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 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 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;
}