int bamreset(::libmaus2::util::ArgInfo const & arginfo)
{
if ( isatty(STDIN_FILENO) )
{
::libmaus2::exception::LibMausException se;
se.getStream() << "Refusing to read binary data from terminal, please redirect standard input to pipe or file." << std::endl;
se.finish();
throw se;
}
if ( isatty(STDOUT_FILENO) )
{
::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 level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
int const resetsortorder = arginfo.getValue<int>("resetsortorder",getDefaultResetSortOrder());
::libmaus2::bambam::BamDecoder dec(std::cin,false);
::libmaus2::bambam::BamHeader const & header = dec.getHeader();
std::string headertext = header.text;
// no replacement header file given
if ( ! arginfo.hasArg("resetheadertext") )
{
// remove SQ lines
std::vector<libmaus2::bambam::HeaderLine> allheaderlines = libmaus2::bambam::HeaderLine::extractLines(headertext);
std::ostringstream upheadstr;
for ( uint64_t i = 0; i < allheaderlines.size(); ++i )
if ( allheaderlines[i].type != "SQ" )
upheadstr << allheaderlines[i].line << std::endl;
headertext = upheadstr.str();
}
// replace header given in file
else
{
std::string const headerfilename = arginfo.getUnparsedValue("resetheadertext","");
uint64_t const headerlen = libmaus2::util::GetFileSize::getFileSize(headerfilename);
libmaus2::aio::CheckedInputStream CIS(headerfilename);
libmaus2::autoarray::AutoArray<char> ctext(headerlen,false);
CIS.read(ctext.begin(),headerlen);
headertext = std::string(ctext.begin(),ctext.end());
}
// add PG line to header
headertext = libmaus2::bambam::ProgramHeaderLineSet::addProgramLine(
headertext,
"bamreset", // ID
"bamreset", // PN
arginfo.commandline, // CL
::libmaus2::bambam::ProgramHeaderLineSet(headertext).getLastIdInChain(), // PP
std::string(PACKAGE_VERSION) // VN
);
// construct new header
libmaus2::bambam::BamHeader uphead(headertext);
if ( resetsortorder )
uphead.changeSortOrder("unknown");
/*
* start index/md5 callbacks
*/
std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
std::string const tmpfileindex = tmpfilenamebase + "_index";
::libmaus2::util::TempFileRemovalContainer::addTempFile(tmpfileindex);
uint32_t const excludeflags = libmaus2::bambam::BamFlagBase::stringToFlags(
arginfo.getValue<std::string>("exclude",getDefaultExcludeFlags()));
std::string md5filename;
std::string indexfilename;
std::vector< ::libmaus2::lz::BgzfDeflateOutputCallback * > cbs;
::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Pmd5cb;
if ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( arginfo.hasArg("md5filename") && arginfo.getUnparsedValue("md5filename","") != "" )
md5filename = arginfo.getUnparsedValue("md5filename","");
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 = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( arginfo.hasArg("indexfilename") && arginfo.getUnparsedValue("indexfilename","") != "" )
indexfilename = arginfo.getUnparsedValue("indexfilename","");
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 = UNIQUE_PTR_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::BamWriter::unique_ptr_type writer(new ::libmaus2::bambam::BamWriter(std::cout,uphead,level,Pcbs));
libmaus2::timing::RealTimeClock rtc; rtc.start();
libmaus2::bambam::BamAlignment & algn = dec.getAlignment();
uint64_t c = 0;
bool const resetaux = arginfo.getValue<int>("resetaux",getDefaultResetAux());
libmaus2::bambam::BamAuxFilterVector::unique_ptr_type const prgfilter(libmaus2::bambam::BamAuxFilterVector::parseAuxFilterList(arginfo));
libmaus2::bambam::BamAuxFilterVector const * rgfilter = prgfilter.get();
while ( dec.readAlignment() )
{
bool const keep = resetAlignment(algn,resetaux /* reset aux */,excludeflags,rgfilter);
if ( keep )
algn.serialise(writer->getStream());
if ( verbose && (++c & (1024*1024-1)) == 0 )
std::cerr << "[V] " << c/(1024*1024) << " " << (c / rtc.getElapsedSeconds()) << std::endl;
}
writer.reset();
if ( Pmd5cb )
{
Pmd5cb->saveDigestAsFile(md5filename);
}
if ( Pindex )
{
Pindex->flush(std::string(indexfilename));
}
return EXIT_SUCCESS;
}
int bamclipreinsert(::libmaus::util::ArgInfo const & arginfo)
{
if ( isatty(STDIN_FILENO) )
{
::libmaus::exception::LibMausException se;
se.getStream() << "Refusing to read binary data from terminal, please redirect standard input to pipe or file." << std::endl;
se.finish();
throw se;
}
if ( isatty(STDOUT_FILENO) )
{
::libmaus::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 level = arginfo.getValue<int>("level",getDefaultLevel());
int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
switch ( level )
{
case Z_NO_COMPRESSION:
case Z_BEST_SPEED:
case Z_BEST_COMPRESSION:
case Z_DEFAULT_COMPRESSION:
break;
default:
{
::libmaus::exception::LibMausException se;
se.getStream()
<< "Unknown compression level, please use"
<< " level=" << Z_DEFAULT_COMPRESSION << " (default) or"
<< " level=" << Z_BEST_SPEED << " (fast) or"
<< " level=" << Z_BEST_COMPRESSION << " (best) or"
<< " level=" << Z_NO_COMPRESSION << " (no compression)" << std::endl;
se.finish();
throw se;
}
break;
}
::libmaus::bambam::BamDecoder dec(std::cin,false);
::libmaus::bambam::BamHeader const & header = dec.getHeader();
std::string const headertext(header.text);
// add PG line to header
std::string const upheadtext = ::libmaus::bambam::ProgramHeaderLineSet::addProgramLine(
headertext,
"bamclipreinsert", // ID
"bamclipreinsert", // PN
arginfo.commandline, // CL
::libmaus::bambam::ProgramHeaderLineSet(headertext).getLastIdInChain(), // PP
std::string(PACKAGE_VERSION) // VN
);
// construct new header
libmaus::bambam::BamHeader const uphead(upheadtext);
/*
* start index/md5 callbacks
*/
std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
std::string const tmpfileindex = tmpfilenamebase + "_index";
::libmaus::util::TempFileRemovalContainer::addTempFile(tmpfileindex);
std::string md5filename;
std::string indexfilename;
std::vector< ::libmaus::lz::BgzfDeflateOutputCallback * > cbs;
::libmaus::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Pmd5cb;
if ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( arginfo.hasArg("md5filename") && arginfo.getUnparsedValue("md5filename","") != "" )
md5filename = arginfo.getUnparsedValue("md5filename","");
else
std::cerr << "[V] no filename for md5 given, not creating hash" << std::endl;
if ( md5filename.size() )
{
::libmaus::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Tmd5cb(new ::libmaus::lz::BgzfDeflateOutputCallbackMD5);
Pmd5cb = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
libmaus::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( arginfo.hasArg("indexfilename") && arginfo.getUnparsedValue("indexfilename","") != "" )
indexfilename = arginfo.getUnparsedValue("indexfilename","");
else
std::cerr << "[V] no filename for index given, not creating index" << std::endl;
if ( indexfilename.size() )
{
libmaus::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Tindex(new libmaus::bambam::BgzfDeflateOutputCallbackBamIndex(tmpfileindex));
Pindex = UNIQUE_PTR_MOVE(Tindex);
cbs.push_back(Pindex.get());
}
}
std::vector< ::libmaus::lz::BgzfDeflateOutputCallback * > * Pcbs = 0;
if ( cbs.size() )
Pcbs = &cbs;
/*
* end md5/index callbacks
*/
::libmaus::bambam::BamWriter::unique_ptr_type writer(new ::libmaus::bambam::BamWriter(std::cout,uphead,level,Pcbs));
libmaus::bambam::BamAuxFilterVector bafv;
// bafv.set('z','z');
// std::vector<uint8_t> R(8);
// std::string const zz("zz");
libmaus::bambam::BamAlignment & algn = dec.getAlignment();
uint64_t c = 0;
libmaus::autoarray::AutoArray < std::pair<uint8_t,uint8_t> > auxtags;
libmaus::autoarray::AutoArray<libmaus::bambam::cigar_operation> cigop;
std::stack < libmaus::bambam::cigar_operation > hardstack;
libmaus::bambam::BamAlignment::D_array_type Tcigar;
while ( dec.readAlignment() )
{
// reinsert clipped parts and attach soft clipping cigar operations as needed
clipReinsert(algn,auxtags,bafv,cigop,Tcigar,hardstack);
algn.serialise(writer->getStream());
++c;
if ( verbose && (c & (1024*1024-1)) == 0 )
std::cerr << "[V] " << c/(1024*1024) << std::endl;
}
writer.reset();
if ( Pmd5cb )
{
Pmd5cb->saveDigestAsFile(md5filename);
}
if ( Pindex )
{
Pindex->flush(std::string(indexfilename));
}
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"
)
{
std::cerr << ::biobambam2::Licensing::license();
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> ( "verbose=<["+::biobambam2::Licensing::formatNumber(getDefaultVerbose())+"]>", "print progress information" ) );
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" ) );
V.push_back ( std::pair<std::string,std::string> ( "resetheadertext=[<>]", "replacement SAM header text file (default: filter header in source BAM file)" ) );
V.push_back ( std::pair<std::string,std::string> ( "exclude=["+getDefaultExcludeFlags()+"]", "drop alignments having any of the given flags set" ) );
V.push_back ( std::pair<std::string,std::string> ( std::string("resetaux=<[")+::biobambam2::Licensing::formatNumber(getDefaultResetAux())+"]>", "reset auxiliary fields" ) );
V.push_back ( std::pair<std::string,std::string> ( "auxfilter=[<>]", "comma separated list of aux tags to keep if resetaux=0 (default: keep all)" ) );
V.push_back ( std::pair<std::string,std::string> ( "resetsortorder=<["+::biobambam2::Licensing::formatNumber(getDefaultResetSortOrder())+"]>", "set sort order to unknown (default: 1)" ) );
::biobambam2::Licensing::printMap(std::cerr,V);
std::cerr << std::endl;
std::cerr << "Alignment flags: PAIRED,PROPER_PAIR,UNMAP,MUNMAP,REVERSE,MREVERSE,READ1,READ2,SECONDARY,QCFAIL,DUP,SUPPLEMENTARY" << std::endl;
