@gmod/cram 3.0.6 → 3.0.7

package/dist/htscodecs/fqzcomp.js.map

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

@@ -0,0 +1,5 @@
+export function r4x8_uncompress(inputBuffer: any, outputBuffer: any): void;
+export function r4x16_uncompress(inputBuffer: any, outputBuffer: any): void;
+export function arith_uncompress(inputBuffer: any, outputBuffer: any): any;
+export function fqzcomp_uncompress(inputBuffer: any, outputBuffer: any): void;
+export function tok3_uncompress(inputBuffer: any, outputBuffer: any): void;

package/dist/htscodecs/index.js

@@ -0,0 +1,70 @@
+/*
+ * Copyright (c) 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.
+ */
+// This is an interface to the htscodecs reference implementation of
+// the CRAM 3.1 codecs.
+// This JavaScript file is not part of the reference implementation
+// and is simply and interface to get a consistent interface for cram-js.
+'use strict';
+var r4x8 = require('./rans');
+var r4x16 = require('./rans4x16');
+var arith = require('./arith_gen');
+var fqzcomp = require('./fqzcomp');
+var tok3 = require('./tok3');
+function r4x8_uncompress(inputBuffer, outputBuffer) {
+    r4x8.decode(inputBuffer).copy(outputBuffer, 0, 0);
+}
+function r4x16_uncompress(inputBuffer, outputBuffer) {
+    r4x16.decode(inputBuffer).copy(outputBuffer, 0, 0);
+}
+function arith_uncompress(inputBuffer, outputBuffer) {
+    // fix by @cmdcolin for CRAM 3.1
+    // xref https://github.com/jkbonfield/htscodecs/pull/1/files
+    return new arith().decode(inputBuffer).copy(outputBuffer, 0, 0);
+}
+function fqzcomp_uncompress(inputBuffer, outputBuffer) {
+    var q_lens = new Array();
+    fqzcomp.decode(inputBuffer, q_lens).copy(outputBuffer, 0, 0);
+}
+function tok3_uncompress(inputBuffer, outputBuffer) {
+    // Returns in string form instead of buffer
+    var out = tok3.decode(inputBuffer, 0, '\0');
+    Buffer.from(out, 'binary').copy(outputBuffer, 0, 0);
+}
+module.exports = {
+    r4x8_uncompress: r4x8_uncompress,
+    r4x16_uncompress: r4x16_uncompress,
+    arith_uncompress: arith_uncompress,
+    fqzcomp_uncompress: fqzcomp_uncompress,
+    tok3_uncompress: tok3_uncompress,
+};
+//# sourceMappingURL=index.js.map

package/dist/htscodecs/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/htscodecs/index.js"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,oEAAoE;AACpE,uBAAuB;AAEvB,mEAAmE;AACnE,yEAAyE;AAEzE,YAAY,CAAA;AAEZ,IAAI,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAA;AAC5B,IAAI,KAAK,GAAG,OAAO,CAAC,YAAY,CAAC,CAAA;AACjC,IAAI,KAAK,GAAG,OAAO,CAAC,aAAa,CAAC,CAAA;AAClC,IAAI,OAAO,GAAG,OAAO,CAAC,WAAW,CAAC,CAAA;AAClC,IAAI,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAA;AAE5B,SAAS,eAAe,CAAC,WAAW,EAAE,YAAY;IAChD,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;AACnD,CAAC;AAED,SAAS,gBAAgB,CAAC,WAAW,EAAE,YAAY;IACjD,KAAK,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;AACpD,CAAC;AAED,SAAS,gBAAgB,CAAC,WAAW,EAAE,YAAY;IACjD,gCAAgC;IAChC,4DAA4D;IAC5D,OAAO,IAAI,KAAK,EAAE,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;AACjE,CAAC;AAED,SAAS,kBAAkB,CAAC,WAAW,EAAE,YAAY;IACnD,IAAI,MAAM,GAAG,IAAI,KAAK,EAAE,CAAA;IACxB,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;AAC9D,CAAC;AAED,SAAS,eAAe,CAAC,WAAW,EAAE,YAAY;IAChD,2CAA2C;IAC3C,IAAI,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAC3C,MAAM,CAAC,IAAI,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;AACrD,CAAC;AAED,MAAM,CAAC,OAAO,GAAG;IACf,eAAe,EAAE,eAAe;IAChC,gBAAgB,EAAE,gBAAgB;IAClC,gBAAgB,EAAE,gBAAgB;IAClC,kBAAkB,EAAE,kBAAkB;IACtC,eAAe,EAAE,eAAe;CACjC,CAAA"}

