[med-svn] [Git][med-team/biobambam2][master] 5 commits: New upstream version 2.0.179+ds
Étienne Mollier
gitlab at salsa.debian.org
Wed Jan 6 17:12:39 GMT 2021
Étienne Mollier pushed to branch master at Debian Med / biobambam2
Commits:
2bf8b52e by Étienne Mollier at 2021-01-03T11:06:30+01:00
New upstream version 2.0.179+ds
- - - - -
5f020f31 by Étienne Mollier at 2021-01-03T11:06:30+01:00
routine-update: New upstream version
- - - - -
66f86564 by Étienne Mollier at 2021-01-03T11:06:31+01:00
Update upstream source from tag 'upstream/2.0.179+ds'
Update to upstream version '2.0.179+ds'
with Debian dir b73edffb6e2287f56964882405b7d32f892ac9b2
- - - - -
181a351a by Étienne Mollier at 2021-01-03T11:06:31+01:00
routine-update: Standards-Version: 4.5.1
- - - - -
7b3de3b6 by Étienne Mollier at 2021-01-03T11:19:43+01:00
routine-update: Ready to upload to unstable
- - - - -
12 changed files:
- ChangeLog
- configure.ac
- debian/changelog
- debian/control
- src/Makefile.am
- src/biobambam2/UpdateNumericalIndex.cpp
- src/biobambam2/UpdateNumericalIndex.hpp
- + src/programs/bamaddne.cpp
- src/programs/bamfastcat.cpp
- src/programs/bamfilterk.cpp
- src/programs/bamreheader.cpp
- src/programs/bamreplacechecksums.cpp
Changes:
=====================================
ChangeLog
=====================================
@@ -1,3 +1,10 @@
+biobambam2 (2.0.178-1) unstable; urgency=medium
+
+ * Add bamaddne
+ * bump libmaus2 version
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Mon, 23 Nov 2020 14:39:27 +0100
+
biobambam2 (2.0.177-1) unstable; urgency=medium
* Versioning cleanup
=====================================
configure.ac
=====================================
@@ -1,4 +1,4 @@
-AC_INIT(biobambam2,2.0.177,[germant at miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])
+AC_INIT(biobambam2,2.0.179,[germant at miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])
AC_CANONICAL_SYSTEM
AC_PROG_LIBTOOL
@@ -165,7 +165,7 @@ if test ! -z "${with_libmaus2}" ; then
fi
fi
-PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.749])
+PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.767])
if test ! -z "${with_libmaus2}" ; then
if test ! -z "${PKGCONFIGPATHSAVE}" ; then
@@ -463,7 +463,7 @@ AC_ARG_ENABLE(install_uncommon,
AS_HELP_STRING([--enable-install-uncommon],[enable installation of some uncommon programs (default no)]),
[install_uncommon=${enableval}],[install_uncommon=no])
-UNCOMMON="bamfilter bamfilterbyname bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname bamdisthist fastabgzfextract bamheap bamfrontback bamrandomtag bamheap2 bamheap3 bamtagconversion fastqtobampar bambisect vcffilterinfo vcfpatchcontigprepend vcfconcat vcfsort filtergtf bamconsensus vcfreplacecontigs vcffiltersamples bamexploderg bamexondepth bamheadercat bammarkduplicatesoptdist vcfdiff bamsimpledepth bamdepthmerge bamcountflags vcffilterfilterflags vcfreplacecontigsmap fastaselectreg"
+UNCOMMON="bamfilter bamfilterbyname bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname bamdisthist fastabgzfextract bamheap bamfrontback bamrandomtag bamheap2 bamheap3 bamtagconversion fastqtobampar bambisect vcffilterinfo vcfpatchcontigprepend vcfconcat vcfsort filtergtf bamconsensus vcfreplacecontigs vcffiltersamples bamexploderg bamexondepth bamheadercat bammarkduplicatesoptdist vcfdiff bamsimpledepth bamdepthmerge bamcountflags vcffilterfilterflags vcfreplacecontigsmap fastaselectreg bamdifference bamaddne"
UNCOMMONINSTALLED=
UNCOMMONUNINSTALLED=
if test "${install_uncommon}" = "yes" ; then
=====================================
debian/changelog
=====================================
@@ -1,9 +1,11 @@
-biobambam2 (2.0.177+ds-2) UNRELEASED; urgency=medium
+biobambam2 (2.0.179+ds-1) unstable; urgency=medium
* Switch d/watch to dversionmangle=auto to fix uscan constantly finding newer
upstream version.
