SYMBOL INDEX (753 symbols across 88 files)

FILE: falcon_kit/FastaReader.py
  function wrap (line 20) | def wrap(s, columns):
  function splitFastaHeader (line 25) | def splitFastaHeader(name):
  function splitFileContents (line 38) | def splitFileContents(f, delimiter, BLOCKSIZE=8192):
  class FastaRecord (line 57) | class FastaRecord(object):
    method __init__ (line 64) | def __init__(self, name, sequence):
    method name (line 77) | def name(self):
    method id (line 85) | def id(self):
    method metadata (line 93) | def metadata(self):
    method sequence (line 101) | def sequence(self):
    method length (line 110) | def length(self):
    method md5 (line 117) | def md5(self):
    method fromString (line 124) | def fromString(cls, s):
    method __eq__ (line 139) | def __eq__(self, other):
    method __ne__ (line 146) | def __ne__(self, other):
    method __str__ (line 149) | def __str__(self):
  function yield_fasta_records (line 160) | def yield_fasta_records(f, fn):
  function stream_stdout (line 174) | def stream_stdout(call, fn):
  function open_fasta_reader (line 181) | def open_fasta_reader(fn):
  class FastaReader (line 215) | class FastaReader(object):
    method __iter__ (line 219) | def __iter__(self):
    method __init__ (line 224) | def __init__(self, f):

FILE: falcon_kit/bash.py
  function mkdir (line 22) | def mkdir(d):
  function make_executable (line 27) | def make_executable(path):
  function write_sub_script (line 35) | def write_sub_script(ofs, script):
  function write_script (line 59) | def write_script(script, script_fn, job_done_fn=None):
  function write_script_and_wrapper_top (line 66) | def write_script_and_wrapper_top(script, wrapper_fn, job_done):
  function select_rundir (line 99) | def select_rundir(tmpdir, wdir, script):
  function write_script_and_wrapper_for_tmp (line 105) | def write_script_and_wrapper_for_tmp(tmpdir, script, wrapper_fn, job_done):
  function filter_DBsplit_option (line 133) | def filter_DBsplit_option(opt):
  function update_dict_entry (line 142) | def update_dict_entry(d, key, func):
  function get_last_block (line 146) | def get_last_block(fn):
  function script_build_rdb (line 164) | def script_build_rdb(config, input_fofn_fn, run_jobs_bfn, length_cutoff_...
  function script_build_pdb (line 215) | def script_build_pdb(config, input_fofn_bfn, run_jobs_bfn):
  function script_run_DB2Falcon (line 240) | def script_run_DB2Falcon(config, preads4falcon_fn, preads_db):
  function scripts_daligner (line 254) | def scripts_daligner(run_jobs_fn, db_prefix, rdb_build_done, nblock, pre...
  function scripts_merge (line 288) | def scripts_merge(config, db_prefix, run_jobs_fn):
  function script_run_consensus (line 335) | def script_run_consensus(config, db_fn, las_fn, out_file_bfn):
  function script_run_falcon_asm (line 374) | def script_run_falcon_asm(config, las_fofn_fn, preads4falcon_fasta_fn, d...
  function script_run_report_pre_assembly (line 422) | def script_run_report_pre_assembly(i_raw_reads_db_fn, i_preads_fofn_fn, ...

FILE: falcon_kit/falcon_kit.py
  class KmerLookup (line 19) | class KmerLookup(Structure):
  class KmerMatch (line 25) | class KmerMatch(Structure):
  class AlnRange (line 31) | class AlnRange(Structure):
  class ConsensusData (line 39) | class ConsensusData(Structure):
  class Alignment (line 86) | class Alignment(Structure):
  function get_alignment (line 125) | def get_alignment(seq1, seq0):

FILE: falcon_kit/fc_asm_graph.py
  function reverse_end (line 11) | def reverse_end(node_id):
  class AsmGraph (line 17) | class AsmGraph(object):
    method __init__ (line 19) | def __init__(self, sg_file, utg_file, ctg_file):
    method load_sg_data (line 34) | def load_sg_data(self, sg_file):
    method load_sg_seq (line 47) | def load_sg_seq(self, fasta_fn):
    method get_seq_from_path (line 81) | def get_seq_from_path(self, path):
    method load_utg_data (line 91) | def load_utg_data(self, utg_file):
    method load_ctg_data (line 103) | def load_ctg_data(self, ctg_file):
    method get_sg_for_utg (line 128) | def get_sg_for_utg(self, utg_id):
    method get_sg_for_ctg (line 142) | def get_sg_for_ctg(self, ctg_id):
    method build_node_map (line 163) | def build_node_map(self):

FILE: falcon_kit/functional.py
  function _verify_pairs (line 17) | def _verify_pairs(pairs1, pairs2):
  function skip_LAcheck (line 28) | def skip_LAcheck(bash):
  function get_daligner_job_descriptions_sans_LAcheck (line 40) | def get_daligner_job_descriptions_sans_LAcheck(run_jobs_stream, db_prefi...
  function get_daligner_job_descriptions (line 56) | def get_daligner_job_descriptions(run_jobs_stream, db_prefix, single=Fal...
  function first_block_las (line 99) | def first_block_las(line):
  function get_las_filenames (line 112) | def get_las_filenames(mjob_data, db_prefix):
  function get_mjob_data (line 152) | def get_mjob_data(run_jobs_stream):
  function yield_args_from_line (line 191) | def yield_args_from_line(bash_line):
  function xform_script_for_preads (line 204) | def xform_script_for_preads(script):
  function xform_script_for_raw_reads (line 210) | def xform_script_for_raw_reads(script):
  function get_script_xformer (line 214) | def get_script_xformer(pread_aln):
  class GenomeCoverageError (line 221) | class GenomeCoverageError(Exception):
  function calc_cutoff_from_reverse_sorted_readlength_counts (line 225) | def calc_cutoff_from_reverse_sorted_readlength_counts(rl_counts, target):
  function num2int (line 247) | def num2int(num):
  function get_reverse_sorted_readlength_counts_from_DBstats (line 255) | def get_reverse_sorted_readlength_counts_from_DBstats(DBstats_output):
  function calc_cutoff (line 277) | def calc_cutoff(target, DBstats_output):
  function parse_2columns_of_ints (line 286) | def parse_2columns_of_ints(data):
  function weighted_average (line 301) | def weighted_average(cols):
  function parsed_readlengths_from_dbdump_output (line 311) | def parsed_readlengths_from_dbdump_output(output):
  function mapped_readlengths_from_dbdump_output (line 325) | def mapped_readlengths_from_dbdump_output(output):
  function average_difference (line 352) | def average_difference(dictA, dictB):
  function calc_metric_fragmentation (line 365) | def calc_metric_fragmentation(perl_counts_output):
  function calc_metric_truncation (line 372) | def calc_metric_truncation(dbdump_output, length_pairs_output):
  function choose_cat_fasta (line 381) | def choose_cat_fasta(fofn):
  function dash_flags (line 404) | def dash_flags(val):
  function cfg_tobool (line 419) | def cfg_tobool(v):
  class LowerDict (line 456) | class LowerDict(dict):  # dicts take a mapping or iterable as their opti...
    method __init__ (line 458) | def __init__(self):
    method __getitem__ (line 461) | def __getitem__(self, k):
    method __setitem__ (line 463) | def __setitem__(self, k, v):
    method __delitem__ (line 465) | def __delitem__(self, k):
    method get (line 467) | def get(self, k, default=None):
    method setdefault (line 469) | def setdefault(self, k, default=None):
    method pop (line 471) | def pop(self, k, v=_RaiseKeyError):
    method __contains__ (line 477) | def __contains__(self, k):
    method fromkeys (line 482) | def fromkeys(cls, keys, v=None):
    method __repr__ (line 484) | def __repr__(self):
  function toLowerDict (line 490) | def toLowerDict(cfg):

