Refactor bam features

CHANGELOG.md

@@ -1,16 +1,13 @@
 ## [2.0.4](https://github.com/GMOD/bam-js/compare/v2.0.3...v2.0.4) (2024-08-09)
 
-
-
 ## [2.0.3](https://github.com/GMOD/bam-js/compare/v2.0.2...v2.0.3) (2024-07-23)
 
-
 ### Reverts
 
-* Revert "Migrate to eslint9" ([65adcbb](https://github.com/GMOD/bam-js/commit/65adcbb2793243659682d30694f8604d241a5337))
-* Revert "Run format" ([2a02535](https://github.com/GMOD/bam-js/commit/2a02535db4df80f245232522cdba771cbf5ea214))
-
-
+- Revert "Migrate to eslint9"
+  ([65adcbb](https://github.com/GMOD/bam-js/commit/65adcbb2793243659682d30694f8604d241a5337))
+- Revert "Run format"
+  ([2a02535](https://github.com/GMOD/bam-js/commit/2a02535db4df80f245232522cdba771cbf5ea214))
 
 ## [2.0.2](https://github.com/GMOD/bam-js/compare/v2.0.1...v2.0.2) (2024-02-21)
 

README.md

@@ -161,7 +161,7 @@ feature.get('end') // 0-based half open end coordinate
 feature.get('name') // QNAME
 feature.get('seq') // feature sequence
 feature.get('qual') // qualities
-feature.get('cigar') // cigar string
+feature.get('CIGAR') // CIGAR string
 feature.get('MD') // MD string
 feature.get('SA') // supplementary alignments
 feature.get('template_length') // TLEN

package.json

@@ -40,8 +40,10 @@
   "dependencies": {
     "@gmod/abortable-promise-cache": "^2.0.0",
     "@gmod/bgzf-filehandle": "^1.4.4",
+    "buffer": "^6.0.3",
     "crc": "^4.3.2",
     "generic-filehandle": "^3.0.0",
+    "long": "^4.0.0",
     "quick-lru": "^4.0.0"
   },
   "devDependencies": {
@@ -53,8 +55,8 @@
     "eslint": "^9.9.0",
     "eslint-config-prettier": "^9.1.0",
     "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-unicorn": "^55.0.0",
-    "prettier": "^3.2.5",
+    "eslint-plugin-unicorn": "^56.0.0",
+    "prettier": "^3.3.3",
     "rimraf": "^6.0.1",
     "standard-changelog": "^6.0.0",
     "typescript": "^5.0.4",

src/bamFile.ts

@@ -288,12 +288,12 @@ export default class BamFile {
 
       const recs = [] as BAMFeature[]
       for (const feature of records) {
-        if (feature.seq_id() === chrId) {
-          if (feature.get('start') >= max) {
+        if (feature.ref_id === chrId) {
+          if (feature.start >= max) {
             // past end of range, can stop iterating
             done = true
             break
-          } else if (feature.get('end') >= min) {
+          } else if (feature.end >= min) {
             // must be in range
             recs.push(feature)
           }
@@ -319,8 +319,8 @@ export default class BamFile {
     feats.map(ret => {
       const readNames: Record<string, number> = {}
       for (const element of ret) {
-        const name = element.name()
-        const id = element.id()
+        const name = element.name
+        const id = element.id
         if (!readNames[name]) {
           readNames[name] = 0
         }
@@ -337,10 +337,10 @@ export default class BamFile {
     const matePromises: Promise<Chunk[]>[] = []
     feats.map(ret => {
       for (const f of ret) {
-        const name = f.name()
-        const start = f.get('start')
-        const pnext = f._next_pos()
-        const rnext = f._next_refid()
+        const name = f.name
+        const start = f.start
+        const pnext = f.next_pos
+        const rnext = f.next_refid
         if (
           this.index &&
           unmatedPairs[name] &&
@@ -377,7 +377,7 @@ export default class BamFile {
           dpositions,
           chunk,
         )) {
-          if (unmatedPairs[feature.get('name')] && !readIds[feature.id()]) {
+          if (unmatedPairs[feature.name] && !readIds[feature.id]) {
             mateRecs.push(feature)
           }
         }