V1.1

This release contains major changes, offering improved functionality and usability!

Merge getDB.py into install.sh
2)
Kept options
-f|--force: Unlink databases.
-o|--organism ORGANISM: Organism to download databases for.
-h|--help: Displays usage information.
3)
Renamed options
-l|--link LINK: Link databases instead of downloading.
-s|--select-db SELECT_DB: Database(s) to download for the specified organism.
New options
-c|--clean: Just remove installed tools.
-d|--db-dest DB_DEST: Change database download location.
-n|--native: Use native python.
4)
Re-implement as a shell script
Kept options
-o|--organism (default: human): Run for the specified organism instead of human.
-b|--bam: Input unmapped reads in .bam format instead of .fastq format.
-z|--gzip: gunzip the input file.
-d|--dev: Keep intermediate FASTA files.
-f|--force: Overwrite the analysis destination directory.
-m|--max: Use a liberal threshold when remapping to reference.
-p|--pe: Reserved but has no effect.
-q|--quiet: Reserved but has no effect.
Renamed options
-s|--steps: Select the analysis modes to use.
-a|--fasta: Input unmapped reads in .fasta format instead of .fastq format.
Forcibly disables low-quality read filtering.
New options
-i|--ignore-extensions: Ignore incorrect .fastq/.fq/.fasta/.fa file extensions. Does not ignore incorrect .gz/.bam file extensions.
-x|--commands: Print all commands (diagnostic mode).
-h|--help: Displays usage information.
5)
Retired options
--qsub
--qsubArray
--maui
--outGz
--rezip
--clean
--nonReductive
6)
Other changes
Use MiniConda for dependencies instead of storing them in the repository.
Update README.md with concise documentation.
7)
Add .gitignore.