bp = {}
bp[:REC_TYPE] = 'SAM'
- bp[:Q_ID] = sam[:QNAME]
- bp[:STRAND] = sam[:FLAG].revcomp? ? '-' : '+'
- bp[:S_ID] = sam[:RNAME]
- bp[:S_BEG] = sam[:POS]
- bp[:MAPQ] = sam[:MAPQ]
- bp[:CIGAR] = sam[:CIGAR]
+ bp[:Q_ID] = sam[:QNAME]
+ bp[:STRAND] = sam[:FLAG].revcomp? ? '-' : '+'
+ bp[:S_ID] = sam[:RNAME]
+ bp[:S_BEG] = sam[:POS]
+ bp[:MAPQ] = sam[:MAPQ]
+ bp[:CIGAR] = sam[:CIGAR].to_s
unless sam[:RNEXT] == '*'
bp[:Q_ID2] = sam[:RNEXT]
bp
end
- # Create align descriptors according to the KISS format description:
+ # Class method to convert a Biopiece record
+ # into a SAM entry.
+ def self.to_sam(bp)
+ "FISK"
+ end
+
+ # Create alignment descriptors according to the KISS
+ # format description:
# http://code.google.com/p/biopieces/wiki/KissFormat
def self.align_descriptors(sam)
offset = 0
sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\tref\t*\t\*\t*\t*\n"))
assert_nothing_raised { sam.each }
end
+
+ def test_Sam_to_bp_returns_correctly
+ string = "ID00036734\t0\tgi48994873\t366089\t37\t37M1I62M\t*\t0\t0\tGTTCCGCTATCGGCTGAATTTGATTGCGAGTGAGATATTTTATGCCAGCCAGCCAGACGCAGACGCGCCGAGACAGAACTTAATGGGCCCGCTAACAGCG\t*\tXT:A:U\tNM:i:1\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:1\tXG:i:1\tMD:Z:99\n"
+
+ sam = Sam.new(StringIO.new(string))
+
+ sam.each do |s|
+ assert_equal("SAM", Sam.to_bp(s)[:REC_TYPE])
+ assert_equal("ID00036734", Sam.to_bp(s)[:Q_ID])
+ assert_equal("-", Sam.to_bp(s)[:STRAND])
+ assert_equal("gi48994873", Sam.to_bp(s)[:S_ID])
+ assert_equal(366089, Sam.to_bp(s)[:S_BEG])
+ assert_equal(37, Sam.to_bp(s)[:MAPQ])
+ assert_equal("37M1I62M", Sam.to_bp(s)[:CIGAR])
+ assert_equal("GTTCCGCTATCGGCTGAATTTGATTGCGAGTGAGATATTTTATGCCAGCCAGCCAGACGCAGACGCGCCGAGACAGAACTTAATGGGCCCGCTAACAGCG", Sam.to_bp(s)[:SEQ])
+ assert_equal("37:->T", Sam.to_bp(s)[:ALIGN])
+ end
+ end
end