/*
* Attempt to open the disk described by (dev) for use by (f).
*
* Note that the philosophy here is "give them exactly what
* they ask for". This is necessary because being too "smart"
* about what the user might want leads to complications.
* (eg. given no slice or partition value, with a disk that is
* sliced - are they after the first BSD slice, or the DOS
* slice before it?)
*/
static int
bd_open(struct open_file *f, ...)
{
va_list ap;
struct i386_devdesc *dev;
struct open_disk *od;
int error;
va_start(ap, f);
dev = va_arg(ap, struct i386_devdesc *);
va_end(ap);
if ((error = bd_opendisk(&od, dev)))
return(error);
BD(dev).bd_open++;
if (BD(dev).bd_bcache == NULL)
BD(dev).bd_bcache = bcache_allocate();
/*
* Save our context
*/
((struct i386_devdesc *)(f->f_devdata))->d_kind.biosdisk.data = od;
DEBUG("open_disk %p, partition at 0x%x", od, od->od_boff);
return(0);
}
static int
bd_close(struct open_file *f)
{
struct i386_devdesc *dev = f->f_devdata;
struct open_disk *od = (struct open_disk *)(dev->d_kind.biosdisk.data);
BD(dev).bd_open--;
if (BD(dev).bd_open == 0) {
bcache_free(BD(dev).bd_bcache);
BD(dev).bd_bcache = NULL;
}
bd_closedisk(od);
return(0);
}
ContainmentResult TestSphereSphere ( Sphere const & A,
Sphere const & B )
{
// ----------
// do a quick outside test first
Vector delta = B.getCenter() - A.getCenter();
real dist2 = delta.magnitudeSquared();
real sumRadius = A.getRadius() + B.getRadius();
real sumRadius2 = sumRadius * sumRadius;
if(dist2 > sumRadius2)
{
return CR_Outside;
}
else if(dist2 == sumRadius2) //lint !e777 // testing floats for equality
{
return CR_TouchingOutside;
}
else
{
// ----------
// and if that fails do the full test
real dist = sqrt(dist2);
Range AD( dist - A.getRadius(), dist + A.getRadius() );
Range BD( -B.getRadius(), B.getRadius() );
return Containment1d::TestRangeRange( AD, BD );
}
}
static int
bd_strategy(void *devdata, int rw, daddr_t dblk, size_t size,
char *buf, size_t *rsize)
{
struct bcache_devdata bcd;
struct i386_devdesc *dev = devdata;
struct open_disk *od = (struct open_disk *)(dev->d_kind.biosdisk.data);
bcd.dv_strategy = bd_realstrategy;
bcd.dv_devdata = devdata;
bcd.dv_cache = BD(dev).bd_bcache;
return(bcache_strategy(&bcd, rw, dblk+od->od_boff, size, buf, rsize));
}
ContainmentResult TestCylinderCylinder ( Cylinder const & A,
Cylinder const & B )
{
Vector delta = B.getBase() - A.getBase();
delta.y = 0;
real dist = delta.magnitude();
Range AD( dist - A.getRadius(), dist + A.getRadius() );
Range BD( -B.getRadius(), B.getRadius() );
ContainmentResult hTest = Containment1d::TestRangeRange( AD, BD );
ContainmentResult vTest = Containment1d::TestRangeRange( A.getRangeY(), B.getRangeY() );
// ----------
return Containment::ComposeAxisTests(hTest,vTest);
}
int bamfilter(libmaus::util::ArgInfo const & arginfo)
{
uint64_t const minmapped = arginfo.getValue<uint64_t>("minmapped",getDefaultMinMapped());
uint64_t const maxmapped = arginfo.getValue<uint64_t>("maxmapped",getDefaultMaxMapped());
uint64_t const minlen = arginfo.getValue<uint64_t>("minlen",getDefaultMinLen());
int const level = libmaus::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
::libmaus::bambam::BamDecoder BD(std::cin);
::libmaus::bambam::BamHeader const & bamheader = BD.getHeader();
::libmaus::bambam::BamAlignment & alignment = BD.getAlignment();
/*
* 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::BamHeader::unique_ptr_type uphead(libmaus::bambam::BamHeaderUpdate::updateHeader(arginfo,bamheader,"bamfilter",std::string(PACKAGE_VERSION)));
::libmaus::bambam::BamWriter::unique_ptr_type writer(new ::libmaus::bambam::BamWriter(std::cout,*uphead,level,Pcbs));
while ( BD.readAlignment() )
{
bool const a_1_mapped = !(alignment.getFlags() & ::libmaus::bambam::BamFlagBase::LIBMAUS_BAMBAM_FUNMAP);
bool const a_2_mapped = !(alignment.getFlags() & ::libmaus::bambam::BamFlagBase::LIBMAUS_BAMBAM_FMUNMAP);
bool const proper = (alignment.getFlags() & ::libmaus::bambam::BamFlagBase::LIBMAUS_BAMBAM_FPROPER_PAIR);
uint64_t const nummapped = (a_1_mapped?1:0)+(a_2_mapped?1:0)+(proper?1:0);
if (
nummapped >= minmapped &&
nummapped <= maxmapped &&
alignment.getLseq() >= static_cast<int64_t>(minlen)
)
alignment.serialise(writer->getStream());
}
writer.reset();
if ( Pmd5cb )
{
Pmd5cb->saveDigestAsFile(md5filename);
}
if ( Pindex )
{
Pindex->flush(std::string(indexfilename));
}
return EXIT_SUCCESS;
}
void CCorrelationFilters::fusion_matrix_inverse(Eigen::ArrayXXcd &X, Eigen::MatrixXi indices)
{
/* We compute the inverse of the fusion matrix by using the schur complement
* on our data structure. We use an inplace implementation therefore it is quite
* memory efficient as well.
