# Uploaded samtools version 0.1.14-1.
[samtools.git] / bam_rmdup.c
1 #include <stdlib.h>
2 #include <string.h>
3 #include <stdio.h>
4 #include <zlib.h>
5 #include <unistd.h>
6 #include "sam.h"
7
8 typedef bam1_t *bam1_p;
9
10 #include "khash.h"
11 KHASH_SET_INIT_STR(name)
12 KHASH_MAP_INIT_INT64(pos, bam1_p)
13
14 #define BUFFER_SIZE 0x40000
15
16 typedef struct {
17         uint64_t n_checked, n_removed;
18         khash_t(pos) *best_hash;
19 } lib_aux_t;
20 KHASH_MAP_INIT_STR(lib, lib_aux_t)
21
22 typedef struct {
23         int n, max;
24         bam1_t **a;
25 } tmp_stack_t;
26
27 static inline void stack_insert(tmp_stack_t *stack, bam1_t *b)
28 {
29         if (stack->n == stack->max) {
30                 stack->max = stack->max? stack->max<<1 : 0x10000;
31                 stack->a = (bam1_t**)realloc(stack->a, sizeof(bam1_t*) * stack->max);
32         }
33         stack->a[stack->n++] = b;
34 }
35
36 static inline void dump_best(tmp_stack_t *stack, samfile_t *out)
37 {
38         int i;
39         for (i = 0; i != stack->n; ++i) {
40                 samwrite(out, stack->a[i]);
41                 bam_destroy1(stack->a[i]);
42         }
43         stack->n = 0;
44 }
45
46 static void clear_del_set(khash_t(name) *del_set)
47 {
48         khint_t k;
49         for (k = kh_begin(del_set); k < kh_end(del_set); ++k)
50                 if (kh_exist(del_set, k))
51                         free((char*)kh_key(del_set, k));
52         kh_clear(name, del_set);
53 }
54
55 static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
56 {
57         khint_t k = kh_get(lib, aux, lib);
58         if (k == kh_end(aux)) {
59                 int ret;
60                 char *p = strdup(lib);
61                 lib_aux_t *q;
62                 k = kh_put(lib, aux, p, &ret);
63                 q = &kh_val(aux, k);
64                 q->n_checked = q->n_removed = 0;
65                 q->best_hash = kh_init(pos);
66                 return q;
67         } else return &kh_val(aux, k);
68 }
69
70 static void clear_best(khash_t(lib) *aux, int max)
71 {
72         khint_t k;
73         for (k = kh_begin(aux); k != kh_end(aux); ++k) {
74                 if (kh_exist(aux, k)) {
75                         lib_aux_t *q = &kh_val(aux, k);
76                         if (kh_size(q->best_hash) >= max)
77                                 kh_clear(pos, q->best_hash);
78                 }
79         }
80 }
81
82 static inline int sum_qual(const bam1_t *b)
83 {
84         int i, q;
85         uint8_t *qual = bam1_qual(b);
86         for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
87         return q;
88 }
89
90 void bam_rmdup_core(samfile_t *in, samfile_t *out)
91 {
92         bam1_t *b;
93         int last_tid = -1, last_pos = -1;
94         tmp_stack_t stack;
95         khint_t k;
96         khash_t(lib) *aux;
97         khash_t(name) *del_set;
98         
99         aux = kh_init(lib);
100         del_set = kh_init(name);
101         b = bam_init1();
102         memset(&stack, 0, sizeof(tmp_stack_t));
103
104         kh_resize(name, del_set, 4 * BUFFER_SIZE);
105         while (samread(in, b) >= 0) {
106                 bam1_core_t *c = &b->core;
107                 if (c->tid != last_tid || last_pos != c->pos) {
108                         dump_best(&stack, out); // write the result
109                         clear_best(aux, BUFFER_SIZE);
110                         if (c->tid != last_tid) {
111                                 clear_best(aux, 0);
112                                 if (kh_size(del_set)) { // check
113                                         fprintf(stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set));
114                                         clear_del_set(del_set);
115                                 }
116                                 if ((int)c->tid == -1) { // append unmapped reads
117                                         samwrite(out, b);
118                                         while (samread(in, b) >= 0) samwrite(out, b);
119                                         break;
120                                 }
121                                 last_tid = c->tid;
122                                 fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", in->header->target_name[c->tid]);
