Changes for version 0.16 - 2018-04-16
- Update quality profile database in order to keep it simple
- Turn read-size option settable only when quality-profile="poisson". Otherwise, if quality-profile comes from database, it will override the default/user-provided value
Documentation
Creates single-end and paired-end fastq reads for transcriptome and genome simulation.
Modules
App builder that simulates single-end and paired-end reads.
Policy and base module to App::SimulateReads project.
Base class for command line interface.
App::SimulateReads::CLI subclass for command line application interface.
App::SimulateReads::CLI subclass for commands interface
simulate command class. Simulate a custom sequencing
expression command class. Manage expression-matrix database.
expression subcommand class. Add an expression-matrix to the database.
expression subcommand class. Remove an expression-matrix from database.
expression subcommand class. Restore database.
simulate command class. Simulate genome sequencing
quality command class. Manage quality profile database.
quality subcommand class. Add a quality profile to the database.
quality subcommand class. Remove a quality profile from database.
quality subcommand class. Restore database.
simulate command class. Simulate transcriptome sequencing
Singleton class to manage database
Class to handle expression-matrix database schemas.
Class to handle quality database schemas.
Base class to simulate fastq entries
App::SimulateReads::Fastq subclass for simulate paired-end fastq entries.
App::SimulateReads::Fastq subclass for simulate single-end fastq entries.
Interlaces the processe id for differents processes, actually for parent, child processes.
Class to simulate quality entries
Base class to simulate reads
App::SimulateReads::Read subclass for simulate paired-end reads.
App::SimulateReads::Read subclass for simulate single-end reads.
Wrapper on Simulator class for genome/transcriptome sequencing
Input and output custom wrappers.
Getopt::Long wrapper.
Extends class with runtime printf like function
Class responsible to make the simulation
Moose type constraints for App::SimulateReads project
Weighted raffle interface.