@gmod/cram 5.0.3 → 5.0.4

package/dist/seek-bzip/stream.d.ts

@@ -1 +1,8 @@
-declare const Stream: () => void;
+export default class Stream {
+    readByte(): void;
+    read(buffer: any, bufOffset: any, length: any): number;
+    writeByte(_byte: any): void;
+    seek(new_pos: any): void;
+    write(buffer: any, bufOffset: any, length: any): any;
+    flush(): void;
+}

package/dist/seek-bzip/stream.js

@@ -1,41 +1,37 @@
 "use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
 // @ts-nocheck
-/// * very simple input/output stream interface */
-const Stream = function () { };
-// input streams //////////////
-/** Returns the next byte, or -1 for EOF. */
-Stream.prototype.readByte = function () {
-    throw new Error('abstract method readByte() not implemented');
-};
-/** Attempts to fill the buffer; returns number of bytes read, or
- *  -1 for EOF. */
-Stream.prototype.read = function (buffer, bufOffset, length) {
-    let bytesRead = 0;
-    while (bytesRead < length) {
-        const c = this.readByte();
-        if (c < 0) {
-            // EOF
-            return bytesRead === 0 ? -1 : bytesRead;
+class Stream {
+    readByte() {
+        throw new Error('abstract method readByte() not implemented');
+    }
+    read(buffer, bufOffset, length) {
+        let bytesRead = 0;
+        while (bytesRead < length) {
+            const c = this.readByte();
+            if (c < 0) {
+                // EOF
+                return bytesRead === 0 ? -1 : bytesRead;
+            }
+            buffer[bufOffset++] = c;
+            bytesRead++;
         }
-        buffer[bufOffset++] = c;
-        bytesRead++;
+        return bytesRead;
+    }
+    writeByte(_byte) {
+        throw new Error('abstract method readByte() not implemented');
     }
-    return bytesRead;
-};
-Stream.prototype.seek = function (new_pos) {
-    throw new Error('abstract method seek() not implemented');
-};
-// output streams ///////////
-Stream.prototype.writeByte = function (_byte) {
-    throw new Error('abstract method readByte() not implemented');
-};
-Stream.prototype.write = function (buffer, bufOffset, length) {
-    let i;
-    for (i = 0; i < length; i++) {
-        this.writeByte(buffer[bufOffset++]);
+    seek(new_pos) {
+        throw new Error('abstract method seek() not implemented');
+    }
+    write(buffer, bufOffset, length) {
+        let i;
+        for (i = 0; i < length; i++) {
+            this.writeByte(buffer[bufOffset++]);
+        }
+        return length;
     }
-    return length;
-};
-Stream.prototype.flush = function () { };
-module.exports = Stream;
+    flush() { }
+}
+exports.default = Stream;
 //# sourceMappingURL=stream.js.map

package/dist/seek-bzip/stream.js.map

@@ -1 +1 @@
-{"version":3,"file":"stream.js","sourceRoot":"","sources":["../../src/seek-bzip/stream.ts"],"names":[],"mappings":";AAAA,cAAc;AACd,kDAAkD;AAClD,MAAM,MAAM,GAAG,cAAa,CAAC,CAAA;AAE7B,+BAA+B;AAC/B,4CAA4C;AAC5C,MAAM,CAAC,SAAS,CAAC,QAAQ,GAAG;IAC1B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;AAC/D,CAAC,CAAA;AACD;kBACkB;AAClB,MAAM,CAAC,SAAS,CAAC,IAAI,GAAG,UAAU,MAAM,EAAE,SAAS,EAAE,MAAM;IACzD,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,OAAO,SAAS,GAAG,MAAM,EAAE,CAAC;QAC1B,MAAM,CAAC,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAA;QACzB,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YACV,MAAM;YACN,OAAO,SAAS,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACzC,CAAC;QACD,MAAM,CAAC,SAAS,EAAE,CAAC,GAAG,CAAC,CAAA;QACvB,SAAS,EAAE,CAAA;IACb,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC,CAAA;AACD,MAAM,CAAC,SAAS,CAAC,IAAI,GAAG,UAAU,OAAO;IACvC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;AAC3D,CAAC,CAAA;AAED,6BAA6B;AAC7B,MAAM,CAAC,SAAS,CAAC,SAAS,GAAG,UAAU,KAAK;IAC1C,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;AAC/D,CAAC,CAAA;AACD,MAAM,CAAC,SAAS,CAAC,KAAK,GAAG,UAAU,MAAM,EAAE,SAAS,EAAE,MAAM;IAC1D,IAAI,CAAC,CAAA;IACL,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC5B,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;IACrC,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC,CAAA;AACD,MAAM,CAAC,SAAS,CAAC,KAAK,GAAG,cAAa,CAAC,CAAA;AAEvC,MAAM,CAAC,OAAO,GAAG,MAAM,CAAA"}
+{"version":3,"file":"stream.js","sourceRoot":"","sources":["../../src/seek-bzip/stream.ts"],"names":[],"mappings":";;AAAA,cAAc;AACd,MAAqB,MAAM;IACzB,QAAQ;QACN,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;IAC/D,CAAC;IACD,IAAI,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM;QAC5B,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,OAAO,SAAS,GAAG,MAAM,EAAE,CAAC;YAC1B,MAAM,CAAC,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAA;YACzB,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBACV,MAAM;gBACN,OAAO,SAAS,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;YACzC,CAAC;YACD,MAAM,CAAC,SAAS,EAAE,CAAC,GAAG,CAAC,CAAA;YACvB,SAAS,EAAE,CAAA;QACb,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,SAAS,CAAC,KAAK;QACb,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;IAC/D,CAAC;IACD,IAAI,CAAC,OAAO;QACV,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;IAC3D,CAAC;IACD,KAAK,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM;QAC7B,IAAI,CAAC,CAAA;QACL,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YAC5B,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QACrC,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IACD,KAAK,KAAI,CAAC;CACX;AA/BD,yBA+BC"}

