Chapter 4 Read tasks

assessSoftClipping	Assessing level of soft clipping in BAM file
BAMDiagnostics	Estimating depth and read property frequencies
downsample	Downsampling a BAM file
filterBAM	Writing reads that pass filters to BAM file
mergeOverlappingReads	Merging paired-end reads in BAM file
mergeRG	Merging read groups in a BAM file
PMDS	Filtering for ancient reads using PMDS
qualityTransformation	Printing Quality Transformation
readOverlap	Estimating distribution of overlap of paired reads
trimSoftClips	Removing soft clipped bases from reads