NAME

Bio::ToolBox::db_helper::alignment_callbacks

DESCRIPTION

This module provides common callback subroutines for working with bam alignments. It is generalized and may be used with either Bio::DB::Sam or Bio::DB::HTS adapter objects.

It's not meant to be used by individuals.

Methods

assign_callback

The only public subroutine used to assign the appropriate callback subroutine based on the parameters requested, such as alignment filtering what and how to score found alignments. This will return a string for the name of the appropriate private subroutine to be used as a callback function code in the low level iterator for the Bam file adapter.

Pass this function the paramater hash as described in either Bio::ToolBox::db_helper::bam or Bio::ToolBox::db_helper::hts.

SEE ALSO

Bio::ToolBox::Data, Bio::ToolBox::db_helper, Bio::ToolBox::db_helper::bam, Bio::ToolBox::db_helper::hts

AUTHOR

Timothy J. Parnell, PhD
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.