@gmod/cram 4.0.1 → 4.0.4

package/esm/htscodecs/tok3.js

@@ -1,4 +1,5 @@
-"use strict";
+/* eslint-disable no-var */
+// @ts-nocheck
 /*
  * Copyright (c) 2019 Genome Research Ltd.
  * Author(s): James Bonfield
@@ -36,26 +37,11 @@
 // 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();
+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;
@@ -69,59 +55,57 @@ 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);
+    let t = -1;
+    const 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;
+        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) {
-            var M = new Array(nnames - 1).fill(TOK_MATCH);
+            const 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();
+            const dup_pos = src.ReadByte();
+            const 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);
+            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) {
-    var str = val + '';
-    while (str.length < len)
+    let 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;
+    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];
     }
-    var t = 1;
+    let t = 1;
     N[n] = '';
     T[n] = new Array(256);
     do {
@@ -160,204 +144,24 @@ function DecodeSingleName(B, N, T, n) {
     } 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) {
+export 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')
+    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 (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])
+    for (let i = 0; i < nnames; i++) {
+        str += DecodeSingleName(B, N, T, i) + separator;
     }
-    T[n][++t] = {
-        type: TOK_END,
-    };
-    return [t + 1, max_len];
+    return str;
 }
-module.exports = { encode, decode };
 //# sourceMappingURL=tok3.js.map

