VCFArray

VCFArray extends the DelayedArray framework to represent VCF data entries as array-like objects with on-disk or remote VCF files as backend, enabling efficient access to variant call data without loading entire files into memory.

Key Features:

• DelayedArray Extension: VCFArray extends the DelayedArray framework to provide array-like representations of VCF data.
• On-disk and Remote Backend Support: VCFArray uses on-disk or remote VCF files as backend storage for data access.
• Multi-field Data Conversion: Data entries from VCF files, including info fields, FORMAT fields, and fixed columns (REF, ALT, QUAL, FILTER), can be converted into VCFArray instances with different dimensions.

Scientific Applications:

• Variant Call Format Data Analysis: VCFArray enables array-based computational operations on VCF file contents for genomic variant analysis.
• Large-scale Genomic Data Processing: VCFArray facilitates memory-efficient analysis of variant data from large VCF files through delayed evaluation and on-disk data access.

Methodology:

VCFArray extends the DelayedArray framework to represent VCF data entries as array-like objects with on-disk or remote VCF file as backend, converting info fields, FORMAT fields, and fixed columns into VCFArray instances with different dimensions.