"""
A corner case: reference sequence contains IUPAC ambiguous nucleotide
characters, which we allow.  This test ensures that we can extract the
transcript from a BAM alignment file, specifically when the reverse complement
is needed.
"""

import os
import pytest
import shutil
import tempfile

import pbcore.io
from pbcore.io.align.BamIO import AlignmentFile

SAM_STR = """\
@HD\tVN:1.5\tSO:coordinate\tpb:3.0.1
@SQ\tSN:genome\tLN:28\tM5:734d5f3b2859595f4bd87a2fe6b7389b
@RG\tID:1\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;Ipd=ip;BASECALLERVERSION=2.0.1.0.123678;FRAMERATEHZ=75.000000;BINDINGKIT=foo;SEQUENCINGKIT=bar\tPU:movie1
@PG\tID:bax2bam-0.0.2\tPN:bax2bam\tVN:0.0.2\tDS:bax2bam
movie1/54130/0_10\t16\tgenome\t12\t30\t10=\t*\t0\t-28\tTCTCAGGAGA\t*\tRG:Z:1\tdq:Z:2222'$22'2\tdt:Z:NNNNAGNNGN\tip:B:C,255,2,0,10,22,34,0,2,3,0,16\tiq:Z:(+#1'$#*1&\tmq:Z:&1~51*5&~2\tnp:i:1\tqe:i:10\tqs:i:0\trq:f:0.854\tsn:B:f,-1,-1,-1,-1\tsq:Z:<32<4<<<<3\tzm:i:54130\tAS:i:-3020\tNM:i:134\tcx:i:2"""

FASTA_STR = ">genome\nAAAATGASGAGATCARAATGASGAGATC"
FAI_STR = "genome  28      8       28      29"


class TestCase:

    def setup_method(self):
        self.tmp_dir = tempfile.mkdtemp()

        f = open(os.path.join(self.tmp_dir, "tst_pbcore.sam"), "w")
        f.write(SAM_STR)
        f.close()
        # convert to bam using pysam
        sam_in = AlignmentFile(os.path.join(
            self.tmp_dir, "tst_pbcore.sam"), "r")
        bam_out = AlignmentFile(os.path.join(self.tmp_dir, "tst_pbcore.bam"), "wb",
                                template=sam_in)
        for s in sam_in:
            bam_out.write(s)
        bam_out.close()
        open(os.path.join(self.tmp_dir, "tst_pbcore.fa"), "w").write(FASTA_STR)
        open(os.path.join(self.tmp_dir, "tst_pbcore.fa.fai"), "w").write(FAI_STR)

    def teardown_method(self):
        shutil.rmtree(self.tmp_dir)

    def test_reverse_complement(self):
        bam_file = pbcore.io.BamReader(os.path.join(self.tmp_dir, "tst_pbcore.bam"),
                                       referenceFastaFname=os.path.join(self.tmp_dir, "tst_pbcore.fa"))
        for aln in bam_file:
            seq = aln.transcript()