NGLess Constants

In NGLess, any variable written in uppercase is a constant, i.e., can only be assigned to once. In addition, there are builtin constants defined by NGLess.

Built in constants

• ARGV

This is string array which contains the arguments passed to the script

• STDIN

Use in place of a filename to read from standard input

• STDOUT

Use in place of a filename to write to standard output

For example:

ngless '0.9'

input = samfile(STDIN)
input = select(input) using |mr|:
    if mr.flag({mapped}):
        discard
write(input, ofile=STDOUT, format={bam})

This file reads a sam stream from stdin, filters it (using the select call) and writes to standard output in bam format.