SYMBOL INDEX (133 symbols across 4 files)

FILE: samplot/__main__.py
  function main (line 11) | def main(args=None):

FILE: samplot/samplot.py
  function strip_chr (line 62) | def strip_chr(chrom):
  class plan_step (line 71) | class plan_step:
    method __init__ (line 74) | def __init__(self, start_pos, end_pos, event, info=None):
    method __str__ (line 80) | def __str__(self):
    method __repr__ (line 104) | def __repr__(self):
  class genome_interval (line 111) | class genome_interval:
    method __init__ (line 112) | def __init__(self, chrm, start, end):
    method __str__ (line 117) | def __str__(self):
    method __repr__ (line 120) | def __repr__(self):
    method __eq__ (line 123) | def __eq__(self, gi2):
    method intersect (line 128) | def intersect(self, gi):
  function get_range_hit (line 140) | def get_range_hit(ranges, chrm, point):
  function map_genome_point_to_range_points (line 155) | def map_genome_point_to_range_points(ranges, chrm, point):
  function points_in_window (line 171) | def points_in_window(points):
  function get_tabix_iter (line 190) | def get_tabix_iter(chrm, start, end, datafile):
  function add_coverage (line 231) | def add_coverage(read, coverage_matrix, offset, column):
  function plot_coverage (line 264) | def plot_coverage(
  class PairedEnd (line 383) | class PairedEnd:
    method __init__ (line 390) | def __init__(self, chrm, start, end, is_reverse, MI_tag, HP_tag):
    method __repr__ (line 410) | def __repr__(self):
  function add_pair_end (line 424) | def add_pair_end(bam_file, read, pairs, linked_reads, ignore_hp):
  function sample_normal (line 479) | def sample_normal(max_depth, pairs, z):
  function get_pairs_insert_sizes (line 538) | def get_pairs_insert_sizes(ranges, pairs):
  function get_pair_insert_size (line 559) | def get_pair_insert_size(ranges, pair):
  function get_pairs_plan (line 585) | def get_pairs_plan(ranges, pairs, linked_plan=False):
  function get_pair_plan (line 612) | def get_pair_plan(ranges, pair, linked_plan=False):
  function get_pair_event_type (line 662) | def get_pair_event_type(pe_read):
  function jitter (line 677) | def jitter(value, bounds: float = 0.1) -> float:
  function plot_pair_plan (line 686) | def plot_pair_plan(ranges, step, ax, marker_size, jitter_bounds):
  function plot_pairs (line 731) | def plot_pairs(
  class SplitRead (line 759) | class SplitRead:
    method __init__ (line 766) | def __init__(self, chrm, start, end, strand, query_pos, MI_tag=None, H...
    method __repr__ (line 787) | def __repr__(self):
  function calc_query_pos_from_cigar (line 802) | def calc_query_pos_from_cigar(cigar, strand):
  function add_split (line 842) | def add_split(read, splits, bam_file, linked_reads, ignore_hp):
  function get_split_plan (line 912) | def get_split_plan(ranges, split, linked_plan=False):
  function get_splits_plan (line 977) | def get_splits_plan(ranges, splits, linked_plan=False):
  function plot_split_plan (line 1005) | def plot_split_plan(ranges, step, ax, marker_size, jitter_bounds):
  function plot_splits (line 1046) | def plot_splits(
  class Alignment (line 1073) | class Alignment:
    method __init__ (line 1080) | def __init__(self, chrm, start, end, strand, query_position):
    method __str__ (line 1090) | def __str__(self):
    method __repr__ (line 1104) | def __repr__(self):
  class LongRead (line 1117) | class LongRead:
    method __init__ (line 1123) | def __init__(self, alignments):
    method __str__ (line 1131) | def __str__(self):
    method __repr__ (line 1134) | def __repr__(self):
  function get_alignments_from_cigar (line 1141) | def get_alignments_from_cigar(chrm, curr_pos, strand, cigartuples, rever...
  function get_cigartuples_from_string (line 1176) | def get_cigartuples_from_string(cigarstring):
  function merge_alignments (line 1193) | def merge_alignments(min_gap, alignments):
  function add_long_reads (line 1218) | def add_long_reads(bam_file, read, long_reads, min_event_size, ignore_hp):
  function add_align_step (line 1277) | def add_align_step(alignment, steps, ranges):
  function get_long_read_plan (line 1355) | def get_long_read_plan(read_name, long_reads, ranges):
  function plot_variant (line 1529) | def plot_variant(sv, sv_type, ax, ranges):
  function plot_confidence_interval (line 1576) | def plot_confidence_interval(chrm, breakpoint, ci, ax, ranges):
  function create_variant_plot (line 1606) | def create_variant_plot(grid, ax_i, sv, sv_type, ranges, start_ci, end_ci):
  function get_linked_plan (line 1638) | def get_linked_plan(ranges, pairs, splits, linked_reads, gem_name):
  function plot_linked_reads (line 1714) | def plot_linked_reads(
  function plot_long_reads (line 1775) | def plot_long_reads(long_reads, ax, ranges, curr_min_insert_size, curr_m...
  function pair (line 1862) | def pair(arg):
  function print_arguments (line 1883) | def print_arguments(options):
  function add_plot (line 1915) | def add_plot(parent_parser):
  function estimate_fragment_len (line 2350) | def estimate_fragment_len(bam, reference):
  function set_plot_dimensions (line 2377) | def set_plot_dimensions(
  function get_read_data (line 2496) | def get_read_data(
  function downsample_pairs (line 2671) | def downsample_pairs(max_depth, z_score, all_pairs):
  function set_haplotypes (line 2686) | def set_haplotypes(curr_coverage):
  function plot_samples (line 2707) | def plot_samples(
  function plot_legend (line 2928) | def plot_legend(fig, legend_fontsize, marker_size):
  function create_gridspec (line 2994) | def create_gridspec(bams, transcript_file, annotation_files, sv_type, re...
  function get_plot_annotation_plan (line 3033) | def get_plot_annotation_plan(ranges, annotation_file):
  function plot_annotations (line 3076) | def plot_annotations(
  function get_interval_range_plan_start_end (line 3144) | def get_interval_range_plan_start_end(ranges, interval):
  function get_transcript_plan (line 3203) | def get_transcript_plan(ranges, transcript_file):
  function plot_transcript (line 3302) | def plot_transcript(
  function plot (line 3424) | def plot(parser, options, extra_args=None):

