package biocaml

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The OCaml Bioinformatics Library

Install

dune-project

Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

Maintainers

B

biocaml@googlegroups.com

Sources

v0.10.0.tar.gz

md5=497e3f2f7128a6ca347d66848da38a3d

sha512=4a76ebbafda3bc944afaff40d69791dfe153a0638ef5d7e6e1bc962b7f991d9545cd0af2d7930b39f8b31dbf067d0603cfa03d9b7a49396ab1ae452df47fd1f3

doc/biocaml.ez/Biocaml_ez/Sam/index.html

Module `Biocaml_ez.Sam`

include module type of struct include Biocaml_unix.Sam end

Types

Header Types

type 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.

val sexp_of_header_item_tag : header_item_tag -> Ppx_sexp_conv_lib.Sexp.t

val header_item_tag_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> header_item_tag

val __header_item_tag_of_sexp__ : Ppx_sexp_conv_lib.Sexp.t -> header_item_tag

type 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.

val sexp_of_tag_value : tag_value -> Ppx_sexp_conv_lib.Sexp.t

val tag_value_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> tag_value

type sort_order = [

| `Unknown
| `Unsorted
| `Query_name
| `Coordinate

]

val sexp_of_sort_order : sort_order -> Ppx_sexp_conv_lib.Sexp.t

val sort_order_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> sort_order

val __sort_order_of_sexp__ : Ppx_sexp_conv_lib.Sexp.t -> sort_order

type group_order = [

| `None
| `Query
| `Reference

]

val sexp_of_group_order : group_order -> Ppx_sexp_conv_lib.Sexp.t

val group_order_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> group_order

val __group_order_of_sexp__ : Ppx_sexp_conv_lib.Sexp.t -> group_order

type header_line = private Biocaml_unix.Sam.header_line = {

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.

val sexp_of_header_line : header_line -> Ppx_sexp_conv_lib.Sexp.t

val header_line_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> header_line

type ref_seq = private Biocaml_unix.Sam.ref_seq = {

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.

val sexp_of_ref_seq : ref_seq -> Ppx_sexp_conv_lib.Sexp.t

val ref_seq_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> ref_seq

type platform = [

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

]

val sexp_of_platform : platform -> Ppx_sexp_conv_lib.Sexp.t

val platform_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> platform

val __platform_of_sexp__ : Ppx_sexp_conv_lib.Sexp.t -> platform

type read_group = private Biocaml_unix.Sam.read_group = {

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.

val sexp_of_read_group : read_group -> Ppx_sexp_conv_lib.Sexp.t

val read_group_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> read_group

type program = private Biocaml_unix.Sam.program = {

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.

val sexp_of_program : program -> Ppx_sexp_conv_lib.Sexp.t

val program_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> program

type 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

]

val sexp_of_header_item : header_item -> Ppx_sexp_conv_lib.Sexp.t

val header_item_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> header_item

val __header_item_of_sexp__ : Ppx_sexp_conv_lib.Sexp.t -> header_item

type header = private Biocaml_unix.Sam.header = {

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.

val empty_header : header

module Flags = Biocaml_unix.Sam.Flags

type 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.

val sexp_of_cigar_op : cigar_op -> Ppx_sexp_conv_lib.Sexp.t

val cigar_op_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> cigar_op

val __cigar_op_of_sexp__ : Ppx_sexp_conv_lib.Sexp.t -> cigar_op

type optional_field_value = private [<

| `A of char
| `i of Core_kernel.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.

val sexp_of_optional_field_value : 
  optional_field_value ->
  Ppx_sexp_conv_lib.Sexp.t

val optional_field_value_of_sexp : 
  Ppx_sexp_conv_lib.Sexp.t ->
  optional_field_value

val __optional_field_value_of_sexp__ : 
  Ppx_sexp_conv_lib.Sexp.t ->
  optional_field_value

type optional_field = private Biocaml_unix.Sam.optional_field = {

tag : string;
value : optional_field_value;

}

val sexp_of_optional_field : optional_field -> Ppx_sexp_conv_lib.Sexp.t

val optional_field_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> optional_field

type rnext = private [<

| `Value of string
| `Equal_to_RNAME

]

val sexp_of_rnext : rnext -> Ppx_sexp_conv_lib.Sexp.t

val rnext_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> rnext

val __rnext_of_sexp__ : Ppx_sexp_conv_lib.Sexp.t -> rnext

type alignment = private Biocaml_unix.Sam.alignment = {

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 : Biocaml_unix.Phred_score.t list;
(*
QUAL
*)
optional_fields : optional_field list;

}

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

val sexp_of_alignment : alignment -> Ppx_sexp_conv_lib.Sexp.t

val alignment_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> alignment

module MakeIO = Biocaml_unix.Sam.MakeIO

include sig ... end

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

val write_file : 
  ?perm:int ->
  ?append:bool ->
  string ->
  ?header:header ->
  alignment Biocaml_unix.Future_unix.Pipe.Reader.t ->
  unit Biocaml_unix.Future_unix.Deferred.t

Low-level Parsers and Constructors

val 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

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

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_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.

