def _new_rec(self, name: str, chrom: str, start: int,
attrs: Optional[Dict[str, Any]]) -> AlignedSegment:
"""Generates a new AlignedSegment. Sets the segment up with the correct
header and adds the RG attribute if not contained in attrs.
Args:
name: the name of the read/template
chrom: the chromosome to which the read is mapped
start: the start position of the read on the chromosome
attrs: an optional dictionary of SAM attributes with two-char keys
Returns:
AlignedSegment: an aligned segment with name, chrom, pos, attributes the
read group, and the unmapped flag all set appropriately.
"""
if chrom is not sam.NO_REF_NAME and chrom not in self._seq_lookup:
raise ValueError(
f"{chrom} is not a valid chromosome name in this builder.")
rec = AlignedSegment(header=self._samheader)
rec.query_name = name
rec.reference_name = chrom
rec.reference_start = start
rec.mapping_quality = self.mapping_quality
if chrom == sam.NO_REF_NAME or start == sam.NO_REF_POS:
rec.is_unmapped = True
attrs = attrs if attrs else dict()
if "RG" not in attrs:
attrs["RG"] = self.rg_id()
rec.set_tags(list(attrs.items()))
return rec
qe=14,
rq=0.80,
sn=[2.0, 3.0, 5.0, 6.0],
ip=[15]*14,
pw=[16]*14,
zm=42,
cx=2,
# Now, the pulse stuff
pc = " GAgggTTACAcccGATaaaTACA",
pa = [5]*23, #pkmean
pm = [4]*23, #pkmid
pd = [3]*23, #prePulseFrames
px = [2]*23, #pulseWidthInFrames
sf = range(3, 1000, 5)[:23] # startFrame
)
pulsePeer.set_tags(tags.items())
mockBamReader = Mock(
readGroupInfo=lambda x: Mock(ID=0,
MovieName="FakeMovie",
ReadType="SUBREAD",
SequencingChemistry="FakeChemistry",
FrameRate=100.0))
bamRecord = BamAlignment(mockBamReader, pulsePeer)
mockVpReader = Mock(movieName="FakeMovie",
pulseFeatureDescs=
{ "preBaseFrames" : FeatureDesc("preBaseFrames" , "Ipd:Frames" , "ip", "identity", np.uint16, np.uint16),
"baseWidthInFrames" : FeatureDesc("baseWidthInFrames" , "PulseWidth:Frames" , "pw", "identity", np.uint16, np.uint16) })
qe=14,
rq=0.80,
sn=[2.0, 3.0, 5.0, 6.0],
ip=[15] * 14,
pw=[16] * 14,
zm=42,
cx=2,
# Now, the pulse stuff
pc=" GAgggTTACAcccGATaaaTACA",
pa=[5] * 23, #pkmean
pm=[4] * 23, #pkmid
pd=[3] * 23, #prePulseFrames
px=[2] * 23, #pulseWidthInFrames
sf=range(3, 1000, 5)[:23] # startFrame
)
pulsePeer.set_tags(tags.items())
mockBamReader = Mock(
readGroupInfo=lambda x: Mock(ID=0,
MovieName="FakeMovie",
ReadType="SUBREAD",
SequencingChemistry="FakeChemistry",
FrameRate=100.0))
bamRecord = BamAlignment(mockBamReader, pulsePeer)
mockVpReader = Mock(movieName="FakeMovie",
pulseFeatureDescs={
"preBaseFrames":
FeatureDesc("preBaseFrames", "Ipd:Frames", "ip",
"identity", np.uint16, np.uint16),
"baseWidthInFrames":
