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jellyfish::parse_qual_dna Class Reference

Inheritance diagram for jellyfish::parse_qual_dna:
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List of all members.

Classes

class  thread

Public Types

typedef
seq_qual_parser::sequence_t
bucket_iterator
typedef seq_qual_parser::sequence_t bucket_t

Public Member Functions

bucket_iterator bucket_begin () const
bucket_iterator bucket_end () const
virtual void fill ()
bool is_closed ()
thread new_thread ()
seq_qual_parser::sequence_tnext ()
 parse_qual_dna (int nb_files, char *argv[], uint_t _mer_len, unsigned int nb_buffers, size_t _buffer_size, const char _qs, const char _min_q)
void release (seq_qual_parser::sequence_t *bucket)
void set_canonical (bool v=true)

Static Public Attributes

static const uint_t CODE_RESET = -1
static const uint_t codes [256]

Protected Member Functions

void close ()
seq_qual_parser::sequence_twrite_next ()
void write_release (seq_qual_parser::sequence_t *bucket)

Private Types

typedef std::vector< const char * > fary_t

Private Attributes

allocators::mmap buffer_data
size_t buffer_size
bool canonical
fary_t::const_iterator current_file
fary_t files
seq_qual_parserfparser
bool have_seam
uint_t mer_len
const char min_q
const char quality_start
char * seam

Friends

class thread

Detailed Description

Definition at line 29 of file parse_qual_dna.hpp.


The documentation for this class was generated from the following files:

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