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_kernel.Or_error.t

val parse_header_item_tag : string -> header_item_tag Core_kernel.Or_error.t

val parse_tag_value : string -> tag_value Core_kernel.Or_error.t

val parse_header_version : string -> string Core_kernel.Or_error.t

val parse_sort_order : string -> sort_order Core_kernel.Or_error.t

val parse_header_line : tag_value list -> header_line Core_kernel.Or_error.t

val parse_ref_seq : tag_value list -> ref_seq Core_kernel.Or_error.t

val parse_platform : string -> platform Core_kernel.Or_error.t

val parse_read_group : tag_value list -> read_group Core_kernel.Or_error.t

val parse_program : tag_value list -> program Core_kernel.Or_error.t

val parse_header_item : 
  Biocaml_unix.Line.t ->
  header_item Core_kernel.Or_error.t

val parse_header : string -> header Core_kernel.Or_error.t

val cigar_op_alignment_match : int -> cigar_op Core_kernel.Or_error.t

Low-level Optional field Parsers and Constructors

val cigar_op_insertion : int -> cigar_op Core_kernel.Or_error.t

val cigar_op_deletion : int -> cigar_op Core_kernel.Or_error.t

val cigar_op_skipped : int -> cigar_op Core_kernel.Or_error.t

val cigar_op_soft_clipping : int -> cigar_op Core_kernel.Or_error.t

val cigar_op_hard_clipping : int -> cigar_op Core_kernel.Or_error.t

val cigar_op_padding : int -> cigar_op Core_kernel.Or_error.t

val cigar_op_seq_match : int -> cigar_op Core_kernel.Or_error.t

val cigar_op_seq_mismatch : int -> cigar_op Core_kernel.Or_error.t

val optional_field_value_A : 
  char ->
  optional_field_value Core_kernel.Or_error.t

Low-level Optional field Parsers and Constructors

val optional_field_value_i : Core_kernel.Int64.t -> optional_field_value

val optional_field_value_f : float -> optional_field_value

val optional_field_value_Z : 
  string ->
  optional_field_value Core_kernel.Or_error.t

val optional_field_value_H : 
  string ->
  optional_field_value Core_kernel.Or_error.t

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

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

val parse_optional_field_value : 
  string ->
  optional_field_value Core_kernel.Or_error.t

val parse_optional_field : string -> optional_field Core_kernel.Or_error.t

val 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:Biocaml_unix.Phred_score.t list ->
  ?optional_fields:optional_field list ->
  unit ->
  alignment Core_kernel.Or_error.t

Low-level Alignment Parsers and Constructors

val parse_qname : string -> string option Core_kernel.Or_error.t

val parse_flags : string -> Flags.t Core_kernel.Or_error.t

val parse_rname : string -> string option Core_kernel.Or_error.t

val parse_pos : string -> int option Core_kernel.Or_error.t

val parse_mapq : string -> int option Core_kernel.Or_error.t

val parse_cigar : string -> cigar_op list Core_kernel.Or_error.t

val parse_rnext : string -> rnext option Core_kernel.Or_error.t

val parse_pnext : string -> int option Core_kernel.Or_error.t

val parse_tlen : string -> int option Core_kernel.Or_error.t

val parse_seq : string -> string option Core_kernel.Or_error.t

val parse_qual : 
  string ->
  Biocaml_unix.Phred_score.t list Core_kernel.Or_error.t

val parse_alignment : 
  ?ref_seqs:Core_kernel.String.Set.t ->
  Biocaml_unix.Line.t ->
  alignment Core_kernel.Or_error.t

Low-level Printers

val print_header_item_tag : header_item_tag -> string

Low-level Header Printers

val print_tag_value : tag_value -> string

val print_header_version : string -> string

val print_sort_order : sort_order -> string

val print_header_line : header_line -> string

val print_ref_seq : ref_seq -> string

val print_platform : platform -> string

val print_read_group : read_group -> string

val print_program : program -> string

val print_other : (string * tag_value list) -> string

val print_qname : string option -> string

Low-level Alignment Printers

val print_flags : Flags.t -> string

val print_rname : string option -> string

val print_pos : int option -> string

val print_mapq : int option -> string

val print_cigar_op : cigar_op -> string

val print_cigar : cigar_op list -> string

val print_rnext : rnext option -> string

val print_pnext : int option -> string

val print_tlen : int option -> string

val print_seq : string option -> string

val print_qual : Biocaml_unix.Phred_score.t list -> string

val print_optional_field : optional_field -> string

val print_alignment : alignment -> string

val read : 
  ?start:Biocaml_unix.Pos.t ->
  Biocaml_unix.Future_unix.Reader.t ->
  header * alignment CFStream.Stream.t