Deals with merging large segment to small segment.

Procedure is overall similar to the previous cases. For case five, we have two options when merging:

• Merge large and small

• Merge small and next large This helper deals with the first option. Note that there is no 'below_thr' parameter for these two helpers, since we already know we're going to merge when they're called in FinalizeSmallSegments.

Usage

MergeSegmentsFiveLargeSmall(
  granges_obj,
  small_segment,
  large_segments,
  j,
  end_of_file
)

Arguments

granges_obj

A GRanges object: is used as reference to obtain true genomic data from specified regions.

small_segment

An array: the given small segment that might be merged into the large_segments frame.

large_segments

A data frame: segment data. Initially contains only segments with size >= 3Mb, but as we merge small segments into it, smaller segments are progressively added.

j

An integer/index: the position of the large segment we're comparing with small_segment, within large_segments.

end_of_file

A boolean: whether there's any large segments after j.