samtools-0.1.2: Binding to the C samtools library

Bio.SamTools.FaIdx

Description

Fetch sequences from an indexed fasta file

Synopsis

data InHandle
filename :: InHandle -> FilePath
open :: FilePath -> IO InHandle
close :: InHandle -> IO ()
withFastaIndex :: FilePath -> (InHandle -> IO a) -> IO a
fetch :: InHandle -> ByteString -> (Int64, Int64) -> IO ByteString
fetchLoc :: Location l => InHandle -> OnSeq l -> IO (Maybe ByteString)
readLoc :: Location l => FilePath -> OnSeq l -> IO (Maybe ByteString)

Documentation

data InHandle Source

Input handle for an indexed fasta file

filename :: InHandle -> FilePath Source

Name of the fasta file

open :: FilePath -> IO InHandle Source

Open an indexed fasta file

close :: InHandle -> IO () Source

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

Arguments

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)Source

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