123                         }
124                 }
125                 if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) {
126                         samwrite(out, b);
127                 } else if (c->isize > 0) { // paired, head
128                         uint64_t key = (uint64_t)c->pos<<32 | c->isize;
129                         const char *lib;
130                         lib_aux_t *q;
131                         int ret;
132                         lib = bam_get_library(in->header, b);
133                         q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
134                         ++q->n_checked;
135                         k = kh_put(pos, q->best_hash, key, &ret);
136                         if (ret == 0) { // found in best_hash
137                                 bam1_t *p = kh_val(q->best_hash, k);
138                                 ++q->n_removed;
139                                 if (sum_qual(p) < sum_qual(b)) { // the current alignment is better; this can be accelerated in principle
140                                         kh_put(name, del_set, strdup(bam1_qname(p)), &ret); // p will be removed
141                                         bam_copy1(p, b); // replaced as b
142                                 } else kh_put(name, del_set, strdup(bam1_qname(b)), &ret); // b will be removed
143                                 if (ret == 0)
144                                         fprintf(stderr, "[bam_rmdup_core] inconsistent BAM file for pair '%s'. Continue anyway.\n", bam1_qname(b));
145                         } else { // not found in best_hash
146                                 kh_val(q->best_hash, k) = bam_dup1(b);
147                                 stack_insert(&stack, kh_val(q->best_hash, k));
148                         }
149                 } else { // paired, tail
150                         k = kh_get(name, del_set, bam1_qname(b));
151                         if (k != kh_end(del_set)) {
152                                 free((char*)kh_key(del_set, k));
153                                 kh_del(name, del_set, k);
154                         } else samwrite(out, b);
155                 }
156                 last_pos = c->pos;
157         }
158
159         for (k = kh_begin(aux); k != kh_end(aux); ++k) {
160                 if (kh_exist(aux, k)) {
161                         lib_aux_t *q = &kh_val(aux, k);                 
162                         dump_best(&stack, out);
163                         fprintf(stderr, "[bam_rmdup_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
164                                         (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
165                         kh_destroy(pos, q->best_hash);
166                         free((char*)kh_key(aux, k));
167                 }
168         }
169         kh_destroy(lib, aux);
170
171         clear_del_set(del_set);
172         kh_destroy(name, del_set);
173         free(stack.a);
174         bam_destroy1(b);
175 }
176
177 void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se);
178
179 int bam_rmdup(int argc, char *argv[])
180 {
181         int c, is_se = 0, force_se = 0;
182         samfile_t *in, *out;
183         while ((c = getopt(argc, argv, "sS")) >= 0) {
184                 switch (c) {
185                 case 's': is_se = 1; break;
186                 case 'S': force_se = is_se = 1; break;
187                 }
188         }
189         if (optind + 2 > argc) {
190                 fprintf(stderr, "\n");
191                 fprintf(stderr, "Usage:  samtools rmdup [-sS] <input.srt.bam> <output.bam>\n\n");
192                 fprintf(stderr, "Option: -s    rmdup for SE reads\n");
193                 fprintf(stderr, "        -S    treat PE reads as SE in rmdup (force -s)\n\n");
194                 return 1;
195         }
196         in = samopen(argv[optind], "rb", 0);
197         out = samopen(argv[optind+1], "wb", in->header);
198         if (in == 0 || out == 0) {
199                 fprintf(stderr, "[bam_rmdup] fail to read/write input files\n");
200                 return 1;
201         }
202         if (is_se) bam_rmdupse_core(in, out, force_se);
203         else bam_rmdup_core(in, out);
204         samclose(in); samclose(out);
205         return 0;
206 }