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