FILE: falcon_kit/gfa_graph.py
  class GFAGraph (line 50) | class GFAGraph:
    method __init__ (line 51) | def __init__(self):
    method add_node (line 63) | def add_node(self, node_name, node_len, node_seq='*', tags={}, labels=...
    method add_edge (line 83) | def add_edge(self, edge_name, source, source_orient, sink, sink_orient...
    method add_path (line 129) | def add_path(self, path_name, path_nodes, path_cigars, tags={}, labels...
    method write_gfa_v1 (line 158) | def write_gfa_v1(self, fp_out):
    method write_gfa_v2 (line 189) | def write_gfa_v2(self, fp_out):
  function serialize_gfa (line 225) | def serialize_gfa(gfa_graph):
  function deserialize_gfa (line 232) | def deserialize_gfa(fp_in):

FILE: falcon_kit/io.py
  function log (line 21) | def log(*msgs):
  function validate_config (line 25) | def validate_config(config):
  function update_env_from_config (line 48) | def update_env_from_config(config, fn):
  function eng (line 57) | def eng(number):
  function read_as_msgpack (line 61) | def read_as_msgpack(stream):
  function read_as_json (line 68) | def read_as_json(stream):
  function write_as_msgpack (line 75) | def write_as_msgpack(stream, val):
  function write_as_json (line 82) | def write_as_json(stream, val):
  function deserialize (line 89) | def deserialize(fn):
  function serialize (line 103) | def serialize(fn, val):
  function yield_bam_fn (line 119) | def yield_bam_fn(input_bam_fofn_fn):
  function yield_abspath_from_fofn (line 132) | def yield_abspath_from_fofn(fofn_fn):
  function rmdirs (line 148) | def rmdirs(*dirnames):
  function rmdir (line 153) | def rmdir(d):
  function rm_force (line 156) | def rm_force(*fns):

FILE: falcon_kit/mains/LAmerge.py
  function log (line 18) | def log(msg):
  function system (line 22) | def system(call, checked=False):
  function main (line 33) | def main(argv=sys.argv):

FILE: falcon_kit/mains/LAsort.py
  function log (line 15) | def log(msg):
  function system (line 19) | def system(call, checked=False):
  function main (line 30) | def main(argv=sys.argv):

FILE: falcon_kit/mains/actg_coordinate.py
  function main (line 8) | def main(argv=sys.argv):

FILE: falcon_kit/mains/build_pdb.py
  function run (line 12) | def run(config_fn, input_fofn_fn, job_done_fn, run_jobs_fn):
  class HelpF (line 24) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 28) | def parse_args(argv):
  function main (line 56) | def main(argv=sys.argv):

FILE: falcon_kit/mains/build_rdb.py
  function run (line 13) | def run(config_fn, length_cutoff_fn, input_fofn_fn, job_done_fn, run_job...
  class HelpF (line 31) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 35) | def parse_args(argv):
  function main (line 67) | def main(argv=sys.argv):

FILE: falcon_kit/mains/calc_cutoff.py
  function main (line 11) | def main(argv=sys.argv):

FILE: falcon_kit/mains/collect_contig_gfa.py
  function run (line 10) | def run(fp_out, p_ctg_tiling_path, a_ctg_tiling_path,
  function parse_args (line 64) | def parse_args(argv):
  function main (line 86) | def main(argv=sys.argv):

FILE: falcon_kit/mains/collect_pread_gfa.py
  function load_seqs (line 11) | def load_seqs(fasta_fn, store_only_seq_len):
  function load_pread_overlaps (line 26) | def load_pread_overlaps(fp_in):
  function load_sg_edges (line 42) | def load_sg_edges(fp_in):
  function add_node (line 57) | def add_node(gfa_graph, v, preads_dict):
  function add_edge (line 62) | def add_edge(gfa_graph, v, w, edge_split_line, preads_overlap_dict, sg_e...
  function add_tiling_paths_to_gfa (line 93) | def add_tiling_paths_to_gfa(gfa_graph, tiling_paths, preads_dict, preads...
  function add_string_graph_to_gfa (line 128) | def add_string_graph_to_gfa(gfa_graph, sg_edges_list, utg_data, ctg_path...
  function run (line 141) | def run(fp_out, p_ctg_tiling_path, a_ctg_tiling_path,
  function parse_args (line 201) | def parse_args(argv):
  function main (line 237) | def main(argv=sys.argv):

FILE: falcon_kit/mains/consensus.py
  function get_longest_reads (line 26) | def get_longest_reads(seqs, max_n_read, max_cov_aln, sort=True):
  function get_alignment (line 48) | def get_alignment(seq1, seq0, edge_tolerance=1000):
  function get_consensus_without_trim (line 102) | def get_consensus_without_trim(c_input):
  function get_consensus_with_trim (line 123) | def get_consensus_with_trim(c_input):
  function get_seq_data (line 161) | def get_seq_data(config, min_n_read, min_len_aln):
  function format_seq (line 212) | def format_seq(seq, col):
  function parse_args (line 216) | def parse_args(argv):
  function run (line 253) | def run(args):
  function main (line 301) | def main(argv=sys.argv):

FILE: falcon_kit/mains/consensus_gather_fasta_fofn.py
  function run (line 17) | def run(gathered_fn, preads_fofn_fn):
  class HelpF (line 32) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 36) | def parse_args(argv):
  function main (line 55) | def main(argv=sys.argv):

FILE: falcon_kit/mains/consensus_scatter.py
  function corrected_relpath (line 15) | def corrected_relpath(p, was_rel_to):
  function read_gathered_las (line 21) | def read_gathered_las(path):
  function run (line 37) | def run(las_fopfn_fn, db_fn, length_cutoff_fn, config_fn, wildcards, sca...
  class HelpF (line 81) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 85) | def parse_args(argv):
  function main (line 121) | def main(argv=sys.argv):

FILE: falcon_kit/mains/consensus_split.py
  function corrected_relpath (line 16) | def corrected_relpath(p, was_rel_to):
  function read_gathered_las (line 22) | def read_gathered_las(path):
  function run (line 37) | def run(p_id2las_fn, db_fn, length_cutoff_fn, config_fn, wildcards,
  class HelpF (line 90) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 94) | def parse_args(argv):
  function main (line 127) | def main(argv=sys.argv):

FILE: falcon_kit/mains/consensus_task.py
  function get_option_with_proper_nproc (line 14) | def get_option_with_proper_nproc(regexp, opt, opt_name, nproc, cpu_count...
  function get_falcon_sense_option (line 44) | def get_falcon_sense_option(opt, nproc):
  function get_pa_dazcon_option (line 56) | def get_pa_dazcon_option(opt, nproc):
  function script_run_consensus (line 70) | def script_run_consensus(config, db_fn, las_fn, out_file_fn, nproc):
  function run (line 107) | def run(config_fn, length_cutoff_fn, las_fn, db_fn, nproc,
  class HelpF (line 123) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 127) | def parse_args(argv):
  function main (line 162) | def main(argv=sys.argv):

FILE: falcon_kit/mains/contig_annotate.py
  function main (line 8) | def main(argv=sys.argv):

FILE: falcon_kit/mains/copy_fofn.py
  function run (line 12) | def run(abs, in_fn, out_fn):
  class HelpF (line 24) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 28) | def parse_args(argv):
  function main (line 52) | def main(argv=sys.argv):

FILE: falcon_kit/mains/copy_mapped.py
  function deserialize (line 16) | def deserialize(fn):
  function assert_exists (line 20) | def assert_exists(fn):
  function mkdir (line 24) | def mkdir(dirname):
  function copy (line 35) | def copy(name, rel_src):
  function run (line 48) | def run(special_split_fn, fn_patterns):
  function parse_args (line 82) | def parse_args(argv):
  function main (line 95) | def main(argv=sys.argv):

