{-# LANGUAGE DeriveDataTypeable #-} {-# LANGUAGE DeriveGeneric #-} {-# LANGUAGE FlexibleContexts #-} {-# LANGUAGE FlexibleInstances #-} {-# LANGUAGE MultiParamTypeClasses #-} {-# LANGUAGE TypeFamilies #-} -- | -- Module : Data.SAM.Version1_6.Read.Error -- Copyright : (c) Matthew Mosior 2023 -- License : BSD-style -- Maintainer : mattm.github@gmail.com -- Portability : portable -- -- = Description -- -- This library enables the decoding/encoding of SAM, BAM and CRAM file formats. module Data.SAM.Version1_6.Read.Error ( -- * SAM version 1.6 data type SAM_V1_6_Error(..) ) where import Data.Data import Generics.Deriving.Base -- | Custom @"SAM_V1_6"@ (SAM version 1.6) error data type. -- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. data SAM_V1_6_Error = -- | @HD tag not in accepted format (only important -- if @HD tag is present). SAM_V1_6_Error_File_Level_Metadata_Tag_Incorrect_Format -- | VN tag missing (only important -- if @HD tag is present). | SAM_V1_6_Error_File_Level_Metadata_Format_Version_Tag_Missing -- | VN tag not in accepted format (only important -- if @HD tag is present). | SAM_V1_6_Error_File_Level_Metadata_Format_Version_Tag_Incorrect_Format -- | VN value not in accepted format (only important -- if @HD tag is present). | SAM_V1_6_Error_File_Level_Metadata_Format_Version_Value_Incorrect_Format -- | Sorting order tag not in accepted format (only important -- if @HD tag is present). | SAM_V1_6_Error_File_Level_Metadata_Sorting_Order_Tag_Incorrect_Format -- | Sorting order invalid value (only important -- if @HD tag is present). | SAM_V1_6_Error_File_Level_Metadata_Sorting_Order_Invalid_Value -- | Grouping of alignments no in accepted format (only important -- if @HD tag is present). | SAM_V1_6_Error_File_Level_Metadata_Grouping_Of_Alignments_Tag_Incorrect_Format -- | Grouping of Alignments invalid value (only important -- if @HD tag is present). | SAM_V1_6_Error_File_Level_Metadata_Grouping_Of_Alignments_Invalid_Value -- | Subsorting order tag not in accepted format (only important -- if @HD tag is present). | SAM_V1_6_Error_File_Level_Metadata_Subsorting_Order_Tag_Incorrect_Format -- | Subsorting order of alignments not in accepted format (only -- if @HD tag is present. | SAM_V1_6_Error_File_Level_Metadata_Subsorting_Order_Incorrect_Format -- | SN tag missing (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Tag_Missing -- | Reference Sequence Name not in accepted format (only important -- if @SQ tag is present. | SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Incorrect_Format -- | Reference Sequence Name invalid value (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Invalid_Value -- | LN tag missing (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Missing -- | Reference Sequence Length not in accepted format (only important -- if @SQ tag is present. | SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Incorrect_Format -- | Reference Sequence Length invalid value (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Invalid_Value -- | Alternative locus not in accepted format (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Locus_Incorrect_Format -- | Alternative Reference Sequence Names not in accepted format (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names_Incorrect_Format -- | Alternative Reference Sequence Names invalid value (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names_Invalid_Value -- | Genome Assembly Identifier not in accepted format (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_Genome_Assembly_Identifier_Incorrect_Format -- | Description not in accepted format (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_Description_Incorrect_Format -- | MD5 checksum not in accepted format (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_MD5_Checksum_Incorrect_Format -- | Species not in accepted format (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_Species_Incorrect_Format -- | Molecule topology not in accepted format (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_Molecule_Topology_Incorrect_Format -- | Molecule topology invalid value (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_Molecule_Topology_Invalid_Value -- | URI not in accepted format (only important -- if @SQ tag is present). | SAM_V1_6_Error_Reference_Sequence_Dictionary_URI_Incorrect_Format -- | ID tag not accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Read_Group_Identifier_Incorrect_Format -- | ID tag is missing (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Read_Group_Identifier_Tag_Missing -- | BC tag not in accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Barcode_Sequence_Incorrect_Format -- | CN tag not in accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Sequencing_Center_Incorrect_Format -- | DS tag not in accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Description_Incorrect_Format -- | DT tag not in accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Date_Run_Produced_Incorrect_Format -- | FO tag not in accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Flow_Order_Incorrect_Format -- | KS tag not in accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Key_Sequence_Incorrect_Format -- | LB tag not in accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Library_Incorrect_Format -- | PG tag not in accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Programs_Incorrect_Format -- | PI tag not in accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Predicted_Median_Insert_Size_Incorrect_Format -- | PL tag not in accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Platform_Incorrect_Format -- | PM tag not in accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Platform_Model_Incorrect_Format -- | PU tag not in accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Platform_Unit_Incorrect_Format -- | SM tag not in accepted format (only important -- if @RG tag is present). | SAM_V1_6_Error_Read_Group_Sample_Incorrect_Format -- | RG tag not in accepted format. | SAM_V1_6_Error_Read_Group_Tag_Incorrect_Format -- | ID tag not in accepted format (only important -- if @PG tag is present). | SAM_V1_6_Error_Program_Identifier_Incorrect_Format -- | PN tag not in accepted format (only important -- if @PG tag is present). | SAM_V1_6_Error_Program_Name_Incorrect_Format -- | CL tag not in accepted format (only important -- if @PG tag is present). | SAM_V1_6_Error_Program_Command_Line_Incorrect_Format -- | PP tag not in accepted format (only important -- if @PG tag is present). | SAM_V1_6_Error_Program_Previous_PG_ID_Incorrect_Format -- | DS tag not in accepted format (only important -- if @PG tag is present). | SAM_V1_6_Error_Program_Description_Incorrect_Format -- | VN tag not in accepted format (only important -- if @PG tag is present). | SAM_V1_6_Error_Program_Version_Incorrect_Format -- | PG tag not in accepted format. | SAM_V1_6_Error_Program_Tag_Incorrect_Format -- | CO tag not in accepted format. | SAM_V1_6_Error_One_Line_Comment_Tag_Incorrect_Format -- | QNAME of alignment section not in accepted format. | SAM_V1_6_Error_Alignment_QNAME_Incorrect_Format -- | FLAG of alignment section not in accepted format. | SAM_V1_6_Error_Alignment_FLAG_Incorrect_Format -- | RNAME of alignment section not in accepted format. | SAM_V1_6_Error_Alignment_RNAME_Incorrect_Format -- | POS of alignment section not in accepted format. | SAM_V1_6_Error_Alignment_POS_Incorrect_Format -- | MAPQ of alignment section not in accepted format. | SAM_V1_6_Error_Alignment_MAPQ_Incorrect_Format -- | CIGAR of alignment section not in accepted format. | SAM_V1_6_Error_Alignment_CIGAR_Incorrect_Format -- | RNEXT of alignment section not in accepted format. | SAM_V1_6_Error_Alignment_RNEXT_Incorrect_Format -- | PNEXT of alignment section not in accepted format. | SAM_V1_6_Error_Alignment_PNEXT_Incorrect_Format -- | TLEN of alignment section not in accpepted format. | SAM_V1_6_Error_Alignment_TLEN_Incorrect_Format -- | SEQ of alignment section not in accepted format. | SAM_V1_6_Error_Alignment_SEQ_Incorrect_Format -- | QUAL of alignment section not in accepted format. | SAM_V1_6_Error_Alignment_QUAL_Incorrect_Format -- | AOPT tag of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_AOPT_Tag_Incorrect_Format -- | AOPT type of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_AOPT_Type_Incorrect_Format -- | AOPT value of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_AOPT_Value_Incorrect_Format -- | IOPT tag of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_IOPT_Tag_Incorrect_Format -- | IOPT type of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_IOPT_Type_Incorrect_Format -- | IOPT value of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_IOPT_Value_Incorrect_Format -- | FOPT tag of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_FOPT_Tag_Incorrect_Format -- | FOPT type of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_FOPT_Type_Incorrect_Format -- | FOPT value of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_FOPT_Value_Incorrect_Format -- | ZOPT tag of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_ZOPT_Tag_Incorrect_Format -- | ZOPT type of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_ZOPT_Type_Incorrect_Format -- | ZOPT value of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_ZOPT_Value_Incorrect_Format -- | HOPT tag of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_HOPT_Tag_Incorrect_Format -- | HOPT type of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_HOPT_Type_Incorrect_Format -- | HOPT value of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_HOPT_Value_Incorrect_Format -- | BOPT tag of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_BOPT_Tag_Incorrect_Format -- | BOPT type of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_BOPT_Type_Incorrect_Format -- | BOPT value type of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_BOPT_Value_Type_Incorrect_Format -- | BOPT value data of the alignment section not in accepted format. | SAM_V1_6_Error_Alignment_BOPT_Value_Data_Incorrect_Format deriving (Eq,Generic,Show,Typeable)