[med-svn] [Git][med-team/biobambam2][master] 8 commits: routine-update: New upstream version
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Tue Aug 24 20:45:49 BST 2021
Étienne Mollier pushed to branch master at Debian Med / biobambam2
Commits:
dd4ab7a2 by Étienne Mollier at 2021-08-24T12:48:30+02:00
routine-update: New upstream version
- - - - -
7709cfd6 by Étienne Mollier at 2021-08-24T12:48:32+02:00
New upstream version 2.0.183+ds
- - - - -
e4daece1 by Étienne Mollier at 2021-08-24T12:48:36+02:00
Update upstream source from tag 'upstream/2.0.183+ds'
Update to upstream version '2.0.183+ds'
with Debian dir 7ed9bf23c110557070e8ca797e109e162d1fde8b
- - - - -
669b5d63 by Étienne Mollier at 2021-08-24T12:48:36+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
e9fd708f by Étienne Mollier at 2021-08-24T12:48:45+02:00
Remove duplicate line from changelog.
Changes-By: lintian-brush
- - - - -
773f6153 by Étienne Mollier at 2021-08-24T15:47:14+02:00
d/control: build depends on libmaus2-dev (>= 2.0.800)
older versions of libmaus2 will cause a configure error at build time.
- - - - -
5b75a6a6 by Étienne Mollier at 2021-08-24T16:36:18+02:00
update changelog
- - - - -
81dd7b7e by Étienne Mollier at 2021-08-24T16:54:23+02:00
routine-update: Ready to upload to unstable
- - - - -
23 changed files:
- ChangeLog
- configure.ac
- debian/changelog
- debian/control
- src/biobambam2/ReadHeader.cpp
- src/programs/bam12split.cpp
- src/programs/bam12strip.cpp
- src/programs/bamauxmerge2.cpp
- src/programs/bamauxsort.cpp
- src/programs/bamfastcat.cpp
- src/programs/bamfilteraux.cpp
- src/programs/bamfilterk.cpp
- src/programs/bamfilternames.cpp
- src/programs/bamfilterrefid.cpp
- src/programs/bamfilterrg.cpp
- src/programs/bamfixmatecoordinates.cpp
- src/programs/bamfixmateinformation.cpp
- src/programs/bamflagsplit.cpp
- src/programs/bammdnm.cpp
- src/programs/bamrandomtag.cpp
- src/programs/bamreheader.cpp
- src/programs/bamreplacechecksums.cpp
- src/programs/bamsort.cpp
Changes:
=====================================
ChangeLog
=====================================
@@ -1,3 +1,9 @@
+biobambam2 (2.0.183-1) unstable; urgency=medium
+
+ * Adapt to change in libmaus2 (rename GetObject to GetCObject)
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Mon, 02 Aug 2021 17:54:00 +0200
+
biobambam2 (2.0.182-1) unstable; urgency=medium
* Add O (output file) option for bamfastcat
=====================================
configure.ac
=====================================
@@ -1,4 +1,4 @@
-AC_INIT(biobambam2,2.0.182,[germant at miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])
+AC_INIT(biobambam2,2.0.183,[germant at miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])
AC_CANONICAL_SYSTEM
AC_PROG_LIBTOOL
@@ -165,7 +165,7 @@ if test ! -z "${with_libmaus2}" ; then
fi
fi
-PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.774])
+PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.800])
if test ! -z "${with_libmaus2}" ; then
if test ! -z "${PKGCONFIGPATHSAVE}" ; then
=====================================
debian/changelog
=====================================
@@ -1,10 +1,13 @@
-biobambam2 (2.0.182+ds-1~0exp0) UNRELEASED; urgency=medium
+biobambam2 (2.0.183+ds-1) unstable; urgency=medium
* New upstream version
* all patches removed after application upstream
* d/control: updated my uploader address
+ * Standards-Version: 4.6.0 (routine-update)
+ * d/control: build depends on libmaus2-dev (>= 2.0.800); fixes configure
+ error at build time.
