def __encrypt_unmapped(alignment: pysam.AlignedSegment, secret: bytes):
"""
Stream cipher encryption / decryption.
alignment + secret => encrypted_alignment
encrypted_alignment + secret => alignment
:param alignment:
:param secret:
:return: encrypter/decrypted alignment
"""
if alignment.is_unmapped:
if secret is None:
raise ValueError(
'Secret key must be present when unmapped alignments are iterated.'
)
# use 64B long hash (encrypts 256 bases)
sha512 = hashlib.sha512()
sha512.update(secret + alignment.query_name.encode())
mut_seq = cmn.stream_cipher(alignment.query_sequence,
sha512.digest())
# change and preserve quality
# TODO: maybe something else with the quality?
quality = alignment.query_qualities
alignment.query_sequence = mut_seq
alignment.query_qualities = quality
def softclip_end_of_alignment_by_query(
rec: AlignedSegment,
bases_to_clip: int,
clipped_base_quality: Optional[int] = None,
tags_to_invalidate: Iterable[str] = TAGS_TO_INVALIDATE
) -> ClippingInfo:
"""
Adds soft-clipping to the end of a read's alignment.
Clipping is applied before any existing hard or soft clipping. E.g. a read with cigar 100M5S
that is clipped with bases_to_clip=10 will yield a cigar of 90M15S.
If the read is unmapped or bases_to_clip < 1 then nothing is done.
If the read has fewer clippable bases than requested the read will be unmapped.
Args:
rec: the BAM record to clip
bases_to_clip: the number of additional bases of clipping desired in the read/query
clipped_base_quality: if not None, set bases in the clipped region to this quality
tags_to_invalidate: the set of extended attributes to remove upon clipping
Returns:
ClippingInfo: a named tuple containing the number of query/read bases and the number
of target/reference bases clipped.
"""
if rec.is_unmapped or bases_to_clip < 1:
return ClippingInfo(0, 0)
num_clippable_bases = rec.query_alignment_length
if bases_to_clip >= num_clippable_bases:
return _clip_whole_read(rec, tags_to_invalidate)
# Reverse the cigar and qualities so we can clip from the start
cigar = Cigar.from_cigartuples(rec.cigartuples).reversed()
quals = rec.query_qualities
quals.reverse()
new_cigar, clipping_info = _clip(cigar, quals, bases_to_clip,
clipped_base_quality)
# Then reverse everything back again
quals.reverse()
rec.query_qualities = quals
rec.cigarstring = str(new_cigar.reversed())
_cleanup(rec, tags_to_invalidate)
return clipping_info
def _set_length_dependent_fields(
self,
rec: pysam.AlignedSegment,
length: int,
bases: Optional[str] = None,
quals: Optional[List[int]] = None,
cigar: Optional[str] = None,
) -> None:
"""Fills in bases, quals and cigar on a record.
If any of bases, quals or cigar are defined, they must all have the same length/query
length. If none are defined then the length parameter is used. Undefined values are
synthesize at the inferred length.
Args:
rec: a SAM record
length: the length to use if all of bases/quals/cigar are None
bases: an optional string of bases for the read
quals: an optional list of qualities for the read
cigar: an optional cigar string for the read
"""
# Do some validation to make sure all defined things have the same lengths
lengths = set()
if bases is not None:
lengths.add(len(bases))
if quals is not None:
lengths.add(len(quals))
if cigar is not None:
cig = sam.Cigar.from_cigarstring(cigar)
lengths.add(sum([elem.length_on_query for elem in cig.elements]))
if not lengths:
lengths.add(length)
if len(lengths) != 1:
raise ValueError(
"Provided bases/quals/cigar are not length compatible.")
# Fill in the record, making any parts that were not defined as params
length = lengths.pop()
rec.query_sequence = bases if bases else self._bases(length)
rec.query_qualities = quals if quals else [self.base_quality] * length
if not rec.is_unmapped:
rec.cigarstring = cigar if cigar else f"{length}M"
def _make_read_unmapped(rec: AlignedSegment) -> None:
"""Removes mapping information from a read."""
if rec.is_reverse:
quals = rec.query_qualities
quals.reverse()
rec.query_sequence = dnautils.reverse_complement(rec.query_sequence)
rec.query_qualities = quals
rec.is_reverse = False
rec.reference_id = sam.NO_REF_INDEX
rec.reference_start = sam.NO_REF_POS
rec.cigar = None
rec.mapping_quality = 0
rec.template_length = 0
rec.is_duplicate = False
rec.is_secondary = False
rec.is_supplementary = False
rec.is_proper_pair = False
rec.is_unmapped = True
