@gmod/cram 3.0.6 → 4.0.0

package/esm/htscodecs/tok3.js

@@ -0,0 +1,363 @@
+"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.
+ */
+// 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.
+const IOStream = require('./iostream');
+const rans = require('./rans4x16');
+const arith_gen = require('./arith_gen');
+function sum(array) {
+    let sum = 0;
+    for (const entry of array) {
+        sum += entry.length;
+    }
+    return sum;
+}
+function concatUint8Array(args) {
+    const mergedArray = new Uint8Array(sum(args));
+    let offset = 0;
+    for (const entry of args) {
+        mergedArray.set(entry, offset);
+        offset += entry.length;
+    }
+    return mergedArray;
+}
+var 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) {
+    var t = -1;
+    var B = new Array(256);
+    while (!src.EOF()) {
+        var ttype = src.ReadByte();
+        var tok_new = ttype & 128;
+        var tok_dup = ttype & 64;
+        var type = ttype & 63;
+        if (tok_new) {
+            t++;
+            B[t] = new Array(13);
+        }
+        if (type != TOK_TYPE && tok_new) {
+            var M = new Array(nnames - 1).fill(TOK_MATCH);
+            B[t][TOK_TYPE] = new IOStream(concatUint8Array([new Uint8Array(type), M]));
+        }
+        if (tok_dup) {
+            var dup_pos = src.ReadByte();
+            var dup_type = src.ReadByte();
+            B[t][type] = new IOStream(B[dup_pos][dup_type].buf);
+        }
+        else {
+            var clen = src.ReadUint7();
+            var data = src.ReadData(clen);
+            if (use_arith)
+                B[t][type] = arith.decode(data);
+            else
+                B[t][type] = rans.decode(data);
+            B[t][type] = new IOStream(B[t][type]);
+        }
+    }
+    return B;
+}
+//----------------------------------------------------------------------
+// Token decode
+function LeftPadNumber(val, len) {
+    var str = val + '';
+    while (str.length < len)
+        str = '0' + str;
+    return str;
+}
+function DecodeSingleName(B, N, T, n) {
+    var type = B[0][TOK_TYPE].ReadByte();
+    var dist = B[0][type].ReadUint32();
+    var m = n - dist;
+    if (type == TOK_DUP) {
+        N[n] = N[m];
+        T[n] = T[m];
+        return N[n];
+    }
+    var 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.
+function decode(src, len, separator) {
+    var src = new IOStream(src);
+    var ulen = src.ReadUint32();
+    var nnames = src.ReadUint32();
+    var use_arith = src.ReadByte();
+    var B = DecodeTokenByteStreams(src, len, use_arith, nnames);
+    var N = new Array(nnames);
+    var T = new Array(nnames);
+    var str = '';
+    if (typeof separator === 'undefined')
+        separator = '\n';
+    for (var i = 0; i < nnames; i++)
+        str += DecodeSingleName(B, N, T, i) + separator;
+    return str;
+}
+//----------------------------------------------------------------------
+// Main tokeniser encode function
+// Encoder is trickier than decode as we have a lot of decisions to make.
+// However here we just make a simple guess without anything complex,
+// to demonstrate the basic idea.  See the C implementation for further
+// expansion on this.
+function encode(src, use_arith) {
+    // Convert buffer to array of names
+    var str = src.toString();
+    if (str[str.length - 1] == '\n')
+        str = str.substring(0, str.length - 1);
+    var names = str.split('\n');
+    var out = new IOStream('', 0, str.length * 2 + 10000); // guess max size
+    out.WriteUint32(str.length);
+    out.WriteUint32(names.length);
+    out.WriteByte(use_arith);
+    // Tokenise names
+    var T = new Array(names.length);
+    var H = {};
+    var F = new Array(256).fill(0); // DELTA vs DIGIT frequency
+    var max_tok = 0;
+    var max_len = 0;
+    for (var i = 0; i < names.length; i++) {
+        var [ntok, len] = TokeniseName(T, H, F, names[i], i);
+        if (max_tok < ntok)
+            max_tok = ntok;
+        if (max_len < len)
+            max_len = len;
+    }
+    // Convert tokens to byte streams and serialise
+    for (var tnum = 0; tnum < max_tok; tnum++) {
+        var B = new Array(TOK_END + 1);
+        for (var type = 0; type <= TOK_END; type++)
+            B[type] = new IOStream('', 0, names.length * max_len);
+        FillByteStreams(B, T, tnum, names, max_tok, max_len);
+        SerialiseByteStreams(B, tnum, use_arith, out);
+    }
+    return out.buf.slice(0, out.pos);
+}
+function FillByteStreams(B, T, tnum, names, max_tok, max_len) {
+    // Create byte streams B[]
+    for (var n = 0; n < names.length; n++) {
