def test_read_sam_paired(): samfile = pysam.Samfile('test.sam', 'r') alignments = gc.read_samfile(samfile, paired=True) alignments = list(alignments) eq_(len(alignments), 11) a = alignments[0] eq_(a.reference_ID, 'gi|30407130|emb|AL954747.1|') eq_(a.read_ID, 'DB775P1:240:D1TE2ACXX:4:1216:12799:92206') eq_(a.start, 2784862) eq_(a.end, 2785034) eq_(a.mismatches, 11)
def test_read_sam(): samfile = pysam.Samfile('test.sam', 'r') alignments = gc.read_samfile(samfile) alignments = list(alignments) eq_(len(alignments), 22) a = alignments[0] eq_(a.reference_ID, 'gi|30407130|emb|AL954747.1|') eq_(a.read_ID, 'DB775P1:240:D1TE2ACXX:4:1216:12799:92206') eq_(a.strand, '+') # See test_pysam_position() above. Pysam uses a 0-based, half-open # interval. I want to transfer back to a 1-based, closed interval. eq_(a.start, 2784862) eq_(a.end, 2784946) eq_(a.mismatches, 6)