Gmap align gtf

GmapAlignGTF class.

Represents a task that wraps Gmap aligment tool. Gmap index is Mandatory to use Gmap tools.

Configuration options: * threads: Multi threading options: number of threads to use. [Default = 8] * min-identity": Do not print alignments with identity less this value (default=70.0, 0.0 would means no filtering). Note that chimeric alignments will be output regardless of this filter. * min-trimmed-coverage: Do not print alignments with trimmed coverage less than this value (default=70.0, 0.0 would means no filtering). Note that chimeric alignments will be output regardless of this filter. * max-hit-number: Maximum number of hits to show (default 5). If set to 1, GMAP will not report chimeric alignments, since those imply two hits. If you want a single alignment plus chimeric alignments, then set this to be 0. [Default = 5] * cross-species: Use a more sensitive search for canonical splicing, which helps especially for cross-species alignments and other difficult cases (genome for a far-related species/family...). [Default = No]