@gmod/cram 8.0.1 → 8.0.2

package/dist/cramFile/record.d.ts

@@ -110,11 +110,7 @@ export default class CramRecord {
      * @returns {String} sequence basepairs
      */
     getReadBases(): string | null | undefined;
-    /**
-     * Get the pair orientation of a paired read. Adapted from igv.js
-     * @returns {String} of paired orientatin
-     */
-    getPairOrientation(): string | null;
+    getPairOrientation(): string | undefined;
     /**
      * Annotates this feature with the given reference sequence basepair
      * information. This will add a `sub` and a `ref` item to base

package/dist/cramFile/record.js

@@ -295,50 +295,30 @@ class CramRecord {
         }
         return this.readBases;
     }
-    /**
-     * Get the pair orientation of a paired read. Adapted from igv.js
-     * @returns {String} of paired orientatin
-     */
+    // adapted from igv.js
+    // inlines flag checks and uses template literal instead of array+join
     getPairOrientation() {
-        if (!this.isSegmentUnmapped() &&
-            this.isPaired() &&
-            !this.isMateUnmapped() &&
-            this.sequenceId === this.mate?.sequenceId) {
-            const s1 = this.isReverseComplemented() ? 'R' : 'F';
-            const s2 = this.isMateReverseComplemented() ? 'R' : 'F';
-            let o1 = ' ';
-            let o2 = ' ';
-            if (this.isRead1()) {
-                o1 = '1';
-                o2 = '2';
-            }
-            else if (this.isRead2()) {
-                o1 = '2';
-                o2 = '1';
-            }
-            const tmp = [];
-            let isize = this.templateLength || this.templateSize;
-            if (isize === undefined) {
-                throw new Error('One of templateSize and templateLength must be set');
-            }
-            if (this.alignmentStart > this.mate.alignmentStart && isize > 0) {
-                isize = -isize;
-            }
-            if (isize > 0) {
-                tmp[0] = s1;
-                tmp[1] = o1;
-                tmp[2] = s2;
-                tmp[3] = o2;
-            }
-            else {
-                tmp[2] = s1;
-                tmp[3] = o1;
-                tmp[0] = s2;
-                tmp[1] = o2;
-            }
-            return tmp.join('');
+        const f = this.flags;
+        // combined check: paired (0x1) set, unmapped (0x4) clear, mate unmapped (0x8) clear
+        if ((f & 0xd) !== 0x1 || this.sequenceId !== this.mate?.sequenceId) {
+            return undefined;
         }
-        return null;
+        const s1 = f & 0x10 ? 'R' : 'F';
+        const s2 = f & 0x20 ? 'R' : 'F';
+        let o1 = ' ';
+        let o2 = ' ';
+        if (f & 0x40) {
+            o1 = '1';
+            o2 = '2';
+        }
+        else if (f & 0x80) {
+            o1 = '2';
+            o2 = '1';
+        }
+        const isize = this.templateLength || this.templateSize || 0;
+        return isize > 0
+            ? `${s1}${o1}${s2}${o2}`
+            : `${s2}${o2}${s1}${o1}`;
     }
     /**
      * Annotates this feature with the given reference sequence basepair

package/dist/cramFile/record.js.map

@@ -1 +1 @@
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package/esm/cramFile/record.d.ts

@@ -110,11 +110,7 @@ export default class CramRecord {
      * @returns {String} sequence basepairs
      */
     getReadBases(): string | null | undefined;
-    /**
-     * Get the pair orientation of a paired read. Adapted from igv.js
-     * @returns {String} of paired orientatin
-     */
-    getPairOrientation(): string | null;
+    getPairOrientation(): string | undefined;
     /**
      * Annotates this feature with the given reference sequence basepair
      * information. This will add a `sub` and a `ref` item to base

