@gmod/cram 3.0.7 → 4.0.0

package/src/rans/constants.ts

@@ -2,4 +2,4 @@ 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 }

package/src/rans/d04.ts

@@ -1,6 +1,5 @@
 // @ts-nocheck
 import { CramMalformedError } from '../errors'
-
 import { TF_SHIFT } from './constants'
 import Decoding from './decoding'
 

package/src/rans/decoding.ts

@@ -1,6 +1,5 @@
 // @ts-nocheck
 import { CramMalformedError } from '../errors'
-
 import { RANS_BYTE_L } from './constants'
 
 class FC {

package/src/rans/frequencies.ts

@@ -1,6 +1,5 @@
 // @ts-nocheck
 import { CramMalformedError } from '../errors'
-
 import { TOTFREQ } from './constants'
 import Decoding from './decoding'
 

package/src/rans/index.ts

@@ -1,12 +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
@@ -155,6 +152,7 @@ function /* static ByteBuffer */ uncompressOrder1Way4(
 class ByteBuffer {
   constructor(nodeBuffer, initialInputPosition = 0) {
     this._buffer = nodeBuffer
+    this._dataView = new DataView(nodeBuffer.buffer)
     this._position = initialInputPosition
     this.length = nodeBuffer.length
   }
@@ -194,7 +192,7 @@ class ByteBuffer {
   }
 
   getInt() {
-    const i = this._buffer.readInt32LE(this._position)
+    const i = this._dataView.getInt32(this._position, true)
     this._position += 4
     return i
   }
@@ -229,7 +227,7 @@ export default function uncompress(
   }
 
   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) {

package/src/unzip.ts

@@ -1 +1,5 @@
-export { gunzipSync as unzip } from 'zlib'
+import { inflate } from 'pako'
+
+export function unzip(input: Uint8Array) {
+  return inflate(input)
+}

package/dist/cramFile/filehandle.d.ts

@@ -1 +0,0 @@
-export { GenericFilehandle as Filehandle } from 'generic-filehandle';

package/dist/cramFile/filehandle.js

@@ -1,3 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-//# sourceMappingURL=filehandle.js.map

package/dist/cramFile/filehandle.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"filehandle.js","sourceRoot":"","sources":["../../src/cramFile/filehandle.ts"],"names":[],"mappings":""}

package/dist/htscodecs/main_arith_gen.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/htscodecs/main_arith_gen.js

@@ -1,86 +0,0 @@
-"use strict";
-/*
- * Copyright (c) 2019,2020 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.
- */
-// Command line tool to manually test the arith_gen.js code.
-var fs = require('fs');
-var RangeCoderGen = require('./arith_gen');
-var argv = require('minimist')(process.argv.slice(2), { boolean: ['d', 'r'] });
-if (argv._.length != 1) {
-    process.stderr.write('Usage: node main_arith_gen.js [-d] [-o order] input-file > output-file\n');
-    process.exit(1);
-}
-var filein = argv._[0];
-var buf = fs.readFileSync(filein);
-var blk_size = 1024 * 1024;
-var raw = argv.r;
-var arith = new RangeCoderGen();
-if (!argv.d) {
-    var order = argv.o != undefined ? argv.o : 0;
-    // -o8.4 => 8+(256*4)
-    order += Math.round((order - (order >> 0)) * 10) * 256;
-    var pos = 0;
-    var out_len = 0;
-    if (raw)
-        blk_size = buf.length;
-    while (pos < buf.length) {
-        var buf2 = arith.encode(buf.slice(pos, pos + blk_size), order);
-        // Compressed buffer size. Used in multi-block format.
-        var csize = new Buffer.allocUnsafe(4);
-        if (!raw) {
-            csize.writeInt32LE(buf2.length, 0);
-            process.stdout.write(csize);
-        }
-        // Write compressed buffer itself
-        process.stdout.write(buf2);
-        pos += blk_size;
-        out_len += buf2.length;
-    }
-    process.stderr.write('Compress order ' + order + ', ' + buf.length + ' => ' + out_len + '\n');
-}
-else {
-    var pos = 0;
-    var out_len = 0;
-    var len = buf.length;
-    while (pos < buf.length) {
-        if (!raw) {
-            len = buf.readInt32LE(pos);
-            pos += 4;
-        }
-        var buf2 = arith.decode(buf.slice(pos, pos + len));
-        process.stdout.write(buf2);
-        out_len += buf2.length;
-        pos += len;
-    }
-    process.stderr.write('Decompress ' + buf.length + ' => ' + out_len + '\n');
-}
-//# sourceMappingURL=main_arith_gen.js.map