*/
int num_blocks=0;
int total_blocks=0;
int size_blocks = X.rows();
if (indices.rows() != indices.cols()){
std::cout << "Something Wrong" << std::endl;
return;
}
else
{
num_blocks = indices.rows();
}
if (num_blocks == 1){
X = X.inverse();
return;
}
if (num_blocks == 2)
{
Eigen::ArrayXXcd temp1;
Eigen::ArrayXXcd temp2;
Eigen::ArrayXXcd DC(size_blocks,1);
Eigen::ArrayXXcd BD(size_blocks,1);
Eigen::ArrayXXcd BDC(size_blocks,1);
Eigen::ArrayXXcd ABDC(size_blocks,1);
DC = X.block(0,indices(1,0),size_blocks,1)/X.block(0,indices(1,1),size_blocks,1);
BD = X.block(0,indices(0,1),size_blocks,1)/X.block(0,indices(1,1),size_blocks,1);
BDC = X.block(0,indices(0,1),size_blocks,1)*DC;
ABDC = (X.block(0,indices(0,0),size_blocks,1)-BDC).inverse();
X.block(0,indices(0,0),size_blocks,1) = ABDC;
X.block(0,indices(0,1),size_blocks,1) = -ABDC*BD;
X.block(0,indices(1,0),size_blocks,1) = -DC*ABDC;
X.block(0,indices(1,1),size_blocks,1) = 1/X.block(0,indices(1,1),size_blocks,1) - X.block(0,indices(1,0),size_blocks,1)*BD;
}
else
{
int num_B = num_blocks-1;
int num_C = num_blocks-1;
Eigen::MatrixXi ind_A;
Eigen::MatrixXi ind_B;
Eigen::MatrixXi ind_C;
Eigen::MatrixXi ind_D;
total_blocks = num_blocks*num_blocks;
ind_D = indices.block(num_blocks-1,num_blocks-1,1,1);
ind_B = indices.block(0,num_blocks-1,num_blocks-1,1);
ind_C = indices.block(num_blocks-1,0,1,num_blocks-1);
ind_A = indices.block(0,0,num_blocks-1,num_blocks-1).transpose();
num_blocks = num_blocks-1;
Eigen::ArrayXXcd D = Eigen::ArrayXXcd::Zero(size_blocks,1);
Eigen::ArrayXXcd DC = Eigen::ArrayXXcd::Zero(size_blocks,num_blocks);
Eigen::ArrayXXcd BD = Eigen::ArrayXXcd::Zero(size_blocks,num_blocks);
Eigen::ArrayXXcd BDC = Eigen::ArrayXXcd::Zero(size_blocks,num_blocks*num_blocks);
Eigen::ArrayXXcd ABDC = Eigen::ArrayXXcd::Zero(size_blocks,num_blocks*num_blocks);
Eigen::ArrayXXcd tmp_B = Eigen::ArrayXXcd::Zero(size_blocks,num_B);
Eigen::ArrayXXcd tmp_C = Eigen::ArrayXXcd::Zero(size_blocks,num_C);
Eigen::ArrayXXcd tmp_D = Eigen::ArrayXXcd::Zero(size_blocks,1);
for(int i=0;i<num_C;i++){
tmp_C.block(0,i,size_blocks,1) = X.block(0,ind_C(0,i),size_blocks,1);
}
for(int i=0;i<num_B;i++){
tmp_B.block(0,i,size_blocks,1) = X.block(0,ind_B(i,0),size_blocks,1);
}
D.block(0,0,size_blocks,1) = X.block(0,total_blocks-1,size_blocks,1).inverse();
Eigen::Vector2i num_blocks_1, num_blocks_2;
num_blocks_1 << 1,1;
num_blocks_2 << 1,num_blocks;
fusion_matrix_multiply(DC,D,tmp_C,num_blocks_1,num_blocks_2);
num_blocks_1 << num_blocks,1;
num_blocks_2 << 1,1;
fusion_matrix_multiply(BD,tmp_B,D,num_blocks_1,num_blocks_2);
num_blocks_1 << num_blocks,1;
num_blocks_2 << 1,num_blocks;
fusion_matrix_multiply(BDC,tmp_B,DC,num_blocks_1,num_blocks_2);
for(int i=0;i<ind_A.rows();i++){
for(int j=0;j<ind_A.cols();j++){
X.block(0,ind_A(i,j),size_blocks,1) -= BDC.block(0,i,size_blocks,1);
}
}
fusion_matrix_inverse(X,ind_A);
tmp_B = Eigen::ArrayXXcd::Zero(size_blocks,num_B);
tmp_C = Eigen::ArrayXXcd::Zero(size_blocks,num_C);
tmp_D = Eigen::ArrayXXcd::Zero(size_blocks,1);
num_blocks_1 << num_blocks,num_blocks;
num_blocks_2 << num_blocks,1;
fusion_matrix_multiply(tmp_B,ABDC,BD,num_blocks_1,num_blocks_2);
for(int i=0;i<num_B;i++){
X.block(0,ind_B(i,0),size_blocks,1) = -tmp_B.block(0,i,size_blocks,1);
