Module `Biocaml_unix.Sam`Source

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

Types

Header Types

Sourcetype header_item_tag = private [<

| `HD
| `SQ
| `RG
| `PG
| `CO
| `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 = [

| `Unknown
| `Unsorted
| `Query_name
| `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 = [

| `None
| `Query
| `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 {

version : string;
(*
VN
*)
sort_order : sort_order option;
(*
SO
*)
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 {

name : string;
(*
SN
*)
length : int;
(*
LN
*)
assembly : string option;
(*
AS
*)
md5 : string option;
(*
M5
*)
species : string option;
(*
SP
*)
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 = [

| `Capillary
| `LS454
| `Illumina
| `Solid
| `Helicos
| `Ion_Torrent
| `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 {

id : string;
(*
ID
*)
seq_center : string option;
(*
CN
*)
description : string option;
(*
DS
*)
run_date : [ `Date of string | `Time of string ] option;
(*
DT
*)
flow_order : string option;
(*
FO
*)
key_seq : string option;
(*
KS
*)
library : string option;
(*
LB
*)
program : string option;
(*
PG
*)
predicted_median_insert_size : int option;
(*
PI
*)
platform : platform option;
(*
PL
*)
platform_unit : string option;
(*
PU
*)
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 {

id : string;
(*
ID
*)
name : string option;
(*
PN
*)
command_line : string option;
(*
CL
*)
previous_id : string option;
(*
PP
*)
description : string option;
(*
DS
*)
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 [<

| `HD of header_line
| `SQ of ref_seq
| `RG of read_group
| `PG of program
| `CO of string
| `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 {

version : string option;
sort_order : sort_order option;
group_order : group_order option;
ref_seqs : ref_seq list;
read_groups : read_group list;
programs : program list;
comments : string list;
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 [<

| `Alignment_match of int
| `Insertion of int
| `Deletion of int
| `Skipped of int
| `Soft_clipping of int
| `Hard_clipping of int
| `Padding of int
| `Seq_match of int
| `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 [<

| `A of char
| `i of Core.Int64.t
| `f of float
| `Z of string
| `H of string
| `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 {

tag : string;
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 [<

| `Value of string
| `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 {

qname : string option;
(*
QNAME
*)
flags : Flags.t;
(*
FLAG
*)
rname : string option;
(*
RNAME
*)
pos : int option;
(*
POS
*)
mapq : int option;
(*
MAPQ
*)
cigar : cigar_op list;
(*
CIGAR
*)
rnext : rnext option;
(*
RNEXT
*)
pnext : int option;
(*
PNEXT
*)
tlen : int option;
(*
TLEN
*)
seq : string option;
(*
SEQ
*)
qual : Phred_score.t list;
(*
QUAL
*)
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

Source

val read : 
  ?start:Pos.t ->
  Future_unix.Reader.t ->
  (header * alignment Core.Or_error.t Future_unix.Pipe.Reader.t)
    Core.Or_error.t
    Future_unix.Deferred.t

Source

val write : 
  Future_unix.Writer.t ->
  ?header:header ->
  alignment Future_unix.Pipe.Reader.t ->
  unit Future_unix.Deferred.t

Source

val 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

Source

val header_line : 
  version:string ->
  ?sort_order:sort_order ->
  ?group_order:group_order ->
  unit ->
  header_line Core.Or_error.t

Low-level Header Parsers and Constructors

Source

val ref_seq : 
  name:string ->
  length:int ->
  ?assembly:string ->
  ?md5:string ->
  ?species:string ->
  ?uri:string ->
  unit ->
  ref_seq Core.Or_error.t

Source

val 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.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.

Source

val 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.Or_error.t

Sourceval parse_header_item_tag : string -> header_item_tag Core.Or_error.t

Sourceval parse_tag_value : string -> tag_value Core.Or_error.t

Sourceval parse_header_version : string -> string Core.Or_error.t

Sourceval parse_sort_order : string -> sort_order Core.Or_error.t

Sourceval parse_header_line : tag_value list -> header_line Core.Or_error.t

Sourceval parse_ref_seq : tag_value list -> ref_seq Core.Or_error.t

Sourceval parse_platform : string -> platform Core.Or_error.t

Sourceval parse_read_group : tag_value list -> read_group Core.Or_error.t

Sourceval parse_program : tag_value list -> program Core.Or_error.t

Sourceval parse_header_item : Line.t -> header_item Core.Or_error.t

Sourceval parse_header : string -> header Core.Or_error.t

Sourceval cigar_op_alignment_match : int -> cigar_op Core.Or_error.t

Low-level Optional field Parsers and Constructors

Sourceval cigar_op_insertion : int -> cigar_op Core.Or_error.t

Sourceval cigar_op_deletion : int -> cigar_op Core.Or_error.t

Sourceval cigar_op_skipped : int -> cigar_op Core.Or_error.t

Sourceval cigar_op_soft_clipping : int -> cigar_op Core.Or_error.t

Sourceval cigar_op_hard_clipping : int -> cigar_op Core.Or_error.t

Sourceval cigar_op_padding : int -> cigar_op Core.Or_error.t

Sourceval cigar_op_seq_match : int -> cigar_op Core.Or_error.t

Sourceval cigar_op_seq_mismatch : int -> cigar_op Core.Or_error.t

Sourceval optional_field_value_A : char -> optional_field_value Core.Or_error.t

Low-level Optional field Parsers and Constructors

Sourceval optional_field_value_i : Core.Int64.t -> optional_field_value

Sourceval optional_field_value_f : float -> optional_field_value

Sourceval optional_field_value_Z : string -> optional_field_value Core.Or_error.t

Sourceval optional_field_value_H : string -> optional_field_value Core.Or_error.t

Source

val optional_field_value_B : 
  char ->
  string list ->
  optional_field_value Core.Or_error.t

Source

val optional_field : 
  string ->
  optional_field_value ->
  optional_field Core.Or_error.t

Sourceval parse_optional_field_value : string -> optional_field_value Core.Or_error.t

Sourceval parse_optional_field : string -> optional_field Core.Or_error.t

Source

val alignment : 
  ?ref_seqs:Core.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.Or_error.t

Low-level Alignment Parsers and Constructors

Sourceval parse_qname : string -> string option Core.Or_error.t

Sourceval parse_flags : string -> Flags.t Core.Or_error.t

Sourceval parse_rname : string -> string option Core.Or_error.t

Sourceval parse_pos : string -> int option Core.Or_error.t

Sourceval parse_mapq : string -> int option Core.Or_error.t

Sourceval parse_cigar : string -> cigar_op list Core.Or_error.t

Sourceval parse_rnext : string -> rnext option Core.Or_error.t

Sourceval parse_pnext : string -> int option Core.Or_error.t

Sourceval parse_tlen : string -> int option Core.Or_error.t

Sourceval parse_seq : string -> string option Core.Or_error.t

Sourceval parse_qual : string -> Phred_score.t list Core.Or_error.t

Source

val parse_alignment : 
  ?ref_seqs:Core.String.Set.t ->
  Line.t ->
  alignment Core.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

Install

Dune Dependency

Authors

Maintainers

Sources

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

Module `Biocaml_unix.Sam`Source

Types

Header Types

Low-level Parsers and Constructors

Low-level Printers

package biocaml

Install

Dune Dependency

Authors

Maintainers

Sources

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

Module Biocaml_unix.SamSource

Types

Header Types

Low-level Parsers and Constructors

Low-level Printers

Module `Biocaml_unix.Sam`Source