from modules.software_base import WorkflowRunnerBase
import os

class Bowtie2SplitRunner(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="runBowtieSplit.py",
            unneeded_args=["-1", "-2", "-S", "-U", "--threads", "-p"],
            output_type="bam",
            mode=mode
        )

    def find_input_files(self,prev_step_files):
        for line in prev_step_files:
            man_item = next((man_item for man_item in self.manifest_list if man_item['id'] == line['id']), None)
            self.input_file_list.append({
                "id": line["id"],
                "horizon": man_item['horizon'],
                "input1": line["output1"],
                "input2": line["output2"],
                "output1": f"{os.path.join(self.output_path, line['id'])}.{self.output_type}",
                "output2": None,
            })
        if self.leaf:
            return prev_step_files
        else:
            return self.input_file_list

    def build_command_queue(self):
        cmd = [
            self.software_name,
            f"-S {self.output_path}",
            self.additional_args,
            f"--rg-id SFM22.SAMPLE.HORIZON.Illumina.Lib01",
            f"--rg SM:SAMPLE",
            f"--threads {self.threads}"
        ]
        for item in self.input_file_list:
            cmd += [
                f"--input_pair {item['input1']},{item['input2']}"
            ]

        self.command_queue.append(" ".join(cmd))