Module Biocaml.Track (.ml)

module Track: Biocaml_track

Track lines define display attributes. They can be thought of as lists of attribute-value pairs. For forward compatibility, this module allows arbitrary attributes to be set. However, the following lists known attributes and specifies restrictions on their values:

name - string enclosed in double quotes if there are spaces; recommended to use only alphanumeric characters and length less than 15 characters but this is not enforced
description - string enclosed in double quotes if there are spaces; recommended to use only alphanumeric characters and length less than 60 characters but this is not enforced
visibility - "hide", "dense", "full", "pack", or "squish"; if type=wiggle_0 then "hide", "dense", or "full"; can also use integer value where 0 = "hide", 1 = "dense", 2 = "full", 3 = "pack", 4 = "squish"
color - "R,G,B" where each of R, G, and B are integers between 0 and 255
altColor - "R,G,B" where each of R, G, and B are integers between 0 and 255
itemRgb - "On" is the only allowed value
useScore - 0 or 1
group - string
priority - integer
autoScale - "on" or "off"
gridDefault - "on" or "off"
maxHeightPixels - "max:default:min" where each of max, default, and min are integers
graphType - "bar" or "points"
viewLimits - "lower:upper" where each of lower and upper are integers
yLineMark - floating point value
yLineOnOff - "on" or "off"
windowingFunction - "maximum", "mean", or "minimum"
smoothingWindow - "off" or an integer between 2 and 16
db - should be a valid UCSC assembly ID, but currently any string is accepted
offset - integer
url - string
htmlUrl - string
type - "wiggle_0" is the only value currently supported, leaving this attribute unset handles other track types

type t = [ `browser of
           [ `hide of [ `all ]
           | `position of string * int * int
           | `unknown of string ]
       | `comment of string
       | `track of (string * string) list ]

The type of the parser "track" lines.

type 'a content = [ `content of 'a ]

The "content" lines of the files.

type parse_error = [ `incomplete_input of Biocaml_pos.t * string list * string option
       | `wrong_browser_position of Biocaml_pos.t * string
       | `wrong_key_value_format of (string * string) list * string * string ]

The possible parsing errors.

module Transform: sig .. end

Low-level transforms.