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 + ".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)