package/esm/cramFile/record.js

@@ -289,50 +289,30 @@ export default class CramRecord {
         }
         return this.readBases;
     }
-    /**
-     * Get the pair orientation of a paired read. Adapted from igv.js
-     * @returns {String} of paired orientatin
-     */
+    // adapted from igv.js
+    // inlines flag checks and uses template literal instead of array+join
     getPairOrientation() {
-        if (!this.isSegmentUnmapped() &&
-            this.isPaired() &&
-            !this.isMateUnmapped() &&
-            this.sequenceId === this.mate?.sequenceId) {
-            const s1 = this.isReverseComplemented() ? 'R' : 'F';
-            const s2 = this.isMateReverseComplemented() ? 'R' : 'F';
-            let o1 = ' ';
-            let o2 = ' ';
-            if (this.isRead1()) {
-                o1 = '1';
-                o2 = '2';
-            }
-            else if (this.isRead2()) {
-                o1 = '2';
-                o2 = '1';
-            }
-            const tmp = [];
-            let isize = this.templateLength || this.templateSize;
-            if (isize === undefined) {
-                throw new Error('One of templateSize and templateLength must be set');
-            }
-            if (this.alignmentStart > this.mate.alignmentStart && isize > 0) {
-                isize = -isize;
-            }
-            if (isize > 0) {
-                tmp[0] = s1;
-                tmp[1] = o1;
-                tmp[2] = s2;
-                tmp[3] = o2;
-            }
-            else {
-                tmp[2] = s1;
-                tmp[3] = o1;
-                tmp[0] = s2;
-                tmp[1] = o2;
-            }
-            return tmp.join('');
+        const f = this.flags;
+        // combined check: paired (0x1) set, unmapped (0x4) clear, mate unmapped (0x8) clear
+        if ((f & 0xd) !== 0x1 || this.sequenceId !== this.mate?.sequenceId) {
+            return undefined;
         }
-        return null;
+        const s1 = f & 0x10 ? 'R' : 'F';
+        const s2 = f & 0x20 ? 'R' : 'F';
+        let o1 = ' ';
+        let o2 = ' ';
+        if (f & 0x40) {
+            o1 = '1';
+            o2 = '2';
+        }
+        else if (f & 0x80) {
+            o1 = '2';
+            o2 = '1';
+        }
+        const isize = this.templateLength || this.templateSize || 0;
+        return isize > 0
+            ? `${s1}${o1}${s2}${o2}`
+            : `${s2}${o2}${s1}${o1}`;
     }
     /**
      * Annotates this feature with the given reference sequence basepair