return EXIT_SUCCESS;
}
return bamreset(arginfo);
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
int main(int argc, char * argv[])
{
try
{
::libmaus::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 << ::biobambam::Licensing::license();
return EXIT_SUCCESS;
}
else if (
arginfo.restargs[i] == "-h"
||
arginfo.restargs[i] == "--help"
)
{
std::cerr << ::biobambam::Licensing::license();
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=<["+::biobambam::Licensing::formatNumber(getDefaultLevel())+"]>", "compression settings for output bam file (0=uncompressed,1=fast,9=best,-1=zlib default)" ) );
V.push_back ( std::pair<std::string,std::string> ( "SO=<["+getDefaultSortOrder()+"]>", "sorting order (coordinate or queryname)" ) );
V.push_back ( std::pair<std::string,std::string> ( "verbose=<["+::biobambam::Licensing::formatNumber(getDefaultVerbose())+"]>", "print progress report" ) );
V.push_back ( std::pair<std::string,std::string> ( "blockmb=<["+::biobambam::Licensing::formatNumber(getDefaultBlockSize())+"]>", "size of internal memory buffer used for sorting in MiB" ) );
V.push_back ( std::pair<std::string,std::string> ( "disablevalidation=<["+::biobambam::Licensing::formatNumber(getDefaultDisableValidation())+"]>", "disable input validation (default is 0)" ) );
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> ( "md5=<["+::biobambam::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" ) );
V.push_back ( std::pair<std::string,std::string> ( "index=<["+::biobambam::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" ) );
V.push_back ( std::pair<std::string,std::string> ( std::string("inputformat=<[")+getDefaultInputFormat()+"]>", std::string("input format (") + libmaus::bambam::BamMultiAlignmentDecoderFactory::getValidInputFormats() + ")" ) );
V.push_back ( std::pair<std::string,std::string> ( std::string("outputformat=<[")+libmaus::bambam::BamBlockWriterBaseFactory::getDefaultOutputFormat()+"]>", std::string("output format (") + libmaus::bambam::BamBlockWriterBaseFactory::getValidOutputFormats() + ")" ) );
V.push_back ( std::pair<std::string,std::string> ( "I=<[stdin]>", "input filename (standard input if unset)" ) );
V.push_back ( std::pair<std::string,std::string> ( "inputthreads=<[1]>", "input helper threads (for inputformat=bam only, default: 1)" ) );
V.push_back ( std::pair<std::string,std::string> ( "reference=<>", "reference FastA (.fai file required, for cram i/o only)" ) );
V.push_back ( std::pair<std::string,std::string> ( "range=<>", "coordinate range to be processed (for coordinate sorted indexed BAM input only)" ) );
V.push_back ( std::pair<std::string,std::string> ( "outputthreads=<[1]>", "output helper threads (for outputformat=bam only, default: 1)" ) );
V.push_back ( std::pair<std::string,std::string> ( "O=<[stdout]>", "output filename (standard output if unset)" ) );
V.push_back ( std::pair<std::string,std::string> ( std::string("fixmates=<[")+::biobambam::Licensing::formatNumber(getDefaultFixMates())+"]>", "fix mate information (for name collated input only, disabled by default)" ) );
::biobambam::Licensing::printMap(std::cerr,V);
std::cerr << std::endl;
return EXIT_SUCCESS;
}
return bamsort(arginfo);
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
int bamchecksort(libmaus2::util::ArgInfo const & arginfo)
{
int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
libmaus2::bambam::BamDecoder bamdec(std::cin);
libmaus2::bambam::BamAlignment & algn = bamdec.getAlignment();
libmaus2::bambam::BamHeader const & header = bamdec.getHeader();
std::string const sortorder = libmaus2::bambam::BamHeader::getSortOrderStatic(header.text);
libmaus2::bambam::BamAlignment prevalgn;
if ( bamdec.readAlignment() )
{
prevalgn.swap(algn);
if ( sortorder == "coordinate" )
{
uint64_t c = 0;
while ( bamdec.readAlignment() )
{
bool const ok =
(static_cast<uint32_t>( algn.getRefID()) >
static_cast<uint32_t>(prevalgn.getRefID())
)
||
(
(static_cast<uint32_t>( algn.getRefID()) ==
static_cast<uint32_t>(prevalgn.getRefID())
)
&&
(static_cast<uint32_t>( algn.getPos()) >=
static_cast<uint32_t>(prevalgn.getPos())
)
);
if ( ! ok )
{
libmaus2::exception::LibMausException se;
se.getStream() << "Broken order:";
se.getStream() << prevalgn.formatAlignment(header) << std::endl;
se.getStream() << algn.formatAlignment(header) << std::endl;
se.finish();
throw se;
}
prevalgn.swap(algn);
if ( verbose && ( ((++c) & ((1ull<<20)-1)) == 0 ) )
std::cerr << "[V] " << c << std::endl;
}
if ( verbose )
std::cerr << "[V] " << c << std::endl;
std::cerr << "Alignments sorted by coordinate." << std::endl;
}
else if ( sortorder == "queryname" )
{
uint64_t c = 0;
while ( bamdec.readAlignment() )
{
// bool const ok = libmaus2::bambam::BamAlignmentNameComparator::compareInt(prevalgn,algn) <= 0;
bool const ok =
!libmaus2::bambam::BamAlignmentNameComparator::compare(algn,prevalgn);
if ( ! ok )
{
libmaus2::exception::LibMausException se;
se.getStream() << "Broken order:";
se.getStream() << prevalgn.formatAlignment(header) << std::endl;
se.getStream() << algn.formatAlignment(header) << std::endl;
se.getStream() << libmaus2::bambam::BamAlignmentNameComparator::compareInt(prevalgn,algn) << std::endl;
se.finish();
throw se;
}
prevalgn.swap(algn);
if ( verbose && ( ((++c) & ((1ull<<20)-1)) == 0 ) )
std::cerr << "[V] " << c << std::endl;
}
if ( verbose )
std::cerr << "[V] " << c << std::endl;
std::cerr << "Alignments sorted by query name." << std::endl;
}
else
{
std::cerr << "[V] not checking order for \"" << sortorder << "\"" << std::endl;
}
}
return EXIT_SUCCESS;
}
int main(int argc, char * argv[])
{
try
{
::libmaus::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 << ::biobambam::Licensing::license();
return EXIT_SUCCESS;
}
else if (
arginfo.restargs[i] == "-h"
||
arginfo.restargs[i] == "--help"
)
{
std::cerr << ::biobambam::Licensing::license();
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> ( "I=<filename>", "input file, can be set multiple times" ) );
V.push_back ( std::pair<std::string,std::string> ( "level=<["+::biobambam::Licensing::formatNumber(getDefaultLevel())+"]>", "compression settings for output bam file (0=uncompressed,1=fast,9=best,-1=zlib default)" ) );
V.push_back ( std::pair<std::string,std::string> ( "verbose=<["+::biobambam::Licensing::formatNumber(getDefaultVerbose())+"]>", "print progress report" ) );
V.push_back ( std::pair<std::string,std::string> ( "md5=<["+::biobambam::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 (default: extend output file name)" ) );
V.push_back ( std::pair<std::string,std::string> ( "index=<["+::biobambam::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 (default: extend output file name)" ) );
V.push_back ( std::pair<std::string,std::string> ( "tmpfile=<filename>", "prefix for temporary files, default: create files in current directory" ) );
::biobambam::Licensing::printMap(std::cerr,V);
std::cerr << std::endl;
return EXIT_SUCCESS;
}
return bamcat(arginfo);
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
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"
)
{
std::cerr << ::biobambam2::Licensing::license();
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> ( "verbose=<["+::biobambam2::Licensing::formatNumber(getDefaultVerbose())+"]>", "print progress report" ) );
V.push_back ( std::pair<std::string,std::string> ( "mod=<["+::biobambam2::Licensing::formatNumber(getDefaultMod())+"]>", "print progress for every mod'th alignment if verbose" ) );
V.push_back ( std::pair<std::string,std::string> ( "ranksplit=<["+::biobambam2::Licensing::formatNumber(getDefaultRankSplit())+"]>", "split rank pairs in names (see bam12split command)" ) );
V.push_back ( std::pair<std::string,std::string> ( "rankstrip=<["+::biobambam2::Licensing::formatNumber(getDefaultRankStrip())+"]>", "strip ranks of names (see bam12strip command)" ) );
V.push_back ( std::pair<std::string,std::string> ( "clipreinsert=<["+::biobambam2::Licensing::formatNumber(getDefaultClipReinsert())+"]>", "reinsert clipped sequence fragments (see bamclipreinsert command)" ) );
V.push_back ( std::pair<std::string,std::string> ( "zztoname=<["+::biobambam2::Licensing::formatNumber(getDefaultZZToName())+"]>", "move rank from zz to name aux field to name (see bamzztoname command)" ) );
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 (default: extend output file name)" ) );
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 (default: extend output file name)" ) );
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> ( "sanity=<["+::biobambam2::Licensing::formatNumber(getDefaultSanity())+"]>", "extra checking of reads" ) );
::biobambam2::Licensing::printMap(std::cerr,V);
std::cerr << std::endl;
return EXIT_SUCCESS;
}
return bam12auxmerge(arginfo);
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
int bamrecalculatecigar(libmaus2::util::ArgInfo const & arginfo)
{
if ( isatty(STDOUT_FILENO) )
{
::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 = arginfo.getValue<int>("verbose",getDefaultVerbose());
// input decoder wrapper
libmaus2::bambam::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
libmaus2::bambam::BamMultiAlignmentDecoderFactory::construct(
arginfo,false // put rank
)
);
libmaus2::bambam::BamAlignmentDecoder & bamdec = decwrapper->getDecoder();
libmaus2::bambam::BamAlignment & algn = bamdec.getAlignment();
libmaus2::bambam::BamHeader const & header = bamdec.getHeader();
::libmaus2::bambam::BamHeader::unique_ptr_type uphead(updateHeader(arginfo,header));
/*
* start index/md5 callbacks
