package biocaml

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The OCaml Bioinformatics Library

Install

Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

  1. S
    Sebastien Mondet
  2. A
    Ashish Agarwal
  3. P
    Philippe Veber
  4. C
    Christophe Troestler
  5. S
    Sergei Lebedev
  6. D
    David Koppstein
  7. A
    Alexander Gryzlov
  8. F
    Francois Berenger

Maintainers

  1. B
    biocaml@googlegroups.com

Sources

v0.11.0.tar.gz
md5=486aeb3e552dabae85839e2af30d6c52
sha512=4ed2df0b7cbd80bd6e29bd8fee9d2dacd9379ad0f4ff142bd8e16ade3f1507f6cc7cbe4c614943b8feb8fa4705935695cb458606b0da813dbf255b1e566a43cf

doc/biocaml.unix/Biocaml_unix/Sam/index.html

Module Biocaml_unix.SamSource

SAM files. Documentation here assumes familiarity with the SAM specification.

Types

Header Types

Sourcetype header_item_tag = private [<
  1. | `HD
  2. | `SQ
  3. | `RG
  4. | `PG
  5. | `CO
  6. | `Other of string
]

Header item tags define the different types of header lines. The term "tag" in this context should not be confused with its use in "tag-value" pairs, which comprise the content of header items.

Sourceval sexp_of_header_item_tag : header_item_tag -> Sexplib0.Sexp.t
Sourceval header_item_tag_of_sexp : Sexplib0.Sexp.t -> header_item_tag
Sourceval __header_item_tag_of_sexp__ : Sexplib0.Sexp.t -> header_item_tag
Sourcetype tag_value = private string * string

A tag-value pair comprising the content of header items. Tag-value pairs occur in other places too, but this type is specifically for those in the header.

Sourceval sexp_of_tag_value : tag_value -> Sexplib0.Sexp.t
Sourceval tag_value_of_sexp : Sexplib0.Sexp.t -> tag_value
Sourcetype sort_order = [
  1. | `Unknown
  2. | `Unsorted
  3. | `Query_name
  4. | `Coordinate
]
Sourceval sexp_of_sort_order : sort_order -> Sexplib0.Sexp.t
Sourceval sort_order_of_sexp : Sexplib0.Sexp.t -> sort_order
Sourceval __sort_order_of_sexp__ : Sexplib0.Sexp.t -> sort_order
Sourcetype group_order = [
  1. | `None
  2. | `Query
  3. | `Reference
]
Sourceval sexp_of_group_order : group_order -> Sexplib0.Sexp.t
Sourceval group_order_of_sexp : Sexplib0.Sexp.t -> group_order
Sourceval __group_order_of_sexp__ : Sexplib0.Sexp.t -> group_order
Sourcetype header_line = private {
  1. version : string;
    (*

    VN

    *)
  2. sort_order : sort_order option;
    (*

    SO

    *)
  3. group_order : group_order option;
    (*

    GO

    *)
}

@HD. A header consists of different types of lines. Confusingly, one of these types is called the "header line", which is what this type refers to. It does not refer generically to any line within a header.

Sourceval sexp_of_header_line : header_line -> Sexplib0.Sexp.t
Sourceval header_line_of_sexp : Sexplib0.Sexp.t -> header_line
Sourcetype ref_seq = private {
  1. name : string;
    (*

    SN

    *)
  2. length : int;
    (*

    LN

    *)
  3. assembly : string option;
    (*

    AS

    *)
  4. md5 : string option;
    (*

    M5

    *)
  5. species : string option;
    (*

    SP

    *)
  6. uri : string option;
    (*

    UR

    *)
}

@SQ. Reference sequence.