}
num_blocks_1 << 1,num_blocks;
num_blocks_2 << num_blocks,num_blocks;
fusion_matrix_multiply(tmp_C,DC,ABDC,num_blocks_1,num_blocks_2);
for(int i=0;i<num_C;i++){
X.block(0,ind_C(0,i),size_blocks,1) = -tmp_C.block(0,i,size_blocks,1);
}
tmp_C = Eigen::ArrayXXcd::Zero(size_blocks,num_C);
num_blocks_1 << 1,num_blocks;
num_blocks_2 << num_blocks,num_blocks;
fusion_matrix_multiply(tmp_C,DC,ABDC,num_blocks_1,num_blocks_2);
num_blocks_1 << 1,num_blocks;
num_blocks_2 << num_blocks,1;
fusion_matrix_multiply(tmp_D,tmp_C,BD,num_blocks_1,num_blocks_2);
tmp_D += D;
X.block(0,total_blocks-1,size_blocks,1) = tmp_D.block(0,0,size_blocks,1);
}
}
/* returns 1 if GPRs have been modified */
int
_rvec_io_write( int dummy_rvec, ulong mphys_ioaddr, void *usr_data )
{
int op, op_ext, rS, rA, rB, d, flag=0, ret=0;
ulong ea, cont, len, inst=mregs->inst_opcode;
enum { byte=1, half=2, word=4, len_mask=7, indexed=8, update=16,
reverse=32, nop=64, fpinst=128 };
/* do_io_write() is considered FPU-unsafe */
shield_fpu( mregs );
/* break instruction into parts */
op = OPCODE_PRIM( inst );
op_ext = OPCODE_EXT( inst );
rS = B1( inst ); /* bit 6-10 */
rA = B2( inst ); /* bit 11-15 */
rB = B3( inst ); /* bit 16-20 */
d = BD( inst ); /* bit 16-31 sign extended */
switch( op ) {
case 38: /* stb rS,d(rA) */
flag = byte ; break;
case 39: /* stbu rS,d(rA) */
flag = byte | update; break;
case 44: /* sth rS,d(rA) */
flag = half ; break;
case 45: /* sthu rS,d(rA) */
flag = half | update; break;
case 36: /* stw rS,d(rA) */
flag = word ; break;
case 37: /* stwud rS,d(rA) */
flag = word | update; break;
case 54: /* stfd frS,d(rA) */ /* FPU */
flag = word | fpinst; break;
case 55: /* stfdu frS,d(rA) */ /* FPU */
flag = word | fpinst | update; break;
}
if( !flag && op==31 ) {
switch( op_ext ) {
case 215: /* stbx rS,rA,rB */
flag = byte | indexed ; break;
case 247: /* stbux rS,rA,rB */
flag = byte | indexed | update; break;
case 407: /* sthx rS,rA,rB */
flag = half | indexed ; break;
case 439: /* sthux rS,rA,rB */
flag = half | indexed | update; break;
case 151: /* stwx rS,rA,rB */
flag = word | indexed ; break;
case 183: /* stwux rS,rA,rB */
flag = word | indexed | update; break;
case 918: /* sthbrx rS,rA,rB */
flag = half | indexed | reverse; break;
case 662: /* stwbrx rS,rA,rB */
flag = word | indexed | reverse; break;
case 727: /* stfdx frS,rA,rB */
/* printm("FPU store inst\n"); */
flag = word | indexed | fpinst; break;
case 759: /* stfdux frS,rA,rB */
/* printm("FPU store inst\n"); */
flag = word | indexed | update | fpinst; break;
}
}
if( flag & len_mask ) { /* instruction found */
if( flag & indexed ) { /* stxxx rS,rA,rB */
ea = mregs->gpr[rB];
ea += rA ? mregs->gpr[rA] : 0;
} else { /* stxxx rS,d(rA) */
ea = rA ? mregs->gpr[rA] : 0;
ea += d;
}
if( !(flag & fpinst ) )
cont = mregs->gpr[rS];
else {
save_fpu_completely( mregs );
cont = mregs->fpr[rS].h;
}
len = flag & len_mask;
if( flag & byte ) {
cont &= 0xff;
} else if( flag & half ) {
if( !(flag & reverse) )
cont &= 0xffff;
else
cont = bswap_16( cont );
} else if( flag & reverse )
cont = ld_le32(&cont);
/* ea is the mac untranslated address,
* mregs->mmu_ioaddr holds the translated address
*/
do_io_write( usr_data, mphys_ioaddr, cont, len );
if( flag & fpinst ) {
