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)
