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

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

jellyfish::parse_dna Class Reference

Inheritance diagram for jellyfish::parse_dna:
Inheritance graph
[legend]
Collaboration diagram for jellyfish::parse_dna:
Collaboration graph
[legend]

List of all members.

Classes

class  thread

Public Types

typedef
sequence_parser::sequence_t
bucket_iterator
typedef sequence_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 ()
sequence_parser::sequence_tnext ()
 parse_dna (int nb_files, const char *argv[], uint_t _mer_len, unsigned int nb_buffers, size_t _buffer_size)
void release (sequence_parser::sequence_t *bucket)
void set_canonical (bool v=true)

Static Public Member Functions

static void mer_binary_to_string (uint64_t mer, uint_t klen, char *out)
static uint64_t mer_string_to_binary (const char *in, uint_t klen)
static uint64_t reverse_complement (uint64_t v, uint_t length)

Static Public Attributes

static const uint_t CODE_COMMENT = -3
static const uint_t CODE_IGNORE = -2
static const uint_t CODE_NOT_DNA = ((uint_t)1) << (bsizeof(uint_t) - 1)
static const uint_t CODE_RESET = -1
static const uint_t codes [256]

Protected Member Functions

void close ()
sequence_parser::sequence_twrite_next ()
void write_release (sequence_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
sequence_parserfparser
bool have_seam
uint_t mer_len
char * seam

Friends

class thread

Detailed Description

Definition at line 29 of file parse_dna.hpp.


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

Generated by  Doxygen 1.6.0   Back to index