@gmod/cram 4.0.3 → 4.0.5

package/dist/cramFile/util.js

@@ -3,17 +3,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.TWO_PWR_56_DBL = exports.TWO_PWR_24_DBL = exports.TWO_PWR_64_DBL = exports.TWO_PWR_32_DBL = exports.TWO_PWR_16_DBL = void 0;
 exports.itf8Size = itf8Size;
 exports.parseItf8 = parseItf8;
 exports.parseLtf8 = parseLtf8;
 exports.parseItem = parseItem;
 exports.tinyMemoize = tinyMemoize;
 exports.sequenceMD5 = sequenceMD5;
-exports.sum = sum;
-exports.concatUint8Array = concatUint8Array;
-const long_1 = __importDefault(require("long"));
 const md5_1 = __importDefault(require("md5"));
-const getBits_1 = require("./codecs/getBits");
+exports.TWO_PWR_16_DBL = 1 << 16;
+exports.TWO_PWR_32_DBL = exports.TWO_PWR_16_DBL * exports.TWO_PWR_16_DBL;
+exports.TWO_PWR_64_DBL = exports.TWO_PWR_32_DBL * exports.TWO_PWR_32_DBL;
+exports.TWO_PWR_24_DBL = 1 << 24;
+exports.TWO_PWR_56_DBL = exports.TWO_PWR_24_DBL * exports.TWO_PWR_32_DBL;
 function itf8Size(v) {
     if (!(v & ~0x7f)) {
         return 1;
@@ -33,29 +35,34 @@ function parseItf8(buffer, initialOffset) {
     let offset = initialOffset;
     const countFlags = buffer[offset];
     let result;
+    // Single byte value (0xxxxxxx)
     if (countFlags < 0x80) {
         result = countFlags;
-        offset = offset + 1;
+        offset += 1;
     }
+    // Two byte value (10xxxxxx)
     else if (countFlags < 0xc0) {
-        result = ((countFlags << 8) | buffer[offset + 1]) & 0x3fff;
-        offset = offset + 2;
+        result = ((countFlags & 0x3f) << 8) | buffer[offset + 1];
+        offset += 2;
     }
+    // Three byte value (110xxxxx)
     else if (countFlags < 0xe0) {
         result =
-            ((countFlags << 16) | (buffer[offset + 1] << 8) | buffer[offset + 2]) &
-                0x1fffff;
-        offset = offset + 3;
+            ((countFlags & 0x1f) << 16) |
+                (buffer[offset + 1] << 8) |
+                buffer[offset + 2];
+        offset += 3;
     }
+    // Four byte value (1110xxxx)
     else if (countFlags < 0xf0) {
         result =
-            ((countFlags << 24) |
+            ((countFlags & 0x0f) << 24) |
                 (buffer[offset + 1] << 16) |
                 (buffer[offset + 2] << 8) |
-                buffer[offset + 3]) &
-                0x0fffffff;
-        offset = offset + 4;
+                buffer[offset + 3];
+        offset += 4;
     }
+    // Five byte value (11110xxx)
     else {
         result =
             ((countFlags & 0x0f) << 28) |
@@ -63,95 +70,104 @@ function parseItf8(buffer, initialOffset) {
                 (buffer[offset + 2] << 12) |
                 (buffer[offset + 3] << 4) |
                 (buffer[offset + 4] & 0x0f);
-        // x=((0xff & 0x0f)<<28) | (0xff<<20) | (0xff<<12) | (0xff<<4) | (0x0f & 0x0f);
-        // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
-        offset = offset + 5;
-    }
-    if (offset > buffer.length) {
-        throw new getBits_1.CramBufferOverrunError('Attempted to read beyond end of buffer; this file seems truncated.');
+        offset += 5;
     }
     return [result, offset - initialOffset];
 }
 function parseLtf8(buffer, initialOffset) {
-    const dataView = new DataView(buffer.buffer);
     let offset = initialOffset;
     const countFlags = buffer[offset];
-    let n;
+    let value;
+    // Single byte value < 0x80
     if (countFlags < 0x80) {
-        n = countFlags;
+        value = countFlags;
         offset += 1;
     }
+    // Two byte value < 0xC0
     else if (countFlags < 0xc0) {
-        n = ((buffer[offset] << 8) | buffer[offset + 1]) & 0x3fff;
+        value = ((countFlags << 8) | buffer[offset + 1]) & 0x3fff;
         offset += 2;
     }
+    // Three byte value < 0xE0
     else if (countFlags < 0xe0) {
-        n =
-            ((buffer[offset] << 16) |
+        value =
+            ((countFlags & 0x3f) << 16) |
                 (buffer[offset + 1] << 8) |
-                buffer[offset + 2]) &
-                0x1fffff;
-        n = ((countFlags & 63) << 16) | dataView.getUint16(offset + 1, true);
+                buffer[offset + 2];
         offset += 3;
     }
+    // Four byte value < 0xF0
     else if (countFlags < 0xf0) {
-        n =
-            ((buffer[offset] << 24) |
+        value =
+            ((countFlags & 0x1f) << 24) |
                 (buffer[offset + 1] << 16) |
                 (buffer[offset + 2] << 8) |
-                buffer[offset + 3]) &
-                0x0fffffff;
+                buffer[offset + 3];
         offset += 4;
     }
+    // Five byte value < 0xF8
     else if (countFlags < 0xf8) {
-        n =
-            ((buffer[offset] & 15) * 2 ** 32 + (buffer[offset + 1] << 24)) |