*/
std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
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 ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( arginfo.hasArg("md5filename") && arginfo.getUnparsedValue("md5filename","") != "" )
md5filename = arginfo.getUnparsedValue("md5filename","");
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 = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( arginfo.hasArg("indexfilename") && arginfo.getUnparsedValue("indexfilename","") != "" )
indexfilename = arginfo.getUnparsedValue("indexfilename","");
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 = UNIQUE_PTR_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::BamBlockWriterBase::unique_ptr_type writer(
libmaus2::bambam::BamBlockWriterBaseFactory::construct(*uphead, arginfo, Pcbs)
);
libmaus2::autoarray::AutoArray<libmaus2::bambam::cigar_operation> cigopin;
libmaus2::autoarray::AutoArray<char> readdata;
libmaus2::bambam::BamAlignment::D_array_type T;
if ( ! arginfo.hasArg("reference") )
{
libmaus2::exception::LibMausException se;
se.getStream() << "reference key is missing." << std::endl;
se.finish();
throw se;
}
std::string const reference = arginfo.getUnparsedValue("reference","");
if ( ! libmaus2::util::GetFileSize::fileExists(reference) )
{
libmaus2::exception::LibMausException se;
se.getStream() << "file " << reference << " does not exist." << std::endl;
se.finish();
throw se;
}
libmaus2::fastx::FastAIndex::unique_ptr_type FAindex(libmaus2::fastx::FastAIndex::load(reference + ".fai"));
libmaus2::aio::InputStreamInstance FAISI(reference);
uint64_t c = 0;
libmaus2::autoarray::AutoArray<char> ref;
int64_t refloaded = -1;
while ( bamdec.readAlignment() )
{
if ( algn.isMapped() )
{
assert ( algn.getRefID() >= 0 );
if ( algn.getRefID() != refloaded )
{
if ( algn.getRefID() < refloaded )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "bamrecalculatecigar: file is not sorted by coordinate" << std::endl;
lme.finish();
throw lme;
}
ref = FAindex->readSequence(FAISI,algn.getRefID());
refloaded = algn.getRefID();
}
uint64_t const numcig = libmaus2::bambam::BamAlignmentDecoderBase::recalculateCigar(
algn.D.begin(),
ref.begin() + algn.getPos(),
cigopin,
readdata
);
algn.replaceCigarString(cigopin,numcig,T);
}
writer->writeAlignment(algn);
if ( ((++c) & ((1ull<<20)-1)) == 0 && verbose )
std::cerr << "[V] " << c << std::endl;
}
if ( verbose )
std::cerr << "[V] " << c << std::endl;
writer.reset();
if ( Pmd5cb )
{
Pmd5cb->saveDigestAsFile(md5filename);
}
if ( Pindex )
{
Pindex->flush(std::string(indexfilename));
}
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"
)
{
std::cerr << ::biobambam2::Licensing::license();
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> ( "verbose=<["+::biobambam2::Licensing::formatNumber(getDefaultVerbose())+"]>", "print stats at the end of a successfull run" ) );
V.push_back ( std::pair<std::string,std::string> ( "basequalhist=<["+::biobambam2::Licensing::formatNumber(getDefaultBaseQualHist())+"]>", "print base quality histogram at end of a successfull run" ) );
V.push_back ( std::pair<std::string,std::string> ( "passthrough=<["+::biobambam2::Licensing::formatNumber(getDefaultPassThrough())+"]>", "write alignments to standard output (default: do not pass through)" ) );
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> ( "tmpfile=<filename>", "prefix for temporary files, default: create files in current directory (passthrough=1, index=1 only)" ) );
V.push_back ( std::pair<std::string,std::string> ( "md5=<["+::biobambam2::Licensing::formatNumber(getDefaultMD5())+"]>", "create md5 check sum (default: 0, passthrough=1 only)" ) );
V.push_back ( std::pair<std::string,std::string> ( "md5filename=<filename>", "file name for md5 check sum" ) );
V.push_back ( std::pair<std::string,std::string> ( "index=<["+::biobambam2::Licensing::formatNumber(getDefaultIndex())+"]>", "create BAM index (default: 0, passthrough=1 only)" ) );
V.push_back ( std::pair<std::string,std::string> ( "indexfilename=<filename>", "file name for BAM index file" ) );
V.push_back ( std::pair<std::string,std::string> ( std::string("inputformat=<[")+getDefaultInputFormat()+"]>", std::string("input format (") + libmaus2::bambam::BamMultiAlignmentDecoderFactory::getValidInputFormats() + ")" ) );
V.push_back ( std::pair<std::string,std::string> ( std::string("outputformat=<[")+libmaus2::bambam::BamBlockWriterBaseFactory::getDefaultOutputFormat()+"]>", std::string("output format (") + libmaus2::bambam::BamBlockWriterBaseFactory::getValidOutputFormats() + ", passthrough=1 only)" ) );
V.push_back ( std::pair<std::string,std::string> ( "I=<[stdin]>", "input filename (standard input if unset)" ) );
V.push_back ( std::pair<std::string,std::string> ( "inputthreads=<[1]>", "input helper threads (for inputformat=bam only, default: 1)" ) );
V.push_back ( std::pair<std::string,std::string> ( "reference=<>", "reference FastA (.fai file required, for cram i/o only)" ) );
V.push_back ( std::pair<std::string,std::string> ( "range=<>", "coordinate range to be processed (for coordinate sorted indexed BAM input only)" ) );
V.push_back ( std::pair<std::string,std::string> ( "outputthreads=<[1]>", "output helper threads (for outputformat=bam only, default: 1, passthrough=1 only)" ) );
V.push_back ( std::pair<std::string,std::string> ( "O=<[stdout]>", "output filename (standard output if unset, passthrough=1 only)" ) );
::biobambam2::Licensing::printMap(std::cerr,V);
std::cerr << std::endl;
return EXIT_SUCCESS;
}
return bamvalidate(arginfo);
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
int bamfiltermc(libmaus2::util::ArgInfo const & arginfo)
{
bool const verbose = arginfo.getValue("verbose",getDefaultVerbose());
libmaus2::bambam::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
libmaus2::bambam::BamMultiAlignmentDecoderFactory::construct(arginfo));
::libmaus2::bambam::BamAlignmentDecoder * ppdec = &(decwrapper->getDecoder());
::libmaus2::bambam::BamAlignmentDecoder & dec = *ppdec;
::libmaus2::bambam::BamHeader const & header = dec.getHeader();
::libmaus2::bambam::BamAlignment & algn = dec.getAlignment();
std::string const tmpfilenamebase = arginfo.getUnparsedValue("tmpfile",arginfo.getDefaultTmpFileName());
uint64_t const numthreads = arginfo.getValueUnsignedNumeric<uint64_t>("numthreads",getDefaultNumThreads());
/*
* start index/md5 callbacks
*/
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 ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( libmaus2::bambam::BamBlockWriterBaseFactory::getMD5FileName(arginfo) != std::string() )
md5filename = libmaus2::bambam::BamBlockWriterBaseFactory::getMD5FileName(arginfo);
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 = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( libmaus2::bambam::BamBlockWriterBaseFactory::getIndexFileName(arginfo) != std::string() )
indexfilename = libmaus2::bambam::BamBlockWriterBaseFactory::getIndexFileName(arginfo);
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 = UNIQUE_PTR_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::BamHeader::unique_ptr_type genuphead(
libmaus2::bambam::BamHeaderUpdate::updateHeader(arginfo,header,"bamfiltermc",std::string(PACKAGE_VERSION))
);
libmaus2::bambam::BamBlockWriterBase::unique_ptr_type Pwriter(libmaus2::bambam::BamBlockWriterBaseFactory::construct(*genuphead,arginfo,Pcbs));
libmaus2::bambam::BamBlockWriterBase & wr = *Pwriter;
// freelist size
uint64_t const flsize = 16*1024;
libmaus2::util::FreeList < libmaus2::bambam::BamAlignment, BamAlignmentFreeListDefaultAllocator, BamAlignmentFreeListDefaultTypeInfo > FL(flsize);
libmaus2::util::SimpleQueue < libmaus2::bambam::BamAlignment::shared_ptr_type > Q;
libmaus2::bambam::BamAuxFilterVector auxvec;
auxvec.set('M','C');
uint64_t alcnt = 0;
while ( dec.readAlignment() )
{
if ( FL.empty() )
handleQueue(Q,FL,wr,auxvec,numthreads);
assert ( ! FL.empty() );
libmaus2::bambam::BamAlignment::shared_ptr_type P = FL.get();
P->swap(algn);
Q.push_back(P);
if ( verbose && ((++alcnt % (1024*1024)) == 0) )
std::cerr << "[V] " << alcnt << std::endl;
}
handleQueue(Q,FL,wr,auxvec,numthreads);
// reset BAM writer
Pwriter.reset();
if ( Pmd5cb )
Pmd5cb->saveDigestAsFile(md5filename);
if ( Pindex )
Pindex->flush(std::string(indexfilename));
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"
)
{
std::cerr << ::biobambam2::Licensing::license();
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> ( "verbose=<["+::biobambam2::Licensing::formatNumber(getDefaultVerbose())+"]>", "print progress report" ) );
V.push_back ( std::pair<std::string,std::string> ( std::string("inputformat=<[")+getDefaultInputFormat()+"]>", std::string("input format (") + libmaus2::bambam::BamMultiAlignmentDecoderFactory::getValidInputFormats() + ")" ) );
V.push_back ( std::pair<std::string,std::string> ( "I=<[stdin]>", "input filename (standard input if unset)" ) );
V.push_back ( std::pair<std::string,std::string> ( "inputthreads=<[1]>", "input helper threads (for inputformat=bam only, default: 1)" ) );
V.push_back ( std::pair<std::string,std::string> ( "outputthreads=<[1]>", "input helper threads (for inputformat=bam only, default: 1)" ) );
V.push_back ( std::pair<std::string,std::string> ( "numthreads=<[1]>", "number of worker threads (default: 1)" ) );
::biobambam2::Licensing::printMap(std::cerr,V);
std::cerr << std::endl;
return EXIT_SUCCESS;
}
return bamfiltermc(arginfo);
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
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"
