@gmod/cram 4.0.3 → 4.0.4

package/esm/htscodecs/iostream.js

@@ -1,4 +1,4 @@
-"use strict";
+// @ts-nocheck
 /*
  * Copyright (c) 2019 Genome Research Ltd.
  * Author(s): James Bonfield
@@ -33,9 +33,9 @@
  */
 // Turn a buffer into a fake stream with get / put commands.
 // This enables up to closely match the published pseudocode.
-module.exports = class IOStream {
+export default class IOStream {
     constructor(buf, start_pos = 0, size = 0) {
-        if (size != 0) {
+        if (size !== 0) {
             this.buf = new Uint8Array(size);
             this.length = size;
         }
@@ -52,7 +52,7 @@ module.exports = class IOStream {
         return this.pos >= this.length;
     }
     ReadData(len) {
-        var A = this.buf.slice(this.pos, this.pos + len);
+        const A = this.buf.slice(this.pos, this.pos + len);
         this.pos += len;
         return A;
     }
@@ -67,7 +67,7 @@ module.exports = class IOStream {
         return String.fromCharCode(b);
     }
     ReadUint16() {
-        var i = this.ReadByte();
+        let i = this.ReadByte();
         i |= this.ReadByte() << 8;
         return i;
     }
@@ -78,39 +78,30 @@ module.exports = class IOStream {
     }
     // nul terminated string
     ReadString() {
-        var s = '';
+        let s = '';
+        let b;
         do {
-            var b = this.buf[this.pos++];
-            if (b)
+            b = this.buf[this.pos++];
+            if (b) {
                 s += String.fromCharCode(b);
+            }
         } while (b);
         return s;
     }
-    //    ReadUint7() {
-    //	// Variable sized unsigned integers
-    //	var i = 0;
-    //	var s = 0;
-    //	do {
-    //	    var c = this.ReadByte();
-    //	    i = i | ((c & 0x7f)<<s);
-    //	    s += 7;
-    //	} while ((c & 0x80))
-    //
-    //	return i;
-    //    }
     ReadUint7() {
         // Variable sized unsigned integers
-        var i = 0;
+        let i = 0;
+        let c;
         do {
-            var c = this.ReadByte();
+            c = this.ReadByte();
             i = (i << 7) | (c & 0x7f);
         } while (c & 0x80);
         return i;
     }
     ReadITF8() {
-        var i = this.buf[this.pos];
+        let i = this.buf[this.pos];
         this.pos++;
-        //process.stderr.write("i="+i+"\n");
+        // process.stderr.write("i="+i+"\n");
         if (i >= 0xf0) {
             // 1111xxxx => +4 bytes
             i = (i & 0x0f) << 28;
@@ -120,7 +111,7 @@ module.exports = class IOStream {
                     (this.buf[this.pos + 2] << 4) +
                     (this.buf[this.pos + 3] >> 4);
             this.pos += 4;
-            //process.stderr.write("  4i="+i+"\n");
+            // process.stderr.write("  4i="+i+"\n");
         }
         else if (i >= 0xe0) {
             // 1110xxxx => +3 bytes
@@ -130,114 +121,25 @@ module.exports = class IOStream {
                     (this.buf[this.pos + 1] << 8) +
                     (this.buf[this.pos + 2] << 0);
             this.pos += 3;
-            //process.stderr.write("  3i="+i+"\n");
+            // process.stderr.write("  3i="+i+"\n");
         }
         else if (i >= 0xc0) {
             // 110xxxxx => +2 bytes
             i = (i & 0x1f) << 16;
             i += (this.buf[this.pos + 0] << 8) + (this.buf[this.pos + 1] << 0);