if( ((mphys_ioaddr+4) & 0xfff) < 4 )
printm("emulate store data inst: Possible MMU translation error\n");
do_io_write( usr_data, mphys_ioaddr+4, mregs->fpr[rS].l, 4 );
}
if( (flag & update) && rA ) {
mregs->gpr[rA] = ea;
ret = 1;
}
}
if( flag )
mregs->nip += 4;
else {
printm("Unimplemented store instruction %08lX\n", inst );
stop_emulation();
}
return ret;
}
/* returns 1 if GPRs have been modified */
int
_rvec_io_read( int dummy_rvec, ulong mphys_ioaddr, void *usr_data )
{
ulong ea, cont, inst=mregs->inst_opcode;
int op, op_ext, rD, rA, rB, d;
int flag=0, ret=1;
enum { byte=1, half=2, word=4, len_mask=7, indexed=8, update=16,
zero=32, reverse=64, nop=128, fpinst=256 };
/* do_io_read() is considered FPU-unsafe */
shield_fpu( mregs );
/* break instruction into parts */
op = OPCODE_PRIM( inst ); /* bit 0-5 */
op_ext = OPCODE_EXT( inst );
rD = B1( inst ); /* bit 6-10 */
rA = B2( inst ); /* bit 11-15 */
rB = B3( inst ); /* bit 16-20 */
d = BD( inst ); /* bit 16-31 sign extended */
switch( op ) {
case 34: /* lbz rD,d(rA) */
flag = byte | zero; break;
case 35: /* lbzu rD,d(rA) */
flag = byte | zero | update; break;
case 40: /* lhz rD,d(rA) */
flag = half | zero; break;
case 41: /* lhzu rD,d(rA) */
flag = half | zero | update; break;
case 42: /* lha rD,d(rA) */
flag = half; break;
case 43: /* lhau rD,d(rA) */
flag = half | update; break;
case 32: /* lwz rD,d(rA) */
flag = word | zero; break;
case 33: /* lwzu, rD,d(rA) */
flag = word | zero | update; break;
case 50: /* lfd frD,d(rA) */ /* FPU */
flag = word | fpinst | zero; break;
case 51: /* lfdu frD, d(rA) */ /* FPU */
flag = word | fpinst | update | zero; break;
}
if( !flag && op==31 ) {
switch( op_ext ) { /* lxxx rD,rA,rB */
case 87: /* lbzx rD,rA,rB */
flag = byte | indexed | zero; break;
case 119: /* lbzux rD,rA,rB */
flag = byte | indexed | zero | update; break;
case 279: /* lhzx rD,rA,rB */
flag = half | indexed | zero; break;
case 311: /* lhzux rD,rA,rB */
flag = half | indexed | zero | update; break;
case 343: /* lhax rD,rA,rB */
flag = half | indexed; break;
case 375: /* lhaux rD,rA,rB */
flag = half | indexed | update; break;
case 23: /* lwzx rD,rA,rB */
flag = word | indexed | zero; break;
case 55: /* lwzux rD,rA,rB */
flag = word | indexed | zero | update; break;
case 790: /* lhbrx rS,rA,rB */
flag = half | indexed | zero | reverse; break;
case 534: /* lwbrx rS,rA,rB */
flag = word | indexed | zero | reverse; break;
case 599: /* lfdx frD,rA,rB */ /* FPU */
flag = word | indexed | zero | fpinst; break;
case 631: /* lfdux frD,rA,rB */ /* FPU */
flag = word | indexed | zero | update | fpinst; break;
case 86: /* dcbf rA,rB - cache instruction*/
/* treat as nop if data-translation is off */
flag = (mregs->msr & MSR_DR) ? 0 : nop; break;
}
}
if( flag & len_mask) { /* instruction found */
if( flag & indexed ) { /* lxxx rD,rA,rB */
ea = mregs->gpr[rB];
ea += rA ? mregs->gpr[rA] : 0;
} else { /* lxxx rD,d(rA) */
ea = rA ? mregs->gpr[rA] : 0;
ea += d;
}
/* ea is the mac untranslated address, */
/* mphys_ioaddr is the mac-physical address */
cont = 0;
do_io_read( usr_data, mphys_ioaddr, (flag & len_mask), &cont );
if( flag & byte ){
cont &= 0xff;
} else if( flag & half ) {
cont &= 0xffff;
if( !(flag & zero) ) /* algebraic */
cont |= (cont & 0x8000)? 0xffff0000 : 0;
