def _setup(self, config, temp):
if self._check_fastqs:
check_fastq_files(self.input_files, self._quality_offset)
os.mkfifo(os.path.join(temp, self._basename + ".discarded"))
os.mkfifo(os.path.join(temp, self._basename + ".pair1.truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".pair2.truncated"))
os.mkfifo(os.path.join(temp, "uncompressed_input_1"))
os.mkfifo(os.path.join(temp, "uncompressed_input_2"))
if self._version == VERSION_15:
if self._collapse:
os.mkfifo(os.path.join(temp, self._basename + ".collapsed"))
os.mkfifo(
os.path.join(temp,
self._basename + ".collapsed.truncated"))
os.mkfifo(
os.path.join(temp, self._basename + ".singleton.truncated"))
else:
os.mkfifo(
os.path.join(temp,
self._basename + ".singleton.aln.truncated"))
os.mkfifo(
os.path.join(temp,
self._basename + ".singleton.unaln.truncated"))
CommandNode._setup(self, config, temp)
def _setup(self, config, temp):
check_fastq_files(self.input_files, self._quality_offset)
os.mkfifo(os.path.join(temp, self._basename + ".truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".discarded"))
os.mkfifo(os.path.join(temp, "uncompressed_input"))
CommandNode._setup(self, config, temp)
def _setup(self, config, temp):
check_fastq_files(self.input_files, self._quality_offset)
os.mkfifo(os.path.join(temp, self._basename + ".truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".discarded"))
os.mkfifo(os.path.join(temp, "uncompressed_input"))
CommandNode._setup(self, config, temp)
def _setup(self, config, temp):
check_fastq_files(self.input_files, self._quality_offset)
os.mkfifo(os.path.join(temp, self._basename + ".discarded"))
os.mkfifo(os.path.join(temp, self._basename + ".pair1.truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".pair2.truncated"))
os.mkfifo(os.path.join(temp, "uncompressed_input_1"))
os.mkfifo(os.path.join(temp, "uncompressed_input_2"))
if self._version == VERSION_15:
if self._collapse:
os.mkfifo(os.path.join(temp, self._basename + ".collapsed"))
os.mkfifo(os.path.join(temp, self._basename + ".collapsed.truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".singleton.truncated"))
else:
os.mkfifo(os.path.join(temp, self._basename + ".singleton.aln.truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".singleton.unaln.truncated"))
CommandNode._setup(self, config, temp)
