int
main( int argc, char *argv[] )
{
extern void dummy( void * );
float aa, *a, *b, *c, *x, *y;
double aad, *ad, *bd, *cd, *xd, *yd;
int i, j, n;
int inner = 0;
int vector = 0;
int matrix = 0;
int double_precision = 0;
int retval = PAPI_OK;
char papi_event_str[PAPI_MIN_STR_LEN] = "PAPI_FP_OPS";
int papi_event;
int EventSet = PAPI_NULL;
/* Parse the input arguments */
for ( i = 0; i < argc; i++ ) {
if ( strstr( argv[i], "-i" ) )
inner = 1;
else if ( strstr( argv[i], "-v" ) )
vector = 1;
else if ( strstr( argv[i], "-m" ) )
matrix = 1;
else if ( strstr( argv[i], "-e" ) ) {
if ( ( argv[i + 1] == NULL ) || ( strlen( argv[i + 1] ) == 0 ) ) {
print_help( argv );
exit( 1 );
}
strncpy( papi_event_str, argv[i + 1], sizeof ( papi_event_str ) );
i++;
} else if ( strstr( argv[i], "-d" ) )
double_precision = 1;
else if ( strstr( argv[i], "-h" ) ) {
print_help( argv );
exit( 1 );
}
}
/* if no options specified, set all tests to TRUE */
if ( inner + vector + matrix == 0 )
inner = vector = matrix = 1;
tests_quiet( argc, argv ); /* Set TESTS_QUIET variable */
if ( !TESTS_QUIET )
printf( "Initializing..." );
/* Initialize PAPI */
retval = PAPI_library_init( PAPI_VER_CURRENT );
if ( retval != PAPI_VER_CURRENT )
test_fail( __FILE__, __LINE__, "PAPI_library_init", retval );
/* Translate name */
retval = PAPI_event_name_to_code( papi_event_str, &papi_event );
if ( retval != PAPI_OK )
test_fail( __FILE__, __LINE__, "PAPI_event_name_to_code", retval );
if ( PAPI_query_event( papi_event ) != PAPI_OK )
test_skip( __FILE__, __LINE__, "PAPI_query_event", PAPI_ENOEVNT );
if ( ( retval = PAPI_create_eventset( &EventSet ) ) != PAPI_OK )
test_fail( __FILE__, __LINE__, "PAPI_create_eventset", retval );
if ( ( retval = PAPI_add_event( EventSet, papi_event ) ) != PAPI_OK )
test_fail( __FILE__, __LINE__, "PAPI_add_event", retval );
printf( "\n" );
retval = PAPI_OK;
/* Inner Product test */
if ( inner ) {
/* Allocate the linear arrays */
if (double_precision) {
xd = malloc( INDEX5 * sizeof(double) );
yd = malloc( INDEX5 * sizeof(double) );
if ( !( xd && yd ) )
retval = PAPI_ENOMEM;
}
else {
x = malloc( INDEX5 * sizeof(float) );
y = malloc( INDEX5 * sizeof(float) );
if ( !( x && y ) )
retval = PAPI_ENOMEM;
}
if ( retval == PAPI_OK ) {
headerlines( "Inner Product Test", TESTS_QUIET );
/* step through the different array sizes */
for ( n = 0; n < INDEX5; n++ ) {
if ( n < INDEX1 || ( ( n + 1 ) % 50 ) == 0 ) {
/* Initialize the needed arrays at this size */
if ( double_precision ) {
for ( i = 0; i <= n; i++ ) {
xd[i] = ( double ) rand( ) * ( double ) 1.1;
yd[i] = ( double ) rand( ) * ( double ) 1.1;
}
} else {
for ( i = 0; i <= n; i++ ) {
x[i] = ( float ) rand( ) * ( float ) 1.1;
y[i] = ( float ) rand( ) * ( float ) 1.1;
}
}
/* reset PAPI flops count */
reset_flops( "Inner Product Test", EventSet );
/* do the multiplication */
if ( double_precision ) {
aad = inner_double( n, xd, yd );
dummy( ( void * ) &aad );
} else {
aa = inner_single( n, x, y );
dummy( ( void * ) &aa );
}
resultline( n, 1, EventSet );
}
}
}
if (double_precision) {
free( xd );
free( yd );
} else {
free( x );
free( y );
}
}
/* Matrix Vector test */