if( flag & reverse )
cont = bswap_16( cont );
} else if( flag & reverse)
cont = ld_le32(&cont);
if( !(flag & fpinst) )
mregs->gpr[rD] = cont;
else {
/* FPU instruction */
save_fpu_completely( mregs );
ret = 0;
mregs->fpr[rD].h = cont;
/* check for 4K boundary crossings... */
if( ((mphys_ioaddr+4) & 0xfff) < 4 )
printm("emulate_load_data_inst: MMU translation might be bad\n");
do_io_read( usr_data, mphys_ioaddr+4, 4, &cont );
mregs->fpr[rD].l = cont;
reload_tophalf_fpu( mregs );
}
if( (flag & update) && rA && (rA!=rD || (flag & fpinst)) ) {
ret = 1;
mregs->gpr[rA] = ea;
}
}
if( flag )
mregs->nip += 4;
else {
printm("Unimplemented load instruction %08lX\n", inst );
stop_emulation();
}
return ret;
}
int main(int argc, char *argv[])
{
{
libmaus2::lz::LineSplittingGzipOutputStream LSG("gzsplit",4,17);
for ( uint64_t i = 0; i < 17; ++i )
LSG << "line_" << i << "\n";
}
{
libmaus2::lz::LineSplittingGzipOutputStream LSG("nogzsplit",4,17);
}
testGzip();
testlz4();
#if 0
maskBamDuplicateFlag(std::cin,std::cout);
return 0;
#endif
#if 0
{
libmaus2::lz::BgzfInflateDeflateParallel BIDP(std::cin,std::cout,Z_DEFAULT_COMPRESSION,32,128);
libmaus2::autoarray::AutoArray<char> B(64*1024,false);
int r;
uint64_t t = 0;
uint64_t last = std::numeric_limits<uint64_t>::max();
uint64_t lcnt = 0;
uint64_t const mod = 64*1024*1024;
libmaus2::timing::RealTimeClock rtc; rtc.start();
libmaus2::timing::RealTimeClock lrtc; lrtc.start();
while ( (r = BIDP.read(B.begin(),B.size())) )
{
BIDP.write(B.begin(),r);
lcnt += r;
t += r;
if ( t/mod != last/mod )
{
if ( isatty(STDERR_FILENO) )
std::cerr
<< "\r" << std::string(60,' ') << "\r";
std::cerr
<< rtc.formatTime(rtc.getElapsedSeconds()) << " " << t/(1024*1024) << "MB, " << (lcnt/lrtc.getElapsedSeconds())/(1024.0*1024.0) << "MB/s";
if ( isatty(STDERR_FILENO) )
std::cerr << std::flush;
else
std::cerr << std::endl;
lrtc.start();
last = t;
lcnt = 0;
}
}
if ( isatty(STDERR_FILENO) )
std::cerr
<< "\r" << std::string(60,' ') << "\r";
std::cerr
<< rtc.formatTime(rtc.getElapsedSeconds()) << " " << t/(1024*1024) << "MB, " << (t/rtc.getElapsedSeconds())/(1024.0*1024.0) << "MB/s";
std::cerr << std::endl;
return 0;
}
#endif
#if 0
{
::libmaus2::lz::BgzfDeflateParallel BDP(std::cout,32,128,Z_DEFAULT_COMPRESSION);
while ( std::cin )
{
libmaus2::autoarray::AutoArray<char> B(16384);
std::cin.read(B.begin(),B.size());
int64_t const r = std::cin.gcount();
BDP.write(B.begin(),r);
}
BDP.flush();
std::cout.flush();
}
return 0;
#endif
#if 0
{
try
{
libmaus2::lz::BgzfInflateParallel BIP(std::cin /* ,4,16 */);
uint64_t c = 0;
uint64_t b = 0;
uint64_t d = 0;
libmaus2::timing::RealTimeClock rtc; rtc.start();
libmaus2::autoarray::AutoArray<uint8_t> adata(64*1024,false);
while ( (d=BIP.read(reinterpret_cast<char *>(adata.begin()),adata.size())) != 0 )
{
b += d;
if ( ++c % (16*1024) == 0 )
{
std::cerr << c << "\t" << b/(1024.0*1024.0*1024.0) << "\t" << static_cast<double>(b)/(1024.0*1024.0*rtc.getElapsedSeconds()) << " MB/s" << std::endl;
}
}
std::cerr << c << "\t" << b/(1024.0*1024.0*1024.0) << "\t" << static_cast<double>(b)/(1024.0*1024.0*rtc.getElapsedSeconds()) << " MB/s" << std::endl;
std::cerr << "decoded " << b << " bytes in " << rtc.getElapsedSeconds() << " seconds." << std::endl;
