trim_and_filter: Trim and Filter a FASTQ
In andrewGhazi/malacoda: Bayesian Analysis of High-Throughput Genomic Assays

Use the FASTX-Toolkit to trim out the barcodes from the FASTQs by position, then quality filter them.

1	trim_and_filter(fastq, temp_dir, quality_cutoff, bc_start, bc_end)

`fastq`	path to a fastq file
`temp_dir`	a character string giving the path to a directory to use for temporary intermediate files
`quality_cutoff`	an integer indicating the quality cutoff to be used
`bc_start`	an integer indicating the position in the read where the barcode starts
`bc_end`	an integer indicating the position in the read where the barcode ends