def retrieve(self, start, end, minreadq):
""" Returns reads fully overlapping [start,end) """
# start at end going backwards, for efficiency
idx = self._bufend
reads = []
while True:
idx = (idx - 1) % len(self._buffer)
# for efficiency, do a quick test first
if self._buffer[idx].pos <= start:
##DEBUG
#rstart0, rend0 = pruned_ref_start_end(self._buffer[idx], minreadq)
rstart, rend = platypusutils.pruned_ref_start_end(
self._buffer[idx], minreadq, 0)
#assert rstart0 == rstart
#assert rend0 == rend
if rend <= start:
# it is theoretically possible that subsequent reads, that start leftward of
# the current read, do still fully overlap [start,end), even though the current
# read is disjoint with [start,end). In practice we will miss very few indel
# errors this way, as long error indels tend to occur in long tandems, and
# errors outside tandems are short.
break
if rstart <= start and rend >= end:
reads.append(self._buffer[idx])
if idx == self._bufend:
break
return reads
def retrieve(self, start, end, minreadq):
""" Returns reads fully overlapping [start,end) """
# start at end going backwards, for efficiency
idx = self._bufend
reads = []
while True:
idx = (idx - 1) % len(self._buffer)
# for efficiency, do a quick test first
if self._buffer[idx].pos <= start:
##DEBUG
#rstart0, rend0 = pruned_ref_start_end(self._buffer[idx], minreadq)
rstart, rend = platypusutils.pruned_ref_start_end(self._buffer[idx], minreadq, 0)
#assert rstart0 == rstart
#assert rend0 == rend
if rend <= start:
# it is theoretically possible that subsequent reads, that start leftward of
# the current read, do still fully overlap [start,end), even though the current
# read is disjoint with [start,end). In practice we will miss very few indel
# errors this way, as long error indels tend to occur in long tandems, and
# errors outside tandems are short.
break
if rstart <= start and rend >= end:
reads.append( self._buffer[idx] )
if idx == self._bufend:
break
return reads
def enter(self, read, minAnchor):
##DEBUG
#pos0, end0 = pruned_ref_start_end( read, self.minReadQ, minAnchor )
pos, end = platypusutils.pruned_ref_start_end( read, self.minReadQ, minAnchor )
#assert pos0 == pos
#assert end0 == end
if end - pos > self.covbuflen:
# read too long
return
self.covbuf[pos % self.covbuflen] += 1
self.covbuf[end % self.covbuflen] -= 1
def enter(self, read, minAnchor):
##DEBUG
#pos0, end0 = pruned_ref_start_end( read, self.minReadQ, minAnchor )
pos, end = platypusutils.pruned_ref_start_end(read, self.minReadQ,
minAnchor)
#assert pos0 == pos
#assert end0 == end
if end - pos > self.covbuflen:
# read too long
return
self.covbuf[pos % self.covbuflen] += 1
self.covbuf[end % self.covbuflen] -= 1
