Internal helper used by gc_cal.
Given the ordered positions of reference genes on a contig,
this function returns the genomic coordinates that mark the
boundary of each candidate cluster.
A boundary is declared whenever the gap between two successive
reference genes exceeds the maximum spacing allowed by the
cluster definition (AllGeneNum - MinConSeq).
gc_cluster(Data = orf_position.tmp, AllGeneNum = 30, MinConSeq = 15)A numeric vector containing every position that marks the end
of a putative gene cluster. These values are subsequently used as
breakpoints to slice the contig into candidate regions in the
downstream functions gc_position() and gc_range().
A numeric vector (ascending order) of ORF positions that carry
one of the reference genes of interest. Usually the vector
orf_position.tmp created inside gc_cal.
Integer. Maximum genomic span (in ORF count) that the
algorithm is allowed to cover when defining a single
cluster. Passed unchanged from gc_cal.
Integer. Minimum number of consecutive reference genes
required to form a cluster. Passed unchanged from
gc_cal.
If the gap between two consecutive reference genes is larger than
AllGeneNum - MinConSeq, the left-hand gene is recorded as the
last member of the preceding cluster.
The final reference gene is always appended to the vector as the last boundary, ensuring the rightmost cluster is not lost.