+        if (tnum > 0 && T[n][0].type == TOK_DUP)
+            continue;
+        if (!T[n][tnum])
+            continue;
+        B[TOK_TYPE].WriteByte(T[n][tnum].type);
+        switch (T[n][tnum].type) {
+            case TOK_DIFF:
+                B[TOK_DIFF].WriteUint32(T[n][tnum].val);
+                break;
+            case TOK_DUP:
+                B[TOK_DUP].WriteUint32(T[n][tnum].val);
+                break;
+            case TOK_STRING:
+                B[TOK_STRING].WriteString(T[n][tnum].val);
+                break;
+            case TOK_CHAR:
+                B[TOK_CHAR].WriteChar(T[n][tnum].val);
+                break;
+            case TOK_DIGITS:
+                B[TOK_DIGITS].WriteUint32(T[n][tnum].val);
+                break;
+            case TOK_DIGITS0:
+                B[TOK_DIGITS0].WriteUint32(T[n][tnum].val);
+                B[TOK_DZLEN].WriteByte(T[n][tnum].val.length);
+                break;
+            case TOK_DELTA:
+                B[T[n][tnum].type].WriteByte(T[n][tnum].val);
+                break;
+            case TOK_DELTA0:
+                B[T[n][tnum].type].WriteByte(T[n][tnum].val);
+                break;
+        }
+    }
+}
+function SerialiseByteStreams(B, tnum, use_arith, out) {
+    // Compress and serialise byte streams B[]
+    for (var type = 0; type <= TOK_END; type++) {
+        if (B[type].pos <= 0)
+            continue;
+        out.WriteByte(type + (type == 0 ? 128 : 0));
+        // IOStream to sized buffer
+        B[type] = B[type].buf.slice(0, B[type].pos);
+        var comp = try_compress(B[type], use_arith);
+        out.WriteUint7(comp.length);
+        out.WriteData(comp, comp.length);
+    }
+}
+function try_compress(src, use_arith) {
+    var best = 1 << 30;
+    var comp;
+    var methods = [0, 1, 64, 65, 128, 129, 193 + 8];
+    for (var i in methods) {
+        var lvl = methods[i];
+        if (lvl & 1 && src.length < 100)
+            continue;
+        if (lvl & 8 && src.length % 4 != 0)
+            continue;
+        try {
+            var tmp = use_arith ? arith.encode(src, lvl) : rans.encode(src, lvl);
+        }
+        catch (e) {
+            var tmp = 0;
+        }
+        if (tmp && best > tmp.length) {
+            best = tmp.length;
+            comp = tmp;
+        }
+    }
+    return comp;
+}
+function TokeniseName(T, H, F, name, n) {
+    var max_len = 0;
+    // Always compare against last name only
+    var p = n - 1;
+    T[n] = new Array(256);
+    if (H[name]) {
+        //console.error(name,H[name],n)
+        T[n][0] = {
+            type: TOK_DUP,
+            val: n - H[name],
+        };
+    }
+    else {
+        T[n][0] = {
+            type: TOK_DIFF,
+            val: n == 0 ? 0 : 1,
+        };
+    }
+    H[name] = n;
+    // Splits on alphanumerics, punctuation
+    var tok = name.match(/([a-zA-Z0-9]{1,9})|([^a-zA-Z0-9]+)/g);
+    for (var i = 0; i < tok.length; i++) {
+        var t = i + 1; // token 0 = DIFF vs DUP
+        var type = TOK_STRING;
+        var val = tok[i];
+        if (tok[i].match(/^0+[0-9]*$/g))
+            type = TOK_DIGITS0;
+        else if (tok[i].match(/^[0-9]+$/g))
+            type = TOK_DIGITS;
+        else if (tok[i].length == 1)
+            type = TOK_CHAR;
+        if (p >= 0 && T[p][t]) {
+            if (T[p][t].str == tok[i]) {
+                type = TOK_MATCH;
+                val = '';
+            }
+            else if (T[p][t].type == TOK_DIGITS || T[p][t].type == TOK_DELTA) {
+                var d = val - T[p][t].str;
+                F[t]++;
+                if (d >= 0 && d < 256 && F[t] > n / 2) {
+                    type = TOK_DELTA;
+                    val = d;
+                }
+            }
+            else if ((T[p][t].type == TOK_DIGITS0 || T[p][t].type == TOK_DELTA0) &&
+                T[p][t].str.length == val.length) {
+                var d = val - T[p][t].str;
+                F[t]++;
+                if (d >= 0 && d < 256 && F[t] > n / 2) {
+                    type = TOK_DELTA0;
+                    val = d;
+                }
+            }
+        }
+        T[n][t] = {
+            str: tok[i],
+            val: val,
+            type: type,
+        };
+        if (max_len < T[n][t].val.length + 3)
+            // +3 for integers; 5 -> (Uint32)5
+            max_len = T[n][t].val.length + 3;
+        //console.error(t,T[n][t])
+    }
+    T[n][++t] = {
+        type: TOK_END,
+    };
+    return [t + 1, max_len];
+}
+module.exports = { encode, decode };
+//# sourceMappingURL=tok3.js.map

