def _flushContigIfCompleted(self, window):
refId, _, _ = window
refEntry = reference.byName[refId]
refName = refEntry.fullName
basesProcessed = self.referenceBasesProcessedById[refId]
requiredBases = reference.numReferenceBases(refId,
options.referenceWindows)
if basesProcessed == requiredBases:
# This contig is done, so we can dump to file and delete
# the data structures.
if self.gffWriter or self.vcfWriter:
variants = sorted(self.variantsByRefId[refId])
if self.gffWriter:
self.gffWriter.writeVariants(variants)
if self.vcfWriter:
self.vcfWriter.writeVariants(variants)
del self.variantsByRefId[refId]
#
# If the user asked to analyze a window or a set of
# windows, we output a FAST[AQ] contig per analyzed
# window. Otherwise we output a fasta contig per
# reference contig.
#
# We try to be intelligent about naming the output
# contigs, to include window information where applicable.
#
for span in reference.enumerateSpans(refId,
options.referenceWindows):
_, s, e = span
if (s == 0) and (e == refEntry.length):
spanName = refName
else:
spanName = refName + "_%d_%d" % (s, e)
cssName = consensus.consensusContigName(
spanName, self._algorithmName)
# Gather just the chunks pertaining to this span
chunksThisSpan = [
chunk for chunk in self.consensusChunksByRefId[refId]
if windows.windowsIntersect(chunk.refWindow, span)
]
css = consensus.join(chunksThisSpan)
if self.fastaWriter:
self.fastaWriter.writeRecord(cssName, css.sequence)
if self.fastqWriter:
self.fastqWriter.writeRecord(cssName, css.sequence,
css.confidence)
del self.consensusChunksByRefId[refId]
def _flushContigIfCompleted(self, window):
refId, _, _ = window
refEntry = reference.byId[refId]
refName = refEntry.name
basesProcessed = self.referenceBasesProcessedById[refId]
requiredBases = reference.numReferenceBases(refId, options.referenceWindows)
if basesProcessed == requiredBases:
# This contig is done, so we can dump to file and delete
# the data structures.
if self.gffWriter:
self.gffWriter.writeVariants(sorted(self.variantsByRefId[refId]))
del self.variantsByRefId[refId]
#
# If the user asked to analyze a window or a set of
# windows, we output a FAST[AQ] contig per analyzed
# window. Otherwise we output a fasta contig per
# reference contig.
#
# We try to be intelligent about naming the output
# contigs, to include window information where applicable.
#
for span in reference.enumerateSpans(refId, options.referenceWindows):
_, s, e = span
if (s == 0) and (e == refEntry.length):
spanName = refName
else:
spanName = refName + ":%d-%d" % (s, e)
cssName = consensus.consensusContigName(spanName,
options.algorithm)
# Gather just the chunks pertaining to this span
chunksThisSpan = [ chunk for chunk in self.consensusChunksByRefId[refId]
if windows.windowsIntersect(chunk.refWindow, span) ]
css = consensus.join(chunksThisSpan)
if self.fastaWriter:
self.fastaWriter.writeRecord(cssName,
css.sequence)
if self.fastqWriter:
self.fastqWriter.writeRecord(cssName,
css.sequence,
css.confidence)
del self.consensusChunksByRefId[refId]