0
|
1 /* test/fieldarith.c -- CIGAR field arithmetic test suite.
|
|
2
|
|
3 Copyright (C) 2013 Genome Research Ltd.
|
|
4
|
|
5 Author: John Marshall <jm18@sanger.ac.uk>
|
|
6
|
|
7 Permission is hereby granted, free of charge, to any person obtaining a copy
|
|
8 of this software and associated documentation files (the "Software"), to deal
|
|
9 in the Software without restriction, including without limitation the rights
|
|
10 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
|
11 copies of the Software, and to permit persons to whom the Software is
|
|
12 furnished to do so, subject to the following conditions:
|
|
13
|
|
14 The above copyright notice and this permission notice shall be included in
|
|
15 all copies or substantial portions of the Software.
|
|
16
|
|
17 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
|
18 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
|
19 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
|
|
20 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
|
21 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
|
22 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
|
|
23 DEALINGS IN THE SOFTWARE. */
|
|
24
|
|
25 #include <stdio.h>
|
|
26
|
|
27 #include "htslib/sam.h"
|
|
28
|
|
29 int ntests = 0;
|
|
30 int nfailures = 0;
|
|
31
|
|
32 void check(const bam1_t *aln, const char *testname, const char *tag, int value)
|
|
33 {
|
|
34 int32_t refvalue;
|
|
35 uint8_t *aux = bam_aux_get(aln, tag);
|
|
36 if (!aux) return;
|
|
37 ntests++;
|
|
38 refvalue = bam_aux2i(aux);
|
|
39 if (value != refvalue) {
|
|
40 fprintf(stderr, "%s FAIL for %s: computed %d != %d expected\n",
|
|
41 testname, bam_get_qname(aln), value, refvalue);
|
|
42 nfailures++;
|
|
43 }
|
|
44 }
|
|
45
|
|
46 int main(int argc, char **argv)
|
|
47 {
|
|
48 bam_hdr_t *header;
|
|
49 bam1_t *aln = bam_init1();
|
|
50 int i;
|
|
51
|
|
52 for (i = 1; i < argc; i++) {
|
|
53 samFile *in = sam_open(argv[i], "r");
|
|
54 if (in == NULL) { perror(argv[1]); return 1; }
|
|
55
|
|
56 header = sam_hdr_read(in);
|
|
57 while (sam_read1(in, header, aln) >= 0) {
|
|
58 check(aln, "cigar2qlen", "XQ",
|
|
59 bam_cigar2qlen(aln->core.n_cigar, bam_get_cigar(aln)));
|
|
60 check(aln, "cigar2rlen", "XR",
|
|
61 bam_cigar2rlen(aln->core.n_cigar, bam_get_cigar(aln)));
|
|
62 check(aln, "endpos", "XE", bam_endpos(aln));
|
|
63 }
|
|
64
|
|
65 bam_hdr_destroy(header);
|
|
66 sam_close(in);
|
|
67 }
|
|
68
|
|
69 bam_destroy1(aln);
|
|
70
|
|
71 return (nfailures > 0);
|
|
72 }
|