-                ((buffer[offset + 2] << 16) |
+        value =
+            (buffer[offset] & 0x0f) * exports.TWO_PWR_32_DBL +
+                ((buffer[offset + 1] << 24) |
+                    (buffer[offset + 2] << 16) |
                     (buffer[offset + 3] << 8) |
                     buffer[offset + 4]);
-        // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
         offset += 5;
     }
+    // Six byte value < 0xFC
     else if (countFlags < 0xfc) {
-        n =
-            ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * 2 ** 32 +
-                (buffer[offset + 2] << 24)) |
-                ((buffer[offset + 3] << 16) |
+        value =
+            (((buffer[offset] & 0x07) << 8) | buffer[offset + 1]) * exports.TWO_PWR_32_DBL +
+                ((buffer[offset + 2] << 24) |
+                    (buffer[offset + 3] << 16) |
                     (buffer[offset + 4] << 8) |
                     buffer[offset + 5]);
         offset += 6;
     }
+    // Seven byte value < 0xFE
     else if (countFlags < 0xfe) {
-        n =
-            ((((buffer[offset] & 3) << 16) |
+        value =
+            (((buffer[offset] & 0x03) << 16) |
                 (buffer[offset + 1] << 8) |
                 buffer[offset + 2]) *
-                2 ** 32 +
-                (buffer[offset + 3] << 24)) |
-                ((buffer[offset + 4] << 16) |
+                exports.TWO_PWR_32_DBL +
+                ((buffer[offset + 3] << 24) |
+                    (buffer[offset + 4] << 16) |
                     (buffer[offset + 5] << 8) |
                     buffer[offset + 6]);
         offset += 7;
     }
+    // Eight byte value < 0xFF
     else if (countFlags < 0xff) {
-        n = long_1.default.fromBytesBE(buffer.slice(offset + 1, offset + 8));
-        if (n.greaterThan(Number.MAX_SAFE_INTEGER) ||
-            n.lessThan(Number.MIN_SAFE_INTEGER)) {
-            throw new Error('integer overflow');
-        }
-        n = n.toNumber();
+        value =
+            ((buffer[offset + 1] << 24) |
+                (buffer[offset + 2] << 16) |
+                (buffer[offset + 3] << 8) |
+                buffer[offset + 4]) *
+                exports.TWO_PWR_32_DBL +
+                ((buffer[offset + 5] << 24) |
+                    (buffer[offset + 6] << 16) |
+                    (buffer[offset + 7] << 8) |
+                    buffer[offset + 8]);
         offset += 8;
     }
+    // Nine byte value
     else {
-        n = long_1.default.fromBytesBE(buffer.slice(offset + 1, offset + 9));
-        if (n.greaterThan(Number.MAX_SAFE_INTEGER) ||
-            n.lessThan(Number.MIN_SAFE_INTEGER)) {
-            throw new Error('integer overflow');
-        }
-        n = n.toNumber();
+        value =
+            buffer[offset + 1] * exports.TWO_PWR_56_DBL +
+                ((buffer[offset + 2] << 24) |
+                    (buffer[offset + 3] << 16) |
+                    (buffer[offset + 4] << 8) |
+                    buffer[offset + 5]) *
+                    exports.TWO_PWR_32_DBL +
+                ((buffer[offset + 6] << 24) |
+                    (buffer[offset + 7] << 16) |
+                    (buffer[offset + 8] << 8) |
+                    buffer[offset + 9]);
         offset += 9;
     }
-    return [n, offset - initialOffset];
+    return [value, offset - initialOffset];
 }
 function parseItem(buffer, parser, startBufferPosition = 0, startFilePosition = 0) {
     const { offset, value } = parser(buffer, startBufferPosition);
@@ -161,10 +177,6 @@ function parseItem(buffer, parser, startBufferPosition = 0, startFilePosition =
         _size: offset - startBufferPosition,
     };
 }
-// this would be nice as a decorator, but i'm a little worried about babel
-// support for it going away or changing. memoizes a method in the stupidest
-// possible way, with no regard for the arguments.  actually, this only works
-// on methods that take no arguments
 function tinyMemoize(_class, methodName) {
     const method = _class.prototype[methodName];
     const memoAttrName = `_memo_${methodName}`;
@@ -182,20 +194,4 @@ function tinyMemoize(_class, methodName) {
 function sequenceMD5(seq) {
     return (0, md5_1.default)(seq.toUpperCase().replaceAll(/[^\u0021-\u007e]/g, ''));
 }
-function sum(array) {
-    let sum = 0;
-    for (const entry of array) {
-        sum += entry.length;
-    }
-    return sum;
-}
-function concatUint8Array(args) {
-    const mergedArray = new Uint8Array(sum(args));
-    let offset = 0;
-    for (const entry of args) {
-        mergedArray.set(entry, offset);
-        offset += entry.length;
-    }
-    return mergedArray;
-}
 //# sourceMappingURL=util.js.map

