def __build_hit_for_match(self):
"""At least one of read or mate are a match"""
if self.__read.type == BWA_TYPE_NO_MATCH:
# the read isn't matched, which implies we have a mate
# and it is matched. We place the read at the mate's position
self.pos = self.__mate.pos
strand = self.__mate.strand
self.flag |= SAM_FSU # query unmapped
ref_len = 1 # ref_len is the length of the reference in the alignment
else:
self.pos = self.__read.pos
strand = self.__read.strand
ref_len = self.__read.get_pos_end() - self.pos
self.qual = self.__read.mapQ
if strand:
self.flag |= SAM_FSR # query on the reverse strand
# Where in the reference is pos?
self.ref_id, self.__nn = bwa.get_seq_id(self.bns, self.pos, ref_len)
self.tid = self.bns.anns[self.ref_id].name
# make the position relative to the start of its reference section
self.pos = self.pos - self.bns.anns[self.ref_id].offset
# Check whether the read alignment bridges two adjacent reference sequences
if (self.__read.type != BWA_TYPE_NO_MATCH and
(self.pos + ref_len > self.bns.anns[self.ref_id].len)):
self.flag |= SAM_FSU # it does, so we set it as unmapped
# presume we can't calculate any of these fields,
# so we set them to the "default" values"
self.mtid = None
self.mpos = 0
self.isize = 0
if self.__mate:
if self.__mate.type != BWA_TYPE_NO_MATCH:
if self.__mate.strand:
self.flag |= SAM_FMR
# XXX: below, self.__mate.len. Shouldn't it be (self.__mate.get_pos_end() - self.__mate.pos) ??
# I posted to the list about this and await a response.
self.m_ref_id, m_nn = bwa.get_seq_id(self.bns, self.__mate.pos, self.__mate.len)
if self.m_ref_id == self.ref_id:
self.mtid = '='
if self.__read.type != BWA_TYPE_NO_MATCH:
self.isize = self.__mate.get_pos_5() - self.__read.get_pos_5()
# else the isize remains at 0
else:
self.mtid = self.bns.anns[self.m_ref_id].name
self.mpos = self.__mate.pos - self.bns.anns[self.m_ref_id].offset
else: # unmapped mate
self.flag |= SAM_FMU
self.mtid = "="
self.mpos = self.__read.pos - self.bns.anns[self.ref_id].offset
self.pos = self.pos + 1 # base 1
self.mpos = self.mpos + 1 # base 1
def __build_hit_for_match(self):
"""At least one of read or mate are a match"""
if self.__read.type == BWA_TYPE_NO_MATCH:
# the read isn't matched, which implies we have a mate
# and it is matched. We place the read at the mate's position
self.pos = self.__mate.pos
strand = self.__mate.strand
self.flag |= SAM_FSU # query unmapped
ref_len = 1 # ref_len is the length of the reference in the alignment
else:
self.pos = self.__read.pos
strand = self.__read.strand
ref_len = self.__read.get_pos_end() - self.pos
self.qual = self.__read.mapQ
if strand:
self.flag |= SAM_FSR # query on the reverse strand
# Where in the reference is pos?
self.ref_id, self.__nn = bwa.get_seq_id(self.bns, self.pos, ref_len)
self.tid = self.bns.anns[self.ref_id].name
# make the position relative to the start of its reference section
self.pos = self.pos - self.bns.anns[self.ref_id].offset
# Check whether the read alignment bridges two adjacent reference sequences
if (self.__read.type != BWA_TYPE_NO_MATCH and
(self.pos + ref_len > self.bns.anns[self.ref_id].len)):
self.flag |= SAM_FSU # it does, so we set it as unmapped
# presume we can't calculate any of these fields,
# so we set them to the "default" values"
self.mtid = None
self.mpos = 0
self.isize = 0
if self.__mate:
if self.__mate.type != BWA_TYPE_NO_MATCH:
if self.__mate.strand:
self.flag |= SAM_FMR
# XXX: below, self.__mate.len. Shouldn't it be (self.__mate.get_pos_end() - self.__mate.pos) ??
# I posted to the list about this and await a response.
self.m_ref_id, m_nn = bwa.get_seq_id(self.bns, self.__mate.pos, self.__mate.len)
if self.m_ref_id == self.ref_id:
self.mtid = '='
if self.__read.type != BWA_TYPE_NO_MATCH:
self.isize = self.__mate.get_pos_5() - self.__read.get_pos_5()
# else the isize remains at 0
else:
self.mtid = self.bns.anns[self.m_ref_id].name
self.mpos = self.__mate.pos - self.bns.anns[self.m_ref_id].offset
else: # unmapped mate
self.flag |= SAM_FMU
self.mtid = "="
self.mpos = self.__read.pos - self.bns.anns[self.ref_id].offset
self.pos = self.pos + 1 # base 1
self.mpos = self.mpos + 1 # base 1
def __analyze_multi(self, i):
multi_hit_chunk = []
q = self.__read.multi[i]
ref_len = q.get_pos_end(len(self.__read)) - q.pos
ref_id, nn = bwa.get_seq_id(self.bns, q.pos, ref_len)
sign = '-' if q.strand else '+'
multi_hit_chunk.append(self.bns.anns[ref_id].name)
multi_hit_chunk.append("%s%d" % (sign, (q.pos - self.bns.anns[ref_id].offset + 1)))
# FIXME: duplicate from samt_adapter, we should centralize formatting
cigar_str = "".join(['%d%s' % t for t in q.get_cigar(len(self.__read))]) or "*"
multi_hit_chunk.append(cigar_str)
multi_hit_chunk.append("%d" % (q.n_gapo + q.n_gape + q.n_mm))
return multi_hit_chunk
def __analyze_multi(self, i):
multi_hit_chunk = []
q = self.__read.multi[i]
ref_len = q.get_pos_end(len(self.__read)) - q.pos
ref_id, nn = bwa.get_seq_id(self.bns, q.pos, ref_len)
sign = '-' if q.strand else '+'
multi_hit_chunk.append(self.bns.anns[ref_id].name)
multi_hit_chunk.append("%s%d" % (sign, (q.pos - self.bns.anns[ref_id].offset + 1)))
# FIXME: duplicate from samt_adapter, we should centralize formatting
cigar_str = "".join(['%d%s' % t for t in q.get_cigar(len(self.__read))]) or "*"
multi_hit_chunk.append(cigar_str)
multi_hit_chunk.append("%d" % (q.n_gapo + q.n_gape + q.n_mm))
return multi_hit_chunk