+ * New upstream version
+ * Standards-Version: 4.5.1 (routine-update)
- -- Étienne Mollier <etienne.mollier at mailoo.org> Wed, 02 Dec 2020 22:19:53 +0100
+ -- Étienne Mollier <etienne.mollier at mailoo.org> Sun, 03 Jan 2021 11:06:34 +0100
biobambam2 (2.0.177+ds-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -6,8 +6,8 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
pkg-config,
- libmaus2-dev (>= 2.0.749)
-Standards-Version: 4.5.0
+ libmaus2-dev
+Standards-Version: 4.5.1
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/Makefile.am
=====================================
@@ -115,6 +115,7 @@ bin_PROGRAMS = \
bamdepthintersect \
bamfilterk \
bamfixpairinfo \
+ bamdifference \
bamfeaturecount @BLASTXMLTOBAMINSTEXP@ @UNCOMMONINSTALLED@
noinst_PROGRAMS = @BAMREFDEPTHPEAKS@ @BLASTXMLTOBAMNOINSTEXP@ @UNCOMMONUNINSTALLED@
@@ -153,7 +154,8 @@ EXTRA_PROGRAMS = blastnxmltobam \
bamsimpledepth \
bamdepthmerge \
bamcountflags \
- fastaselectreg
+ fastaselectreg \
+ bamaddne
populaterefcache_SOURCES = programs/populaterefcache.cpp biobambam2/Licensing.cpp
populaterefcache_LDADD = ${LIBMAUS2LIBS}
@@ -709,3 +711,13 @@ fastaselectreg_SOURCES = programs/fastaselectreg.cpp biobambam2/Licensing.cpp
fastaselectreg_LDADD = ${LIBMAUS2LIBS}
fastaselectreg_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
fastaselectreg_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}
+
+bamdifference_SOURCES = programs/bamdifference.cpp biobambam2/Licensing.cpp
+bamdifference_LDADD = ${LIBMAUS2LIBS}
+bamdifference_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
+bamdifference_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}
+
+bamaddne_SOURCES = programs/bamaddne.cpp biobambam2/Licensing.cpp
+bamaddne_LDADD = ${LIBMAUS2LIBS}
+bamaddne_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
+bamaddne_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}
=====================================
src/biobambam2/UpdateNumericalIndex.cpp
=====================================
@@ -22,7 +22,17 @@
namespace biobambam2
{
- void updateNumericalIndex(std::string const & bamfn, std::pair<uint64_t,std::string> const & compdata)
+ /**
+ * update numerical index
+ *
+ * @param bamfn: file name of BAM file
+ * @param compdata: (input header size, output data)
+ **/
+ void updateNumericalIndex(
+ std::string const & bamfn,
+ std::pair<uint64_t,std::string> const & compdata,
+ std::ostream * verbstr
+ )
{
std::string const indexfn = libmaus2::bambam::BamNumericalIndexBase::getIndexName(bamfn);
@@ -37,12 +47,21 @@ namespace biobambam2
// get index stats
uint64_t alcnt, mod, numblocks;
+
+ try
{
libmaus2::bambam::BamNumericalIndexDecoder indexdec(indexfn);
mod = indexdec.getBlockSize();
alcnt = indexdec.getAlignmentCount();
numblocks = indexdec.size();
}
+ catch(std::exception const & ex)
+ {
+ libmaus2::exception::LibMausException lme;
+ lme.getStream() << "[E] updateNumericalIndex: unable to get index stats: " << ex.what() << std::endl;
+ lme.finish();
+ throw lme;
+ }
// replace values for recompressed part
std::istringstream compistr(compdata.second + libmaus2::lz::BgzfDeflateBase::getEOFBlock());
@@ -64,7 +83,8 @@ namespace biobambam2
uint64_t const blockid = i / mod;
std::pair<uint64_t,uint64_t> const & start = P.second.start;
- // std::cerr << "replacing index position for " << i << " by " << start.first << "," << start.second << std::endl;
+ if ( verbstr )
+ (*verbstr) << "replacing index position for " << i << " by " << start.first << "," << start.second << std::endl;
libmaus2::bambam::BamNumericalIndexGenerator::ReplaceObject(
blockid,start.first,start.second
@@ -89,14 +109,25 @@ namespace biobambam2
libmaus2::aio::FileRemoval::removeFile(replfn);
- // std::cerr << "shifting index positions for [" << highestSet+1 << "," << numblocks << ")" << " by " << static_cast<int64_t>(compdata.second.size()) - static_cast<int64_t>(compdata.first) << std::endl;