package/esm/htscodecs/tok3.js.map

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+{"version":3,"file":"tok3.js","sourceRoot":"","sources":["../../src/htscodecs/tok3.ts"],"names":[],"mappings":"AAAA,2BAA2B;AAC3B,cAAc;AAEd;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,iBAAiB;AACjB,EAAE;AACF,2DAA2D;AAC3D,6DAA6D;AAC7D,uDAAuD;AAEvD,OAAO,EAAE,gBAAgB,EAAE,MAAM,SAAS,CAAA;AAC1C,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,KAAK,IAAI,MAAM,YAAY,CAAA;AAElC,MAAM,KAAK,GAAG,IAAI,SAAS,EAAE,CAAA;AAE7B,MAAM,QAAQ,GAAG,CAAC,CAAA;AAClB,MAAM,UAAU,GAAG,CAAC,CAAA;AACpB,MAAM,QAAQ,GAAG,CAAC,CAAA;AAClB,MAAM,WAAW,GAAG,CAAC,CAAA;AACrB,MAAM,SAAS,GAAG,CAAC,CAAA;AACnB,MAAM,OAAO,GAAG,CAAC,CAAA;AACjB,MAAM,QAAQ,GAAG,CAAC,CAAA;AAClB,MAAM,UAAU,GAAG,CAAC,CAAA;AACpB,MAAM,SAAS,GAAG,CAAC,CAAA;AACnB,MAAM,UAAU,GAAG,CAAC,CAAA;AACpB,MAAM,SAAS,GAAG,EAAE,CAAA;AACpB,MAAM,OAAO,GAAG,EAAE,CAAA;AAClB,MAAM,OAAO,GAAG,EAAE,CAAA;AAElB,yEAAyE;AACzE,qBAAqB;AACrB,SAAS,sBAAsB,CAAC,GAAG,EAAE,OAAO,EAAE,SAAS,EAAE,MAAM;IAC7D,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;IAEV,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IAExB,OAAO,CAAC,GAAG,CAAC,GAAG,EAAE,EAAE,CAAC;QAClB,MAAM,KAAK,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;QAC5B,MAAM,OAAO,GAAG,KAAK,GAAG,GAAG,CAAA;QAC3B,MAAM,OAAO,GAAG,KAAK,GAAG,EAAE,CAAA;QAC1B,MAAM,IAAI,GAAG,KAAK,GAAG,EAAE,CAAA;QAEvB,IAAI,OAAO,EAAE,CAAC;YACZ,CAAC,EAAE,CAAA;YACH,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,EAAE,CAAC,CAAA;QACtB,CAAC;QAED,IAAI,IAAI,IAAI,QAAQ,IAAI,OAAO,EAAE,CAAC;YAChC,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;YAC/C,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,IAAI,QAAQ,CAAC,gBAAgB,CAAC,CAAC,IAAI,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;QAC5E,CAAC;QAED,IAAI,OAAO,EAAE,CAAC;YACZ,MAAM,OAAO,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;YAC9B,MAAM,QAAQ,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;YAC/B,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,IAAI,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAA;QACrD,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,GAAG,GAAG,CAAC,SAAS,EAAE,CAAA;YAC5B,MAAM,IAAI,GAAG,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;YAE/B,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YAC/D,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,IAAI,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;QACvC,CAAC;IACH,CAAC;IAED,OAAO,CAAC,CAAA;AACV,CAAC;AAED,yEAAyE;AACzE,eAAe;AACf,SAAS,aAAa,CAAC,GAAG,EAAE,GAAG;IAC7B,IAAI,GAAG,GAAG,GAAG,GAAG,EAAE,CAAA;IAClB,OAAO,GAAG,CAAC,MAAM,GAAG,GAAG,EAAE,CAAC;QACxB,GAAG,GAAG,GAAG,GAAG,GAAG,CAAA;IACjB,CAAC;IAED,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,SAAS,gBAAgB,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC;IAClC,IAAI,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,QAAQ,EAAE,CAAA;IACpC,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,UAAU,EAAE,CAAA;IACpC,MAAM,CAAC,GAAG,CAAC,GAAG,IAAI,CAAA;IAElB,IAAI,IAAI,IAAI,OAAO,EAAE,CAAC;QACpB,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;QACX,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;IACb,CAAC;IAED,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;IACT,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IACrB,GAAG,CAAC;QACF,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,QAAQ,EAAE,CAAA;QAEhC,QAAQ,IAAI,EAAE,CAAC;YACb,KAAK,QAAQ;gBACX,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,QAAQ,EAAE,CAAA;gBACnC,MAAK;YAEP,KAAK,UAAU;gBACb,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,UAAU,EAAE,CAAA;gBACvC,MAAK;YAEP,KAAK,UAAU;gBACb,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,UAAU,EAAE,CAAA;gBACvC,MAAK;YAEP,KAAK,WAAW;gBACd,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,UAAU,EAAE,CAAA;gBACtC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,QAAQ,EAAE,CAAA;gBAClC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;gBAC7B,MAAK;YAEP,KAAK,SAAS;gBACZ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,QAAQ,EAAE,CAAA;gBACrD,MAAK;YAEP,KAAK,UAAU;gBACb,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,QAAQ,EAAE,CAAA;gBACpD,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;gBACtB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;gBAC7B,MAAK;YAEP,KAAK,SAAS;gBACZ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBACjB,MAAK;YAEP;gBACE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gBACZ,MAAK;QACT,CAAC;QAED,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;IACnB,CAAC,QAAQ,IAAI,IAAI,OAAO,EAAC;IAEzB,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;AACb,CAAC;AAED,yEAAyE;AACzE,qEAAqE;AACrE,mCAAmC;AACnC,MAAM,UAAU,MAAM,CAAC,GAAG,EAAE,GAAG,EAAE,SAAS;IACxC,IAAI,GAAG,GAAG,IAAI,QAAQ,CAAC,GAAG,CAAC,CAAA;IAC3B,MAAM,IAAI,GAAG,GAAG,CAAC,UAAU,EAAE,CAAA;IAC7B,MAAM,MAAM,GAAG,GAAG,CAAC,UAAU,EAAE,CAAA;IAC/B,MAAM,SAAS,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;IAEhC,MAAM,CAAC,GAAG,sBAAsB,CAAC,GAAG,EAAE,GAAG,EAAE,SAAS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package/esm/indexedCramFile.d.ts

@@ -19,10 +19,17 @@ export default class IndexedCramFile {
      *
      * @param {object} args
      * @param {CramFile} args.cram
-     * @param {Index-like} args.index object that supports getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
-     * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
-     * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
-     * 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.
+     *
+     * @param {Index-like} args.index object that supports
+     * getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
+     *
+     * @param {number} [args.cacheSize] optional maximum number of CRAM records
+     * to cache.  default 20,000
+     *
+     * @param {boolean} [args.checkSequenceMD5] - default true. if false,
+     * disables verifying the MD5 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: {
         index: CramIndexLike;
@@ -36,10 +43,9 @@ export default class IndexedCramFile {
     } & CramFileSource)));
     /**
      *
-     * @param {number} seq numeric ID of the reference sequence
-     * @param {number} start start of the range of interest. 1-based closed coordinates.
-     * @param {number} end end of the range of interest. 1-based closed coordinates.
-     * @returns {Promise[Array[CramRecord]]}
+     * @param seq numeric ID of the reference sequence
+     * @param start start of the range of interest. 1-based closed coordinates.
+     * @param end end of the range of interest. 1-based closed coordinates.
      */
     getRecordsForRange(seq: number, start: number, end: number, opts?: {
         viewAsPairs?: boolean;

