correctly parse FILER "bed"-like files

[fossilfriend]

all files are in a bedX+Y (e.g., bed4+12 means chr, start, end, name+ 12 more non-standard BED fields)

• [x] assign example tracks a bedX+Y format in their config
• [x] create a custom bed decoder that is a copy of the igv.js decodeBed decoder, but logs a message to indicate that the custom decoder is called
• [x] set track.config.decode (resolveDecoder) to the custom bed decoder when resolving tracks, if format matches bedX+Y regexp

decode functions only take tokens and header, and cannot see the track config, so need to figure out how to pass X+Y to decoder so it can determine how to interpret fields

it looks like we can use the header, which is assigned a format: see featureParser.js line 62

• [ ] modify custom bed decoder to pull X and Y out of header.format and then modify code to dynamically propagate standard & optional fields based on X,Y values
  • X = number of standard BED fields
  • Y = number of optional fields

[fossilfriend]

will need to expose UCSCBedFeature in NIAGADS/igv.js so that it can be imported by the decoder; error is caused by the following line of code in decodeBedXY:

const feature = new igv.UCSCBedFeature({chr: chr, start: start, end: end, score: 1000})

[fossilfriend]

in bedDecoder.tsx define a new Feature class BedXYFeature to use instead of UCSCBedFeature.

Should be modeled after UCSCBedFeature, but modifies the getAttributeValue function to check info field instead of attributes field and returns null on key errors.

decodeBedXY should return a BedXYFeature instead of a UCSCBedFeature. Also, update to build properties in entirety before creating the feature object.

[fossilfriend]

closed by https://github.com/NIAGADS/niagads-igv-webapp/pull/30