@gmod/cram 3.0.6 → 3.0.7

package/dist/htscodecs/arith_sh.js

@@ -0,0 +1,128 @@
+"use strict";
+/*
+ * Copyright (c) 2019 Genome Research Ltd.
+ * Author(s): James Bonfield
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ *    1. Redistributions of source code must retain the above copyright notice,
+ *       this list of conditions and the following disclaimer.
+ *
+ *    2. Redistributions in binary form must reproduce the above
+ *       copyright notice, this list of conditions and the following
+ *       disclaimer in the documentation and/or other materials provided
+ *       with the distribution.
+ *
+ *    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+ *       Institute nor the names of its contributors may be used to endorse
+ *       or promote products derived from this software without specific
+ *       prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
+ * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+// An arithmetic coder, based on Eugene Shelwien's reimplementation of
+// Michael Schindler range coder.
+//
+// Order-0 byte stream of ~/scratch/data/q40b
+// C:              3.1s decode  (approx same vs 32-bit and 64-bit)
+// Arith_sh.js     6.7s decode  (32-bit with carries)
+// Arith.js      317.0s decode  (64-bit no carries); int64 crippling it.
+//----------------------------------------------------------------------
+// Arithmetic (range) coder
+module.exports = class RangeCoder {
+    constructor(src) {
+        this.low = 0;
+        this.range = 0xffffffff;
+        this.code = 0;
+        this.FFnum = 0;
+        this.carry = 0;
+        this.cache = 0;
+    }
+    RangeStartDecode(src) {
+        for (var i = 0; i < 5; i++)
+            this.code = (this.code << 8) + src.ReadByte();
+        this.code &= 0xffffffff;
+        this.code >>>= 0; // force to be +ve int
+    }
+    RangeGetFrequency(tot_freq) {
+        this.range = Math.floor(this.range / tot_freq);
+        //return this.code / this.range;
+        return Math.floor(this.code / this.range);
+        // Conceptual scenario; return freq only and don't modify range yet
+        //return Math.floor(this.code / (Math.floor(this.range / tot_freq)));
+    }
+    RangeDecode(src, sym_low, sym_freq, tot_freq) {
+        // Conceptually we divide range here, but in practice we cached it earlier
+        //this.range = Math.floor(this.range / tot_freq);
+        this.code -= sym_low * this.range;
+        this.range *= sym_freq;
+        while (this.range < 1 << 24) {
+            this.range *= 256;
+            this.code = this.code * 256 + src.ReadByte();
+        }
+    }
+    RangeShiftLow(dst) {
+        // We know range is < (1<<24) as we got here.  We already have a
+        // cached copy of 8 bits from low.  Is this correct, or does it need
+        // fixing?  Possible scenarios.
+        // 1. Low < 0xff000000 thus low+range < 0xffffffff and cache
+        //    cannot possibly change.  Output cache and as many ffs as needed.
+        // 2. We already detected an overflow in RangeEncode, setting carry.
+        //    In this case output cached byte + 1 and any 00s needed.
+        // 3. Neither case - range is low but we haven't yet detected if we're
+        //    XXffffff or XY000000 scenario.  Increase counter for ff/00s.
+        if ((this.low < 0xff000000) | this.carry) {
+            // cached byte if no overflow, byte+1 otherwise
+            dst.WriteByte(this.cache + this.carry);
+            // Flush any tracked FFs (no carry) or 00s (carry).
+            while (this.FFnum) {
+                dst.WriteByte(this.carry - 1);
+                this.FFnum--;
+            }
+            // Take a copy of top byte ready for next flush
+            this.cache = this.low >>> 24;
+            this.carry = 0;
+        }
+        else {
+            this.FFnum++; // keep track of number of trailing ff/00 bytes to write
+        }
+        this.low <<= 8;
+        this.low >>>= 0; // force to be +ve int
+    }
+    RangeEncode(dst, sym_low, sym_freq, tot_freq) {
+        var old_low = this.low;
+        this.range = Math.floor(this.range / tot_freq);
+        this.low += sym_low * this.range;
+        this.low >>>= 0; // Truncate to +ve int so we can spot overflow
+        this.range *= sym_freq;
+        // "low + sym*range < old_low" means we overflow; set carry.
+        // NB: can this.low < old_low occur twice before range < (1<<24)?
+        // We claim not, but prove it!
+        if (this.low < old_low) {
+            if (this.carry != 0)
+                console.log('ERROR: Multiple carry');
+            this.carry = 1;
+        }
+        // Renormalise if range gets too small
+        while (this.range < 1 << 24) {
+            this.range *= 256;
+            this.RangeShiftLow(dst);
+        }
+    }
+    RangeFinishEncode(dst) {
+        for (var i = 0; i < 5; i++)
+            this.RangeShiftLow(dst);
+    }
+};
+//# sourceMappingURL=arith_sh.js.map

package/dist/htscodecs/arith_sh.js.map

@@ -0,0 +1 @@
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package/dist/htscodecs/byte_model.d.ts

