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src/s/e/seq_crumbs-HEAD/crumbs/filters.py   seq_crumbs(Download)
from crumbs.statistics import calculate_dust_score, IntCounter, draw_histogram
from crumbs.settings import get_setting
from crumbs.mapping import (get_or_create_bowtie2_index, map_with_bowtie2,
                            map_process_to_bam, sort_mapped_reads,
                            get_or_create_bwa_index, map_with_bwamem,
                        else:
                            kind = UNKNOWN
            read = [alignedread_to_seqitem(alignments_group[0], file_format),
                    kind]
            #read = [alignments_group, kind]
            kind = UNKNOWN
        if out_format == SEQITEM:
            pair = [alignedread_to_seqitem(read[0], file_format) for read in mates_alignments]
        elif out_format == 'aligned_read':
            pair = mates_alignments