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comparison PsiCLASS-1.0.2/samtools-0.1.19/bam_rmdup.c @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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-1:000000000000 0:903fc43d6227
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 }