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App-Sandy-0.25
River stage zero No dependents
3 ++

Changes for version 0.25 - 2023-09-19

  • Remove version from transcript_id, example: ENST00006666.9 will become ENST00006666

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::BGZF
Wrapper around Compress::BGZF::Writer in order
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::Citation
citation command class. Print citation
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::Dump
expression subcommand class. Dump an expression-matrix from 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::Dump
quality subcommand class. Dump a quality profile from 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::Variation
variation command class. Manage structural variation database.
App::Sandy::Command::Variation::Add
variation subcommand class. Add structural variation to the database.
App::Sandy::Command::Variation::Dump
variation subcommand class. Dump structural variation from database.
App::Sandy::Command::Variation::Remove
variation subcommand class. Remove structural variation from database.
App::Sandy::Command::Variation::Restore
variation subcommand class. Restore database.
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::Handle::Variation
Class to handle structural variation database schemas.
App::Sandy::DB::Schema
App::Sandy::DB::Schema::Result::ExpressionMatrix
App::Sandy::DB::Schema::Result::QualityProfile
App::Sandy::DB::Schema::Result::StructuralVariation
App::Sandy::InterlaceProcesses
Interlaces the processe id for differents processes, actually for parent, child processes.
App::Sandy::PieceTable
Implement a piece table data structure class
App::Sandy::Quality
Class to simulate quality entries
App::Sandy::RNG
Generates random numbers
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::BSearch
Binary search role
App::Sandy::Role::Counter
Bayes counter
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::Role::SeqID
Role for seqid standardization
App::Sandy::Role::Statistic
Basic statistics
App::Sandy::Role::Template::Fastq
Fastq template role
App::Sandy::Role::Template::Sam
Sam template role
App::Sandy::Seq
Base class to simulate seq entries
App::Sandy::Seq::PairedEnd
App::Sandy::Seq subclass for simulate paired-end entries.
App::Sandy::Seq::SingleEnd
App::Sandy::Seq subclass for simulate single-end entries.
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