Make methylation look different from other mismatches on small scale

[iromeo]

Methylation mismatches look like T and C by our initial design, idea was that unmethylated cytosine coloured like ordinary cytosine and methylated cytosine looks like changed cytosine. Also, it is consistent with IGV and often people show methylated CpG using red/green/black colors and not methylated using blue/white colours. Maybe the intuition of colors selection is a bit misleading, because red is color of T and T are mismatches where cytosine wasn't protected by methylation, so maybe other color scheme will be easier to memorise.

On the other hand, we want to visualize mismatches that cannot be explained by bisulfite treatment., e.g. to highlight SNP and combination for SNP+methylaiton.

At the moment, SNP looks like methylation:

Let's fix it. Suggestions:

• change the shape of the mismatch bar, e.g. make methylation-related bars shorter with equal gaps above and below the bar
  • bars will be still visible in coverage in a same way
• do not show non-methylated mismatches in coverage
  • bars in reads will be still look same + SNP will be less noticeable
• Use colours that different from A/T/G/C/N colors , e.g.:

          this == METHYLATED_C -> Color(255,80,180)
          this == UNMETHYLATED_C -> Color(0 ,100,250)

and with reads coloring:

[iromeo]

Additional examples for new colors:

[iromeo]

The color scheme was updated. For my examples looks good.