package/esm/htscodecs/tok3.js.map

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package/esm/index.d.ts

@@ -1,3 +1,3 @@
-export { default as CramFile, CramRecord } from './cramFile';
+export { CramRecord, default as CramFile } from './cramFile';
 export { default as CraiIndex } from './craiIndex';
 export { default as IndexedCramFile } from './indexedCramFile';

package/esm/index.js

@@ -1,4 +1,4 @@
-export { default as CramFile, CramRecord } from './cramFile';
+export { CramRecord, default as CramFile } from './cramFile';
 export { default as CraiIndex } from './craiIndex';
 export { default as IndexedCramFile } from './indexedCramFile';
 //# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,QAAQ,EAAE,UAAU,EAAE,MAAM,YAAY,CAAA;AAC5D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;AAClD,OAAO,EAAE,OAAO,IAAI,eAAe,EAAE,MAAM,mBAAmB,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,OAAO,IAAI,QAAQ,EAAE,MAAM,YAAY,CAAA;AAC5D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;AAClD,OAAO,EAAE,OAAO,IAAI,eAAe,EAAE,MAAM,mBAAmB,CAAA"}

package/esm/indexedCramFile.d.ts

@@ -1,10 +1,10 @@
+import { Slice } from './craiIndex';
 import CramFile from './cramFile';
-import CramRecord from './cramFile/record';
 import { SeqFetch } from './cramFile/file';
-import { Filehandle } from './cramFile/filehandle';
-import { Slice } from './craiIndex';
+import CramRecord from './cramFile/record';
+import type { GenericFilehandle } from 'generic-filehandle2';
 export interface CramFileSource {
-    cramFilehandle?: Filehandle;
+    cramFilehandle?: GenericFilehandle;
     cramUrl?: string;
     cramPath?: string;
 }

package/esm/indexedCramFile.js

@@ -1,5 +1,5 @@
-import { CramUnimplementedError } from './errors';
 import CramFile from './cramFile';
+import { CramUnimplementedError } from './errors';
 export default class IndexedCramFile {
     /**
      *
@@ -11,17 +11,17 @@ export default class IndexedCramFile {
      * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
      */
     constructor(args) {
-        var _a;
         // { cram, index, seqFetch /* fasta, fastaIndex */ }) {
         this.cram =
-            (_a = args.cram) !== null && _a !== void 0 ? _a : new CramFile({
-                url: args.cramUrl,
-                path: args.cramPath,
-                filehandle: args.cramFilehandle,
-                seqFetch: args.seqFetch,
-                checkSequenceMD5: args.checkSequenceMD5,
-                cacheSize: args.cacheSize,
-            });
+            args.cram ??
+                new CramFile({
+                    url: args.cramUrl,
+                    path: args.cramPath,
+                    filehandle: args.cramFilehandle,
+                    seqFetch: args.seqFetch,
+                    checkSequenceMD5: args.checkSequenceMD5,
+                    cacheSize: args.cacheSize,
+                });
         if (!(this.cram instanceof CramFile)) {
             throw new Error('invalid arguments: no cramfile');
         }

package/esm/indexedCramFile.js.map

@@ -1 +1 @@
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package/esm/io/index.d.ts

