@gmod/cram 4.0.3 → 4.0.4

package/src/htscodecs/tok3.ts

@@ -0,0 +1,197 @@
+/* eslint-disable no-var */
+// @ts-nocheck
+
+/*
+ * 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.
+ */
+
+// Name tokeniser
+//
+// This is a reference implementation designed to match the
+// written specification as closely as possible.  It is *NOT*
+// an efficient implementation, but see comments below.
+
+import { concatUint8Array } from '../util'
+import arith_gen from './arith_gen'
+import IOStream from './iostream'
+import * as rans from './rans4x16'
+
+const arith = new arith_gen()
+
+const TOK_TYPE = 0
+const TOK_STRING = 1
+const TOK_CHAR = 2
+const TOK_DIGITS0 = 3
+const TOK_DZLEN = 4
+const TOK_DUP = 5
+const TOK_DIFF = 6
+const TOK_DIGITS = 7
+const TOK_DELTA = 8
+const TOK_DELTA0 = 9
+const TOK_MATCH = 10
+const TOK_NOP = 11
+const TOK_END = 12
+
+// ----------------------------------------------------------------------
+// Token byte streams
+function DecodeTokenByteStreams(src, in_size, use_arith, nnames) {
+  let t = -1
+
+  const B = new Array(256)
+
+  while (!src.EOF()) {
+    const ttype = src.ReadByte()
+    const tok_new = ttype & 128
+    const tok_dup = ttype & 64
+    const type = ttype & 63
+
+    if (tok_new) {
+      t++
+      B[t] = new Array(13)
+    }
+
+    if (type != TOK_TYPE && tok_new) {
+      const M = new Array(nnames - 1).fill(TOK_MATCH)
+      B[t][TOK_TYPE] = new IOStream(concatUint8Array([new Uint8Array(type), M]))
+    }
+
+    if (tok_dup) {
+      const dup_pos = src.ReadByte()
+      const dup_type = src.ReadByte()
+      B[t][type] = new IOStream(B[dup_pos][dup_type].buf)
+    } else {
+      const clen = src.ReadUint7()
+      const data = src.ReadData(clen)
+
+      B[t][type] = use_arith ? arith.decode(data) : rans.decode(data)
+      B[t][type] = new IOStream(B[t][type])
+    }
+  }
+
+  return B
+}
+
+// ----------------------------------------------------------------------
+// Token decode
+function LeftPadNumber(val, len) {
+  let str = val + ''
+  while (str.length < len) {
+    str = '0' + str
+  }
+
+  return str
+}
+
+function DecodeSingleName(B, N, T, n) {
+  let type = B[0][TOK_TYPE].ReadByte()
+  const dist = B[0][type].ReadUint32()
+  const m = n - dist
+
+  if (type == TOK_DUP) {
+    N[n] = N[m]
+    T[n] = T[m]
+    return N[n]
+  }
+
+  let t = 1
+  N[n] = ''
+  T[n] = new Array(256)
+  do {
+    type = B[t][TOK_TYPE].ReadByte()
+
+    switch (type) {
+      case TOK_CHAR:
+        T[n][t] = B[t][TOK_CHAR].ReadChar()
+        break
+
+      case TOK_STRING:
+        T[n][t] = B[t][TOK_STRING].ReadString()
+        break
+
+      case TOK_DIGITS:
+        T[n][t] = B[t][TOK_DIGITS].ReadUint32()
+        break
+
+      case TOK_DIGITS0:
+        var d = B[t][TOK_DIGITS0].ReadUint32()
+        var l = B[t][TOK_DZLEN].ReadByte()
+        T[n][t] = LeftPadNumber(d, l)
+        break
+
+      case TOK_DELTA:
+        T[n][t] = (T[m][t] >> 0) + B[t][TOK_DELTA].ReadByte()
+        break
+
+      case TOK_DELTA0:
+        var d = (T[m][t] >> 0) + B[t][TOK_DELTA0].ReadByte()
+        var l = T[m][t].length
+        T[n][t] = LeftPadNumber(d, l)
+        break
+
+      case TOK_MATCH:
+        T[n][t] = T[m][t]
+        break
+
+      default:
+        T[n][t] = ''
+        break
+    }
+
+    N[n] += T[n][t++]
+  } while (type != TOK_END)
+
+  return N[n]
+}
+
+// ----------------------------------------------------------------------
+// Main tokeniser decode entry function: decodes a compressed src and
+// returns the uncompressed buffer.
+export function decode(src, len, separator) {
+  var src = new IOStream(src)
+  const ulen = src.ReadUint32()
+  const nnames = src.ReadUint32()
+  const use_arith = src.ReadByte()
+
+  const B = DecodeTokenByteStreams(src, len, use_arith, nnames)
+  const N = new Array(nnames)
+  const T = new Array(nnames)
+
+  let str = ''
+  if (separator === undefined) {
+    separator = '\n'
+  }
+  for (let i = 0; i < nnames; i++) {
+    str += DecodeSingleName(B, N, T, i) + separator
+  }
+
+  return str
+}