package/dist/htscodecs/main_arith_gen.js.map

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

@@ -1 +0,0 @@
-export {};

package/dist/htscodecs/main_fqzcomp.js

@@ -1,112 +0,0 @@
-"use strict";
-/*
- * Copyright (c) 2019,2020 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.
- */
-var fs = require('fs');
-var fqz = require('./fqzcomp');
-var argv = require('minimist')(process.argv.slice(2), { boolean: ['d', 'r'] });
-if (argv._.length != 1) {
-    process.stderr.write('Usage: node main_fqzcomp.js [-d] input-file > output-file\n');
-    process.exit(1);
-}
-var filein = argv._[0];
-var buf = fs.readFileSync(filein);
-var raw = argv.r;
-if (!argv.d) {
-    // Line breaks to get sequence length, but then stitch together into
-    // a single non-breaking buffer.
-    var len = 0;
-    var j = 0;
-    var q_lens = new Array();
-    var q_dirs = new Array();
-    var q_len = 0;
-    for (var i = 0; i < buf.length; i++) {
-        if (buf[i] == '\n'.charCodeAt(0) || buf[i] == '\t'.charCodeAt(0)) {
-            q_lens.push(len);
-            if (q_len == 0)
-                q_len = len;
-            else if (q_len != len)
-                q_len = -1; // marker for multiple lengths
-            len = 0;
-            if (buf[i] == '\t'.charCodeAt(0)) {
-                // parse 2nd token for read1/read2 status
-                var dir = '';
-                for (i++; i < buf.length && buf[i] != '\n'.charCodeAt(0); i++)
-                    dir += String.fromCharCode(buf[i]);
-                q_dirs.push(dir);
-            }
-            else {
-                q_dirs.push(0);
-            }
-        }
-        else {
-            buf[j++] = buf[i] - 33; // ASCII phred to raw
-            len++;
-        }
-    }
-    buf = buf.slice(0, j);
-    if (q_len > 0)
-        q_lens = [q_lens[0]];
-    var buf2 = fqz.encode(buf, q_lens, q_dirs);
-    process.stderr.write('Compress ' + buf.length + ' => ' + buf2.length + '\n');
-    if (!raw) {
-        var hdr = new Buffer.allocUnsafe(8);
-        hdr.writeInt32LE(buf.length, 0);
-        hdr.writeInt32LE(buf2.length, 4);
-        process.stdout.write(hdr);
-    }
-    process.stdout.write(buf2);
-}
-else {
-    var q_lens = new Array();
-    // Consume ulen and clen from outer test harness (pointless as non-blocking atm)
-    var buf2;
-    if (raw)
-        buf2 = fqz.decode(buf, q_lens);
-    else
-        buf2 = fqz.decode(buf.slice(8), q_lens);
-    // Split into newlines so we can do easy data comparison
-    var buf3 = new Buffer.allocUnsafe(buf2.length + q_lens.length);
-    var rec = 0;
-    var len = q_lens[rec++];
-    var j = 0;
-    for (var i = 0; i < buf2.length; i++) {
-        buf3[j++] = buf2[i] + 33;
-        if (--len == 0) {
-            buf3[j++] = '\n'.charCodeAt(0);
-            len = q_lens[rec++];
-        }
-    }
-    process.stderr.write('Decompress ' + buf.length + ' => ' + buf3.length + '\n');
-    process.stdout.write(buf3);
-}
-//# sourceMappingURL=main_fqzcomp.js.map

