Add TAF format documentation and improve code comments

- Add reference to TAF format documentation (ComparativeGenomicsToolkit/taffy)
- Document row instruction types and their meaning
- Add function documentation to parseRowInstructions
- Improve class documentation for BgzipTaffyAdapter
- Add block documentation for lowerBound function

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

Author: cmdcolin

src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts

@@ -50,7 +50,9 @@ interface TafFeature {
   seq: string
 }
 
-// Binary search to find the index of the first element >= target
+/**
+ * Binary search to find the index of the first element >= target
+ */
 function lowerBound<T>(arr: T[], target: number, getKey: (item: T) => number) {
   let lo = 0
   let hi = arr.length
@@ -65,6 +67,12 @@ function lowerBound<T>(arr: T[], target: number, getKey: (item: T) => number) {
   return lo
 }
 
+/**
+ * Adapter for TAF (Taffy Alignment Format) files compressed with BGZIP
+ * Implements streaming parsing of TAF blocks into MAF features
+ *
+ * TAF Format: https://github.com/ComparativeGenomicsToolkit/taffy
+ */
 export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
   public setupP?: Promise<SetupData>
 

src/BgzipTaffyAdapter/rowInstructions.ts

@@ -1,3 +1,15 @@
+/**
+ * TAF (Taffy Alignment Format) row instruction types
+ * Reference: https://github.com/ComparativeGenomicsToolkit/taffy
+ *
+ * Instruction types:
+ * 'i' - insert: add a new sequence row
+ * 's' - substitute: replace coordinates of an existing row
+ * 'd' - delete: remove a sequence row
+ * 'g' - gap: add a fixed-length gap to sequence start
+ * 'G' - gap substring: add variable-length gap from substring
+ */
+
 interface RowInsert {
   type: 'i'
   row: number
@@ -60,6 +72,10 @@ export function filterFirstLineInstructions(
     })
 }
 
+/**
+ * Parses TAF row instruction string into structured RowInstruction objects
+ * Each instruction token sequence is parsed according to TAF format rules
+ */
 export function parseRowInstructions(meta: string) {
   const ret = meta.split(' ')
   const rows = [] as RowInstruction[]