+ if ( verbstr )
+ (*verbstr) << "shifting index positions for [" << highestSet+1 << "," << numblocks << ")" << " by " << static_cast<int64_t>(compdata.second.size()) - static_cast<int64_t>(compdata.first) << std::endl;
- // shift values in part we moved as is
- libmaus2::bambam::BamNumericalIndexGenerator::shiftValuesStreaming(
- indexfn,
- highestSet + 1,numblocks,
- static_cast<int64_t>(compdata.second.size()) - static_cast<int64_t>(compdata.first)
- );
+ try
+ {
+ // shift values in part we moved as is
+ libmaus2::bambam::BamNumericalIndexGenerator::shiftValuesStreaming(
+ indexfn,
+ highestSet + 1,numblocks,
+ static_cast<int64_t>(compdata.second.size()) - static_cast<int64_t>(compdata.first)
+ );
+ }
+ catch(std::exception const & ex)
+ {
+ libmaus2::exception::LibMausException lme;
+ lme.getStream() << "[E] updateNumericalIndex: failed in shiftValuesStreaming: " << ex.what() << std::endl;
+ lme.finish();
+ throw lme;
+ }
}
}
}
=====================================
src/biobambam2/UpdateNumericalIndex.hpp
=====================================
@@ -23,6 +23,6 @@
namespace biobambam2
{
- void updateNumericalIndex(std::string const & bamfn, std::pair<uint64_t,std::string> const & compdata);
+ void updateNumericalIndex(std::string const & bamfn, std::pair<uint64_t,std::string> const & compdata, std::ostream * verbstr = nullptr);
}
#endif
=====================================
src/programs/bamaddne.cpp
=====================================
@@ -0,0 +1,246 @@
+/**
+ bambam
+ Copyright (C) 2009-2013 German Tischler
+ Copyright (C) 2011-2013 Genome Research Limited
+
+ 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 "config.h"
+
+#include <iostream>
+#include <queue>
+
+#include <libmaus2/util/ArgInfo.hpp>
+#include <libmaus2/util/ArgParser.hpp>
+#include <libmaus2/timing/RealTimeClock.hpp>
+#include <libmaus2/bambam/BamBlockWriterBaseFactory.hpp>
+#include <libmaus2/bambam/BamMergeCoordinate.hpp>
+#include <libmaus2/bambam/BamMergeQueryName.hpp>
+#include <libmaus2/bambam/BamWriter.hpp>
+#include <libmaus2/bambam/BamMultiAlignmentDecoderFactory.hpp>
+#include <libmaus2/lz/BgzfDeflateOutputCallbackMD5.hpp>
+#include <libmaus2/bambam/BgzfDeflateOutputCallbackBamIndex.hpp>
+
+#include <biobambam2/Licensing.hpp>
+
+static int getDefaultVerbose() { return 1; }
+static int getDefaultMD5() { return 0; }
+static int getDefaultIndex() { return 0; }
+
+::libmaus2::bambam::BamHeader::unique_ptr_type updateHeader(
+ ::libmaus2::util::ArgParser const & arg,
+ ::libmaus2::bambam::BamHeader const & header
+)
+{
+ std::string const headertext(header.text);
+
+ // add PG line to header
+ std::string const upheadtext = ::libmaus2::bambam::ProgramHeaderLineSet::addProgramLine(
+ headertext,
+ "bamaddne", // ID
+ "bamaddne", // PN
+ arg.commandline, // CL
+ ::libmaus2::bambam::ProgramHeaderLineSet(headertext).getLastIdInChain(), // PP
+ std::string(PACKAGE_VERSION) // VN
+ );
+ // construct new header
+ ::libmaus2::bambam::BamHeader::unique_ptr_type uphead(new ::libmaus2::bambam::BamHeader(upheadtext));
+
+ return uphead;
+}
+
+int bamaddne(libmaus2::util::ArgParser const & arg)
+{
+ arg.printArgs(std::cerr);
+
+ libmaus2::timing::RealTimeClock rtc;
+ rtc.start();
+
+ if ( isatty(STDOUT_FILENO) && (!arg.uniqueArgPresent("O")) )
+ {
+ ::libmaus2::exception::LibMausException se;
+ se.getStream() << "Refusing write binary data to terminal, please redirect standard output to pipe or file." << std::endl;
+ se.finish();
+ throw se;
+ }
+
+ int const verbose = arg.getParsedArgOrDefault<int>("verbose",getDefaultVerbose());
+
+ /*
+ * start index/md5 callbacks
+ */
+ std::string const tmpfilenamebase = arg.getStringArgOrDefault("tmpfile",libmaus2::util::ArgInfo::getDefaultTmpFileName(arg.progname));
+ std::string const tmpfileindex = tmpfilenamebase + "_index";