package/dist/cramFile/util.js.map

@@ -1 +1 @@
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package/dist/htscodecs/arith_gen.d.ts

@@ -1,18 +1,16 @@
-export = RangeCoderGen;
-declare class RangeCoderGen {
-    decode(src: any): Uint8Array<any>;
-    stream: IOStream | undefined;
-    decodeStream(stream: any, n_out?: number): Uint8Array<any>;
+import IOStream from './iostream';
+export default class RangeCoderGen {
+    stream: IOStream;
+    decode(src: Uint8Array): Uint8Array<any>;
+    decodeStream(stream: IOStream, n_out?: number): Uint8Array<any>;
     decode0(stream: any, n_out: any): Uint8Array<any>;
     decode1(stream: any, n_out: any): Uint8Array<any>;
     decodeExt(stream: any, n_out: any): Uint8Array<ArrayBuffer>;
     decodeRLE0(stream: any, n_out: any): Uint8Array<any>;
     decodeRLE1(stream: any, n_out: any): Uint8Array<any>;
     decodePackMeta(stream: any): any[];
-    nsym: any;
     decodePack(data: any, M: any, len: any): any;
     packMeta(src: any): (number | any[] | IOStream)[];
     decodeStripe(stream: any, len: any): Uint8Array<any>;
     decodeCat(stream: any, len: any): Uint8Array<any>;
 }
-import IOStream = require("./iostream");