FILE: falcon_kit/mains/ctg_link_analysis.py
  function main (line 8) | def main(argv=sys.argv):

FILE: falcon_kit/mains/daligner.py
  function run (line 12) | def run(daligner_settings_fn, daligner_script_fn, job_done_fn):
  class HelpF (line 24) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 28) | def parse_args(argv):
  function main (line 52) | def main(argv=sys.argv):

FILE: falcon_kit/mains/daligner_gather_las_list.py
  function run (line 18) | def run(gathered_fn, las_paths_fn):
  class HelpF (line 45) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 49) | def parse_args(argv):
  function main (line 69) | def main(argv=sys.argv):

FILE: falcon_kit/mains/daligner_scatter.py
  function run (line 14) | def run(db_prefix, pread_aln, skip_checks, run_jobs_fn, db_fn, stage, wi...
  class HelpF (line 50) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 54) | def parse_args(argv):
  function main (line 98) | def main(argv=sys.argv):

FILE: falcon_kit/mains/daligner_split.py
  function run (line 15) | def run(bash_template_fn, db_prefix, pread_aln, skip_checks, run_jobs_fn...
  class HelpF (line 60) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 64) | def parse_args(argv):
  function main (line 104) | def main(argv=sys.argv):

FILE: falcon_kit/mains/dazzler.py
  function filter_DBsplit_option (line 69) | def filter_DBsplit_option(opt):
  function script_build_db (line 76) | def script_build_db(config, input_fofn_fn, db):
  function script_length_cutoff (line 99) | def script_length_cutoff(config, db, length_cutoff_fn='length_cutoff'):
  function script_DBsplit (line 112) | def script_DBsplit(config, db):
  function build_db (line 122) | def build_db(config, input_fofn_fn, db_fn, length_cutoff_fn):
  function script_HPC_daligner (line 143) | def script_HPC_daligner(config, db, length_cutoff_fn, tracks, prefix='da...
  function script_HPC_TANmask (line 157) | def script_HPC_TANmask(db, prefix):
  function symlink (line 171) | def symlink(actual, symbolic=None, force=True):
  function symlink_db (line 201) | def symlink_db(db_fn):
  function tan_split (line 220) | def tan_split(config_fn, db_fn, uows_fn, bash_template_fn):
  function tan_apply (line 294) | def tan_apply(db_fn, script_fn, job_done_fn):
  function tan_combine (line 303) | def tan_combine(db_fn, gathered_fn, new_db_fn):
  function split_db (line 329) | def split_db(config_fn, daligner_uows_fn, db_fn):
  function get_tracks (line 331) | def get_tracks(db_fn):
  function daligner_split (line 339) | def daligner_split(config, config_fn, db_fn, nproc, wildcards, length_cu...
  function daligner_apply (line 422) | def daligner_apply(db_fn, script_fn, job_done_fn):
  class MissingLas (line 427) | class MissingLas(Exception):
  function is_perfect_square (line 430) | def is_perfect_square(n):
  function daligner_combine (line 435) | def daligner_combine(db_fn, gathered_fn, las_paths_fn):
  function merge_split (line 484) | def merge_split(config_fn, dbname, las_paths_fn, split_fn, bash_template...
  function ichunked (line 533) | def ichunked(seq, chunksize):
  function merge_apply (line 542) | def merge_apply(las_paths_fn, las_fn):
  function merge_combine (line 576) | def merge_combine(gathered_fn, las_paths_fn, block2las_fn):
  function setup_logging (line 650) | def setup_logging(log_level):
  function cmd_build (line 658) | def cmd_build(args):
  function cmd_tan_split (line 661) | def cmd_tan_split(args):
  function cmd_tan_apply (line 663) | def cmd_tan_apply(args):
  function cmd_tan_combine (line 665) | def cmd_tan_combine(args):
  function cmd_daligner_split (line 667) | def cmd_daligner_split(args):
  function cmd_daligner_apply (line 670) | def cmd_daligner_apply(args):
  function cmd_daligner_combine (line 672) | def cmd_daligner_combine(args):
  function cmd_merge_split (line 674) | def cmd_merge_split(args):
  function cmd_merge_apply (line 676) | def cmd_merge_apply(args):
  function cmd_merge_combine (line 678) | def cmd_merge_combine(args):
  function get_ours (line 698) | def get_ours(config_fn, db_fn):
  function add_build_arguments (line 720) | def add_build_arguments(parser):
  function add_tan_split_arguments (line 729) | def add_tan_split_arguments(parser):
  function add_tan_apply_arguments (line 738) | def add_tan_apply_arguments(parser):
  function add_tan_combine_arguments (line 747) | def add_tan_combine_arguments(parser):
  function add_daligner_split_arguments (line 756) | def add_daligner_split_arguments(parser):
  function add_daligner_apply_arguments (line 773) | def add_daligner_apply_arguments(parser):
  function add_daligner_combine_arguments (line 782) | def add_daligner_combine_arguments(parser):
  function add_merge_split_arguments (line 790) | def add_merge_split_arguments(parser):
  function add_merge_apply_arguments (line 807) | def add_merge_apply_arguments(parser):
  function add_merge_combine_arguments (line 815) | def add_merge_combine_arguments(parser):
  function add_split_arguments (line 827) | def add_split_arguments(parser):
  class HelpF (line 845) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 848) | def parse_args(argv):
  function main (line 970) | def main(argv=sys.argv):

FILE: falcon_kit/mains/dedup_a_tigs.py
  function parse_args (line 9) | def parse_args(argv):
  function main (line 22) | def main(argv=sys.argv):

FILE: falcon_kit/mains/fasta2fasta.py
  function complement (line 39) | def complement(x): return (COMPLEMENT[base] for base in x)
  function WriteSplit (line 45) | def WriteSplit(write, seq, split=8000):
  function parse_header (line 54) | def parse_header(header, zmw_counter=None):
  function process_fasta (line 83) | def process_fasta(ifs, movie2write):
  function process_fastq (line 116) | def process_fastq(ifs, movie2write):
  function process_try_both (line 136) | def process_try_both(ifs, movie2write):
  function process (line 144) | def process(ifn, movie2write):
  class WriterMap (line 168) | class WriterMap(object):
    method basenames (line 169) | def basenames(self):
    method close (line 172) | def close(self):
    method __getitem__ (line 176) | def __getitem__(self, movie):
    method __init__ (line 191) | def __init__(self, Basename, Open):
  function get_writer (line 198) | def get_writer(Gzip=False):
  function fixall (line 214) | def fixall(ifns, Gzip=False):
  function main (line 227) | def main():

FILE: falcon_kit/mains/fetch_reads.py
  function fetch_ref_and_reads (line 15) | def fetch_ref_and_reads(base_dir, fofn, ctg_id, out_dir, min_ctg_lenth):
  function parse_args (line 129) | def parse_args(argv):
  function main (line 152) | def main(argv=sys.argv):

FILE: falcon_kit/mains/gen_gfa_v1.py
  function run (line 9) | def run(fp_out, collected_gfa):
  function parse_args (line 15) | def parse_args(argv):
  function main (line 23) | def main(argv=sys.argv):

FILE: falcon_kit/mains/gen_gfa_v2.py
  function run (line 9) | def run(fp_out, collected_gfa):
  function parse_args (line 15) | def parse_args(argv):
  function main (line 23) | def main(argv=sys.argv):

FILE: falcon_kit/mains/generate_read_to_ctg_map.py
  function run (line 12) | def run(rawread_id_fn, pread_id_fn, sg_edges_list_fn, utg_data_fn, ctg_p...
  class HelpF (line 44) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 48) | def parse_args(argv):
  function main (line 90) | def main(argv=sys.argv):

