hs-samtools-0.10.0.0: src/Data/SAM/Version1_6/Write/Base.hs
{-# LANGUAGE FlexibleContexts #-}
{-# LANGUAGE FlexibleInstances #-}
{-# LANGUAGE MultiParamTypeClasses #-}
{-# LANGUAGE TypeFamilies #-}
-- |
-- Module : Data.SAM.Version1_6.Write.Base
-- Copyright : (c) Matthew Mosior 2024
-- License : BSD-style
-- Maintainer : mattm.github@gmail.com
-- Portability : portable
--
-- = Description
--
-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.
module Data.SAM.Version1_6.Write.Base ( -- * Writing
writeSAM_V1_6
) where
import Data.SAM.Version1_6.Base
import Data.SAM.Version1_6.Header.HD
import Data.SAM.Version1_6.Header.SQ
import Data.SAM.Version1_6.Header.RG
import Data.SAM.Version1_6.Header.PG
import Data.SAM.Version1_6.Header.CO
import Data.SAM.Version1_6.Alignment.Base
import Data.SAM.Version1_6.Alignment.OptionalFields.Base
import Data.SAM.Version1_6.Alignment.OptionalFields.AOPT
import Data.SAM.Version1_6.Alignment.OptionalFields.IOPT
import Data.SAM.Version1_6.Alignment.OptionalFields.FOPT
import Data.SAM.Version1_6.Alignment.OptionalFields.ZOPT
import Data.SAM.Version1_6.Alignment.OptionalFields.HOPT
import Data.SAM.Version1_6.Alignment.OptionalFields.BOPT
import Control.Monad (forM)
import Data.ByteString as DB (pack,singleton)
import Data.ByteString.Lazy as DBL (filter)
import Data.ByteString.Lazy.Char8 as DBLC8 (fromStrict,unpack)
import Data.Foldable (toList)
import Data.List (intercalate)
import Data.Word
import Data.ByteString.Builder (toLazyByteString,word16LE,word32LE)
import System.IO (hFlush,hClose,hPutStr,IOMode(..),openFile,Handle)
-- | Deconstruct a @"SAM_V1_6"@ to a `String`.
deconstructSAM_V1_6 :: SAM_V1_6
-> String
deconstructSAM_V1_6 samv16 =
( intercalate "\n" $
Prelude.filter (not . Prelude.null)
[ sam_v1_6_file_level_metadata_tos
, sam_v1_6_reference_sequence_dictionary_tos
, sam_v1_6_read_group_tos
, sam_v1_6_program_tos
, sam_v1_6_one_line_comment_tos
, sam_v1_6_alignment_tos
]
)
++ "\n"
where
sam_v1_6_file_level_metadata_format_version_tos x = "VN:" ++
( unpack $
fromStrict $
sam_v1_6_file_level_metadata_format_version_value $
sam_v1_6_file_level_metadata_format_version x
)
sam_v1_6_file_level_metadata_sorting_order_tos x = case (sam_v1_6_file_level_metadata_sorting_order x) of
Nothing ->
""
Just rgf ->
"SO:" ++
( unpack $
fromStrict $
sam_v1_6_file_level_metadata_sorting_order_value rgf
)
sam_v1_6_file_level_metadata_alignment_grouping_tos x = case (sam_v1_6_file_level_metadata_alignment_grouping x) of
Nothing ->
""
Just rgf ->
"GO:" ++
( unpack $
fromStrict $
sam_v1_6_file_level_metadata_alignment_grouping_value rgf
)
sam_v1_6_file_level_metadata_subsorting_order_tos x = case (sam_v1_6_file_level_metadata_subsorting_order x) of
Nothing ->
""
Just rgf ->
"SS:" ++
( unpack $
fromStrict $
sam_v1_6_file_level_metadata_subsorting_order_value rgf
)
sam_v1_6_file_level_metadata_tos = case (sam_v1_6_file_level_metadata samv16) of
Nothing ->
""
Just hdf ->
intercalate "\t" $
Prelude.filter (not . Prelude.null)
[ "@HD"
, sam_v1_6_file_level_metadata_format_version_tos hdf
, sam_v1_6_file_level_metadata_sorting_order_tos hdf
, sam_v1_6_file_level_metadata_alignment_grouping_tos hdf
, sam_v1_6_file_level_metadata_subsorting_order_tos hdf
]
sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tos x = "SN:" ++
( unpack $
fromStrict $
sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value $
sam_v1_6_reference_sequence_dictionary_reference_sequence_name x
)
sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tos x = "LN:" ++
( unpack $
fromStrict $
sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value $
sam_v1_6_reference_sequence_dictionary_reference_sequence_length x
