from modules.software_base import WorkflowRunnerBase
import os

class PicardRunner(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="picard",
            unneeded_args=["--INPUT", "-I", "-O", "--OUTPUT"],
            output_type="bam",
            leaf=False,
            mode=mode
        )
    def dynamic_flags_from_args(self):
        # Different subcommands require different flags :[
        if "MarkDuplicates" in self.additional_args:
            self.unneeded_args.append("-M")

        if "ValidateSamTools" in self.additional_args:
            self.leaf = True

    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": 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):
        # Written with specifically ValidateSamFile and MarkDuplicates in mind.
        for item in self.input_file_list:
            cmd = [
                self.software_name,
                self.additional_args,
                f"--INPUT {item['input1']}",
                f"--OUTPUT {item['output1']}"
            ]

            if "MarkDuplicates" in self.additional_args:
                cmd += [
                    f"--METRICS_FILE {os.path.join(self.output_path, "input-dedupe-stats.txt")}"
                ]

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