package/dist/htscodecs/main_fqzcomp.js.map

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

@@ -1 +0,0 @@
-export {};

package/dist/htscodecs/main_rans.js

@@ -1,83 +0,0 @@
-"use strict";
-/*
- * Copyright (c) 2019-2020 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.
- */
-var fs = require('fs');
-var rans = require('./rans');
-var argv = require('minimist')(process.argv.slice(2), { boolean: ['d', 'r'] });
-if (argv._.length != 1) {
-    process.stderr.write('Usage: node main_rans.js [-d] [-o order] input-file > output-file\n');
-    process.exit(1);
-}
-var filein = argv._[0];
-var buf = fs.readFileSync(filein);
-var blk_size = 1024 * 1024;
-var raw = argv.r;
-if (!argv.d) {
-    var order = argv.o != undefined ? argv.o : 0;
-    var pos = 0;
-    var out_len = 0;
-    if (raw)
-        blk_size = buf.length;
-    while (pos < buf.length) {
-        var buf2 = rans.encode(buf.slice(pos, pos + blk_size), order);
-        var header = new Buffer.allocUnsafe(5);
-        if (!raw) {
-            header[0] = order;
-            header.writeInt32LE(buf2.length, 1);
-            process.stdout.write(header);
-        }
-        process.stdout.write(buf2);
-        pos += blk_size;
-        out_len += buf2.length;
-    }
-    process.stderr.write('Compress order ' + order + ', ' + buf.length + ' => ' + out_len + '\n');
-}
-else {
-    var pos = 0;
-    var out_len = 0;
-    var len = buf.length;
-    while (pos < buf.length) {
-        if (!raw) {
-            var order = buf[0];
-            pos++;
-            len = buf.readInt32LE(pos);
-            pos += 4;
-        }
-        var buf2 = rans.decode(buf.slice(pos, pos + len));
-        process.stdout.write(buf2);
-        out_len += buf2.length;
-        pos += len;
-    }
-    process.stderr.write('Decompress ' + buf.length + ' => ' + out_len + '\n');
-}
-//# sourceMappingURL=main_rans.js.map

package/dist/htscodecs/main_rans.js.map

@@ -1 +0,0 @@
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package/dist/htscodecs/main_rans4x16.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/htscodecs/main_rans4x16.js

@@ -1,82 +0,0 @@
-"use strict";
-/*
- * Copyright (c) 2019-2020 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.
- */
-var fs = require('fs');
-var rans = require('./rans4x16');
-var argv = require('minimist')(process.argv.slice(2), { boolean: ['d', 'r'] });
-if (argv._.length != 1) {
-    processf.stderr.write('Usage: node main_rans4x16.js [-d] [-o order] input-file > output-file\n');
-    process.exit(1);
-}
-var filein = argv._[0];
-var buf = fs.readFileSync(filein);
-var blk_size = 1024 * 1024;
-var raw = argv.r;
-if (!argv.d) {
-    var order = argv.o != undefined ? argv.o : 0;
-    // -o8.4 => 8+(256*4)
-    order += Math.round((order - (order >> 0)) * 10) * 256;
-    var pos = 0;
-    var out_len = 0;
-    if (raw)
-        blk_size = buf.length;
-    while (pos < buf.length) {
-        var buf2 = rans.encode(buf.slice(pos, pos + blk_size), order);
-        var header = new Buffer.allocUnsafe(4);
-        if (!raw) {
-            header.writeInt32LE(buf2.length, 0);
-            process.stdout.write(header);
-        }
-        process.stdout.write(buf2);
-        pos += blk_size;
-        out_len += buf2.length + 4;
-    }
-    process.stderr.write('Compress order ' + order + ', ' + buf.length + ' => ' + out_len + '\n');
-}
-else {
-    var pos = 0;
-    var out_len = 0;
-    var len = buf.length;
-    while (pos < buf.length) {
-        if (!raw) {
-            len = buf.readInt32LE(pos);
-            pos += 4;
-        }
-        var buf2 = rans.decode(buf.slice(pos, pos + len));
-        process.stdout.write(buf2);
-        out_len += buf2.length;
-        pos += len;
-    }
-    process.stderr.write('Decompress ' + buf.length + ' => ' + out_len + '\n');
-}
-//# sourceMappingURL=main_rans4x16.js.map

package/dist/htscodecs/main_rans4x16.js.map

@@ -1 +0,0 @@
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package/dist/htscodecs/main_tok3.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/htscodecs/main_tok3.js

