@gmod/cram 3.0.6 → 3.0.7

package/src/htscodecs/arith_sh.js

@@ -0,0 +1,138 @@
+/*
+ * 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)
+  }
+}

package/src/htscodecs/byte_model.js

@@ -0,0 +1,126 @@
+/*
+ * 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
+    }
+  }
+}