diff --git a/CHANGELOG.md b/CHANGELOG.md --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -64,3 +64,11 @@ ## 0.5.0.3 -- 2023-09-01 * Added homepage and bug-reports fields to cabal file. + +## 0.5.0.4 -- 2023-09-01 + +* Added small initial test suite. + +## 0.6.0.0 -- 2023-09-04 + +* Removed tag section of headers and changed those affected from data to newtypes. diff --git a/hs-samtools.cabal b/hs-samtools.cabal --- a/hs-samtools.cabal +++ b/hs-samtools.cabal @@ -20,7 +20,7 @@ -- PVP summary: +-+------- breaking API changes -- | | +----- non-breaking API additions -- | | | +--- code changes with no API change -version: 0.5.0.3 +version: 0.6.0.0 -- A short (one-line) description of the package. synopsis: Read and write SAM, BAM, and CRAM files. @@ -176,4 +176,5 @@ -- Test dependencies. build-depends: base ^>=4.17.1.0, + hspec == 2.11.4, hs-samtools diff --git a/src/Data/SAM/Version1_6/Alignment/BOPT.hs b/src/Data/SAM/Version1_6/Alignment/BOPT.hs --- a/src/Data/SAM/Version1_6/Alignment/BOPT.hs +++ b/src/Data/SAM/Version1_6/Alignment/BOPT.hs @@ -269,10 +269,10 @@ value ) = "SAM_V1_6_Alignment_BOPT_Float { " ++ - "tag = " ++ - (show tag) ++ - " , type = " ++ - (show bopttype) ++ - " , value = " ++ - (show value) ++ + "tag = " ++ + (show tag) ++ + " , type = " ++ + (show bopttype) ++ + " , value = " ++ + (show value) ++ " }" diff --git a/src/Data/SAM/Version1_6/Header/CO.hs b/src/Data/SAM/Version1_6/Header/CO.hs --- a/src/Data/SAM/Version1_6/Header/CO.hs +++ b/src/Data/SAM/Version1_6/Header/CO.hs @@ -33,8 +33,8 @@ -- | Custom SAM (version 1.6) @"SAM_V1_6_One_Line_Comment"@ data type. -- -- See section 1.3 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. -data SAM_V1_6_One_Line_Comment = SAM_V1_6_One_Line_Comment { sam_v1_6_one_line_comment_value :: ByteString - } +newtype SAM_V1_6_One_Line_Comment = SAM_V1_6_One_Line_Comment { sam_v1_6_one_line_comment_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_One_Line_Comment where @@ -42,6 +42,6 @@ instance Show SAM_V1_6_One_Line_Comment where show (SAM_V1_6_One_Line_Comment value) = "SAM_V1_6_One_Line_Comment { " ++ - "value = " ++ - (show value) ++ - " }" + "value = " ++ + (show value) ++ + " }" diff --git a/src/Data/SAM/Version1_6/Header/HD.hs b/src/Data/SAM/Version1_6/Header/HD.hs --- a/src/Data/SAM/Version1_6/Header/HD.hs +++ b/src/Data/SAM/Version1_6/Header/HD.hs @@ -33,8 +33,6 @@ import Data.ByteString import Data.Data -import Data.Sequence -import Data.Word import Generics.Deriving.Base -- | Custom SAM (version 1.6) @"SAM_V1_6_File_Level_Metadata"@ data type. @@ -61,73 +59,61 @@ " }" -- | VN tag for @"SAM_V1_6_File_Level_Metadata"@. -data SAM_V1_6_File_Level_Metadata_Format_Version = SAM_V1_6_File_Level_Metadata_Format_Version { sam_v1_6_file_level_metadata_format_version_tag :: Seq Word8 - , sam_v1_6_file_level_metadata_format_version_value :: ByteString - } +newtype SAM_V1_6_File_Level_Metadata_Format_Version = SAM_V1_6_File_Level_Metadata_Format_Version { sam_v1_6_file_level_metadata_format_version_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_File_Level_Metadata_Format_Version where - SAM_V1_6_File_Level_Metadata_Format_Version sam_v1_6_file_level_metadata_format_version_tag1 sam_v1_6_file_level_metadata_format_version_value1 == SAM_V1_6_File_Level_Metadata_Format_Version sam_v1_6_file_level_metadata_format_version_tag2 sam_v1_6_file_level_metadata_format_version_value2 = sam_v1_6_file_level_metadata_format_version_tag1 == sam_v1_6_file_level_metadata_format_version_tag2 && sam_v1_6_file_level_metadata_format_version_value1 == sam_v1_6_file_level_metadata_format_version_value2 + SAM_V1_6_File_Level_Metadata_Format_Version sam_v1_6_file_level_metadata_format_version_value1 == SAM_V1_6_File_Level_Metadata_Format_Version sam_v1_6_file_level_metadata_format_version_value2 = sam_v1_6_file_level_metadata_format_version_value1 == sam_v1_6_file_level_metadata_format_version_value2 instance Show SAM_V1_6_File_Level_Metadata_Format_Version where - show (SAM_V1_6_File_Level_Metadata_Format_Version tag value) = + show (SAM_V1_6_File_Level_Metadata_Format_Version value) = "SAM_V1_6_File_Level_Metadata_Format_Version { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | SO tag for @"SAM_V1_6_File_Level_Metadata"@. -data SAM_V1_6_File_Level_Metadata_Sorting_Order = SAM_V1_6_File_Level_Metadata_Sorting_Order { sam_v1_6_file_level_metadata_sorting_order_tag :: Seq Word8 - , sam_v1_6_file_level_metadata_sorting_order_value :: ByteString - } +newtype SAM_V1_6_File_Level_Metadata_Sorting_Order = SAM_V1_6_File_Level_Metadata_Sorting_Order { sam_v1_6_file_level_metadata_sorting_order_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_File_Level_Metadata_Sorting_Order where - SAM_V1_6_File_Level_Metadata_Sorting_Order sam_v1_6_file_level_metadata_sorting_order_tag1 sam_v1_6_file_level_metadata_sorting_order_value1 == SAM_V1_6_File_Level_Metadata_Sorting_Order sam_v1_6_file_level_metadata_sorting_order_tag2 sam_v1_6_file_level_metadata_sorting_order_value2 = sam_v1_6_file_level_metadata_sorting_order_tag1 == sam_v1_6_file_level_metadata_sorting_order_tag2 && sam_v1_6_file_level_metadata_sorting_order_value1 == sam_v1_6_file_level_metadata_sorting_order_value2 + SAM_V1_6_File_Level_Metadata_Sorting_Order sam_v1_6_file_level_metadata_sorting_order_value1 == SAM_V1_6_File_Level_Metadata_Sorting_Order sam_v1_6_file_level_metadata_sorting_order_value2 = sam_v1_6_file_level_metadata_sorting_order_value1 == sam_v1_6_file_level_metadata_sorting_order_value2 instance Show SAM_V1_6_File_Level_Metadata_Sorting_Order where - show (SAM_V1_6_File_Level_Metadata_Sorting_Order tag value) = + show (SAM_V1_6_File_Level_Metadata_Sorting_Order value) = "SAM_V1_6_File_Level_Metadata_Sorting_Order { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | GO tag for @"SAM_V1_6_File_Level_Metadata"@. -data SAM_V1_6_File_Level_Metadata_Alignment_Grouping = SAM_V1_6_File_Level_Metadata_Alignment_Grouping { sam_v1_6_file_level_metadata_alignment_grouping_tag :: Seq Word8 - , sam_v1_6_file_level_metadata_alignment_grouping_value :: ByteString - } +newtype SAM_V1_6_File_Level_Metadata_Alignment_Grouping = SAM_V1_6_File_Level_Metadata_Alignment_Grouping { sam_v1_6_file_level_metadata_alignment_grouping_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_File_Level_Metadata_Alignment_Grouping where - SAM_V1_6_File_Level_Metadata_Alignment_Grouping sam_v1_6_file_level_metadata_alignment_grouping_tag1 sam_v1_6_file_level_metadata_alignment_grouping_value1 == SAM_V1_6_File_Level_Metadata_Alignment_Grouping sam_v1_6_file_level_metadata_alignment_grouping_tag2 sam_v1_6_file_level_metadata_alignment_grouping_value2 = sam_v1_6_file_level_metadata_alignment_grouping_tag1 == sam_v1_6_file_level_metadata_alignment_grouping_tag2 && sam_v1_6_file_level_metadata_alignment_grouping_value1 == sam_v1_6_file_level_metadata_alignment_grouping_value2 + SAM_V1_6_File_Level_Metadata_Alignment_Grouping sam_v1_6_file_level_metadata_alignment_grouping_value1 == SAM_V1_6_File_Level_Metadata_Alignment_Grouping sam_v1_6_file_level_metadata_alignment_grouping_value2 = sam_v1_6_file_level_metadata_alignment_grouping_value1 == sam_v1_6_file_level_metadata_alignment_grouping_value2 instance Show SAM_V1_6_File_Level_Metadata_Alignment_Grouping where - show (SAM_V1_6_File_Level_Metadata_Alignment_Grouping tag value) = + show (SAM_V1_6_File_Level_Metadata_Alignment_Grouping value) = "SAM_V1_6_File_Level_Metadata_Alignment_Grouping { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | SS tag for @"SAM_V1_6_File_Level_Metadata"@. -data SAM_V1_6_File_Level_Metadata_SubSorting_Order = SAM_V1_6_File_Level_Metadata_SubSorting_Order { sam_v1_6_file_level_metadata_subsorting_order_tag :: Seq Word8 - , sam_v1_6_file_level_metadata_subsorting_order_value :: ByteString - } +newtype SAM_V1_6_File_Level_Metadata_SubSorting_Order = SAM_V1_6_File_Level_Metadata_SubSorting_Order { sam_v1_6_file_level_metadata_subsorting_order_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_File_Level_Metadata_SubSorting_Order where - SAM_V1_6_File_Level_Metadata_SubSorting_Order sam_v1_6_file_level_metadata_subsorting_order_tag1 sam_v1_6_file_level_metadata_subsorting_order_value1 == SAM_V1_6_File_Level_Metadata_SubSorting_Order sam_v1_6_file_level_metadata_subsorting_order_tag2 sam_v1_6_file_level_metadata_subsorting_order_value2 = sam_v1_6_file_level_metadata_subsorting_order_tag1 == sam_v1_6_file_level_metadata_subsorting_order_tag2 && sam_v1_6_file_level_metadata_subsorting_order_value1 == sam_v1_6_file_level_metadata_subsorting_order_value2 + SAM_V1_6_File_Level_Metadata_SubSorting_Order sam_v1_6_file_level_metadata_subsorting_order_value1 == SAM_V1_6_File_Level_Metadata_SubSorting_Order sam_v1_6_file_level_metadata_subsorting_order_value2 = sam_v1_6_file_level_metadata_subsorting_order_value1 == sam_v1_6_file_level_metadata_subsorting_order_value2 instance Show SAM_V1_6_File_Level_Metadata_SubSorting_Order where - show (SAM_V1_6_File_Level_Metadata_SubSorting_Order tag value) = + show (SAM_V1_6_File_Level_Metadata_SubSorting_Order value) = "SAM_V1_6_File_Level_Metadata_SubSorting_Order { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" diff --git a/src/Data/SAM/Version1_6/Header/PG.hs b/src/Data/SAM/Version1_6/Header/PG.hs --- a/src/Data/SAM/Version1_6/Header/PG.hs +++ b/src/Data/SAM/Version1_6/Header/PG.hs @@ -35,8 +35,6 @@ import Data.ByteString import Data.Data -import Data.Sequence -import Data.Word import Generics.Deriving.Base -- | Custom SAM (version 1.6) @"SAM_V1_6_Program"@ data type. @@ -69,109 +67,91 @@ " }" -- | ID tag for @"SAM_V1_6_Program"@. -data SAM_V1_6_Program_Record_Identifier = SAM_V1_6_Program_Record_Identifier { sam_v1_6_program_record_identifier_tag :: Seq Word8 - , sam_v1_6_program_record_identifier_value :: ByteString - } +newtype SAM_V1_6_Program_Record_Identifier = SAM_V1_6_Program_Record_Identifier { sam_v1_6_program_record_identifier_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Program_Record_Identifier where - SAM_V1_6_Program_Record_Identifier sam_v1_6_program_record_identifier_tag1 sam_v1_6_program_record_identifier_value1 == SAM_V1_6_Program_Record_Identifier sam_v1_6_program_record_identifier_tag2 sam_v1_6_program_record_identifier_value2 = sam_v1_6_program_record_identifier_tag1 == sam_v1_6_program_record_identifier_tag2 && sam_v1_6_program_record_identifier_value1 == sam_v1_6_program_record_identifier_value2 + SAM_V1_6_Program_Record_Identifier sam_v1_6_program_record_identifier_value1 == SAM_V1_6_Program_Record_Identifier sam_v1_6_program_record_identifier_value2 = sam_v1_6_program_record_identifier_value1 == sam_v1_6_program_record_identifier_value2 instance Show SAM_V1_6_Program_Record_Identifier where - show (SAM_V1_6_Program_Record_Identifier tag value) = + show (SAM_V1_6_Program_Record_Identifier value) = "SAM_V1_6_Program_Record_Identifier { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | PN tag for @"SAM_V1_6_Program"@. -data SAM_V1_6_Program_Name = SAM_V1_6_Program_Name { sam_v1_6_program_name_tag :: Seq Word8 - , sam_v1_6_program_name_value :: ByteString - } +newtype SAM_V1_6_Program_Name = SAM_V1_6_Program_Name { sam_v1_6_program_name_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Program_Name where - SAM_V1_6_Program_Name sam_v1_6_program_name_tag1 sam_v1_6_program_name_value1 == SAM_V1_6_Program_Name sam_v1_6_program_name_tag2 sam_v1_6_program_name_value2 = sam_v1_6_program_name_tag1 == sam_v1_6_program_name_tag2 && sam_v1_6_program_name_value1 == sam_v1_6_program_name_value2 + SAM_V1_6_Program_Name sam_v1_6_program_name_value1 == SAM_V1_6_Program_Name sam_v1_6_program_name_value2 = sam_v1_6_program_name_value1 == sam_v1_6_program_name_value2 instance Show SAM_V1_6_Program_Name where - show (SAM_V1_6_Program_Name tag value) = + show (SAM_V1_6_Program_Name value) = "SAM_V1_6_Program_Name { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | CL tag for @"SAM_V1_6_Program"@. -data SAM_V1_6_Program_Command_Line = SAM_V1_6_Program_Command_Line { sam_v1_6_program_command_line_tag :: Seq Word8 - , sam_v1_6_program_command_line_value :: ByteString - } +newtype SAM_V1_6_Program_Command_Line = SAM_V1_6_Program_Command_Line { sam_v1_6_program_command_line_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Program_Command_Line where - SAM_V1_6_Program_Command_Line sam_v1_6_program_command_line_tag1 sam_v1_6_program_command_line_value1 == SAM_V1_6_Program_Command_Line sam_v1_6_program_command_line_tag2 sam_v1_6_program_command_line_value2 = sam_v1_6_program_command_line_tag1 == sam_v1_6_program_command_line_tag2 && sam_v1_6_program_command_line_value1 == sam_v1_6_program_command_line_value2 + SAM_V1_6_Program_Command_Line sam_v1_6_program_command_line_value1 == SAM_V1_6_Program_Command_Line sam_v1_6_program_command_line_value2 = sam_v1_6_program_command_line_value1 == sam_v1_6_program_command_line_value2 instance Show SAM_V1_6_Program_Command_Line where - show (SAM_V1_6_Program_Command_Line tag value) = + show (SAM_V1_6_Program_Command_Line value) = "SAM_V1_6_Program_Command_Line { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | PP tag for @"SAM_V1_6_Program"@. -data SAM_V1_6_Program_Previous_PG_ID = SAM_V1_6_Program_Previous_PG_ID { sam_v1_6_program_previous_pg_id_tag :: Seq Word8 - , sam_v1_6_program_previous_pg_id_value :: ByteString - } +newtype SAM_V1_6_Program_Previous_PG_ID = SAM_V1_6_Program_Previous_PG_ID { sam_v1_6_program_previous_pg_id_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Program_Previous_PG_ID