Bed file format: https://genome.ucsc.edu/FAQ/FAQformat.html#format1

Start with module: Plugin - BED file format handler

Update:

• Figured out a way to get the min_blocks and max_blocks data from the object.
• The type of the object that is passed to function is SeqSymmetry(Parent class), but it does not have information about blocks. Therefore it needs to by type casted with class UcscBedDetailSym, child class of SeqSymmetry, in order to access the getters methods of min_blocks and max_blocks.
• on coming monday, I will be creating a new branch and start working on the coding part.

Since the bedsym logic may be applied to data that is not showing gene models (exons), label the blocks as "Block: " for Selection Info.

Some general notes from walking through the debugger:
SeqUtils.java - collectLeafSpans - loops through blocks and calls UcscBedSym getChild
UcscBedSym.java - getChild - creates new BedChildSingletonSeqSym for each child (I think these equate to exons). Right now these just take three properties, seq, start, end (they are effectively just a SimpleSeqSpan). Unclear if we can add the index position to the BedChildSingletonSeqSym (i.e. what should be the exon). The SimpleSeqSpan is used in a lot of places, so would be hard to modify. Maybe we can modify BedChildSingletonSeqSym to have the index position?
SeqMapView - determineProps - this is where the properties are assigned to the view, but I'm not sure exactly how this works.

• Implemented a feature that shows block number of a selected gene model in selection info.
• pull and checkout to this branch.
• added comments for each code change.
  Testing Instructions:
• select the single genome, click on the selection info and check for a property named "block number".
• Hover on single genome model and look for the property called "block number".
• The block number represents the sequence number or position of the block.

Testing on Mac:

• Default data from IGB Quickload shows block number correctly for +/- strands.
• ncbiRefSeqCurated in the hg38 human genome does not show the block number (I think these DAS files load as bigBed, which IGB cannot currently fully parse).
• Local bed file shows block number correctly for +/- strands.
• Narrowpeak and broadpeak files do not show block number (this is the correct behavior).
• Local GFF3 file (from smoketesting) does not show block number (correct behavior), but does show a "rank" property that seems to correlate with exon number, so no need to implement this feature for GFF3?
• Local GTF file (from smoketesting) does not show block number (correct behavior), but does have a "exon_number" property, so no need to implement the feature for GTF.
• Local bigbed file (see IGBF-2978) shows block number correctly for +/- strands.
• A FindJunctions file is showing the block number. This isn't exactly correct as the block number for findJunctions is always going to be 1 - 2 and will not change based on the exons associated with the junction. Odd that the findJunctions file is being parsed as a ucscBedSym, but I think it should be fine assuming we leave the property as "Block number" instead of exon, which could be confusing.

Everything seems to be working well. GFF/GTF already seem to implement the exon number, so we have now added bed/bigBed files. It's odd that the UCSC DAS files are not showing the block number, but I have a few theories (I will make a new ticket).

One quirk is that the first and last "thick" exons when overlapping a "thin" UTR will not show the block number. This is because the "thin" UTR is the actual child sym that the block number appears in, the thick part is drawn over top of it, and it is unclear where that sym is coming from.

Ready for pull request.

new pull request submitted after rebasing branch with main-JDK8.

PR is merged and main-JDK8 branch installers are newly built and ready for testing in the Downloads section of the team repo as usual: https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/

Tested main-JDK8 installer on Mac.

Block number is working correctly, no errors in the log.

Closing ticket.