| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Bio.Glf
- data GlfSeq = GlfSeq {
- glf_seqname :: !ByteString
- glf_seqlen :: !Int
- data GlfRec
- = SNP {
- glf_refbase :: !Char
- glf_offset :: !Int
- glf_depth :: !Int
- glf_min_lk :: !Int
- glf_mapq :: !Int
- glf_lk :: [Int]
- | Indel {
- glf_refbase :: !Char
- glf_offset :: !Int
- glf_depth :: !Int
- glf_min_lk :: !Int
- glf_mapq :: !Int
- glf_lk_hom1 :: !Int
- glf_lk_hom2 :: !Int
- glf_lk_het :: !Int
- glf_is_ins1 :: !Bool
- glf_is_ins2 :: !Bool
- glf_seq1 :: !ByteString
- glf_seq2 :: !ByteString
- = SNP {
- enee_glf_file :: Monad m => (GlfSeq -> Enumeratee [GlfRec] a m b) -> (ByteString -> Enumerator a m b) -> Enumeratee ByteString a m b
- enum_glf_file :: (MonadIO m, MonadMask m) => FilePath -> (GlfSeq -> Enumeratee [GlfRec] a m b) -> (ByteString -> Enumerator a m b) -> Enumerator a m b
- enum_glf_handle :: (MonadIO m, MonadMask m) => Handle -> (GlfSeq -> Enumeratee [GlfRec] a m b) -> (ByteString -> Enumerator a m b) -> Enumerator a m b
Documentation
Constructors
| GlfSeq | |
Fields
| |
Constructors
| SNP | |
Fields
| |
| Indel | |
Fields
| |
enee_glf_file :: Monad m => (GlfSeq -> Enumeratee [GlfRec] a m b) -> (ByteString -> Enumerator a m b) -> Enumeratee ByteString a m b Source
Iterates over a GLF file. In get_glf_file per_seq per_file, the
enumerator per_file genome_name, where genome_name is the name
stored in the GLF header, is run once, then the enumeratee per_seq
glfseq is iterated over the records in each sequence.
enum_glf_file :: (MonadIO m, MonadMask m) => FilePath -> (GlfSeq -> Enumeratee [GlfRec] a m b) -> (ByteString -> Enumerator a m b) -> Enumerator a m b Source
Enumerate the contents of a GLF file, apply suitable Enumeratees to both sequences and records, resulting in an Enumerator of whatever, typically output Strings or records...
This type is positively weird and I'm not entirely sure this is the right way to go about it.
enum_glf_handle :: (MonadIO m, MonadMask m) => Handle -> (GlfSeq -> Enumeratee [GlfRec] a m b) -> (ByteString -> Enumerator a m b) -> Enumerator a m b Source