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
return 0;
#endif
std::cerr << "Testing random data on bgzf...";
testBgzfRandom();
std::cerr << "done." << std::endl;
std::cerr << "Testing mono...";
testBgzfMono();
std::cerr << "done." << std::endl;
::libmaus2::lz::BgzfDeflate<std::ostream> bdefl(std::cout);
char const * str = "Hello, world.\n";
bdefl.write(reinterpret_cast<char const *>(str),strlen(str));
bdefl.flush();
bdefl.write(reinterpret_cast<char const *>(str),strlen(str));
bdefl.flush();
bdefl.addEOFBlock();
return 0;
::libmaus2::lz::BgzfInflateStream SW(std::cin);
::libmaus2::autoarray::AutoArray<char> BB(200,false);
while ( SW.read(BB.begin(),BB.size()) )
{
}
if ( argc < 2 )
return EXIT_FAILURE;
return 0;
#if 0
::libmaus2::lz::GzipHeader GZH(argv[1]);
return 0;
#endif
std::ostringstream ostr;
::libmaus2::autoarray::AutoArray<uint8_t> message = ::libmaus2::util::GetFileSize::readFile(argv[1]);
std::cerr << "Deflating message of length " << message.size() << "...";
::libmaus2::lz::Deflate DEFL(ostr);
DEFL.write ( reinterpret_cast<char const *>(message.begin()), message.size() );
DEFL.flush();
std::cerr << "done." << std::endl;
std::cerr << "Checking output...";
std::istringstream istr(ostr.str());
::libmaus2::lz::Inflate INFL(istr);
int c;
uint64_t i = 0;
while ( (c=INFL.get()) >= 0 )
{
assert ( c == message[i] );
i++;
}
std::cerr << "done." << std::endl;
// std::cerr << "Message size " << message.size() << std::endl;
std::string testfilename = "test";
::libmaus2::lz::BlockDeflate BD(testfilename);
BD.write ( message.begin(), message.size() );
BD.flush();
uint64_t const decpos = message.size() / 3;
::libmaus2::lz::BlockInflate BI(testfilename,decpos);
::libmaus2::autoarray::AutoArray<uint8_t> dmessage (message.size(),false);
uint64_t const red = BI.read(dmessage.begin()+decpos,dmessage.size());
assert ( red == dmessage.size()-decpos );
std::cerr << "(";
for ( uint64_t i = decpos; i < message.size(); ++i )
assert ( message[i] == dmessage[i] );
std::cerr << ")\n";
std::string shortmes1("123456789");
std::string shortmes2("AA");
std::string shortmes3("BB");
std::string shortmes4("CC");
std::string textfile1("test1");
std::string textfile2("test2");
std::string textfile3("test3");
std::string textfile4("test4");
::libmaus2::lz::BlockDeflate BD1(textfile1);
BD1.write ( reinterpret_cast<uint8_t const *>(shortmes1.c_str()), shortmes1.size() );
BD1.flush();
::libmaus2::lz::BlockDeflate BD2(textfile2);
BD2.write ( reinterpret_cast<uint8_t const *>(shortmes2.c_str()), shortmes2.size() );
BD2.flush();
::libmaus2::lz::BlockDeflate BD3(textfile3);
BD3.write ( reinterpret_cast<uint8_t const *>(shortmes3.c_str()), shortmes3.size() );
BD3.flush();
::libmaus2::lz::BlockDeflate BD4(textfile4);
BD4.write ( reinterpret_cast<uint8_t const *>(shortmes4.c_str()), shortmes4.size() );
BD4.flush();
std::vector < std::string > filenames;
filenames.push_back(textfile1);
filenames.push_back(textfile2);
filenames.push_back(textfile3);
filenames.push_back(textfile4);
for ( uint64_t j = 0; j <= 15; ++j )
{
::libmaus2::lz::ConcatBlockInflate CBI(filenames,j);
for ( uint64_t i = 0; i < j; ++i )
std::cerr << ' ';
for ( uint64_t i = 0; i < CBI.n-j; ++i )
std::cerr << (char)CBI.get();
std::cerr << std::endl;
