Crate dnacomb 

Library supporting the DNAComb structured sequence read processing tool. The GitHub and Crates.io page give documentation for the CLI tool with these pages documenting the library,

Provides structs and functions for:

• Defining DNA molecule forms and libraries (libspec)
• Reading and filtering paired sequence reads (parsing, filters)
• Extracting the defined regions from reads (counting, containers)
• Comparing the observed region sequences to the library (libspec, containers)
• Supporting constructs for CLI usage (logging, errors)

The main module brings this together to define the main CLI program. The library can equally be used programatically to support other workflows although it is designed primarily to support the CLI tool.

Re-exports

pub use combinations::ObservedCombinations;

pub use counting::CountMode;

pub use counting::count_reads;

pub use lib_spec::Library;

pub use lib_spec::LibrarySpec;

Modules

combination

Observed combination of sequence regions from a sequencing experiment

combinations

Store collections of observed combinations

counting

Counting the occurance of different reads in sequence files

errors

Custom error types for DNAComb

filters

Filters to identify and count failing reads

lib_spec

Specification for DNA constructs and libraries

library_combination

Library matches from sequencing data

logging

A simple logging based progress counter using count and timing information

parsing

Parse Fasta and Fastq files with a consistent interface

region

Observed sequence regions from a sequencing experiment

seqs

Core data structures for DNA sequence objects

utils

Utility fucntions for use throughout the library