hs-samtools-0.10.0.0: src/Data/BAM/Version1_6/Read/Error.hs
{-# LANGUAGE DeriveDataTypeable #-}
{-# LANGUAGE DeriveGeneric #-}
{-# LANGUAGE FlexibleContexts #-}
{-# LANGUAGE FlexibleInstances #-}
{-# LANGUAGE MultiParamTypeClasses #-}
{-# LANGUAGE StrictData #-}
{-# LANGUAGE TypeFamilies #-}
-- |
-- Module : Data.BAM.Version1_6.Read.Error
-- Copyright : (c) Matthew Mosior 2024
-- License : BSD-style
-- Maintainer : mattm.github@gmail.com
-- Portability : portable
--
-- = Description
--
-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.
module Data.BAM.Version1_6.Read.Error ( -- * BAM version 1.6 data type
BAM_V1_6_Read_Error(..)
) where
import Data.Data
import Generics.Deriving.Base
-- | Custom @"BAM_V1_6_Read_Error"@ (BAM version 1.6) error data type.
-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.
data BAM_V1_6_Read_Error = -- | Identification 1 (IDentification 1; ID1) field
-- of the GZip header not in accepted format.
BAM_V1_6_Read_Error_GZipHeader_ID1_Incorrect_Format
-- | Identification 2 (IDentification 2; ID2) field
-- of the GZip header not in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_ID2_Incorrect_Format
-- | Compression Method (CM) field of the GZip header not
-- in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_Compression_Method_Incorrect_Format
-- | Flag (FLG) field of the GZip header not in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_Flag_Incorrect_Format
-- | Modification TIME (MTIME) field of the GZip header not
-- in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_Modification_TIME_Incorrect_Format
-- | Extra flags (eXtra FLags; XFL) field of the GZip header
-- not in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_Extra_Flags_Incorrect_Format
-- | Operating System (OS) field of the GZip header
-- not in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_Operating_System_Incorrect_Format
-- | Extra Length (eXtra LENgth; XLEN) field of the
-- GZip header is not in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_Extra_Length_Incorrect_Format
-- | Subfield Identifier 1 (Subfield Identifier1; SI1)
-- field of the GZip header is not in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_Subfield_Identifier_1_Incorrect_Format
-- | Subfield Identifier 2 (Subfield Identifier2; SI2)
-- field of the GZip header is not in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_Subfield_Identifier_2_Incorrect_Format
-- | Subfield Length (Subfield LENgth; SLEN)
-- field of the GZip header is not in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_Subfield_Length_Incorrect_Format
-- | Total block size minus 1 (total Block SIZE minus 1; BSIZE)
-- field of the GZip header is not in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_Total_Block_SIZE_Minus_1_Incorrect_Format
-- | Compressed DATA by zlib::deflate() (CDATA) is not
-- in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_Compressed_DATA_Incorrect_Format
-- | @HD tag not in accepted format (only important
-- if @HD tag is present).
| BAM_V1_6_Read_Error_File_Level_Metadata_Tag_Incorrect_Format
-- | VN tag missing (only important
-- if @HD tag is present).
| BAM_V1_6_Read_Error_File_Level_Metadata_Format_Version_Tag_Missing
-- | VN tag not in accepted format (only important
-- if @HD tag is present).
| BAM_V1_6_Read_Error_File_Level_Metadata_Format_Version_Tag_Incorrect_Format
-- | VN value not in accepted format (only important
-- if @HD tag is present).
| BAM_V1_6_Read_Error_File_Level_Metadata_Format_Version_Value_Incorrect_Format
-- | Sorting order tag not in accepted format (only important
-- if @HD tag is present).
| BAM_V1_6_Read_Error_File_Level_Metadata_Sorting_Order_Tag_Incorrect_Format
-- | Sorting order invalid value (only important
-- if @HD tag is present).
| BAM_V1_6_Read_Error_File_Level_Metadata_Sorting_Order_Invalid_Value
-- | Grouping of alignments no in accepted format (only important
-- if @HD tag is present).
| BAM_V1_6_Read_Error_File_Level_Metadata_Grouping_Of_Alignments_Tag_Incorrect_Format
-- | Grouping of Alignments invalid value (only important
-- if @HD tag is present).
| BAM_V1_6_Read_Error_File_Level_Metadata_Grouping_Of_Alignments_Invalid_Value
-- | Subsorting order tag not in accepted format (only important
-- if @HD tag is present).
| BAM_V1_6_Read_Error_File_Level_Metadata_Subsorting_Order_Tag_Incorrect_Format
-- | Subsorting order of alignments not in accepted format (only
-- if @HD tag is present.
| BAM_V1_6_Read_Error_File_Level_Metadata_Subsorting_Order_Incorrect_Format
-- | The BAM magic string in the BAM header is not BAM\SOH (BAM\1).
| BAM_V1_6_Read_Error_BAMHeader_BAM_Magic_String_Invalid_Value
-- | SN tag missing (only important
-- if @SQ tag is present).
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Tag_Missing
-- | Reference Sequence Name not in accepted format (only important
-- if @SQ tag is present.
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Incorrect_Format
-- | Reference Sequence Name invalid value (only important
-- if @SQ tag is present).
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Invalid_Value
-- | LN tag missing (only important
-- if @SQ tag is present).
| BAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Missing
-- | Reference Sequence Length not in accepted format (only important
-- if @SQ tag is present.
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Incorrect_Format
-- | Reference Sequence Length invalid value (only important
-- if @SQ tag is present).
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Invalid_Value
-- | Alternative locus not in accepted format (only important
-- if @SQ tag is present).
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Alternative_Locus_Incorrect_Format
-- | Alternative Reference Sequence Names not in accepted format (only important
-- if @SQ tag is present).
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names_Incorrect_Format
-- | Alternative Reference Sequence Names invalid value (only important
-- if @SQ tag is present).
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names_Invalid_Value
-- | Genome Assembly Identifier not in accepted format (only important
-- if @SQ tag is present).
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Genome_Assembly_Identifier_Incorrect_Format
-- | Description not in accepted format (only important
-- if @SQ tag is present).
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Description_Incorrect_Format
-- | MD5 checksum not in accepted format (only important
-- if @SQ tag is present).
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_MD5_Checksum_Incorrect_Format
-- | Species not in accepted format (only important
-- if @SQ tag is present).
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Species_Incorrect_Format
-- | Molecule topology not in accepted format (only important
-- if @SQ tag is present).
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Molecule_Topology_Incorrect_Format
-- | Molecule topology invalid value (only important
-- if @SQ tag is present).
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Molecule_Topology_Invalid_Value
-- | URI not in accepted format (only important
-- if @SQ tag is present).
| BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_URI_Incorrect_Format
-- | ID tag not accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Read_Group_Identifier_Incorrect_Format
-- | ID tag is missing (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Read_Group_Identifier_Tag_Missing
-- | BC tag not in accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Barcode_Sequence_Incorrect_Format
-- | CN tag not in accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Sequencing_Center_Incorrect_Format
-- | DS tag not in accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Description_Incorrect_Format
-- | DT tag not in accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Date_Run_Produced_Incorrect_Format
-- | FO tag not in accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Flow_Order_Incorrect_Format
-- | KS tag not in accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Key_Sequence_Incorrect_Format
-- | LB tag not in accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Library_Incorrect_Format
-- | PG tag not in accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Programs_Incorrect_Format
-- | PI tag not in accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Predicted_Median_Insert_Size_Incorrect_Format
-- | PL tag not in accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Platform_Incorrect_Format
-- | PM tag not in accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Platform_Model_Incorrect_Format
-- | PU tag not in accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Platform_Unit_Incorrect_Format
-- | SM tag not in accepted format (only important
-- if @RG tag is present).
| BAM_V1_6_Read_Error_Read_Group_Sample_Incorrect_Format
-- | RG tag not in accepted format.
| BAM_V1_6_Read_Error_Read_Group_Tag_Incorrect_Format
-- | ID tag not in accepted format (only important
-- if @PG tag is present).
| BAM_V1_6_Read_Error_Program_Identifier_Incorrect_Format
-- | PN tag not in accepted format (only important
-- if @PG tag is present).
| BAM_V1_6_Read_Error_Program_Name_Incorrect_Format
-- | CL tag not in accepted format (only important
-- if @PG tag is present).
| BAM_V1_6_Read_Error_Program_Command_Line_Incorrect_Format
-- | PP tag not in accepted format (only important
-- if @PG tag is present).
| BAM_V1_6_Read_Error_Program_Previous_PG_ID_Incorrect_Format
-- | DS tag not in accepted format (only important
-- if @PG tag is present).
| BAM_V1_6_Read_Error_Program_Description_Incorrect_Format
-- | VN tag not in accepted format (only important
-- if @PG tag is present).
| BAM_V1_6_Read_Error_Program_Version_Incorrect_Format
-- | PG tag not in accepted format.
| BAM_V1_6_Read_Error_Program_Tag_Incorrect_Format
-- | CO tag not in accepted format.
