Module commands

Command functions that implement each of the granges subcommands.

Structs

FeatureDensity

Calculate the density of features in a BED4 file, per window. There are two modes:

FilterChroms

Filter out ranges not in the specified “genome” file.

Merge

Merges all the genomic ranges if they overlap by distance.

Enums

ProcessingMode

An enum to indicate whether an streaming or in-memory algorithm should be used.

Functions

build_tsv_writer

Build a new TSV writer

build_tsv_writer_with_config

Build a new TSV writer with config, i.e. for manual headers, metadata etc.

granges_adjust

Adjusts genomic ranges in a BED file by a specified amount.

granges_filter

Filters genomic ranges based on overlaps with another set of ranges.

granges_flank

Generates flanking regions for genomic ranges in a BED file.

granges_map

Developer Notes

granges_random_bed

Generate a random BED-like file with genomic ranges.

granges_windows

Generate a BED3 file of genomic windows.