1 /* sample.c -- group data by sample.
2
3 Copyright (C) 2010, 2011 Broad Institute.
4 Copyright (C) 2013 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 <stdlib.h>
29 #include <string.h>
30 #include "sample.h"
31 #include "htslib/khash.h"
KHASH_MAP_INIT_STR(sm,int)32 KHASH_MAP_INIT_STR(sm, int)
33
34 bam_sample_t *bam_smpl_init(void)
35 {
36 bam_sample_t *s;
37 s = calloc(1, sizeof(bam_sample_t));
38 s->rg2smid = kh_init(sm);
39 s->sm2id = kh_init(sm);
40 return s;
41 }
42
bam_smpl_destroy(bam_sample_t * sm)43 void bam_smpl_destroy(bam_sample_t *sm)
44 {
45 int i;
46 khint_t k;
47 khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
48 if (sm == 0) return;
49 for (i = 0; i < sm->n; ++i) free(sm->smpl[i]);
50 free(sm->smpl);
51 for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k)
52 if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k));
53 kh_destroy(sm, sm->rg2smid);
54 kh_destroy(sm, sm->sm2id);
55 free(sm);
56 }
57
add_pair(bam_sample_t * sm,khash_t (sm)* sm2id,const char * key,const char * val)58 static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val)
59 {
60 khint_t k_rg, k_sm;
61 int ret;
62 khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
63 k_rg = kh_get(sm, rg2smid, key);
64 if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID
65 k_rg = kh_put(sm, rg2smid, strdup(key), &ret);
66 k_sm = kh_get(sm, sm2id, val);
67 if (k_sm == kh_end(sm2id)) { // absent
68 if (sm->n == sm->m) {
69 sm->m = sm->m? sm->m<<1 : 1;
70 sm->smpl = realloc(sm->smpl, sizeof(char*) * sm->m);
71 }
72 sm->smpl[sm->n] = strdup(val);
73 k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret);
74 kh_val(sm2id, k_sm) = sm->n++;
75 }
76 kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm);
77 }
78
bam_smpl_add(bam_sample_t * sm,const char * fn,const char * txt)79 int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
80 {
81 const char *p = txt, *q, *r;
82 kstring_t buf, first_sm;
83 int n = 0;
84 khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id;
85 if (txt == 0) {
86 add_pair(sm, sm2id, fn, fn);
87 return 0;
88 }
89 memset(&buf, 0, sizeof(kstring_t));
90 memset(&first_sm, 0, sizeof(kstring_t));
91 while ((q = strstr(p, "@RG")) != 0) {
92 p = q + 3;
93 r = q = 0;
94 if ((q = strstr(p, "\tID:")) != 0) q += 4;
95 if ((r = strstr(p, "\tSM:")) != 0) r += 4;
96 if (r && q) {
97 char *u, *v;
98 int oq, or;
99 for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
100 for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
101 oq = *u; or = *v; *u = *v = '\0';
102 buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
103 add_pair(sm, sm2id, buf.s, r);
104 if ( !first_sm.s )
105 kputs(r,&first_sm);
106 *u = oq; *v = or;
107 } else break;
108 p = q > r? q : r;
109 ++n;
110 }
111 if (n == 0) add_pair(sm, sm2id, fn, fn);
112 // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but
113 // use the tag instead.
114 else if ( n==1 && first_sm.s )
115 add_pair(sm,sm2id,fn,first_sm.s);
116 if ( first_sm.s )
117 free(first_sm.s);
118
119 // add_pair(sm, sm2id, fn, fn);
120 free(buf.s);
121 return 0;
122 }
123
bam_smpl_rg2smid(const bam_sample_t * sm,const char * fn,const char * rg,kstring_t * str)124 int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str)
125 {
126 khint_t k;
127 khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
128 if (rg) {
129 str->l = 0;
130 kputs(fn, str); kputc('/', str); kputs(rg, str);
131 k = kh_get(sm, rg2smid, str->s);
132 } else k = kh_get(sm, rg2smid, fn);
133 return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k);
134 }
135