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remove bedtools as dependency for converting BAM -> FASTQ. Now AMPtk will first try to use samtools if it exists, then bedtools if it exists, and will default to pybam native python parser to convert. Pybam is 10X slower than samtools, but is written in python thus no extra dependencies needed.
added threshold filtering to amptk remove and amptk select, so you could remove all samples with reads less than 5000 by running, amptk remove -i input.demux.fq -t 5000 -o output.demux.fq