@gmod/cram 3.0.7 → 4.0.0

package/esm/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/esm/htscodecs/main_arith_gen.js.map

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

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

package/esm/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/esm/htscodecs/main_fqzcomp.js.map

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

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

package/esm/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/esm/htscodecs/main_rans.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"main_rans.js","sourceRoot":"","sources":["../../src/htscodecs/main_rans.js"],"names":[],"mappings":";AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,IAAI,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAAA;AACtB,IAAI,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAA;AAC5B,IAAI,IAAI,GAAG,OAAO,CAAC,UAAU,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,OAAO,EAAE,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,CAAC,CAAA;AAE9E,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC;IACvB,OAAO,CAAC,MAAM,CAAC,KAAK,CAClB,qEAAqE,CACtE,CAAA;IACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;AACjB,CAAC;AAED,IAAI,MAAM,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAEtB,IAAI,GAAG,GAAG,EAAE,CAAC,YAAY,CAAC,MAAM,CAAC,CAAA;AACjC,IAAI,QAAQ,GAAG,IAAI,GAAG,IAAI,CAAA;AAC1B,IAAI,GAAG,GAAG,IAAI,CAAC,CAAC,CAAA;AAEhB,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;IACZ,IAAI,KAAK,GAAG,IAAI,CAAC,CAAC,IAAI,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC5C,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IAAI,OAAO,GAAG,CAAC,CAAA;IACf,IAAI,GAAG;QAAE,QAAQ,GAAG,GAAG,CAAC,MAAM,CAAA;IAC9B,OAAO,GAAG,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;QACxB,IAAI,IAAI,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,EAAE,GAAG,GAAG,QAAQ,CAAC,EAAE,KAAK,CAAC,CAAA;QAC7D,IAAI,MAAM,GAAG,IAAI,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACtC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,MAAM,CAAC,CAAC,CAAC,GAAG,KAAK,CAAA;YACjB,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC,CAAA;YACnC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC9B,CAAC;QACD,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1B,GAAG,IAAI,QAAQ,CAAA;QACf,OAAO,IAAI,IAAI,CAAC,MAAM,CAAA;IACxB,CAAC;IACD,OAAO,CAAC,MAAM,CAAC,KAAK,CAClB,iBAAiB,GAAG,KAAK,GAAG,IAAI,GAAG,GAAG,CAAC,MAAM,GAAG,MAAM,GAAG,OAAO,GAAG,IAAI,CACxE,CAAA;AACH,CAAC;KAAM,CAAC;IACN,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IAAI,OAAO,GAAG,CAAC,CAAA;IACf,IAAI,GAAG,GAAG,GAAG,CAAC,MAAM,CAAA;IACpB,OAAO,GAAG,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;QACxB,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,IAAI,KAAK,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;YAClB,GAAG,EAAE,CAAA;YACL,GAAG,GAAG,GAAG,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;YAC1B,GAAG,IAAI,CAAC,CAAA;QACV,CAAC;QACD,IAAI,IAAI,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,EAAE,GAAG,GAAG,GAAG,CAAC,CAAC,CAAA;QACjD,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1B,OAAO,IAAI,IAAI,CAAC,MAAM,CAAA;QACtB,GAAG,IAAI,GAAG,CAAA;IACZ,CAAC;IACD,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,aAAa,GAAG,GAAG,CAAC,MAAM,GAAG,MAAM,GAAG,OAAO,GAAG,IAAI,CAAC,CAAA;AAC5E,CAAC"}

package/esm/htscodecs/main_rans4x16.d.ts

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

package/esm/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/esm/htscodecs/main_rans4x16.js.map

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

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

package/esm/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/esm/htscodecs/main_tok3.js.map