)
sam_v1_6_reference_sequence_dictionary_alternative_locus_tos x = case (sam_v1_6_reference_sequence_dictionary_alternative_locus x) of
Nothing ->
""
Just sqf ->
"AH:" ++
( unpack $
fromStrict $
sam_v1_6_reference_sequence_dictionary_alternative_locus_value sqf
)
sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tos x = case (sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names x) of
Nothing ->
""
Just sqf ->
"AN:" ++
( unpack $
fromStrict $
sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value sqf
)
sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tos x = case (sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier x) of
Nothing ->
""
Just sqf ->
"AS:" ++
( unpack $
fromStrict $
sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value sqf
)
sam_v1_6_reference_sequence_dictionary_description_tos x = case (sam_v1_6_reference_sequence_dictionary_description x) of
Nothing ->
""
Just sqf ->
"DS:" ++
( unpack $
fromStrict $
sam_v1_6_reference_sequence_dictionary_description_value sqf
)
sam_v1_6_reference_sequence_dictionary_md5_checksum_tos x = case (sam_v1_6_reference_sequence_dictionary_md5_checksum x) of
Nothing ->
""
Just sqf ->
"M5:" ++
( unpack $
fromStrict $
sam_v1_6_reference_sequence_dictionary_md5_checksum_value sqf
)
sam_v1_6_reference_sequence_dictionary_species_tos x = case (sam_v1_6_reference_sequence_dictionary_species x) of
Nothing ->
""
Just sqf ->
"SP:" ++
( unpack $
fromStrict $
sam_v1_6_reference_sequence_dictionary_species_value sqf
)
sam_v1_6_reference_sequence_dictionary_molecule_topology_tos x = case (sam_v1_6_reference_sequence_dictionary_molecule_topology x) of
Nothing ->
""
Just sqf ->
"TP:" ++
( unpack $
fromStrict $
sam_v1_6_reference_sequence_dictionary_molecule_topology_value sqf
)
sam_v1_6_reference_sequence_dictionary_uri_tos x = case (sam_v1_6_reference_sequence_dictionary_uri x) of
Nothing ->
""
Just sqf ->
"UR:" ++
( unpack $
fromStrict $
sam_v1_6_reference_sequence_dictionary_uri_value sqf
)
sam_v1_6_reference_sequence_dictionary_tos = case (sam_v1_6_reference_sequence_dictionary samv16) of
Nothing ->
""
Just sqf ->
intercalate "\n" $
map (\x -> intercalate "\t" $
Prelude.filter (not . Prelude.null)
[ "@SQ"
, sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tos x
, sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tos x
, sam_v1_6_reference_sequence_dictionary_alternative_locus_tos x
, sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tos x
, sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tos x
, sam_v1_6_reference_sequence_dictionary_description_tos x
, sam_v1_6_reference_sequence_dictionary_md5_checksum_tos x
, sam_v1_6_reference_sequence_dictionary_species_tos x
, sam_v1_6_reference_sequence_dictionary_molecule_topology_tos x
, sam_v1_6_reference_sequence_dictionary_uri_tos x
]
) (toList sqf)
sam_v1_6_read_group_identifer_tos x = "ID:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_identifier_value $
sam_v1_6_read_group_identifier x
)
sam_v1_6_read_group_barcode_sequence_tos x = case (sam_v1_6_read_group_barcode_sequence x) of
Nothing ->
""
Just rgf ->
"BC:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_barcode_sequence_value rgf
)
sam_v1_6_read_group_sequencing_center_tos x = case (sam_v1_6_read_group_sequencing_center x) of
Nothing ->
""
Just rgf ->
"CN:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_sequencing_center_value rgf
)
sam_v1_6_read_group_description_tos x = case (sam_v1_6_read_group_description x) of
Nothing ->
""
Just rgf ->
"DS:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_description_value rgf
)
sam_v1_6_read_group_run_date_tos x = case (sam_v1_6_read_group_run_date x) of