package/esm/seek-bzip/stream.d.ts

@@ -1 +1,8 @@
-declare const Stream: () => void;
+export default class Stream {
+    readByte(): void;
+    read(buffer: any, bufOffset: any, length: any): number;
+    writeByte(_byte: any): void;
+    seek(new_pos: any): void;
+    write(buffer: any, bufOffset: any, length: any): any;
+    flush(): void;
+}

package/esm/seek-bzip/stream.js

@@ -1,41 +1,34 @@
-"use strict";
 // @ts-nocheck
-/// * very simple input/output stream interface */
-const Stream = function () { };
-// input streams //////////////
-/** Returns the next byte, or -1 for EOF. */
-Stream.prototype.readByte = function () {
-    throw new Error('abstract method readByte() not implemented');
-};
-/** Attempts to fill the buffer; returns number of bytes read, or
- *  -1 for EOF. */
-Stream.prototype.read = function (buffer, bufOffset, length) {
-    let bytesRead = 0;
-    while (bytesRead < length) {
-        const c = this.readByte();
-        if (c < 0) {
-            // EOF
-            return bytesRead === 0 ? -1 : bytesRead;
+export default class Stream {
+    readByte() {
+        throw new Error('abstract method readByte() not implemented');
+    }
+    read(buffer, bufOffset, length) {
+        let bytesRead = 0;
+        while (bytesRead < length) {
+            const c = this.readByte();
+            if (c < 0) {
+                // EOF
+                return bytesRead === 0 ? -1 : bytesRead;
+            }
+            buffer[bufOffset++] = c;
+            bytesRead++;
         }
-        buffer[bufOffset++] = c;
-        bytesRead++;
+        return bytesRead;
+    }
+    writeByte(_byte) {
+        throw new Error('abstract method readByte() not implemented');
     }
-    return bytesRead;
-};
-Stream.prototype.seek = function (new_pos) {
-    throw new Error('abstract method seek() not implemented');
-};
-// output streams ///////////
-Stream.prototype.writeByte = function (_byte) {
-    throw new Error('abstract method readByte() not implemented');
-};
-Stream.prototype.write = function (buffer, bufOffset, length) {
-    let i;
-    for (i = 0; i < length; i++) {
-        this.writeByte(buffer[bufOffset++]);
+    seek(new_pos) {
+        throw new Error('abstract method seek() not implemented');
+    }
+    write(buffer, bufOffset, length) {
+        let i;
+        for (i = 0; i < length; i++) {
+            this.writeByte(buffer[bufOffset++]);
+        }
+        return length;
     }
-    return length;
-};
-Stream.prototype.flush = function () { };
-module.exports = Stream;
+    flush() { }
+}
 //# sourceMappingURL=stream.js.map

