This pull request updates the codebase to require and use indexed, compressed VCF files (.vcf.gz with CSI index) for variant highlighting, improving performance and reliability when querying genomic intervals. It also refactors the VCF reading logic to use IndexedReader and adds error handling for missing index files. The test suite and wizard file discovery have been updated accordingly.

VCF file handling improvements:

• Switched from Reader to IndexedReader for VCF files in VcfHighlight, enabling efficient region-based queries and requiring CSI index files. The code now fetches only the relevant region from the VCF file instead of reading all records. (src/highlight.rs, [1] [2]
• Added error handling in main.rs to check for the existence of the CSI index file before processing a VCF file, and provide a helpful error message if missing. (src/main.rs, src/main.rsR49-R58)

Test and file discovery updates:

• Updated tests to use compressed VCF files (.vcf.gz) instead of uncompressed VCFs, reflecting the new requirements. (src/highlight.rs, [1] [2]
• Modified wizard mode file discovery to only include .vcf.gz and .bcf files, excluding uncompressed VCFs. (src/wizard.rs, src/wizard.rsL34-R34)

Code cleanup and minor changes:

• Removed the old uncompressed VCF test file from the repository. (tests/sample_3/1257A.vcf, tests/sample_3/1257A.vcfL1-L4)
• Renamed the Region::contains method to _contains (now unused), reflecting its removal from active use in the highlighting logic. (src/cli.rs, src/cli.rsL296-R296)
• Minor import and error handling improvements in main.rs. (src/main.rs, src/main.rsL11-R11)