where - SAM_V1_6_Program_Previous_PG_ID sam_v1_6_program_previous_pg_id_tag1 sam_v1_6_program_previous_pg_id_value1 == SAM_V1_6_Program_Previous_PG_ID sam_v1_6_program_previous_pg_id_tag2 sam_v1_6_program_previous_pg_id_value2 = sam_v1_6_program_previous_pg_id_tag1 == sam_v1_6_program_previous_pg_id_tag2 && sam_v1_6_program_previous_pg_id_value1 == sam_v1_6_program_previous_pg_id_value2 + SAM_V1_6_Program_Previous_PG_ID sam_v1_6_program_previous_pg_id_value1 == SAM_V1_6_Program_Previous_PG_ID sam_v1_6_program_previous_pg_id_value2 = sam_v1_6_program_previous_pg_id_value1 == sam_v1_6_program_previous_pg_id_value2 instance Show SAM_V1_6_Program_Previous_PG_ID where - show (SAM_V1_6_Program_Previous_PG_ID tag value) = + show (SAM_V1_6_Program_Previous_PG_ID value) = "SAM_V1_6_Program_Previous_PG_ID { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | DS tag for @"SAM_V1_6_Program"@. -data SAM_V1_6_Program_Description = SAM_V1_6_Program_Description { sam_v1_6_program_description_tag :: Seq Word8 - , sam_v1_6_program_description_value :: ByteString - } +newtype SAM_V1_6_Program_Description = SAM_V1_6_Program_Description { sam_v1_6_program_description_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Program_Description where - SAM_V1_6_Program_Description sam_v1_6_program_description_tag1 sam_v1_6_program_description_value1 == SAM_V1_6_Program_Description sam_v1_6_program_description_tag2 sam_v1_6_program_description_value2 = sam_v1_6_program_description_tag1 == sam_v1_6_program_description_tag2 && sam_v1_6_program_description_value1 == sam_v1_6_program_description_value2 + SAM_V1_6_Program_Description sam_v1_6_program_description_value1 == SAM_V1_6_Program_Description sam_v1_6_program_description_value2 = sam_v1_6_program_description_value1 == sam_v1_6_program_description_value2 instance Show SAM_V1_6_Program_Description where - show (SAM_V1_6_Program_Description tag value) = + show (SAM_V1_6_Program_Description value) = "SAM_V1_6_Program_Description { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | VN tag for @"SAM_V1_6_Program"@. -data SAM_V1_6_Program_Version = SAM_V1_6_Program_Version { sam_v1_6_program_version_tag :: Seq Word8 - , sam_v1_6_program_version_value :: ByteString - } +newtype SAM_V1_6_Program_Version = SAM_V1_6_Program_Version { sam_v1_6_program_version_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Program_Version where - SAM_V1_6_Program_Version sam_v1_6_program_version_tag1 sam_v1_6_program_version_value1 == SAM_V1_6_Program_Version sam_v1_6_program_version_tag2 sam_v1_6_program_version_value2 = sam_v1_6_program_version_tag1 == sam_v1_6_program_version_tag2 && sam_v1_6_program_version_value1 == sam_v1_6_program_version_value2 + SAM_V1_6_Program_Version sam_v1_6_program_version_value1 == SAM_V1_6_Program_Version sam_v1_6_program_version_value2 = sam_v1_6_program_version_value1 == sam_v1_6_program_version_value2 instance Show SAM_V1_6_Program_Version where - show (SAM_V1_6_Program_Version tag value) = + show (SAM_V1_6_Program_Version value) = "SAM_V1_6_Program_Version { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" diff --git a/src/Data/SAM/Version1_6/Header/RG.hs b/src/Data/SAM/Version1_6/Header/RG.hs --- a/src/Data/SAM/Version1_6/Header/RG.hs +++ b/src/Data/SAM/Version1_6/Header/RG.hs @@ -43,8 +43,6 @@ import Data.ByteString import Data.Data -import Data.Sequence -import Data.Word import Generics.Deriving.Base -- | Custom SAM (version 1.6) @"SAM_V1_6_Read_Group"@ data type. @@ -114,253 +112,211 @@ " }" -- | ID tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Identifier = SAM_V1_6_Read_Group_Identifier { sam_v1_6_read_group_identifier_tag :: Seq Word8 - , sam_v1_6_read_group_identifier_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Identifier = SAM_V1_6_Read_Group_Identifier { sam_v1_6_read_group_identifier_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Identifier where - SAM_V1_6_Read_Group_Identifier sam_v1_6_read_group_identifier_tag1 sam_v1_6_read_group_identifier_value1 == SAM_V1_6_Read_Group_Identifier sam_v1_6_read_group_identifier_tag2 sam_v1_6_read_group_identifier_value2 = sam_v1_6_read_group_identifier_tag1 == sam_v1_6_read_group_identifier_tag2 && sam_v1_6_read_group_identifier_value1 == sam_v1_6_read_group_identifier_value2 + SAM_V1_6_Read_Group_Identifier sam_v1_6_read_group_identifier_value1 == SAM_V1_6_Read_Group_Identifier sam_v1_6_read_group_identifier_value2 = sam_v1_6_read_group_identifier_value1 == sam_v1_6_read_group_identifier_value2 instance Show SAM_V1_6_Read_Group_Identifier where - show (SAM_V1_6_Read_Group_Identifier tag value) = + show (SAM_V1_6_Read_Group_Identifier value) = "SAM_V1_6_Read_Group_Identifier { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | BC tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Barcode_Sequence = SAM_V1_6_Read_Group_Barcode_Sequence { sam_v1_6_read_group_barcode_sequence_tag :: Seq Word8 - , sam_v1_6_read_group_barcode_sequence_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Barcode_Sequence = SAM_V1_6_Read_Group_Barcode_Sequence { sam_v1_6_read_group_barcode_sequence_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Barcode_Sequence where - SAM_V1_6_Read_Group_Barcode_Sequence sam_v1_6_read_group_barcode_sequence_tag1 sam_v1_6_read_group_barcode_sequence_value1 == SAM_V1_6_Read_Group_Barcode_Sequence sam_v1_6_read_group_barcode_sequence_tag2 sam_v1_6_read_group_barcode_sequence_value2 = sam_v1_6_read_group_barcode_sequence_tag1 == sam_v1_6_read_group_barcode_sequence_tag2 && sam_v1_6_read_group_barcode_sequence_value1 == sam_v1_6_read_group_barcode_sequence_value2 + SAM_V1_6_Read_Group_Barcode_Sequence sam_v1_6_read_group_barcode_sequence_value1 == SAM_V1_6_Read_Group_Barcode_Sequence sam_v1_6_read_group_barcode_sequence_value2 = sam_v1_6_read_group_barcode_sequence_value1 == sam_v1_6_read_group_barcode_sequence_value2 instance Show SAM_V1_6_Read_Group_Barcode_Sequence where - show (SAM_V1_6_Read_Group_Barcode_Sequence tag value) = + show (SAM_V1_6_Read_Group_Barcode_Sequence value) = "SAM_V1_6_Read_Group_Barcode_Sequence { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | CN tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Sequencing_Center = SAM_V1_6_Read_Group_Sequencing_Center { sam_v1_6_read_group_sequencing_center_tag :: Seq Word8 - , sam_v1_6_read_group_sequencing_center_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Sequencing_Center = SAM_V1_6_Read_Group_Sequencing_Center { sam_v1_6_read_group_sequencing_center_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Sequencing_Center where - SAM_V1_6_Read_Group_Sequencing_Center sam_v1_6_read_group_sequencing_center_tag1 sam_v1_6_read_group_sequencing_center_value1 == SAM_V1_6_Read_Group_Sequencing_Center sam_v1_6_read_group_sequencing_center_tag2 sam_v1_6_read_group_sequencing_center_value2 = sam_v1_6_read_group_sequencing_center_tag1 == sam_v1_6_read_group_sequencing_center_tag2 && sam_v1_6_read_group_sequencing_center_value1 == sam_v1_6_read_group_sequencing_center_value2 + SAM_V1_6_Read_Group_Sequencing_Center sam_v1_6_read_group_sequencing_center_value1 == SAM_V1_6_Read_Group_Sequencing_Center sam_v1_6_read_group_sequencing_center_value2 = sam_v1_6_read_group_sequencing_center_value1 == sam_v1_6_read_group_sequencing_center_value2 instance Show SAM_V1_6_Read_Group_Sequencing_Center where - show (SAM_V1_6_Read_Group_Sequencing_Center tag value) = + show (SAM_V1_6_Read_Group_Sequencing_Center value) = "SAM_V1_6_Read_Group_Sequencing_Center { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | DS tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Description = SAM_V1_6_Read_Group_Description { sam_v1_6_read_group_description_tag :: Seq Word8 - , sam_v1_6_read_group_description_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Description = SAM_V1_6_Read_Group_Description { sam_v1_6_read_group_description_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Description where - SAM_V1_6_Read_Group_Description sam_v1_6_read_group_description_tag1 sam_v1_6_read_group_description_value1 == SAM_V1_6_Read_Group_Description sam_v1_6_read_group_description_tag2 sam_v1_6_read_group_description_value2 = sam_v1_6_read_group_description_tag1 == sam_v1_6_read_group_description_tag2 && sam_v1_6_read_group_description_value1 == sam_v1_6_read_group_description_value2 + SAM_V1_6_Read_Group_Description sam_v1_6_read_group_description_value1 == SAM_V1_6_Read_Group_Description sam_v1_6_read_group_description_value2 = sam_v1_6_read_group_description_value1 == sam_v1_6_read_group_description_value2 instance Show SAM_V1_6_Read_Group_Description where - show (SAM_V1_6_Read_Group_Description tag value) = + show (SAM_V1_6_Read_Group_Description value) = "SAM_V1_6_Read_Group_Description { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | DT tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Run_Date = SAM_V1_6_Read_Group_Run_Date { sam_v1_6_read_group_run_date_tag :: Seq Word8 - , sam_v1_6_read_group_run_date_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Run_Date = SAM_V1_6_Read_Group_Run_Date { sam_v1_6_read_group_run_date_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Run_Date where - SAM_V1_6_Read_Group_Run_Date sam_v1_6_read_group_run_date_tag1 sam_v1_6_read_group_run_date_value1 == SAM_V1_6_Read_Group_Run_Date sam_v1_6_read_group_run_date_tag2 sam_v1_6_read_group_run_date_value2 = sam_v1_6_read_group_run_date_tag1 == sam_v1_6_read_group_run_date_tag2 && sam_v1_6_read_group_run_date_value1 == sam_v1_6_read_group_run_date_value2 + SAM_V1_6_Read_Group_Run_Date sam_v1_6_read_group_run_date_value1 == SAM_V1_6_Read_Group_Run_Date sam_v1_6_read_group_run_date_value2 = sam_v1_6_read_group_run_date_value1 == sam_v1_6_read_group_run_date_value2 instance Show SAM_V1_6_Read_Group_Run_Date where - show (SAM_V1_6_Read_Group_Run_Date tag value) = + show (SAM_V1_6_Read_Group_Run_Date value) = "SAM_V1_6_Read_Group_Run_Date { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | FO tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Flow_Order = SAM_V1_6_Read_Group_Flow_Order { sam_v1_6_read_group_flow_order_tag :: Seq Word8 - , sam_v1_6_read_group_flow_order_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Flow_Order = SAM_V1_6_Read_Group_Flow_Order { sam_v1_6_read_group_flow_order_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Flow_Order where - SAM_V1_6_Read_Group_Flow_Order sam_v1_6_read_group_flow_order_tag1 sam_v1_6_one_line_comment_value1 == SAM_V1_6_Read_Group_Flow_Order sam_v1_6_read_group_flow_order_tag2 sam_v1_6_read_group_flow_order_value2 = sam_v1_6_read_group_flow_order_tag1 == sam_v1_6_read_group_flow_order_tag2 && sam_v1_6_one_line_comment_value1 == sam_v1_6_read_group_flow_order_value2 + SAM_V1_6_Read_Group_Flow_Order sam_v1_6_one_line_comment_value1 == SAM_V1_6_Read_Group_Flow_Order sam_v1_6_read_group_flow_order_value2 = sam_v1_6_one_line_comment_value1 == sam_v1_6_read_group_flow_order_value2 instance Show SAM_V1_6_Read_Group_Flow_Order where - show (SAM_V1_6_Read_Group_Flow_Order tag value) = + show (SAM_V1_6_Read_Group_Flow_Order value) = "SAM_V1_6_Read_Group_Flow_Order { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | KS tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Key_Sequence = SAM_V1_6_Read_Group_Key_Sequence { sam_v1_6_read_group_key_sequence_tag :: Seq Word8 - , sam_v1_6_read_group_key_sequence_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Key_Sequence = SAM_V1_6_Read_Group_Key_Sequence { sam_v1_6_read_group_key_sequence_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Key_Sequence where - SAM_V1_6_Read_Group_Key_Sequence sam_v1_6_read_group_key_sequence_tag1 sam_v1_6_read_group_key_sequence_value1 == SAM_V1_6_Read_Group_Key_Sequence sam_v1_6_read_group_key_sequence_tag2 sam_v1_6_read_group_key_sequence_value2 = sam_v1_6_read_group_key_sequence_tag1 == sam_v1_6_read_group_key_sequence_tag2 && sam_v1_6_read_group_key_sequence_value1 == sam_v1_6_read_group_key_sequence_value2 + SAM_V1_6_Read_Group_Key_Sequence sam_v1_6_read_group_key_sequence_value1 == SAM_V1_6_Read_Group_Key_Sequence sam_v1_6_read_group_key_sequence_value2 = sam_v1_6_read_group_key_sequence_value1 == sam_v1_6_read_group_key_sequence_value2 instance Show SAM_V1_6_Read_Group_Key_Sequence where - show (SAM_V1_6_Read_Group_Key_Sequence tag value) = + show (SAM_V1_6_Read_Group_Key_Sequence value) = "SAM_V1_6_Read_Group_Key_Sequence { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | LB tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Library = SAM_V1_6_Read_Group_Library { sam_v1_6_read_group_library_tag :: Seq Word8 - , sam_v1_6_read_group_library_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Library = SAM_V1_6_Read_Group_Library { sam_v1_6_read_group_library_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Library where - SAM_V1_6_Read_Group_Library sam_v1_6_read_group_library_tag1 sam_v1_6_read_group_library_value1 == SAM_V1_6_Read_Group_Library sam_v1_6_read_group_library_tag2 sam_v1_6_read_group_library_value2 = sam_v1_6_read_group_library_tag1 == sam_v1_6_read_group_library_tag2 && sam_v1_6_read_group_library_value1 == sam_v1_6_read_group_library_value2 + SAM_V1_6_Read_Group_Library sam_v1_6_read_group_library_value1 == SAM_V1_6_Read_Group_Library sam_v1_6_read_group_library_value2 = sam_v1_6_read_group_library_value1 == sam_v1_6_read_group_library_value2 instance Show SAM_V1_6_Read_Group_Library where - show (SAM_V1_6_Read_Group_Library tag value) = + show (SAM_V1_6_Read_Group_Library value) = "SAM_V1_6_Read_Group_Library { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | PG tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Programs = SAM_V1_6_Read_Group_Programs { sam_v1_6_read_group_programs_tag :: Seq Word8 - , sam_v1_6_read_group_programs_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Programs = SAM_V1_6_Read_Group_Programs { sam_v1_6_read_group_programs_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Programs where - SAM_V1_6_Read_Group_Programs sam_v1_6_read_group_programs_tag1 sam_v1_6_read_group_programs_value1 == SAM_V1_6_Read_Group_Programs sam_v1_6_read_group_programs_tag2 sam_v1_6_read_group_programs_value2 = sam_v1_6_read_group_programs_tag1 == sam_v1_6_read_group_programs_tag2 && sam_v1_6_read_group_programs_value1 == sam_v1_6_read_group_programs_value2 + SAM_V1_6_Read_Group_Programs sam_v1_6_read_group_programs_value1 == SAM_V1_6_Read_Group_Programs sam_v1_6_read_group_programs_value2 = sam_v1_6_read_group_programs_value1 == sam_v1_6_read_group_programs_value2 instance Show SAM_V1_6_Read_Group_Programs where - show (SAM_V1_6_Read_Group_Programs tag value) = + show (SAM_V1_6_Read_Group_Programs value) = "SAM_V1_6_Read_Group_Programs { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | PI tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Predicted_Median_Insert_Size = SAM_V1_6_Read_Group_Predicted_Median_Insert_Size { sam_v1_6_read_group_predicted_median_insert_size_tag :: Seq Word8 - , sam_v1_6_read_group_predicted_median_insert_size_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Predicted_Median_Insert_Size = SAM_V1_6_Read_Group_Predicted_Median_Insert_Size { sam_v1_6_read_group_predicted_median_insert_size_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Predicted_Median_Insert_Size where - SAM_V1_6_Read_Group_Predicted_Median_Insert_Size sam_v1_6_read_group_predicted_median_insert_size_tag1 sam_v1_6_one_line_comment_value1 == SAM_V1_6_Read_Group_Predicted_Median_Insert_Size sam_v1_6_read_group_predicted_median_insert_size_tag2 sam_v1_6_read_group_predicted_median_insert_size_value2 = sam_v1_6_read_group_predicted_median_insert_size_tag1 == sam_v1_6_read_group_predicted_median_insert_size_tag2 && sam_v1_6_one_line_comment_value1 == sam_v1_6_read_group_predicted_median_insert_size_value2 + SAM_V1_6_Read_Group_Predicted_Median_Insert_Size sam_v1_6_read_group_predicted_median_insert_size_value1 == SAM_V1_6_Read_Group_Predicted_Median_Insert_Size sam_v1_6_read_group_predicted_median_insert_size_value2 = sam_v1_6_read_group_predicted_median_insert_size_value1 == sam_v1_6_read_group_predicted_median_insert_size_value2 instance Show SAM_V1_6_Read_Group_Predicted_Median_Insert_Size where - show (SAM_V1_6_Read_Group_Predicted_Median_Insert_Size tag value) = + show (SAM_V1_6_Read_Group_Predicted_Median_Insert_Size value) = "SAM_V1_6_Read_Group_Predicted_Median_Insert_Size { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | PL tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Platform = SAM_V1_6_Read_Group_Platform { sam_v1_6_read_group_platform_tag :: Seq Word8 - , sam_v1_6_read_group_platform_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Platform = SAM_V1_6_Read_Group_Platform { sam_v1_6_read_group_platform_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Platform where - SAM_V1_6_Read_Group_Platform sam_v1_6_read_group_platform_tag1 sam_v1_6_read_group_platform_value1 == SAM_V1_6_Read_Group_Platform sam_v1_6_read_group_platform_tag2 sam_v1_6_read_group_platform_value2 = sam_v1_6_read_group_platform_tag1 == sam_v1_6_read_group_platform_tag2 && sam_v1_6_read_group_platform_value1 == sam_v1_6_read_group_platform_value2 + SAM_V1_6_Read_Group_Platform sam_v1_6_read_group_platform_value1 == SAM_V1_6_Read_Group_Platform sam_v1_6_read_group_platform_value2 = sam_v1_6_read_group_platform_value1 == sam_v1_6_read_group_platform_value2 instance Show SAM_V1_6_Read_Group_Platform where - show (SAM_V1_6_Read_Group_Platform tag value) = + show (SAM_V1_6_Read_Group_Platform value) = "SAM_V1_6_Read_Group_Platform { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | PM tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Platform_Model = SAM_V1_6_Read_Group_Platform_Model { sam_v1_6_read_group_platform_model_tag :: Seq Word8 - , sam_v1_6_read_group_platform_model_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Platform_Model = SAM_V1_6_Read_Group_Platform_Model { sam_v1_6_read_group_platform_model_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Platform_Model where - SAM_V1_6_Read_Group_Platform_Model sam_v1_6_read_group_platform_model_tag1 sam_v1_6_read_group_platform_model_value1 == SAM_V1_6_Read_Group_Platform_Model sam_v1_6_read_group_platform_model_tag2 sam_v1_6_read_group_platform_model_value2 = sam_v1_6_read_group_platform_model_tag1 == sam_v1_6_read_group_platform_model_tag2 && sam_v1_6_read_group_platform_model_value1 == sam_v1_6_read_group_platform_model_value2 + SAM_V1_6_Read_Group_Platform_Model sam_v1_6_read_group_platform_model_value1 == SAM_V1_6_Read_Group_Platform_Model sam_v1_6_read_group_platform_model_value2 = sam_v1_6_read_group_platform_model_value1 == sam_v1_6_read_group_platform_model_value2 instance Show SAM_V1_6_Read_Group_Platform_Model where - show (SAM_V1_6_Read_Group_Platform_Model tag value) = + show (SAM_V1_6_Read_Group_Platform_Model value) = "SAM_V1_6_Read_Group_Platform_Model { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | PU tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Platform_Unit = SAM_V1_6_Read_Group_Platform_Unit { sam_v1_6_read_group_platform_unit_tag :: Seq Word8 - , sam_v1_6_read_group_platform_unit_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Platform_Unit = SAM_V1_6_Read_Group_Platform_Unit { sam_v1_6_read_group_platform_unit_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Platform_Unit where - SAM_V1_6_Read_Group_Platform_Unit sam_v1_6_read_group_platform_unit_tag1 sam_v1_6_read_group_platform_unit_value1 == SAM_V1_6_Read_Group_Platform_Unit sam_v1_6_read_group_platform_unit_tag2 sam_v1_6_read_group_platform_unit_value2 = sam_v1_6_read_group_platform_unit_tag1 == sam_v1_6_read_group_platform_unit_tag2 && sam_v1_6_read_group_platform_unit_value1 == sam_v1_6_read_group_platform_unit_value2 + SAM_V1_6_Read_Group_Platform_Unit sam_v1_6_read_group_platform_unit_value1 == SAM_V1_6_Read_Group_Platform_Unit sam_v1_6_read_group_platform_unit_value2 = sam_v1_6_read_group_platform_unit_value1 == sam_v1_6_read_group_platform_unit_value2 instance Show SAM_V1_6_Read_Group_Platform_Unit where - show (SAM_V1_6_Read_Group_Platform_Unit tag value) = + show (SAM_V1_6_Read_Group_Platform_Unit value) = "SAM_V1_6_Read_Group_Platform_Unit { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | SM tag for @"SAM_V1_6_Read_Group"@. -data SAM_V1_6_Read_Group_Sample = SAM_V1_6_Read_Group_Sample { sam_v1_6_read_group_sample_tag :: Seq Word8 - , sam_v1_6_read_group_sample_value :: ByteString - } +newtype SAM_V1_6_Read_Group_Sample = SAM_V1_6_Read_Group_Sample { sam_v1_6_read_group_sample_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Read_Group_Sample where - SAM_V1_6_Read_Group_Sample sam_v1_6_read_group_sample_tag1 sam_v1_6_read_group_sample_value1 == SAM_V1_6_Read_Group_Sample sam_v1_6_read_group_sample_tag2 sam_v1_6_read_group_sample_value2 = sam_v1_6_read_group_sample_tag1 == sam_v1_6_read_group_sample_tag2 && sam_v1_6_read_group_sample_value1 == sam_v1_6_read_group_sample_value2 + SAM_V1_6_Read_Group_Sample sam_v1_6_read_group_sample_value1 == SAM_V1_6_Read_Group_Sample sam_v1_6_read_group_sample_value2 = sam_v1_6_read_group_sample_value1 == sam_v1_6_read_group_sample_value2 instance Show SAM_V1_6_Read_Group_Sample where - show (SAM_V1_6_Read_Group_Sample tag value) = + show (SAM_V1_6_Read_Group_Sample value) = "SAM_V1_6_Read_Group_Sample { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" diff --git a/src/Data/SAM/Version1_6/Header/SQ.hs b/src/Data/SAM/Version1_6/Header/SQ.hs --- a/src/Data/SAM/Version1_6/Header/SQ.hs +++ b/src/Data/SAM/Version1_6/Header/SQ.hs @@ -39,8 +39,6 @@ import Data.ByteString import Data.Data -import Data.Sequence -import Data.Word import Generics.Deriving.Base -- | Custom SAM (version 1.6) @"SAM_V1_6_Reference_Sequence_Dictionary"@ data type. @@ -95,177 +93,151 @@ " }" -- | SN tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@. -data SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name { sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag :: Seq Word8 - , sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value :: ByteString - } +newtype SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name { sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name where - SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag1 sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag2 sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value2 = sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag1 == sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag2 && sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value1 == sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value2 + SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value2 = sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value1 == sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value2 instance Show SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name where - show (SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name tag value) = + show (SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name value) = "SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | LN tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@. -data SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length { sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag :: Seq Word8 - , sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value :: ByteString - } +newtype SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length { sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length where - SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag1 sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag2 sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value2 = sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag1 == sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag2 && sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value1 == sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value2 + SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value2 = sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value1 == sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value2 instance Show SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length where - show (SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length tag value) = + show (SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length value) = "SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | AH tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@. -data SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus = SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus { sam_v1_6_reference_sequence_dictionary_alternative_locus_tag :: Seq Word8 - , sam_v1_6_reference_sequence_dictionary_alternative_locus_value :: ByteString - } +newtype SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus = SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus { sam_v1_6_reference_sequence_dictionary_alternative_locus_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus where - SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus sam_v1_6_reference_sequence_dictionary_alternative_locus_tag1 sam_v1_6_reference_sequence_dictionary_alternative_locus_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus sam_v1_6_reference_sequence_dictionary_alternative_locus_tag2 sam_v1_6_reference_sequence_dictionary_alternative_locus_value2 = sam_v1_6_reference_sequence_dictionary_alternative_locus_tag1 == sam_v1_6_reference_sequence_dictionary_alternative_locus_tag2 && sam_v1_6_reference_sequence_dictionary_alternative_locus_value1 == sam_v1_6_reference_sequence_dictionary_alternative_locus_value2 + SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus sam_v1_6_reference_sequence_dictionary_alternative_locus_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus sam_v1_6_reference_sequence_dictionary_alternative_locus_value2 = sam_v1_6_reference_sequence_dictionary_alternative_locus_value1 == sam_v1_6_reference_sequence_dictionary_alternative_locus_value2 instance Show SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus where - show (SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus tag value) = + show (SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus value) = "SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | AN tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@. -data SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names = SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names { sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tag :: Seq Word8 - , sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value :: ByteString - } +newtype SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names = SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names { sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names where - SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tag1 sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tag2 sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value2 = sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tag1 == sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tag2 && sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value1 == sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value2 + SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value2 = sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value1 == sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value2 instance Show SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names where - show (SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names tag value) = "SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ - (show value) ++ - " }" + show (SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names value) = + "SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names { " ++ + "value = " ++ + (show value) ++ + " }" -- | AS tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@. -data SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier = SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier { sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag :: Seq Word8 - , sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value :: ByteString - } +newtype SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier = SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier { sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier where - SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag1 sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag2 sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value2 = sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag1 == sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag2 && sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value1 == sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value2 + SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value2 = sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value1 == sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value2 instance Show SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier where - show (SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier tag value) = "SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ - (show value) ++ - " }" + show (SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier value) = + "SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier { " ++ + "value = " ++ + (show value) ++ + " }" -- | DS tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@. -data SAM_V1_6_Reference_Sequence_Dictionary_Description = SAM_V1_6_Reference_Sequence_Dictionary_Description { sam_v1_6_reference_sequence_dictionary_description_tag :: Seq Word8 - , sam_v1_6_reference_sequence_dictionary_description_value :: ByteString - } +newtype SAM_V1_6_Reference_Sequence_Dictionary_Description = SAM_V1_6_Reference_Sequence_Dictionary_Description { sam_v1_6_reference_sequence_dictionary_description_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Description where - SAM_V1_6_Reference_Sequence_Dictionary_Description sam_v1_6_reference_sequence_dictionary_description_tag1 sam_v1_6_reference_sequence_dictionary_description_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Description sam_v1_6_reference_sequence_dictionary_description_tag2 sam_v1_6_reference_sequence_dictionary_description_value2 = sam_v1_6_reference_sequence_dictionary_description_tag1 == sam_v1_6_reference_sequence_dictionary_description_tag2 && sam_v1_6_reference_sequence_dictionary_description_value1 == sam_v1_6_reference_sequence_dictionary_description_value2 + SAM_V1_6_Reference_Sequence_Dictionary_Description sam_v1_6_reference_sequence_dictionary_description_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Description sam_v1_6_reference_sequence_dictionary_description_value2 = sam_v1_6_reference_sequence_dictionary_description_value1 == sam_v1_6_reference_sequence_dictionary_description_value2 instance Show SAM_V1_6_Reference_Sequence_Dictionary_Description where - show (SAM_V1_6_Reference_Sequence_Dictionary_Description tag value) = "SAM_V1_6_Reference_Sequence_Dictionary_Description { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ - (show value) ++ - " }" + show (SAM_V1_6_Reference_Sequence_Dictionary_Description value) = + "SAM_V1_6_Reference_Sequence_Dictionary_Description { " ++ + "value = " ++ + (show value) ++ + " }" -- | M5 tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@. -data SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum = SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum { sam_v1_6_reference_sequence_dictionary_md5_checksum_tag :: Seq Word8 - , sam_v1_6_reference_sequence_dictionary_md5_checksum_value :: ByteString - } +newtype SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum = SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum { sam_v1_6_reference_sequence_dictionary_md5_checksum_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum where - SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum sam_v1_6_reference_sequence_dictionary_md5_checksum_tag1 sam_v1_6_reference_sequence_dictionary_md5_checksum_value1 == SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum sam_v1_6_reference_sequence_dictionary_md5_checksum_tag2 sam_v1_6_reference_sequence_dictionary_md5_checksum_value2 = sam_v1_6_reference_sequence_dictionary_md5_checksum_tag1 == sam_v1_6_reference_sequence_dictionary_md5_checksum_tag2 && sam_v1_6_reference_sequence_dictionary_md5_checksum_value1 == sam_v1_6_reference_sequence_dictionary_md5_checksum_value2 + SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum sam_v1_6_reference_sequence_dictionary_md5_checksum_value1 == SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum sam_v1_6_reference_sequence_dictionary_md5_checksum_value2 = sam_v1_6_reference_sequence_dictionary_md5_checksum_value1 == sam_v1_6_reference_sequence_dictionary_md5_checksum_value2 instance Show SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum where - show (SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum tag value) = "SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ - (show value) ++ - " }" + show (SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum value) = + "SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum { " ++ + "value = " ++ + (show value) ++ + " }" -- | SP tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@. -data SAM_V1_6_Reference_Sequence_Dictionary_Species = SAM_V1_6_Reference_Sequence_Dictionary_Species { sam_v1_6_reference_sequence_dictionary_species_tag :: Seq Word8 - , sam_v1_6_reference_sequence_dictionary_species_value :: ByteString - } +newtype SAM_V1_6_Reference_Sequence_Dictionary_Species = SAM_V1_6_Reference_Sequence_Dictionary_Species { sam_v1_6_reference_sequence_dictionary_species_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Species where - SAM_V1_6_Reference_Sequence_Dictionary_Species sam_v1_6_reference_sequence_dictionary_species_tag1 sam_v1_6_reference_sequence_dictionary_species_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Species sam_v1_6_reference_sequence_dictionary_species_tag2 sam_v1_6_reference_sequence_dictionary_species_value2 = sam_v1_6_reference_sequence_dictionary_species_tag1 == sam_v1_6_reference_sequence_dictionary_species_tag2 && sam_v1_6_reference_sequence_dictionary_species_value1 == sam_v1_6_reference_sequence_dictionary_species_value2 + SAM_V1_6_Reference_Sequence_Dictionary_Species sam_v1_6_reference_sequence_dictionary_species_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Species sam_v1_6_reference_sequence_dictionary_species_value2 = sam_v1_6_reference_sequence_dictionary_species_value1 == sam_v1_6_reference_sequence_dictionary_species_value2 instance Show SAM_V1_6_Reference_Sequence_Dictionary_Species where - show (SAM_V1_6_Reference_Sequence_Dictionary_Species tag value) = + show (SAM_V1_6_Reference_Sequence_Dictionary_Species value) = "SAM_V1_6_Reference_Sequence_Dictionary_Species { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | TP tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@. -data SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology = SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology { sam_v1_6_reference_sequence_dictionary_molecule_topology_tag :: Seq Word8 - , sam_v1_6_reference_sequence_dictionary_molecule_topology_value :: ByteString - } +newtype SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology = SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology { sam_v1_6_reference_sequence_dictionary_molecule_topology_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology where - SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology sam_v1_6_reference_sequence_dictionary_molecule_topology_tag1 sam_v1_6_reference_sequence_dictionary_molecule_topology_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology sam_v1_6_reference_sequence_dictionary_molecule_topology_tag2 sam_v1_6_reference_sequence_dictionary_molecule_topology_value2 = sam_v1_6_reference_sequence_dictionary_molecule_topology_tag1 == sam_v1_6_reference_sequence_dictionary_molecule_topology_tag2 && sam_v1_6_reference_sequence_dictionary_molecule_topology_value1 == sam_v1_6_reference_sequence_dictionary_molecule_topology_value2 + SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology sam_v1_6_reference_sequence_dictionary_molecule_topology_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology sam_v1_6_reference_sequence_dictionary_molecule_topology_value2 = sam_v1_6_reference_sequence_dictionary_molecule_topology_value1 == sam_v1_6_reference_sequence_dictionary_molecule_topology_value2 instance Show SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology where - show (SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology tag value) = + show (SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology value) = "SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" -- | UR tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@. -data SAM_V1_6_Reference_Sequence_Dictionary_URI = SAM_V1_6_Reference_Sequence_Dictionary_URI { sam_v1_6_reference_sequence_dictionary_uri_tag :: Seq Word8 - , sam_v1_6_reference_sequence_dictionary_uri_value :: ByteString - } +newtype SAM_V1_6_Reference_Sequence_Dictionary_URI = SAM_V1_6_Reference_Sequence_Dictionary_URI { sam_v1_6_reference_sequence_dictionary_uri_value :: ByteString + } deriving (Generic,Typeable) instance Eq SAM_V1_6_Reference_Sequence_Dictionary_URI where - SAM_V1_6_Reference_Sequence_Dictionary_URI sam_v1_6_reference_sequence_dictionary_uri_tag1 sam_v1_6_reference_sequence_dictionary_uri_value1 == SAM_V1_6_Reference_Sequence_Dictionary_URI sam_v1_6_reference_sequence_dictionary_uri_tag2 sam_v1_6_reference_sequence_dictionary_uri_value2 = sam_v1_6_reference_sequence_dictionary_uri_tag1 == sam_v1_6_reference_sequence_dictionary_uri_tag2 && sam_v1_6_reference_sequence_dictionary_uri_value1 == sam_v1_6_reference_sequence_dictionary_uri_value2 + SAM_V1_6_Reference_Sequence_Dictionary_URI sam_v1_6_reference_sequence_dictionary_uri_value1 == SAM_V1_6_Reference_Sequence_Dictionary_URI sam_v1_6_reference_sequence_dictionary_uri_value2 = sam_v1_6_reference_sequence_dictionary_uri_value1 == sam_v1_6_reference_sequence_dictionary_uri_value2 instance Show SAM_V1_6_Reference_Sequence_Dictionary_URI where - show (SAM_V1_6_Reference_Sequence_Dictionary_URI tag value) = + show (SAM_V1_6_Reference_Sequence_Dictionary_URI value) = "SAM_V1_6_Reference_Sequence_Dictionary_URI { " ++ - "tag = " ++ - (show tag) ++ - " , value = " ++ + "value = " ++ (show value) ++ " }" diff --git a/src/Data/SAM/Version1_6/Read/Parser/Alignment/Base.hs b/src/Data/SAM/Version1_6/Read/Parser/Alignment/Base.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Alignment/Base.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Alignment/Base.hs @@ -141,7 +141,7 @@ _ <- word8 09 qual <- do qualp <- DABL.takeTill (== 09) -- Parse QUAL field of the alignment section. - case (qualp =~ [re|[!-~]+|]) of + case (qualp =~ [re|[!-~?]+|\*|]) of False -> fail $ show SAM_V1_6_Error_Alignment_QUAL_Incorrect_Format True -> -- QUAL is in the accepted format. return qualp diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/HD/GO.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/GO.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/HD/GO.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/GO.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the GO tag of the @HD tag section of the SAM v1.6 file format. @@ -57,12 +55,12 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_File_Level_Metadata_GO :: Parser SAM_V1_6_File_Level_Metadata_Alignment_Grouping parse_SAM_V1_6_File_Level_Metadata_GO = do - hdheaderalignmentgroupingtag <- do hdheaderalignmentgroupingtagp <- DABL.takeTill (== 58) - -- Parse GO tag of the header section. - case (hdheaderalignmentgroupingtagp =~ [re|[G][O]|]) of - False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Grouping_Of_Alignments_Tag_Incorrect_Format - True -> -- GO tag is in the accepted format. - return hdheaderalignmentgroupingtagp + _ <- do hdheaderalignmentgroupingtagp <- DABL.takeTill (== 58) + -- Parse GO tag of the header section. + case (hdheaderalignmentgroupingtagp =~ [re|[G][O]|]) of + False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Grouping_Of_Alignments_Tag_Incorrect_Format + True -> -- GO tag is in the accepted format. + return hdheaderalignmentgroupingtagp _ <- word8 58 hdheaderalignmentgroupingvalue <- do hdheaderalignmentgroupingvaluep <- DABL.takeTill (== 09) -- Parse GO value of the header section. @@ -70,6 +68,5 @@ False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Grouping_Of_Alignments_Invalid_Value True -> -- GO value is in the accepted format. return hdheaderalignmentgroupingvaluep - return SAM_V1_6_File_Level_Metadata_Alignment_Grouping { sam_v1_6_file_level_metadata_alignment_grouping_tag = DSeq.fromList $ DB.unpack hdheaderalignmentgroupingtag - , sam_v1_6_file_level_metadata_alignment_grouping_value = hdheaderalignmentgroupingvalue + return SAM_V1_6_File_Level_Metadata_Alignment_Grouping { sam_v1_6_file_level_metadata_alignment_grouping_value = hdheaderalignmentgroupingvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SO.