Sourceval sexp_of_ref_seq : ref_seq -> Sexplib0.Sexp.t
Sourceval ref_seq_of_sexp : Sexplib0.Sexp.t -> ref_seq
Sourcetype platform = [
  1. | `Capillary
  2. | `LS454
  3. | `Illumina
  4. | `Solid
  5. | `Helicos
  6. | `Ion_Torrent
  7. | `Pac_Bio
]
Sourceval sexp_of_platform : platform -> Sexplib0.Sexp.t
Sourceval platform_of_sexp : Sexplib0.Sexp.t -> platform
Sourceval __platform_of_sexp__ : Sexplib0.Sexp.t -> platform
Sourcetype read_group = private {
  1. id : string;
    (*

    ID

    *)
  2. seq_center : string option;
    (*

    CN

    *)
  3. description : string option;
    (*

    DS

    *)
  4. run_date : [ `Date of string | `Time of string ] option;
    (*

    DT

    *)
  5. flow_order : string option;
    (*

    FO

    *)
  6. key_seq : string option;
    (*

    KS

    *)
  7. library : string option;
    (*

    LB

    *)
  8. program : string option;
    (*

    PG

    *)
  9. predicted_median_insert_size : int option;
    (*

    PI

    *)
  10. platform : platform option;
    (*

    PL

    *)
  11. platform_unit : string option;
    (*

    PU

    *)
  12. sample : string option;
    (*

    SM

    *)
}

@RG.

Sourceval sexp_of_read_group : read_group -> Sexplib0.Sexp.t
Sourceval read_group_of_sexp : Sexplib0.Sexp.t -> read_group
Sourcetype program = private {
  1. id : string;
    (*

    ID

    *)
  2. name : string option;
    (*

    PN

    *)
  3. command_line : string option;
    (*

    CL

    *)
  4. previous_id : string option;
    (*

    PP

    *)
  5. description : string option;
    (*

    DS

    *)
  6. version : string option;
    (*

    VN

    *)
}

@PG.

Sourceval sexp_of_program : program -> Sexplib0.Sexp.t
Sourceval program_of_sexp : Sexplib0.Sexp.t -> program
Sourcetype header_item = private [<
  1. | `HD of header_line
  2. | `SQ of ref_seq
  3. | `RG of read_group
  4. | `PG of program
  5. | `CO of string
  6. | `Other of string * tag_value list
]
Sourceval sexp_of_header_item : header_item -> Sexplib0.Sexp.t
Sourceval header_item_of_sexp : Sexplib0.Sexp.t -> header_item
Sourceval __header_item_of_sexp__ : Sexplib0.Sexp.t -> header_item
Sourcetype header = private {
  1. version : string option;
  2. sort_order : sort_order option;
  3. group_order : group_order option;
  4. ref_seqs : ref_seq list;
  5. read_groups : read_group list;
  6. programs : program list;
  7. comments : string list;
  8. others : (string * tag_value list) list;
}
  • sort_order: Guaranteed to be None if version = None.
  • ref_seqs: List of @SQ items. Order matters; it dictates alignment sorting order when sort_order = `Coordinate.
  • read_groups: Unordered list of @RG items.
  • programs: List of @PG lines. Currently unordered, but we should topologically sort.
  • comments: Unordered list of @CO lines.
Sourceval empty_header : header
Sourcemodule Flags : sig ... end
Sourcetype cigar_op = private [<
  1. | `Alignment_match of int
  2. | `Insertion of int
  3. | `Deletion of int
  4. | `Skipped of int
  5. | `Soft_clipping of int
  6. | `Hard_clipping of int
  7. | `Padding of int
  8. | `Seq_match of int
  9. | `Seq_mismatch of int
]

CIGAR operations.

Sourceval sexp_of_cigar_op : cigar_op -> Sexplib0.Sexp.t
Sourceval cigar_op_of_sexp : Sexplib0.Sexp.t -> cigar_op
Sourceval __cigar_op_of_sexp__ : Sexplib0.Sexp.t -> cigar_op
Sourcetype optional_field_value = private [<
  1. | `A of char
  2. | `i of Core_kernel.Int64.t
  3. | `f of float
  4. | `Z of string
  5. | `H of string
  6. | `B of char * string list
]

The constructor encodes the TYPE and each carries its corresponding VALUE.