| BAM_V1_6_Read_Error_One_Line_Comment_Tag_Incorrect_Format
-- | QNAME of alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_QNAME_Incorrect_Format
-- | FLAG of alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_FLAG_Incorrect_Format
-- | RNAME of alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_RNAME_Incorrect_Format
-- | POS of alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_POS_Incorrect_Format
-- | MAPQ of alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_MAPQ_Incorrect_Format
-- | CIGAR of alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_CIGAR_Incorrect_Format
-- | RNEXT of alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_RNEXT_Incorrect_Format
-- | PNEXT of alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_PNEXT_Incorrect_Format
-- | TLEN of alignment section not in accpepted format.
| BAM_V1_6_Read_Error_Alignment_TLEN_Incorrect_Format
-- | SEQ of alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_SEQ_Incorrect_Format
-- | QUAL of alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_QUAL_Incorrect_Format
-- | Optional field is missing a type.
| BAM_V1_6_Read_Error_Alignment_OptionalFields_Missing_Type
-- | Optional field BOPT is missing a type.
| BAM_V1_6_Read_Error_Alignment_OptionalFields_BOPT_Missing_Type
-- | Optional field doesn't have a type.
| BAM_V1_6_Read_Error_Alignment_OptionalFields_Index_Missing
-- | Optional field has left-over bytes following parsing.
| BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes
-- | AOPT tag of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_AOPT_Tag_Incorrect_Format
-- | AOPT type of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_AOPT_Type_Incorrect_Format
-- | AOPT value of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_AOPT_Value_Incorrect_Format
-- | BigCOPT tag of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_BigCOPT_Tag_Incorrect_Format
-- | BigCOPT type of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_BigCOPT_Type_Incorrect_Format
-- | BigIOPT tag of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_BigIOPT_Tag_Incorrect_Format
-- | BigIOPT type of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_BigIOPT_Type_Incorrect_Format
-- | BigSOPT tag of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_BigSOPT_Tag_Incorrect_Format
-- | BigSOPT type of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_BigSOPT_Type_Incorrect_Format
-- | SmallCOPT tag of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_SmallCOPT_Tag_Incorrect_Format
-- | SmallCOPT type of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_SmallCOPT_Type_Incorrect_Format
-- | SmallIOPT tag of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_SmallIOPT_Tag_Incorrect_Format
-- | SmallIOPT type of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_SmallIOPT_Type_Incorrect_Format
-- | SmallSOPT tag of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_SmallSOPT_Tag_Incorrect_Format
-- | SmallSOPT type of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_SmallSOPT_Type_Incorrect_Format
-- | FOPT tag of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_FOPT_Tag_Incorrect_Format
-- | FOPT type of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_FOPT_Type_Incorrect_Format
-- | FOPT value of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_FOPT_Value_Incorrect_Format
-- | ZOPT tag of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_ZOPT_Tag_Incorrect_Format
-- | ZOPT type of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_ZOPT_Type_Incorrect_Format
-- | ZOPT value of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_ZOPT_Value_Incorrect_Format
-- | HOPT tag of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_HOPT_Tag_Incorrect_Format
-- | HOPT type of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_HOPT_Type_Incorrect_Format
-- | HOPT value of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_HOPT_Value_Incorrect_Format
-- | BOPT tag of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_BOPT_Tag_Incorrect_Format
-- | BOPT type of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_BOPT_Type_Incorrect_Format
-- | BOPT value type of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_BOPT_Value_Type_Incorrect_Format
-- | BOPT value data of the alignment section not in accepted format.
| BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format
-- | The CDATA field of a BGZF block not in accepted format.
| BAM_V1_6_Read_Error_CDATA_Incorrect_Format
-- | A CDATA BAM block alignment optional fields
-- are not in accepted format.
| BAM_V1_6_Read_Error_CDATA_BAM_Alignment_Optional_Fields_Incorrect_Format
-- | CRC-32 (CRC32) field of the GZip header
-- not in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_CRC32_Incorrect_Format
-- | Input Size (Input SIZE, i.e. length of uncompressed data)
-- not in accepted format.
| BAM_V1_6_Read_Error_GZipHeader_Input_Size_Incorrect_Format
-- | The calculated crc32 of the uncompressed CDATA
-- is not equivalent to the CRC32 field of the BGZF block.
| BAM_V1_6_Read_Error_Calculated_CRC32_Not_Equivalent_To_CRC32
-- | The last 28 bytes of the BAM file are not equivalent
-- to the standardized 28 byte end-of-file marker.
| BAM_V1_6_Read_Error_End_Of_File_Marker_Incorrect_Format
deriving (Eq,Generic,Show,Typeable)