Crate fqgrep_lib

Modules§

AMINO_ACIDS
DNA_BASES
DNA_MASK_VALUES: The encoded 4-bit mask values for the four standard DNA bases (A=1, C=2, G=4, T=8). Used to distinguish DNA-only patterns from those containing IUPAC ambiguity codes.
IUPAC_BASES
IUPAC_BASES_COMPLEMENT
IUPAC_MASKS: Lookup table mapping ASCII byte values to their 4-bit IUPAC bitmask encodings. A=1, C=2, G=4, T=8, and ambiguity codes are the bitwise OR of their constituents.
MAX_IUPAC_EXPANSIONS: The maximum number of expanded patterns allowed before returning an error.

encode: Encodes a sequence of ASCII bases into a BitEnc using 4-bit IUPAC mask values.
expand_iupac_fixed_pattern: Expands the pattern containing IUPAC bases into one or more patterns.
expand_iupac_regex: Converts an IUPAC pattern into a regex pattern by replacing each ambiguity code with a character class of its constituent DNA bases (e.g., R becomes [AG]).
is_fastq_path: Returns true if the path ends with a recognized FASTQ file extension
is_gzip_path: Returns true if the path ends with a recognized GZIP file extension