Nothing ->
""
Just rgf ->
"DT:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_run_date_value rgf
)
sam_v1_6_read_group_flow_order_tos x = case (sam_v1_6_read_group_flow_order x) of
Nothing ->
""
Just rgf ->
"FO:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_flow_order_value rgf
)
sam_v1_6_read_group_key_sequence_tos x = case (sam_v1_6_read_group_key_sequence x) of
Nothing ->
""
Just rgf ->
"KS:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_key_sequence_value rgf
)
sam_v1_6_read_group_library_tos x = case (sam_v1_6_read_group_library x) of
Nothing ->
""
Just rgf ->
"LB:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_library_value rgf
)
sam_v1_6_read_group_programs_tos x = case (sam_v1_6_read_group_programs x) of
Nothing ->
""
Just rgf ->
"PG:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_programs_value rgf
)
sam_v1_6_read_group_predicted_median_insert_size_tos x = case (sam_v1_6_read_group_predicted_median_insert_size x) of
Nothing ->
""
Just rgf ->
"PI:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_predicted_median_insert_size_value rgf
)
sam_v1_6_read_group_platform_tos x = case (sam_v1_6_read_group_platform x) of
Nothing ->
""
Just rgf ->
"PL:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_platform_value rgf
)
sam_v1_6_read_group_platform_model_tos x = case (sam_v1_6_read_group_platform_model x) of
Nothing ->
""
Just rgf ->
"PM:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_platform_model_value rgf
)
sam_v1_6_read_group_platform_unit_tos x = case (sam_v1_6_read_group_platform_unit x) of
Nothing ->
""
Just rgf ->
"PU:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_platform_unit_value rgf
)
sam_v1_6_read_group_sample_tos x = case (sam_v1_6_read_group_sample x) of
Nothing ->
""
Just rgf ->
"SM:" ++
( unpack $
fromStrict $
sam_v1_6_read_group_sample_value rgf
)
sam_v1_6_read_group_tos = case (sam_v1_6_read_group samv16) of
Nothing ->
""
Just rgf ->
intercalate "\n" $
map (\x -> intercalate "\t" $
Prelude.filter (not . Prelude.null)
[ "@RG"
, sam_v1_6_read_group_identifer_tos x
, sam_v1_6_read_group_barcode_sequence_tos x
, sam_v1_6_read_group_sequencing_center_tos x
, sam_v1_6_read_group_description_tos x
, sam_v1_6_read_group_run_date_tos x
, sam_v1_6_read_group_flow_order_tos x
, sam_v1_6_read_group_key_sequence_tos x
, sam_v1_6_read_group_library_tos x
, sam_v1_6_read_group_programs_tos x
, sam_v1_6_read_group_predicted_median_insert_size_tos x
, sam_v1_6_read_group_platform_tos x
, sam_v1_6_read_group_platform_model_tos x
, sam_v1_6_read_group_platform_unit_tos x
, sam_v1_6_read_group_sample_tos x
]
) (toList rgf)
sam_v1_6_program_record_identifier_tos x = "ID:" ++
( unpack $
fromStrict $
sam_v1_6_program_record_identifier_value $
sam_v1_6_program_record_identifier x
)
sam_v1_6_program_name_tos x = case (sam_v1_6_program_name x) of
Nothing ->
""
Just rgf ->
"PN:" ++
( unpack $
fromStrict $
sam_v1_6_program_name_value rgf
)
sam_v1_6_program_command_line_tos x = case (sam_v1_6_program_command_line x) of
Nothing ->
""
Just rgf ->
"CL:" ++
( unpack $
fromStrict $
sam_v1_6_program_command_line_value rgf
)
sam_v1_6_program_previous_pg_id_tos x = case (sam_v1_6_program_previous_pg_id x) of
Nothing ->
""
Just rgf ->
"PP:" ++
( unpack $
fromStrict $
sam_v1_6_program_previous_pg_id_value rgf
)
sam_v1_6_program_description_tos x = case (sam_v1_6_program_description x) of
Nothing ->
""
Just rgf ->
"DS:" ++
( unpack $
fromStrict $
sam_v1_6_program_description_value rgf
)
sam_v1_6_program_version_tos x = case (sam_v1_6_program_version x) of
Nothing ->
""
Just rgf ->
"VN:" ++
( unpack $
fromStrict $
