Bio.SamTools.FaIdx

Fetch sequences from an indexed fasta file

Documentation

data InHandle

Input handle for an indexed fasta file

filename :: InHandle -> FilePath

Name of the fasta file

open :: FilePath -> IO InHandle

Open an indexed fasta file

close :: InHandle -> IO ()

withFastaIndex :: FilePath -> (InHandle -> IO a) -> IO a

fetch

Arguments

:: InHandle

-> ByteString

Sequence name

-> (Int64, Int64)

(Starting, ending) position, 0-based

-> IO ByteString

Fetch a region specified by sequence name and coordinates, or the empty string when the sequence is not found.

fetchLoc :: Location l => InHandle -> OnSeq l -> IO (Maybe ByteString)

readLoc :: Location l => FilePath -> OnSeq l -> IO (Maybe ByteString)