package/src/util.ts

@@ -0,0 +1,16 @@
+function sum(array: Uint8Array[]) {
+  let sum = 0
+  for (const entry of array) {
+    sum += entry.length
+  }
+  return sum
+}
+export function concatUint8Array(args: Uint8Array[]) {
+  const mergedArray = new Uint8Array(sum(args))
+  let offset = 0
+  for (const entry of args) {
+    mergedArray.set(entry, offset)
+    offset += entry.length
+  }
+  return mergedArray
+}

package/src/htscodecs/iostream.js

@@ -1,257 +0,0 @@
-/*
- * 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.
- */
-
-// Turn a buffer into a fake stream with get / put commands.
-// This enables up to closely match the published pseudocode.
-module.exports = class IOStream {
-  constructor(buf, start_pos = 0, size = 0) {
-    if (size != 0) {
-      this.buf = new Uint8Array(size)
-      this.length = size
-    } else {
-      this.buf = buf
-      this.length = buf.length
-    }
-    this.dataView = new DataView(this.buf.buffer)
-    this.pos = start_pos
-  }
-
-  // ----------
-  // Reading
-  EOF() {
-    return this.pos >= this.length
-  }
-
-  ReadData(len) {
-    var A = this.buf.slice(this.pos, this.pos + len)
-    this.pos += len
-    return A
-  }
-
-  ReadByte() {
-    const b = this.buf[this.pos]
-    this.pos++
-    return b
-  }
-
-  ReadChar() {
-    const b = this.buf[this.pos]
-    this.pos++
-    return String.fromCharCode(b)
-  }
-
-  ReadUint16() {
-    var i = this.ReadByte()
-    i |= this.ReadByte() << 8
-    return i
-  }
-
-  ReadUint32() {
-    const i = this.dataView.getInt32(this.pos, true)
-    this.pos += 4
-    return i
-  }
-
-  // nul terminated string
-  ReadString() {
-    var s = ''
-    do {
-      var 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
-    do {
-      var c = this.ReadByte()
-      i = (i << 7) | (c & 0x7f)
-    } while (c & 0x80)
-
-    return i
-  }
-
-  ReadITF8() {
-    var i = this.buf[this.pos]
-    this.pos++
-
-    //process.stderr.write("i="+i+"\n");
-
-    if (i >= 0xf0) {
-      // 1111xxxx => +4 bytes
-      i = (i & 0x0f) << 28
-      i +=
-        (this.buf[this.pos + 0] << 20) +
-        (this.buf[this.pos + 1] << 12) +
-        (this.buf[this.pos + 2] << 4) +
-        (this.buf[this.pos + 3] >> 4)
-      this.pos += 4
-      //process.stderr.write("  4i="+i+"\n");
-    } else if (i >= 0xe0) {
-      // 1110xxxx => +3 bytes
-      i = (i & 0x0f) << 24
-      i +=
-        (this.buf[this.pos + 0] << 16) +
-        (this.buf[this.pos + 1] << 8) +
-        (this.buf[this.pos + 2] << 0)
-      this.pos += 3
-      //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");
-    } 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
-  }
-}