def __get_configuration(self, ctx):
# TODO: refactor settings common to mapper and reducer
jc = ctx.getJobConf()
jobconf = deprecation_utils.convert_job_conf(jc, self.DeprecationMap, self.logger)
jc_configure(self, jobconf, 'seal.seqal.log.level', 'log_level', 'INFO')
jc_configure(self, jobconf, "seal.seqal.fastq-subformat", "format", self.DEFAULT_FORMAT)
jc_configure_int(self, jobconf, 'seal.seqal.alignment.max.isize', 'max_isize', 1000)
jc_configure_int(self, jobconf, 'seal.seqal.alignment.min.isize', 'min_isize', None)
jc_configure_int(self, jobconf, 'seal.seqal.pairing.batch.size', 'batch_size', 10000)
jc_configure_int(self, jobconf, 'seal.seqal.min_hit_quality', 'min_hit_quality', 0)
jc_configure_bool(self, jobconf, 'seal.seqal.remove_unmapped', 'remove_unmapped', False)
jc_configure_int(self, jobconf, 'seal.seqal.nthreads', 'nthreads', 1)
jc_configure_int(self, jobconf, 'seal.seqal.trim.qual', 'trim_qual', 0)
try:
self.log_level = getattr(logging, self.log_level)
except AttributeError:
raise ValueError("Unsupported log level: %r" % self.log_level)
if self.format not in self.SUPPORTED_FORMATS:
raise_pydoop_exception(
"seal.seqal.fastq-subformat must be one of %r" %
(self.SUPPORTED_FORMATS,)
)
if self.remove_unmapped:
raise NotImplementedError("seal.seqal.remove_unmapped is currently unsupported")
if self.min_hit_quality > 0:
raise NotImplementedError("seal.seqal.min_hit_quality is currently unsupported")
if self.trim_qual > 0:
raise NotImplementedError("seal.seqal.trim_qual is currently unsupported")
if self.max_isize <= 0:
raise ValueError("'seal.seqal.alignment.max.isize' must be > 0, if specified [1000]")
if self.batch_size <= 0:
raise ValueError("'seal.seqal.pairing.batch.size' must be > 0, if specified [10000]")
# minimum qual value required for a hit to be kept. By default outputs all the
# hits BWA returns.
if self.min_hit_quality < 0:
raise ValueError("'seal.seqal.min_hit_quality' must be >= 0, if specified [0]")
# number of concurrent threads for main alignment operation
if self.nthreads <= 0:
raise ValueError("'seal.seqal.nthreads' must be > 0, if specified [1]")
# trim quality parameter used by BWA from read trimming. Equivalent to
# the -q parameter for bwa align
if self.trim_qual < 0:
raise ValueError("'seal.seqal.trim.qual' must be >= 0, if specified [0]")
if jc.hasKey('mapred.reduce.tasks') and jc.getInt('mapred.reduce.tasks') > 0:
self.__map_only = False
else:
self.__map_only = True
def __init__(self, ctx):
super(reducer, self).__init__(ctx)
jc = ctx.getJobConf()
logger = logging.getLogger("seqal")
jobconf = deprecation_utils.convert_job_conf(jc, self.DeprecationMap, logger)
jc_configure(self, jobconf, 'seal.seqal.log.level', 'log_level', 'INFO')
jc_configure_bool(self, jobconf, 'seal.seqal.discard_duplicates', 'discard_duplicates', False)
logging.basicConfig(level=self.log_level)
self.event_monitor = HadoopEventMonitor(self.COUNTER_CLASS, logging.getLogger("reducer"), ctx)
self.__output_sink = EmitSamLink(ctx, self.event_monitor)
def __init__(self, ctx):
super(reducer, self).__init__(ctx)
jc = ctx.getJobConf()
logger = logging.getLogger("seqal")
jobconf = deprecation_utils.convert_job_conf(jc, self.DeprecationMap, logger)
jc_configure(self, jobconf, 'seal.seqal.log.level', 'log_level', 'INFO')
jc_configure_bool(self, jobconf, 'seal.seqal.discard_duplicates', 'discard_duplicates', False)
logging.basicConfig(level=self.log_level)
self.event_monitor = HadoopEventMonitor(self.COUNTER_CLASS, logging.getLogger("reducer"), ctx)
self.__output_sink = EmitSamLink(ctx, self.event_monitor)
