package biocaml

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Track files in UCSC Genome Browser format. The following documentation assumes knowledge of concepts explained on the UCSC Genome Browser's website. Basically, a track file is one of several types of data (WIG, GFF, etc.), possibly preceded by comments, browser lines, and a track line. This module allows only a single data track within a file, although the UCSC specifies that multiple tracks may be provided together.

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

Item Types

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

The type of the parser "track" lines.

type 'a content = [
  1. | `content of 'a
]

The "content" lines of the files.

Error Types

module Error : sig ... end

Low-level transforms.

module Transform : sig ... end

Low-level transforms.