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SO.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SO.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SO.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the SO tag of the @HD tag section of the SAM v1.6 file format. @@ -57,12 +55,12 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_File_Level_Metadata_SO :: Parser SAM_V1_6_File_Level_Metadata_Sorting_Order parse_SAM_V1_6_File_Level_Metadata_SO = do - hdheadersortingordertag <- do hdheadersortingordertagp <- DABL.takeTill (== 58) - -- Parse SO tag of the header section. - case (hdheadersortingordertagp =~ [re|[S][O]|]) of - False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Sorting_Order_Tag_Incorrect_Format - True -> -- SO tag is in the accepted format. - return hdheadersortingordertagp + _ <- do hdheadersortingordertagp <- DABL.takeTill (== 58) + -- Parse SO tag of the header section. + case (hdheadersortingordertagp =~ [re|[S][O]|]) of + False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Sorting_Order_Tag_Incorrect_Format + True -> -- SO tag is in the accepted format. + return hdheadersortingordertagp _ <- word8 58 hdheadersortingordervalue <- do hdheadersortingordervaluep <- DABL.takeTill (== 09) -- Parse SO value of the header section. @@ -70,6 +68,5 @@ False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Sorting_Order_Invalid_Value True -> -- SO value is in the accepted format. return hdheadersortingordervaluep - return SAM_V1_6_File_Level_Metadata_Sorting_Order { sam_v1_6_file_level_metadata_sorting_order_tag = DSeq.fromList $ DB.unpack hdheadersortingordertag - , sam_v1_6_file_level_metadata_sorting_order_value = hdheadersortingordervalue + return SAM_V1_6_File_Level_Metadata_Sorting_Order { sam_v1_6_file_level_metadata_sorting_order_value = hdheadersortingordervalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SS.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SS.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SS.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SS.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the SS tag of the @HD tag section of the SAM v1.6 file format. @@ -57,12 +55,12 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_File_Level_Metadata_SS :: Parser SAM_V1_6_File_Level_Metadata_SubSorting_Order parse_SAM_V1_6_File_Level_Metadata_SS = do - hdheadersubsortingordertag <- do hdheadersubsortingordertagp <- DABL.takeTill (== 58) - -- Parse SS tag of the header section. - case (hdheadersubsortingordertagp =~ [re|[S][S]|]) of - False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Subsorting_Order_Tag_Incorrect_Format - True -> -- SS tag is in the accepted format. - return hdheadersubsortingordertagp + _ <- do hdheadersubsortingordertagp <- DABL.takeTill (== 58) + -- Parse SS tag of the header section. + case (hdheadersubsortingordertagp =~ [re|[S][S]|]) of + False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Subsorting_Order_Tag_Incorrect_Format + True -> -- SS tag is in the accepted format. + return hdheadersubsortingordertagp _ <- word8 58 hdheadersubsortingordervalue <- do hdheadersubsortingordervaluep <- DABL.takeTill (== 09) -- Parse SS value of the header section. @@ -70,6 +68,5 @@ False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Subsorting_Order_Incorrect_Format True -> -- SS value is in the accepted format. return hdheadersubsortingordervaluep - return SAM_V1_6_File_Level_Metadata_SubSorting_Order { sam_v1_6_file_level_metadata_subsorting_order_tag = DSeq.fromList $ DB.unpack hdheadersubsortingordertag - , sam_v1_6_file_level_metadata_subsorting_order_value = hdheadersubsortingordervalue + return SAM_V1_6_File_Level_Metadata_SubSorting_Order { sam_v1_6_file_level_metadata_subsorting_order_value = hdheadersubsortingordervalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/HD/VN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/VN.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/HD/VN.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/VN.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the VN tag of the @HD tag section of the SAM v1.6 file format. @@ -57,12 +55,12 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_File_Level_Metadata_VN :: Parser SAM_V1_6_File_Level_Metadata_Format_Version parse_SAM_V1_6_File_Level_Metadata_VN = do - hdheaderversiontag <- do hdheaderversiontagp <- DABL.takeTill (== 58) - -- Parse VN tag of the header section. - case (hdheaderversiontagp =~ [re|[V][N]|]) of - False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Format_Version_Tag_Incorrect_Format - True -> -- VN tag is in the accepted format. - return hdheaderversiontagp + _ <- do hdheaderversiontagp <- DABL.takeTill (== 58) + -- Parse VN tag of the header section. + case (hdheaderversiontagp =~ [re|[V][N]|]) of + False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Format_Version_Tag_Incorrect_Format + True -> -- VN tag is in the accepted format. + return hdheaderversiontagp _ <- word8 58 hdheaderversionvalue <- do hdheaderversionvaluep <- DABL.takeTill (== 09) -- Parse VN value of the header section. @@ -70,6 +68,5 @@ False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Format_Version_Value_Incorrect_Format True -> -- VN value is in the accepted format. return hdheaderversionvaluep - return SAM_V1_6_File_Level_Metadata_Format_Version { sam_v1_6_file_level_metadata_format_version_tag = DSeq.fromList $ DB.unpack hdheaderversiontag - , sam_v1_6_file_level_metadata_format_version_value = hdheaderversionvalue + return SAM_V1_6_File_Level_Metadata_Format_Version { sam_v1_6_file_level_metadata_format_version_value = hdheaderversionvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/CL.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/CL.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/CL.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/CL.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the CL tag of the @PG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Program_CL :: Parser SAM_V1_6_Program_Command_Line parse_SAM_V1_6_SAM_V1_6_Program_CL = do - pgheadercommandlinetag <- do pgheadercommandlinetagp <- DABL.takeTill (== 58) - -- Parse CL tag of the header section. - case (pgheadercommandlinetagp =~ [re|[C][L]|]) of - False -> fail $ show SAM_V1_6_Error_Program_Command_Line_Incorrect_Format - True -> -- CL tag is in the accepted format. - return pgheadercommandlinetagp + _ <- do pgheadercommandlinetagp <- DABL.takeTill (== 58) + -- Parse CL tag of the header section. + case (pgheadercommandlinetagp =~ [re|[C][L]|]) of + False -> fail $ show SAM_V1_6_Error_Program_Command_Line_Incorrect_Format + True -> -- CL tag is in the accepted format. + return pgheadercommandlinetagp _ <- word8 58 pgheadercommandlinevalue <- DABL.takeTill (== 09) - return SAM_V1_6_Program_Command_Line { sam_v1_6_program_command_line_tag = DSeq.fromList $ DB.unpack pgheadercommandlinetag - , sam_v1_6_program_command_line_value = pgheadercommandlinevalue + return SAM_V1_6_Program_Command_Line { sam_v1_6_program_command_line_value = pgheadercommandlinevalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/DS.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/DS.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/DS.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/DS.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the DS tag of the @PG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Program_DS :: Parser SAM_V1_6_Program_Description parse_SAM_V1_6_SAM_V1_6_Program_DS = do - pgheaderdescriptiontag <- do pgheaderdescriptiontagp <- DABL.takeTill (== 58) - -- Parse DS tag of the header section. - case (pgheaderdescriptiontagp =~ [re|[D][S]|]) of - False -> fail $ show SAM_V1_6_Error_Program_Description_Incorrect_Format - True -> -- DS tag is in the accepted format. - return pgheaderdescriptiontagp + _ <- do pgheaderdescriptiontagp <- DABL.takeTill (== 58) + -- Parse DS tag of the header section. + case (pgheaderdescriptiontagp =~ [re|[D][S]|]) of + False -> fail $ show SAM_V1_6_Error_Program_Description_Incorrect_Format + True -> -- DS tag is in the accepted format. + return pgheaderdescriptiontagp _ <- word8 58 pgheaderdescriptionvalue <- DABL.takeTill (== 09) - return SAM_V1_6_Program_Description { sam_v1_6_program_description_tag = DSeq.fromList $ DB.unpack pgheaderdescriptiontag - , sam_v1_6_program_description_value = pgheaderdescriptionvalue + return SAM_V1_6_Program_Description { sam_v1_6_program_description_value = pgheaderdescriptionvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/ID.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/ID.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/ID.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/ID.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the ID tag of the @PG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Program_ID :: Parser SAM_V1_6_Program_Record_Identifier parse_SAM_V1_6_SAM_V1_6_Program_ID = do - pgheaderidentifiertag <- do pgheaderidentifiertagp <- DABL.takeTill (== 58) - -- Parse ID tag of the header section. - case (pgheaderidentifiertagp =~ [re|[I][D]|]) of - False -> fail $ show SAM_V1_6_Error_Program_Identifier_Incorrect_Format - True -> -- ID tag is in the accepted format. - return pgheaderidentifiertagp + _ <- do pgheaderidentifiertagp <- DABL.takeTill (== 58) + -- Parse ID tag of the header section. + case (pgheaderidentifiertagp =~ [re|[I][D]|]) of + False -> fail $ show SAM_V1_6_Error_Program_Identifier_Incorrect_Format + True -> -- ID tag is in the accepted format. + return pgheaderidentifiertagp _ <- word8 58 pgheaderidentifiervalue <- DABL.takeTill (== 09) - return SAM_V1_6_Program_Record_Identifier { sam_v1_6_program_record_identifier_tag = DSeq.fromList $ DB.unpack pgheaderidentifiertag - , sam_v1_6_program_record_identifier_value = pgheaderidentifiervalue + return SAM_V1_6_Program_Record_Identifier { sam_v1_6_program_record_identifier_value = pgheaderidentifiervalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PN.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PN.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PN.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the PN tag of the @PG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Program_PN :: Parser SAM_V1_6_Program_Name parse_SAM_V1_6_SAM_V1_6_Program_PN = do - pgheadernametag <- do pgheadernametagp <- DABL.takeTill (== 58) - -- Parse PN tag of the header section. - case (pgheadernametagp =~ [re|[P][N]|]) of - False -> fail $ show SAM_V1_6_Error_Program_Name_Incorrect_Format - True -> -- PN tag is in the accepted format. - return pgheadernametagp + _ <- do pgheadernametagp <- DABL.takeTill (== 58) + -- Parse PN tag of the header section. + case (pgheadernametagp =~ [re|[P][N]|]) of + False -> fail $ show SAM_V1_6_Error_Program_Name_Incorrect_Format + True -> -- PN tag is in the accepted format. + return pgheadernametagp _ <- word8 58 pgheadernamevalue <- DABL.takeTill (== 09) - return SAM_V1_6_Program_Name { sam_v1_6_program_name_tag = DSeq.fromList $ DB.unpack pgheadernametag - , sam_v1_6_program_name_value = pgheadernamevalue + return SAM_V1_6_Program_Name { sam_v1_6_program_name_value = pgheadernamevalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PP.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PP.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PP.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PP.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the PP tag of the @PG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Program_PP :: Parser SAM_V1_6_Program_Previous_PG_ID parse_SAM_V1_6_SAM_V1_6_Program_PP = do - pgheaderpreviouspgidtag <- do pgheaderpreviouspgidtagp <- DABL.takeTill (== 58) - -- Parse PP tag of the header section. - case (pgheaderpreviouspgidtagp =~ [re|[P][P]|]) of - False -> fail $ show SAM_V1_6_Error_Program_Previous_PG_ID_Incorrect_Format - True -> -- PP tag is in the accepted format. - return pgheaderpreviouspgidtagp + _ <- do pgheaderpreviouspgidtagp <- DABL.takeTill (== 58) + -- Parse PP tag of the header section. + case (pgheaderpreviouspgidtagp =~ [re|[P][P]|]) of + False -> fail $ show SAM_V1_6_Error_Program_Previous_PG_ID_Incorrect_Format + True -> -- PP tag is in the accepted format. + return pgheaderpreviouspgidtagp _ <- word8 58 pgheaderpreviouspgidvalue <- DABL.takeTill (== 09) - return SAM_V1_6_Program_Previous_PG_ID { sam_v1_6_program_previous_pg_id_tag = DSeq.fromList $ DB.unpack pgheaderpreviouspgidtag - , sam_v1_6_program_previous_pg_id_value = pgheaderpreviouspgidvalue + return SAM_V1_6_Program_Previous_PG_ID { sam_v1_6_program_previous_pg_id_value = pgheaderpreviouspgidvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/VN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/VN.