Changes for version 0.25 - 2023-09-19
- Remove version from transcript_id, example: ENST00006666.9 will become ENST00006666
Documentation
A straightforward and complete next-generation sequencing read simulator
Modules
App builder that simulates single-end and paired-end reads.
Wrapper around Compress::BGZF::Writer in order
Policy and base module to App::Sandy project.
Base class for command line interface.
App::Sandy::CLI subclass for command line application interface.
App::Sandy::CLI subclass for commands interface
citation command class. Print citation
expression command class. Manage expression-matrix database.
expression subcommand class. Add an expression-matrix to the database.
expression subcommand class. Dump an expression-matrix from 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. Dump a quality profile from database.
quality subcommand class. Remove a quality profile from database.
quality subcommand class. Restore database.
simulate command class. Simulate transcriptome sequencing
variation command class. Manage structural variation database.
variation subcommand class. Add structural variation to the database.
variation subcommand class. Dump structural variation from database.
variation subcommand class. Remove structural variation from database.
variation subcommand class. Restore database.
version command class. Print version
Singleton class to manage database
Class to handle expression-matrix database schemas.
Class to handle quality database schemas.
Class to handle structural variation database schemas.
Interlaces the processe id for differents processes, actually for parent, child processes.
Implement a piece table data structure class
Class to simulate quality entries
Generates random numbers
Base class to simulate reads
App::Sandy::Read subclass for simulate paired-end reads.
App::Sandy::Read subclass for simulate single-end reads.
Binary search role
Bayes counter
Wrapper on Simulator class for genome/transcriptome sequencing
Input and output custom wrappers.
Getopt::Long wrapper.
Extends class with runtime printf like function
Role for seqid standardization
Basic statistics
Fastq template role
Sam template role
Base class to simulate seq entries
App::Sandy::Seq subclass for simulate paired-end entries.
App::Sandy::Seq subclass for simulate single-end entries.
Class responsible to make the simulation
Moose type constraints for App::Sandy project
Weighted raffle interface.