package/esm/seek-bzip/stream.js.map

@@ -1 +1 @@
-{"version":3,"file":"stream.js","sourceRoot":"","sources":["../../src/seek-bzip/stream.ts"],"names":[],"mappings":";AAAA,cAAc;AACd,kDAAkD;AAClD,MAAM,MAAM,GAAG,cAAa,CAAC,CAAA;AAE7B,+BAA+B;AAC/B,4CAA4C;AAC5C,MAAM,CAAC,SAAS,CAAC,QAAQ,GAAG;IAC1B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;AAC/D,CAAC,CAAA;AACD;kBACkB;AAClB,MAAM,CAAC,SAAS,CAAC,IAAI,GAAG,UAAU,MAAM,EAAE,SAAS,EAAE,MAAM;IACzD,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,OAAO,SAAS,GAAG,MAAM,EAAE,CAAC;QAC1B,MAAM,CAAC,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAA;QACzB,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YACV,MAAM;YACN,OAAO,SAAS,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACzC,CAAC;QACD,MAAM,CAAC,SAAS,EAAE,CAAC,GAAG,CAAC,CAAA;QACvB,SAAS,EAAE,CAAA;IACb,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC,CAAA;AACD,MAAM,CAAC,SAAS,CAAC,IAAI,GAAG,UAAU,OAAO;IACvC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;AAC3D,CAAC,CAAA;AAED,6BAA6B;AAC7B,MAAM,CAAC,SAAS,CAAC,SAAS,GAAG,UAAU,KAAK;IAC1C,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;AAC/D,CAAC,CAAA;AACD,MAAM,CAAC,SAAS,CAAC,KAAK,GAAG,UAAU,MAAM,EAAE,SAAS,EAAE,MAAM;IAC1D,IAAI,CAAC,CAAA;IACL,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC5B,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;IACrC,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC,CAAA;AACD,MAAM,CAAC,SAAS,CAAC,KAAK,GAAG,cAAa,CAAC,CAAA;AAEvC,MAAM,CAAC,OAAO,GAAG,MAAM,CAAA"}
+{"version":3,"file":"stream.js","sourceRoot":"","sources":["../../src/seek-bzip/stream.ts"],"names":[],"mappings":"AAAA,cAAc;AACd,MAAM,CAAC,OAAO,OAAO,MAAM;IACzB,QAAQ;QACN,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;IAC/D,CAAC;IACD,IAAI,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM;QAC5B,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,OAAO,SAAS,GAAG,MAAM,EAAE,CAAC;YAC1B,MAAM,CAAC,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAA;YACzB,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBACV,MAAM;gBACN,OAAO,SAAS,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;YACzC,CAAC;YACD,MAAM,CAAC,SAAS,EAAE,CAAC,GAAG,CAAC,CAAA;YACvB,SAAS,EAAE,CAAA;QACb,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,SAAS,CAAC,KAAK;QACb,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;IAC/D,CAAC;IACD,IAAI,CAAC,OAAO;QACV,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;IAC3D,CAAC;IACD,KAAK,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM;QAC7B,IAAI,CAAC,CAAA;QACL,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YAC5B,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QACrC,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IACD,KAAK,KAAI,CAAC;CACX"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "5.0.3",
+  "version": "5.0.4",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",

package/src/seek-bzip/stream.ts

@@ -1,42 +1,33 @@
 // @ts-nocheck
-/// * very simple input/output stream interface */
-const Stream = function () {}
-
-// input streams //////////////
-/** Returns the next byte, or -1 for EOF. */
-Stream.prototype.readByte = function () {
-  throw new Error('abstract method readByte() not implemented')
-}
-/** Attempts to fill the buffer; returns number of bytes read, or
- *  -1 for EOF. */
-Stream.prototype.read = function (buffer, bufOffset, length) {
-  let bytesRead = 0
-  while (bytesRead < length) {
-    const c = this.readByte()
-    if (c < 0) {
-      // EOF
-      return bytesRead === 0 ? -1 : bytesRead
+export default class Stream {
+  readByte() {
+    throw new Error('abstract method readByte() not implemented')
+  }
+  read(buffer, bufOffset, length) {
+    let bytesRead = 0
+    while (bytesRead < length) {
+      const c = this.readByte()
+      if (c < 0) {
+        // EOF
+        return bytesRead === 0 ? -1 : bytesRead
+      }
+      buffer[bufOffset++] = c
+      bytesRead++
     }
-    buffer[bufOffset++] = c
-    bytesRead++
+    return bytesRead
   }
-  return bytesRead
-}
-Stream.prototype.seek = function (new_pos) {
-  throw new Error('abstract method seek() not implemented')
-}
-
-// output streams ///////////
-Stream.prototype.writeByte = function (_byte) {
-  throw new Error('abstract method readByte() not implemented')
-}
-Stream.prototype.write = function (buffer, bufOffset, length) {
-  let i
-  for (i = 0; i < length; i++) {
-    this.writeByte(buffer[bufOffset++])
+  writeByte(_byte) {
+    throw new Error('abstract method readByte() not implemented')
+  }
+  seek(new_pos) {
+    throw new Error('abstract method seek() not implemented')
+  }
+  write(buffer, bufOffset, length) {
+    let i
+    for (i = 0; i < length; i++) {
+      this.writeByte(buffer[bufOffset++])
+    }
+    return length
   }
-  return length
+  flush() {}
 }
-Stream.prototype.flush = function () {}
-
-module.exports = Stream