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/VN.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/VN.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the VN tag of the @PG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Program_VN :: Parser SAM_V1_6_Program_Version parse_SAM_V1_6_SAM_V1_6_Program_VN = do - pgheaderversiontag <- do pgheaderversiontagp <- DABL.takeTill (== 58) - -- Parse VN tag of the header section. - case (pgheaderversiontagp =~ [re|[V][N]|]) of - False -> fail $ show SAM_V1_6_Error_Program_Version_Incorrect_Format - True -> -- VN tag is in the accepted format. - return pgheaderversiontagp + _ <- do pgheaderversiontagp <- DABL.takeTill (== 58) + -- Parse VN tag of the header section. + case (pgheaderversiontagp =~ [re|[V][N]|]) of + False -> fail $ show SAM_V1_6_Error_Program_Version_Incorrect_Format + True -> -- VN tag is in the accepted format. + return pgheaderversiontagp _ <- word8 58 pgheaderversionvalue <- DABL.takeTill (== 09) - return SAM_V1_6_Program_Version { sam_v1_6_program_version_tag = DSeq.fromList $ DB.unpack pgheaderversiontag - , sam_v1_6_program_version_value = pgheaderversionvalue + return SAM_V1_6_Program_Version { sam_v1_6_program_version_value = pgheaderversionvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/BC.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/BC.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/BC.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/BC.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the BC tag of the @RG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_BC :: Parser SAM_V1_6_Read_Group_Barcode_Sequence parse_SAM_V1_6_SAM_V1_6_Read_Group_BC = do - rgheaderbarcodesequencetag <- do rgheaderbarcodesequencetagp <- DABL.takeTill (== 58) - -- Parse BC tag of the header section. - case (rgheaderbarcodesequencetagp =~ [re|[B][C]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Barcode_Sequence_Incorrect_Format - True -> -- BC tag is in the accepted format. - return rgheaderbarcodesequencetagp + _ <- do rgheaderbarcodesequencetagp <- DABL.takeTill (== 58) + -- Parse BC tag of the header section. + case (rgheaderbarcodesequencetagp =~ [re|[B][C]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Barcode_Sequence_Incorrect_Format + True -> -- BC tag is in the accepted format. + return rgheaderbarcodesequencetagp _ <- word8 58 rgheaderbarcodesequencevalue <- DABL.takeTill (== 09) - return SAM_V1_6_Read_Group_Barcode_Sequence { sam_v1_6_read_group_barcode_sequence_tag = DSeq.fromList $ DB.unpack rgheaderbarcodesequencetag - , sam_v1_6_read_group_barcode_sequence_value = rgheaderbarcodesequencevalue + return SAM_V1_6_Read_Group_Barcode_Sequence { sam_v1_6_read_group_barcode_sequence_value = rgheaderbarcodesequencevalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/CN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/CN.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/CN.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/CN.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the CN tag of the @RG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_CN :: Parser SAM_V1_6_Read_Group_Sequencing_Center parse_SAM_V1_6_SAM_V1_6_Read_Group_CN = do - rgheadersequencingcentertag <- do rgheadersequencingcentertagp <- DABL.takeTill (== 58) - -- Parse CN tag of the header section. - case (rgheadersequencingcentertagp =~ [re|[C][N]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Sequencing_Center_Incorrect_Format - True -> -- CN tag is in the accepted format. - return rgheadersequencingcentertagp + _ <- do rgheadersequencingcentertagp <- DABL.takeTill (== 58) + -- Parse CN tag of the header section. + case (rgheadersequencingcentertagp =~ [re|[C][N]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Sequencing_Center_Incorrect_Format + True -> -- CN tag is in the accepted format. + return rgheadersequencingcentertagp _ <- word8 58 rgheadersequencingcentervalue <- DABL.takeTill (== 09) - return SAM_V1_6_Read_Group_Sequencing_Center { sam_v1_6_read_group_sequencing_center_tag = DSeq.fromList $ DB.unpack rgheadersequencingcentertag - , sam_v1_6_read_group_sequencing_center_value = rgheadersequencingcentervalue + return SAM_V1_6_Read_Group_Sequencing_Center { sam_v1_6_read_group_sequencing_center_value = rgheadersequencingcentervalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DS.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DS.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DS.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DS.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the DS tag of the @RG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_DS :: Parser SAM_V1_6_Read_Group_Description parse_SAM_V1_6_SAM_V1_6_Read_Group_DS = do - rgheaderdescriptiontag <- do rgheaderdescriptiontagp <- DABL.takeTill (== 58) - -- Parse DS tag of the header section. - case (rgheaderdescriptiontagp =~ [re|[D][S]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Description_Incorrect_Format - True -> -- DS tag is in the accepted format. - return rgheaderdescriptiontagp + _ <- do rgheaderdescriptiontagp <- DABL.takeTill (== 58) + -- Parse DS tag of the header section. + case (rgheaderdescriptiontagp =~ [re|[D][S]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Description_Incorrect_Format + True -> -- DS tag is in the accepted format. + return rgheaderdescriptiontagp _ <- word8 58 rgheaderdescriptionvalue <- DABL.takeTill (== 09) - return SAM_V1_6_Read_Group_Description { sam_v1_6_read_group_description_tag = DSeq.fromList $ DB.unpack rgheaderdescriptiontag - , sam_v1_6_read_group_description_value = rgheaderdescriptionvalue + return SAM_V1_6_Read_Group_Description { sam_v1_6_read_group_description_value = rgheaderdescriptionvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DT.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DT.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DT.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DT.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DTeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the DT tag of the @RG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_DT :: Parser SAM_V1_6_Read_Group_Run_Date parse_SAM_V1_6_SAM_V1_6_Read_Group_DT = do - rgheaderrundatetag <- do rgheaderrundatetagp <- DABL.takeTill (== 58) - -- Parse DT tag of the header section. - case (rgheaderrundatetagp =~ [re|[D][T]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Date_Run_Produced_Incorrect_Format - True -> -- DT tag is in the accepted format. - return rgheaderrundatetagp + _ <- do rgheaderrundatetagp <- DABL.takeTill (== 58) + -- Parse DT tag of the header section. + case (rgheaderrundatetagp =~ [re|[D][T]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Date_Run_Produced_Incorrect_Format + True -> -- DT tag is in the accepted format. + return rgheaderrundatetagp _ <- word8 58 rgheaderrundatevalue <- DABL.takeTill (== 09) - return SAM_V1_6_Read_Group_Run_Date { sam_v1_6_read_group_run_date_tag = DTeq.fromList $ DB.unpack rgheaderrundatetag - , sam_v1_6_read_group_run_date_value = rgheaderrundatevalue + return SAM_V1_6_Read_Group_Run_Date { sam_v1_6_read_group_run_date_value = rgheaderrundatevalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/FO.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/FO.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/FO.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/FO.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the FO tag of the @RG tag section of the SAM v1.6 file format. @@ -57,12 +55,12 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_FO :: Parser SAM_V1_6_Read_Group_Flow_Order parse_SAM_V1_6_SAM_V1_6_Read_Group_FO = do - rgheaderflowordertag <- do rgheaderflowordertagp <- DABL.takeTill (== 58) - -- Parse FO tag of the header section. - case (rgheaderflowordertagp =~ [re|[F][O]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Flow_Order_Incorrect_Format - True -> -- FO tag is in the accepted format. - return rgheaderflowordertagp + _ <- do rgheaderflowordertagp <- DABL.takeTill (== 58) + -- Parse FO tag of the header section. + case (rgheaderflowordertagp =~ [re|[F][O]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Flow_Order_Incorrect_Format + True -> -- FO tag is in the accepted format. + return rgheaderflowordertagp _ <- word8 58 rgheaderflowordervalue <- do rgheaderflowordervaluep <- DABL.takeTill (== 09) -- Parse FO value of the header section. @@ -70,6 +68,5 @@ False -> fail $ show SAM_V1_6_Error_Read_Group_Flow_Order_Incorrect_Format True -> -- FO value is in the accepted format. return rgheaderflowordervaluep - return SAM_V1_6_Read_Group_Flow_Order { sam_v1_6_read_group_flow_order_tag = DSeq.fromList $ DB.unpack rgheaderflowordertag - , sam_v1_6_read_group_flow_order_value = rgheaderflowordervalue + return SAM_V1_6_Read_Group_Flow_Order { sam_v1_6_read_group_flow_order_value = rgheaderflowordervalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/ID.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/ID.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/ID.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/ID.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the ID tag of the @RG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_ID :: Parser SAM_V1_6_Read_Group_Identifier parse_SAM_V1_6_SAM_V1_6_Read_Group_ID = do - rgheaderreadgroupidentifiertag <- do rgheaderreadgroupidentifiertagp <- DABL.takeTill (== 58) - -- Parse ID tag of the header section. - case (rgheaderreadgroupidentifiertagp =~ [re|[I][D]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Read_Group_Identifier_Incorrect_Format - True -> -- ID tag is in the accepted format. - return rgheaderreadgroupidentifiertagp + _ <- do rgheaderreadgroupidentifiertagp <- DABL.takeTill (== 58) + -- Parse ID tag of the header section. + case (rgheaderreadgroupidentifiertagp =~ [re|[I][D]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Read_Group_Identifier_Incorrect_Format + True -> -- ID tag is in the accepted format. + return rgheaderreadgroupidentifiertagp _ <- word8 58 rgheaderreadgroupidentifiervalue <- DABL.takeTill (== 09) - return SAM_V1_6_Read_Group_Identifier { sam_v1_6_read_group_identifier_tag = DSeq.fromList $ DB.unpack rgheaderreadgroupidentifiertag - , sam_v1_6_read_group_identifier_value = rgheaderreadgroupidentifiervalue + return SAM_V1_6_Read_Group_Identifier { sam_v1_6_read_group_identifier_value = rgheaderreadgroupidentifiervalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/KS.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/KS.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/KS.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/KS.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the KS tag of the @RG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_KS :: Parser SAM_V1_6_Read_Group_Key_Sequence parse_SAM_V1_6_SAM_V1_6_Read_Group_KS = do - rgheaderkeysequencetag <- do rgheaderkeysequencetagp <- DABL.takeTill (== 58) - -- Parse KS tag of the header section. - case (rgheaderkeysequencetagp =~ [re|[K][S]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Key_Sequence_Incorrect_Format - True -> -- KS tag is in the accepted format. - return rgheaderkeysequencetagp + _ <- do rgheaderkeysequencetagp <- DABL.takeTill (== 58) + -- Parse KS tag of the header section. + case (rgheaderkeysequencetagp =~ [re|[K][S]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Key_Sequence_Incorrect_Format + True -> -- KS tag is in the accepted format. + return rgheaderkeysequencetagp _ <- word8 58 rgheaderkeysequencevalue <- DABL.takeTill (== 09) - return SAM_V1_6_Read_Group_Key_Sequence { sam_v1_6_read_group_key_sequence_tag = DSeq.fromList $ DB.unpack rgheaderkeysequencetag - , sam_v1_6_read_group_key_sequence_value = rgheaderkeysequencevalue + return SAM_V1_6_Read_Group_Key_Sequence { sam_v1_6_read_group_key_sequence_value = rgheaderkeysequencevalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/LB.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/LB.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/LB.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/LB.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the LB tag of the @RG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_LB :: Parser SAM_V1_6_Read_Group_Library parse_SAM_V1_6_SAM_V1_6_Read_Group_LB = do - rgheaderlibrarytag <- do rgheaderlibrarytagp <- DABL.takeTill (== 58) - -- Parse LB tag of the header section. - case (rgheaderlibrarytagp =~ [re|[L][B]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Library_Incorrect_Format - True -> -- LB tag is in the accepted format. - return rgheaderlibrarytagp + _ <- do rgheaderlibrarytagp <- DABL.takeTill (== 58) + -- Parse LB tag of the header section. + case (rgheaderlibrarytagp =~ [re|[L][B]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Library_Incorrect_Format + True -> -- LB tag is in the accepted format. + return rgheaderlibrarytagp _ <- word8 58 rgheaderlibraryvalue <- DABL.takeTill (== 09) - return SAM_V1_6_Read_Group_Library { sam_v1_6_read_group_library_tag = DSeq.fromList $ DB.unpack rgheaderlibrarytag - , sam_v1_6_read_group_library_value = rgheaderlibraryvalue + return SAM_V1_6_Read_Group_Library { sam_v1_6_read_group_library_value = rgheaderlibraryvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PG.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PG.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PG.