}
return 0;
}
int bammaskflags(::libmaus2::util::ArgInfo const & arginfo)
{
uint64_t const maskpos = arginfo.getValue<uint64_t>("maskpos",0xFFFFUL);
uint64_t const maskneg = arginfo.getValue<uint64_t>("maskneg",getDefaultMaskNeg());
uint64_t const mask = maskpos & (~maskneg);
if ( mask )
{
std::cerr << "Keeping flags ";
for ( uint64_t i = 1; i <= ::libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_FSUPPLEMENTARY; i <<= 1 )
if ( mask & i )
std::cerr << static_cast< ::libmaus2::bambam::BamFlagBase::bam_flags >(i) << ";";
std::cerr << std::endl;
std::cerr << "Erasing flags ";
for ( uint64_t i = 1; i <= ::libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_FSUPPLEMENTARY; i <<= 1 )
if ( !(mask & i) )
std::cerr << static_cast< ::libmaus2::bambam::BamFlagBase::bam_flags >(i) << ";";
std::cerr << std::endl;
}
else
{
std::cerr << "Erasing all flags." << std::endl;
}
int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
int const resetmatecoord = arginfo.getValue<int>("resetmatecoord",0);
::libmaus2::bambam::BamDecoder BD(std::cin);
::libmaus2::bambam::BamHeader const & bamheader = BD.getHeader();
std::string const headertext(bamheader.text);
// add PG line to header
std::string const upheadtext = ::libmaus2::bambam::ProgramHeaderLineSet::addProgramLine(
headertext,
"bammaskflags", // ID
"bammaskflags", // PN
arginfo.commandline, // CL
::libmaus2::bambam::ProgramHeaderLineSet(headertext).getLastIdInChain(), // PP
std::string(PACKAGE_VERSION) // VN
);
// construct new header
::libmaus2::bambam::BamHeader uphead(upheadtext);
::libmaus2::bambam::BamAlignment & alignment = BD.getAlignment();
/*
* 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));
while ( BD.readAlignment() )
{
alignment.putFlags(alignment.getFlags() & mask);
if ( resetmatecoord )
{
alignment.putNextRefId(-1);
alignment.putNextPos(-1);
}
alignment.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[])
{
Pooma::initialize(argc,argv);
Pooma::Tester tester(argc,argv);
#if POOMA_EXCEPTIONS
try {
#endif
tester.out() << "\n\nTesting 5D slice-range subsetting...\n\n";
Interval<1> I(5);
Interval<5> BD(I,I,I,I,I);
Brick5_t b(BD);
for (int i4 = 0; i4 < b.domain()[4].length(); ++i4)
for (int i3 = 0; i3 < b.domain()[3].length(); ++i3)
for (int i2 = 0; i2 < b.domain()[2].length(); ++i2)
for (int i1 = 0; i1 < b.domain()[1].length(); ++i1)
for (int i0 = 0; i0 < b.domain()[0].length(); ++i0)
b(i0,i1,i2,i3,i4) = i4+10*(i3+10*(i2+10*(i1+10*i0)));
tester.out() << "b.domain() = " << b.domain() << std::endl;
tester.out() << std::endl;
typedef NewDomain5<int, Range<1>, int, AllDomain<1>, Interval<1> >
NewDomain_t;
typedef NewDomain_t::SliceType_t SliceType_t;
SliceType_t VD;
AllDomain<1> A;
Interval<1> I1(1,3);
Range<1> R(0,4,2);
NewDomain_t::fillSlice(VD, b.domain(), 2, R, 1, A, I1);
tester.out() << "VD = " << VD << std::endl;
typedef NewEngine<Brick5_t, SliceType_t>::Type_t Engine_t;
Engine_t v(b, VD);
// v.domain() should be: [0:2:1,0:4:1,0:2:1]
tester.out() << "v.domain() = " << v.domain() << std::endl;
// v's values should be 2 | 0,2,4 | 1 | 0,1,2,3,4 | 1,2,3
tester.out() << "v = \n";
for (int i2 = 0; i2 < v.domain()[2].length(); ++i2)
for (int i1 = 0; i1 < v.domain()[1].length(); ++i1)
for (int i0 = 0; i0 < v.domain()[0].length(); ++i0)
