c_cpp/lib/htslib/test/test_view.c

   1 /*  test/test_view.c -- simple view tool, purely for use in a test harness.
   2
   3     Copyright (C) 2012 Broad Institute.
   4     Copyright (C) 2013-2014 Genome Research Ltd.
   5
   6     Author: Heng Li <lh3@sanger.ac.uk>
   7
   8 Permission is hereby granted, free of charge, to any person obtaining a copy
   9 of this software and associated documentation files (the "Software"), to deal
  10 in the Software without restriction, including without limitation the rights
  11 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  12 copies of the Software, and to permit persons to whom the Software is
  13 furnished to do so, subject to the following conditions:
  14
  15 The above copyright notice and this permission notice shall be included in
  16 all copies or substantial portions of the Software.
  17
  18 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  19 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  20 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
  21 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  22 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  23 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  24 DEALINGS IN THE SOFTWARE.  */
  25
  26 #include <config.h>
  27
  28 #include <stdio.h>
  29 #include <unistd.h>
  30 #include <stdlib.h>
  31 #include <string.h>
  32 #include <getopt.h>
  33
  34 #include "cram/cram.h"
  35
  36 #include "htslib/sam.h"
  37
  38 int main(int argc, char *argv[])
  39 {
  40     samFile *in;
  41     char *fn_ref = 0;
  42     int flag = 0, c, clevel = -1, ignore_sam_err = 0;
  43     char moder[8];
  44     bam_hdr_t *h;
  45     bam1_t *b;
  46     htsFile *out;
  47     char modew[800];
  48     int r = 0, exit_code = 0;
  49     hts_opt *in_opts = NULL, *out_opts = NULL;
  50     int nreads = 0;
  51     int extra_hdr_nuls = 0;
  52     int benchmark = 0;
  53     int nthreads = 0; // shared pool
  54
  55     while ((c = getopt(argc, argv, "IbDCSl:t:i:o:N:BZ:@:")) >= 0) {
  56         switch (c) {
  57         case 'S': flag |= 1; break;
  58         case 'b': flag |= 2; break;
  59         case 'D': flag |= 4; break;
  60         case 'C': flag |= 8; break;
  61         case 'B': benchmark = 1; break;
  62         case 'l': clevel = atoi(optarg); flag |= 2; break;
  63         case 't': fn_ref = optarg; break;
  64         case 'I': ignore_sam_err = 1; break;
  65         case 'i': if (hts_opt_add(&in_opts,  optarg)) return 1; break;
  66         case 'o': if (hts_opt_add(&out_opts, optarg)) return 1; break;
  67         case 'N': nreads = atoi(optarg); break;
  68         case 'Z': extra_hdr_nuls = atoi(optarg); break;
  69         case '@': nthreads = atoi(optarg); break;
  70         }
  71     }
  72     if (argc == optind) {
  73         fprintf(stderr, "Usage: samview [-bSCSIB] [-N num_reads] [-l level] [-o option=value] [-Z hdr_nuls] <in.bam>|<in.sam>|<in.cram> [region]\n");
  74         return 1;
  75     }
  76     strcpy(moder, "r");
  77     if (flag&4) strcat(moder, "c");
  78     else if ((flag&1) == 0) strcat(moder, "b");
  79
  80     in = sam_open(argv[optind], moder);
  81     if (in == NULL) {
  82         fprintf(stderr, "Error opening \"%s\"\n", argv[optind]);
  83         return EXIT_FAILURE;
  84     }
  85     h = sam_hdr_read(in);
  86     if (h == NULL) {
  87         fprintf(stderr, "Couldn't read header for \"%s\"\n", argv[optind]);
  88         return EXIT_FAILURE;
  89     }
  90     h->ignore_sam_err = ignore_sam_err;
  91     if (extra_hdr_nuls) {
  92         char *new_text = realloc(h->text, h->l_text + extra_hdr_nuls);
  93         if (new_text == NULL) {
  94             fprintf(stderr, "Error reallocing header text\n");
  95             return EXIT_FAILURE;
  96         }
  97         h->text = new_text;
  98         memset(&h->text[h->l_text], 0, extra_hdr_nuls);
  99         h->l_text += extra_hdr_nuls;
 100     }
 101
 102     b = bam_init1();
 103
 104     strcpy(modew, "w");
 105     if (clevel >= 0 && clevel <= 9) sprintf(modew + 1, "%d", clevel);
 106     if (flag&8) strcat(modew, "c");
 107     else if (flag&2) strcat(modew, "b");
 108     out = hts_open("-", modew);
 109     if (out == NULL) {
 110         fprintf(stderr, "Error opening standard output\n");
 111         return EXIT_FAILURE;
 112     }
 113
 114     /* CRAM output */
 115     if (flag & 8) {
 116         int ret;
 117
 118         // Parse input header and use for CRAM output
 119         out->fp.cram->header = sam_hdr_parse_(h->text, h->l_text);
 120
 121         // Create CRAM references arrays
 122         if (fn_ref)
 123             ret = cram_set_option(out->fp.cram, CRAM_OPT_REFERENCE, fn_ref);
 124         else
 125             // Attempt to fill out a cram->refs[] array from @SQ headers
 126             ret = cram_set_option(out->fp.cram, CRAM_OPT_REFERENCE, NULL);
 127
 128         if (ret != 0)
 129             return EXIT_FAILURE;
 130     }
 131
 132     // Process any options; currently cram only.
