For a single channel of input, creates wiggle files showing binned coverage, which can be visualized using the UCSC Genome Browser, IGV and other browsers. See http://genome.ucsc.edu/goldenPath/help/wiggle.html.

For multiple channels, generates tables of binned coverage which cannot be visualized.

usage: usage="binReads [options] <alignment_file(s)>"

options:
  -h, --help            show this help message and exit
  -b BINSIZE, --binsize=BINSIZE
                        binsize [default=1000]
  -o OUTFILE, --outfile=OUTFILE
                        output filename [default=<uses base filename>]
  -v, --verbose         print debugging output [default=False]
  -s, --sort            sort files first [default=False]
  -z, --gzip            gzip resulting file [defualt=False]
  -m REFMAP, --refMap=REFMAP
                        transform refIDs to refnames in the map file (e.g. the
                        output of align2txt -map <file>)
  --merge               create a single binning based on multiple alignment
                        files
  --aggregate           creates a tab-deliminated (e.g. not WIGGLE) formated
                        tally with count columns for each input file for each
                        reference bin
  --zero                include bins with a zero count
  --minCount=MINCOUNT   report only bins with counts >= minCount  [default=1]
  --bufferSize=MEM      Buffer Size to allocate when sorting text files
                        (default=1G)
  -n TRACK_NAME, --track_name=TRACK_NAME
                        name to display on browser track
  -r, --reads_per_million
                        report bin counts in reads/million units
                        (default=False)