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NVBIO
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This module contains a series of classes to load and represent read streams. The idea is that a read stream is an object implementing a simple interface, ReadDataStream, which allows to stream through a file or other set of reads in batches, which are represented in memory with an object inheriting from ReadData. There are several kinds of ReadData containers to keep the reads in the host RAM, or in CUDA device memory. Additionally, the same container can be viewed with different ReadDataView's, in order to allow reinterpreting the base arrays as arrays of different types, e.g. to perform vector loads or use LDG.
Modules | |
| ReadsIODetail | |
Typedefs | |
| typedef ReadDataView< uint32 *, uint32 *, char *, char * > | nvbio::io::ReadDataCore |
| typedef ReadDataRAM | nvbio::io::ReadDataHost |
| typedef ReadDataDevice | nvbio::io::ReadDataCUDA |
Enumerations | |
| enum | nvbio::io::QualityEncoding { nvbio::io::Phred = 0, nvbio::io::Phred33 = 1, nvbio::io::Phred64 = 2, nvbio::io::Solexa = 3, nvbio::io::Phred = 0, nvbio::io::Phred33 = 1, nvbio::io::Phred64 = 2, nvbio::io::Solexa = 3 } |
| enum | nvbio::io::ReadEncoding { nvbio::io::FORWARD = 0x0001, nvbio::io::REVERSE = 0x0002, nvbio::io::FORWARD_COMPLEMENT = 0x0004, nvbio::io::REVERSE_COMPLEMENT = 0x0008 } |
| enum | nvbio::io::PairedEndPolicy { nvbio::io::PE_POLICY_FF = 0, nvbio::io::PE_POLICY_FR = 1, nvbio::io::PE_POLICY_RF = 2, nvbio::io::PE_POLICY_RR = 3, nvbio::io::PE_POLICY_FF = 0, nvbio::io::PE_POLICY_FR = 1, nvbio::io::PE_POLICY_RF = 2, nvbio::io::PE_POLICY_RR = 3 } |
Functions | |
| ReadDataStream * | nvbio::io::open_read_file (const char *read_file_name, const QualityEncoding qualities, const uint32 max_reads, const uint32 truncate_read_len, const ReadEncoding flags) |
| typedef ReadDataView<uint32*,uint32*,char*,char*> nvbio::io::ReadDataCore |
| typedef ReadDataDevice nvbio::io::ReadDataCUDA |
| typedef ReadDataRAM nvbio::io::ReadDataHost |
| ReadDataStream * nvbio::io::open_read_file | ( | const char * | read_file_name, |
| const QualityEncoding | qualities, | ||
| const uint32 | max_reads = uint32(-1), |
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| const uint32 | max_read_len = uint32(-1), |
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| const ReadEncoding | flags = REVERSE |
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| ) |
factory method to open a read file
| read_file_name | the file to open |
| qualities | the encoding of the qualities |
| max_reads | maximum number of reads to input |
| max_read_len | maximum read length - reads will be truncated |
| flags | a set of flags indicating which strands to encode in the batch for each read. For example, passing FORWARD | REVERSE_COMPLEMENT will result in a stream containing BOTH the forward and reverse-complemented strands. |
1.8.4
