Commit fcb2ab68 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 2.0.152+dfsg

parent 2d665349

.gitignore

+2 −1
Original line number Diff line number Diff line
@@ -65,3 +65,4 @@ src/vcfconcat 
src/vcfsort

removespace.sh

src/filtergtf

src/vcfreplacecontigs

ChangeLog

+32 −0
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biobambam2 (2.0.152-1) unstable; urgency=medium



  * update libmaus2 version to 2.0.694



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 22 Jan 2020 09:58:27 +0100



biobambam2 (2.0.151-1) unstable; urgency=medium



  * bump libmaus2 version



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 21 Jan 2020 16:41:38 +0100



biobambam2 (2.0.150-1) unstable; urgency=medium



  * Add cols (line wrapping) option in bamtofastq



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 07 Jan 2020 16:37:02 +0100



biobambam2 (2.0.149-1) unstable; urgency=medium



  * use kmerCallbackPosFR instead of kmerCallbackPos in bamfilterk

  * Add vcfreplacecontigs program



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 07 Jan 2020 09:02:29 +0100



biobambam2 (2.0.148-1) unstable; urgency=medium



  * compute maximum depth in bamfeaturecount

  * fix output of wrong reference id in bamfeaturecount if GTF chrom set is a subset of BAM chrom set



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 13 Nov 2019 12:53:00 +0100



biobambam2 (2.0.147-1) unstable; urgency=medium



  * fix heap comparisons in bamconsensus

configure.ac

+4 −4
Original line number Diff line number Diff line 
AC_INIT(biobambam2,2.0.147,[germant@miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])

AC_INIT(biobambam2,2.0.152,[germant@miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])

AC_CANONICAL_SYSTEM

AC_PROG_LIBTOOL
@@ -165,7 +165,7 @@ if test ! -z "${with_libmaus2}" ; then 
	fi

fi



PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.683])

PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.694])



if test ! -z "${with_libmaus2}" ; then

	if test ! -z "${PKGCONFIGPATHSAVE}" ; then
@@ -300,7 +300,7 @@ if test "${have_libmaus2_irods}" = "yes" ; then 
		fi

	fi



	PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.683])

	PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.694])



	LIBMAUS2IRODSCPPFLAGS="${libmaus2irods_CFLAGS}"

	LIBMAUS2IRODSLIBS="${libmaus2irods_LIBS}"
@@ -463,7 +463,7 @@ AC_ARG_ENABLE(install_uncommon, 
        AS_HELP_STRING([--enable-install-uncommon],[enable installation of some uncommon programs (default no)]),

        [install_uncommon=${enableval}],[install_uncommon=no])



UNCOMMON="bamfilter bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname bamdisthist fastabgzfextract bamheap bamfrontback bamrandomtag bamheap2 bamheap3 bamtagconversion fastqtobampar bambisect vcffilterinfo vcfpatchcontigprepend vcfconcat vcfsort filtergtf bamconsensus"

UNCOMMON="bamfilter bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname bamdisthist fastabgzfextract bamheap bamfrontback bamrandomtag bamheap2 bamheap3 bamtagconversion fastqtobampar bambisect vcffilterinfo vcfpatchcontigprepend vcfconcat vcfsort filtergtf bamconsensus vcfreplacecontigs"

UNCOMMONINSTALLED=

UNCOMMONUNINSTALLED=

if test "${install_uncommon}" = "yes" ; then

src/Makefile.am

+6 −0
Original line number Diff line number Diff line
@@ -138,6 +138,7 @@ EXTRA_PROGRAMS = blastnxmltobam \ 
	vcfpatchcontigprepend \

	vcfconcat \

	vcfsort \

	vcfreplacecontigs \

	filtergtf



populaterefcache_SOURCES = programs/populaterefcache.cpp biobambam2/Licensing.cpp
@@ -600,6 +601,11 @@ vcfsort_LDADD = ${LIBMAUS2LIBS} 
vcfsort_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}

vcfsort_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}



vcfreplacecontigs_SOURCES = programs/vcfreplacecontigs.cpp biobambam2/Licensing.cpp

vcfreplacecontigs_LDADD = ${LIBMAUS2LIBS}

vcfreplacecontigs_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}

vcfreplacecontigs_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}



bamfiltereofblocks_SOURCES = programs/bamfiltereofblocks.cpp biobambam2/Licensing.cpp biobambam2/RunEOFFilter.cpp

bamfiltereofblocks_LDADD = ${LIBMAUS2LIBS}

bamfiltereofblocks_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}

src/programs/bamauxmerge2.cpp

+1 −0
Original line number Diff line number Diff line
@@ -47,6 +47,7 @@ 
#include <libmaus2/util/LELoad.hpp>

#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>

#include <libmaus2/fastx/FastAReader.hpp>

#include <libmaus2/bambam/StrCmpNum.hpp>



#include <biobambam2/BamBamConfig.hpp>

#include <biobambam2/Licensing.hpp>