)
{
std::cerr << ::biobambam2::Licensing::license();
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> ( "verbose=<["+::biobambam2::Licensing::formatNumber(getDefaultVerbose())+"]>", "print progress report" ) );
V.push_back ( std::pair<std::string,std::string> ( std::string("inputformat=<[")+getDefaultInputFormat()+"]>", std::string("input format (") + libmaus2::bambam::BamMultiAlignmentDecoderFactory::getValidInputFormats() + ")" ) );
V.push_back ( std::pair<std::string,std::string> ( std::string("outputformat=<[")+libmaus2::bambam::BamBlockWriterBaseFactory::getDefaultOutputFormat()+"]>", std::string("output format (") + libmaus2::bambam::BamBlockWriterBaseFactory::getValidOutputFormats() + ")" ) );
V.push_back ( std::pair<std::string,std::string> ( "I=<[stdin]>", "input filename (standard input if unset)" ) );
V.push_back ( std::pair<std::string,std::string> ( "inputthreads=<[1]>", "input helper threads (for inputformat=bam only, default: 1)" ) );
V.push_back ( std::pair<std::string,std::string> ( "reference=<>", "reference FastA (.fai file required, for cram i/o only)" ) );
V.push_back ( std::pair<std::string,std::string> ( "range=<>", "coordinate range to be processed (for coordinate sorted indexed BAM input only)" ) );
V.push_back ( std::pair<std::string,std::string> ( "outputthreads=<[1]>", "output helper threads (for outputformat=bam only, default: 1)" ) );
V.push_back ( std::pair<std::string,std::string> ( "O=<[stdout]>", "output filename (standard output if unset)" ) );
V.push_back ( std::pair<std::string,std::string> ( std::string("prefix=<[")+getDefaultPrefix()+"]>", "prefix of output file names" ) );
V.push_back ( std::pair<std::string,std::string> ( "thres=<["+::biobambam2::Licensing::formatNumber(getDefaultSizeThres())+"]>", "size threshold for the creation of next file" ) );
::biobambam2::Licensing::printMap(std::cerr,V);
std::cerr << std::endl;
return EXIT_SUCCESS;
}
return bamexplode(arginfo);
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
int bamheap2(libmaus2::util::ArgInfo const & arginfo)
{
bool const verbose = arginfo.getValue("verbose",getDefaultVerbose());
std::string const reference = arginfo.getUnparsedValue("reference",std::string());
std::string const outputprefix = arginfo.getUnparsedValue("outputprefix",std::string());
libmaus2::bambam::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
libmaus2::bambam::BamMultiAlignmentDecoderFactory::construct(arginfo));
::libmaus2::bambam::BamAlignmentDecoder * ppdec = &(decwrapper->getDecoder());
::libmaus2::bambam::BamAlignmentDecoder & dec = *ppdec;
::libmaus2::bambam::BamHeader const & header = dec.getHeader();
::libmaus2::bambam::BamAlignment const & algn = dec.getAlignment();
double const damult = arginfo.getValue<double>("amult",1);
double const dcmult = arginfo.getValue<double>("cmult",1);
double const dgmult = arginfo.getValue<double>("gmult",1);
double const dtmult = arginfo.getValue<double>("tmult",1);
double const dpadmult = arginfo.getValue<double>("padmult",1);
double maxmult = 0;
maxmult = std::max(damult,maxmult);
maxmult = std::max(dcmult,maxmult);
maxmult = std::max(dgmult,maxmult);
maxmult = std::max(dtmult,maxmult);
maxmult = std::max(dpadmult,maxmult);
uint64_t const amult = std::floor((damult / maxmult) * (1ull<<16) + 0.5);
uint64_t const cmult = std::floor((dcmult / maxmult) * (1ull<<16) + 0.5);
uint64_t const gmult = std::floor((dgmult / maxmult) * (1ull<<16) + 0.5);
uint64_t const tmult = std::floor((dtmult / maxmult) * (1ull<<16) + 0.5);
uint64_t const padmult = std::floor((dpadmult / maxmult) * (1ull<<16) + 0.5);
libmaus2::fastx::FastAIndex::unique_ptr_type Pindex;
libmaus2::aio::InputStreamInstance::unique_ptr_type PCIS;
if ( reference.size() )
{
libmaus2::fastx::FastAIndex::unique_ptr_type Tindex(
libmaus2::fastx::FastAIndex::load(reference+".fai")
);
Pindex = UNIQUE_PTR_MOVE(Tindex);
libmaus2::aio::InputStreamInstance::unique_ptr_type TCIS(new libmaus2::aio::InputStreamInstance(reference));
PCIS = UNIQUE_PTR_MOVE(TCIS);
}
libmaus2::autoarray::AutoArray<libmaus2::bambam::cigar_operation> cigop;
libmaus2::autoarray::AutoArray<char> bases;
int64_t prevrefid = -1;
std::string refidname = "*";
std::map< uint64_t, HeapEntry > M;
uint64_t alcnt = 0;
std::vector< std::pair<char,uint8_t> > pendinginserts;
int64_t loadedRefId = -1;
int64_t streamRefId = -1;
libmaus2::autoarray::AutoArray<char> refseqbases;
ConsensusAccuracy * consacc = 0;
std::map<uint64_t,ConsensusAccuracy> Mconsacc;
typedef libmaus2::util::shared_ptr<std::ostringstream>::type stream_ptr_type;
stream_ptr_type Pstream;
ConsensusAux Caux;
Caux.M['a'] = Caux.M['A'] = amult;
Caux.M['c'] = Caux.M['C'] = cmult;
Caux.M['g'] = Caux.M['G'] = gmult;
Caux.M['t'] = Caux.M['T'] = tmult;
Caux.M[padsym] = padmult;
while ( dec.readAlignment() )
{
if (
algn.isMapped() && (!algn.isQCFail()) &&
algn.getLseq()
)
{
assert ( ! pendinginserts.size() );
uint32_t const numcigop = algn.getCigarOperations(cigop);
uint64_t readpos = 0;
uint64_t refpos = algn.getPos();
uint64_t const seqlen = algn.decodeRead(bases);
uint8_t const * qual = libmaus2::bambam::BamAlignmentDecoderBase::getQual(algn.D.begin());
// handle finished columns
if ( algn.getRefID() != prevrefid )
{
while ( M.size() )
{
HeapEntry & H = M.begin()->second;
if ( outputprefix.size() && (streamRefId != prevrefid) )
{
if ( Pstream )
{
std::ostringstream fnostr;
fnostr << outputprefix << "_" << header.getRefIDName(streamRefId);
libmaus2::aio::OutputStreamInstance PFOS(fnostr.str());
PFOS << ">" << header.getRefIDName(streamRefId) << '\n';
PFOS << Pstream->str() << '\n';
Pstream.reset();
}
stream_ptr_type Tstream(new std::ostringstream);
Pstream = Tstream;
streamRefId = prevrefid;
}
if ( Pindex && (loadedRefId != prevrefid) )
{
refseqbases = Pindex->readSequence(*PCIS, Pindex->getSequenceIdByName(refidname));
loadedRefId = prevrefid;
if ( Mconsacc.find(loadedRefId) == Mconsacc.end() )
Mconsacc[loadedRefId] = ConsensusAccuracy(refseqbases.size());
consacc = &(Mconsacc[loadedRefId]);
}
H.toStream(std::cout,M.begin()->first,refidname,(M.begin()->first < refseqbases.size()) ? static_cast<int>(refseqbases[M.begin()->first]) : -1,Caux,consacc,Pstream.get());
M.erase(M.begin());
}
prevrefid = algn.getRefID();
refidname = header.getRefIDName(prevrefid);
}
else
{
while ( M.size() && M.begin()->first < refpos )
{
HeapEntry & H = M.begin()->second;
if ( outputprefix.size() && (streamRefId != prevrefid) )
{
if ( Pstream )
{
std::ostringstream fnostr;
fnostr << outputprefix << "_" << header.getRefIDName(streamRefId);
libmaus2::aio::OutputStreamInstance PFOS(fnostr.str());
PFOS << ">" << header.getRefIDName(streamRefId) << '\n';
PFOS << Pstream->str() << '\n';
Pstream.reset();
}
stream_ptr_type Tstream(new std::ostringstream);
Pstream = Tstream;
streamRefId = prevrefid;
}
if ( Pindex && (loadedRefId != prevrefid) )
{
refseqbases = Pindex->readSequence(*PCIS, Pindex->getSequenceIdByName(refidname));
loadedRefId = prevrefid;
if ( Mconsacc.find(loadedRefId) == Mconsacc.end() )
Mconsacc[loadedRefId] = ConsensusAccuracy(refseqbases.size());
consacc = &(Mconsacc[loadedRefId]);
}
H.toStream(std::cout,M.begin()->first,refidname,(M.begin()->first < refseqbases.size()) ? static_cast<int>(refseqbases[M.begin()->first]) : -1,Caux,consacc,Pstream.get());
M.erase(M.begin());
}
}
for ( uint64_t ci = 0; ci < numcigop; ++ci )
{
uint64_t const ciglen = cigop[ci].second;
switch ( cigop[ci].first )
{
case libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_CMATCH:
case libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_CEQUAL:
case libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_CDIFF:
{
if ( pendinginserts.size() )
{
M[refpos].I.push_back(pendinginserts);
pendinginserts.resize(0);
}
for ( uint64_t i = 0; i < ciglen; ++i )
{
M[refpos].V.push_back(std::make_pair(bases[readpos],qual[readpos]));
readpos++;
refpos++;
}
break;
}
case libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_CINS:
{
for ( uint64_t i = 0; i < ciglen; ++i, ++readpos )
pendinginserts.push_back(std::make_pair(bases[readpos],qual[readpos]));
break;
}
case libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_CDEL:
// handle pending inserts
if ( pendinginserts.size() )
{
M[refpos].I.push_back(pendinginserts);
pendinginserts.resize(0);
}
// deleting bases from the reference
for ( uint64_t i = 0; i < ciglen; ++i, ++refpos )
M[refpos].V.push_back(std::make_pair(padsym,0));
break;
case libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_CREF_SKIP:
// handle pending inserts
if ( pendinginserts.size() )
{
M[refpos].I.push_back(pendinginserts);
pendinginserts.resize(0);
}
// skip bases on reference
for ( uint64_t i = 0; i < ciglen; ++i )
{
refpos++;
}
break;
case libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_CSOFT_CLIP:
// skip bases on read
for ( uint64_t i = 0; i < ciglen; ++i )
{
readpos++;
}
break;
case libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_CHARD_CLIP:
break;
case libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_CPAD:
{
for ( uint64_t i = 0; i < ciglen; ++i, ++readpos )
pendinginserts.push_back(std::make_pair(padsym,0));
break;
}
}
}
if ( pendinginserts.size() )
{
M[refpos].I.push_back(pendinginserts);
M[refpos].iadd++;
pendinginserts.resize(0);
}
assert ( readpos == seqlen );
}
if ( verbose && ((++alcnt % (1024*1024)) == 0) )
std::cerr << "[V] " << alcnt << std::endl;
}
while ( M.size() )
{
HeapEntry & H = M.begin()->second;
if ( outputprefix.size() && (streamRefId != prevrefid) )
{
if ( Pstream )
{
std::ostringstream fnostr;
