@gmod/cram 3.0.6 → 3.0.7

package/dist/htscodecs/main_rans.js

@@ -0,0 +1,83 @@
+"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

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

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

package/dist/htscodecs/main_rans4x16.js

@@ -0,0 +1,82 @@
+"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

@@ -0,0 +1 @@
+{"version":3,"file":"main_rans4x16.js","sourceRoot":"","sources":["../../src/htscodecs/main_rans4x16.js"],"names":[],"mappings":";AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,IAAI,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAAA;AACtB,IAAI,IAAI,GAAG,OAAO,CAAC,YAAY,CAAC,CAAA;AAChC,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,QAAQ,CAAC,MAAM,CAAC,KAAK,CACnB,yEAAyE,CAC1E,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,qBAAqB;IACrB,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,GAAG,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,GAAG,GAAG,CAAA;IACtD,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,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,GAAG,CAAC,CAAA;IAC5B,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,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/dist/htscodecs/main_tok3.d.ts

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

package/dist/htscodecs/main_tok3.js

@@ -0,0 +1,84 @@
+"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

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

@@ -0,0 +1,2 @@
+export function decode(src: any): any;
+export function encode(src: any, order: any): Buffer;