@@ -0,0 +1,11 @@
+export = ByteModel;
+declare class ByteModel {
+    constructor(max_sym?: number);
+    total_freq: number;
+    max_sym: number;
+    S: any[];
+    F: any[];
+    ModelDecode(src: any, rc: any): any;
+    ModelRenormalise(): void;
+    ModelEncode(dst: any, rc: any, sym: any): void;
+}

package/dist/htscodecs/byte_model.js

@@ -0,0 +1,113 @@
+"use strict";
+/*
+ * Copyright (c) 2019 Genome Research Ltd.
+ * Author(s): James Bonfield
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ *    1. Redistributions of source code must retain the above copyright notice,
+ *       this list of conditions and the following disclaimer.
+ *
+ *    2. Redistributions in binary form must reproduce the above
+ *       copyright notice, this list of conditions and the following
+ *       disclaimer in the documentation and/or other materials provided
+ *       with the distribution.
+ *
+ *    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+ *       Institute nor the names of its contributors may be used to endorse
+ *       or promote products derived from this software without specific
+ *       prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
+ * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+// An adaptive probability model for encoding and decoding of symbols
+// within a given alphabet, using the range coder to get/put the
+// compressed data.
+const MAX_FREQ = (1 << 16) - 17;
+const STEP = 16;
+module.exports = class ByteModel {
+    constructor(max_sym = 256) {
+        this.total_freq = max_sym;
+        this.max_sym = max_sym - 1;
+        this.S = new Array();
+        this.F = new Array();
+        for (var i = 0; i <= this.max_sym; i++) {
+            this.S[i] = i;
+            this.F[i] = 1;
+        }
+    }
+    ModelDecode(src, rc) {
+        // Find symbol
+        var freq = rc.RangeGetFrequency(this.total_freq);
+        // Linear scan to find cumulative frequency 'freq'
+        var acc = 0;
+        var x = 0;
+        while (acc + this.F[x] <= freq)
+            acc += this.F[x++];
+        //	for (var acc = 0; (acc += this.F[x]) <= freq; x++)
+        //	    ;
+        //	acc -= this.F[x];
+        // Update range coder
+        rc.RangeDecode(src, acc, this.F[x], this.total_freq);
+        // Update model
+        this.F[x] += STEP;
+        this.total_freq += STEP;
+        if (this.total_freq > MAX_FREQ)
+            this.ModelRenormalise();
+        // Keep symbols approximately frequency sorted
+        var sym = this.S[x];
+        if (x > 0 && this.F[x] > this.F[x - 1]) {
+            var tmp = this.F[x];
+            this.F[x] = this.F[x - 1];
+            this.F[x - 1] = tmp;
+            tmp = this.S[x];
+            this.S[x] = this.S[x - 1];
+            this.S[x - 1] = tmp;
+        }
+        return sym;
+    }
+    ModelRenormalise() {
+        // Halve all the frequencies, being careful not to hit zero
+        this.total_freq = 0;
+        for (var i = 0; i <= this.max_sym; i++) {
+            this.F[i] -= Math.floor(this.F[i] / 2);
+            this.total_freq += this.F[i];
+        }
+    }
+    ModelEncode(dst, rc, sym) {
+        // Find cumulative frequency
+        var acc = 0;
+        for (var x = 0; this.S[x] != sym; x++)
+            acc += this.F[x];
+        // Encode
+        rc.RangeEncode(dst, acc, this.F[x], this.total_freq);
+        // Update model
+        this.F[x] += STEP;
+        this.total_freq += STEP;
+        if (this.total_freq > MAX_FREQ)
+            // FIXME x2
+            this.ModelRenormalise();
+        // Keep symbols approximately frequency sorted
+        var sym = this.S[x];
+        if (x > 0 && this.F[x] > this.F[x - 1]) {
+            var tmp = this.F[x];
+            this.F[x] = this.F[x - 1];
+            this.F[x - 1] = tmp;
+            tmp = this.S[x];
+            this.S[x] = this.S[x - 1];
+            this.S[x - 1] = tmp;
+        }
+    }
+};
+//# sourceMappingURL=byte_model.js.map

package/dist/htscodecs/byte_model.js.map

@@ -0,0 +1 @@
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package/dist/htscodecs/fqzcomp.d.ts

@@ -0,0 +1,2 @@
+export function decode(src: any, q_lens: any): any;
+export function encode(src: any, q_lens: any, q_dirs: any): any;