fnostr << outputprefix << "_" << header.getRefIDName(streamRefId);
libmaus2::aio::OutputStreamInstance PFOS(fnostr.str());
PFOS << ">" << header.getRefIDName(streamRefId) << '\n';
PFOS << Pstream->str() << '\n';
Pstream.reset();
}
stream_ptr_type Tstream(new std::ostringstream);
Pstream = Tstream;
streamRefId = prevrefid;
}
if ( Pindex && (loadedRefId != prevrefid) )
{
refseqbases = Pindex->readSequence(*PCIS, Pindex->getSequenceIdByName(refidname));
loadedRefId = prevrefid;
if ( Mconsacc.find(loadedRefId) == Mconsacc.end() )
Mconsacc[loadedRefId] = ConsensusAccuracy(refseqbases.size());
consacc = &(Mconsacc[loadedRefId]);
}
H.toStream(std::cout,M.begin()->first,refidname,(M.begin()->first < refseqbases.size()) ? static_cast<int>(refseqbases[M.begin()->first]) : -1,Caux,consacc,Pstream.get());
M.erase(M.begin());
}
if ( Pstream )
{
std::ostringstream fnostr;
fnostr << outputprefix << "_" << header.getRefIDName(streamRefId);
libmaus2::aio::OutputStreamInstance PFOS(fnostr.str());
PFOS << ">" << header.getRefIDName(streamRefId) << '\n';
PFOS << Pstream->str() << '\n';
Pstream.reset();
}
ConsensusAccuracy constotal;
for ( std::map<uint64_t,ConsensusAccuracy>::const_iterator ita = Mconsacc.begin(); ita != Mconsacc.end(); ++ita )
{
std::cerr << header.getRefIDName(ita->first) << "\t" << ita->second << std::endl;
std::map<uint64_t,uint64_t> const M = ita->second.depthhistogram.get();
uint64_t total = 0;
uint64_t preavg = 0;
for ( std::map<uint64_t,uint64_t>::const_iterator aita = M.begin(); aita != M.end(); ++aita )
{
total += aita->second;
preavg += aita->first * aita->second;
}
uint64_t acc = 0;
for ( std::map<uint64_t,uint64_t>::const_iterator aita = M.begin(); aita != M.end(); ++aita )
{
acc += aita->second;
std::cerr << "H[" << header.getRefIDName(ita->first) << "," << aita->first << ",+]"
<< "\t" << aita->second << "\t" << static_cast<double>(aita->second)/total
<< "\t" << acc << "\t" << static_cast<double>(acc)/total << std::endl;
}
acc = 0;
for ( std::map<uint64_t,uint64_t>::const_reverse_iterator aita = M.rbegin(); aita != M.rend(); ++aita )
{
acc += aita->second;
std::cerr << "H[" << header.getRefIDName(ita->first) << "," << aita->first << ",-]"
<< "\t" << aita->second << "\t" << static_cast<double>(aita->second)/total
<< "\t" << acc << "\t" << static_cast<double>(acc)/total << std::endl;
}
std::cerr << "H[" << header.getRefIDName(ita->first) << ",avg]\t" <<
static_cast<double>(preavg)/total << std::endl;
constotal += ita->second;
}
if ( Mconsacc.size() )
{
std::cerr << "all\t" << constotal << std::endl;
std::map<uint64_t,uint64_t> const M = constotal.depthhistogram.get();
uint64_t total = 0;
uint64_t preavg = 0;
for ( std::map<uint64_t,uint64_t>::const_iterator aita = M.begin(); aita != M.end(); ++aita )
{
total += aita->second;
preavg += aita->first * aita->second;
}
uint64_t acc = 0;
for ( std::map<uint64_t,uint64_t>::const_iterator aita = M.begin(); aita != M.end(); ++aita )
{
acc += aita->second;
std::cerr << "H[" << "all" << "," << aita->first << ",+]"
<< "\t" << aita->second << "\t" << static_cast<double>(aita->second)/total
<< "\t" << acc << "\t" << static_cast<double>(acc)/total << std::endl;
}
acc = 0;
for ( std::map<uint64_t,uint64_t>::const_reverse_iterator aita = M.rbegin(); aita != M.rend(); ++aita )
{
acc += aita->second;
std::cerr << "H[" << "all" << "," << aita->first << ",-]"
<< "\t" << aita->second << "\t" << static_cast<double>(aita->second)/total
<< "\t" << acc << "\t" << static_cast<double>(acc)/total << std::endl;
}
std::cerr << "H[all,avg]\t" << static_cast<double>(preavg) / total << std::endl;
}
return EXIT_SUCCESS;
}
int bamsort(::libmaus::util::ArgInfo const & arginfo)
{
::libmaus::util::TempFileRemovalContainer::setup();
bool const inputisstdin = (!arginfo.hasArg("I")) || (arginfo.getUnparsedValue("I","-") == "-");
bool const outputisstdout = (!arginfo.hasArg("O")) || (arginfo.getUnparsedValue("O","-") == "-");
if ( isatty(STDIN_FILENO) && inputisstdin && (arginfo.getValue<std::string>("inputformat","bam") != "sam") )
{
::libmaus::exception::LibMausException se;
se.getStream() << "Refusing to read binary data from terminal, please redirect standard input to pipe or file." << std::endl;
se.finish();
throw se;
}
if ( isatty(STDOUT_FILENO) && outputisstdout && (arginfo.getValue<std::string>("outputformat","bam") != "sam") )
{
::libmaus::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 = arginfo.getValue<int>("verbose",getDefaultVerbose());
bool const disablevalidation = arginfo.getValue<int>("disablevalidation",getDefaultDisableValidation());
std::string const inputformat = arginfo.getUnparsedValue("inputformat",getDefaultInputFormat());
int const level = arginfo.getValue<int>("level",getDefaultLevel());
switch ( level )
{
case Z_NO_COMPRESSION:
case Z_BEST_SPEED:
case Z_BEST_COMPRESSION:
case Z_DEFAULT_COMPRESSION:
break;
default:
{
::libmaus::exception::LibMausException se;
se.getStream()
<< "Unknown compression level, please use"
<< " level=" << Z_DEFAULT_COMPRESSION << " (default) or"
<< " level=" << Z_BEST_SPEED << " (fast) or"
<< " level=" << Z_BEST_COMPRESSION << " (best) or"
<< " level=" << Z_NO_COMPRESSION << " (no compression)" << std::endl;
se.finish();
throw se;
}
break;
}
// prefix for tmp files
std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
std::string const tmpfilenameout = tmpfilenamebase + "_bamsort";
::libmaus::util::TempFileRemovalContainer::addTempFile(tmpfilenameout);
uint64_t blockmem = arginfo.getValue<uint64_t>("blockmb",getDefaultBlockSize())*1024*1024;
std::string const sortorder = arginfo.getValue<std::string>("SO","coordinate");
bool const fixmates = arginfo.getValue<int>("fixmates",getDefaultFixMates());
uint64_t sortthreads = arginfo.getValue<uint64_t>("sortthreads",getDefaultSortThreads());
// input decoder wrapper
libmaus::bambam::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
libmaus::bambam::BamMultiAlignmentDecoderFactory::construct(
arginfo,false // put rank
)
);
::libmaus::bambam::BamAlignmentDecoder * ppdec = &(decwrapper->getDecoder());
::libmaus::bambam::BamAlignmentDecoder & dec = *ppdec;
if ( disablevalidation )
dec.disableValidation();
::libmaus::bambam::BamHeader const & header = dec.getHeader();
std::string const headertext(header.text);
// add PG line to header
std::string const upheadtext = ::libmaus::bambam::ProgramHeaderLineSet::addProgramLine(
headertext,
"bamsort", // ID
"bamsort", // PN
arginfo.commandline, // CL
::libmaus::bambam::ProgramHeaderLineSet(headertext).getLastIdInChain(), // PP
std::string(PACKAGE_VERSION) // VN
);
// construct new header
::libmaus::bambam::BamHeader uphead(upheadtext);
/*
* start index/md5 callbacks
*/
std::string const tmpfileindex = tmpfilenamebase + "_index";
::libmaus::util::TempFileRemovalContainer::addTempFile(tmpfileindex);
std::string md5filename;
std::string indexfilename;
std::vector< ::libmaus::lz::BgzfDeflateOutputCallback * > cbs;
::libmaus::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Pmd5cb;
if ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( arginfo.hasArg("md5filename") && arginfo.getUnparsedValue("md5filename","") != "" )
md5filename = arginfo.getUnparsedValue("md5filename","");
else
std::cerr << "[V] no filename for md5 given, not creating hash" << std::endl;
if ( md5filename.size() )
{
::libmaus::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Tmd5cb(new ::libmaus::lz::BgzfDeflateOutputCallbackMD5);
Pmd5cb = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
libmaus::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( arginfo.hasArg("indexfilename") && arginfo.getUnparsedValue("indexfilename","") != "" )
indexfilename = arginfo.getUnparsedValue("indexfilename","");
else
std::cerr << "[V] no filename for index given, not creating index" << std::endl;
if ( indexfilename.size() )
{
libmaus::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Tindex(new libmaus::bambam::BgzfDeflateOutputCallbackBamIndex(tmpfileindex));
Pindex = UNIQUE_PTR_MOVE(Tindex);
cbs.push_back(Pindex.get());
}
}
std::vector< ::libmaus::lz::BgzfDeflateOutputCallback * > * Pcbs = 0;
if ( cbs.size() )
Pcbs = &cbs;
/*
* end md5/index callbacks
*/
if ( sortorder != "queryname" )
uphead.changeSortOrder("coordinate");
else
uphead.changeSortOrder("queryname");
libmaus::bambam::BamBlockWriterBase::unique_ptr_type Pout ( libmaus::bambam::BamBlockWriterBaseFactory::construct(uphead, arginfo, Pcbs) );
if ( fixmates )
{
if ( sortorder != "queryname" )
{
::libmaus::bambam::BamEntryContainer< ::libmaus::bambam::BamAlignmentPosComparator >
BEC(blockmem,tmpfilenameout,sortthreads);
if ( verbose )
std::cerr << "[V] Reading alignments from source." << std::endl;
uint64_t incnt = 0;
// current alignment
libmaus::bambam::BamAlignment & curalgn = dec.getAlignment();
// previous alignment
libmaus::bambam::BamAlignment prevalgn;
// previous alignment valid
bool prevalgnvalid = false;
// MQ field filter
libmaus::bambam::BamAuxFilterVector MQfilter;
MQfilter.set("MQ");
while ( dec.readAlignment() )
{
if ( curalgn.isSecondary() || curalgn.isSupplementary() )
{
BEC.putAlignment(curalgn);
}
else if ( prevalgnvalid )
{
// different name
if ( strcmp(curalgn.getName(),prevalgn.getName()) )
{
BEC.putAlignment(prevalgn);
curalgn.swap(prevalgn);
}
// same name
else
{
libmaus::bambam::BamAlignment::fixMateInformation(prevalgn,curalgn,MQfilter);
BEC.putAlignment(prevalgn);
BEC.putAlignment(curalgn);
prevalgnvalid = false;
}
}
else
{
prevalgn.swap(curalgn);
prevalgnvalid = true;
}
