Fast5-research

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* Update way reads classifications are parsed from the bulk to use modal classification as Minknow now does.

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* Add filter_from_bam command to create filter tsv file from BAM and sequencing summary file.

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* Add `index_reads` program to build read_id->file index tsv file.

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* Add program to produce read summary text file from Bulk .fast5.

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* Allow `extract_reads` to extract only reads present in a given read_summary.txt

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* Allow `filter_reads` to be given full filename/read_id information

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