History

Coverage and covtobed

covtobed

ℹ️ We adopted the semantic versioning.

📁 Stable releases are released via Miniconda, and are available here.

• version 1.2.0: introduced the -z flag to skip reference shorter than a specified length (useful in fragmented metagenomic datasets)
• version 1.1.4: will warn to use samtools fixmate on unexpected physical coverage (before: the program was terminating with error) [issue #11]
• version 1.1.2: code cleanup [including Dockerfile], added Code Quality scrutiny and badge
• version 1.1.0: new feature, a switch (-a) to discard invalid alignments (PCR duplicates, failing QC, supplementary) Not released yet
• version 1.0.1: Support for coverage > 65k [issue #7], update documentation [incl. issue #5]
• version 1.0: Finalized tests; Improved code comments; Updated manuscript; Updated Wiki

Pre-releases:

• version 0.8: Removed test constraints; Target Enrichment dataset released;
• version 0.7: Extended tests with TravisCI; Fixed splash screen;
• version 0.6: Bug fix [issue #2]: physical coverage
• version 0.4: Bug fix [issue #1]
• version 0.3: Bug fixes and added minimum feature-length switch. Dockerfile provided, also including the legacy coverage tool.
• version 0.1: Rewrite of coverage with a focus on simplicity and adhesion to UNIX programming philosophy.

coverage (legacy)

The coverage tool, now provided via Docker, is a legacy tool developed to generate internal reports for the MD-PAEDIGREE project, to analyze the gene panels targeting genes linked to cardiomyopathies.

It has been used, for example, in the analysis of target enrichment experiments (like Poloni 2019)

The development of coverage was stopped and the core engine rewritten as foundation for the simpler covtobed.