entry = Seq.new_bp(record)
if options[:forward] and record[:SEQ].length >= options[:forward].length
- if m = entry.patmatch(options[:forward], 0, fmis, fins, fdel)
+ if m = entry.patmatch(options[:forward], max_mismatches: fmis, max_insertions: fins, max_deletions: fdel)
record[:ADAPTOR_POS_LEFT] = m.pos
record[:ADAPTOR_LEN_LEFT] = m.length
record[:ADAPTOR_PAT_LEFT] = m.match
pat = pat[1 ... pat.length]
- if m = entry.patmatch(pat, [0, len], fmis, fins, fdel)
+ if m = entry.patmatch(pat, start: 0, stop: len, max_mismatches: fmis, max_insertions: fins, max_deletions: fdel)
record[:ADAPTOR_POS_LEFT] = m.pos
record[:ADAPTOR_LEN_LEFT] = m.length
record[:ADAPTOR_PAT_LEFT] = m.match
end
if options[:reverse] and record[:SEQ].length >= options[:reverse].length
- if m = entry.patmatch(options[:reverse], 0, rmis, rins, rdel)
+ if m = entry.patmatch(options[:reverse], max_mismatches: rmis, max_insertions: rins, max_deletions: rdel)
record[:ADAPTOR_POS_RIGHT] = m.pos
record[:ADAPTOR_LEN_RIGHT] = m.length
record[:ADAPTOR_PAT_RIGHT] = m.match
pat = pat[0 ... pat.length - 1]
- if m = entry.patmatch(pat, entry.length - len, rmis, rins, rdel)
+ if m = entry.patmatch(pat, start: entry.length - len, max_mismatches: rmis, max_insertions: rins, max_deletions: rdel)
record[:ADAPTOR_POS_RIGHT] = m.pos
record[:ADAPTOR_LEN_RIGHT] = m.length
record[:ADAPTOR_PAT_RIGHT] = m.match