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Module Biocaml_bam.Error (.ml)

module Error:
sig

The possible errors returned by parsing and printing functions.
type raw_bam = [ `read_name_not_null_terminated of string
       | `reference_information_name_not_null_terminated of string
       | `reference_information_overflow of int * string
       | `wrong_int32 of string
       | `wrong_magic_number of string ]
The possible non-gzip-related errors encountered while parsing a BAM file.
type parse_optional = [ `wrong_auxiliary_data of
           [ `array_size of int
           | `null_terminated_hexarray
           | `null_terminated_string
           | `out_of_bounds
           | `unknown_type of char
           | `wrong_int32 of string ] * string ]
The potential failures while parsing the optional content in BAM alignments.
type parse_cigar = [ `wrong_cigar of string | `wrong_cigar_length of int ]
The potential failures while parsing the so-called CIGAR operations
type raw_to_item = [ `header_line_not_first of int
       | `header_line_without_version of (string * string) list
       | `header_line_wrong_sorting of string
       | `invalid_header_tag of int * string
       | `invalid_tag_value_list of int * string list
       | `reference_sequence_not_found of Biocaml_bam.raw_alignment
       | `wrong_auxiliary_data of
           [ `array_size of int
           | `null_terminated_hexarray
           | `null_terminated_string
           | `out_of_bounds
           | `unknown_type of char
           | `wrong_int32 of string ] * string
       | `wrong_cigar of string
       | `wrong_cigar_length of int
       | `wrong_flag of Biocaml_bam.raw_alignment
       | `wrong_mapq of Biocaml_bam.raw_alignment
       | `wrong_pnext of Biocaml_bam.raw_alignment
       | `wrong_pos of Biocaml_bam.raw_alignment
       | `wrong_qname of Biocaml_bam.raw_alignment
       | `wrong_tlen of Biocaml_bam.raw_alignment ]
All the possible errors one can encounter while going from raw_items to Sam.items.
type item_to_raw = [ `cannot_get_sequence of Biocaml_sam.alignment
       | `header_item_not_first of string
       | `reference_name_not_found of Biocaml_sam.alignment * string ]
Inconsistency errors that may happen while trnasforming a Sam.item to a raw_item.
type t = [ `cannot_get_sequence of Biocaml_sam.alignment
       | `header_item_not_first of string
       | `header_line_not_first of int
       | `header_line_without_version of (string * string) list
       | `header_line_wrong_sorting of string
       | `invalid_header_tag of int * string
       | `invalid_tag_value_list of int * string list
       | `read_name_not_null_terminated of string
       | `reference_information_name_not_null_terminated of string
       | `reference_information_overflow of int * string
       | `reference_name_not_found of Biocaml_sam.alignment * string
       | `reference_sequence_not_found of Biocaml_bam.raw_alignment
       | `wrong_auxiliary_data of
           [ `array_size of int
           | `null_terminated_hexarray
           | `null_terminated_string
           | `out_of_bounds
           | `unknown_type of char
           | `wrong_int32 of string ] * string
       | `wrong_cigar of string
       | `wrong_cigar_length of int
       | `wrong_flag of Biocaml_bam.raw_alignment
       | `wrong_int32 of string
       | `wrong_magic_number of string
       | `wrong_mapq of Biocaml_bam.raw_alignment
       | `wrong_pnext of Biocaml_bam.raw_alignment
       | `wrong_pos of Biocaml_bam.raw_alignment
       | `wrong_qname of Biocaml_bam.raw_alignment
       | `wrong_tlen of Biocaml_bam.raw_alignment ]
The union of all the errors.
val raw_bam_of_sexp : Sexplib.Sexp.t -> raw_bam
val sexp_of_raw_bam : raw_bam -> Sexplib.Sexp.t
val parse_optional_of_sexp : Sexplib.Sexp.t -> parse_optional
val sexp_of_parse_optional : parse_optional -> Sexplib.Sexp.t
val parse_cigar_of_sexp : Sexplib.Sexp.t -> parse_cigar
val sexp_of_parse_cigar : parse_cigar -> 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 t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
end