@gmod/cram 3.0.5 → 3.0.7

package/dist/cramFile/file.js

@@ -15,7 +15,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const buffer_1 = require("buffer");
 const crc32_1 = __importDefault(require("crc/crc32"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
-const htscodecs_1 = __importDefault(require("@jkbonfield/htscodecs"));
+const htscodecs_1 = __importDefault(require("../htscodecs"));
 const bzip2_1 = __importDefault(require("bzip2"));
 const xz_decompress_1 = require("xz-decompress");
 const errors_1 = require("../errors");
@@ -102,12 +102,8 @@ class CramFile {
                 return (0, sam_1.parseHeaderText)('');
             }
             const content = firstBlock.content;
-            // find the end of the trailing zeros in the header text
             const headerLength = content.readInt32LE(0);
             const textStart = 4;
-            // let textEnd = content.length - 1
-            // while (textEnd >= textStart && !content[textEnd]) textEnd -= 1
-            // trim off the trailing zeros
             const text = content.toString('utf8', textStart, textStart + headerLength);
             this.header = text;
             return (0, sam_1.parseHeaderText)(text);
@@ -153,7 +149,8 @@ class CramFile {
                     }
                 }
                 else {
-                    // otherwise, just traverse to the next container using the container's length
+                    // otherwise, just traverse to the next container using the container's
+                    // length
                     position += currentHeader._size + currentHeader.length;
                 }
             }
@@ -186,9 +183,9 @@ class CramFile {
                 if (!currentHeader) {
                     break;
                 }
-                // if this is the first container, read all the blocks in the
-                // container, because we cannot trust the container
-                // header's given length due to a bug somewhere in htslib
+                // if this is the first container, read all the blocks in the container,
+                // because we cannot trust the container header's given length due to a
+                // bug somewhere in htslib
                 if (containerCount === 0) {
                     position = currentHeader._endPosition;
                     for (let j = 0; j < currentHeader.numBlocks; j++) {
@@ -200,7 +197,8 @@ class CramFile {
                     }
                 }
                 else {
-                    // otherwise, just traverse to the next container using the container's length
+                    // otherwise, just traverse to the next container using the container's
+                    // length
                     position += currentHeader._size + currentHeader.length;
                 }
                 containerCount += 1;

package/dist/cramFile/file.js.map

@@ -1 +1 @@
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package/dist/cramFile/slice/decodeRecord.js

@@ -21,7 +21,9 @@ function readNullTerminatedString(buffer) {
  */
 function parseTagValueArray(buffer) {
     const arrayType = String.fromCharCode(buffer[0]);
-    const length = Int32Array.from(buffer.slice(1))[0];
+    const dataView = new DataView(buffer.buffer);
+    const littleEndian = true;
+    const length = dataView.getUint32(1, littleEndian);
     const array = new Array(length);
     buffer = buffer.slice(5);
     if (arrayType === 'c') {

package/dist/cramFile/slice/decodeRecord.js.map

@@ -1 +1 @@
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package/dist/cramFile/util.js.map

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

@@ -0,0 +1,26 @@
+export = RangeCoderGen;
+declare class RangeCoderGen {
+    decode(src: any): any;
+    stream: IOStream | undefined;
+    decodeStream(stream: any, n_out?: number): any;
+    encode(src: any, flags: any): any;
+    decode0(stream: any, n_out: any): any;
+    encode0(src: any, n_in: any, out: any): any;
+    decode1(stream: any, n_out: any): any;
+    encode1(src: any, n_in: any, out: any): any;
+    decodeExt(stream: any, n_out: any): any;
+    encodeExt(stream: any, n_out: any): void;
+    decodeRLE0(stream: any, n_out: any): any;
+    encodeRLE0(src: any, n_in: any, out: any): any;
+    decodeRLE1(stream: any, n_out: any): any;
+    encodeRLE1(src: any, n_in: any, out: any): any;
+    decodePackMeta(stream: any): any[];
+    nsym: any;
+    decodePack(data: any, M: any, len: any): any;
+    packMeta(src: any): (number | any[] | IOStream)[];
+    encodePack(data: any): any[];
+    encodeStripe(hdr: any, src: any, N: any): any;
+    decodeStripe(stream: any, len: any): any;
+    decodeCat(stream: any, len: any): any;
+}
+import IOStream = require("./iostream");