tester.out() << v(i0,i1,i2) << std::endl;
typedef NewDomain3<int, Range<1>, Interval<1> > NewDomain2_t;
typedef NewDomain2_t::SliceType_t SliceType2_t;
SliceType2_t VD2;
Interval<1> I2(1,2);
Range<1> R2(0,2,2);
NewDomain2_t::fillSlice(VD2, v.domain(), 0, R2, I2);
tester.out() << "VD2 = " << VD2 << std::endl;
NewEngine<Engine_t, SliceType2_t>::Type_t v2(v, VD2);
// v2.domain() should be: [0:1:1,0:1:1]
tester.out() << "v2.domain() = " << v2.domain() << std::endl;
// v2's values should be 2 | 0 | 1 | 0,2 | 2,3
tester.out() << "v2 = \n";
for (int i1 = 0; i1 < v2.domain()[1].length(); ++i1)
for (int i0 = 0; i0 < v2.domain()[0].length(); ++i0)
tester.out() << v2(i0,i1) << std::endl;
#if POOMA_EXCEPTIONS
}
catch(const char *err)
{
tester.exceptionHandler( err );
tester.set( false );
}
catch(const Pooma::Assertion &err)
{
tester.exceptionHandler( err );
tester.set( false );
}
#endif
int ret = tester.results("brickview_test1");
Pooma::finalize();
return ret;
}
int bamfilterflags(::libmaus2::util::ArgInfo const & arginfo)
{
uint32_t const excludeflags = libmaus2::bambam::BamFlagBase::stringToFlags(arginfo.getValue<std::string>("exclude",""));
std::cerr << "[V] excluding " << excludeflags << std::endl;
int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",Z_DEFAULT_COMPRESSION));
uint64_t const numthreads = arginfo.getValue<uint64_t>("numthreads",1);
uint64_t cnt = 0;
uint64_t kept = 0;
/*
* 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
*/
if ( numthreads == 1 )
{
::libmaus2::bambam::BamDecoder BD(std::cin);
::libmaus2::bambam::BamHeader const & bamheader = BD.getHeader();
::libmaus2::bambam::BamHeader::unique_ptr_type uphead(libmaus2::bambam::BamHeaderUpdate::updateHeader(arginfo,bamheader,"bamfilterflags",std::string(PACKAGE_VERSION)));
::libmaus2::bambam::BamAlignment & alignment = BD.getAlignment();
::libmaus2::bambam::BamWriter::unique_ptr_type writer(new ::libmaus2::bambam::BamWriter(std::cout,*uphead,level,Pcbs));
for ( ; BD.readAlignment(); ++cnt )
{
if ( cnt % (1024*1024) == 0 )
std::cerr << "[V] processed " << cnt << " kept " << kept << " removed " << (cnt-kept) << std::endl;
if ( ! (alignment.getFlags() & excludeflags) )
{
alignment.serialise(writer->getStream());
++kept;
}
}
std::cerr << "[V] " << cnt << std::endl;
}
else
{
::libmaus2::bambam::BamHeaderUpdate UH(arginfo,"bamfilterflags",std::string(PACKAGE_VERSION));
libmaus2::bambam::BamParallelRewrite BPR(std::cin,UH,std::cout,Z_DEFAULT_COMPRESSION,numthreads,4 /* blocks per thread */,Pcbs);
libmaus2::bambam::BamAlignmentDecoder & dec = BPR.getDecoder();
libmaus2::bambam::BamParallelRewrite::writer_type & writer = BPR.getWriter();
libmaus2::bambam::BamAlignment const & algn = dec.getAlignment();
for ( ; dec.readAlignment(); ++cnt )
{
if ( cnt % (1024*1024) == 0 )
std::cerr << "[V] processed " << cnt << " kept " << kept << " removed " << (cnt-kept) << std::endl;
if ( ! (algn.getFlags() & excludeflags) )
{
algn.serialise(writer.getStream());
++kept;
}
}
std::cerr << "[V] " << cnt << std::endl;
}
std::cerr << "[V] kept " << kept << " removed " << cnt-kept << std::endl;
if ( Pmd5cb )
{
Pmd5cb->saveDigestAsFile(md5filename);
}
if ( Pindex )
{
Pindex->flush(std::string(indexfilename));
}
return EXIT_SUCCESS;
}