package/dist/htscodecs/iostream.d.ts

@@ -0,0 +1,26 @@
+export = IOStream;
+declare class IOStream {
+    constructor(buf: any, start_pos?: number, size?: number);
+    buf: any;
+    length: any;
+    pos: number;
+    EOF(): boolean;
+    ReadData(len: any): any;
+    ReadByte(): any;
+    ReadChar(): string;
+    ReadUint16(): any;
+    ReadUint32(): any;
+    ReadString(): string;
+    ReadUint7(): number;
+    ReadITF8(): any;
+    WriteByte(b: any): void;
+    WriteChar(b: any): void;
+    WriteString(str: any): void;
+    WriteData(buf: any, len: any): void;
+    WriteStream(stream: any): void;
+    WriteUint16(u: any): void;
+    WriteUint32(u: any): void;
+    WriteUint7(i: any): void;
+    WriteITF8(i: any): void;
+    WriteByteNeg(b: any): void;
+}

package/dist/htscodecs/iostream.js

@@ -0,0 +1,242 @@
+"use strict";
+/*
+ * Copyright (c) 2019 Genome Research Ltd.
+ * Author(s): James Bonfield
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ *    1. Redistributions of source code must retain the above copyright notice,
+ *       this list of conditions and the following disclaimer.
+ *
+ *    2. Redistributions in binary form must reproduce the above
+ *       copyright notice, this list of conditions and the following
+ *       disclaimer in the documentation and/or other materials provided
+ *       with the distribution.
+ *
+ *    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+ *       Institute nor the names of its contributors may be used to endorse
+ *       or promote products derived from this software without specific
+ *       prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
+ * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+// Turn a buffer into a fake stream with get / put commands.
+// This enables up to closely match the published pseudocode.
+module.exports = class IOStream {
+    constructor(buf, start_pos = 0, size = 0) {
+        if (size != 0) {
+            this.buf = Buffer.allocUnsafe(size);
+            this.length = size;
+        }
+        else {
+            this.buf = buf;
+            this.length = buf.length;
+        }
+        this.pos = start_pos;
+    }
+    // ----------
+    // Reading
+    EOF() {
+        return this.pos >= this.length;
+    }
+    ReadData(len) {
+        var A = this.buf.slice(this.pos, this.pos + len);
+        this.pos += len;
+        return A;
+    }
+    ReadByte() {
+        const b = this.buf[this.pos];
+        this.pos++;
+        return b;
+    }
+    ReadChar() {
+        const b = this.buf[this.pos];
+        this.pos++;
+        return String.fromCharCode(b);
+    }
+    ReadUint16() {
+        var i = this.ReadByte();
+        i |= this.ReadByte() << 8;
+        return i;
+    }
+    ReadUint32() {
+        const i = this.buf.readInt32LE(this.pos);
+        this.pos += 4;
+        return i;
+    }
+    // nul terminated string
+    ReadString() {
+        var s = '';
+        do {
+            var b = this.buf[this.pos++];
+            if (b)
+                s += String.fromCharCode(b);
+        } while (b);
+        return s;
+    }
+    //    ReadUint7() {
+    //	// Variable sized unsigned integers
+    //	var i = 0;
+    //	var s = 0;
+    //	do {
+    //	    var c = this.ReadByte();
+    //	    i = i | ((c & 0x7f)<<s);
+    //	    s += 7;
+    //	} while ((c & 0x80))
+    //
+    //	return i;
+    //    }
+    ReadUint7() {
+        // Variable sized unsigned integers
+        var i = 0;
+        do {
+            var c = this.ReadByte();
+            i = (i << 7) | (c & 0x7f);
+        } while (c & 0x80);
+        return i;
+    }
+    ReadITF8() {
+        var i = this.buf[this.pos];
+        this.pos++;
+        //process.stderr.write("i="+i+"\n");
+        if (i >= 0xf0) {
+            // 1111xxxx => +4 bytes
+            i = (i & 0x0f) << 28;
+            i +=
+                (this.buf[this.pos + 0] << 20) +
+                    (this.buf[this.pos + 1] << 12) +
+                    (this.buf[this.pos + 2] << 4) +
+                    (this.buf[this.pos + 3] >> 4);
+            this.pos += 4;
+            //process.stderr.write("  4i="+i+"\n");
+        }
+        else if (i >= 0xe0) {
+            // 1110xxxx => +3 bytes
+            i = (i & 0x0f) << 24;
+            i +=
+                (this.buf[this.pos + 0] << 16) +
+                    (this.buf[this.pos + 1] << 8) +
+                    (this.buf[this.pos + 2] << 0);
+            this.pos += 3;
+            //process.stderr.write("  3i="+i+"\n");
+        }
+        else if (i >= 0xc0) {
+            // 110xxxxx => +2 bytes
+            i = (i & 0x1f) << 16;
+            i += (this.buf[this.pos + 0] << 8) + (this.buf[this.pos + 1] << 0);
+            this.pos += 2;
+            //process.stderr.write("  2i="+i+"\n");
+        }
+        else if (i >= 0x80) {
+            // 10xxxxxx => +1 bytes
+            i = (i & 0x3f) << 8;
+            i += this.buf[this.pos];
+            this.pos++;
+            //process.stderr.write("  1i="+i+"\n");
+        }
+        else {
+            // 0xxxxxxx => +0 bytes
+        }
+        return i;
+    }
+    // ----------
+    // Writing
+    WriteByte(b) {
+        this.buf[this.pos++] = b;
+    }
+    WriteChar(b) {
+        this.buf[this.pos++] = b.charCodeAt(0);
+    }
+    WriteString(str) {
+        for (var i = 0; i < str.length; i++)
+            this.buf[this.pos++] = str.charCodeAt(i);
+        this.buf[this.pos++] = 0;
+    }
+    WriteData(buf, len) {
+        for (var i = 0; i < len; i++)
+            this.buf[this.pos++] = buf[i];
+    }
+    WriteStream(stream) {
+        this.WriteData(stream.buf, stream.pos);
+    }
+    WriteUint16(u) {
+        //this.buf.writeInt16LE(u, this.pos);
+        this.WriteByte(u & 0xff);
+        this.WriteByte((u >> 8) & 0xff);
+    }
+    WriteUint32(u) {
+        this.buf.writeInt32LE(u, this.pos);
+        this.pos += 4;
+    }
+    //    WriteUint7(i) {
+    //	do {
+    //	    this.WriteByte((i & 0x7f) | ((i > 0x80) << 7));
+    //	    i >>= 7;
+    //	} while (i > 0);
+    //    }
+    WriteUint7(i) {
+        var s = 0;
+        var X = i;
+        do {
+            s += 7;
+            X >>= 7;
+        } while (X > 0);
+        do {
+            s -= 7;
+            this.WriteByte(((i >> s) & 0x7f) + ((s > 0) << 7));
+        } while (s > 0);
+    }
+    WriteITF8(i) {
+        // Horrid, ITF8 is unsigned, but we still write signed into it
+        if (i < 0)
+            i = (1 << 32) + i;
+        if (i <= 0x0000007f) {
+            // 1 byte
+            this.buf[this.pos++] = i;
+        }
+        else if (i <= 0x00003fff) {
+            // 2 bytes
+            this.buf[this.pos++] = 0x80 | Math.floor(i / 256);
+            this.buf[this.pos++] = i & 0xff;
+        }
+        else if (i < 0x0001ffff) {
+            // 3 bytes
+            this.buf[this.pos++] = 0xc0 | Math.floor(i / 65536);
+            this.buf[this.pos++] = Math.floor(i / 256) & 0xff;
+            this.buf[this.pos++] = i & 0xff;
+        }
+        else if (i < 0x0fffffff) {
+            // 4 bytes
+            this.buf[this.pos++] = 0xe0 | Math.floor(i / 16777216);
+            this.buf[this.pos++] = Math.floor(i / 65536) & 0xff;
+            this.buf[this.pos++] = Math.floor(i / 256) & 0xff;
+            this.buf[this.pos++] = i & 0xff;
+        }
+        else {
+            // 5 bytes; oddly using 4.5 bytes
+            this.buf[this.pos++] = 0xf0 | Math.floor(i / 268435456);
+            this.buf[this.pos++] = Math.floor(i / 1048576) & 0xff;
+            this.buf[this.pos++] = Math.floor(i / 4096) & 0xff;
+            this.buf[this.pos++] = Math.floor(i / 4) & 0xff;
+            this.buf[this.pos++] = i & 0x0f;
+        }
+    }
+    // ----------
+    // Writing from end of buffer going backwards.
+    // Needed by rANS codec.
+    WriteByteNeg(b) {
+        this.buf[--this.pos] = b;
+    }
+};
+//# sourceMappingURL=iostream.js.map