FILE: falcon_kit/mains/generic_gather.py
  function run (line 12) | def run(gathered_fn, scattered_fn):
  class HelpF (line 37) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 41) | def parse_args(argv):
  function main (line 61) | def main(argv=sys.argv):

FILE: falcon_kit/mains/generic_run_units_of_work.py
  function validate (line 16) | def validate(bash_template, inputs, outputs, parameterss):
  function update_values_rel_to (line 30) | def update_values_rel_to(things, dn):
  function run (line 39) | def run(bash_template_fn, units_of_work_fn, nproc,
  class HelpF (line 80) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 84) | def parse_args(argv):
  function main (line 108) | def main(argv=sys.argv):

FILE: falcon_kit/mains/generic_scatter_one_uow.py
  function validate (line 16) | def validate(bash_template, inputs, outputs, parameterss):
  function run (line 31) | def run(all_uow_list_fn, split_idx, one_uow_list_fn):
  class HelpF (line 51) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 55) | def parse_args(argv):
  function main (line 76) | def main(argv=sys.argv):

FILE: falcon_kit/mains/generic_unsplit.py
  function run (line 12) | def run(result_fn_list_fn, gathered_fn):
  class HelpF (line 38) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 42) | def parse_args(argv):
  function main (line 61) | def main(argv=sys.argv):

FILE: falcon_kit/mains/get_read_ctg_map.py
  function make_dirs (line 19) | def make_dirs(d):
  function get_read_ctg_map (line 25) | def get_read_ctg_map(rawread_dir, pread_dir, asm_dir):
  function parse_args (line 84) | def parse_args(argv):
  function main (line 94) | def main(argv=sys.argv):

FILE: falcon_kit/mains/graph_to_contig.py
  class TooLongError (line 40) | class TooLongError(Exception): pass
  function log (line 43) | def log(msg):
  function rc (line 48) | def rc(seq):
  function get_aln_data (line 52) | def get_aln_data(t_seq, q_seq):
  function reverse_end (line 107) | def reverse_end(node_id):
  function yield_first_seq (line 113) | def yield_first_seq(one_path_edges, seqs):
  function run (line 127) | def run(improper_p_ctg, proper_a_ctg):
  function main (line 397) | def main(argv=sys.argv):

FILE: falcon_kit/mains/graph_to_utgs.py
  function rc (line 15) | def rc(seq):
  function get_aln_data (line 19) | def get_aln_data(t_seq, q_seq):
  function main (line 59) | def main(argv=sys.argv):

FILE: falcon_kit/mains/hgap4_adapt.py
  function mkcd (line 167) | def mkcd(newdir):
  function symlink (line 173) | def symlink(jo):
  function get_parser (line 425) | def get_parser():
  function main (line 464) | def main(argv=sys.argv):

FILE: falcon_kit/mains/las_merge.py
  function run (line 12) | def run(p_id_num, las_paths_fn, merge_script_fn, las_merged_fn_fn,
  class HelpF (line 44) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 48) | def parse_args(argv):
  function main (line 81) | def main(argv=sys.argv):

FILE: falcon_kit/mains/las_merge_gather.py
  function run (line 17) | def run(gathered_fn, las_fn, p_id2las_fn):
  class HelpF (line 33) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 37) | def parse_args(argv):
  function main (line 58) | def main(argv=sys.argv):

FILE: falcon_kit/mains/las_merge_scatter.py
  function read_gathered_las (line 13) | def read_gathered_las(path):
  function run (line 26) | def run(run_jobs_fn, gathered_las_fn, db_prefix, stage, wildcards, scatt...
  class HelpF (line 75) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 79) | def parse_args(argv):
  function main (line 116) | def main(argv=sys.argv):

FILE: falcon_kit/mains/las_merge_split.py
  function get_block (line 19) | def get_block(las_fn):
  function read_gathered_las (line 33) | def read_gathered_las(las_fns):
  function run (line 44) | def run(run_jobs_fn, gathered_las_fn, db_prefix, wildcards,
  class HelpF (line 109) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 113) | def parse_args(argv):
  function main (line 143) | def main(argv=sys.argv):

FILE: falcon_kit/mains/ovlp_filter.py
  function run_filter_stage1 (line 14) | def run_filter_stage1(db_fn, fn, max_diff, max_ovlp, min_ovlp, min_len):
  function filter_stage1 (line 21) | def filter_stage1(readlines, max_diff, max_ovlp, min_ovlp, min_len):
  function run_filter_stage2 (line 71) | def run_filter_stage2(db_fn, fn, max_diff, max_ovlp, min_ovlp, min_len, ...
  function filter_stage2 (line 78) | def filter_stage2(readlines, max_diff, max_ovlp, min_ovlp, min_len, igno...
  function run_filter_stage3 (line 105) | def run_filter_stage3(db_fn, fn, max_diff, max_ovlp, min_ovlp, min_len, ...
  function filter_stage3 (line 112) | def filter_stage3(readlines, max_diff, max_ovlp, min_ovlp, min_len, igno...
  function run_ovlp_filter (line 194) | def run_ovlp_filter(outs, exe_pool, file_list, max_diff, max_cov, min_co...
  function try_run_ovlp_filter (line 235) | def try_run_ovlp_filter(out_fn, n_core, fofn, max_diff, max_cov, min_cov...
  function ovlp_filter (line 255) | def ovlp_filter(out_fn, n_core, las_fofn, max_diff, max_cov, min_cov, mi...
  function parse_args (line 268) | def parse_args(argv):
  function main (line 319) | def main(argv=sys.argv):

FILE: falcon_kit/mains/ovlp_stats.py
  function filter_stats (line 16) | def filter_stats(readlines, min_len):
  function run_filter_stats (line 67) | def run_filter_stats(db_fn, fn, min_len):
  function run_ovlp_stats (line 78) | def run_ovlp_stats(exe_pool, db_fn, file_list, min_len):
  function try_run_ovlp_stats (line 88) | def try_run_ovlp_stats(n_core, db_fn, fofn, min_len):
  function ovlp_stats (line 103) | def ovlp_stats(db_fn, fofn, min_len, n_core, stream, debug, silent):
  function parse_args (line 115) | def parse_args(argv):
  function main (line 136) | def main(argv=sys.argv):

FILE: falcon_kit/mains/ovlp_to_graph.py
  class SGNode (line 17) | class SGNode(object):
    method __init__ (line 22) | def __init__(self, node_name):
    method add_out_edge (line 27) | def add_out_edge(self, out_edge):
    method add_in_edge (line 30) | def add_in_edge(self, in_edge):
  class SGEdge (line 34) | class SGEdge(object):
    method __init__ (line 39) | def __init__(self, in_node, out_node):
    method set_attribute (line 44) | def set_attribute(self, attr, value):
  function reverse_end (line 48) | def reverse_end(node_name):
  class StringGraph (line 59) | class StringGraph(object):
    method __init__ (line 64) | def __init__(self):
    method add_node (line 73) | def add_node(self, node_name):
    method add_edge (line 80) | def add_edge(self, in_node_name, out_node_name, **attributes):
    method init_reduce_dict (line 99) | def init_reduce_dict(self):
    method bfs_nodes (line 103) | def bfs_nodes(self, n, exclude=None, depth=5):
    method mark_chimer_edges (line 123) | def mark_chimer_edges(self):
    method mark_spur_edge (line 193) | def mark_spur_edge(self):
    method mark_tr_edges (line 219) | def mark_tr_edges(self):
    method mark_best_overlap (line 279) | def mark_best_overlap(self):
    method resolve_repeat_edges (line 323) | def resolve_repeat_edges(self):
    method get_out_edges_for_node (line 411) | def get_out_edges_for_node(self, name, mask=True):
    method get_in_edges_for_node (line 420) | def get_in_edges_for_node(self, name, mask=True):
    method get_best_out_edge_for_node (line 429) | def get_best_out_edge_for_node(self, name, mask=True):
    method get_best_in_edge_for_node (line 440) | def get_best_in_edge_for_node(self, name, mask=True):
  function reverse_edge (line 451) | def reverse_edge(e):
  function reverse_path (line 456) | def reverse_path(p):
  function find_bundle (line 461) | def find_bundle(ug, u_edge_data, start_node, depth_cutoff, width_cutoff,...
  function generate_string_graph (line 654) | def generate_string_graph(args):
  function construct_compound_paths (line 907) | def construct_compound_paths(ug, u_edge_data):
  function identify_simple_paths (line 1029) | def identify_simple_paths(sg2, edge_data):
  function identify_spurs (line 1143) | def identify_spurs(ug, u_edge_data, spur_len):
  function remove_dup_simple_path (line 1219) | def remove_dup_simple_path(ug, u_edge_data):
  function construct_c_path_from_utgs (line 1246) | def construct_c_path_from_utgs(ug, u_edge_data, sg):
  function ovlp_to_graph (line 1359) | def ovlp_to_graph(args):
  function main (line 1554) | def main(argv=sys.argv):

