from lqc.cs import CS
from lqc.indel import Indel
from lqc.mismatch import Mismatch
from lqc.splice import Splice
from lqc.stat import stat_element_from_bam_by_contig
from lqc.utils import check_bam_with_cs_or_md
from lqc.utils import bam_or_sam
from lqc.utils import write_readcs
from lqc.report_table import create_readstat_table
from lqc.report_table import create_indel_summary_table
from lqc.report_table import create_mismatch_normalized_read_location_table
from lqc.report_table import create_splice_table
from lqc.report_figure import plot_readstat_bar
from lqc.report_figure import plot_readstat_bar_mean_element_per_read
from lqc.report_figure import plot_readstat_bar_mean_element_per_read_per_kb
from lqc.report_figure import plot_readstat_cumulative_length
from lqc.report_figure import plot_readstat_bar_ratio_with_element
from lqc.report_figure import plot_readstat_length_hist
from lqc.report_figure import plot_element_total_count
from lqc.report_figure import plot_indel_hist_length
from lqc.report_figure import plot_indel_hist_location
from lqc.report_figure import plot_mismatch_type_count
from lqc.report_figure import plot_mismatch_hist_location
from lqc.report_figure import plot_splice_type_count
from lqc.template import get_html_template
from lqc.template import copy_logo
from lqc.report_html import html_add_readstat_table
from lqc.report_html import html_add_mismatch_table
from lqc.report_html import html_add_insertion_table
from lqc.report_html import html_add_deletion_table
from lqc.report_html import html_add_splice_table


__all__ = [
    'CS',
    'Indel',
    'Mismatch',
    'Splice',
    'stat_element_from_bam_by_contig',
    'check_bam_with_cs_or_md',
    'bam_or_sam',
    'write_readcs',
    'create_readstat_table',
    'create_indel_summary_table',
    'create_mismatch_normalized_read_location_table',
    'create_splice_table',
    'plot_readstat_bar',
    'plot_readstat_bar_mean_element_per_read',
    'plot_readstat_bar_mean_element_per_read_per_kb',
    'plot_readstat_cumulative_length',
    'plot_readstat_bar_ratio_with_element',
    'plot_readstat_length_hist',
    'plot_element_total_count',
    'plot_indel_hist_length',
    'plot_indel_hist_location',
    'plot_mismatch_type_count',
    'plot_mismatch_hist_location',
    'plot_splice_type_count',
    'get_html_template',
    'copy_logo',
    'html_add_readstat_table',
    'html_add_mismatch_table',
    'html_add_insertion_table',
    'html_add_deletion_table',
    'html_add_splice_table'
]