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PG.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the PG tag of the @RG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_PG :: Parser SAM_V1_6_Read_Group_Programs parse_SAM_V1_6_SAM_V1_6_Read_Group_PG = do - rgheaderprogramstag <- do rgheaderprogramstagp <- DABL.takeTill (== 58) - -- Parse PG tag of the header section. - case (rgheaderprogramstagp =~ [re|[P][G]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Programs_Incorrect_Format - True -> -- PG tag is in the accepted format. - return rgheaderprogramstagp + _ <- do rgheaderprogramstagp <- DABL.takeTill (== 58) + -- Parse PG tag of the header section. + case (rgheaderprogramstagp =~ [re|[P][G]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Programs_Incorrect_Format + True -> -- PG tag is in the accepted format. + return rgheaderprogramstagp _ <- word8 58 rgheaderprogramsvalue <- DABL.takeTill (== 09) - return SAM_V1_6_Read_Group_Programs { sam_v1_6_read_group_programs_tag = DSeq.fromList $ DB.unpack rgheaderprogramstag - , sam_v1_6_read_group_programs_value = rgheaderprogramsvalue + return SAM_V1_6_Read_Group_Programs { sam_v1_6_read_group_programs_value = rgheaderprogramsvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PI.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PI.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PI.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PI.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the PI tag of the @RG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_PI :: Parser SAM_V1_6_Read_Group_Predicted_Median_Insert_Size parse_SAM_V1_6_SAM_V1_6_Read_Group_PI = do - rgheaderpredictedmedianinsertsizetag <- do rgheaderpredictedmedianinsertsizetagp <- DABL.takeTill (== 58) - -- Parse PI tag of the header section. - case (rgheaderpredictedmedianinsertsizetagp =~ [re|[P][I]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Predicted_Median_Insert_Size_Incorrect_Format - True -> -- PI tag is in the accepted format. - return rgheaderpredictedmedianinsertsizetagp + _ <- do rgheaderpredictedmedianinsertsizetagp <- DABL.takeTill (== 58) + -- Parse PI tag of the header section. + case (rgheaderpredictedmedianinsertsizetagp =~ [re|[P][I]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Predicted_Median_Insert_Size_Incorrect_Format + True -> -- PI tag is in the accepted format. + return rgheaderpredictedmedianinsertsizetagp _ <- word8 58 rgheaderpredictedmedianinsertsizevalue <- DABL.takeTill (== 09) - return SAM_V1_6_Read_Group_Predicted_Median_Insert_Size { sam_v1_6_read_group_predicted_median_insert_size_tag = DSeq.fromList $ DB.unpack rgheaderpredictedmedianinsertsizetag - , sam_v1_6_read_group_predicted_median_insert_size_value = rgheaderpredictedmedianinsertsizevalue + return SAM_V1_6_Read_Group_Predicted_Median_Insert_Size { sam_v1_6_read_group_predicted_median_insert_size_value = rgheaderpredictedmedianinsertsizevalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PL.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PL.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PL.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PL.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the PL tag of the @RG tag section of the SAM v1.6 file format. @@ -57,12 +55,12 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_PL :: Parser SAM_V1_6_Read_Group_Platform parse_SAM_V1_6_SAM_V1_6_Read_Group_PL = do - rgheaderplatformtag <- do rgheaderplatformtagp <- DABL.takeTill (== 58) - -- Parse PL tag of the header section. - case (rgheaderplatformtagp =~ [re|[P][L]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Platform_Incorrect_Format - True -> -- PL tag is in the accepted format. - return rgheaderplatformtagp + _ <- do rgheaderplatformtagp <- DABL.takeTill (== 58) + -- Parse PL tag of the header section. + case (rgheaderplatformtagp =~ [re|[P][L]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Platform_Incorrect_Format + True -> -- PL tag is in the accepted format. + return rgheaderplatformtagp _ <- word8 58 rgheaderplatformvalue <- do rgheaderplatformvaluep <- DABL.takeTill (== 09) -- Parse PL value of the header section. @@ -70,6 +68,5 @@ False -> fail $ show SAM_V1_6_Error_Read_Group_Platform_Incorrect_Format True -> -- PL value is in the accepted format. return rgheaderplatformvaluep - return SAM_V1_6_Read_Group_Platform { sam_v1_6_read_group_platform_tag = DSeq.fromList $ DB.unpack rgheaderplatformtag - , sam_v1_6_read_group_platform_value = rgheaderplatformvalue + return SAM_V1_6_Read_Group_Platform { sam_v1_6_read_group_platform_value = rgheaderplatformvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PM.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PM.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PM.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PM.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the PM tag of the @RG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_PM :: Parser SAM_V1_6_Read_Group_Platform_Model parse_SAM_V1_6_SAM_V1_6_Read_Group_PM = do - rgheaderplatformmodeltag <- do rgheaderplatformmodeltagp <- DABL.takeTill (== 58) - -- Parse PM tag of the header section. - case (rgheaderplatformmodeltagp =~ [re|[P][M]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Platform_Model_Incorrect_Format - True -> -- PM tag is in the accepted format. - return rgheaderplatformmodeltagp + _ <- do rgheaderplatformmodeltagp <- DABL.takeTill (== 58) + -- Parse PM tag of the header section. + case (rgheaderplatformmodeltagp =~ [re|[P][M]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Platform_Model_Incorrect_Format + True -> -- PM tag is in the accepted format. + return rgheaderplatformmodeltagp _ <- word8 58 rgheaderplatformmodelvalue <- DABL.takeTill (== 09) - return SAM_V1_6_Read_Group_Platform_Model { sam_v1_6_read_group_platform_model_tag = DSeq.fromList $ DB.unpack rgheaderplatformmodeltag - , sam_v1_6_read_group_platform_model_value = rgheaderplatformmodelvalue + return SAM_V1_6_Read_Group_Platform_Model { sam_v1_6_read_group_platform_model_value = rgheaderplatformmodelvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PU.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PU.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PU.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PU.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the PU tag of the @RG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_PU :: Parser SAM_V1_6_Read_Group_Platform_Unit parse_SAM_V1_6_SAM_V1_6_Read_Group_PU = do - rgheaderplatformunittag <- do rgheaderplatformunittagp <- DABL.takeTill (== 58) - -- Parse PU tag of the header section. - case (rgheaderplatformunittagp =~ [re|[P][U]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Platform_Unit_Incorrect_Format - True -> -- PU tag is in the accepted format. - return rgheaderplatformunittagp + _ <- do rgheaderplatformunittagp <- DABL.takeTill (== 58) + -- Parse PU tag of the header section. + case (rgheaderplatformunittagp =~ [re|[P][U]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Platform_Unit_Incorrect_Format + True -> -- PU tag is in the accepted format. + return rgheaderplatformunittagp _ <- word8 58 rgheaderplatformunitvalue <- DABL.takeTill (== 09) - return SAM_V1_6_Read_Group_Platform_Unit { sam_v1_6_read_group_platform_unit_tag = DSeq.fromList $ DB.unpack rgheaderplatformunittag - , sam_v1_6_read_group_platform_unit_value = rgheaderplatformunitvalue + return SAM_V1_6_Read_Group_Platform_Unit { sam_v1_6_read_group_platform_unit_value = rgheaderplatformunitvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/SM.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/SM.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/SM.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/SM.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the SM tag of the @RG tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Read_Group_SM :: Parser SAM_V1_6_Read_Group_Sample parse_SAM_V1_6_SAM_V1_6_Read_Group_SM = do - rgheadersampletag <- do rgheadersampletagp <- DABL.takeTill (== 58) - -- Parse SM tag of the header section. - case (rgheadersampletagp =~ [re|[S][M]|]) of - False -> fail $ show SAM_V1_6_Error_Read_Group_Sample_Incorrect_Format - True -> -- SM tag is in the accepted format. - return rgheadersampletagp + _ <- do rgheadersampletagp <- DABL.takeTill (== 58) + -- Parse SM tag of the header section. + case (rgheadersampletagp =~ [re|[S][M]|]) of + False -> fail $ show SAM_V1_6_Error_Read_Group_Sample_Incorrect_Format + True -> -- SM tag is in the accepted format. + return rgheadersampletagp _ <- word8 58 rgheadersamplevalue <- DABL.takeTill (== 09) - return SAM_V1_6_Read_Group_Sample { sam_v1_6_read_group_sample_tag = DSeq.fromList $ DB.unpack rgheadersampletag - , sam_v1_6_read_group_sample_value = rgheadersamplevalue + return SAM_V1_6_Read_Group_Sample { sam_v1_6_read_group_sample_value = rgheadersamplevalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AH.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AH.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AH.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AH.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the AH tag of the @SQ tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AH :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AH = do - sqheaderalternativelocustag <- do sqheaderalternativelocustagp <- DABL.takeTill (== 58) - -- Parse AH tag of the header section. - case (sqheaderalternativelocustagp =~ [re|[A][H]|]) of - False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Locus_Incorrect_Format - True -> -- AH tag is in the accepted format. - return sqheaderalternativelocustagp + _ <- do sqheaderalternativelocustagp <- DABL.takeTill (== 58) + -- Parse AH tag of the header section. + case (sqheaderalternativelocustagp =~ [re|[A][H]|]) of + False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Locus_Incorrect_Format + True -> -- AH tag is in the accepted format. + return sqheaderalternativelocustagp _ <- word8 58 sqheaderalternativelocusvalue <- DABL.takeTill (== 09) - return SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus { sam_v1_6_reference_sequence_dictionary_alternative_locus_tag = DSeq.fromList $ DB.unpack sqheaderalternativelocustag - , sam_v1_6_reference_sequence_dictionary_alternative_locus_value = sqheaderalternativelocusvalue + return SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus { sam_v1_6_reference_sequence_dictionary_alternative_locus_value = sqheaderalternativelocusvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AN.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AN.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AN.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the AN tag of the @SQ tag section of the SAM v1.6 file format. @@ -57,12 +55,12 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AN :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AN = do - sqheaderalternativereferencesequencenamestag <- do sqheaderalternativereferencesequencenamestagp <- DABL.takeTill (== 58) - -- Parse AN tag of the header section. - case (sqheaderalternativereferencesequencenamestagp =~ [re|[A][N]|]) of - False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names_Incorrect_Format - True -> -- AN tag is in the accepted format. - return sqheaderalternativereferencesequencenamestagp + _ <- do sqheaderalternativereferencesequencenamestagp <- DABL.takeTill (== 58) + -- Parse AN tag of the header section. + case (sqheaderalternativereferencesequencenamestagp =~ [re|[A][N]|]) of + False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names_Incorrect_Format + True -> -- AN tag is in the accepted format. + return sqheaderalternativereferencesequencenamestagp _ <- word8 58 sqheaderalternativereferencesequencenamesvalue <- do sqheaderalternativereferencesequencenamesvaluep <- DABL.takeTill (== 09) -- Parse AN value of the header section. @@ -70,6 +68,5 @@ False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names_Invalid_Value True -> -- AN value is in the accepted format. return sqheaderalternativereferencesequencenamesvaluep - return SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names { sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tag = DSeq.fromList $ DB.unpack sqheaderalternativereferencesequencenamestag - , sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value = sqheaderalternativereferencesequencenamesvalue + return SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names { sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value = sqheaderalternativereferencesequencenamesvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AS.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AS.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AS.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AS.