+ # Class method to create a new SAM entry from a Biopiece record.
+ # FIXME
+ def self.new_bp(bp)
+ qname = bp[:Q_ID]
+ flag = 0
+ rname = bp[:S_ID]
+ pos = bp[:S_BEG]
+ mapq = bp[:MAPQ]
+ cigar = bp[:CIGAR]
+ rnext = bp[:Q_ID2] || '*'
+ pnext = bp[:S_BEG2] || 0
+ tlen = bp[:TLEN] || 0
+ seq = bp[:SEQ]
+ qual = bp[:SCORES] || '*'
+ nm = "NM:i:#{bp[:NM]}" if bp[:NM]
+ md = "MD:Z:#{bp[:MD]}" if bp[:MD]
+
+ flag |= FLAG_REVCOMP if bp[:STRAND] == '+'
+
+ if qname && flag && rname && pos && mapq && cigar && rnext && pnext && tlen && seq && qual
+ ary = [qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual]
+ ary << nm if nm
+ ary << md if md
+
+ ary.join("\t")
+ end