package/esm/indexedCramFile.js

@@ -5,13 +5,19 @@ export default class IndexedCramFile {
      *
      * @param {object} args
      * @param {CramFile} args.cram
-     * @param {Index-like} args.index object that supports getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
-     * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
-     * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
-     * 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.
+     *
+     * @param {Index-like} args.index object that supports
+     * getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
+     *
+     * @param {number} [args.cacheSize] optional maximum number of CRAM records
+     * to cache.  default 20,000
+     *
+     * @param {boolean} [args.checkSequenceMD5] - default true. if false,
+     * disables verifying the MD5 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) {
-        // { cram, index, seqFetch /* fasta, fastaIndex */ }) {
         this.cram =
             args.cram ??
                 new CramFile({
@@ -29,10 +35,9 @@ export default class IndexedCramFile {
     }
     /**
      *
-     * @param {number} seq numeric ID of the reference sequence
-     * @param {number} start start of the range of interest. 1-based closed coordinates.
-     * @param {number} end end of the range of interest. 1-based closed coordinates.
-     * @returns {Promise[Array[CramRecord]]}
+     * @param seq numeric ID of the reference sequence
+     * @param start start of the range of interest. 1-based closed coordinates.
+     * @param end end of the range of interest. 1-based closed coordinates.
      */
     async getRecordsForRange(seq, start, end, opts = {}) {
         opts.viewAsPairs = opts.viewAsPairs || false;
@@ -44,13 +49,11 @@ export default class IndexedCramFile {
         }
         const seqId = seq;
         const slices = await this.index.getEntriesForRange(seqId, start, end);
-        // TODO: do we need to merge or de-duplicate the blocks?
         // fetch all the slices and parse the feature data
-        const filter = (feature) => feature.sequenceId === seq &&
+        const sliceResults = await Promise.all(slices.map(slice => this.getRecordsInSlice(slice, feature => feature.sequenceId === seq &&
             feature.alignmentStart <= end &&
             feature.lengthOnRef !== undefined &&
-            feature.alignmentStart + feature.lengthOnRef - 1 >= start;
-        const sliceResults = await Promise.all(slices.map(slice => this.getRecordsInSlice(slice, filter)));
+            feature.alignmentStart + feature.lengthOnRef - 1 >= start)));
         let ret = Array.prototype.concat(...sliceResults);
         if (opts.viewAsPairs) {
             const readNames = {};

package/esm/indexedCramFile.js.map

@@ -1 +1 @@
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package/esm/util.d.ts

@@ -0,0 +1 @@
+export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;

package/esm/util.js

@@ -0,0 +1,17 @@
+function sum(array) {
+    let sum = 0;
+    for (const entry of array) {
+        sum += entry.length;
+    }
+    return sum;
+}
+export 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;
+}
+//# sourceMappingURL=util.js.map

