Scope

Alignment analysis.

Expected behavior

This function is expected to perform the analysis of a single part or (if no splicing plan was prepared) of all the input alignments. Splicing plan are prepared with plugin_alignment_analysis_num_parts

Input arguments

The function receives the following arguments:

  • $1: the file with the splicing plan (if available)
  • $2: the current part to process (if available)

Environment

The function has access to the following environment variables: