<commit_before>"""
.. module:: freebayes
   :platform: Unix, OSX
   :synopsis: A wrapper module for calling ScanIndel.

.. moduleauthor:: <NAME> <<EMAIL>>
"""

from ddb_ngsflow import pipeline<commit_msg>ITDSeek method wrapper<commit_after>"""
.. module:: freebayes
   :platform: Unix, OSX
   :synopsis: A wrapper module for calling ScanIndel.

.. moduleauthor:: <NAME> <<EMAIL>>
"""

from ddb_ngsflow import pipeline


def run_flt3_itdseek(job, config, name, samples):
    """Run ITDseek without a matched normal sample
    :param config: The configuration dictionary.
    :type config: dict.
    :param name: sample name.
    :type name: str.
    :param samples: The samples configuration dictionary.
    :type config: dict.
    :returns:  str -- The output vcf file name.
    """

    itdseek_vcf = "{}.flt3.itdseek.vcf".format(name)
    itdseek_logfile = "{}.flt3.itdseek.log".format(name)

    itdseek_command = ["{}".format(config['itdseek']['bin']),
                       "{}.rg.sorted.bam".format(name),
                       "{}".format(config['reference']),
                       "{}".format(config['samtools-0.19']['bin']),
                       ">",
                       "{}".format(itdseek_vcf)]

    job.fileStore.logToMaster("ITDSeek Command: {}\n".format(itdseek_command))
    pipeline.run_and_log_command(" ".join(itdseek_command), itdseek_logfile)

    return itdseek_vcf
{'fraction_non_alphanumeric': 0.14910394265232976, 'fraction_numerical': 0.004301075268817204, 'mean_word_length': 2.932394366197183, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 10, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5267997', 'n_tokens_mistral': 464, 'n_tokens_neox': 448, 'n_words': 102}