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App-SimulateReads-0.16
River stage zero No dependents
++

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

simulate_reads
Creates single-end and paired-end fastq reads for transcriptome and genome simulation.

Modules

App::SimulateReads
App builder that simulates single-end and paired-end reads.
App::SimulateReads::Base
Policy and base module to App::SimulateReads project.
App::SimulateReads::CLI
Base class for command line interface.
App::SimulateReads::CLI::App
App::SimulateReads::CLI subclass for command line application interface.
App::SimulateReads::CLI::Command
App::SimulateReads::CLI subclass for commands interface
App::SimulateReads::Command::Custom
simulate command class. Simulate a custom sequencing
App::SimulateReads::Command::Expression
expression command class. Manage expression-matrix database.
App::SimulateReads::Command::Expression::Add
expression subcommand class. Add an expression-matrix to the database.
App::SimulateReads::Command::Expression::Remove
expression subcommand class. Remove an expression-matrix from database.
App::SimulateReads::Command::Expression::Restore
expression subcommand class. Restore database.
App::SimulateReads::Command::Genome
simulate command class. Simulate genome sequencing
App::SimulateReads::Command::Quality
quality command class. Manage quality profile database.
App::SimulateReads::Command::Quality::Add
quality subcommand class. Add a quality profile to the database.
App::SimulateReads::Command::Quality::Remove
quality subcommand class. Remove a quality profile from database.
App::SimulateReads::Command::Quality::Restore
quality subcommand class. Restore database.
App::SimulateReads::Command::Transcriptome
simulate command class. Simulate transcriptome sequencing
App::SimulateReads::DB
Singleton class to manage database
App::SimulateReads::DB::Handle::Expression
Class to handle expression-matrix database schemas.
App::SimulateReads::DB::Handle::Quality
Class to handle quality database schemas.
App::SimulateReads::DB::Schema
App::SimulateReads::DB::Schema::Result::ExpressionMatrix
App::SimulateReads::DB::Schema::Result::QualityProfile
App::SimulateReads::Fastq
Base class to simulate fastq entries
App::SimulateReads::Fastq::PairedEnd
App::SimulateReads::Fastq subclass for simulate paired-end fastq entries.
App::SimulateReads::Fastq::SingleEnd
App::SimulateReads::Fastq subclass for simulate single-end fastq entries.
App::SimulateReads::InterlaceProcesses
Interlaces the processe id for differents processes, actually for parent, child processes.
App::SimulateReads::Quality
Class to simulate quality entries
App::SimulateReads::Read
Base class to simulate reads
App::SimulateReads::Read::PairedEnd
App::SimulateReads::Read subclass for simulate paired-end reads.
App::SimulateReads::Read::SingleEnd
App::SimulateReads::Read subclass for simulate single-end reads.
App::SimulateReads::Role::Digest
Wrapper on Simulator class for genome/transcriptome sequencing
App::SimulateReads::Role::IO
Input and output custom wrappers.
App::SimulateReads::Role::ParseArgv
Getopt::Long wrapper.
App::SimulateReads::Role::RunTimeTemplate
Extends class with runtime printf like function
App::SimulateReads::Simulator
Class responsible to make the simulation
App::SimulateReads::Types
Moose type constraints for App::SimulateReads project
App::SimulateReads::WeightedRaffle
Weighted raffle interface.

Other files