             this.pos += 2;
-            //process.stderr.write("  2i="+i+"\n");
+            // process.stderr.write("  2i="+i+"\n");
         }
         else if (i >= 0x80) {
             // 10xxxxxx => +1 bytes
             i = (i & 0x3f) << 8;
             i += this.buf[this.pos];
             this.pos++;
-            //process.stderr.write("  1i="+i+"\n");
         }
         else {
             // 0xxxxxxx => +0 bytes
         }
         return i;
     }
-    // ----------
-    // Writing
-    WriteByte(b) {
-        this.buf[this.pos++] = b;
-    }
-    WriteChar(b) {
-        this.buf[this.pos++] = b.charCodeAt(0);
-    }
-    WriteString(str) {
-        for (var i = 0; i < str.length; i++)
-            this.buf[this.pos++] = str.charCodeAt(i);
-        this.buf[this.pos++] = 0;
-    }
-    WriteData(buf, len) {
-        for (var i = 0; i < len; i++)
-            this.buf[this.pos++] = buf[i];
-    }
-    WriteStream(stream) {
-        this.WriteData(stream.buf, stream.pos);
-    }
-    WriteUint16(u) {
-        //this.buf.writeInt16LE(u, this.pos);
-        this.WriteByte(u & 0xff);
-        this.WriteByte((u >> 8) & 0xff);
-    }
-    WriteUint32(u) {
-        this.buf.writeInt32LE(u, this.pos);
-        this.pos += 4;
-    }
-    //    WriteUint7(i) {
-    //	do {
-    //	    this.WriteByte((i & 0x7f) | ((i > 0x80) << 7));
-    //	    i >>= 7;
-    //	} while (i > 0);
-    //    }
-    WriteUint7(i) {
-        var s = 0;
-        var X = i;
-        do {
-            s += 7;
-            X >>= 7;
-        } while (X > 0);
-        do {
-            s -= 7;
-            this.WriteByte(((i >> s) & 0x7f) + ((s > 0) << 7));
-        } while (s > 0);
-    }
-    WriteITF8(i) {
-        // Horrid, ITF8 is unsigned, but we still write signed into it
-        if (i < 0)
-            i = (1 << 32) + i;
-        if (i <= 0x0000007f) {
-            // 1 byte
-            this.buf[this.pos++] = i;
-        }
-        else if (i <= 0x00003fff) {
-            // 2 bytes
-            this.buf[this.pos++] = 0x80 | Math.floor(i / 256);
-            this.buf[this.pos++] = i & 0xff;
-        }
-        else if (i < 0x0001ffff) {
-            // 3 bytes
-            this.buf[this.pos++] = 0xc0 | Math.floor(i / 65536);
-            this.buf[this.pos++] = Math.floor(i / 256) & 0xff;
-            this.buf[this.pos++] = i & 0xff;
-        }
-        else if (i < 0x0fffffff) {
-            // 4 bytes
-            this.buf[this.pos++] = 0xe0 | Math.floor(i / 16777216);
-            this.buf[this.pos++] = Math.floor(i / 65536) & 0xff;
-            this.buf[this.pos++] = Math.floor(i / 256) & 0xff;
-            this.buf[this.pos++] = i & 0xff;
-        }
-        else {
-            // 5 bytes; oddly using 4.5 bytes
-            this.buf[this.pos++] = 0xf0 | Math.floor(i / 268435456);
-            this.buf[this.pos++] = Math.floor(i / 1048576) & 0xff;
-            this.buf[this.pos++] = Math.floor(i / 4096) & 0xff;
-            this.buf[this.pos++] = Math.floor(i / 4) & 0xff;
-            this.buf[this.pos++] = i & 0x0f;
-        }
-    }
-    // ----------
-    // Writing from end of buffer going backwards.
-    // Needed by rANS codec.
-    WriteByteNeg(b) {
-        this.buf[--this.pos] = b;
-    }
-};
+}
 //# sourceMappingURL=iostream.js.map

