qc_alignment: Generate some alignment statistics on reads
In anilchalisey/chompR: ChIP and ATAC-seq data processing pipeline

Generate some alignment statistics on reads

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qc_alignment(samtools = "samtools", bam.files = NULL,
  filtered.bam.files = NULL, threads = 1,
  remove.mitochondrial = "MT")

`samtools`	character string specifying path to samtools. [DEFAULT = "samtools"]
`bam.files`	character vector specifying path to pre-filtered bam files. [DEFAULT = NULL]
`filtered.bam.files`	character vector specifying path to filtered bam files. [DEFAULT = NULL]
`threads`	positive integer specifying the number of cores to use
`remove.mitochondrial`	character string. If set, this will count reads mapping to the mitochondrial genome. The string should match the reference name for the mitochondrial genome in the alignment file. Examples include "ChrM", "M" and "MT".