Copyright	(c) Matthew Mosior 2024
License	BSD-style
Maintainer	mattm.github@gmail.com
Portability	portable
Safe Haskell	Safe-Inferred
Language	Haskell2010

Data.BAM.Version1_6.BGZFBlock

Contents

BAM_V1_6_BGZFBlock version 1.6 data type

Description

This library enables the decoding/encoding of SAM, BAM and CRAM file formats.

Synopsis

data BAM_V1_6_BGZFBlock = BAM_V1_6_BGZFBlock {
}

BAM_V1_6_BGZFBlock version 1.6 data type

data BAM_V1_6_BGZFBlock Source #

Custom BAM_V1_6_BGZFBlock (BAM version 1.6) data type.

See the SAM v1.6 specification documentation.

Constructors

BAM_V1_6_BGZFBlock

Fields

bam_v1_6_bgzfblock_gzip_header :: BAM_V1_6_GZipHeader
GZip 10 byte header. This contains a magic number (1f 08), the compression method (08 for DEFLATE), 1-byte of header flags, a 4-byte timestamp, compression flags, and the operating system ID.
bam_v1_6_bgzfblock_subfield_identifier_one :: Word8
This should be B.
bam_v1_6_bgzfblock_subfield_identifier_two :: Word8
This should be C.
bam_v1_6_bgzfblock_subfield_length :: Word16
This should be '02 00'.
bam_v1_6_bgzfblock_total_block_size_minus_one :: Word16
The payload of the BGZF extra field is a 16-bit unsigned integer in little endian format. This integer gives the size of the containing BGZF block minus one.
bam_v1_6_bgzfblock_cdata :: BAM_V1_6_BAM
Compressed DATA by zlib::deflate(). The data in this field will be in a decompressed and useable state.
bam_v1_6_bgzfblock_crc32 :: Word32
CRC-32.
bam_v1_6_bgzfblock_isize :: Word32
Input SIZE (length of uncompressed data).

Instances

Instances details

Generic BAM_V1_6_BGZFBlock Source #
Instance details Defined in Data.BAM.Version1_6.BGZFBlock Associated Types type Rep BAM_V1_6_BGZFBlock :: Type -> Type # Methods from :: BAM_V1_6_BGZFBlock -> Rep BAM_V1_6_BGZFBlock x # to :: Rep BAM_V1_6_BGZFBlock x -> BAM_V1_6_BGZFBlock #
Show BAM_V1_6_BGZFBlock Source #
Instance details Defined in Data.BAM.Version1_6.BGZFBlock Methods showsPrec :: Int -> BAM_V1_6_BGZFBlock -> ShowS # show :: BAM_V1_6_BGZFBlock -> String # showList :: [BAM_V1_6_BGZFBlock] -> ShowS #
Eq BAM_V1_6_BGZFBlock Source #
Instance details Defined in Data.BAM.Version1_6.BGZFBlock Methods (==) :: BAM_V1_6_BGZFBlock -> BAM_V1_6_BGZFBlock -> Bool # (/=) :: BAM_V1_6_BGZFBlock -> BAM_V1_6_BGZFBlock -> Bool #
type Rep BAM_V1_6_BGZFBlock Source #
Instance details Defined in Data.BAM.Version1_6.BGZFBlock type Rep BAM_V1_6_BGZFBlock = D1 ('MetaData "BAM_V1_6_BGZFBlock" "Data.BAM.Version1_6.BGZFBlock" "hs-samtools-0.10.0.3-inplace" 'False) (C1 ('MetaCons "BAM_V1_6_BGZFBlock" 'PrefixI 'True) (((S1 ('MetaSel ('Just "bam_v1_6_bgzfblock_gzip_header") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 BAM_V1_6_GZipHeader) :: S1 ('MetaSel ('Just "bam_v1_6_bgzfblock_subfield_identifier_one") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Word8)) :: (S1 ('MetaSel ('Just "bam_v1_6_bgzfblock_subfield_identifier_two") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Word8) :: S1 ('MetaSel ('Just "bam_v1_6_bgzfblock_subfield_length") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Word16))) :: ((S1 ('MetaSel ('Just "bam_v1_6_bgzfblock_total_block_size_minus_one") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Word16) :: S1 ('MetaSel ('Just "bam_v1_6_bgzfblock_cdata") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 BAM_V1_6_BAM)) :: (S1 ('MetaSel ('Just "bam_v1_6_bgzfblock_crc32") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Word32) :*: S1 ('MetaSel ('Just "bam_v1_6_bgzfblock_isize") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Word32)))))