| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Bio.Bam.Header
- data BamMeta = BamMeta {
- meta_hdr :: !BamHeader
- meta_refs :: !Refs
- meta_other_shit :: [(BamKey, BamOtherShit)]
- meta_comment :: [ByteString]
- parseBamMeta :: Parser BamMeta
- parseBamMetaLine :: Parser (BamMeta -> BamMeta)
- showBamMeta :: BamMeta -> Builder
- addPG :: Maybe Version -> IO (BamMeta -> BamMeta)
- newtype BamKey = BamKey Word16
- data BamHeader = BamHeader {
- hdr_version :: (Int, Int)
- hdr_sorting :: !BamSorting
- hdr_other_shit :: BamOtherShit
- data BamSQ = BamSQ {}
- data BamSorting
- type BamOtherShit = [(BamKey, ByteString)]
- newtype Refseq = Refseq {}
- invalidRefseq :: Refseq
- isValidRefseq :: Refseq -> Bool
- invalidPos :: Int
- isValidPos :: Int -> Bool
- unknownMapq :: Int
- isKnownMapq :: Int -> Bool
- type Refs = Seq BamSQ
- noRefs :: Refs
- getRef :: Refs -> Refseq -> BamSQ
- compareNames :: Seqid -> Seqid -> Ordering
- flagPaired :: Int
- flagProperlyPaired :: Int
- flagUnmapped :: Int
- flagMateUnmapped :: Int
- flagReversed :: Int
- flagMateReversed :: Int
- flagFirstMate :: Int
- flagSecondMate :: Int
- flagAuxillary :: Int
- flagFailsQC :: Int
- flagDuplicate :: Int
- eflagTrimmed :: Int
- eflagMerged :: Int
- distinctBin :: Int -> Int -> Int
- data MdOp
- = MdNum Int
- | MdRep Nucleotides
- | MdDel [Nucleotides]
- readMd :: ByteString -> Maybe [MdOp]
- showMd :: [MdOp] -> ByteString
Documentation
Constructors
| BamMeta | |
Fields
| |
parseBamMetaLine :: Parser (BamMeta -> BamMeta) Source
showBamMeta :: BamMeta -> Builder Source
Exactly two characters, for the "named" fields in bam.
Constructors
| BamHeader | |
Fields
| |
Constructors
| BamSQ | |
Fields
| |
data BamSorting Source
Possible sorting orders from bam header. Thanks to samtools, which
doesn't declare sorted files properly, we have to have the stupid
Unknown state, too.
Constructors
| Unknown | |
| Unsorted | |
| Grouped | |
| Queryname | |
| Coordinate | |
| GroupSorted |
Instances
type BamOtherShit = [(BamKey, ByteString)] Source
Reference sequence in Bam Bam enumerates the reference sequences and then sorts by index. We need to track that index if we want to reproduce the sorting order.
invalidRefseq :: Refseq Source
The invalid Refseq. Bam uses this value to encode a missing reference sequence.
isValidRefseq :: Refseq -> Bool Source
Tests whether a reference sequence is valid.
Returns true unless the the argument equals invalidRefseq.
invalidPos :: Int Source
The invalid position. Bam uses this value to encode a missing position.
isValidPos :: Int -> Bool Source
Tests whether a position is valid.
Returns true unless the the argument equals invalidPos.
unknownMapq :: Int Source
isKnownMapq :: Int -> Bool Source
The empty list of references. Needed for BAM files that don't really store alignments.
compareNames :: Seqid -> Seqid -> Ordering Source
Compares two sequence names the way samtools does. samtools sorts by "strnum_cmp": . if both strings start with a digit, parse the initial sequence of digits and compare numerically, if equal, continue behind the numbers . else compare the first characters (possibly NUL), if equal continue behind them . else both strings ended and the shorter one counts as smaller (and that part is stupid)
flagPaired :: Int Source
flagFailsQC :: Int Source
eflagMerged :: Int Source
distinctBin :: Int -> Int -> Int Source
Computes the "distinct bin" according to the BAM binning scheme. If
an alignment starts at pos and its CIGAR implies a length of len
on the reference, then it goes into bin distinctBin pos len.
Constructors
| MdNum Int | |
| MdRep Nucleotides | |
| MdDel [Nucleotides] |
readMd :: ByteString -> Maybe [MdOp] Source
showMd :: [MdOp] -> ByteString Source
Normalizes a series of MdOps and encodes them in the way BAM and
SAM expect it.