<commit_before>samtools view $1 | awk '{if ($2 == 77) print ">"$1"/1\n"$10; if ($2 == 141) print ">"$1"/2\n"$10; if (($2 != 77) && ($2 != 141)) print ">"$1"\n"$10;}' - > $2.fasta<commit_msg>does not save the seq if it fails quality checks.<commit_after>samtools view $1 | gawk '{if (and($2,0x0200)) next; if (and($2,0x0040)) print ">"$1"/1\n"$10; if (and($2,0x0080)) print ">"$1"/2\n"$10; else print ">"$1"\n"$10;}' - > $2.fasta
{'fraction_non_alphanumeric': 0.29906542056074764, 'fraction_numerical': 0.13551401869158877, 'mean_word_length': 4.72, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 11, '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': '3595600', 'n_tokens_mistral': 220, 'n_tokens_neox': 190, 'n_words': 49}