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Module Biocaml_sam.Error (.ml)

module Error:
sig

The possible errors.
type optional_content_parsing = [ `wrong_optional of
           (string * char * string) list *
           [ `not_a_char of string
           | `not_a_float of string
           | `not_an_int of string
           | `unknown_type of char
           | `wrong_array of
               [ `not_a_char of string
               | `not_a_float of string
               | `not_an_int of string
               | `unknown_type of char
               | `wrong_type of string ]
           | `wrong_type of string ] ]
Errors which can happen while parsing optional content.
type string_to_raw = [ `incomplete_input of Biocaml_pos.t * string list * string option
       | `invalid_header_tag of Biocaml_pos.t * string
       | `invalid_tag_value_list of Biocaml_pos.t * string list
       | `not_an_int of Biocaml_pos.t * string * string
       | `wrong_alignment of Biocaml_pos.t * string
       | `wrong_optional_field of Biocaml_pos.t * string ]
The possible errors one can get while parsing SAM files.
type raw_to_item = [ `comment_after_end_of_header of int * string
       | `duplicate_in_reference_sequence_dictionary of
           Biocaml_sam.reference_sequence array
       | `header_after_end_of_header of int * (string * (string * string) list)
       | `header_line_not_first of int
       | `header_line_without_version of (string * string) list
       | `header_line_wrong_sorting of string
       | `missing_ref_sequence_length of (string * string) list
       | `missing_ref_sequence_name of (string * string) list
       | `wrong_cigar_text of string
       | `wrong_flag of Biocaml_sam.raw_alignment
       | `wrong_mapq of Biocaml_sam.raw_alignment
       | `wrong_optional of
           (string * char * string) list *
           [ `not_a_char of string
           | `not_a_float of string
           | `not_an_int of string
           | `unknown_type of char
           | `wrong_array of
               [ `not_a_char of string
               | `not_a_float of string
               | `not_an_int of string
               | `unknown_type of char
               | `wrong_type of string ]
           | `wrong_type of string ]
       | `wrong_phred_scores of Biocaml_sam.raw_alignment
       | `wrong_pnext of Biocaml_sam.raw_alignment
       | `wrong_pos of Biocaml_sam.raw_alignment
       | `wrong_qname of Biocaml_sam.raw_alignment
       | `wrong_ref_sequence_length of (string * string) list
       | `wrong_tlen of Biocaml_sam.raw_alignment ]
The possible errors one can get while lifting SAM raw_items to higher-level representations. (Note: raw_to_item explicitly contains optional_content_parsing but OCamldoc pastes it inline)
type item_to_raw = [ `wrong_phred_scores of Biocaml_sam.alignment ]
The error that may happen while downgrading the higher-level represtation of an alignment.
type parse = [ `comment_after_end_of_header of int * string
       | `duplicate_in_reference_sequence_dictionary of
           Biocaml_sam.reference_sequence array
       | `header_after_end_of_header of int * (string * (string * string) list)
       | `header_line_not_first of int
       | `header_line_without_version of (string * string) list
       | `header_line_wrong_sorting of string
       | `incomplete_input of Biocaml_pos.t * string list * string option
       | `invalid_header_tag of Biocaml_pos.t * string
       | `invalid_tag_value_list of Biocaml_pos.t * string list
       | `missing_ref_sequence_length of (string * string) list
       | `missing_ref_sequence_name of (string * string) list
       | `not_an_int of Biocaml_pos.t * string * string
       | `wrong_alignment of Biocaml_pos.t * string
       | `wrong_cigar_text of string
       | `wrong_flag of Biocaml_sam.raw_alignment
       | `wrong_mapq of Biocaml_sam.raw_alignment
       | `wrong_optional of
           (string * char * string) list *
           [ `not_a_char of string
           | `not_a_float of string
           | `not_an_int of string
           | `unknown_type of char
           | `wrong_array of
               [ `not_a_char of string
               | `not_a_float of string
               | `not_an_int of string
               | `unknown_type of char
               | `wrong_type of string ]
           | `wrong_type of string ]
       | `wrong_optional_field of Biocaml_pos.t * string
       | `wrong_phred_scores of Biocaml_sam.raw_alignment
       | `wrong_pnext of Biocaml_sam.raw_alignment
       | `wrong_pos of Biocaml_sam.raw_alignment
       | `wrong_qname of Biocaml_sam.raw_alignment
       | `wrong_ref_sequence_length of (string * string) list
       | `wrong_tlen of Biocaml_sam.raw_alignment ]
All possible parsing errors. It is defined as: 
      type parse = [

      | string_to_raw

      | raw_to_item

      ]

      

type t = parse
The union of all possible errors.

S-Expressions conversions for Errors


val optional_content_parsing_of_sexp : Sexplib.Sexp.t -> optional_content_parsing
val sexp_of_optional_content_parsing : optional_content_parsing -> Sexplib.Sexp.t
val string_to_raw_of_sexp : Sexplib.Sexp.t -> string_to_raw
val sexp_of_string_to_raw : string_to_raw -> Sexplib.Sexp.t
val raw_to_item_of_sexp : Sexplib.Sexp.t -> raw_to_item
val sexp_of_raw_to_item : raw_to_item -> Sexplib.Sexp.t
val item_to_raw_of_sexp : Sexplib.Sexp.t -> item_to_raw
val sexp_of_item_to_raw : item_to_raw -> Sexplib.Sexp.t
val parse_of_sexp : Sexplib.Sexp.t -> parse
val sexp_of_parse : parse -> Sexplib.Sexp.t
val t_of_sexp : Sexplib.Sexp.t -> parse
val sexp_of_t : parse -> Sexplib.Sexp.t
end