Index

Symbols

--cutoff <int>, -C <int> filter-abund-single.py command line option filter-abund.py command line option --keep-subsets do-partition.py command line option merge-partition.py command line option --ksize <int>, -k <int> abundance-dist-single.py command line option annotate-partitions.py command line option count-overlap.py command line option do-partition.py command line option filter-abund-single.py command line option filter-abund.py command line option filter-stoptags.py command line option load-graph.py command line option load-into-counting.py command line option make-initial-stoptags.py command line option merge-partition.py command line option normalize-by-median.py command line option --max-size <int>, -X <int> extract-partitions.py command line option --min-partition-size <int>, -m <int> extract-partitions.py command line option --min-tablesize <float>, -x <float> abundance-dist-single.py command line option count-overlap.py command line option do-partition.py command line option filter-abund-single.py command line option filter-abund.py command line option find-knots.py command line option load-graph.py command line option load-into-counting.py command line option make-initial-stoptags.py command line option normalize-by-median.py command line option --n_tables <int>, -N <int> abundance-dist-single.py command line option count-overlap.py command line option do-partition.py command line option filter-abund-single.py command line option filter-abund.py command line option find-knots.py command line option load-graph.py command line option load-into-counting.py command line option make-initial-stoptags.py command line option normalize-by-median.py command line option --no-big-traverse do-partition.py command line option partition-graph.py command line option --no-build-tagset, -n load-graph.py command line option --no-output-groups, -n extract-partitions.py command line option --normalize-to <int>, -Z <int> filter-abund.py command line option --output-unassigned, -U extract-partitions.py command line option --report-total-kmers, -t abundance-dist-single.py command line option filter-abund-single.py command line option load-graph.py command line option load-into-counting.py command line option normalize-by-median.py command line option --save-on-failure normalize-by-median.py command line option --savetable <filename> abundance-dist-single.py command line option filter-abund-single.py command line option --stoptags <filename>, -S <filename> make-initial-stoptags.py command line option partition-graph.py command line option --subset-size <float>, -s <float> do-partition.py command line option make-initial-stoptags.py command line option partition-graph.py command line option --threads <int>, -T <int> abundance-dist-single.py command line option filter-abund-single.py command line option filter-abund.py command line option load-graph.py command line option load-into-counting.py command line option partition-graph.py command line option --threads, -T do-partition.py command line option --variable-coverage, -V filter-abund.py command line option --version abundance-dist-single.py command line option abundance-dist.py command line option annotate-partitions.py command line option count-median.py command line option count-overlap.py command line option do-partition.py command line option extract-paired-reads.py command line option extract-partitions.py command line option filter-abund-single.py command line option filter-abund.py command line option filter-stoptags.py command line option find-knots.py command line option interleave-reads.py command line option load-graph.py command line option load-into-counting.py command line option make-initial-stoptags.py command line option merge-partition.py command line option normalize-by-median.py command line option partition-graph.py command line option sample-reads-randomly.py command line option split-paired-reads.py command line option -b, --no-bigcount abundance-dist-single.py command line option load-into-counting.py command line option

