binned coverage plot option in align_and_plot

[lakras]

added binning for coverage plots with large reference genomes generated by align_and_plot:

• off by default, can be turned on with option bin_large_plots = True
• plots maximum or minimum read depth in each bin (option binning_summary_statistic = "max" or "min", default is max)
• bin size set to one bin per pixel (bin size displayed in y axis label--Plasmodium bin size is 27 kb)
• binning results in Plasmodium coverage plots with file size 20 KB, compared to 140 MB without binning (unopenable and indecipherable if it does open)

also:

• made sample name field in plot_coverage optional to allow running with new batch tool runner on DNA nexus (gets sample name from reads_unmapped_bam)
• fixed indentation, repeated code in plot_coverage

Here's a coverage plot for the first chromosome of P. falciparum without binning (left; 5.2 MB) and with binning (right; 21 KB).

And here's a coverage plot for the whole P. falciparum genome without binning (left; 136.4 MB) and with binning (right; 21 KB).