FILE: falcon_kit/mains/pr_ctg_track.py
  function get_pid_to_ctg (line 16) | def get_pid_to_ctg(fn):
  function run_tr_stage1 (line 27) | def run_tr_stage1(db_fn, fn, min_len, bestn, pid_to_ctg):
  function tr_stage1 (line 34) | def tr_stage1(readlines, min_len, bestn, pid_to_ctg):
  function run_track_reads (line 60) | def run_track_reads(exe_pool, base_dir, file_list, min_len, bestn, db_fn):
  function try_run_track_reads (line 118) | def try_run_track_reads(n_core, base_dir, min_len, bestn):
  function track_reads (line 135) | def track_reads(n_core, base_dir, min_len, bestn, debug, silent, stream):
  function parse_args (line 147) | def parse_args(argv):
  function main (line 172) | def main(argv=sys.argv):

FILE: falcon_kit/mains/report_pre_assembly.py
  function do_report (line 12) | def do_report(db, preads_fofn, genome_length, length_cutoff, out):
  function main (line 25) | def main():

FILE: falcon_kit/mains/rr_ctg_track.py
  function get_rid_to_ctg (line 15) | def get_rid_to_ctg(fn):
  function run_tr_stage1 (line 26) | def run_tr_stage1(db_fn, fn, min_len, bestn, rid_to_ctg):
  function tr_stage1 (line 33) | def tr_stage1(readlines, min_len, bestn, rid_to_ctg):
  function run_track_reads (line 59) | def run_track_reads(exe_pool, base_dir, file_list, min_len, bestn, db_fn):
  function try_run_track_reads (line 119) | def try_run_track_reads(n_core, base_dir, min_len, bestn):
  function track_reads (line 141) | def track_reads(n_core, base_dir, min_len, bestn, debug, silent, stream):
  function parse_args (line 154) | def parse_args(argv):
  function main (line 179) | def main(argv=sys.argv):

FILE: falcon_kit/mains/run1.py
  function create_daligner_tasks (line 24) | def create_daligner_tasks(basedir, scatter_fn):
  function create_merge_tasks (line 53) | def create_merge_tasks(basedir, scatter_fn):
  function create_consensus_tasks (line 78) | def create_consensus_tasks(basedir, scatter_fn):
  function create_merge_gather_task (line 102) | def create_merge_gather_task(wd, inputs):
  function create_consensus_gather_task (line 115) | def create_consensus_gather_task(wd, inputs):
  function main1 (line 127) | def main1(prog_name, input_config_fn, logger_config_fn=None):
  function run (line 160) | def run(wf, config, rule_writer,
  function main (line 685) | def main(argv=sys.argv):

FILE: falcon_kit/mains/symlink_mapped.py
  function deserialize (line 12) | def deserialize(fn):
  function assert_exists (line 16) | def assert_exists(fn):
  function mkdir (line 20) | def mkdir(dirname):
  function symlink (line 25) | def symlink(name, target):
  function run (line 31) | def run(special_split_fn, fn_patterns):
  function parse_args (line 65) | def parse_args(argv):
  function main (line 78) | def main(argv=sys.argv):

FILE: falcon_kit/mains/task_report_pre_assembly.py
  function run (line 14) | def run(config_fn, length_cutoff_fn, raw_reads_db_fn, preads_fofn_fn, pr...
  class HelpF (line 33) | class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelp...
  function parse_args (line 37) | def parse_args(argv):
  function main (line 69) | def main(argv=sys.argv):

FILE: falcon_kit/mains/tasks.py
  function help (line 14) | def help():
  function main_make_fofn_abs (line 25) | def main_make_fofn_abs(i_fofn_fn, o_fofn_fn):
  function main (line 29) | def main(argv=sys.argv):

FILE: falcon_kit/multiproc.py
  class FakePool (line 10) | class FakePool(object):
    method map (line 14) | def map(self, func, iterable, chunksize=None):
    method imap (line 17) | def imap(self, func, iterable, chunksize=None):
    method terminate (line 20) | def terminate(self):
    method __init__ (line 23) | def __init__(self, initializer=None, initargs=[], *args, **kwds):
  function Pool (line 28) | def Pool(processes, *args, **kwds):

FILE: falcon_kit/pype.py
  function wrap_gen_task (line 31) | def wrap_gen_task(rule_writer, script, inputs, outputs, parameters=None,...
  function gen_parallel_tasks (line 62) | def gen_parallel_tasks(
  function dict_rel_paths (line 184) | def dict_rel_paths(dict_paths):

FILE: falcon_kit/pype_tasks.py
  function fn (line 167) | def fn(p): return p
  function system (line 170) | def system(call, check=False):
  function remove (line 183) | def remove(*fns):
  function mkdir (line 192) | def mkdir(d):
  function task_make_fofn_abs_raw (line 197) | def task_make_fofn_abs_raw(self):
  function task_make_fofn_abs_preads (line 204) | def task_make_fofn_abs_preads(self):
  function task_build_rdb (line 211) | def task_build_rdb(self):
  function task_build_pdb (line 233) | def task_build_pdb(self):
  function task_run_db2falcon (line 254) | def task_run_db2falcon(self):
  function task_run_falcon_asm (line 274) | def task_run_falcon_asm(self):
  function task_report_pre_assembly (line 297) | def task_report_pre_assembly(self):
  function task_run_daligner (line 326) | def task_run_daligner(self):
  function read_gathered_las (line 346) | def read_gathered_las(path):
  function task_run_las_merge (line 360) | def task_run_las_merge(self):
  function task_run_consensus (line 395) | def task_run_consensus(self):
  function task_daligner_scatter (line 421) | def task_daligner_scatter(self):
  function task_merge_scatter (line 459) | def task_merge_scatter(self):
  function task_consensus_scatter (line 498) | def task_consensus_scatter(self):
  function task_daligner_gather (line 549) | def task_daligner_gather(self):
  function task_cns_gather (line 563) | def task_cns_gather(self):
  function task_merge_gather (line 570) | def task_merge_gather(self):
  function task_dump_rawread_ids (line 587) | def task_dump_rawread_ids(self):
  function task_dump_pread_ids (line 597) | def task_dump_pread_ids(self):
  function task_generate_read_to_ctg_map (line 607) | def task_generate_read_to_ctg_map(self):