-C <int>, --cutoff <int> normalize-by-median.py command line option -d <int>, --dump-frequency <int> normalize-by-median.py command line option -f, --fault-tolerant normalize-by-median.py command line option -h, --help abundance-dist-single.py command line option abundance-dist.py command line option annotate-partitions.py command line option count-median.py command line option count-overlap.py command line option do-partition.py command line option extract-long-sequences.py command line option extract-paired-reads.py command line option extract-partitions.py command line option fastq-to-fasta.py command line option filter-abund-single.py command line option filter-abund.py command line option filter-stoptags.py command line option find-knots.py command line option interleave-reads.py command line option load-graph.py command line option load-into-counting.py command line option make-initial-stoptags.py command line option merge-partition.py command line option normalize-by-median.py command line option partition-graph.py command line option sample-reads-randomly.py command line option split-paired-reads.py command line option -l <filename>, --loadtable <filename> normalize-by-median.py command line option -l <int>, --length <int> extract-long-sequences.py command line option -M <int>, --max_reads <int> sample-reads-randomly.py command line option -N <int>, --num_reads <int> sample-reads-randomly.py command line option -n, --n_keep fastq-to-fasta.py command line option -o <filename>, --out <filename> normalize-by-median.py command line option -o <filename>, --output <filename> interleave-reads.py command line option -o <optional_output_filename>, --out <optional_output_filename> filter-abund.py command line option -o <output_file>, --output <output_file> sample-reads-randomly.py command line option -o, --output extract-long-sequences.py command line option fastq-to-fasta.py command line option -p, --paired normalize-by-median.py command line option -q, --quiet abundance-dist-single.py command line option count-overlap.py command line option do-partition.py command line option filter-abund-single.py command line option filter-abund.py command line option load-graph.py command line option load-into-counting.py command line option make-initial-stoptags.py command line option normalize-by-median.py command line option -R <filename>, --report <filename> normalize-by-median.py command line option -R <int>, --random-seed <int> sample-reads-randomly.py command line option -s <filename>, --savetable <filename> normalize-by-median.py command line option -S <int>, --samples <int> sample-reads-randomly.py command line option -s, --squash abundance-dist-single.py command line option abundance-dist.py command line option -z, --no-zero abundance-dist-single.py command line option abundance-dist.py command line option

A

abundance-dist-single.py command line option --ksize <int>, -k <int> --min-tablesize <float>, -x <float> --n_tables <int>, -N <int> --report-total-kmers, -t --savetable <filename> --threads <int>, -T <int> --version -b, --no-bigcount -h, --help -q, --quiet -s, --squash -z, --no-zero input_sequence_filename output_histogram_filename abundance-dist.py command line option --version -h, --help -s, --squash -z, --no-zero input_counting_table_filename input_sequence_filename output_histogram_filename accuracy (khmer.Read attribute)

annotate-partitions.py command line option --ksize <int>, -k <int> --version -h, --help graphbase input_sequence_filename annotations (khmer.Read attribute)

B

basename partition-graph.py command line option

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) count-median.py command line option --version -h, --help input_counting_table_filename input_sequence_filename output_summary_filename count-overlap.py command line option --ksize <int>, -k <int> --min-tablesize <float>, -x <float> --n_tables <int>, -N <int> --version -h, --help -q, --quiet input_presence_table_filename input_sequence_filename output_report_filename

D

do-partition.py command line option --keep-subsets --ksize <int>, -k <int> --min-tablesize <float>, -x <float> --n_tables <int>, -N <int> --no-big-traverse --subset-size <float>, -s <float> --threads, -T --version -h, --help -q, --quiet graphbase input_sequence_filename

E

extract-long-sequences.py command line option -h, --help -l <int>, --length <int> -o, --output input_filenames extract-paired-reads.py command line option --version -h, --help infile

extract-partitions.py command line option --max-size <int>, -X <int> --min-partition-size <int>, -m <int> --no-output-groups, -n --output-unassigned, -U --version -h, --help input_partition_filename output_filename_prefix

F

FastaParser (C++ class) fastq-to-fasta.py command line option -h, --help -n, --n_keep -o, --output input_sequence FastqParser (C++ class) filenames sample-reads-randomly.py command line option

filter-abund-single.py command line option --cutoff <int>, -C <int> --ksize <int>, -k <int> --min-tablesize <float>, -x <float> --n_tables <int>, -N <int> --report-total-kmers, -t --savetable <filename> --threads <int>, -T <int> --version -h, --help -q, --quiet input_sequence_filename filter-abund.py command line option --cutoff <int>, -C <int> --ksize <int>, -k <int> --min-tablesize <float>, -x <float> --n_tables <int>, -N <int> --normalize-to <int>, -Z <int> --threads <int>, -T <int> --variable-coverage, -V --version -h, --help -o <optional_output_filename>, --out <optional_output_filename> -q, --quiet input_presence_table_filename input_sequence_filename filter-stoptags.py command line option --ksize <int>, -k <int> --version -h, --help input_sequence_filename input_stoptags_filename find-knots.py command line option --min-tablesize <float>, -x <float> --n_tables <int>, -N <int> --version -h, --help graphbase

