Home

Functionalities to implement

• Infer organism from which samples were derived
• Infer read layout: single vs paired
• Infer read layout: stranded/unstranded
• Infer read layout: sense/antisense for each mate
• Infer sequences of any adapters present in reads

Stretch goals

• Infer type of captured molecule (RNA, DNA)
• Infer method type (RNA-Seq vs CLIP vs A-Seq etc.)

Issues to add

• validate against duplicate IDs
• handle SRA library types
• handle potential mates for unknown file types (mapping)
• check SRA metadata
• allow passing SRA identifiers & download
• implement --fast option (no validation & fix --records)
• fix ValueError traceback thrown when passing more than 2 files
• implement adapter inference properly
• move CleanupRegimes and RunStates from htsinfer.py to models.py

Checklist for new commits

• Check version: minor versions should be incremented for every new feature; currently we are at v0.5.0, so the next feature added should have v0.6.0 and so on; for fixes, on the other hand, you should bump the patch version
• Check CLI args: if you have added CLI args, you need to (1) manually update the usage string in cli.py (this is necessary because the auto-generated one is wrong because and patching argparse is too much work), (2) add the parameter to the argument parser in cli.py, (3) update the usage and parameter descriptions in the README.md accordingly, (4) pass the parameter to the HtsInfer() instantiation in cli.py, (5) add the argument to the HtsInfer() signature in htsinfer.py, (6) add the argument and attribute description to its docstring, (7) define a corresponding attribute in its constructor and assign the argument value to it, and (8) pass it on to whatever class you need it
• Implement/update any required models and enumerators in models.py
• Add any required exceptions to exceptions.py
• See if you want to add anything to the Travis config and make sure that all commands listed in the script section run fine before pushing (this includes tests and linters)
• Make sure all test files and data files added have meaningful names
• Add data files (e.g., the transcripts) in a directory data/ in the project root
• Make sure you update any dependencies, if necessary