package/esm/htscodecs/iostream.js.map

@@ -1 +1 @@
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package/esm/htscodecs/rans.d.ts

@@ -1 +1 @@
-export function decode(src: any): Uint8Array<any>;
+export declare function decode(src: any): Uint8Array<any>;

package/esm/htscodecs/rans.js

@@ -1,4 +1,5 @@
-"use strict";
+/* eslint-disable no-var */
+// @ts-nocheck
 /*
  * Copyright (c) 2019-2020 Genome Research Ltd.
  * Author(s): James Bonfield
@@ -31,8 +32,8 @@
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-const IOStream = require('./iostream');
-//----------------------------------------------------------------------
+import IOStream from './iostream';
+// ----------------------------------------------------------------------
 // rANS primitives itself
 //
 // RansGet* is decoder side
@@ -43,17 +44,19 @@ function RansGetSymbolFromFreq(C, f) {
     // NOTE: Inefficient.
     // In practice we would implement this via a precomputed
     // lookup table C2S[f]; see RansBuildC2S below.
-    var s = 0;
-    while (f >= C[s + 1])
+    let s = 0;
+    while (f >= C[s + 1]) {
         s++;
+    }
     return s;
 }
 function RansBuildC2S(C) {
-    var C2S = new Array(0x1000);
-    var s = 0;
-    for (var f = 0; f < 0x1000; f++) {
-        while (f >= C[s + 1])
+    const C2S = new Array(0x1000);
+    let s = 0;
+    for (let f = 0; f < 0x1000; f++) {
+        while (f >= C[s + 1]) {
             s++;
+        }
         C2S[f] = s;
     }
     return C2S;
@@ -62,39 +65,36 @@ function RansAdvanceStep(R, c, f) {
     return f * (R >> 12) + (R & 0xfff) - c;
 }
 function RansRenorm(src, R) {
-    while (R < 1 << 23)
+    while (R < 1 << 23) {
         R = (R << 8) + src.ReadByte();
+    }
     return R;
 }
-//----------------------------------------------------------------------
+// ----------------------------------------------------------------------
 // Main rANS entry function: decodes a compressed src and
 // returns the uncompressed buffer.
-function decode(src) {
-    var stream = new IOStream(src);
-    var order = stream.ReadByte();
-    var n_in = stream.ReadUint32();
-    var n_out = stream.ReadUint32();
-    if (order == 0) {
-        return RansDecode0(stream, n_out);
-    }
-    else {
-        return RansDecode1(stream, n_out);
-    }
+export function decode(src) {
+    const stream = new IOStream(src);
+    const order = stream.ReadByte();
+    const n_in = stream.ReadUint32();
+    const n_out = stream.ReadUint32();
+    return order == 0 ? RansDecode0(stream, n_out) : RansDecode1(stream, n_out);
 }
-//----------------------------------------------------------------------
+// ----------------------------------------------------------------------
 // Order-0 decoder
 // Decode a single table of order-0 frequences,
 // filling out the F and C arrays.
 function ReadFrequencies0(src, F, C) {
     // Initialise; not in the specification - implicit?
-    for (var i = 0; i < 256; i++)
+    for (var i = 0; i < 256; i++) {
         F[i] = 0;
-    var sym = src.ReadByte();
-    var last_sym = sym;
-    var rle = 0;
+    }
+    let sym = src.ReadByte();
+    let last_sym = sym;
+    let rle = 0;
     // Read F[]
     do {
-        var f = src.ReadITF8();
+        const f = src.ReadITF8();
         F[sym] = f;
         if (rle > 0) {
             rle--;
@@ -102,54 +102,58 @@ function ReadFrequencies0(src, F, C) {
         }
         else {
             sym = src.ReadByte();
-            if (sym == last_sym + 1)
+            if (sym == last_sym + 1) {
                 rle = src.ReadByte();
+            }
         }
         last_sym = sym;
     } while (sym != 0);
     // Compute C[] from F[]
     C[0] = 0;
-    for (var i = 0; i <= 255; i++)
+    for (var i = 0; i <= 255; i++) {
         C[i + 1] = C[i] + F[i];
+    }
 }
 function RansDecode0(src, nbytes) {
     // Decode frequencies
-    var F = new Array(256);
