mergeStrandseqFiles: Merge Strand-seq libraries
In AneuFinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Merge strand libraries to generate a high-coverage Strand-seq library.

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mergeStrandseqFiles(files, assembly, chromosomes = NULL,
  pairedEndReads = FALSE, min.mapq = 10, remove.duplicate.reads = TRUE,
  max.fragment.width = 1000)

`files`	A character vector with files with aligned reads.
`assembly`	Please see `fetchExtendedChromInfoFromUCSC` for available assemblies. Only necessary when importing BED files. BAM files are handled automatically. Alternatively a data.frame with columns 'chromosome' and 'length'.
`chromosomes`	If only a subset of the chromosomes should be imported, specify them here.
`pairedEndReads`	Set to `TRUE` if you have paired-end reads in your BAM files (not implemented for BED files).
`min.mapq`	Minimum mapping quality when importing from BAM files. Set `min.mapq=NA` to keep all reads.
`remove.duplicate.reads`	A logical indicating whether or not duplicate reads should be removed.
`max.fragment.width`	Maximum allowed fragment length. This is to filter out erroneously wrong fragments due to mapping errors of paired end reads.