sam_v1_6_program_version_value rgf
)
sam_v1_6_program_tos = case (sam_v1_6_program samv16) of
Nothing ->
""
Just pgf ->
intercalate "\t" $
Prelude.filter (not . Prelude.null)
[ "@PG"
, sam_v1_6_program_record_identifier_tos pgf
, sam_v1_6_program_name_tos pgf
, sam_v1_6_program_command_line_tos pgf
, sam_v1_6_program_previous_pg_id_tos pgf
, sam_v1_6_program_description_tos pgf
, sam_v1_6_program_version_tos pgf
]
sam_v1_6_one_line_comment_tos = case (sam_v1_6_one_line_comment samv16) of
Nothing ->
""
Just cof ->
intercalate "\n" $
map (\x -> intercalate "\t" $
Prelude.filter (not . Prelude.null)
[ "@CO"
, unpack $
fromStrict $
sam_v1_6_one_line_comment_value x
]
) (toList cof)
sam_v1_6_alignment_tos = intercalate "\n" $
map (\x -> case (Prelude.null $ sam_v1_6_alignment_opts x) of
True ->
sam_v1_6_alignment_mand x
False ->
intercalate "\t"
[ sam_v1_6_alignment_mand x
, sam_v1_6_alignment_opts x
]
) ( toList $
sam_v1_6_alignment samv16
)
sam_v1_6_alignment_mand x = intercalate "\t" $
Prelude.filter (not . Prelude.null)
[ unpack $ fromStrict $ sam_v1_6_alignment_qname x
, show $ sam_v1_6_alignment_flag x
, unpack $ fromStrict $ sam_v1_6_alignment_rname x
, show $ sam_v1_6_alignment_pos x
, show $ sam_v1_6_alignment_mapq x
, unpack $ fromStrict $ sam_v1_6_alignment_cigar x
, unpack $ fromStrict $ sam_v1_6_alignment_rnext x
, show $ sam_v1_6_alignment_pnext x
, show $ sam_v1_6_alignment_tlen x
, unpack $ fromStrict $ sam_v1_6_alignment_seq x
, unpack $ fromStrict $ sam_v1_6_alignment_qual x
]
--sam_v1_6_alignment_opts x = intercalate "\t" $
-- Prelude.filter (not . Prelude.null)
-- [ sam_v1_6_alignment_aopt_d x
-- , sam_v1_6_alignment_iopt_d x
-- , sam_v1_6_alignment_fopt_d x
-- , sam_v1_6_alignment_zopt_d x
-- , sam_v1_6_alignment_hopt_d x
-- , sam_v1_6_alignment_bopt_d x
-- ]
sam_v1_6_alignment_opts x = case (sam_v1_6_alignment_optionalfields x) of
Nothing ->
""
Just optionalfields ->
concat $ forM (toList optionalfields) $ \currentoptionalfield ->
intercalate "\t" $
Prelude.filter (not . Prelude.null)
[ case (sam_v1_6_alignment_optionalfields_aopt currentoptionalfield) of
Nothing ->
""
Just aopt ->
( unpack $
fromStrict $
sam_v1_6_alignment_optionalfields_aopt_tag aopt
)
++
":A:"
++
( unpack $
fromStrict $
sam_v1_6_alignment_optionalfields_aopt_value aopt
)
, case (sam_v1_6_alignment_optionalfields_iopt currentoptionalfield) of
Nothing ->
""
Just iopt ->
( unpack $
fromStrict $
sam_v1_6_alignment_optionalfields_iopt_tag iopt
)
++
":i:"
++
( show $
sam_v1_6_alignment_optionalfields_iopt_value iopt
)
, case (sam_v1_6_alignment_optionalfields_fopt currentoptionalfield) of
Nothing ->
""
Just fopt ->
( unpack $
fromStrict $
sam_v1_6_alignment_optionalfields_fopt_tag fopt
)
++
":f:"
++
( show $
sam_v1_6_alignment_optionalfields_fopt_value fopt
)
, case (sam_v1_6_alignment_optionalfields_zopt currentoptionalfield) of
Nothing ->
""
Just zopt ->
( unpack $
fromStrict $
sam_v1_6_alignment_optionalfields_zopt_tag zopt
)
++
":Z:"
++
( unpack $
fromStrict $
sam_v1_6_alignment_optionalfields_zopt_value zopt
)
, case (sam_v1_6_alignment_optionalfields_hopt currentoptionalfield) of
Nothing ->
""
Just hopt ->
( unpack $
fromStrict $
sam_v1_6_alignment_optionalfields_hopt_tag hopt
)
++
":H:"
++
( unpack $
fromStrict $
sam_v1_6_alignment_optionalfields_hopt_value hopt
)
, case (sam_v1_6_alignment_optionalfields_bopt currentoptionalfield) of
Nothing ->
""
Just bopt ->
concat $
Prelude.filter (not . Prelude.null)
[ case (sam_v1_6_alignment_optionalfields_bopt_int8 bopt) of
Nothing ->
""
Just bopt_int8 ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_optionalfields_bopt_int8_tag bopt_int8