if ( vector && retval != PAPI_ENOMEM ) {
/* Allocate the needed arrays */
if (double_precision) {
ad = malloc( INDEX5 * INDEX5 * sizeof(double) );
xd = malloc( INDEX5 * sizeof(double) );
yd = malloc( INDEX5 * sizeof(double) );
if ( !( ad && xd && yd ) )
retval = PAPI_ENOMEM;
} else {
a = malloc( INDEX5 * INDEX5 * sizeof(float) );
x = malloc( INDEX5 * sizeof(float) );
y = malloc( INDEX5 * sizeof(float) );
if ( !( a && x && y ) )
retval = PAPI_ENOMEM;
}
if ( retval == PAPI_OK ) {
headerlines( "Matrix Vector Test", TESTS_QUIET );
/* step through the different array sizes */
for ( n = 0; n < INDEX5; n++ ) {
if ( n < INDEX1 || ( ( n + 1 ) % 50 ) == 0 ) {
/* Initialize the needed arrays at this size */
if ( double_precision ) {
for ( i = 0; i <= n; i++ ) {
yd[i] = 0.0;
xd[i] = ( double ) rand( ) * ( double ) 1.1;
for ( j = 0; j <= n; j++ )
ad[i * n + j] =
( double ) rand( ) * ( double ) 1.1;
}
} else {
for ( i = 0; i <= n; i++ ) {
y[i] = 0.0;
x[i] = ( float ) rand( ) * ( float ) 1.1;
for ( j = 0; j <= n; j++ )
a[i * n + j] =
( float ) rand( ) * ( float ) 1.1;
}
}
/* reset PAPI flops count */
reset_flops( "Matrix Vector Test", EventSet );
/* compute the resultant vector */
if ( double_precision ) {
vector_double( n, ad, xd, yd );
dummy( ( void * ) yd );
} else {
vector_single( n, a, x, y );
dummy( ( void * ) y );
}
resultline( n, 2, EventSet );
}
}
}
if (double_precision) {
free( ad );
free( xd );
free( yd );
} else {
free( a );
free( x );
free( y );
}
}
/* Matrix Multiply test */
if ( matrix && retval != PAPI_ENOMEM ) {
/* Allocate the needed arrays */
if (double_precision) {
ad = malloc( INDEX5 * INDEX5 * sizeof(double) );
bd = malloc( INDEX5 * INDEX5 * sizeof(double) );
cd = malloc( INDEX5 * INDEX5 * sizeof(double) );
if ( !( ad && bd && cd ) )
retval = PAPI_ENOMEM;
} else {
a = malloc( INDEX5 * INDEX5 * sizeof(float) );
b = malloc( INDEX5 * INDEX5 * sizeof(float) );
c = malloc( INDEX5 * INDEX5 * sizeof(float) );
if ( !( a && b && c ) )
retval = PAPI_ENOMEM;
}
if ( retval == PAPI_OK ) {
headerlines( "Matrix Multiply Test", TESTS_QUIET );
/* step through the different array sizes */
for ( n = 0; n < INDEX5; n++ ) {
if ( n < INDEX1 || ( ( n + 1 ) % 50 ) == 0 ) {
/* Initialize the needed arrays at this size */
if ( double_precision ) {
for ( i = 0; i <= n * n + n; i++ ) {
cd[i] = 0.0;
ad[i] = ( double ) rand( ) * ( double ) 1.1;
bd[i] = ( double ) rand( ) * ( double ) 1.1;
}
} else {
for ( i = 0; i <= n * n + n; i++ ) {
c[i] = 0.0;
a[i] = ( float ) rand( ) * ( float ) 1.1;
b[i] = ( float ) rand( ) * ( float ) 1.1;
}
}
/* reset PAPI flops count */
reset_flops( "Matrix Multiply Test", EventSet );
/* compute the resultant matrix */
if ( double_precision ) {
matrix_double( n, cd, ad, bd );
dummy( ( void * ) c );
} else {
matrix_single( n, c, a, b );
dummy( ( void * ) c );
}
resultline( n, 3, EventSet );
}
}
}
if (double_precision) {
free( ad );
free( bd );
free( cd );
} else {
free( a );
free( b );
free( c );
}
}
/* exit with status code */
if ( retval == PAPI_ENOMEM )
test_fail( __FILE__, __LINE__, "malloc", retval );
else
test_pass( __FILE__, NULL, 0 );
exit( 1 );
}
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;
}