/**
* interval alignment input method
*
* @param delayPutRank if true, then rank aux tag will not be inserted by this call
* @return true iff next alignment could be successfully read, false if no more alignment were available
**/
bool readAlignmentInternal(bool const delayPutRank = false)
{
bool const ok = readAlignmentInRange();
if ( ! ok )
return false;
if ( ! delayPutRank )
putRank();
return true;
}
/**
* interval alignment input method
*
* @param delayPutRank if true, then rank aux tag will not be inserted by this call
* @return true iff next alignment could be successfully read, false if no more alignment were available
**/
bool readAlignmentInternal(bool const delayPutRank = false)
{
char const * pa = 0;
char const * pe = 0;
bool const ok = lb.getline(&pa,&pe);
if ( ! ok )
return false;
samline.parseSamLine(pa,pe);
if ( ! delayPutRank )
putRank();
return true;
}
/**
* input method
*
* @return bool if alignment input was successfull and a new alignment was stored
**/
virtual bool readAlignmentInternal(bool const delayPutRank = false)
{
while ( true )
{
if ( expect_false(! decoder) )
{
if ( static_cast<uint64_t>(++fileid) == infos.size() )
{
return false;
}
else
{
if ( Pwrappers.get() )
{
decoder = &((*Pwrappers)[fileid]->getDecoder());
}
else
{
libmaus::bambam::BamAlignmentDecoderWrapper::unique_ptr_type tptr ( libmaus::bambam::BamAlignmentDecoderFactory::construct(infos[fileid]) );
wrapper = UNIQUE_PTR_MOVE(tptr);
decoder = &(wrapper->getDecoder());
}
algnptr = &(decoder->getAlignment());
}
}
bool const ok = decoder->readAlignment();
if ( expect_true(ok) )
{
alignment.swap(*algnptr);
if ( ! delayPutRank )
putRank();
header.updateAlignment(fileid,alignment);
return true;
}
else
{
wrapper.reset();
decoder = 0;
algnptr = 0;
}
}
}
bool readAlignmentInternal(bool const delayPutRank = false)
{
int const r = d_decode.func(dec);
// std::cerr << "got code " << r << std::endl;
if ( r == -2 )
{
::libmaus::exception::LibMausException se;
se.getStream() << "ScramDecoder::readAlignment(): failed to read alignment without reaching EOF" << std::endl;
se.finish();
throw se;
}
else if ( r == -1 )
{
return false;
}
if ( dec->blocksize > alignment.D.size() )
alignment.D = ::libmaus::bambam::BamAlignment::D_array_type(dec->blocksize,false);
memcpy(alignment.D.begin(),dec->buffer,dec->blocksize);
alignment.blocksize = dec->blocksize;
if ( validate )
{
libmaus_bambam_alignment_validity const validity = alignment.valid(bamheader);
if ( validity != ::libmaus::bambam::libmaus_bambam_alignment_validity_ok )
{
::libmaus::exception::LibMausException se;
se.getStream() << "Invalid alignment: " << validity << std::endl;
se.finish();
throw se;
}
}
if ( ! delayPutRank )
putRank();
return true;
}
