1 /*  test/pileup.c -- simple pileup tester
2 
3     Copyright (C) 2014,2018-2019 Genome Research Ltd.
4 
5     Author: James Bonfield <jkb@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 /*
26   The output from this program isn't quite the same as that from
27   `samtools mpileup`.  It doesn't print the reference base column,
28   it puts brackets around insertion sequences to make them easier to spot
29   and it writes empty brackets after a reported deletion.
30 
31   The output from `samtools mpileup` can be converted to the same format like
32   this:
33 
34 samtools mpileup -B -Q 0 in.bam | perl -lane \
35   'pop(@F);
36    splice(@F, 2, 1);
37    $F[3] =~ s/\+(\d+)([ACGTN]+)/sprintf("+%d(%s)%s",$1,substr($2,0,$1),substr($2,$1))/ieg;
38    $F[3] =~ s/\-(\d+)([ACGTN]+)/sprintf("-%d()%s",$1,substr($2,$1))/ieg;
39    print join("\t", @F);'
40 
41  */
42 
43 #include <config.h>
44 
45 #include <stdio.h>
46 #include <string.h>
47 #include <errno.h>
48 #include <ctype.h>
49 #include <unistd.h>
50 
51 #include "../htslib/sam.h"
52 #include "../htslib/kstring.h"
53 
54 #define MIN(a,b) ((a)<(b)?(a):(b))
55 
56 typedef struct ptest_t {
57     const char *fname;
58     samFile *fp;
59     sam_hdr_t *fp_hdr;
60 } ptest_t;
61 
readaln(void * data,bam1_t * b)62 static int readaln(void *data, bam1_t *b) {
63     ptest_t *g = (ptest_t*)data;
64     int ret;
65 
66     while (1) {
67         ret = sam_read1(g->fp, g->fp_hdr, b);
68         if (ret < 0) break;
69         if ( b->core.flag & (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) ) continue;
70         break;
71     }
72 
73     return ret;
74 }
75 
print_pileup_seq(const bam_pileup1_t * p,int n)76 static int print_pileup_seq(const bam_pileup1_t *p, int n) {
77     kstring_t ks = { 0, 0, NULL };
78     int i;
79 
80     for (i = 0; i < n; i++, p++) {
81         uint8_t *seq = bam_get_seq(p->b);
82         int del_len, is_rev = bam_is_rev(p->b);
83 
84         if (p->is_head)
85             putchar('^'), putchar('!'+MIN(p->b->core.qual,93));
86 
87         if (p->is_del)
88             putchar(p->is_refskip ? (is_rev ? '<' : '>') : '*');
89         else {
90             unsigned char c = seq_nt16_str[bam_seqi(seq, p->qpos)];
91             putchar(is_rev ? tolower(c) : toupper(c));
92         }
93 
94         del_len = -p->indel;
95         if (p->indel > 0) {
96             int j, len = bam_plp_insertion(p, &ks, &del_len);
97             if (len < 0) {
98                 perror("bam_plp_insertion");
99                 goto fail;
100             }
101             printf("%+d(", len);
102             for (j = 0; j < len; j++)
103                 putchar(is_rev ?
