package biocaml

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

Error Types

Low-level transforms.