<jupyter_start><jupyter_text>Read BAM file and get information about mappingAuthor: <NAME>, 2016-2018<jupyter_code>%pylab inline
from sequana import BAM, sequana_data
b = BAM(sequana_data('test.bam', 'testing'))
b.plot_bar_mapq()
b.get_flags_as_df().sum()
b.get_full_stats_as_df()<jupyter_output><empty_output>
{'fraction_non_alphanumeric': 0.12903225806451613, 'fraction_numerical': 0.025806451612903226, 'mean_word_length': 9.724137931034482, 'pattern_counts': {'":': 0, '<': 6, '<?xml version=': 0, '>': 6, '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}}
{'chain_length': '1', 'dir': 'jupyter-structured-clean-dedup', 'id': '96824', 'license': 'BSD-3-Clause', 'n_tokens_mistral': 130, 'n_tokens_neox': 124, 'n_words': 22, 'path': 'notebooks/BAM.ipynb', 'repo_name': 'vladsaveliev/sequana', 'size': '319'}