- -- Étienne Mollier <emollier at debian.org> Tue, 29 Jun 2021 23:14:44 +0200
+ -- Étienne Mollier <emollier at debian.org> Tue, 24 Aug 2021 16:37:12 +0200
biobambam2 (2.0.179+ds-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -6,8 +6,8 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
pkg-config,
- libmaus2-dev
-Standards-Version: 4.5.1
+ libmaus2-dev (>= 2.0.800)
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/biobambam2
Vcs-Git: https://salsa.debian.org/med-team/biobambam2.git
Homepage: https://gitlab.com/german.tischler/biobambam2
=====================================
src/biobambam2/ReadHeader.cpp
=====================================
@@ -20,8 +20,8 @@
#include <libmaus2/lz/BgzfInflate.hpp>
#include <libmaus2/bambam/BamHeader.hpp>
-#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/lz/BgzfDeflate.hpp>
+#include <libmaus2/util/GetCObject.hpp>
std::pair<uint64_t,std::string> readHeader(std::istream & in, biobambam2::HeaderUpdate const & HU, int const level, bool const dropheader)
{
@@ -45,7 +45,7 @@ std::pair<uint64_t,std::string> readHeader(std::istream & in, biobambam2::Header
libmaus2::lz::BgzfInflateBase::BaseBlockInfo const BBI = base.readBlock(in);
uint64_t const decompsize = base.decompressBlock(decompBuffer.begin(),BBI);
unsigned char const * udecomp = reinterpret_cast<unsigned char const *>(decompBuffer.begin());
- libmaus2::util::GetObject<unsigned char const *> GO(udecomp);
+ libmaus2::util::GetCObject<unsigned char const *> GO(udecomp);
std::pair<bool,uint64_t> const P = BHPS.parseHeader(GO,decompsize);
=====================================
src/programs/bam12split.cpp
=====================================
@@ -33,7 +33,6 @@
#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>
#include <libmaus2/util/ArgInfo.hpp>
-#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/PutObject.hpp>
#include <libmaus2/util/TempFileRemovalContainer.hpp>
=====================================
src/programs/bam12strip.cpp
=====================================
@@ -33,7 +33,6 @@
#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>
#include <libmaus2/util/ArgInfo.hpp>
-#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/PutObject.hpp>
#include <libmaus2/util/TempFileRemovalContainer.hpp>
=====================================
src/programs/bamauxmerge2.cpp
=====================================
@@ -43,7 +43,7 @@
#include <libmaus2/util/Histogram.hpp>
#include <biobambam2/KmerPoisson.hpp>
#include <libmaus2/bambam/BamHeaderParserState.hpp>
-#include <libmaus2/util/GetObject.hpp>
+#include <libmaus2/util/GetCObject.hpp>
#include <libmaus2/util/LELoad.hpp>
#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>
#include <libmaus2/fastx/FastAReader.hpp>
@@ -1002,7 +1002,7 @@ struct BlockProcessDispatcher : public libmaus2::parallel::SimpleThreadWorkPacka
DataBlockTypeInfo::pointer_type tptr = info.deFSH.pop();
libmaus2::bambam::BamHeaderParserState & BHPS = info.BHPS;
- libmaus2::util::GetObject<uint8_t const *> GO(reinterpret_cast<uint8_t const *>(tptr->c));
+ libmaus2::util::GetCObject<uint8_t const *> GO(reinterpret_cast<uint8_t const *>(tptr->c));
std::pair<bool,uint64_t> const HPB = BHPS.parseHeader(GO, 0);
std::pair<bool,uint64_t> const HP = BHPS.parseHeader(GO, tptr->n);
=====================================
src/programs/bamauxsort.cpp
=====================================
@@ -33,7 +33,6 @@
#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>
#include <libmaus2/util/ArgInfo.hpp>
-#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/PutObject.hpp>
#include <libmaus2/util/TempFileRemovalContainer.hpp>
=====================================
src/programs/bamfastcat.cpp
=====================================
@@ -19,7 +19,6 @@
#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>
=====================================
src/programs/bamfilteraux.cpp
=====================================
@@ -33,7 +33,6 @@
#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>
#include <libmaus2/util/ArgInfo.hpp>
-#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/PutObject.hpp>
