Example #1
0
			void put(libmaus::fastx::FastQReader::pattern_type const & pattern)
			{
				uint64_t const patlen = getFastQLength(pattern);
				
				while ( (C.end() - pc) < static_cast<ptrdiff_t>(patlen) )
				{
					uint64_t const off = pc-C.begin();
					uint64_t const newclen = std::max(2*C.size(),static_cast<uint64_t>(1ull));
					C.resize(newclen);
					pc = C.begin()+off;
				}

				*(pc)++ = '@';
				std::copy(pattern.sid.begin(),pattern.sid.end(),pc);
				pc += pattern.sid.size();
				*(pc++) = '\n';

				std::copy(pattern.spattern.begin(), pattern.spattern.end(),pc);
				pc += pattern.spattern.size();
				*(pc++) = '\n';

				*(pc)++ = '+';
				std::copy(pattern.plus.begin(), pattern.plus.end(),pc);
				pc += pattern.plus.size();
				*(pc++) = '\n';

				std::copy(pattern.quality.begin(), pattern.quality.end(),pc);
				pc += pattern.quality.size();
				*(pc++) = '\n';
				
				assert ( pc <= C.end() );
				
				lnumsyms += pattern.spattern.size();
				minlen = std::min(minlen,static_cast<uint64_t>(pattern.spattern.size()));
				maxlen = std::max(maxlen,static_cast<uint64_t>(pattern.spattern.size()));
				pathigh++;
				
				if ( pathigh - patlow == patperblock )
					internalFlush();
			}
Example #2
0
			/* decode next block */
			bool decodeBlock()
			{
				/* open new file if necessary */
				bool changedfile = false;
				while ( fileptr < idda.data.size() && blockptr == idda.data[fileptr].numentries )
				{
					fileptr++;
					blockptr = 0;
					changedfile = true;
				}
				if ( fileptr == idda.data.size() )
					return false;
				if ( changedfile )
					openNewFile();

				/* align to word boundary */
				GD->flush();
				/* read block size */
				uint64_t const blocksize = GD->decodeWord(32);

				/* increase size of memory buffer if necessary */
				if ( blocksize > decodebuf.size() )
					decodebuf.resize(blocksize);

				/* set buffer pointers */
				pa = decodebuf.begin();
				pc = pa;
				pe = pa + blocksize;

				/* decode block */
				for ( uint64_t i = 0; i < blocksize; ++i )
					decodebuf[i] = GD->decode();

				/* increment block pointer */
				blockptr++;
				
				return true;
			}