 133     if (hts_opt_apply(in, in_opts))
 134         return EXIT_FAILURE;
 135     hts_opt_free(in_opts);
 136
 137     if (hts_opt_apply(out, out_opts))
 138         return EXIT_FAILURE;
 139     hts_opt_free(out_opts);
 140
 141     // Create and share the thread pool
 142     htsThreadPool p = {NULL, 0};
 143     if (nthreads > 0) {
 144         p.pool = hts_tpool_init(nthreads);
 145         if (!p.pool) {
 146             fprintf(stderr, "Error creating thread pool\n");
 147             exit_code = 1;
 148         } else {
 149             hts_set_opt(in,  HTS_OPT_THREAD_POOL, &p);
 150             hts_set_opt(out, HTS_OPT_THREAD_POOL, &p);
 151         }
 152     }
 153
 154     if (!benchmark && sam_hdr_write(out, h) < 0) {
 155         fprintf(stderr, "Error writing output header.\n");
 156         exit_code = 1;
 157     }
 158     if (optind + 1 < argc && !(flag&1)) { // BAM input and has a region
 159         int i;
 160         hts_idx_t *idx;
 161         if ((idx = sam_index_load(in, argv[optind])) == 0) {
 162             fprintf(stderr, "[E::%s] fail to load the BAM index\n", __func__);
 163             return 1;
 164         }
 165         for (i = optind + 1; i < argc; ++i) {
 166             hts_itr_t *iter;
 167             if ((iter = sam_itr_querys(idx, h, argv[i])) == 0) {
 168                 fprintf(stderr, "[E::%s] fail to parse region '%s'\n", __func__, argv[i]);
 169                 continue;
 170             }
 171             while ((r = sam_itr_next(in, iter, b)) >= 0) {
 172                 if (!benchmark && sam_write1(out, h, b) < 0) {
 173                     fprintf(stderr, "Error writing output.\n");
 174                     exit_code = 1;
 175                     break;
 176                 }
 177                 if (nreads && --nreads == 0)
 178                     break;
 179             }
 180             hts_itr_destroy(iter);
 181         }
 182         hts_idx_destroy(idx);
 183     } else while ((r = sam_read1(in, h, b)) >= 0) {
 184         if (!benchmark && sam_write1(out, h, b) < 0) {
 185             fprintf(stderr, "Error writing output.\n");
 186             exit_code = 1;
 187             break;
 188         }
 189         if (nreads && --nreads == 0)
 190             break;
 191     }
 192
 193     if (r < -1) {
 194         fprintf(stderr, "Error parsing input.\n");
 195         exit_code = 1;
 196     }
 197
 198     r = sam_close(out);
 199     if (r < 0) {
 200         fprintf(stderr, "Error closing output.\n");
 201         exit_code = 1;
 202     }
 203
 204     bam_destroy1(b);
 205     bam_hdr_destroy(h);
 206
 207     r = sam_close(in);
 208     if (r < 0) {
 209         fprintf(stderr, "Error closing input.\n");
 210         exit_code = 1;
 211     }
 212
 213     if (p.pool)
 214         hts_tpool_destroy(p.pool);
 215
 216     return exit_code;
 217 }