def _createMutRow(self,m):
if m is None:
return None
# Calculate values
# TODO: This is a sloppy way to do GT
n_lod = self._extract_lod(m, 'init_n_lod')
t_lod = self._extract_lod(m, 't_lod_fstar')
# Nothing to call if both LODs are too low.
if (t_lod < 0) and (n_lod < 0):
return
qual = max(t_lod, 0)
gtN, gtT = self.genotype(n_lod, t_lod)
ref,alt,new_start = MutUtils.retrievePrecedingBaseFromReference(m)
ss,ssCode = self.determineSomaticStatus(gtN, gtT, qual)
if ss is None or ssCode is None:
return
n_alt_count = self._get_annotation_value(m, 'n_alt_count', '0', is_blank_default=True)
n_ref_count = self._get_annotation_value(m, 'n_ref_count', '0', is_blank_default=True)
n_alt_sum = self._get_annotation_value(m, 'n_alt_sum', '0', is_blank_default=True)
t_alt_count = self._get_annotation_value(m, 't_alt_count', '0', is_blank_default=True)
t_ref_count = self._get_annotation_value(m, 't_ref_count', '0', is_blank_default=True)
t_alt_sum = self._get_annotation_value(m, 't_alt_sum', '0', is_blank_default=True)
mq0=0
normalFormat = self._generateFormatFieldWithValues(gtN, n_alt_count, n_ref_count, mq0,
self._generateBQ(n_alt_count, n_alt_sum), ssCode)
primaryFormat = self._generateFormatFieldWithValues(gtT, t_alt_count, t_ref_count, mq0,
self._generateBQ(t_alt_count, t_alt_sum), ssCode)
filterVal = self._generateFilterField(m)
info = self._generateInfoField(m,filterVal, mq0, ss)
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL PRIMARY
mutRow = dict()
mutRow['CHROM'] = self._renderChrom(m.chr)
mutRow['POS'] = new_start
mutRow['ID'] = self.renderID(m)
mutRow['REF'] = ref
mutRow['ALT'] = alt
mutRow['QUAL'] = qual
mutRow['FILTER'] = filterVal
mutRow['INFO'] = info
mutRow['FORMAT'] = self._generateFormatField()
mutRow['NORMAL'] = normalFormat
mutRow['PRIMARY'] = primaryFormat
return mutRow
def _createMutRow(self, m):
if m is None:
return None
# Calculate values
# TODO: This is a sloppy way to do GT
n_lod = self._extract_lod(m, 'init_n_lod')
t_lod = self._extract_lod(m, 't_lod_fstar')
# Nothing to call if both LODs are too low.
if (t_lod < 0) and (n_lod < 0):
return
qual = max(t_lod, 0)
gtN, gtT = self.genotype(n_lod, t_lod)
ref, alt, new_start = MutUtils.retrievePrecedingBaseFromReference(m)
ss, ssCode = self.determineSomaticStatus(gtN, gtT, qual)
if ss is None or ssCode is None:
return
n_alt_count = self._get_annotation_value(m,
'n_alt_count',
'0',
is_blank_default=True)
n_ref_count = self._get_annotation_value(m,
'n_ref_count',
'0',
is_blank_default=True)
n_alt_sum = self._get_annotation_value(m,
'n_alt_sum',
'0',
is_blank_default=True)
t_alt_count = self._get_annotation_value(m,
't_alt_count',
'0',
is_blank_default=True)
t_ref_count = self._get_annotation_value(m,
't_ref_count',
'0',
is_blank_default=True)
t_alt_sum = self._get_annotation_value(m,
't_alt_sum',
'0',
is_blank_default=True)
mq0 = 0
normalFormat = self._generateFormatFieldWithValues(
gtN, n_alt_count, n_ref_count, mq0,
self._generateBQ(n_alt_count, n_alt_sum), ssCode)
primaryFormat = self._generateFormatFieldWithValues(
gtT, t_alt_count, t_ref_count, mq0,
self._generateBQ(t_alt_count, t_alt_sum), ssCode)
filterVal = self._generateFilterField(m)
info = self._generateInfoField(m, filterVal, mq0, ss)
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL PRIMARY
mutRow = dict()
mutRow['CHROM'] = self._renderChrom(m.chr)
mutRow['POS'] = new_start
mutRow['ID'] = self.renderID(m)
mutRow['REF'] = ref
mutRow['ALT'] = alt
mutRow['QUAL'] = qual
mutRow['FILTER'] = filterVal
mutRow['INFO'] = info
mutRow['FORMAT'] = self._generateFormatField()
mutRow['NORMAL'] = normalFormat
mutRow['PRIMARY'] = primaryFormat
return mutRow