#include <libmaus2/util/TempFileRemovalContainer.hpp>
=====================================
src/programs/bamfilterk.cpp
=====================================
@@ -19,7 +19,6 @@
#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>
=====================================
src/programs/bamfilternames.cpp
=====================================
@@ -30,7 +30,6 @@
#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>
#include <libmaus2/util/ArgInfo.hpp>
-#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/PutObject.hpp>
#include <libmaus2/util/TempFileRemovalContainer.hpp>
=====================================
src/programs/bamfilterrefid.cpp
=====================================
@@ -30,7 +30,6 @@
#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>
#include <libmaus2/util/ArgInfo.hpp>
-#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/PutObject.hpp>
#include <libmaus2/util/TempFileRemovalContainer.hpp>
=====================================
src/programs/bamfilterrg.cpp
=====================================
@@ -30,7 +30,6 @@
#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>
#include <libmaus2/util/ArgInfo.hpp>
-#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/PutObject.hpp>
#include <libmaus2/util/TempFileRemovalContainer.hpp>
=====================================
src/programs/bamfixmatecoordinates.cpp
=====================================
@@ -29,7 +29,6 @@
#include <libmaus2/fastx/CompactFastEncoder.hpp>
#include <libmaus2/bambam/BamAlignmentEncoderBase.hpp>
-#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/CountPutObject.hpp>
#include <libmaus2/util/ArgInfo.hpp>
=====================================
src/programs/bamfixmateinformation.cpp
=====================================
@@ -34,7 +34,6 @@
#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>
#include <libmaus2/util/ArgInfo.hpp>
-#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/PutObject.hpp>
#include <libmaus2/util/TempFileRemovalContainer.hpp>
=====================================
src/programs/bamflagsplit.cpp
=====================================
@@ -35,7 +35,6 @@
#include <libmaus2/aio/OutputStreamInstance.hpp>
#include <libmaus2/util/ArgInfo.hpp>
-#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/PutObject.hpp>
#include <libmaus2/util/TempFileRemovalContainer.hpp>
=====================================
src/programs/bammdnm.cpp
=====================================
@@ -147,7 +147,7 @@ static int bammdnm(libmaus2::util::ArgInfo const & arginfo)
if ( (! haveheader) && (pa != pc) )
{
- ::libmaus2::util::GetObject<uint8_t const *> G(pa);
+ ::libmaus2::util::GetCObject<uint8_t const *> G(pa);
std::pair<bool,uint64_t> const P = bamheaderparsestate.parseHeader(G,bgzfinfo.uncompressed);
// header complete?
=====================================
src/programs/bamrandomtag.cpp
=====================================
@@ -33,7 +33,6 @@
#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>
#include <libmaus2/util/ArgInfo.hpp>
-#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/PutObject.hpp>
#include <libmaus2/util/TempFileRemovalContainer.hpp>
=====================================
src/programs/bamreheader.cpp
=====================================
@@ -20,7 +20,6 @@
#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>
=====================================
src/programs/bamreplacechecksums.cpp
=====================================
@@ -20,7 +20,6 @@
#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>
=====================================
src/programs/bamsort.cpp
=====================================
@@ -38,7 +38,6 @@
#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>
#include <libmaus2/util/ArgInfo.hpp>
-#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/PutObject.hpp>
#include <libmaus2/util/TempFileRemovalContainer.hpp>
#include <libmaus2/bambam/ChecksumsFactory.hpp>
View it on GitLab: https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638
--
View it on GitLab: https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638
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