Improved Validation#9
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Add comprehensive validation features matching GATK ValidateVariants: - ALT allele observation check (ALLELES validation) - Empty VCF detection with --allow-empty override - Header Type/Number field validation - Variant sorting check (disable with -S) - AN/AC consistency check in strict mode (CHR_COUNTS) - REF validation against FASTA reference (-R) - dbSNP ID validation (-D) - GVCF format validation (-g) Additional improvements: - Add -i/--input flag for mmap file input - Update documentation with all new options - Add test cases for new validations - Maintain ~110 MB/s throughput performance
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Thank you for contributing to VCFX! Before submitting your pull request, please confirm the following:
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