NVBIO
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SequenceDataFile from a FASTQ file contains the code to parse FASTQ files and dump the results into a SequenceDataRAM object file access is done via derived classes
Definition at line 53 of file sequence_fastq.h.
#include <sequence_fastq.h>
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SequenceDataFile_FASTQ_parser (const char *read_file_name, const SequenceDataFile::Options &options, const uint32 buffer_size=64536u) | |
virtual int | nextChunk (struct SequenceDataEncoder *output, uint32 max_reads, uint32 max_bps) |
virtual FileState | fillBuffer (void)=0 |
virtual bool | gets (char *buffer, int len)=0 |
Proteced Methods inherited from nvbio::io::SequenceDataFile | |
SequenceDataFile (const Options &options) | |
Protected Members | |
const char * | m_file_name |
std::vector< char > | m_buffer |
uint32 | m_buffer_size |
uint32 | m_buffer_pos |
uint32 | m_line |
uint8 | m_error_char |
std::vector< char > | m_name |
std::vector< uint8 > | m_read_bp |
std::vector< uint8 > | m_read_q |
Protected Members inherited from nvbio::io::SequenceDataFile | |
Options | m_options |
uint32 | m_loaded |
FileState | m_file_state |
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Definition at line 56 of file sequence_fastq.h.
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protectedpure virtual |
Implemented in nvbio::io::SequenceDataFile_FASTQ_gz.
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protectedpure virtual |
Implemented in nvbio::io::SequenceDataFile_FASTQ_gz.
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Definition at line 91 of file sequence_fastq.h.
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Definition at line 93 of file sequence_fastq.h.
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Definition at line 92 of file sequence_fastq.h.
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Definition at line 99 of file sequence_fastq.h.
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Definition at line 88 of file sequence_fastq.h.
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Definition at line 96 of file sequence_fastq.h.
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Definition at line 102 of file sequence_fastq.h.
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Definition at line 103 of file sequence_fastq.h.
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Definition at line 104 of file sequence_fastq.h.