Index

A | B | C | F | G | H | I | K | N | P | R | S | T

A

accuracy (khmer.Read attribute)
annotations (khmer.Read attribute)

B

Bz2StreamReader (C++ class)

C

CacheManager (C++ class)
CacheManager::get_bytes (C++ function)
CacheManager::has_more_data (C++ function)
CacheManager::split_at (C++ function)
CacheManagerSegment (C++ class)
CacheManger::_get_segment (C++ function)
Config (C++ class)
Config::get_number_of_threads (C++ function)
Config::get_reads_input_buffer_size (C++ function)
Config::set_number_of_threads (C++ function)
Config::set_reads_input_buffer_size (C++ function)
consume_fasta_and_tag_with_reads_parser() (khmer.new_counting_hash method)
consume_fasta_with_reads_parser() (khmer.new_hashtable method)

F

FastaParser (C++ class)
FastqParser (C++ class)

G

get_active_config (C++ function)
get_config() (in module khmer)
GzStreamReader (C++ class)

H

Hashbits (C++ class)
Hashbits::consume_fasta_and_tag (C++ function)
Hasher (C++ class)
Hashtable (C++ class)
Hashtable::consume_fasta (C++ function)

I

IParser (C++ class)
IParser::get_parser (C++ function)
IParser::imprint_next_read (C++ function)
IParser::imprint_next_read_pair (C++ function)
IParser::is_complete (C++ function)
IPerformanceMetrics (C++ class)
IPerformanceMetrics::accumulate_timer_deltas (C++ function)
IPerformanceMetrics::start_timers (C++ function)
IPerformanceMetrics::stop_timers (C++ function)
IStreamReader (C++ class)
iter_read_pairs() (khmer.ReadParser method)

K

khmer (module)

N

name (khmer.Read attribute)

P

ParserState (C++ class)

R

RawStreamReader (C++ class)
Read (C++ class)
(class in khmer)
read_into_cache (C++ function)
ReadParser (class in khmer)

S

sequence (khmer.Read attribute)
set_active_config (C++ function)
set_config() (in module khmer)

T

ThreadIDMap (C++ class)
ThreadIDMap::get_thread_id (C++ function)
TraceLogger (C++ class)
TraceLogger::operator() (C++ function)