package/esm/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,SAAS,GAAG,CAAC,KAAmB;IAC9B,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,KAAK,MAAM,KAAK,IAAI,KAAK,EAAE,CAAC;QAC1B,GAAG,IAAI,KAAK,CAAC,MAAM,CAAA;IACrB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AACD,MAAM,UAAU,gBAAgB,CAAC,IAAkB;IACjD,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAA;IAC7C,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC9B,MAAM,IAAI,KAAK,CAAC,MAAM,CAAA;IACxB,CAAC;IACD,OAAO,WAAW,CAAA;AACpB,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "4.0.1",
+  "version": "4.0.4",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -25,13 +25,13 @@
     "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "format": "prettier --write .",
     "docs": "documentation readme --shallow src/indexedCramFile.ts --section=IndexedCramFile; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/craiIndex.ts --section=CraiIndex;  documentation readme --shallow errors.ts '--section=Exception Classes'; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/cramFile/record.ts --section=CramRecord",
-    "prebuild": "npm run clean",
+    "prebuild": "yarn clean",
     "clean": "rimraf dist esm",
     "build:esm": "tsc --outDir esm",
     "build:es5": "tsc --module commonjs --outDir dist",
-    "build": "npm run build:esm && npm run build:es5",
+    "build": "yarn build:esm && yarn build:es5",
     "postbuild": "webpack",
-    "prepack": "npm test run && npm run build && cp dist/errors.js errors.js",
+    "preversion": "yarn test --run && yarn build && cp dist/errors.js errors.js",
     "postpublish": "rm errors.js",
     "postversion": "git push --follow-tags"
   },
@@ -44,16 +44,15 @@
   "dependencies": {
     "bzip2": "^0.1.1",
     "crc": "^4.3.2",
-    "generic-filehandle2": "^0.0.2",
-    "long": "^4.0.0",
+    "generic-filehandle2": "^1.0.0",
+    "longfn": "^1.3.1",
     "md5": "^2.2.1",
     "pako": "^1.0.4",
     "quick-lru": "^4.0.1",
     "xz-decompress": "^0.2.1"
   },
   "devDependencies": {
-    "@gmod/indexedfasta": "^2.1.0",
-    "@types/long": "^4.0.0",
+    "@gmod/indexedfasta": "^3.0.0",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
     "@typescript-eslint/eslint-plugin": "^8.0.0",
@@ -63,7 +62,7 @@
     "documentation": "^14.0.3",
     "eslint": "^9.9.0",
     "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-unicorn": "^55.0.0",
+    "eslint-plugin-unicorn": "^56.0.1",
     "mock-fs": "^5.2.0",
     "prettier": "^3.2.5",
     "rimraf": "^6.0.1",

package/src/cramFile/file.ts

@@ -4,11 +4,12 @@ import QuickLRU from 'quick-lru'
 import { XzReadableStream } from 'xz-decompress'
 
 import { CramMalformedError, CramUnimplementedError } from '../errors'
-import htscodecs from '../htscodecs'
+import * as htscodecs from '../htscodecs'
 import { open } from '../io'
 import ransuncompress from '../rans'
 import { parseHeaderText } from '../sam'
 import { unzip } from '../unzip'
+import { concatUint8Array } from '../util'
 import CramContainer from './container'
 import CramRecord from './record'
 import {
@@ -17,7 +18,7 @@ import {
   cramFileDefinition,
   getSectionParsers,
 } from './sectionParsers'
-import { concatUint8Array, parseItem, tinyMemoize } from './util'
+import { parseItem, tinyMemoize } from './util'
 
 import type { GenericFilehandle } from 'generic-filehandle2'
 

package/src/cramFile/slice/decodeRecord.ts

@@ -141,16 +141,14 @@ function decodeReadFeatures(
     const data = decodeDataSeries(dataSeriesName)
     if (type === 'character') {
       return String.fromCharCode(data)
-    }
-    if (type === 'string') {
+    } else if (type === 'string') {
       let r = ''
       for (let i = 0; i < data.byteLength; i++) {
         r += String.fromCharCode(data[i])
       }
       return r
-    }
-    if (type === 'numArray') {
-      return data.toArray()
+    } else if (type === 'numArray') {
+      return Array.from(data)
     }
     // else if (type === 'number') {
     //   return data[0]

package/src/cramFile/slice/index.ts

@@ -267,6 +267,7 @@ export default class CramSlice {
 
   async getReferenceRegion() {
     // read the slice header
+    const decoder = new TextDecoder('utf8')
     const sliceHeader = (await this.getHeader()).parsedContent
     if (!isMappedSliceHeader(sliceHeader)) {
       throw new Error('slice header not mapped')
@@ -298,7 +299,8 @@ export default class CramSlice {
 
       // TODO verify
       return {
-        seq: (refBlock as any).data.toString('utf8'),
+        // @ts-expect-error
+        seq: decoder.decode(refBlock.data),
         start: sliceHeader.refSeqStart,
         end: sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1,
         span: sliceHeader.refSeqSpan,