def test_single_alignment(fastq_record: FastqRecord, ref_fasta: Path) -> None:
# run BWA
results = list(align(reads=[fastq_record], idxbase=ref_fasta))
# Check the returned alignments
assert len(results) == 1
_assert_alignment_for_fastq_record(read=fastq_record, results=results[0])
def test_paired_end_reads(fastq_record: FastqRecord, ref_fasta: Path) -> None:
# run BWA
r1 = attr.evolve(fastq_record, read_number=1)
r2 = attr.evolve(r1, read_number=2)
io_opts = InputOutputOptions(interleaved_pairs=True)
results = list(align(reads=[r1, r2], idxbase=ref_fasta, io_opts=io_opts))
_assert_alignment_for_fastq_record(read=r1, results=results[0])
_assert_alignment_for_fastq_record(read=r2, results=results[1])
def test_no_alignment(ref_fasta: Path) -> None:
fastq_record = FastqRecord(name="unmapped",
bases="A" * 60,
quals="I" * 60,
needs_alignment=False)
# run BWA
results = list(align(reads=[fastq_record], idxbase=ref_fasta))
# Check the returned alignments
assert len(results) == 1
fastq, alignments = results[0]
assert len(alignments) == 0
assert fastq_record == fastq
def test_needs_alignment(fastq_record: FastqRecord, ref_fasta: Path) -> None:
# run BWA
rec1 = fastq_record
rec2 = FastqRecord(name="needs_alignment=False",
bases=rec1.bases,
quals=rec1.quals,
needs_alignment=False)
results = list(align(reads=[rec1, rec2], idxbase=ref_fasta))
# Check the returned alignments
assert len(results) == 2
for result in results:
fastq, alignments = result
if fastq.needs_alignment:
assert fastq == rec1
_assert_alignment_for_fastq_record(read=fastq_record,
results=result)
else:
assert len(alignments) == 0
assert fastq.name == "needs_alignment=False"
assert fastq == rec2
def test_fails_consecutive_reads_with_the_same_name_and_number(
fastq_record: FastqRecord, ref_fasta: Path) -> None:
# run BWA
with pytest.raises(Exception, match="Consecutive reads"):
list(align(reads=[fastq_record, fastq_record], idxbase=ref_fasta))