-    var C = new Array(256);
+    const F = new Array(256);
+    const C = new Array(256);
     ReadFrequencies0(src, F, C);
     // Fast lookup to avoid slow RansGetSymbolFromFreq
-    var C2S = RansBuildC2S(C);
+    const C2S = RansBuildC2S(C);
     // Initialise rANS state
-    var R = new Array(4);
-    for (var i = 0; i < 4; i++)
+    const R = new Array(4);
+    for (var i = 0; i < 4; i++) {
         R[i] = src.ReadUint32();
+    }
     // Main decode loop
-    var output = new Uint8Array(nbytes);
+    const output = new Uint8Array(nbytes);
     for (var i = 0; i < nbytes; i++) {
-        var i4 = i % 4;
-        var f = RansGetCumulativeFreq(R[i4]);
-        var s = C2S[f]; // Equiv to RansGetSymbolFromFreq(C, f);
+        const i4 = i % 4;
+        const f = RansGetCumulativeFreq(R[i4]);
+        const s = C2S[f]; // Equiv to RansGetSymbolFromFreq(C, f);
         output[i] = s;
         R[i4] = RansAdvanceStep(R[i4], C[s], F[s]);
         R[i4] = RansRenorm(src, R[i4]);
     }
     return output;
 }
-//----------------------------------------------------------------------
+// ----------------------------------------------------------------------
 // Order-1 decoder
 // Decode a table of order-1 frequences,
 // filling out the F and C arrays.
 function ReadFrequencies1(src, F, C) {
     // Initialise; not in the specification - implicit?
-    for (var i = 0; i < 256; i++) {
+    for (let i = 0; i < 256; i++) {
         F[i] = new Array(256);
         C[i] = new Array(256);
-        for (var j = 0; j < 256; j++)
+        for (let j = 0; j < 256; j++) {
             F[i][j] = 0;
+        }
     }
-    var sym = src.ReadByte();
-    var last_sym = sym;
-    var rle = 0;
+    let sym = src.ReadByte();
+    let last_sym = sym;
+    let rle = 0;
     // Read F[]
     do {
         ReadFrequencies0(src, F[sym], C[sym]);
@@ -159,35 +163,37 @@ function ReadFrequencies1(src, F, C) {
         }
         else {
             sym = src.ReadByte();
-            if (sym == last_sym + 1)
+            if (sym == last_sym + 1) {
                 rle = src.ReadByte();
+            }
         }
         last_sym = sym;
     } while (sym != 0);
 }
 function RansDecode1(src, nbytes) {
     // Decode frequencies
-    var F = new Array(256);
-    var C = new Array(256);
+    const F = new Array(256);
+    const C = new Array(256);
     ReadFrequencies1(src, F, C);
     // Fast lookup to avoid slow RansGetSymbolFromFreq
-    var C2S = new Array(256);
-    for (var i = 0; i < 256; i++)
+    const C2S = new Array(256);
+    for (var i = 0; i < 256; i++) {
         C2S[i] = RansBuildC2S(C[i]);
+    }
     // Initialise rANS state
-    var R = new Array(4);
-    var L = new Array(4);
+    const R = new Array(4);
+    const L = new Array(4);
     for (var j = 0; j < 4; j++) {
         R[j] = src.ReadUint32();
         L[j] = 0;
     }
     // Main decode loop
-    var output = new Uint8Array(nbytes);
-    var nbytes4 = Math.floor(nbytes / 4);
+    const output = new Uint8Array(nbytes);
+    const nbytes4 = Math.floor(nbytes / 4);
     for (var i = 0; i < nbytes4; i++) {
         for (var j = 0; j < 4; j++) {
             var f = RansGetCumulativeFreq(R[j]);
-            //var s = RansGetSymbolFromFreq(C[L[j]], f);
+            // var s = RansGetSymbolFromFreq(C[L[j]], f);
             var s = C2S[L[j]][f]; // Precomputed version of above
             output[i + j * nbytes4] = s;
             R[j] = RansAdvanceStep(R[j], C[L[j]][s], F[L[j]][s]);
@@ -209,5 +215,4 @@ function RansDecode1(src, nbytes) {
     }
     return output;
 }
-module.exports = { decode };
 //# sourceMappingURL=rans.js.map

package/esm/htscodecs/rans.js.map

@@ -1 +1 @@
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package/esm/htscodecs/rans4x16.d.ts

@@ -1 +1 @@
-export function decode(src: any): any;
+export declare function decode(src: any): any;