FILE: falcon_kit/run_support.py
  function _prepend_env_paths (line 26) | def _prepend_env_paths(content, names):
  function update_env_in_script (line 42) | def update_env_in_script(fn, names):
  function use_tmpdir_for_files (line 52) | def use_tmpdir_for_files(basenames, src_dir, link_dir):
  function make_job_data (line 78) | def make_job_data(url, script_fn):
  function update_HPCdaligner_option (line 95) | def update_HPCdaligner_option(option):
  function clean_falcon_options (line 107) | def clean_falcon_options(fc):
  function get_config (line 120) | def get_config(config):
  function dict2config (line 131) | def dict2config(jdict, section):
  function parse_config (line 140) | def parse_config(config_fn):
  function parse_cfg_file (line 146) | def parse_cfg_file(config_fn):
  function process_job_defaults (line 165) | def process_job_defaults(job_defaults):
  function update_job_defaults_section (line 177) | def update_job_defaults_section(config):
  function update_job_sections (line 256) | def update_job_sections(config):
  function parse_cfg_with_sections (line 278) | def parse_cfg_with_sections(stream):
  function check_config_sections (line 311) | def check_config_sections(cfg):
  function update_dash_flags (line 332) | def update_dash_flags(cfg, key):
  function update_defaults (line 347) | def update_defaults(cfg):
  function check_unexpected_keys (line 432) | def check_unexpected_keys(cfg):
  function _setup_logging (line 497) | def _setup_logging(logging_config_fn):
  function setup_logger (line 517) | def setup_logger(logging_config_fn):
  function get_nblock (line 537) | def get_nblock(db_file):
  function daligner_gather_las (line 554) | def daligner_gather_las(job_rundirs):
  function get_length_cutoff (line 570) | def get_length_cutoff(length_cutoff, fn):
  function build_rdb (line 577) | def build_rdb(input_fofn_fn, config, job_done, script_fn, run_jobs_fn):
  function build_pdb (line 583) | def build_pdb(input_fofn_fn, config, job_done, script_fn, run_jobs_fn):
  function run_db2falcon (line 589) | def run_db2falcon(config, preads4falcon_fn, preads_db, job_done, script_...
  function run_falcon_asm (line 594) | def run_falcon_asm(config, las_fofn_fn, preads4falcon_fasta_fn, db_file_...
  function run_report_pre_assembly (line 600) | def run_report_pre_assembly(i_raw_reads_db_fn, i_preads_fofn_fn, genome_...
  function run_daligner (line 606) | def run_daligner(daligner_script, db_prefix, config, job_done, script_fn):
  function run_las_merge (line 610) | def run_las_merge(script, job_done, config, script_fn):
  function run_consensus (line 614) | def run_consensus(db_fn, las_fn, out_file_fn, config, job_done, script_fn):

FILE: falcon_kit/snakemake.py
  function find_wildcards (line 16) | def find_wildcards(pattern):
  class SnakemakeRuleWriter (line 25) | class SnakemakeRuleWriter(object):
    method legalize (line 26) | def legalize(self, rule_name):
    method unique_rule_name (line 28) | def unique_rule_name(self, basename):
    method write_dynamic_rules (line 37) | def write_dynamic_rules(self, rule_name, input_json, inputs, shell_tem...
    method write_script_rule (line 126) | def write_script_rule(self, inputs, outputs, parameters, shell_templat...
    method __call__ (line 160) | def __call__(self, inputs, outputs, parameters, shell_template, rule_n...
    method __init__ (line 162) | def __init__(self, writer):
  class SnakemakeDynamic (line 232) | class SnakemakeDynamic(object):
    method __init__ (line 234) | def __init__(self, path):
  function snake_string_path (line 236) | def snake_string_path(p):
  function snake_shell (line 245) | def snake_shell(template, rundir):

FILE: falcon_kit/stats_preassembly.py
  function get_fasta_readlengths (line 35) | def get_fasta_readlengths(fasta_file):
  function get_db_readlengths (line 48) | def get_db_readlengths(fn):
  class FastaContainer (line 56) | class FastaContainer(object):
    method __init__ (line 58) | def __init__(self, nreads, total, file_name):
    method from_file (line 64) | def from_file(file_name):
    method __str__ (line 71) | def __str__(self):
  function _validate_file (line 75) | def _validate_file(file_name):
  function cutoff_reads (line 84) | def cutoff_reads(read_lens, min_read_len):
  function read_len_above (line 88) | def read_len_above(read_lens, threshold):
  function percentile (line 97) | def percentile(read_lens, p):
  function stats_from_sorted_readlengths (line 102) | def stats_from_sorted_readlengths(read_lens):
  function read_lens_from_fofn (line 114) | def read_lens_from_fofn(fofn_fn):
  function read_lens_from_db (line 122) | def read_lens_from_db(db_fn):
  function abs_filenames (line 128) | def abs_filenames(fofn_fn):
  function metric_fragmentation (line 139) | def metric_fragmentation(preads_fofn):
  function metric_truncation (line 149) | def metric_truncation(db, preads_fofn):
  function stats_dict (line 161) | def stats_dict(stats_raw_reads, stats_seed_reads, stats_corrected_reads,...
  function make_dict (line 209) | def make_dict(
  function calc_dict (line 237) | def calc_dict(

FILE: falcon_kit/tiling_path.py
  class TilingPathEdge (line 1) | class TilingPathEdge:
    method __init__ (line 3) | def __init__(self, split_line = None):
    method set_from (line 10) | def set_from(self, split_line):
    method get_split_line (line 23) | def get_split_line(self):
  class TilingPath (line 29) | class TilingPath:
    method __init__ (line 30) | def __init__(self, tiling_edge_list, contig_sequence_len = None):
    method dump_as_split_lines (line 64) | def dump_as_split_lines(self):
    method get_subpath (line 67) | def get_subpath(self, start_coord, end_coord):
  function calc_node_coords (line 111) | def calc_node_coords(tiling_edge_list, first_node_offset=0):
  function yield_split_line (line 138) | def yield_split_line(fp_in):
  function load_tiling_paths (line 145) | def load_tiling_paths(tp_file, contig_lens=None, whitelist_seqs=None):
  function load_tiling_paths_from_stream (line 150) | def load_tiling_paths_from_stream(fp_in, contig_lens=None, whitelist_seq...
  function load_tiling_paths_from_split_lines (line 154) | def load_tiling_paths_from_split_lines(split_lines, contig_lens=None, wh...
  function find_a_ctg_placement (line 182) | def find_a_ctg_placement(p_paths, a_paths):

FILE: falcon_kit/util/io.py
  function write_nothing (line 17) | def write_nothing(*args):
  function write_with_pid (line 24) | def write_with_pid(*args):
  function logstats (line 32) | def logstats():
  function reprarg (line 38) | def reprarg(arg):
  function run_func (line 46) | def run_func(args):
  function system (line 73) | def system(call, check=False):
  function syscall (line 86) | def syscall(cmd):
  function slurplines (line 100) | def slurplines(cmd):
  function streamlines (line 104) | def streamlines(cmd):
  class DataReaderContext (line 115) | class DataReaderContext(object):
    method readlines (line 116) | def readlines(self):
    method __enter__ (line 121) | def __enter__(self):
    method __exit__ (line 124) | def __exit__(self, *args):
    method __init__ (line 127) | def __init__(self, data):
  class ProcessReaderContext (line 131) | class ProcessReaderContext(object):
    method readlines (line 134) | def readlines(self):
    method __enter__ (line 140) | def __enter__(self):
    method __exit__ (line 144) | def __exit__(self, etype, evalue, etb):
    method __init__ (line 157) | def __init__(self, cmd):
  function splitlines_iter (line 161) | def splitlines_iter(text):
  class CapturedProcessReaderContext (line 177) | class CapturedProcessReaderContext(ProcessReaderContext):
    method readlines (line 178) | def readlines(self):
  class StreamedProcessReaderContext (line 197) | class StreamedProcessReaderContext(ProcessReaderContext):
    method readlines (line 198) | def readlines(self):
  function filesize (line 221) | def filesize(fn):
  function validated_fns (line 229) | def validated_fns(fofn):
  function yield_validated_fns (line 233) | def yield_validated_fns(fofn):

