<commit_before>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import subprocess
import fileinput
import itertools
import click
import pipes
import sys
import os
import io

from . import _io, _common, _headerops, cli

UTIL_NAME = 'pairsam_parse'

@cli.command()
@click.argument(
    'sam_path', 
    type=str,
    required=False)

@click.option(
    "-o", "--output", 
    type=str, 
    default="", 
    help='output file.'
        ' If the path ends with .gz, the output is bgzip-compressed.'
        ' By default, the output is printed into stdout.')
@click.option(
    "--assembly", 
    type=str, 
    help='Name of genome assembly (e.g. hg19, mm10)')
@click.option(
    "--min-mapq", 
    type=int, 
    default=10,
    help='The minimal MAPQ score of a mapped read')
@click.option(
    "--max-molecule-size", <commit_msg>parse:revert premature transition to _io<commit_after>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import subprocess
import fileinput
import itertools
import click
import pipes
import sys
import os
import io

from . import _common, _headerops, cli

UTIL_NAME = 'pairsam_parse'

@cli.command()
@click.argument(
    'sam_path', 
    type=str,
    required=False)

@click.option(
    "-o", "--output", 
    type=str, 
    default="", 
    help='output file.'
        ' If the path ends with .gz, the output is bgzip-compressed.'
        ' By default, the output is printed into stdout.')
@click.option(
    "--assembly", 
    type=str, 
    help='Name of genome assembly (e.g. hg19, mm10)')
@click.option(
    "--min-mapq", 
    type=int, 
    default=10,
    help='The minimal MAPQ score of a mapped read')
@click.option(
    "--max-molecule-size", 
{'fraction_non_alphanumeric': 0.13978494623655913, 'fraction_numerical': 0.008363201911589008, 'mean_word_length': 2.931924882629108, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, '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': '4306694', 'n_tokens_mistral': 594, 'n_tokens_neox': 562, 'n_words': 167}