Read Origin Protocol v1.1.2

Re-enable metaphlan

Read Origin Protocol v1.1.1

Build fixes.

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.

v1.0.8

This release contains major changes and improvements:

• The low-quality reads are identified but NOT filter out from the analysis. Those reads are marked as "low-quality" in the read name and are used in the downstream analysis
• The commands by ROP are easy to change. Commands are stored in rop.commands.txt
• The --max option has been added. This option allows accounting for the maximum number of unmapped reads. We use liberal threshold to account for maximum number of reads
• The option --pe option has been added (beta version). This option allows reporting number of discordant read pairs, with the reads from the same pair classified as different categories. This is the beta version. Please use with caution.
• Starting from release v1.0.8 due to the computational burden we have replaced bacterial genomes database (NCBI) with informative marker genes (prepared by Metahplan2)
• ROP now accepts reads of variable length
• The following options are temporarily disabled: [--organism ORGANISM] [--skipLowq] [--skipQC] [--skipPreliminary] [--circRNA] [--bacteria]
• The following options are disabled and will be removed in next release: [--qsub] [--qsubArray] [--maui] [--nonReductive]
• We have done major changes to the installation script. To guarantee that ROP uses the latest version of the open source tools (developed by other groups or developed by our group). Starting from this release install.sh will download and install such tools. Before these tools were redistributed with ROP.
• Install miniconda (https://conda.io/miniconda.html) as part of the installation of ROP. This way ROP doesn't require python to be installed on the system.