README.md

BAM Parser

To parser a BAM header:

• In methods.config, include the bam_parser.config file and call bam_parser.parse_bam_header(</path/to/bam>)

The function returns a Map, with the following information:

• read_group: A list of Maps, where each Map contains one parsed read group from the BAM header.

Available functions

• parse_bam_header - Function for parsing a BAM header
  • Positional args:

    position	name	type	required	default	description
    1	bam_path	String	Yes	none	String representing path to BAM file for parsing

Example

To load a BAM header from a file defined at params.bam_file_path:

includeConfig "/path/to/bam_parser.config"
...
methods {
    ...
    bam_header = bam_parser.parse_bam_header(params.bam_file_path)
}