def _mainLoop(self): # Split up reference genome into chunks and farm out the # a chunk as a unit of work. logging.debug("Starting main loop.") ids = reference.enumerateIds(options.referenceWindows) for _id in ids: if options.fancyChunking: chunks = reference.fancyEnumerateChunks(self._inCmpH5, _id, options.referenceChunkSize, options.minCoverage, options.minMapQV, options.referenceWindows) else: chunks = reference.enumerateChunks(_id, options.referenceChunkSize, options.referenceWindows) for chunk in chunks: if self._aborting: return try: self._workQueue.put(chunk, True, options.queueTimeout) except: return # Write sentinels ("end-of-work-stream") for i in xrange(options.numWorkers): self._workQueue.put(None)
def _mainLoop(self): # Split up reference genome into chunks and farm out the # a chunk as a unit of work. logging.debug("Starting main loop.") ids = reference.enumerateIds(options.referenceWindows) for _id in ids: if options.fancyChunking: chunks = reference.fancyEnumerateChunks( self._inAlnFile, _id, options.referenceChunkSize, options.minCoverage, options.minMapQV, options.referenceWindows) else: chunks = reference.enumerateChunks(_id, options.referenceChunkSize, options.referenceWindows) for chunk in chunks: if self._aborting: return self._workQueue.put(chunk) # Write sentinels ("end-of-work-stream") for i in xrange(options.numWorkers): self._workQueue.put(None)