# Empty -- temporary to avoid import errors
def run(bam_file, data, out_dir):
    pass

import collections
import glob
import os
import pandas as pd
import shutil
import toolz as tz

from bcbio import utils
from bcbio import broad
from bcbio.broad.metrics import PicardMetricsParser, PicardMetrics
from bcbio import bam
from bcbio.distributed.transaction import tx_tmpdir
from bcbio.provenance import do
from bcbio.pipeline import datadict as dd

def run(bam_file, data, out_dir):
    config = data["config"]
    if "picard" not in dd.get_tools_on(data):
        return {}
    ref_file = dd.get_ref_file(data)
    sample = dd.get_sample_name(data)
    target_file = dd.get_variant_regions(data)
    broad_runner = broad.PicardCmdRunner("picard", config)
    bam_fname = os.path.abspath(bam_file)
    path = os.path.dirname(bam_fname)
    utils.safe_makedir(out_dir)
    hsmetric_file = os.path.join(out_dir, "%s-sort.hs_metrics" % sample)
    if utils.file_exists(hsmetric_file):
        return hsmetric_file
    with utils.chdir(out_dir):
        with tx_tmpdir() as tmp_dir:
            cur_bam = os.path.basename(bam_fname)
            if not os.path.exists(cur_bam):
                os.symlink(bam_fname, cur_bam)
            gen_metrics = PicardMetrics(broad_runner, tmp_dir)
            gen_metrics.report(cur_bam, ref_file,
                               bam.is_paired(bam_fname),
                               target_file, target_file, None, config)
    do.run("sed -i 's/-sort.bam//g' %s" % hsmetric_file, "")
    return hsmetric_file



update current picard file.