@@ -1,84 +0,0 @@
-"use strict";
-/*
- * Copyright (c) 2019,2020 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.
- */
-var fs = require('fs');
-var tok3 = require('./tok3');
-var argv = require('minimist')(process.argv.slice(2), {
-    boolean: ['d', 'a', 'r'],
-});
-if (argv._.length != 1) {
-    process.stderr.write('Usage: node main_tok3.js [-a] [-d] input-file > output-file\n');
-    process.exit(1);
-}
-var filein = argv._[0];
-var buf = fs.readFileSync(filein);
-var blk_size = 1024 * 1024;
-var raw = argv.r;
-if (!argv.d) {
-    var pos = 0;
-    var out_len = 0;
-    if (raw)
-        blk_size = buf.length;
-    while (pos < buf.length) {
-        var blk_end = blk_size;
-        while (pos + blk_end < buf.length && buf[pos + blk_end - 1] != 10)
-            blk_end--;
-        var buf2 = tok3.encode(buf.slice(pos, pos + blk_end), argv.a);
-        var header = new Buffer.allocUnsafe(4);
-        if (!raw) {
-            header.writeInt32LE(buf2.length, 0);
-            process.stdout.write(header);
-        }
-        process.stdout.write(buf2);
-        pos += blk_end;
-        out_len += buf2.length + 4;
-    }
-    process.stderr.write('Compress ' + buf.length + ' => ' + out_len + '\n');
-}
-else {
-    var pos = 0;
-    var out_len = 0;
-    var len = buf.length;
-    while (pos < buf.length) {
-        if (!raw) {
-            len = buf.readInt32LE(pos);
-            pos += 4;
-        }
-        var buf2 = tok3.decode(buf.slice(pos, pos + len), len);
-        process.stdout.write(buf2);
-        out_len += buf2.length;
-        pos += len;
-    }
-    process.stderr.write('Decompress ' + buf.length + ' => ' + out_len + '\n');
-}
-//# sourceMappingURL=main_tok3.js.map

package/dist/htscodecs/main_tok3.js.map

@@ -1 +0,0 @@
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package/dist/unzip-pako.d.ts

@@ -1,2 +0,0 @@
-import { Buffer } from 'buffer';
-export declare function unzip(input: Buffer): Buffer;

package/dist/unzip-pako.js

@@ -1,9 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.unzip = unzip;
-const pako_1 = require("pako");
-const buffer_1 = require("buffer");
-function unzip(input) {
-    return buffer_1.Buffer.from((0, pako_1.inflate)(input));
-}
-//# sourceMappingURL=unzip-pako.js.map

package/dist/unzip-pako.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":";;AAGA,sBAEC;AALD,+BAA8B;AAC9B,mCAA+B;AAE/B,SAAgB,KAAK,CAAC,KAAa;IACjC,OAAO,eAAM,CAAC,IAAI,CAAC,IAAA,cAAO,EAAC,KAAK,CAAC,CAAC,CAAA;AACpC,CAAC"}

package/esm/cramFile/filehandle.d.ts

@@ -1 +0,0 @@
-export { GenericFilehandle as Filehandle } from 'generic-filehandle';

package/esm/cramFile/filehandle.js

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=filehandle.js.map

package/esm/cramFile/filehandle.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"filehandle.js","sourceRoot":"","sources":["../../src/cramFile/filehandle.ts"],"names":[],"mappings":""}

package/esm/htscodecs/main_arith_gen.d.ts

@@ -1 +0,0 @@
-export {};