@@ -1,4 +1,4 @@
-import { Filehandle } from '../cramFile/filehandle';
-declare function open(maybeUrl?: string, maybePath?: string, maybeFilehandle?: Filehandle): Filehandle;
+import type { GenericFilehandle } from 'generic-filehandle2';
+declare function open(maybeUrl?: string, maybePath?: string, maybeFilehandle?: GenericFilehandle): GenericFilehandle;
 export { open };
 export { LocalFile, RemoteFile } from 'generic-filehandle';

package/esm/io/index.js

@@ -1,4 +1,4 @@
-import { LocalFile, RemoteFile } from 'generic-filehandle';
+import { LocalFile, RemoteFile } from 'generic-filehandle2';
 function open(maybeUrl, maybePath, maybeFilehandle) {
     if (maybeFilehandle) {
         return maybeFilehandle;

package/esm/io/index.js.map

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

@@ -1,4 +1,4 @@
 declare const TF_SHIFT = 12;
 declare const TOTFREQ: number;
 declare const RANS_BYTE_L: number;
-export { TF_SHIFT, TOTFREQ, RANS_BYTE_L };
+export { RANS_BYTE_L, TF_SHIFT, TOTFREQ };

package/esm/rans/constants.js

@@ -1,5 +1,5 @@
 const TF_SHIFT = 12;
 const TOTFREQ = 1 << TF_SHIFT;
 const RANS_BYTE_L = 1 << 23;
-export { TF_SHIFT, TOTFREQ, RANS_BYTE_L };
+export { RANS_BYTE_L, TF_SHIFT, TOTFREQ };
 //# sourceMappingURL=constants.js.map

package/esm/rans/constants.js.map

@@ -1 +1 @@
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package/esm/rans/d04.js.map

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package/esm/rans/decoding.js.map

@@ -1 +1 @@
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package/esm/rans/frequencies.js.map

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package/esm/rans/index.js

@@ -1,10 +1,9 @@
 // @ts-nocheck
-import { Buffer } from 'buffer';
 import { CramMalformedError } from '../errors';
-import Decoding from './decoding';
-import { readStatsO0, readStatsO1 } from './frequencies';
 import D04 from './d04';
 import D14 from './d14';
+import Decoding from './decoding';
+import { readStatsO0, readStatsO1 } from './frequencies';
 // const /* int */ ORDER_BYTE_LENGTH = 1
 // const /* int */ COMPRESSED_BYTE_LENGTH = 4
 const /* int */ RAW_BYTE_LENGTH = 4;
@@ -124,6 +123,7 @@ function uncompressOrder1Way4(
 class ByteBuffer {
     constructor(nodeBuffer, initialInputPosition = 0) {
         this._buffer = nodeBuffer;
+        this._dataView = new DataView(nodeBuffer.buffer);
         this._position = initialInputPosition;
         this.length = nodeBuffer.length;
     }
@@ -155,7 +155,7 @@ class ByteBuffer {
         return pos;
     }
     getInt() {
-        const i = this._buffer.readInt32LE(this._position);
+        const i = this._dataView.getInt32(this._position, true);
         this._position += 4;
         return i;
     }
@@ -180,7 +180,7 @@ export default function uncompress(inputBuffer, outputBuffer, initialInputPositi
         throw new CramMalformedError('Incorrect input length.');
     }
     const /* int */ outputSize = input.getInt();
-    const output = new ByteBuffer(outputBuffer || Buffer.allocUnsafe(outputSize));
+    const output = new ByteBuffer(outputBuffer || new Uint8Array(outputSize));
     // TODO output.limit(outputSize)
     if (output.length < outputSize) {
         throw new CramMalformedError(`Output buffer too small to fit ${outputSize} bytes.`);