )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "[E] failed to write output to standard output channel" << std::endl;
lme.finish();
throw lme;
}
return EXIT_SUCCESS;
}
int main(int argc, char * argv[])
{
try
{
libmaus2::util::ArgInfo const arginfo(argc,argv);
for ( uint64_t i = 0; i < arginfo.restargs.size(); ++i )
if (
arginfo.restargs[i] == "-v"
||
arginfo.restargs[i] == "--version"
)
{
std::cerr << ::biobambam2::Licensing::license();
return EXIT_SUCCESS;
}
else if (
arginfo.restargs[i] == "-h"
||
arginfo.restargs[i] == "--help"
)
{
printHelpMessage(arginfo);
return EXIT_SUCCESS;
}
return bamfilterk(arginfo);
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
src/programs/bamrecalculatecigar.cpp
View file @ c9fb903f
......@@ -179,7 +179,11 @@ int bamrecalculatecigar(libmaus2::util::ArgInfo const & arginfo)
if ( algn.getRefID() < refloaded )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "bamrecalculatecigar: file is not sorted by coordinate" << std::endl;
lme.getStream()
<< "bamrecalculatecigar: file is not sorted by coordinate: "
<< "alignment for ref id " << algn.getRefID()
<< " follows alignment for ref id " << refloaded
<< std::endl;
lme.finish();
throw lme;
}
......
src/programs/bamsormadup.1
View file @ c9fb903f
......@@ -85,6 +85,12 @@ store numerical index in the given file. By default numerical index is not store
.PP
.B numericalindexmod=1024:
use this block size for producing numerical index
.PP
.B fragmergepar=1:
number of threads used for merging fragment lists in duplicate marking. The
run-time will generally benefit from an increased number here, but parallel
merging requires a large number of simultaneously open files, which will
cause problems on some systems.
.SH AUTHOR
Written by German Tischler.
.SH "REPORTING BUGS"
......