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

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

package/esm/unzip-pako.js

@@ -1,6 +0,0 @@
-import { inflate } from 'pako';
-import { Buffer } from 'buffer';
-export function unzip(input) {
-    return Buffer.from(inflate(input));
-}
-//# sourceMappingURL=unzip-pako.js.map

package/esm/unzip-pako.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAE/B,MAAM,UAAU,KAAK,CAAC,KAAa;IACjC,OAAO,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAA;AACpC,CAAC"}

package/src/cramFile/filehandle.ts

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

package/src/htscodecs/Makefile

@@ -1,142 +0,0 @@
-all: test
-
-CBIN=../build/tests
-NODE=node
-NODE_OPTS=--use-strict
-
-TESTS=test_r4x8 test_r4x16 test_arith test_fqzcomp test_tok3
-CORPUS=../tests
-
-modules: node_modules/bzip2 node_modules/minimist
-
-node_modules/bzip2:
-	-mkdir node_modules
-	npm install bzip2
-
-node_modules/minimist:
-	-mkdir node_modules
-	npm install minimist
-
-test check: modules ${TESTS}
-
-test_r4x8:
-	@echo
-	@echo === Checking r4x8
-	@if [ ! -e ${CBIN}/rans4x8 ]; then echo "Set CBIN if you wish to validate against C version"; fi
-	@for i in ${CORPUS}/dat/r4x8/*; do \
-            echo $$i;\
-	    base=`echo $$i | sed 's/\.[0-9]*$$//;s#/q#/../q#'`; \
-	    level=`echo $$i | sed 's/.*\.//'`;\
-	    # Decode predefined data set\
-	    a=`${NODE} ${NODE_OPTS} main_rans.js -d -r $$i 2>/dev/null | md5sum`; \
-	    b=`cut -f 1 < $$base | tr -d '\012' | md5sum`; \
-	    test "$$a" = "$$b" || echo $<: Mismatch for $$i; \
-	    # Round trip. \
-	    cut -f 1 < $$base | tr -d '\012' > _nonl; \
-	    ${NODE} ${NODE_OPTS} main_rans.js -o $$level -r _nonl 2>/dev/null > _; \
-	    a=`${NODE} ${NODE_OPTS} main_rans.js -d -r _ 2>/dev/null | md5sum`; \
-	    test "$$a" = "$$b" || echo $<: Fail round-trip for $$base with level $$level; \
-	    if [ -e ${CBIN}/rans4x8 ]; \
-	    then \
-	      a=`${CBIN}/rans4x8 -d -r < _ 2>/dev/null | tr '\000' '\012' | md5sum`; \
-	      test "$$a" = "$$b" || echo $<: Fail JS to C round-trip for $$base; \
-	    fi; \
-	done
-
-test_r4x16:
-	@echo
-	@echo === Checking r4x16
-	@if [ ! -e ${CBIN}/rans4x16pr ]; then echo "Set CBIN if you wish to validate against C version"; fi
-	@for i in ${CORPUS}/dat/r4x16/*; do \
-            echo $$i;\
-	    base=`echo $$i | sed 's/\.[0-9]*$$//;s#/q#/../q#'`; \
-	    level=`echo $$i | sed 's/.*\.//'`;\
-	    # Decode predefined data set\
-	    a=`${NODE} ${NODE_OPTS} main_rans4x16.js -d -r $$i 2>/dev/null | md5sum`; \
-	    b=`cut -f 1 < $$base | tr -d '\012' | md5sum`; \
-	    test "$$a" = "$$b" || echo $<: Mismatch for $$i; \
-	    # Round trip. \
-	    cut -f 1 < $$base | tr -d '\012' > _nonl; \
-	    ${NODE} ${NODE_OPTS} main_rans4x16.js -o $$level -r _nonl 2>/dev/null > _; \
-	    a=`${NODE} ${NODE_OPTS} main_rans4x16.js -d -r _ 2>/dev/null | md5sum`; \
-	    test "$$a" = "$$b" || echo $<: Fail round-trip for $$base with level $$level; \
-	    if [ -e ${CBIN}/rans4x16pr ]; \
-	    then \
-	      a=`${CBIN}/rans4x16pr -d -r < _ 2>/dev/null | tr '\000' '\012' | md5sum`; \
-	      test "$$a" = "$$b" || echo $<: Fail JS to C round-trip for $$base; \
-	    fi; \
-	done
-
-test_arith:
