usage: __main__.py [-h] --bed BED --signal SIGNAL --output OUTPUT
                   [--genome-size-file GENOME_SIZE_FILE] [--no-residualize]
                   [--genome-fasta GENOME_FASTA]
                   [--summary {max,mean,center_max,center_mean}]
                   [--window-bp WINDOW_BP]

Extract ChIP signal over DNase/ATAC regions from either BigWig or BedGraph.
Outputs: region_key<TAB>signal, where region_key is chrom:start-end of the
ORIGINAL regions.

options:
  -h, --help            show this help message and exit
  --bed BED             Path to DNase-seq/ATAC-seq BED file (-a)
  --signal SIGNAL       Path to ChIP-seq BedGraph OR BigWig file (-b)
  --output OUTPUT       Output file path
  --genome-size-file GENOME_SIZE_FILE
                        Optional genome chrom sizes file for bedtools sort
                        (-g)
  --no-residualize      Skip residualization and output raw extracted signal.
                        By default EUbar outputs residualized log1p(signal)
                        after adjusting for GC.
  --genome-fasta GENOME_FASTA
                        Genome FASTA (required unless --no-residualize is
                        used).
  --summary {max,mean,center_max,center_mean}
                        How to summarize signal: max/mean over full interval,
                        or center_max/center_mean over a fixed window.
  --window-bp WINDOW_BP
                        Window size (bp) for center_* summaries (default:
                        100). Ignored for max/mean.