104                         tolower((uint8_t) ks.s[j]) :
105                         toupper((uint8_t) ks.s[j]));
106             putchar(')');
107         }
108         if (del_len > 0) {
109             printf("-%d()", del_len);
110         }
111         if (p->is_tail)
112             putchar('$');
113     }
114     free(ks.s);
115     return 0;
116 
117  fail:
118     free(ks.s);
119     return -1;
120 }
121 
test_pileup(ptest_t * input)122 static int test_pileup(ptest_t *input) {
123     bam_plp_t plp = NULL;
124     const bam_pileup1_t *p;
125     int tid, pos, n = 0;
126 
127     plp = bam_plp_init(readaln, input);
128     if (!plp) {
129         perror("bam_plp_init");
130         goto fail;
131     }
132     while ((p = bam_plp_auto(plp, &tid, &pos, &n)) != 0) {
133         if (tid < 0) break;
134         if (tid >= input->fp_hdr->n_targets) {
135             fprintf(stderr,
136                     "bam_plp_auto returned tid %d >= header n_targets %d\n",
137                     tid, input->fp_hdr->n_targets);
138             goto fail;
139         }
140 
141         printf("%s\t%d\t%d\t", input->fp_hdr->target_name[tid], pos+1, n);
142 
143         if (print_pileup_seq(p, n) < 0)
144             goto fail;
145 
146         putchar('\n');
147     }
148     if (n < 0) {
149         fprintf(stderr, "bam_plp_auto failed for \"%s\"\n", input->fname);
150         goto fail;
151     }
152 
153     bam_plp_destroy(plp);
154     return 0;
155 
156  fail:
157     bam_plp_destroy(plp);
158     return -1;
159 }
160 
test_mpileup(ptest_t * input)161 static int test_mpileup(ptest_t *input) {
162     bam_mplp_t iter = NULL;
163     const bam_pileup1_t *pileups[1] = { NULL };
164     int n_plp[1] = { 0 };
165     int tid, pos, n = 0;
166 
167     iter = bam_mplp_init(1, readaln, (void **) &input);
168     if (!iter) {
169         perror("bam_plp_init");
170         goto fail;
171     }
172     if (bam_mplp_init_overlaps(iter) < 0) {
173         perror("bam_mplp_init_overlaps");
174         goto fail;
175     }
176 
177     while ((n = bam_mplp_auto(iter, &tid, &pos, n_plp, pileups)) > 0) {
178         if (tid < 0) break;
179         if (tid >= input->fp_hdr->n_targets) {
180             fprintf(stderr,
181                     "bam_mplp_auto returned tid %d >= header n_targets %d\n",
182                     tid, input->fp_hdr->n_targets);
183             goto fail;
184         }
185 
186         printf("%s\t%d\t%d\t", input->fp_hdr->target_name[tid], pos+1, n_plp[0]);
187 
188         if (print_pileup_seq(pileups[0], n_plp[0]) < 0)
189             goto fail;
190 
191         putchar('\n');
192     }
193     if (n < 0) {
194         fprintf(stderr, "bam_plp_auto failed for \"%s\"\n", input->fname);
195         goto fail;
196     }
197 
198     bam_mplp_destroy(iter);
199     return 0;
200 
201  fail:
202     bam_mplp_destroy(iter);
203     return -1;
204 }
205 
main(int argc,char ** argv)206 int main(int argc, char **argv) {
207     ptest_t g = { NULL, NULL, NULL };
208     int use_mpileup = 0, opt;
209 
210     while ((opt = getopt(argc, argv, "m")) != -1) {
211         switch (opt) {
212         case 'm':
213             use_mpileup = 1;
214             break;
215         default:
216             fprintf(stderr, "Usage: %s [-m] <sorted.sam>\n", argv[0]);
217             return EXIT_FAILURE;
218         }
219     }
220 
221     if (optind >= argc) {
222         fprintf(stderr, "Usage: %s [-m] <sorted.sam>\n", argv[0]);
223         return EXIT_FAILURE;
224     }
225 
226     g.fname = argv[optind];
227     g.fp = sam_open(g.fname, "r");
228     if (!g.fp) {
229         fprintf(stderr, "Couldn't open \"%s\" : %s", g.fname, strerror(errno));
230         goto fail;
231     }
232     g.fp_hdr = sam_hdr_read(g.fp);
233     if (!g.fp_hdr) {
234         fprintf(stderr, "Couldn't read header from \"%s\" : %s",
235                 g.fname, strerror(errno));
236         goto fail;
237     }
238 
239     if (use_mpileup) {
240         if (test_mpileup(&g) < 0)
241             goto fail;
242     } else {
243         if (test_pileup(&g) < 0)
244             goto fail;
245     }
246 
247     sam_hdr_destroy(g.fp_hdr);
248     sam_close(g.fp);
249 
250     return EXIT_SUCCESS;
251 
252  fail:
253     if (g.fp_hdr) sam_hdr_destroy(g.fp_hdr);
254     if (g.fp) sam_close(g.fp);
255     return EXIT_FAILURE;
256 }
257