hts-sys 2.2.0

This library provides HTSlib bindings.
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77

/*
 * 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) {
    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,
};