package/dist/htscodecs/iostream.js.map

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

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

package/dist/htscodecs/main_arith_gen.js

@@ -0,0 +1,86 @@
+"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

@@ -0,0 +1 @@
+{"version":3,"file":"main_arith_gen.js","sourceRoot":"","sources":["../../src/htscodecs/main_arith_gen.js"],"names":[],"mappings":";AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,4DAA4D;AAE5D,IAAI,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAAA;AACtB,IAAI,aAAa,GAAG,OAAO,CAAC,aAAa,CAAC,CAAA;AAE1C,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,0EAA0E,CAC3E,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,KAAK,GAAG,IAAI,aAAa,EAAE,CAAA;AAC/B,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,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,EAAE,GAAG,GAAG,QAAQ,CAAC,EAAE,KAAK,CAAC,CAAA;QAE9D,sDAAsD;QACtD,IAAI,KAAK,GAAG,IAAI,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACrC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC,CAAA;YAClC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;QAC7B,CAAC;QAED,iCAAiC;QACjC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAE1B,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,GAAG,GAAG,GAAG,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;YAC1B,GAAG,IAAI,CAAC,CAAA;QACV,CAAC;QACD,IAAI,IAAI,GAAG,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,EAAE,GAAG,GAAG,GAAG,CAAC,CAAC,CAAA;QAClD,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_fqzcomp.d.ts

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

package/dist/htscodecs/main_fqzcomp.js

@@ -0,0 +1,112 @@
+"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

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

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