[CALCITE-2025] Create adapter(s) for standard bioinformatics database files

• Type: New Feature
• Status: Open
• Priority: Minor
• Resolution: Unresolved
• Labels: features
• Assignee: Edmon Begoli
• Reporter: Edmon Begoli
• Created: 31/Oct/17 12:07
• Updated: 31/Oct/17 14:11

Description

Common bioinformatics files, used mostly in genomic medicine, and life sciences research are VCF, SAM, and FASTQ/FASTA files [1,2,3,4].

They are structured text files, with metadata headers, and (generally) column oriented layout.

Having calcite support for these formats would enable it to serve as the front end for processing of a very large body of important data, and to facilitate the integration of these datasets into a downstream frameworks that incorporate or use calcite.

This issue will serve as the parent issues for each format that will be implemented (SAM, VCF, etc.)

1. SAM file format, https://en.wikipedia.org/wiki/SAM_(file_format)
2. VCF file format, https://en.wikipedia.org/wiki/Variant_Call_Format
3. FASTQ file format, https://en.wikipedia.org/wiki/FASTQ_format
4.Other, https://bioinf.comav.upv.es/courses/sequence_analysis/sequence_file_formats.html