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)