Bio.HTS

Documentation

type HeaderState = ResourceT (ReaderT FileHeader IO)

withBamFile :: FilePath -> (BamFileHandle -> HeaderState a) -> IO a

readBam :: BamFileHandle -> ConduitT () Bam HeaderState ()

writeBam :: FilePath -> ConduitT Bam o HeaderState ()

inline_c_ffi_6989586621679078141 :: Ptr HTSFile -> Ptr BamHdr -> IO CInt

inline_c_ffi_6989586621679077971 :: Ptr HTSFile -> Ptr Bam' -> IO CInt

openBamFile :: FilePath -> IOMode -> IO BamFileHandle

inline_c_ffi_6989586621679078167 :: Ptr CChar -> IO (Ptr HTSFile)

inline_c_ffi_6989586621679078175 :: Ptr CChar -> IO (Ptr HTSFile)

readBamHeader :: BamFileHandle -> IO FileHeader

inline_c_ffi_6989586621679078185 :: Ptr HTSFile -> IO (Ptr BamHdr)

closeBamFile :: BamFileHandle -> IO ()

inline_c_ffi_6989586621679078194 :: Ptr HTSFile -> IO ()

showBamHeader :: FileHeader -> ByteString

inline_c_ffi_6989586621679078222 :: Ptr BamHdr -> IO (Ptr CChar)

inline_c_ffi_6989586621679078231 :: Ptr BamHdr -> IO Word32

data SortOrder

Constructors

Unknown

Unsorted

Queryname

Coordinate

getSortOrder :: FileHeader -> SortOrder

bamRead1 :: BamFileHandle -> IO (Maybe Bam)

inline_c_ffi_6989586621679078421 :: Ptr CInt -> Ptr HTSFile -> IO (Ptr Bam')

bamDestory :: FunPtr (Ptr Bam' -> IO ())

getChrId :: Bam -> Int32

Return the chromosome id.

inline_c_ffi_6989586621679078433 :: Ptr Bam' -> IO Int32

getChr :: Ptr BamHdr -> Bam -> Maybe ByteString

Return the chromosome name given the bam file header.

inline_c_ffi_6989586621679078446 :: Ptr BamHdr -> Int32 -> IO (Ptr CChar)

position :: Bam -> Int32

Return the 0-based starting location.

inline_c_ffi_6989586621679078456 :: Ptr Bam' -> IO Int32

endPos :: Bam -> Int32

For a mapped read, this is just position + cigar2rlen. For an unmapped read (either according to its flags or if it has no cigar string), we return position + 1 by convention.

inline_c_ffi_6989586621679078466 :: Ptr Bam' -> IO Int32

queryLen :: Bam -> Int32

Return the query length (read length).

inline_c_ffi_6989586621679078476 :: Ptr Bam' -> IO Int32

isRev :: Bam -> Bool

Whether the query is on the reverse strand.

inline_c_ffi_6989586621679078486 :: Ptr Bam' -> IO CInt

flag :: Bam -> Word16

Return the flag.

inline_c_ffi_6989586621679078497 :: Ptr Bam' -> IO Word16

mapq :: Bam -> Word8

MAPping Quality. It equals −10 log10 Pr{mapping position is wrong}, rounded to the nearest integer. A value 255 indicates that the mapping quality is not available.

inline_c_ffi_6989586621679078507 :: Ptr Bam' -> IO Word8

getSeq :: Bam -> Maybe ByteString

Return the DNA sequence.

inline_c_ffi_6989586621679078517 :: Ptr Bam' -> IO Int32

inline_c_ffi_6989586621679078531 :: Ptr Bam' -> Int32 -> Ptr CChar -> IO ()

qName :: Bam -> ByteString

Get the name of the query.

inline_c_ffi_6989586621679078541 :: Ptr Bam' -> IO (Ptr CChar)

quality :: Bam -> Maybe ByteString

inline_c_ffi_6989586621679078551 :: Ptr Bam' -> IO Int32

inline_c_ffi_6989586621679078560 :: Ptr Bam' -> IO Int8

inline_c_ffi_6989586621679078574 :: Ptr Bam' -> Int32 -> Ptr CChar -> IO ()

cigar :: Bam -> Maybe [(Int, Char)]

inline_c_ffi_6989586621679078584 :: Ptr Bam' -> IO Word16

inline_c_ffi_6989586621679078601 :: Ptr Bam' -> Word16 -> Ptr CInt -> Ptr CChar -> IO ()

mateChrId :: Bam -> Int32

inline_c_ffi_6989586621679078613 :: Ptr Bam' -> IO Int32

mateChr :: Ptr BamHdr -> Bam -> Maybe ByteString

inline_c_ffi_6989586621679078626 :: Ptr BamHdr -> Int32 -> IO (Ptr CChar)

matePos :: Bam -> Int32

0-based

inline_c_ffi_6989586621679078636 :: Ptr Bam' -> IO Int32

tLen :: Bam -> Int32

inline_c_ffi_6989586621679078646 :: Ptr Bam' -> IO Int32

bamToSam :: Ptr BamHdr -> Bam -> Sam

Convert Bam record to Sam record.

hasMultiSegments :: Word16 -> Bool

Template having multiple segments in sequencing

isProperAligned :: Word16 -> Bool

Each segment properly aligned according to the aligner

isUnmapped :: Word16 -> Bool

Segment unmapped

isNextUnmapped :: Word16 -> Bool

Next segment in the template unmapped

isRC :: Word16 -> Bool

SEQ being reverse complemented

isNextRC :: Word16 -> Bool

SEQ of the next segment in the template being reverse complemented

isFirstSegment :: Word16 -> Bool

The first segment in the template

isLastSegment :: Word16 -> Bool

The last segment in the template

isSecondary :: Word16 -> Bool

Secondary alignment

isBadQual :: Word16 -> Bool

Not passing filters, such as platform/vendor quality controls

isDup :: Word16 -> Bool

PCR or optical duplicate

isSupplementary :: Word16 -> Bool

Supplementary alignment