FILE: samplot/samplot_vcf.py
  class Sample (line 44) | class Sample(object):
    method __init__ (line 56) | def __init__(self, line):
    method __repr__ (line 65) | def __repr__(self):
  function flatten (line 71) | def flatten(value, sep=","):
  function get_format_fields (line 97) | def get_format_fields(ids, variant):
  function get_format_title (line 119) | def get_format_title(samples, ids, variant):
  function make_plot_titles (line 133) | def make_plot_titles(samples, attr_values):
  function get_overlap (line 165) | def get_overlap(
  function parse_ped (line 239) | def parse_ped(path, vcf_samples=None):
  function get_names_to_bams (line 268) | def get_names_to_bams(bams, name_list=None):
  function tryfloat (line 297) | def tryfloat(v):
  function to_exprs (line 304) | def to_exprs(astr):
  function check_expr (line 332) | def check_expr(vdict, expr):
  function make_single (line 369) | def make_single(vdict):
  function get_dn_row (line 381) | def get_dn_row(ped_samples):
  function read_important_regions (line 388) | def read_important_regions(bedfilename):
  function var_in_important_regions (line 403) | def var_in_important_regions(important_regions, chrom, start, end, svtype):
  function cram_input (line 426) | def cram_input(bams):
  function above_call_rate (line 433) | def above_call_rate(gts, sample_count, min_call_rate, svtype, chrom, sta...
  function below_max_hets (line 452) | def below_max_hets(gts, max_hets, svtype, chrom, start, end):
  function no_variant_found (line 472) | def no_variant_found(gts, svtype, chrom, start, end):
  function get_plottable_samples (line 486) | def get_plottable_samples(
  function get_variant_samples (line 531) | def get_variant_samples(
  function get_denovos (line 551) | def get_denovos(
  function get_family_controls (line 589) | def get_family_controls(
  function get_nonfamily_controls (line 637) | def get_nonfamily_controls(
  function create_metadata (line 659) | def create_metadata(
  function format_template (line 692) | def format_template(
  function write_site (line 810) | def write_site(table_data, out_dir, output_type, annotations, denovo_row):
  function is_simply_skippable (line 830) | def is_simply_skippable(
  function generate_commands (line 911) | def generate_commands(
  function run_plot_command (line 1108) | def run_plot_command(command_string: str):
  function vcf (line 1127) | def vcf(parser, args, pass_through_args):
  function add_vcf (line 1224) | def add_vcf(parent_parser):

FILE: test/unit/samplot_test.py
  class Test_set_plot_dimensions (line 19) | class Test_set_plot_dimensions(unittest.TestCase):
    method test_set_plot_dimensions (line 21) | def test_set_plot_dimensions(self):
    method test_get_read_data (line 144) | def test_get_read_data(self):
  class Test_genome_interval (line 211) | class Test_genome_interval(unittest.TestCase):
    method test_init (line 213) | def test_init(self):
    method test_intersect (line 221) | def test_intersect(self):
    method test_get_range_hit (line 260) | def test_get_range_hit(self):
    method test_map_genome_point_to_range_points (line 278) | def test_map_genome_point_to_range_points(self):
  class Test_long_read_plan (line 419) | class Test_long_read_plan(unittest.TestCase):
    method test_add_align_step (line 421) | def test_add_align_step(self):
    method test_get_alignments_from_cigar (line 523) | def test_get_alignments_from_cigar(self):
    method test_get_long_read_plan (line 565) | def test_get_long_read_plan(self):
  class Test_annotation_plan (line 707) | class Test_annotation_plan(unittest.TestCase):
    method test_get_alignments_from_cigar (line 709) | def test_get_alignments_from_cigar(self):
  class Test_splits (line 784) | class Test_splits(unittest.TestCase):
    method test_get_split_plan (line 786) | def test_get_split_plan(self):
    method test_get_splits_plan (line 953) | def test_get_splits_plan(self):
  class Test_pairs (line 1002) | class Test_pairs(unittest.TestCase):
    method test_get_pair_insert_size (line 1004) | def test_get_pair_insert_size(self):
    method test_get_pair_plan (line 1093) | def test_get_pair_plan(self):
  class Test_linked (line 1122) | class Test_linked(unittest.TestCase):
    method test_get_linked_plan (line 1124) | def test_get_linked_plan(self):