from modules.software_base import WorkflowRunnerBase
import os

class SplitByRefRunner(WorkflowRunnerBase):
    def __init__(self, logger, manifest_list, input_path, output_path="", additional_args="", threads=2, stepname="", mode=None):
        super().__init__(
            logger=logger,
            manifest_list=manifest_list,
            input_path=input_path,
            output_path=output_path,
            additional_args=additional_args,
            threads=threads,
            stepname=stepname,
            software_name="splitByRef.py",
            unneeded_args=["-i", "-o", "-s", "-t", "--input_bam", "--output_dir", "--sample_id", "--threads"],
            output_type="bam",
            rescan_output=True,
            mode=mode
        )

    def find_input_files(self,prev_step_files):
        for line in prev_step_files:
            self.input_file_list.append({
                "id": line["id"],
                "input1": line["output1"],
                "input2": None,
                "output1": None,
                "output2": None,
            })
        if self.leaf:
            return prev_step_files
        else:
            return None

    def build_command_queue(self):
        for item in self.input_file_list:
            cmd = [
                self.software_name,
                f"--input_bam {item['input1']}",
                f"--output_dir {self.output_path}",
                f"--sample_id {item['id']}",
                f"--threads {self.threads}"
            ]
            
            self.command_queue.append(" ".join(cmd))