G

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

graphbase annotate-partitions.py command line option do-partition.py command line option find-knots.py command line option make-initial-stoptags.py command line option merge-partition.py command line option 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

infile extract-paired-reads.py command line option split-paired-reads.py command line option infiles interleave-reads.py command line option input_counting_table_filename abundance-dist.py command line option count-median.py command line option input_filenames extract-long-sequences.py command line option input_partition_filename extract-partitions.py command line option input_presence_table_filename count-overlap.py command line option filter-abund.py command line option input_sequence fastq-to-fasta.py command line option input_sequence_filename abundance-dist-single.py command line option abundance-dist.py command line option annotate-partitions.py command line option count-median.py command line option count-overlap.py command line option do-partition.py command line option filter-abund-single.py command line option filter-abund.py command line option filter-stoptags.py command line option load-graph.py command line option load-into-counting.py command line option normalize-by-median.py command line option input_stoptags_filename filter-stoptags.py command line option interleave-reads.py command line option --version -h, --help -o <filename>, --output <filename> infiles 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)

L

load-graph.py command line option --ksize <int>, -k <int> --min-tablesize <float>, -x <float> --n_tables <int>, -N <int> --no-build-tagset, -n --report-total-kmers, -t --threads <int>, -T <int> --version -h, --help -q, --quiet input_sequence_filename output_presence_table_filename

load-into-counting.py command line option --ksize <int>, -k <int> --min-tablesize <float>, -x <float> --n_tables <int>, -N <int> --report-total-kmers, -t --threads <int>, -T <int> --version -b, --no-bigcount -h, --help -q, --quiet input_sequence_filename output_countingtable_filename

M

make-initial-stoptags.py command line option --ksize <int>, -k <int> --min-tablesize <float>, -x <float> --n_tables <int>, -N <int> --stoptags <filename>, -S <filename> --subset-size <float>, -s <float> --version -h, --help -q, --quiet graphbase

merge-partition.py command line option --keep-subsets --ksize <int>, -k <int> --version -h, --help graphbase

N

name (khmer.Read attribute)

normalize-by-median.py command line option --ksize <int>, -k <int> --min-tablesize <float>, -x <float> --n_tables <int>, -N <int> --report-total-kmers, -t --save-on-failure --version -C <int>, --cutoff <int> -R <filename>, --report <filename> -d <int>, --dump-frequency <int> -f, --fault-tolerant -h, --help -l <filename>, --loadtable <filename> -o <filename>, --out <filename> -p, --paired -q, --quiet -s <filename>, --savetable <filename> input_sequence_filename

O

output_countingtable_filename load-into-counting.py command line option output_filename_prefix extract-partitions.py command line option output_histogram_filename abundance-dist-single.py command line option abundance-dist.py command line option

output_presence_table_filename load-graph.py command line option output_report_filename count-overlap.py command line option output_summary_filename count-median.py command line option

P

ParserState (C++ class)

partition-graph.py command line option --no-big-traverse --stoptags <filename>, -S <filename> --subset-size <float>, -s <float> --threads <int>, -T <int> --version -h, --help basename

R

RawStreamReader (C++ class) Read (C++ class) (class in khmer)

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

S

sample-reads-randomly.py command line option --version -M <int>, --max_reads <int> -N <int>, --num_reads <int> -R <int>, --random-seed <int> -S <int>, --samples <int> -h, --help -o <output_file>, --output <output_file> filenames sequence (khmer.Read attribute) set_active_config (C++ function)

set_config() (in module khmer) split-paired-reads.py command line option --version -h, --help infile

T

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

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