FILE: falcon_kit/util/system.py
  function only_these_symlinks (line 14) | def only_these_symlinks(dir2paths):
  function lfs_setstripe_maybe (line 45) | def lfs_setstripe_maybe(path='.', stripe=12):
  function find_files (line 57) | def find_files(root_path, pattern):
  function abs_fns (line 71) | def abs_fns(ifofns, idir=None):
  function make_fofn_abs (line 84) | def make_fofn_abs(i_fofn_fn, o_fofn_fn):
  function make_dirs (line 95) | def make_dirs(d):
  function touch (line 101) | def touch(*paths):

FILE: src/c/DW_banded.c
  function compare_d_path (line 65) | int compare_d_path(const void * a, const void * b)
  function d_path_sort (line 77) | void d_path_sort( d_path_data2 * base, unsigned long max_idx) {
  function d_path_data2 (line 81) | d_path_data2 * get_dpath_idx( seq_coor_t d, seq_coor_t k, unsigned long ...
  function print_d_path (line 93) | void print_d_path(  d_path_data2 * base, unsigned long max_idx) {
  function alignment (line 115) | alignment * align(char * query_seq, seq_coor_t q_len,
  function free_alignment (line 333) | void free_alignment(alignment * aln) {

FILE: src/c/common.h
  type seq_coor_t (line 57) | typedef int seq_coor_t;
  type alignment (line 59) | typedef struct {
  type d_path_data (line 72) | typedef struct {
  type d_path_data2 (line 80) | typedef struct {
  type path_point (line 90) | typedef struct {
  type kmer_lookup (line 95) | typedef struct {
  type base (line 101) | typedef unsigned char base;
  type base (line 102) | typedef base * seq_array;
  type seq_coor_t (line 103) | typedef seq_coor_t seq_addr;
  type seq_addr (line 104) | typedef seq_addr * seq_addr_array;
  type kmer_match (line 107) | typedef struct {
  type aln_range (line 114) | typedef struct {
  type consensus_data (line 123) | typedef struct {

FILE: src/c/ext_falcon.c
  function PyMODINIT_FUNC (line 5) | PyMODINIT_FUNC

FILE: src/c/falcon.c
  type align_tag_t (line 64) | typedef struct {
  type align_tags_t (line 74) | typedef struct {
  type align_tag_col_t (line 80) | typedef struct {
  type msa_base_group_t (line 94) | typedef struct {
  type msa_delta_group_t (line 98) | typedef struct {
  type msa_delta_group_t (line 104) | typedef msa_delta_group_t * msa_pos_t;
  function align_tags_t (line 106) | align_tags_t * get_align_tags( char * aln_q_seq,
  function free_align_tags (line 164) | void free_align_tags( align_tags_t * tags) {
  function allocate_aln_col (line 170) | void allocate_aln_col( align_tag_col_t * col) {
  function realloc_aln_col (line 177) | void realloc_aln_col( align_tag_col_t * col ) {
  function free_aln_col (line 184) | void free_aln_col( align_tag_col_t * col) {
  function allocate_delta_group (line 192) | void allocate_delta_group( msa_delta_group_t * g) {
  function realloc_delta_group (line 205) | void realloc_delta_group( msa_delta_group_t * g, uint16_t new_size ) {
  function free_delta_group (line 220) | void free_delta_group( msa_delta_group_t * g) {
  function update_col (line 232) | void update_col( align_tag_col_t * col, seq_coor_t p_t_pos, uint8_t p_de...
  function msa_pos_t (line 266) | msa_pos_t * get_msa_working_sapce(unsigned int max_t_len) {
  function clean_msa_working_space (line 278) | void clean_msa_working_space( msa_pos_t * msa_array, unsigned int max_t_...
  function consensus_data (line 308) | consensus_data * get_cns_from_align_tags( align_tags_t ** tag_seqs,
  function consensus_data (line 562) | consensus_data * generate_consensus( char ** input_seq,
  function consensus_data (line 668) | consensus_data * generate_utg_consensus( char ** input_seq,
  function free_consensus_data (line 776) | void free_consensus_data( consensus_data * consensus ){

FILE: src/c/kmer_lookup.c
  function compare_seq_coor (line 64) | int compare_seq_coor(const void * a, const void * b) {
  function kmer_lookup (line 71) | kmer_lookup * allocate_kmer_lookup ( seq_coor_t size ) {
  function init_kmer_lookup (line 80) | void init_kmer_lookup ( kmer_lookup * kl,  seq_coor_t size ) {
  function free_kmer_lookup (line 91) | void free_kmer_lookup( kmer_lookup *  ptr) {
  function seq_array (line 95) | seq_array allocate_seq(seq_coor_t size) {
  function init_seq_array (line 102) | void init_seq_array( seq_array sa, seq_coor_t size) {
  function free_seq_array (line 109) | void free_seq_array( seq_array sa) {
  function seq_addr_array (line 113) | seq_addr_array allocate_seq_addr(seq_coor_t size) {
  function free_seq_addr_array (line 117) | void free_seq_addr_array(seq_addr_array sda) {
  function seq_coor_t (line 121) | seq_coor_t get_kmer_bitvector(seq_array sa, unsigned int K) {
  function add_sequence (line 140) | void add_sequence ( seq_coor_t start,
  function mask_k_mer (line 195) | void mask_k_mer(seq_coor_t size, kmer_lookup * kl, seq_coor_t threshold) {
  function kmer_match (line 207) | kmer_match * find_kmer_pos_for_seq( char * seq, seq_coor_t seq_len, unsi...
  function free_kmer_match (line 288) | void free_kmer_match( kmer_match * ptr) {
  function aln_range (line 294) | aln_range* find_best_aln_range(kmer_match * km_ptr,
  function aln_range (line 429) | aln_range* find_best_aln_range2(kmer_match * km_ptr,
  function free_aln_range (line 587) | void free_aln_range( aln_range * arange) {

FILE: test/helpers.py
  function equal_list (line 11) | def equal_list(a, b):
  function equal_dict (line 15) | def equal_dict(a, b):
  function equal_multiline (line 22) | def equal_multiline(a, b):
  function get_test_data_dir (line 28) | def get_test_data_dir():
  function assert_filecmp (line 32) | def assert_filecmp(got, expected_path):

FILE: test/test_calc_cutoff.py
  function test_help (line 9) | def test_help():
  function test_calc_cutoff (line 18) | def test_calc_cutoff(capsys):
  function test_calc_cutoff_err (line 35) | def test_calc_cutoff_err():
  function test_calc_cutoff_errfile (line 44) | def test_calc_cutoff_errfile(monkeypatch, tmpdir):

FILE: test/test_collect_contig_gfa.py
  function test_help (line 13) | def test_help():
  function generate_seq (line 42) | def generate_seq(seq_len):
  function setup_test (line 45) | def setup_test(fp_p_ctg, fp_p_tp, fp_a_ctg, fp_a_tp):
  function test_main_1 (line 135) | def test_main_1(tmpdir, capsys):
  function test_main_2 (line 163) | def test_main_2(tmpdir, capsys):
  function test_main_3 (line 196) | def test_main_3(tmpdir, capsys):
  function test_main_4 (line 238) | def test_main_4(tmpdir, capsys):

FILE: test/test_collect_pread_gfa.py
  function test_help (line 6) | def test_help():
  function test_load_seqs (line 12) | def test_load_seqs():
  function test_load_pread_overlaps (line 16) | def test_load_pread_overlaps():
  function test_load_sg_edges (line 20) | def test_load_sg_edges():
  function test_add_node (line 24) | def test_add_node():
  function test_add_edge (line 28) | def test_add_edge():
  function test_add_tiling_paths_to_gfa (line 32) | def test_add_tiling_paths_to_gfa():
  function test_add_string_graph_to_gfa (line 36) | def test_add_string_graph_to_gfa():
  function test_main_1 (line 40) | def test_main_1():