package/esm/cramFile/record.js.map

@@ -1 +1 @@
-{"version":3,"file":"record.js","sourceRoot":"","sources":["../../src/cramFile/record.ts"],"names":[],"mappings":"AAAA,OAAO,SAAS,MAAM,gBAAgB,CAAA;AAyBtC,MAAM,CAAC,MAAM,oBAAoB,GAA4B;IAC3D,UAAU,EAAE,IAAI;CACjB,CAAA;AAED,SAAS,kBAAkB,CAAC,UAAsB,EAAE,SAAoB;IACtE,0CAA0C;IAC1C,IAAI,CAAC,UAAU,CAAC,WAAW,IAAI,CAAC,UAAU,CAAC,UAAU,EAAE,CAAC;QACtD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,IAAI,UAAU,CAAC,cAAc,EAAE,EAAE,CAAC;QAChC,OAAO,IAAI,CAAA;IACb,CAAC;IAED,+CAA+C;IAC/C,MAAM,eAAe,GAAG,UAAU,CAAC,cAAc,GAAG,SAAS,CAAC,KAAK,CAAA;IAEnE,IAAI,CAAC,UAAU,CAAC,YAAY,EAAE,CAAC;QAC7B,OAAO,SAAS,CAAC,GAAG;aACjB,KAAK,CAAC,eAAe,EAAE,eAAe,GAAG,CAAC,UAAU,CAAC,WAAW,IAAI,CAAC,CAAC,CAAC;aACvE,WAAW,EAAE,CAAA;IAClB,CAAC;IAED,IAAI,KAAK,GAAG,EAAE,CAAA;IACd,IAAI,SAAS,GAAG,eAAe,CAAA;IAC/B,IAAI,kBAAkB,GAAG,CAAC,CAAA;IAC1B,OAAO,KAAK,CAAC,MAAM,GAAG,UAAU,CAAC,UAAU,EAAE,CAAC;QAC5C,IAAI,kBAAkB,GAAG,UAAU,CAAC,YAAY,CAAC,MAAM,EAAE,CAAC;YACxD,MAAM,OAAO,GAAG,UAAU,CAAC,YAAY,CAAC,kBAAkB,CAAE,CAAA;YAC5D,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;gBACjD,kBAAkB,IAAI,CAAC,CAAA;YACzB,CAAC;iBAAM,IAAI,OAAO,CAAC,GAAG,KAAK,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAC5C,2BAA2B;gBAC3B,kBAAkB,IAAI,CAAC,CAAA;gBAEvB,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBACzB,sCAAsC;oBACtC,MAAM,KAAK,GAAG,OAAO,CAAC,IAAI,CAAA;oBAC1B,KAAK,IAAI,KAAK,CAAA;oBACd,SAAS,IAAI,KAAK,CAAC,MAAM,CAAA;gBAC3B,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,mCAAmC;oBACnC,0DAA0D;oBAC1D,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;oBACxB,SAAS,IAAI,CAAC,CAAA;gBAChB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,oBAAoB;oBACpB,KAAK,IAAI,OAAO,CAAC,GAAG,CAAA;oBACpB,SAAS,IAAI,CAAC,CAAA;gBAChB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,YAAY;oBACZ,KAAK,IAAI,OAAO,CAAC,IAAI,CAAA;gBACvB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,WAAW;oBACX,SAAS,IAAI,OAAO,CAAC,IAAI,CAAA;gBAC3B,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,qBAAqB;oBACrB,KAAK,IAAI,OAAO,CAAC,IAAI,CAAA;gBACvB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,oCAAoC;oBACpC,aAAa;oBACb,iDAAiD;oBACjD,SAAS,IAAI,OAAO,CAAC,IAAI,CAAA;gBAC3B,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,4DAA4D;oBAC5D,iEAAiE;oBACjE,KAAK,IAAI,OAAO,CAAC,IAAI,CAAA;gBACvB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,sBAAsB;gBACxB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,wBAAwB;gBAC1B,CAAC;YACH,CAAC;iBAAM,IAAI,kBAAkB,GAAG,UAAU,CAAC,YAAY,CAAC,MAAM,EAAE,CAAC;gBAC/D,2DAA2D;gBAC3D,MAAM,KAAK,GAAG,SAAS,CAAC,GAAG,CAAC,KAAK,CAC/B,SAAS,EACT,SAAS,GAAG,OAAO,CAAC,GAAG,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,CAC3C,CAAA;gBACD,KAAK,IAAI,KAAK,CAAA;gBACd,SAAS,IAAI,KAAK,CAAC,MAAM,CAAA;YAC3B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,2DAA2D;YAC3D,MAAM,KAAK,GAAG,SAAS,CAAC,GAAG,CAAC,KAAK,CAC/B,SAAS,EACT,SAAS,GAAG,UAAU,CAAC,UAAU,GAAG,KAAK,CAAC,MAAM,CACjD,CAAA;YACD,KAAK,IAAI,KAAK,CAAA;YACd,SAAS,IAAI,KAAK,CAAC,MAAM,CAAA;QAC3B,CAAC;IACH,CAAC;IAED,OAAO,KAAK,CAAC,WAAW,EAAE,CAAA;AAC5B,CAAC;AAED,MAAM,WAAW,GAAG;IAClB,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;CACL,CAAA;AAED,SAAS,sBAAsB,CAC7B,UAAsB,EACtB,SAAoB,EACpB,iBAAiD,EACjD,WAAwB;IAExB,8DAA8D;IAC9D,MAAM,QAAQ,GAAG,WAAW,CAAC,MAAM,GAAG,SAAS,CAAC,KAAK,CAAA;IACrD,MAAM,OAAO,GAAG,SAAS,CAAC,GAAG,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;IAC9C,IAAI,OAAO,EAAE,CAAC;QACZ,WAAW,CAAC,GAAG,GAAG,OAAO,CAAA;IAC3B,CAAC;IACD,IAAI,UAAU,GAAI,WAAmB,CAAC,OAAO,CAAC,CAAA;IAC9C,IAAI,UAAU,KAAK,SAAS,EAAE,CAAC;QAC7B,UAAU,GAAG,CAAC,CAAA;IAChB,CAAC;IACD,MAAM,kBAAkB,GAAG,iBAAiB,CAAC,kBAAkB,CAAC,UAAU,CAAE,CAAA;IAC5E,MAAM,IAAI,GAAG,kBAAkB,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACjD,IAAI,IAAI,EAAE,CAAC;QACT,WAAW,CAAC,GAAG,GAAG,IAAI,CAAA;IACxB,CAAC;AACH,CAAC;AAWD,MAAM,CAAC,MAAM,QAAQ,GAAG;IACtB,CAAC,GAAG,EAAE,QAAQ,CAAC;IACf,CAAC,GAAG,EAAE,gBAAgB,CAAC;IACvB,CAAC,GAAG,EAAE,iBAAiB,CAAC;IACxB,CAAC,GAAG,EAAE,cAAc,CAAC;IACrB,CAAC,IAAI,EAAE,qBAAqB,CAAC;IAC7B,4CAA4C;IAC5C,CAAC,IAAI,EAAE,yBAAyB,CAAC;IACjC,iBAAiB;IACjB,CAAC,IAAI,EAAE,OAAO,CAAC;IACf,iBAAiB;IACjB,CAAC,IAAI,EAAE,OAAO,CAAC;IACf,yBAAyB;IACzB,CAAC,KAAK,EAAE,WAAW,CAAC;IACpB,cAAc;IACd,CAAC,KAAK,EAAE,UAAU,CAAC;IACnB,4BAA4B;IAC5B,CAAC,KAAK,EAAE,WAAW,CAAC;IACpB,2BAA2B;IAC3B,CAAC,KAAK,EAAE,eAAe,CAAC;CAChB,CAAA;AAEV,MAAM,CAAC,MAAM,SAAS,GAAG;IACvB,CAAC,GAAG,EAAE,yBAAyB,CAAC;IAChC,CAAC,GAAG,EAAE,UAAU,CAAC;IACjB,CAAC,GAAG,EAAE,oBAAoB,CAAC;IAC3B,CAAC,GAAG,EAAE,sBAAsB,CAAC;CACrB,CAAA;AAEV,MAAM,CAAC,MAAM,SAAS,GAAG;IACvB,CAAC,GAAG,EAAE,kBAAkB,CAAC;IACzB,CAAC,GAAG,EAAE,UAAU,CAAC;CACT,CAAA;AAcV,SAAS,eAAe,CACtB,CAAoC;IAEpC,MAAM,CAAC,GAAQ,EAAE,CAAA;IACjB,KAAK,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QAC7B,CAAC,CAAC,KAAK,IAAI,EAAE,CAAC,GAAG,CAAC,KAAa,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,CAAA;QACpD,CAAC,CAAC,MAAM,IAAI,EAAE,CAAC,GAAG,CAAC,KAAa,EAAE,EAAE,CAAC,KAAK,GAAG,IAAI,CAAA;IACnD,CAAC;IAED,OAAO,CAAC,CAAA;AACV,CAAC;AAED,MAAM,CAAC,MAAM,eAAe,GAAG,eAAe,CAAC,QAAQ,CAAC,CAAA;AACxD,MAAM,CAAC,MAAM,gBAAgB,GAAG,eAAe,CAAC,SAAS,C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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "8.0.1",
+  "version": "8.0.2",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -65,7 +65,7 @@
     "documentation": "^14.0.3",
     "eslint": "^9.29.0",
     "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-unicorn": "^62.0.0",
+    "eslint-plugin-unicorn": "^63.0.0",
     "mock-fs": "^5.2.0",
     "prettier": "^3.8.1",
     "rimraf": "^6.0.1",