if ( verbose && ( ( ++incnt & ((1ull<<20)-1) ) == 0 ) )
std::cerr << "[V] " << incnt << std::endl;
}
if ( prevalgnvalid )
{
BEC.putAlignment(prevalgn);
prevalgnvalid = false;
}
if ( verbose )
std::cerr << "[V] read " << incnt << " alignments" << std::endl;
// BEC.createOutput(std::cout, uphead, level, verbose, Pcbs);
BEC.createOutput(*Pout, verbose);
}
else
{
::libmaus::bambam::BamEntryContainer< ::libmaus::bambam::BamAlignmentNameComparator >
BEC(blockmem,tmpfilenameout,sortthreads);
if ( verbose )
std::cerr << "[V] Reading alignments from source." << std::endl;
uint64_t incnt = 0;
// current alignment
libmaus::bambam::BamAlignment & curalgn = dec.getAlignment();
// previous alignment
libmaus::bambam::BamAlignment prevalgn;
// previous alignment valid
bool prevalgnvalid = false;
// MQ field filter
libmaus::bambam::BamAuxFilterVector MQfilter;
MQfilter.set("MQ");
while ( dec.readAlignment() )
{
if ( curalgn.isSecondary() || curalgn.isSupplementary() )
{
BEC.putAlignment(curalgn);
}
else if ( prevalgnvalid )
{
// different name
if ( strcmp(curalgn.getName(),prevalgn.getName()) )
{
BEC.putAlignment(prevalgn);
curalgn.swap(prevalgn);
}
// same name
else
{
libmaus::bambam::BamAlignment::fixMateInformation(prevalgn,curalgn,MQfilter);
BEC.putAlignment(prevalgn);
BEC.putAlignment(curalgn);
prevalgnvalid = false;
}
}
else
{
prevalgn.swap(curalgn);
prevalgnvalid = true;
}
if ( verbose && ( ( ++incnt & ((1ull<<20)-1) ) == 0 ) )
std::cerr << "[V] " << incnt << std::endl;
}
if ( prevalgnvalid )
{
BEC.putAlignment(prevalgn);
prevalgnvalid = false;
}
if ( verbose )
std::cerr << "[V] read " << incnt << " alignments" << std::endl;
// BEC.createOutput(std::cout, uphead, level, verbose, Pcbs);
BEC.createOutput(*Pout, verbose);
}
}
else
{
if ( sortorder != "queryname" )
{
::libmaus::bambam::BamEntryContainer< ::libmaus::bambam::BamAlignmentPosComparator > BEC(blockmem,tmpfilenameout,sortthreads);
if ( verbose )
std::cerr << "[V] Reading alignments from source." << std::endl;
uint64_t incnt = 0;
while ( dec.readAlignment() )
{
BEC.putAlignment(dec.getAlignment());
incnt++;
if ( verbose && (incnt % (1024*1024) == 0) )
std::cerr << "[V] " << incnt/(1024*1024) << "M" << std::endl;
}
if ( verbose )
std::cerr << "[V] read " << incnt << " alignments" << std::endl;
// BEC.createOutput(std::cout, uphead, level, verbose, Pcbs);
BEC.createOutput(*Pout, verbose);
}
else
{
::libmaus::bambam::BamEntryContainer< ::libmaus::bambam::BamAlignmentNameComparator > BEC(blockmem,tmpfilenameout,sortthreads);
if ( verbose )
std::cerr << "[V] Reading alignments from source." << std::endl;
uint64_t incnt = 0;
while ( dec.readAlignment() )
{
BEC.putAlignment(dec.getAlignment());
incnt++;
if ( verbose && (incnt % (1024*1024) == 0) )
std::cerr << "[V] " << incnt/(1024*1024) << "M" << std::endl;
}
if ( verbose )
std::cerr << "[V] read " << incnt << " alignments" << std::endl;
// BEC.createOutput(std::cout, uphead, level, verbose, Pcbs);
BEC.createOutput(*Pout, verbose);
}
}
// flush encoder so callbacks see all output data
Pout.reset();
if ( Pmd5cb )
{
Pmd5cb->saveDigestAsFile(md5filename);
}
if ( Pindex )
{
Pindex->flush(std::string(indexfilename));
}
return EXIT_SUCCESS;
}
int bam12split(::libmaus::util::ArgInfo const & arginfo)
{
::libmaus::util::TempFileRemovalContainer::setup();
if ( isatty(STDIN_FILENO) )
{
::libmaus::exception::LibMausException se;
se.getStream() << "Refusing to read binary data from terminal, please redirect standard input to pipe or file." << std::endl;
se.finish();
throw se;
}
if ( isatty(STDOUT_FILENO) )
{
::libmaus::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;
}
if ( arginfo.hasArg("keep") && arginfo.hasArg("remove") )
{
::libmaus::exception::LibMausException se;
se.getStream() << "The keep and remove keys are mutually exclusive." << std::endl;
se.finish();
throw se;
}
int const level = libmaus::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
::libmaus::bambam::BamDecoder dec(std::cin,false);
::libmaus::bambam::BamHeader const & header = dec.getHeader();
std::string const headertext(header.text);
// add PG line to header
std::string const upheadtext = ::libmaus::bambam::ProgramHeaderLineSet::addProgramLine(
headertext,
"bam12split", // ID
"bam12split", // PN
arginfo.commandline, // CL
::libmaus::bambam::ProgramHeaderLineSet(headertext).getLastIdInChain(), // PP
std::string(PACKAGE_VERSION) // VN
);
// construct new header
libmaus::bambam::BamHeader uphead(upheadtext);
uphead.changeSortOrder("unknown");
/*
* start index/md5 callbacks
*/
std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
std::string const tmpfileindex = tmpfilenamebase + "_index";
::libmaus::util::TempFileRemovalContainer::addTempFile(tmpfileindex);
std::string md5filename;
std::string indexfilename;
std::vector< ::libmaus::lz::BgzfDeflateOutputCallback * > cbs;
::libmaus::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Pmd5cb;
if ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( arginfo.hasArg("md5filename") && arginfo.getUnparsedValue("md5filename","") != "" )
md5filename = arginfo.getUnparsedValue("md5filename","");
else
std::cerr << "[V] no filename for md5 given, not creating hash" << std::endl;
if ( md5filename.size() )
{
::libmaus::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Tmd5cb(new ::libmaus::lz::BgzfDeflateOutputCallbackMD5);
Pmd5cb = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
libmaus::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( arginfo.hasArg("indexfilename") && arginfo.getUnparsedValue("indexfilename","") != "" )
indexfilename = arginfo.getUnparsedValue("indexfilename","");
else
std::cerr << "[V] no filename for index given, not creating index" << std::endl;
if ( indexfilename.size() )
{
libmaus::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Tindex(new libmaus::bambam::BgzfDeflateOutputCallbackBamIndex(tmpfileindex));
Pindex = UNIQUE_PTR_MOVE(Tindex);
cbs.push_back(Pindex.get());
}
}
std::vector< ::libmaus::lz::BgzfDeflateOutputCallback * > * Pcbs = 0;
if ( cbs.size() )
Pcbs = &cbs;
/*
* end md5/index callbacks
*/
::libmaus::bambam::BamWriter::unique_ptr_type writer(new ::libmaus::bambam::BamWriter(std::cout,uphead,level,Pcbs));
libmaus::bambam::BamAlignment & algn = dec.getAlignment();
uint64_t c = 0;
while ( dec.readAlignment() )
{
bool const ok = split12(algn);
if ( ok )
algn.serialise(writer->getStream());
if ( verbose && (++c & (1024*1024-1)) == 0 )
std::cerr << "[V] " << c/(1024*1024) << std::endl;
}
writer.reset();
if ( Pmd5cb )
{
Pmd5cb->saveDigestAsFile(md5filename);
}
if ( Pindex )
{
Pindex->flush(std::string(indexfilename));
}
return EXIT_SUCCESS;
}
int bamvalidateTemplate(::libmaus2::util::ArgInfo const & arginfo)
{
libmaus2::timing::RealTimeClock rtc; rtc.start();
bool const verbose = arginfo.getValue("verbose",getDefaultVerbose());
bool const basequalhist = arginfo.getValue("basequalhist",getDefaultBaseQualHist());
libmaus2::bambam::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
libmaus2::bambam::BamMultiAlignmentDecoderFactory::construct(
arginfo,false // put rank
)
);
::libmaus2::bambam::BamAlignmentDecoder * ppdec = &(decwrapper->getDecoder());
::libmaus2::bambam::BamAlignmentDecoder & dec = *ppdec;
::libmaus2::bambam::BamHeader const & header = dec.getHeader();
::libmaus2::bambam::BamAlignment const & algn = dec.getAlignment();
// add PG line to header
std::string const upheadtext = ::libmaus2::bambam::ProgramHeaderLineSet::addProgramLine(
header.text,
"bamvalidate", // ID
"bamvalidate", // PN
arginfo.commandline, // CL
::libmaus2::bambam::ProgramHeaderLineSet(header.text).getLastIdInChain(), // PP
std::string(PACKAGE_VERSION) // VN
);
// construct new header
::libmaus2::bambam::BamHeader uphead(upheadtext);
/*
* start index/md5 callbacks and alignment writer
*/
std::string md5filename;
std::string indexfilename;
std::vector< ::libmaus2::lz::BgzfDeflateOutputCallback * > cbs;
::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Pmd5cb;
libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
libmaus2::bambam::BamBlockWriterBase::unique_ptr_type Pout;
if ( passthrough )
{
std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
std::string const tmpfileindex = tmpfilenamebase + "_index";
::libmaus2::util::TempFileRemovalContainer::addTempFile(tmpfileindex);
if ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( arginfo.hasArg("md5filename") && arginfo.getUnparsedValue("md5filename","") != "" )
md5filename = arginfo.getUnparsedValue("md5filename","");
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 = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( arginfo.hasArg("indexfilename") && arginfo.getUnparsedValue("indexfilename","") != "" )
indexfilename = arginfo.getUnparsedValue("indexfilename","");
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 = UNIQUE_PTR_MOVE(Tindex);
cbs.push_back(Pindex.get());
}
}
std::vector< ::libmaus2::lz::BgzfDeflateOutputCallback * > * Pcbs = 0;
if ( cbs.size() )
Pcbs = &cbs;
libmaus2::bambam::BamBlockWriterBase::unique_ptr_type Tout (
libmaus2::bambam::BamBlockWriterBaseFactory::construct(uphead, arginfo, Pcbs)
);
Pout = UNIQUE_PTR_MOVE(Tout);
}
libmaus2::autoarray::AutoArray<char> lastvalidname(256); // max valid read name is 255 bytes
uint64_t alsok = 0;
::libmaus2::autoarray::AutoArray<char> qual;
libmaus2::autoarray::AutoArray<uint64_t> H(static_cast<uint64_t>(std::numeric_limits<uint8_t>::max())+1);
std::fill(H.begin(),H.end(),0ull);
try
{
while ( dec.readAlignment() )
{
if ( passthrough )
Pout->writeAlignment(algn);
if ( basequalhist )
{
