Commit 2c80e62a authored by James Gilbert's avatar James Gilbert
Browse files

Added explanation of NOT clauses in SQL

to get overlapping contigs from static_golden_path table
parent 4fbe4e0d
......@@ -329,6 +329,14 @@ sub fetch_RawContigs_by_chr_start_end {
# PL: is the query below correct? The 'NOT
# <' looks odd, the join is different from e.g. the branch version
# (e.g., look at 1.3.2.41). We'll keep it for now :-)
#
# JGRG: The NOT clauses are slightly counterintuitive,
# but fetch every contig that overlaps start and end.
# We search for every contig that doesn't begin after
# our end (doesn't overlap) and doesn't end before
# our start (doesn't overlap), and therefore get every
# contig that overlaps. This takes care of the condition
# where our start and end lie within a contig.
my $sth = $self->dbobj->prepare("
SELECT c.id
, c.internal_id
......
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