FILE: test/test_consensus.py
  function test_help (line 5) | def test_help():

FILE: test/test_functional.py
  function eq_ (line 14) | def eq_(a, b):
  function test_get_daligner_job_descriptions (line 18) | def test_get_daligner_job_descriptions():
  function test_get_daligner_job_descriptions_with_bad_arg (line 30) | def test_get_daligner_job_descriptions_with_bad_arg():
  function test_get_daligner_job_descriptions_small (line 37) | def test_get_daligner_job_descriptions_small():
  function test_get_daligner_job_descriptions_se161 (line 50) | def test_get_daligner_job_descriptions_se161():
  function test_get_mjob_data (line 57) | def test_get_mjob_data():
  function test_skip_LAcheck (line 70) | def test_skip_LAcheck():
  function test_first_block_las (line 93) | def test_first_block_las():
  function test_xform_script_for_preads (line 109) | def test_xform_script_for_preads():
  function check (line 131) | def check(target, expected):
  function test_calc_cutoff_from_reverse_sorted_readlength_counts (line 145) | def test_calc_cutoff_from_reverse_sorted_readlength_counts(n_target, n_e...
  function test_calc_cutoff_from_reverse_sorted_readlength_counts_raises (line 149) | def test_calc_cutoff_from_reverse_sorted_readlength_counts_raises():
  function test_get_reverse_sorted_readlength_counts_from_DBstats (line 174) | def test_get_reverse_sorted_readlength_counts_from_DBstats():
  function test_num2int (line 180) | def test_num2int():
  function test_calc_cutoff (line 195) | def test_calc_cutoff():
  function test_calc_cutoff_bad_coverage (line 202) | def test_calc_cutoff_bad_coverage():
  function test_parsed_readlengths_from_dbdump_output (line 226) | def test_parsed_readlengths_from_dbdump_output():
  function test_mapped_readlengths_from_dbdump_output (line 232) | def test_mapped_readlengths_from_dbdump_output():
  function test_average_difference (line 237) | def test_average_difference():
  function test_calc_metric_truncation (line 254) | def test_calc_metric_truncation():
  function test_calc_metric_fragmentation (line 267) | def test_calc_metric_fragmentation():
  function test_args_from_line (line 272) | def test_args_from_line():
  function test_splitlines_iter (line 285) | def test_splitlines_iter():
  function test_Readers (line 290) | def test_Readers():
  function test_get_falcon_sense_option (line 303) | def test_get_falcon_sense_option():
  function test_get_pa_dazcon_option (line 307) | def test_get_pa_dazcon_option():
  function test_get_option_with_proper_nproc (line 311) | def test_get_option_with_proper_nproc():

FILE: test/test_gen_gfa_v1.py
  function test_help (line 6) | def test_help():
  function test_main_1 (line 12) | def test_main_1(tmpdir, capsys):

FILE: test/test_gen_gfa_v2.py
  function test_help (line 6) | def test_help():
  function test_main_1 (line 12) | def test_main_1(tmpdir, capsys):

FILE: test/test_gfa_graph.py
  function test_gfa_graph (line 15) | def test_gfa_graph():
  function test_add_node_1 (line 18) | def test_add_node_1():
  function test_add_node_2 (line 29) | def test_add_node_2():
  function test_add_edge_1 (line 47) | def test_add_edge_1():
  function test_add_edge_2 (line 68) | def test_add_edge_2():
  function test_add_path_1 (line 104) | def test_add_path_1():
  function test_add_path_2 (line 118) | def test_add_path_2():
  function test_write_gfa_v1 (line 154) | def test_write_gfa_v1():
  function test_write_gfa_v2 (line 173) | def test_write_gfa_v2():
  function test_serialize (line 192) | def test_serialize():
  function test_deserialize (line 204) | def test_deserialize():

FILE: test/test_ovlp_filter.py
  function assert_equal (line 5) | def assert_equal(expected, got):
  function test_help (line 9) | def test_help():
  function test_several (line 19) | def test_several():
  function test_one_not_ignored (line 41) | def test_one_not_ignored():
  function test_one_line_ignored (line 54) | def test_one_line_ignored():
  function test_empty (line 67) | def test_empty():

FILE: test/test_ovlp_stats.py
  function test_help (line 5) | def test_help():
  function test (line 12) | def test():

FILE: test/test_ovlp_to_graph.py
  function test_help (line 6) | def test_help():
  function test_reverse_end (line 13) | def test_reverse_end():

FILE: test/test_run_support.py
  function parse_config (line 6) | def parse_config(content):
  function test_check_config_sections (line 95) | def test_check_config_sections():
  function test_check_config_sections_foo (line 106) | def test_check_config_sections_foo():
  function test_update_job_sections0 (line 125) | def test_update_job_sections0():
  function test_update_job_sections1 (line 140) | def test_update_job_sections1():
  function test_update_job_sections2 (line 157) | def test_update_job_sections2():
  function test_update_job_sections3 (line 171) | def test_update_job_sections3():
  function test_clean_falcon_options (line 177) | def test_clean_falcon_options():

FILE: test/test_stats_preassembly.py
  function test_stats_from_sorted_readlengths (line 7) | def test_stats_from_sorted_readlengths():
  function test_stats_dict (line 13) | def test_stats_dict():

FILE: test/test_tiling_path.py
  function test_tiling_path_1 (line 62) | def test_tiling_path_1():
  function test_tiling_path_2 (line 103) | def test_tiling_path_2():
  function test_tiling_path_3 (line 143) | def test_tiling_path_3():
  function test_tiling_path_4_expect_crash (line 178) | def test_tiling_path_4_expect_crash():
  function test_tiling_path_5 (line 199) | def test_tiling_path_5(tmpdir):
  function test_calc_node_coords_1 (line 226) | def test_calc_node_coords_1():
  function test_calc_node_coords_2 (line 257) | def test_calc_node_coords_2():
  function test_calc_node_coords_3 (line 266) | def test_calc_node_coords_3():
  function test_calc_node_coords_1 (line 305) | def test_calc_node_coords_1():
  function test_find_a_ctg_placement_1 (line 317) | def test_find_a_ctg_placement_1():
  function test_find_a_ctg_placement_2 (line 335) | def test_find_a_ctg_placement_2():
  function test_find_a_ctg_placement_3 (line 347) | def test_find_a_ctg_placement_3():
  function test_get_subpath_1 (line 359) | def test_get_subpath_1():
  function test_get_subpath_2 (line 379) | def test_get_subpath_2():
  function test_get_subpath_3 (line 399) | def test_get_subpath_3():
  function test_get_subpath_4 (line 420) | def test_get_subpath_4():
  function test_get_subpath_5 (line 440) | def test_get_subpath_5():
  function test_get_subpath_6 (line 461) | def test_get_subpath_6():
  function test_get_subpath_7 (line 482) | def test_get_subpath_7():
  function test_get_subpath_8 (line 502) | def test_get_subpath_8():

FILE: test/test_util_io.py
  function test_io_se1331 (line 8) | def test_io_se1331():
  function test_str_type (line 24) | def test_str_type(Context):

FILE: test/test_util_system.py
  function touchtree (line 12) | def touchtree(*fns):
  function dirtree (line 21) | def dirtree(tmpdir_factory):
  function picture (line 29) | def picture(fns):
  function test_system_find_files (line 44) | def test_system_find_files(dirtree):
  function test_make_fofn_abs (line 84) | def test_make_fofn_abs(tmpdir):