uint64_t const l = algn.getLseq();
uint8_t const * Qc = libmaus2::bambam::BamAlignmentDecoderBase::getQual(algn.D.begin());
uint8_t const * const Qe = Qc + l;
while ( Qc != Qe )
H[*(Qc++)]++;
}
uint64_t const lname = algn.getLReadName();
char const * name = algn.getName();
std::copy(name,name+lname+1,lastvalidname.begin());
alsok += 1;
}
}
catch(std::exception const & ex)
{
std::cerr << "[E] name of last valid alignment was " << lastvalidname.begin() << std::endl;
std::cerr << "[E] read " << alsok << " valid alignments" << std::endl;
throw;
}
Pout.reset();
if ( Pmd5cb )
{
Pmd5cb->saveDigestAsFile(md5filename);
}
if ( Pindex )
{
Pindex->flush(std::string(indexfilename));
}
if ( verbose )
std::cerr << "[V] checked " << alsok << " alignments in " << rtc.formatTime(rtc.getElapsedSeconds())
<< " (" << alsok / rtc.getElapsedSeconds() << " al/s)" << std::endl;
if ( basequalhist )
{
uint64_t const s = std::accumulate(H.begin(),H.end(),0ull);
uint64_t a = 0;
uint64_t minq = std::numeric_limits<uint64_t>::max();
uint64_t maxq = 0;
for ( uint64_t i = 0; i < H.size(); ++i )
if ( H[i] )
{
minq = std::min(minq,i);
maxq = std::max(maxq,i);
a += H[i];
std::cerr
<< "[H]\t" << i << "\t";
if ( ( static_cast<uint64_t>(i+33) < static_cast<uint64_t>(std::numeric_limits<char>::max()) && isprint(i+33)) )
std::cerr << static_cast<char>(i+33);
std::cerr << "\t"
<< H[i] << "\t"
<< (H[i] / static_cast<double>(s)) << "\t"
<< (a / static_cast<double>(s))
<< std::endl;
}
if ( s )
{
std::cerr << "[H]\tmin\t" << minq << "\t";
if ( ( static_cast<uint64_t>(minq+33) < static_cast<uint64_t>(std::numeric_limits<char>::max()) && isprint(minq+33)) )
std::cerr << static_cast<char>(minq+33);
std::cerr << std::endl;
std::cerr << "[H]\tmax\t" << maxq << "\t";
if ( ( static_cast<uint64_t>(maxq+33) < static_cast<uint64_t>(std::numeric_limits<char>::max()) && isprint(maxq+33)) )
std::cerr << static_cast<char>(maxq+33);
std::cerr << std::endl;
}
}
return EXIT_SUCCESS;
}
int main(int argc, char * argv[])
{
try
{
::libmaus::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 << ::biobambam::Licensing::license();
return EXIT_SUCCESS;
}
else if (
arginfo.restargs[i] == "-h"
||
arginfo.restargs[i] == "--help"
)
{
std::cerr << ::biobambam::Licensing::license();
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=<["+::biobambam::Licensing::formatNumber(getDefaultLevel())+"]>", "compression settings for output bam file (0=uncompressed,1=fast,9=best,-1=zlib default)" ) );
V.push_back ( std::pair<std::string,std::string> ( "minmapped=<["+::biobambam::Licensing::formatNumber(getDefaultMinMapped())+"]>", "minimum number of mapped fragments in a template" ) );
V.push_back ( std::pair<std::string,std::string> ( "maxmapped=<["+::biobambam::Licensing::formatNumber(getDefaultMaxMapped())+"]>", "maximum number of mapped fragments in a template" ) );
V.push_back ( std::pair<std::string,std::string> ( "minlen=<["+::biobambam::Licensing::formatNumber(getDefaultMinLen())+"]>", "minimum sequence length" ) );
V.push_back ( std::pair<std::string,std::string> ( "verbose=<["+::biobambam::Licensing::formatNumber(getDefaultVerbose())+"]>", "print progress report (default: 1)" ) );
V.push_back ( std::pair<std::string,std::string> ( "md5=<["+::biobambam::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 (default: extend output file name)" ) );
V.push_back ( std::pair<std::string,std::string> ( "index=<["+::biobambam::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 (default: extend output file name)" ) );
::biobambam::Licensing::printMap(std::cerr,V);
std::cerr << std::endl;
return EXIT_SUCCESS;
}
return bamfilter(arginfo);
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
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"
)
{
std::cerr << ::biobambam2::Licensing::license();
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> ( "verbose=<["+::biobambam2::Licensing::formatNumber(getDefaultVerbose())+"]>", "print progress report" ) );
V.push_back ( std::pair<std::string,std::string> ( "I=<[input filename]>", "name of the input file" ) );
// V.push_back ( std::pair<std::string,std::string> ( "numthreads=<["+::biobambam2::Licensing::formatNumber(getDefaultNumThreads())+"]>", "number of recoding threads" ) );
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 (default: extend output file name)" ) );
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 (default: extend output file name)" ) );
V.push_back ( std::pair<std::string,std::string> ( "tmpfile=<filename>", "prefix for temporary files, default: create files in current directory" ) );
::biobambam2::Licensing::printMap(std::cerr,V);
std::cerr << std::endl;
return EXIT_SUCCESS;
}
return bamheaderfilter(arginfo);
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
int bamcat(libmaus::util::ArgInfo const & arginfo)
{
if ( isatty(STDOUT_FILENO) )
{
::libmaus::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 level = arginfo.getValue<int>("level",getDefaultLevel());
int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
switch ( level )
{
case Z_NO_COMPRESSION:
case Z_BEST_SPEED:
case Z_BEST_COMPRESSION:
case Z_DEFAULT_COMPRESSION:
break;
default:
{
::libmaus::exception::LibMausException se;
se.getStream()
<< "Unknown compression level, please use"
<< " level=" << Z_DEFAULT_COMPRESSION << " (default) or"
<< " level=" << Z_BEST_SPEED << " (fast) or"
<< " level=" << Z_BEST_COMPRESSION << " (best) or"
<< " level=" << Z_NO_COMPRESSION << " (no compression)" << std::endl;
se.finish();
throw se;
}
break;
}
std::vector<std::string> inputfilenames = arginfo.getPairValues("I");
for ( uint64_t i = 0; i < arginfo.restargs.size(); ++i )
inputfilenames.push_back(arginfo.restargs[i]);
libmaus::bambam::BamCat bamdec(inputfilenames /* ,true */);
libmaus::bambam::BamAlignment const & algn = bamdec.getAlignment();
libmaus::bambam::BamHeader const & header = bamdec.getHeader();
::libmaus::bambam::BamHeader::unique_ptr_type uphead(updateHeader(arginfo,header));
/*
* start index/md5 callbacks
*/
std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
std::string const tmpfileindex = tmpfilenamebase + "_index";
::libmaus::util::TempFileRemovalContainer::addTempFile(tmpfileindex);
std::string md5filename;
std::string indexfilename;
std::vector< ::libmaus::lz::BgzfDeflateOutputCallback * > cbs;
::libmaus::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Pmd5cb;
if ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( arginfo.hasArg("md5filename") && arginfo.getUnparsedValue("md5filename","") != "" )
md5filename = arginfo.getUnparsedValue("md5filename","");
else
std::cerr << "[V] no filename for md5 given, not creating hash" << std::endl;
if ( md5filename.size() )
{
::libmaus::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Tmd5cb(new ::libmaus::lz::BgzfDeflateOutputCallbackMD5);
Pmd5cb = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
libmaus::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( arginfo.hasArg("indexfilename") && arginfo.getUnparsedValue("indexfilename","") != "" )
indexfilename = arginfo.getUnparsedValue("indexfilename","");
else
std::cerr << "[V] no filename for index given, not creating index" << std::endl;
if ( indexfilename.size() )
{
libmaus::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Tindex(new libmaus::bambam::BgzfDeflateOutputCallbackBamIndex(tmpfileindex));
Pindex = UNIQUE_PTR_MOVE(Tindex);
cbs.push_back(Pindex.get());
}
}
std::vector< ::libmaus::lz::BgzfDeflateOutputCallback * > * Pcbs = 0;
if ( cbs.size() )
Pcbs = &cbs;
/*
* end md5/index callbacks
*/
::libmaus::bambam::BamWriter::unique_ptr_type writer(new ::libmaus::bambam::BamWriter(std::cout,*uphead,level,Pcbs));
libmaus::bambam::BamWriter::stream_type & bamoutstr = writer->getStream();
if ( verbose )
{
uint64_t c = 0;
while ( bamdec.readAlignment() )
{
algn.serialise(bamoutstr);
if ( ((++c) & ((1ull<<20)-1)) == 0 )
std::cerr << "[V] " << c << std::endl;
}
std::cerr << "[V] " << c << std::endl;
}
else
while ( bamdec.readAlignment() )
algn.serialise(bamoutstr);
writer.reset();
if ( Pmd5cb )
{
Pmd5cb->saveDigestAsFile(md5filename);
}
if ( Pindex )
{
Pindex->flush(std::string(indexfilename));
}
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"
)
{
std::cerr << ::biobambam2::Licensing::license();
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> ( "verbose=<["+::biobambam2::Licensing::formatNumber(getDefaultVerbose())+"]>", "print progress report" ) );
::biobambam2::Licensing::printMap(std::cerr,V);
std::cerr << std::endl;
return EXIT_SUCCESS;
}
return bamchecksort(arginfo);
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
int bam12auxmerge(::libmaus2::util::ArgInfo const & arginfo)
{
if ( isatty(STDIN_FILENO) )
{
::libmaus2::exception::LibMausException se;
se.getStream() << "Refusing to read binary data from terminal, please redirect standard input to pipe or file." << std::endl;
se.finish();
throw se;
}
if ( isatty(STDOUT_FILENO) )
{
::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;
}
std::string const prefilename = arginfo.getRestArg<std::string>(0);
libmaus2::bambam::BamDecoder bampredec(prefilename);
int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
int const ranksplit = arginfo.getValue<int>("ranksplit",getDefaultRankSplit());
int const rankstrip = arginfo.getValue<int>("rankstrip",getDefaultRankSplit());
int const clipreinsert = arginfo.getValue<int>("clipreinsert",getDefaultClipReinsert());
int const zztoname = arginfo.getValue<int>("zztoname",getDefaultZZToName());
int const sanity = arginfo.getValue<int>("sanity",getDefaultSanity());