package/src/cramFile/record.ts

@@ -410,51 +410,30 @@ export default class CramRecord {
     return this.readBases
   }
 
-  /**
-   * Get the pair orientation of a paired read. Adapted from igv.js
-   * @returns {String} of paired orientatin
-   */
+  // adapted from igv.js
+  // inlines flag checks and uses template literal instead of array+join
   getPairOrientation() {
-    if (
-      !this.isSegmentUnmapped() &&
-      this.isPaired() &&
-      !this.isMateUnmapped() &&
-      this.sequenceId === this.mate?.sequenceId
-    ) {
-      const s1 = this.isReverseComplemented() ? 'R' : 'F'
-      const s2 = this.isMateReverseComplemented() ? 'R' : 'F'
-      let o1 = ' '
-      let o2 = ' '
-      if (this.isRead1()) {
-        o1 = '1'
-        o2 = '2'
-      } else if (this.isRead2()) {
-        o1 = '2'
-        o2 = '1'
-      }
-
-      const tmp = []
-      let isize = this.templateLength || this.templateSize
-      if (isize === undefined) {
-        throw new Error('One of templateSize and templateLength must be set')
-      }
-      if (this.alignmentStart > this.mate.alignmentStart && isize > 0) {
-        isize = -isize
-      }
-      if (isize > 0) {
-        tmp[0] = s1
-        tmp[1] = o1
-        tmp[2] = s2
-        tmp[3] = o2
-      } else {
-        tmp[2] = s1
-        tmp[3] = o1
-        tmp[0] = s2
-        tmp[1] = o2
-      }
-      return tmp.join('')
+    const f = this.flags
+    // combined check: paired (0x1) set, unmapped (0x4) clear, mate unmapped (0x8) clear
+    if ((f & 0xd) !== 0x1 || this.sequenceId !== this.mate?.sequenceId) {
+      return undefined
     }
-    return null
+    const s1 = f & 0x10 ? 'R' : 'F'
+    const s2 = f & 0x20 ? 'R' : 'F'
+    let o1 = ' '
+    let o2 = ' '
+    if (f & 0x40) {
+      o1 = '1'
+      o2 = '2'
+    } else if (f & 0x80) {
+      o1 = '2'
+      o2 = '1'
+    }
+
+    const isize = this.templateLength || this.templateSize || 0
+    return isize > 0
+      ? `${s1}${o1}${s2}${o2}`
+      : `${s2}${o2}${s1}${o1}`
   }
 
   /**