-	@echo
-	@echo === Checking arith
-	@if [ ! -e ${CBIN}/arith_dynamic ]; then echo "Set CBIN if you wish to validate against C version"; fi
-	@for i in ${CORPUS}/dat/arith/*; do \
-            echo $$i;\
-	    base=`echo $$i | sed 's/\.[0-9]*$$//;s#/q#/../q#'`; \
-	    level=`echo $$i | sed 's/.*\.//'`;\
-	    # Decode predefined data set\
-	    a=`${NODE} ${NODE_OPTS} main_arith_gen.js -d -r $$i 2>/dev/null | md5sum`; \
-	    b=`cut -f 1 < $$base | tr -d '\012' | md5sum`; \
-	    test "$$a" = "$$b" || echo $<: Mismatch for $$i; \
-	    # Round trip. \
-	    cut -f 1 < $$base | tr -d '\012' > _nonl; \
-	    ${NODE} ${NODE_OPTS} main_arith_gen.js -o $$level -r _nonl 2>/dev/null > _; \
-	    a=`${NODE} ${NODE_OPTS} main_arith_gen.js -d -r _ 2>/dev/null | md5sum`; \
-	    test "$$a" = "$$b" || echo $<: Fail round-trip for $$base with level $$level; \
-	    if [ -e ${CBIN}/arith_dynamic ]; \
-	    then \
-	      a=`${CBIN}/arith_dynamic -d -r < _ 2>/dev/null | tr '\000' '\012' | md5sum`; \
-	      test "$$a" = "$$b" || echo $<: Fail JS to C round-trip for $$base; \
-	    fi; \
-	done
-
-test_fqzcomp:
-	@echo
-	@echo === Checking fqzcomp
-	@if [ ! -e ${CBIN}/fqzcomp_qual ]; then echo "Set CBIN if you wish to validate against C version"; fi
-	@for i in ${CORPUS}/dat/fqzcomp/q*; do \
-            echo $$i;\
-	    base=`echo $$i | sed 's/\.[0-9]*$$//;s#/q#/../q#'`; \
-	    level=`echo $$i | sed 's/.*\.//'`;\
-	    # Decode predefined data set\
-	    a=`${NODE} ${NODE_OPTS} main_fqzcomp.js -d -r $$i 2>/dev/null | md5sum`; \
-	    b=`awk '{print $$1}' $$base | md5sum`; \
-	    test "$$a" = "$$b" || echo $<: Mismatch for $$i; \
-	    # Round trip. \
-	    ${NODE} ${NODE_OPTS} main_fqzcomp.js -s $$level -r $$base 2>/dev/null > _; \
-	    a=`${NODE} ${NODE_OPTS} main_fqzcomp -d -r _ 2>/dev/null | md5sum`; \
-	    test "$$a" = "$$b" || echo $<: Fail round-trip for $$base with level $$level; \
-	    if [ -e ${CBIN}/fqzcomp_qual ]; \
-	    then \
-	      a=`${CBIN}/fqzcomp_qual -d -r < _ 2>/dev/null | tr '\000' '\012' | md5sum`; \
-	      test "$$a" = "$$b" || echo $<: Fail JS to C round-trip for $$base; \
-	    fi; \
-	done
-
-test_tok3:
-	@echo
-	@echo === Checking tok3
-	@if [ ! -e ${CBIN}/tokenise_name3 ]; then echo "Set CBIN if you wish to validate against C version"; fi
-	@for base in ${CORPUS}/names/*.names; do \
-	    echo -n "$$base  	";\
-	    ${NODE} ${NODE_OPTS} main_tok3.js -a -r $$base 2>/dev/null > _; \
-	    a=`${NODE} ${NODE_OPTS} main_tok3 -d -r _ 2>/dev/null | md5sum`; \
-	    cat _ | wc -c;\
-	    b=`cat $$base | md5sum`; \
-	    test "$$a" = "$$b" || echo $<: Fail round-trip for $$base; \
-	    if [ -e ${CBIN}/tokenise_name3 ]; \
-	    then \
-	      a=`${CBIN}/tokenise_name3 -d -r < _ | tr '\000' '\012' | md5sum`; \
-	      test "$$a" = "$$b" || echo $<: Fail JS to C round-trip for $$base; \
-	    fi; \
-	done;
-	@for i in ${CORPUS}/names/tok3/*; do \
-	   echo $$i;\
-	    base=`echo $$i | sed 's/\.[0-9]*$$//;s#/tok3##'`; \
-	    level=`echo $$i | sed 's/.*\.//'`;\
-	    # Decode predefined data set\
-	    a=`${NODE} ${NODE_OPTS} main_tok3 -d -r $$i 2>/dev/null | md5sum`; \
-	    b=`cat $$base | md5sum`; \
-	    test "$$a" = "$$b" || echo $<: Mismatch for $$i; \
-	done;