uint64_t const mod = arginfo.getValue<int>("mod",getDefaultMod());
uint64_t const bmod = libmaus2::math::nextTwoPow(mod);
uint64_t const bmask = bmod-1;
libmaus2::autoarray::AutoArray<char> Aread;
::libmaus2::bambam::BamDecoder bamdec(std::cin,false);
::libmaus2::bambam::BamHeader const & header = bamdec.getHeader();
::libmaus2::bambam::BamHeader const & preheader = bampredec.getHeader();
std::string const headertext(header.text);
std::string const preheadertext(libmaus2::bambam::HeaderLine::removeSequenceLines(preheader.text));
libmaus2::bambam::ProgramHeaderLineSet headerlines(headertext);
libmaus2::bambam::ProgramHeaderLineSet preheaderlines(preheadertext);
std::vector<libmaus2::bambam::HeaderLine> allheaderlines = libmaus2::bambam::HeaderLine::extractLines(headertext);
std::string const lastid = preheaderlines.getLastIdInChain();
std::stack < std::pair<uint64_t,std::string> > pgtodo;
for ( uint64_t i = 0; i < headerlines.roots.size(); ++i )
pgtodo.push(std::pair<uint64_t,std::string>(headerlines.roots[i],lastid));
std::string upheadtext = preheadertext;
while ( pgtodo.size() )
{
uint64_t const hid = pgtodo.top().first;
std::string const PP = pgtodo.top().second;
pgtodo.pop();
libmaus2::bambam::HeaderLine const & line = headerlines.lines[hid];
// ID, PP, PN, CL, VN
std::string ID = (line.M.find("ID") != line.M.end()) ? line.M.find("ID")->second : "";
std::string const PN = (line.M.find("PN") != line.M.end()) ? line.M.find("PN")->second : "";
std::string const CL = (line.M.find("CL") != line.M.end()) ? line.M.find("CL")->second : "";
std::string const VN = (line.M.find("VN") != line.M.end()) ? line.M.find("VN")->second : "";
upheadtext = ::libmaus2::bambam::ProgramHeaderLineSet::addProgramLineRef(
upheadtext,
ID,
PN,
CL,
PP,
VN
);
if ( headerlines.edges.find(hid) != headerlines.edges.end() )
{
std::vector<uint64_t> const & children = headerlines.edges.find(hid)->second;
for ( uint64_t j = 0; j < children.size(); ++j )
pgtodo.push(std::pair<uint64_t,std::string>(children[j],ID));
}
}
/* copy SQ lines */
std::ostringstream sqconcstr;
sqconcstr << upheadtext;
for ( uint64_t i = 0; i < allheaderlines.size(); ++i )
if ( allheaderlines[i].type == "SQ" )
sqconcstr << allheaderlines[i].line << "\n";
upheadtext = sqconcstr.str();
::libmaus2::bambam::BamHeader uphead(upheadtext);
uphead.changeSortOrder("unknown");
/*
* start index/md5 callbacks
*/
std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
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 ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( arginfo.hasArg("md5filename") && arginfo.getUnparsedValue("md5filename","") != "" )
md5filename = arginfo.getUnparsedValue("md5filename","");
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 = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( arginfo.hasArg("indexfilename") && arginfo.getUnparsedValue("indexfilename","") != "" )
indexfilename = arginfo.getUnparsedValue("indexfilename","");
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 = UNIQUE_PTR_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::BamWriter::unique_ptr_type writer(new ::libmaus2::bambam::BamWriter(std::cout,uphead,level,Pcbs));
::libmaus2::bambam::BamAlignment & algn = bamdec.getAlignment();
::libmaus2::bambam::BamAlignment & prealgn = bampredec.getAlignment();
int64_t curid = -1;
libmaus2::autoarray::AutoArray< std::pair<uint8_t,uint8_t> > auxpre;
libmaus2::autoarray::AutoArray< std::pair<uint8_t,uint8_t> > auxnew;
libmaus2::bambam::BamAuxFilterVector auxfilter;
// helpers for clipReinsert
libmaus2::autoarray::AutoArray < std::pair<uint8_t,uint8_t> > auxtags;
libmaus2::autoarray::AutoArray<libmaus2::bambam::cigar_operation> cigop;
std::stack < libmaus2::bambam::cigar_operation > hardstack;
libmaus2::bambam::BamAlignment::D_array_type Tcigar;
libmaus2::bambam::BamAuxFilterVector bafv;
libmaus2::bambam::BamAuxFilterVector auxfilterout;
auxfilterout.set('q','s');
auxfilterout.set('q','q');
// helpers for zztoname
libmaus2::bambam::BamAuxFilterVector zzbafv;
zzbafv.set('z','z');
// tag filters for secondary/supplementary reads
libmaus2::bambam::BamAuxFilterVector auxfiltersec;
auxfiltersec.set('q','s');
auxfiltersec.set('q','q');
auxfiltersec.set('a','s');
auxfiltersec.set('a','h');
auxfiltersec.set('a','a');
auxfiltersec.set('a','f');
auxfiltersec.set('a','r');
auxfiltersec.set('a','3');
// loop over aligned BAM file
while ( bamdec.readAlignment() )
{
if ( ranksplit )
split12(algn);
// extract rank
char const * name = algn.getName();
char const * u1 = name;
bool ok = true;
uint64_t rank = 0;
while ( *u1 && *u1 != '_' )
{
rank *= 10;
rank += (*u1-'0');
ok = ok && isdigit(*u1);
++u1;
}
// unable to find rank? write out as is and continue
if ( ! ok )
{
algn.serialise(writer->getStream());
continue;
}
// loop over unaligned BAM file
while ( curid != static_cast<int64_t>(rank) )
{
bool const a_ok = bampredec.readAlignment();
if ( ! a_ok )
{
libmaus2::exception::LibMausException se;
se.getStream() << "Found unexpected EOF on file " << prefilename << std::endl;
se.finish();
throw se;
}
assert ( a_ok );
++curid;
if ( verbose && (! (curid & bmask)) )
std::cerr << "[V] " << (curid / bmod) << std::endl;
}
if ( verbose > 1 )
std::cerr << "Merging:\n" << algn.formatAlignment(header) << "\n" << prealgn.formatAlignment(preheader) << std::endl;
uint64_t pretagnum = prealgn.enumerateAuxTags(auxpre);
uint64_t newtagnum = algn.enumerateAuxTags(auxnew);
// do some sanity checking
if ( sanity )
{
// first do a name check
char const * prename = prealgn.getName();
u1++; // put on the first letter of readname
if ( verbose > 1 )
std::cerr << "Sanity: comparing " << name << " and " << prename << std::endl;
if ( !is_suffix(prename, u1) ) // names do not match
{
libmaus2::exception::LibMausException se;
se.getStream() << "Sanity check failed on read names, found " << name << " and " << prename << std::endl;
se.finish();
throw se;
}
// now the names match so try the flags
if ( !(algn.isPaired() == prealgn.isPaired() &&
algn.isRead1() == prealgn.isRead1() &&
algn.isRead2() == prealgn.isRead2()) )
{
libmaus2::exception::LibMausException se;
se.getStream() << "Sanity check failed on flags, " << std::endl
<< "Aligned " << name << " paired " << algn.isPaired() << " first " << algn.isRead1() << " last " << algn.isRead2() << std::endl
<< "Unaligned " << prename << " paired " << prealgn.isPaired() << " first " << prealgn.isRead1() << " last " << prealgn.isRead2() << std::endl;
se.finish();
throw se;
}
if ( verbose > 1 )
std::cerr << "Sanity check on flags: " << std::endl
<< "Aligned " << name << " paired " << algn.isPaired() << " first " << algn.isRead1() << " last " << algn.isRead2() << std::endl
<< "Unaligned " << prename << " paired " << prealgn.isPaired() << " first " << prealgn.isRead1() << " last " << prealgn.isRead2() << std::endl;
}
std::sort(auxpre.begin(),auxpre.begin()+pretagnum);
std::sort(auxnew.begin(),auxnew.begin()+newtagnum);
if ( verbose > 1 )
std::cerr << "pretagnum=" << pretagnum << " newtagnum=" << newtagnum << std::endl;
std::pair<uint8_t,uint8_t> * prec = auxpre.begin();
std::pair<uint8_t,uint8_t> * pree = prec + pretagnum;
std::pair<uint8_t,uint8_t> * preo = prec;
std::pair<uint8_t,uint8_t> * newc = auxnew.begin();
std::pair<uint8_t,uint8_t> * newe = newc + newtagnum;
std::pair<uint8_t,uint8_t> * newo = newc;
while ( prec != pree && newc != newe )
{
// pre which is not in new
if ( *prec < *newc )
{
*(preo++) = *(prec++);
}
// tag in both, drop pre
else if ( *prec == *newc )
{
*(newo++) = *(newc++);
prec++;
}
// new not in pre
else
{
*(newo++) = *(newc++);
}
}
while ( prec != pree )
*(preo++) = *(prec++);
while ( newc != newe )
*(newo++) = *(newc++);
pretagnum = preo-auxpre.begin();
newtagnum = newo-auxnew.begin();
for ( uint64_t i = 0; i < pretagnum; ++i )
auxfilter.set(auxpre[i].first,auxpre[i].second);
algn.copyAuxTags(prealgn, auxfilter);
for ( uint64_t i = 0; i < pretagnum; ++i )
auxfilter.clear(auxpre[i].first,auxpre[i].second);
if ( verbose > 1 )
{
std::cerr << "pretagnum=" << pretagnum << " newtagnum=" << newtagnum << std::endl;
std::cerr << "result: " << algn.formatAlignment(header) << std::endl;
}
if ( algn.isSecondary() || algn.isSupplementary() )
{
// adding adapter clip data to secondary/supplementary reads
// can lead to incorrect clip reinserts so remove these tags
algn.filterOutAux(auxfiltersec);
}
// copy QC fail flag from original file to aligner output
if ( prealgn.isQCFail() )
algn.putFlags( algn.getFlags() | libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_FQCFAIL );
if ( rankstrip )
strip12(algn);
if ( clipreinsert )
clipReinsert(algn,auxtags,bafv,cigop,Tcigar,hardstack,auxfilterout);
if ( zztoname )
zzToRank(algn,zzbafv);
algn.serialise(writer->getStream());
}
writer.reset();
if ( Pmd5cb )
{
Pmd5cb->saveDigestAsFile(md5filename);
}
if ( Pindex )
{
Pindex->flush(std::string(indexfilename));
}
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"
)
{
std::cerr << ::biobambam2::Licensing::license();
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> ( "n=<["+::biobambam2::Licensing::formatNumber(getDefaultN())+"]>", "number of entries" ) );
V.push_back ( std::pair<std::string,std::string> ( "prefix=<["+getDefaultFilePrefix(arginfo)+"]>", "default output file prefix" ) );
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" ) );
::biobambam2::Licensing::printMap(std::cerr,V);
std::cerr << std::endl;
return EXIT_SUCCESS;
}
return bamsplit(arginfo);
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}