Sourceval sexp_of_optional_field_value : optional_field_value -> Sexplib0.Sexp.t
Sourceval optional_field_value_of_sexp : Sexplib0.Sexp.t -> optional_field_value
Sourceval __optional_field_value_of_sexp__ : Sexplib0.Sexp.t -> optional_field_value
Sourcetype optional_field = private {
  1. tag : string;
  2. value : optional_field_value;
}
Sourceval sexp_of_optional_field : optional_field -> Sexplib0.Sexp.t
Sourceval optional_field_of_sexp : Sexplib0.Sexp.t -> optional_field
Sourcetype rnext = private [<
  1. | `Value of string
  2. | `Equal_to_RNAME
]
Sourceval sexp_of_rnext : rnext -> Sexplib0.Sexp.t
Sourceval rnext_of_sexp : Sexplib0.Sexp.t -> rnext
Sourceval __rnext_of_sexp__ : Sexplib0.Sexp.t -> rnext
Sourcetype alignment = private {
  1. qname : string option;
    (*

    QNAME

    *)
  2. flags : Flags.t;
    (*

    FLAG

    *)
  3. rname : string option;
    (*

    RNAME

    *)
  4. pos : int option;
    (*

    POS

    *)
  5. mapq : int option;
    (*

    MAPQ

    *)
  6. cigar : cigar_op list;
    (*

    CIGAR

    *)
  7. rnext : rnext option;
    (*

    RNEXT

    *)
  8. pnext : int option;
    (*

    PNEXT

    *)
  9. tlen : int option;
    (*

    TLEN

    *)
  10. seq : string option;
    (*

    SEQ

    *)
  11. qual : Phred_score.t list;
    (*

    QUAL

    *)
  12. optional_fields : optional_field list;
}

For cigar and qual, empty list indicates no value, i.e. '*', was given.

Sourceval sexp_of_alignment : alignment -> Sexplib0.Sexp.t
Sourceval alignment_of_sexp : Sexplib0.Sexp.t -> alignment
Sourcemodule MakeIO (Future : Future.S) : sig ... end
include sig ... end
Sourceval read : ?start:Pos.t -> Future_unix.Reader.t -> (header * alignment Core_kernel.Or_error.t Future_unix.Pipe.Reader.t) Core_kernel.Or_error.t Future_unix.Deferred.t
Sourceval write_file : ?perm:int -> ?append:bool -> string -> ?header:header -> alignment Future_unix.Pipe.Reader.t -> unit Future_unix.Deferred.t

Low-level Parsers and Constructors

Sourceval header_line : version:string -> ?sort_order:sort_order -> ?group_order:group_order -> unit -> header_line Core_kernel.Or_error.t

Low-level Header Parsers and Constructors

Sourceval ref_seq : name:string -> length:int -> ?assembly:string -> ?md5:string -> ?species:string -> ?uri:string -> unit -> ref_seq Core_kernel.Or_error.t
Sourceval read_group : id:string -> ?seq_center:string -> ?description:string -> ?run_date:string -> ?flow_order:string -> ?key_seq:string -> ?library:string -> ?program:string -> ?predicted_median_insert_size:int -> ?platform:platform -> ?platform_unit:string -> ?sample:string -> unit -> read_group Core_kernel.Or_error.t

The run_date string will be parsed as a Date.t or Time.t, whichever is possible. If it is a time without a timezone, local timezone will be assumed.

Sourceval header : ?version:string -> ?sort_order:sort_order -> ?group_order:group_order -> ?ref_seqs:ref_seq list -> ?read_groups:read_group list -> ?programs:program list -> ?comments:string list -> ?others:(string * tag_value list) list -> unit -> header Core_kernel.Or_error.t
Sourceval parse_header_item_tag : string -> header_item_tag Core_kernel.Or_error.t
Sourceval parse_tag_value : string -> tag_value Core_kernel.Or_error.t
Sourceval parse_header_version : string -> string Core_kernel.Or_error.t
Sourceval parse_sort_order : string -> sort_order Core_kernel.Or_error.t
Sourceval parse_header_line : tag_value list -> header_line Core_kernel.Or_error.t
Sourceval parse_ref_seq : tag_value list -> ref_seq Core_kernel.Or_error.t
Sourceval parse_platform : string -> platform Core_kernel.Or_error.t
Sourceval parse_read_group : tag_value list -> read_group Core_kernel.Or_error.t
Sourceval parse_program : tag_value list -> program Core_kernel.Or_error.t
Sourceval parse_header_item : Line.t -> header_item Core_kernel.Or_error.t
Sourceval parse_header : string -> header Core_kernel.Or_error.t
Sourceval cigar_op_alignment_match : int -> cigar_op Core_kernel.Or_error.t