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the AS tag of the @SQ tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AS :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AS = do - sqheadergenomeassemblyidentifiertag <- do sqheadergenomeassemblyidentifiertagp <- DABL.takeTill (== 58) - -- Parse AS tag of the header section. - case (sqheadergenomeassemblyidentifiertagp =~ [re|[A][S]|]) of - False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Genome_Assembly_Identifier_Incorrect_Format - True -> -- AS tag is in the accepted format. - return sqheadergenomeassemblyidentifiertagp + _ <- do sqheadergenomeassemblyidentifiertagp <- DABL.takeTill (== 58) + -- Parse AS tag of the header section. + case (sqheadergenomeassemblyidentifiertagp =~ [re|[A][S]|]) of + False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Genome_Assembly_Identifier_Incorrect_Format + True -> -- AS tag is in the accepted format. + return sqheadergenomeassemblyidentifiertagp _ <- word8 58 sqheadergenomeassemblyidentifiervalue <- DABL.takeTill (== 09) - return SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier { sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag = DSeq.fromList $ DB.unpack sqheadergenomeassemblyidentifiertag - , sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value = sqheadergenomeassemblyidentifiervalue + return SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier { sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value = sqheadergenomeassemblyidentifiervalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/DS.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/DS.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/DS.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/DS.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the DS tag of the @SQ tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_DS :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Description parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_DS = do - sqheaderdescriptiontag <- do sqheaderdescriptiontagp <- DABL.takeTill (== 58) - -- Parse DS tag of the header section. - case (sqheaderdescriptiontagp =~ [re|[D][S]|]) of - False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Description_Incorrect_Format - True -> -- DS tag is in the accepted format. - return sqheaderdescriptiontagp + _ <- do sqheaderdescriptiontagp <- DABL.takeTill (== 58) + -- Parse DS tag of the header section. + case (sqheaderdescriptiontagp =~ [re|[D][S]|]) of + False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Description_Incorrect_Format + True -> -- DS tag is in the accepted format. + return sqheaderdescriptiontagp _ <- word8 58 sqheaderdescriptionvalue <- DABL.takeTill (== 09) - return SAM_V1_6_Reference_Sequence_Dictionary_Description { sam_v1_6_reference_sequence_dictionary_description_tag = DSeq.fromList $ DB.unpack sqheaderdescriptiontag - , sam_v1_6_reference_sequence_dictionary_description_value = sqheaderdescriptionvalue + return SAM_V1_6_Reference_Sequence_Dictionary_Description { sam_v1_6_reference_sequence_dictionary_description_value = sqheaderdescriptionvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/LN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/LN.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/LN.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/LN.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the LN tag of the @SQ tag section of the SAM v1.6 file format. @@ -57,12 +55,12 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_LN :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_LN = do - sqheadersequencelengthtag <- do sqheadersequencelengthtagp <- DABL.takeTill (== 58) - -- Parse LN tag of the header section. - case (sqheadersequencelengthtagp =~ [re|[L][N]|]) of - False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Incorrect_Format - True -> -- LN tag is in the accepted format. - return sqheadersequencelengthtagp + _ <- do sqheadersequencelengthtagp <- DABL.takeTill (== 58) + -- Parse LN tag of the header section. + case (sqheadersequencelengthtagp =~ [re|[L][N]|]) of + False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Incorrect_Format + True -> -- LN tag is in the accepted format. + return sqheadersequencelengthtagp _ <- word8 58 sqheadersequencelengthvalue <- do sqheadersequencelengthvaluep <- DABL.takeTill (== 09) -- Parse LN value of the header section. @@ -70,6 +68,5 @@ False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Invalid_Value True -> -- LN value is in the accepted format. return sqheadersequencelengthvaluep - return SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length { sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag = DSeq.fromList $ DB.unpack sqheadersequencelengthtag - , sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value = sqheadersequencelengthvalue + return SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length { sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value = sqheadersequencelengthvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/M5.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/M5.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/M5.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/M5.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the M5 tag of the @SQ tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_M5 :: Parser SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_M5 = do - sqheadermd5checksumtag <- do sqheadermd5checksumtagp <- DABL.takeTill (== 58) - -- Parse M5 tag of the header section. - case (sqheadermd5checksumtagp =~ [re|[M][5]|]) of - False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_MD5_Checksum_Incorrect_Format - True -> -- M5 tag is in the accepted format. - return sqheadermd5checksumtagp + _ <- do sqheadermd5checksumtagp <- DABL.takeTill (== 58) + -- Parse M5 tag of the header section. + case (sqheadermd5checksumtagp =~ [re|[M][5]|]) of + False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_MD5_Checksum_Incorrect_Format + True -> -- M5 tag is in the accepted format. + return sqheadermd5checksumtagp _ <- word8 58 sqheadermd5checksumvalue <- DABL.takeTill (== 09) - return SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum { sam_v1_6_reference_sequence_dictionary_md5_checksum_tag = DSeq.fromList $ DB.unpack sqheadermd5checksumtag - , sam_v1_6_reference_sequence_dictionary_md5_checksum_value = sqheadermd5checksumvalue + return SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum { sam_v1_6_reference_sequence_dictionary_md5_checksum_value = sqheadermd5checksumvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SN.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SN.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SN.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the SN tag of the @SQ tag section of the SAM v1.6 file format. @@ -57,12 +55,12 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_SN :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_SN = do - sqheadersequencenametag <- do sqheadersequencenametagp <- DABL.takeTill (== 58) - -- Parse SN tag of the header section. - case (sqheadersequencenametagp =~ [re|[S][N]|]) of - False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Incorrect_Format - True -> -- SN tag is in the accepted format. - return sqheadersequencenametagp + _ <- do sqheadersequencenametagp <- DABL.takeTill (== 58) + -- Parse SN tag of the header section. + case (sqheadersequencenametagp =~ [re|[S][N]|]) of + False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Incorrect_Format + True -> -- SN tag is in the accepted format. + return sqheadersequencenametagp _ <- word8 58 sqheadersequencenamevalue <- do sqheadersequencenamevaluep <- DABL.takeTill (== 09) -- Parse SN value of the header section. @@ -70,6 +68,5 @@ False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Invalid_Value True -> -- SN value is in the accepted format. return sqheadersequencenamevaluep - return SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name { sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag = DSeq.fromList $ DB.unpack sqheadersequencenametag - , sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value = sqheadersequencenamevalue + return SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name { sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value = sqheadersequencenamevalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SP.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SP.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SP.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SP.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the SP tag of the @SQ tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_SP :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Species parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_SP = do - sqheaderspeciestag <- do sqheaderspeciestagp <- DABL.takeTill (== 58) - -- Parse SP tag of the header section. - case (sqheaderspeciestagp =~ [re|[S][P]|]) of - False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Species_Incorrect_Format - True -> -- SP tag is in the accepted format. - return sqheaderspeciestagp + _ <- do sqheaderspeciestagp <- DABL.takeTill (== 58) + -- Parse SP tag of the header section. + case (sqheaderspeciestagp =~ [re|[S][P]|]) of + False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Species_Incorrect_Format + True -> -- SP tag is in the accepted format. + return sqheaderspeciestagp _ <- word8 58 sqheaderspeciesvalue <- DABL.takeTill (== 09) - return SAM_V1_6_Reference_Sequence_Dictionary_Species { sam_v1_6_reference_sequence_dictionary_species_tag = DSeq.fromList $ DB.unpack sqheaderspeciestag - , sam_v1_6_reference_sequence_dictionary_species_value = sqheaderspeciesvalue + return SAM_V1_6_Reference_Sequence_Dictionary_Species { sam_v1_6_reference_sequence_dictionary_species_value = sqheaderspeciesvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/TP.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/TP.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/TP.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/TP.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the TP tag of the @SQ tag section of the SAM v1.6 file format. @@ -57,12 +55,12 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_TP :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_TP = do - sqheadermoleculetopologytag <- do sqheadermoleculetopologytagp <- DABL.takeTill (== 58) - -- Parse TP tag of the header section. - case (sqheadermoleculetopologytagp =~ [re|[T][P]|]) of - False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Molecule_Topology_Incorrect_Format - True -> -- TP tag is in the accepted format. - return sqheadermoleculetopologytagp + _ <- do sqheadermoleculetopologytagp <- DABL.takeTill (== 58) + -- Parse TP tag of the header section. + case (sqheadermoleculetopologytagp =~ [re|[T][P]|]) of + False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Molecule_Topology_Incorrect_Format + True -> -- TP tag is in the accepted format. + return sqheadermoleculetopologytagp _ <- word8 58 sqheadermoleculetopologyvalue <- do sqheadermoleculetopologyvaluep <- DABL.takeTill (== 09) -- Parse TP value of the header section. @@ -70,6 +68,5 @@ False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Molecule_Topology_Invalid_Value True -> -- TP value is in the accepted format. return sqheadermoleculetopologyvaluep - return SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology { sam_v1_6_reference_sequence_dictionary_molecule_topology_tag = DSeq.fromList $ DB.unpack sqheadermoleculetopologytag - , sam_v1_6_reference_sequence_dictionary_molecule_topology_value = sqheadermoleculetopologyvalue + return SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology { sam_v1_6_reference_sequence_dictionary_molecule_topology_value = sqheadermoleculetopologyvalue } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/UR.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/UR.hs --- a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/UR.hs +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/UR.hs @@ -48,8 +48,6 @@ import Data.SAM.Version1_6.Read.Error import Data.Attoparsec.ByteString.Lazy as DABL -import qualified Data.ByteString as DB (unpack) -import Data.Sequence as DSeq import Text.Regex.PCRE.Heavy -- | Defines a parser for the UR tag of the @SQ tag section of the SAM v1.6 file format. @@ -57,14 +55,13 @@ -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_UR :: Parser SAM_V1_6_Reference_Sequence_Dictionary_URI parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_UR = do - sqheaderuritag <- do sqheaderuritagp <- DABL.takeTill (== 58) - -- Parse UR tag of the header section. - case (sqheaderuritagp =~ [re|[U][R]|]) of - False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_URI_Incorrect_Format - True -> -- UR tag is in the accepted format. - return sqheaderuritagp + _ <- do sqheaderuritagp <- DABL.takeTill (== 58) + -- Parse UR tag of the header section. + case (sqheaderuritagp =~ [re|[U][R]|]) of + False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_URI_Incorrect_Format + True -> -- UR tag is in the accepted format. + return sqheaderuritagp _ <- word8 58 sqheaderurivalue <- DABL.takeTill (== 09) - return SAM_V1_6_Reference_Sequence_Dictionary_URI { sam_v1_6_reference_sequence_dictionary_uri_tag = DSeq.fromList $ DB.unpack sqheaderuritag - , sam_v1_6_reference_sequence_dictionary_uri_value = sqheaderurivalue + return SAM_V1_6_Reference_Sequence_Dictionary_URI { sam_v1_6_reference_sequence_dictionary_uri_value = sqheaderurivalue } diff --git a/test/Main.hs b/test/Main.hs --- a/test/Main.hs +++ b/test/Main.hs @@ -1,4 +1,14 @@ module Main (main) where +import Data.SAM.Version1_6.Read.Base + +import Test.Hspec + main :: IO () -main = putStrLn "Test suite not yet implemented." +main = do --hspec $ do + -- describe "Data.SAM.Version1_6.Read.Base" $ do + -- describe "readSAM_V1_6" $ do + -- describe "toy1.sam" $ do + -- it "Ensures that readSAM_V1_6 can read and parse: toy1.sam" $ do + toy1sam <- readSAM_V1_6 "test/examples/toy4.sam" + print toy1sam