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_optionalfields_bopt_int8_type bopt_int8
) ++
"," ++
( concat $
map show $
toList $
sam_v1_6_alignment_optionalfields_bopt_int8_value bopt_int8
)
, case (sam_v1_6_alignment_optionalfields_bopt_word8 bopt) of
Nothing ->
""
Just bopt_word8 ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_optionalfields_bopt_word8_tag bopt_word8
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_optionalfields_bopt_word8_type bopt_word8
) ++
"," ++
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_optionalfields_bopt_word8_value bopt_word8
)
, case (sam_v1_6_alignment_optionalfields_bopt_int16 bopt) of
Nothing ->
""
Just bopt_int16 ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_optionalfields_bopt_int16_tag bopt_int16
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_optionalfields_bopt_int16_type bopt_int16
) ++
"," ++
( concat $
map show $
toList $
sam_v1_6_alignment_optionalfields_bopt_int16_value bopt_int16
)
, case (sam_v1_6_alignment_optionalfields_bopt_word16 bopt) of
Nothing ->
""
Just bopt_word16 ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_optionalfields_bopt_word16_tag bopt_word16
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_optionalfields_bopt_word16_type bopt_word16
) ++
"," ++
( concat $
map encodeWord16 $
toList $
sam_v1_6_alignment_optionalfields_bopt_word16_value bopt_word16
)
, case (sam_v1_6_alignment_optionalfields_bopt_int32 bopt) of
Nothing ->
""
Just bopt_int32 ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_optionalfields_bopt_int32_tag bopt_int32
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_optionalfields_bopt_int32_type bopt_int32
) ++
"," ++
( concat $
map show $
toList $
sam_v1_6_alignment_optionalfields_bopt_int32_value bopt_int32
)
, case (sam_v1_6_alignment_optionalfields_bopt_word32 bopt) of
Nothing ->
""
Just bopt_word32 ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_optionalfields_bopt_word32_tag bopt_word32
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_optionalfields_bopt_word32_type bopt_word32
) ++
"," ++
( concat $
map encodeWord32 $
toList $
sam_v1_6_alignment_optionalfields_bopt_word32_value bopt_word32
)
, case (sam_v1_6_alignment_optionalfields_bopt_float bopt) of
Nothing ->
""
Just bopt_float ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_optionalfields_bopt_float_tag bopt_float
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_optionalfields_bopt_float_type bopt_float
) ++
"," ++
( concat $
map show $
toList $
sam_v1_6_alignment_optionalfields_bopt_float_value bopt_float
)
]
]
{-
sam_v1_6_alignment_aopt_d x = ( unpack $
fromStrict $
sam_v1_6_alignment_aopt_tag aopt
)
++
":A:"
++
( unpack $
fromStrict $
sam_v1_6_alignment_aopt_value aopt
)
sam_v1_6_alignment_iopt_d x = case (sam_v1_6_alignment_iopt x) of
Nothing ->
""
Just iopt ->
( unpack $
fromStrict $
sam_v1_6_alignment_iopt_tag iopt
)
++
":i:"
++
( show $
sam_v1_6_alignment_iopt_value iopt
)
sam_v1_6_alignment_fopt_d x = case (sam_v1_6_alignment_fopt x) of
Nothing ->
""
Just fopt ->
( unpack $
fromStrict $
sam_v1_6_alignment_fopt_tag fopt
)
++
":f:"
++
( show $
sam_v1_6_alignment_fopt_value fopt
)
sam_v1_6_alignment_zopt_d x = case (sam_v1_6_alignment_zopt x) of
Nothing ->
""
Just zopt ->
( unpack $
fromStrict $
sam_v1_6_alignment_zopt_tag zopt
)
++
":Z:"
++
( unpack $
fromStrict $
sam_v1_6_alignment_zopt_value zopt
)
sam_v1_6_alignment_hopt_d x = case (sam_v1_6_alignment_hopt x) of
Nothing ->
""
Just hopt ->
( unpack $
fromStrict $
sam_v1_6_alignment_hopt_tag hopt
)
++
":H:"
++
( unpack $
fromStrict $
sam_v1_6_alignment_hopt_value hopt
)
sam_v1_6_alignment_bopt_d x = case (sam_v1_6_alignment_bopt x) of