Low-level Optional field Parsers and Constructors

Sourceval cigar_op_insertion : int -> cigar_op Core_kernel.Or_error.t
Sourceval cigar_op_deletion : int -> cigar_op Core_kernel.Or_error.t
Sourceval cigar_op_skipped : int -> cigar_op Core_kernel.Or_error.t
Sourceval cigar_op_soft_clipping : int -> cigar_op Core_kernel.Or_error.t
Sourceval cigar_op_hard_clipping : int -> cigar_op Core_kernel.Or_error.t
Sourceval cigar_op_padding : int -> cigar_op Core_kernel.Or_error.t
Sourceval cigar_op_seq_match : int -> cigar_op Core_kernel.Or_error.t
Sourceval cigar_op_seq_mismatch : int -> cigar_op Core_kernel.Or_error.t
Sourceval optional_field_value_A : char -> optional_field_value Core_kernel.Or_error.t

Low-level Optional field Parsers and Constructors

Sourceval optional_field_value_i : Core_kernel.Int64.t -> optional_field_value
Sourceval optional_field_value_f : float -> optional_field_value
Sourceval optional_field_value_Z : string -> optional_field_value Core_kernel.Or_error.t
Sourceval optional_field_value_H : string -> optional_field_value Core_kernel.Or_error.t
Sourceval optional_field_value_B : char -> string list -> optional_field_value Core_kernel.Or_error.t
Sourceval optional_field : string -> optional_field_value -> optional_field Core_kernel.Or_error.t
Sourceval parse_optional_field_value : string -> optional_field_value Core_kernel.Or_error.t
Sourceval parse_optional_field : string -> optional_field Core_kernel.Or_error.t
Sourceval alignment : ?ref_seqs:Core_kernel.String.Set.t -> ?qname:string -> flags:Flags.t -> ?rname:string -> ?pos:int -> ?mapq:int -> ?cigar:cigar_op list -> ?rnext:rnext -> ?pnext:int -> ?tlen:int -> ?seq:string -> ?qual:Phred_score.t list -> ?optional_fields:optional_field list -> unit -> alignment Core_kernel.Or_error.t

Low-level Alignment Parsers and Constructors

Sourceval parse_qname : string -> string option Core_kernel.Or_error.t
Sourceval parse_flags : string -> Flags.t Core_kernel.Or_error.t
Sourceval parse_rname : string -> string option Core_kernel.Or_error.t
Sourceval parse_pos : string -> int option Core_kernel.Or_error.t
Sourceval parse_mapq : string -> int option Core_kernel.Or_error.t
Sourceval parse_cigar : string -> cigar_op list Core_kernel.Or_error.t
Sourceval parse_rnext : string -> rnext option Core_kernel.Or_error.t
Sourceval parse_pnext : string -> int option Core_kernel.Or_error.t
Sourceval parse_tlen : string -> int option Core_kernel.Or_error.t
Sourceval parse_seq : string -> string option Core_kernel.Or_error.t
Sourceval parse_qual : string -> Phred_score.t list Core_kernel.Or_error.t
Sourceval parse_alignment : ?ref_seqs:Core_kernel.String.Set.t -> Line.t -> alignment Core_kernel.Or_error.t

Low-level Printers

Sourceval print_header_item_tag : header_item_tag -> string

Low-level Header Printers

Sourceval print_tag_value : tag_value -> string
Sourceval print_header_version : string -> string
Sourceval print_sort_order : sort_order -> string
Sourceval print_header_line : header_line -> string
Sourceval print_ref_seq : ref_seq -> string
Sourceval print_platform : platform -> string
Sourceval print_read_group : read_group -> string
Sourceval print_program : program -> string
Sourceval print_other : (string * tag_value list) -> string
Sourceval print_qname : string option -> string

Low-level Alignment Printers

Sourceval print_flags : Flags.t -> string
Sourceval print_rname : string option -> string
Sourceval print_pos : int option -> string
Sourceval print_mapq : int option -> string
Sourceval print_cigar_op : cigar_op -> string
Sourceval print_cigar : cigar_op list -> string
Sourceval print_rnext : rnext option -> string
Sourceval print_pnext : int option -> string
Sourceval print_tlen : int option -> string
Sourceval print_seq : string option -> string
Sourceval print_qual : Phred_score.t list -> string
Sourceval print_optional_field : optional_field -> string
Sourceval print_alignment : alignment -> string
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