+ ::libmaus2::util::TempFileRemovalContainer::addTempFile(tmpfileindex);
+
+ std::string md5filename;
+ std::string indexfilename;
+
+ std::vector< ::libmaus2::lz::BgzfDeflateOutputCallback * > cbs;
+ ::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Pmd5cb;
+ if ( arg.getParsedArgOrDefault<int>("md5",getDefaultMD5()) )
+ {
+ if ( libmaus2::bambam::BamBlockWriterBaseFactory::getMD5FileName(arg) != std::string() )
+ md5filename = libmaus2::bambam::BamBlockWriterBaseFactory::getMD5FileName(arg);
+ else
+ std::cerr << "[V] no filename for md5 given, not creating hash" << std::endl;
+
+ if ( md5filename.size() )
+ {
+ ::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Tmd5cb(new ::libmaus2::lz::BgzfDeflateOutputCallbackMD5);
+ Pmd5cb = std::move(Tmd5cb);
+ cbs.push_back(Pmd5cb.get());
+ }
+ }
+ libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
+ if ( arg.getParsedArgOrDefault<int>("index",getDefaultIndex()) )
+ {
+ if ( libmaus2::bambam::BamBlockWriterBaseFactory::getIndexFileName(arg) != std::string() )
+ indexfilename = libmaus2::bambam::BamBlockWriterBaseFactory::getIndexFileName(arg);
+ else
+ std::cerr << "[V] no filename for index given, not creating index" << std::endl;
+
+ if ( indexfilename.size() )
+ {
+ libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Tindex(new libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex(tmpfileindex));
+ Pindex = std::move(Tindex);
+ cbs.push_back(Pindex.get());
+ }
+ }
+ std::vector< ::libmaus2::lz::BgzfDeflateOutputCallback * > * Pcbs = 0;
+ if ( cbs.size() )
+ Pcbs = &cbs;
+ /*
+ * end md5/index callbacks
+ */
+
+ libmaus2::bambam::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
+ libmaus2::bambam::BamMultiAlignmentDecoderFactory::construct(arg)
+ );
+ libmaus2::bambam::BamAlignmentDecoder & decoder = decwrapper->getDecoder();
+ libmaus2::bambam::BamAlignment & algn = decoder.getAlignment();
+ ::libmaus2::bambam::BamHeader::unique_ptr_type uphead(updateHeader(arg,decoder.getHeader()));
+ std::string ne("1:N:0:AAAAAAAA");
+
+ libmaus2::bambam::BamBlockWriterBase::unique_ptr_type Pwriter(
+ libmaus2::bambam::BamBlockWriterBaseFactory::construct(*uphead,arg,Pcbs));
+
+ std::size_t lineid = 0;
+ for ( ; decoder.readAlignment(); )
+ {
+ int const isread1 = algn.isRead1();
+ int const isread2 = algn.isRead2();
+
+ if ( isread1 + isread2 != 1 )
+ {
+ libmaus2::exception::LibMausException lme;
+ lme.getStream() << "[E] invalid flags " << algn.getFlags() << " for PE read with name " << algn.getName() << std::endl;
+ lme.finish();
+ throw lme;
+ }
+
+ if ( isread1 )
+ ne[0] = '1';
+ else
+ ne[0] = '2';
+
+ if ( ! algn.hasAux("ne") )
+ {
+ algn.putAuxString("ne",ne);
+ }
+
+ std::size_t const llineid = ++lineid;
+
+ Pwriter->writeAlignment(algn);
+
+ if ( verbose && llineid%(1024*1024) == 0 )
+ {
+ std::cerr << "[V] " << llineid << "\t" << rtc.getElapsedSeconds() << "\t" << (llineid/rtc.getElapsedSeconds()) << "/s" << std::endl;
+ }
+ }
+
+ std::cerr << "[V] " << lineid << "\t" << rtc.getElapsedSeconds() << "\t" << lineid/rtc.getElapsedSeconds() << "/s" << std::endl;
+
+ Pwriter.reset();
+
+ if ( Pmd5cb )
+ {
+ Pmd5cb->saveDigestAsFile(md5filename);
+ }
+ if ( Pindex )
+ {
+ Pindex->flush(std::string(indexfilename));
+ }
+
+ return EXIT_SUCCESS;
+}
+
+int main(int argc, char * argv[])
+{
+ try
+ {
+ std::vector<libmaus2::util::ArgParser::ArgumentDefinition> Vformatcons;
+ Vformatcons.push_back(libmaus2::util::ArgParser::ArgumentDefinition("v","verbose",true));
+ Vformatcons.push_back(libmaus2::util::ArgParser::ArgumentDefinition("h","help",true));
+ Vformatcons.push_back(libmaus2::util::ArgParser::ArgumentDefinition("T","tmpfile",true));
+
+ std::vector<libmaus2::util::ArgParser::ArgumentDefinition> const Vformatin = libmaus2::bambam::BamAlignmentDecoderInfo::getArgumentDefinitions();
