Logo Search packages:      
Sourcecode: jellyfish version File versions  Download package

Classes | Public Types | Public Member Functions | Static Public Attributes | Protected Member Functions | Private Types | Private Attributes | Friends

jellyfish::parse_qual_dna Class Reference

Inheritance diagram for jellyfish::parse_qual_dna:
Inheritance graph
Collaboration diagram for jellyfish::parse_qual_dna:
Collaboration graph

List of all members.


class  thread

Public Types

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
bool have_seam
uint_t mer_len
const char min_q
const char quality_start
char * seam


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:

Generated by  Doxygen 1.6.0   Back to index