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Module Biocaml.Sam (.ml)

module Sam: Biocaml_sam
type raw_alignment = {
   qname :string;
   flag :int;
   rname :string;
   pos :int;
   mapq :int;
   cigar :string;
   rnext :string;
   pnext :int;
   tlen :int;
   seq :string;
   qual :string;
   optional :(string * char * string) list;
}
The contents of an alignment line.
type raw_item = [ `alignment of raw_alignment
       | `comment of string
       | `header of string * (string * string) list ]
The "items" of a parsed SAM file stream.
type reference_sequence = {
   ref_name :string;
   ref_length :int;
   ref_assembly_identifier :string option;
   ref_checksum :string option;
   ref_species :string option;
   ref_uri :string option;
   ref_unknown :(string * string) list;
} 
val reference_sequence : ?assembly_identifier:string ->
       ?checksum:string ->
       ?species:string ->
       ?uri:string ->
       ?unknown_data:(string * string) list ->
       string -> int -> reference_sequence
module Flags: sig .. end
type cigar_op = [ `D of int
       | `Eq of int
       | `H of int
       | `I of int
       | `M of int
       | `N of int
       | `P of int
       | `S of int
       | `X of int ] 
type optional_content_value = [ `array of char * optional_content_value array
       | `char of char
       | `float of float
       | `int of int
       | `string of string ] 
type optional_content = (string * char * optional_content_value) list 
type alignment = {
   query_template_name :string;
   flags :Flags.t;
   reference_sequence :[ `name of string
| `none
| `reference_sequence of reference_sequence ];
   position :int option;
   mapping_quality :int option;
   cigar_operations :cigar_op array;
   next_reference_sequence :[ `name of string
| `none
| `qname
| `reference_sequence of reference_sequence ];
   next_position :int option;
   template_length :int option;
   sequence :[ `none | `reference | `string of string ];
   quality :Biocaml_phred_score.t array;
   optional_content :optional_content;
} 
type item = [ `alignment of alignment
       | `comment of string
       | `header of string * (string * string) list
       | `header_line of
           string * [ `coordinate | `queryname | `unknown | `unsorted ] *
           (string * string) list
       | `reference_sequence_dictionary of reference_sequence array ] 
module Error: sig .. end
val in_channel_to_item_stream : ?buffer_size:int ->
       ?filename:string ->
       Pervasives.in_channel ->
       (item, Error.parse) Core.Result.t Stream.t
module Low_level_parsing: sig .. end
module Transform: sig .. end
val raw_alignment_of_sexp : Sexplib.Sexp.t -> raw_alignment
val sexp_of_raw_alignment : raw_alignment -> Sexplib.Sexp.t
The contents of an alignment line.
val raw_item_of_sexp : Sexplib.Sexp.t -> raw_item
val raw_item_of_sexp__ : Sexplib.Sexp.t -> raw_item
val sexp_of_raw_item : raw_item -> Sexplib.Sexp.t
The "items" of a parsed SAM file stream.
val reference_sequence_of_sexp : Sexplib.Sexp.t -> reference_sequence
val sexp_of_reference_sequence : reference_sequence -> Sexplib.Sexp.t
val cigar_op_of_sexp : Sexplib.Sexp.t -> cigar_op
val cigar_op_of_sexp__ : Sexplib.Sexp.t -> cigar_op
val sexp_of_cigar_op : cigar_op -> Sexplib.Sexp.t
val optional_content_value_of_sexp : Sexplib.Sexp.t -> optional_content_value
val optional_content_value_of_sexp__ : Sexplib.Sexp.t -> optional_content_value
val sexp_of_optional_content_value : optional_content_value -> Sexplib.Sexp.t
val optional_content_of_sexp : Sexplib.Sexp.t -> optional_content
val sexp_of_optional_content : optional_content -> Sexplib.Sexp.t
val alignment_of_sexp : Sexplib.Sexp.t -> alignment
val sexp_of_alignment : alignment -> Sexplib.Sexp.t
val item_of_sexp : Sexplib.Sexp.t -> item
val item_of_sexp__ : Sexplib.Sexp.t -> item
val sexp_of_item : item -> Sexplib.Sexp.t

The possible errors one can get while parsing SAM files.

Create a parsing "stoppable" transform.

Create a printing "stoppable" transform.