New upstream version 2.0.134 (4c533d60) · Commits · Debian Med / biobambam2

.gitignore

+1 −1

Original line number	Diff line number	Diff line
		@@ -37,7 +37,7 @@ src/kmerprob
		src/fastqtobam
		src/normalisefasta
		src/fastabgzfextract
		src/fastaexplode
		src/fastaexplod
		test/*.log
		test/*.trs
		src/*/.deps

ChangeLog

+33 −0

Original line number	Diff line number	Diff line
		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

+46 −46

Original line number	Diff line number	Diff line
		@%:@! /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

+46 −46

File changed.

Preview size limit exceeded, changes collapsed.

autom4te.cache/output.2

+46 −46

File changed.

Preview size limit exceeded, changes collapsed.