Nothing ->
""
Just bopt ->
concat $
Prelude.filter (not . Prelude.null)
[ sam_v1_6_alignment_bopt_int8_d bopt
, sam_v1_6_alignment_bopt_word8_d bopt
, sam_v1_6_alignment_bopt_int16_d bopt
, sam_v1_6_alignment_bopt_word16_d bopt
, sam_v1_6_alignment_bopt_int32_d bopt
, sam_v1_6_alignment_bopt_word32_d bopt
, sam_v1_6_alignment_bopt_float_d bopt
]
sam_v1_6_alignment_bopt_int8_d x = case (sam_v1_6_alignment_bopt_int8 x) of
Nothing ->
""
Just bopt_int8 ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_bopt_int8_tag bopt_int8
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_bopt_int8_type bopt_int8
) ++
"," ++
( concat $
map show $
toList $
sam_v1_6_alignment_bopt_int8_value bopt_int8
)
sam_v1_6_alignment_bopt_word8_d x = case (sam_v1_6_alignment_bopt_word8 x) of
Nothing ->
""
Just bopt_word8 ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_bopt_word8_tag bopt_word8
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_bopt_word8_type bopt_word8
) ++
"," ++
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_bopt_word8_value bopt_word8
)
sam_v1_6_alignment_bopt_int16_d x = case (sam_v1_6_alignment_bopt_int16 x) of
Nothing ->
""
Just bopt_int16 ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_bopt_int16_tag bopt_int16
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_bopt_int16_type bopt_int16
) ++
"," ++
( concat $
map show $
toList $
sam_v1_6_alignment_bopt_int16_value bopt_int16
)
sam_v1_6_alignment_bopt_word16_d x = case (sam_v1_6_alignment_bopt_word16 x) of
Nothing ->
""
Just bopt_word16 ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_bopt_word16_tag bopt_word16
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_bopt_word16_type bopt_word16
) ++
"," ++
( concat $
map encodeWord16 $
toList $
sam_v1_6_alignment_bopt_word16_value bopt_word16
)
sam_v1_6_alignment_bopt_int32_d x = case (sam_v1_6_alignment_bopt_int32 x) of
Nothing ->
""
Just bopt_int32 ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_bopt_int32_tag bopt_int32
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_bopt_int32_type bopt_int32
) ++
"," ++
( concat $
map show $
toList $
sam_v1_6_alignment_bopt_int32_value bopt_int32
)
sam_v1_6_alignment_bopt_word32_d x = case (sam_v1_6_alignment_bopt_word32 x) of
Nothing ->
""
Just bopt_word32 ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_bopt_word32_tag bopt_word32
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_bopt_word32_type bopt_word32
) ++
"," ++
( concat $
map encodeWord32 $
toList $
sam_v1_6_alignment_bopt_word32_value bopt_word32
)
sam_v1_6_alignment_bopt_float_d x = case (sam_v1_6_alignment_bopt_float x) of
Nothing ->
""
Just bopt_float ->
( unpack $
fromStrict $
pack $
toList $
sam_v1_6_alignment_bopt_float_tag bopt_float
) ++
":" ++
"B" ++
":" ++
( unpack $
fromStrict $
DB.singleton $
sam_v1_6_alignment_bopt_float_type bopt_float
) ++
"," ++
( concat $
map show $
toList $
sam_v1_6_alignment_bopt_float_value bopt_float
)
-}
encodeWord16 :: Word16
-> [Char]
encodeWord16 = unpack .
DBL.filter (\x -> x /= 0) .
toLazyByteString .
word16LE
encodeWord32 :: Word32
-> [Char]
encodeWord32 = unpack .
DBL.filter (\x -> x /= 0) .
toLazyByteString .
word32LE
-- | Write @"SAM_V1_6"@ to a file.
-- Calls deconstructSAM_V1_6.
hPutSAM_V1_6 :: Handle
-> SAM_V1_6
-> IO ()
hPutSAM_V1_6 h samv16 = System.IO.hPutStr h
(deconstructSAM_V1_6 samv16)
-- | Write a @"SAM_V1_6"@ to a file.
--
-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.
writeSAM_V1_6 :: FilePath -- ^ Output path to SAM file.
-> SAM_V1_6
-> IO ()
writeSAM_V1_6 fp samv16 = do
h <- openFile fp
WriteMode
hPutSAM_V1_6 h
samv16
hFlush h
hClose h