-# Copyright (C) 2007-2011 Martin A. Hansen.
+# Copyright (C) 2007-2013 Martin A. Hansen.
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
end
if sam.has_key? :NM and sam[:NM].to_i > 0
+ bp[:NM] = sam[:NM]
+ bp[:MD] = sam[:MD]
bp[:ALIGN] = self.align_descriptors(sam)
end
bp
end
- # Class method to convert a Biopiece record
- # into a SAM entry.
- def self.to_sam(bp)
- "FISK" # FIXME
+ # 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
end
# Create alignment descriptors according to the KISS