+ std::vector<libmaus2::util::ArgParser::ArgumentDefinition> const Vformatout = libmaus2::bambam::BamBlockWriterBaseFactory::getArgumentDefinitions();
+
+ std::vector<libmaus2::util::ArgParser::ArgumentDefinition> Vformat =
+ libmaus2::util::ArgParser::mergeFormat(libmaus2::util::ArgParser::mergeFormat(Vformatin,Vformatout),Vformatcons);
+
+ libmaus2::util::ArgParser const arg(argc,argv,Vformat);
+
+ if ( arg.uniqueArgPresent("help") )
+ {
+ std::cerr << ::biobambam2::Licensing::license();
+ std::cerr << std::endl;
+
+ #if 0
+ 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> ( "I=<[filename]>", "input file, can be set multiple times" ) );
+ V.push_back ( std::pair<std::string,std::string> ( "SO=<["+getDefaultSortOrder()+"]>]", "sort order (coordinate or queryname)" ) );
+ 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> ( "verbose=<["+::biobambam2::Licensing::formatNumber(getDefaultVerbose())+"]>", "print progress report" ) );
+ V.push_back ( std::pair<std::string,std::string> ( "md5=<["+::biobambam2::Licensing::formatNumber(getDefaultMD5())+"]>", "create md5 check sum (default: 0)" ) );
+ V.push_back ( std::pair<std::string,std::string> ( "md5filename=<filename>", "file name for md5 check sum (no checksum is computed if md5filename is unset)" ) );
+ V.push_back ( std::pair<std::string,std::string> ( "index=<["+::biobambam2::Licensing::formatNumber(getDefaultIndex())+"]>", "create BAM index (default: 0)" ) );
+ V.push_back ( std::pair<std::string,std::string> ( "indexfilename=<filename>", "file name for BAM index file (no BAM index is produced if indexfilename is unset)" ) );
+ V.push_back ( std::pair<std::string,std::string> ( "tmpfile=<filename>", "prefix for temporary files, default: create files in current directory" ) );
+ V.push_back ( std::pair<std::string,std::string> ( "IL=<filename>", "name of file containing input file names" ) );
+ #endif
+
+ std::vector< std::pair<std::string,std::string> > V;
+
+ V.push_back ( std::pair<std::string,std::string> ( "-v/--verbose=0/1", "print progress report" ) );
+
+ ::biobambam2::Licensing::printMap(std::cerr,V);
+
+ std::cerr << std::endl;
+ return EXIT_SUCCESS;
+ }
+
+ return bamaddne(arg);
+ }
+ catch(std::exception const & ex)
+ {
+ std::cerr << ex.what() << std::endl;
+ return EXIT_FAILURE;
+ }
+}
=====================================
src/programs/bamfastcat.cpp
=====================================
@@ -25,7 +25,6 @@
#include <libmaus2/bambam/BamBlockWriterBaseFactory.hpp>
#include <libmaus2/bambam/BamNumericalIndexDecoder.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>
=====================================
src/programs/bamfilterk.cpp
=====================================
@@ -27,7 +27,6 @@
#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>
=====================================
src/programs/bamreheader.cpp
=====================================
@@ -235,7 +235,7 @@ int bamreheader(libmaus2::util::ArgInfo const & arginfo)
}
}
- biobambam2::updateNumericalIndex(bamfn,compdata);
+ biobambam2::updateNumericalIndex(bamfn,compdata,&std::cerr);
}
}
=====================================
src/programs/bamreplacechecksums.cpp
=====================================
@@ -260,7 +260,7 @@ int bamreplacechecksums(libmaus2::util::ArgInfo const & arginfo)
}
}
- biobambam2::updateNumericalIndex(bamfn,compdata);
+ biobambam2::updateNumericalIndex(bamfn,compdata,&std::cerr);
}
}
View it on GitLab: https://salsa.debian.org/med-team/biobambam2/-/compare/743ab1642bee9b480336d6b6cc0ce6297dfd9ae0...7b3de3b693f8cc756be7e653178856cd002a24b9
--
View it on GitLab: https://salsa.debian.org/med-team/biobambam2/-/compare/743ab1642bee9b480336d6b6cc0ce6297dfd9ae0...7b3de3b693f8cc756be7e653178856cd002a24b9
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20210106/d1be4bcf/attachment-0001.html>
More information about the debian-med-commit
mailing list