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App-Sandy-0.17
River stage zero No dependents
3 ++

Changes for version 0.17 - 2018-05-05

  • Fix bug in fasta_tree and fasta_rtree
  • Populate quality and expression databases
  • Improve documentation
  • Rename project from App-SimulateReads to App-Sandy

Documentation

Sandy
A straightforward and complete next-generation sequencing read simulator

Modules

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

Other files