Enable IGB users to show or hide soft-clipped bases in BAM tracks.
Add option to track label context menu - "Show soft-clipped bases"
See image for wording and placement relative to other menu items.

Adding David's comments here for future reference:
Initial thoughts:
1. You need to store everything you need to dynamically visualize the read in the data model when the file is loading.
2. My understanding is likely very poor at this stage, but this probably means creating a custom "Sym" type that cares for the details of rendering.

Additional quick thought that may or may not be useful:

It seems the start position of the sym/glph is impacted by the soft clipping toggle. I think instead of hard-coding the position of the BAMSym at parse time you could instead capture fields in BamSym like softClipStartPosition and defaultStartPosition and then dynamically return one or the other depending on the preferences based toggle.

i.e. in the getter for this property you could have an if condition that references this global preferences boolean

boundaries of the glyph are important in steps such as packing, so I think you will need to take special care to repack/refresh the view when this toggle is triggered and the data model is parsed again for rendering.

I am going to try to implement soft-clipping visualization similar to how insertions are drawn.
This will most likely involve editing the following files:

1. BAMSym.java
2. XAM.java
3. BAM.java
4. SAM.java
5. AnnotationGlyphFactory.java

When testing, it will be important to look at memory use, as we will be drawing new glyphs for each instance of soft-clipping.
We will also need to check paired-end reads, as they add an additional layer of complexity.

My current branch with implemented softclipping:
https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-1291-Softclipping

New implementation showing soft clips as black rectangles with red triangles. The soft clip glyph shows up on the first/last nucleotide that is matched (M on cigar string) after/before the soft clip.

New implementation shows the entire length of the soft clip. Soft clip is selectable and has tooltips and edge matching.

New implementation has more options, better selection through menu. Appears to be working with the changes to HTSJDK.

Tested using master branch of Loraine Lab and also using local build on Windows.
The functionality is working correctly and the menu options are also easy to understand now. The code is not breaking anywhere.