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comparison PsiCLASS-1.0.2/samtools-0.1.19/bam_rmdupse.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 <math.h>
2 #include "sam.h"
3 #include "khash.h"
4 #include "klist.h"
5
6 #define QUEUE_CLEAR_SIZE 0x100000
7 #define MAX_POS 0x7fffffff
8
9 typedef struct {
10 int endpos;
11 uint32_t score:31, discarded:1;
12 bam1_t *b;
13 } elem_t, *elem_p;
14 #define __free_elem(p) bam_destroy1((p)->data.b)
15 KLIST_INIT(q, elem_t, __free_elem)
16 typedef klist_t(q) queue_t;
17
18 KHASH_MAP_INIT_INT(best, elem_p)
19 typedef khash_t(best) besthash_t;
20
21 typedef struct {
22 uint64_t n_checked, n_removed;
23 besthash_t *left, *rght;
24 } lib_aux_t;
25 KHASH_MAP_INIT_STR(lib, lib_aux_t)
26
27 static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
28 {
29 khint_t k = kh_get(lib, aux, lib);
30 if (k == kh_end(aux)) {
31 int ret;
32 char *p = strdup(lib);
33 lib_aux_t *q;
34 k = kh_put(lib, aux, p, &ret);
35 q = &kh_val(aux, k);
36 q->left = kh_init(best);
37 q->rght = kh_init(best);
38 q->n_checked = q->n_removed = 0;
39 return q;
40 } else return &kh_val(aux, k);
41 }
42
43 static inline int sum_qual(const bam1_t *b)
44 {
45 int i, q;
46 uint8_t *qual = bam1_qual(b);
47 for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
48 return q;
49 }
50
51 static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score)
52 {
53 elem_t *p = kl_pushp(q, queue);
54 p->discarded = 0;
55 p->endpos = endpos; p->score = score;
56 if (p->b == 0) p->b = bam_init1();
57 bam_copy1(p->b, b);
58 return p;
59 }
60
61 static void clear_besthash(besthash_t *h, int32_t pos)
62 {
63 khint_t k;
64 for (k = kh_begin(h); k != kh_end(h); ++k)
65 if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos)
66 kh_del(best, h, k);
67 }
68
69 static void dump_alignment(samfile_t *out, queue_t *queue, int32_t pos, khash_t(lib) *h)
70 {
71 if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) {
72 khint_t k;
73 while (1) {
74 elem_t *q;
75 if (queue->head == queue->tail) break;
76 q = &kl_val(queue->head);
77 if (q->discarded) {
78 q->b->data_len = 0;
79 kl_shift(q, queue, 0);
80 continue;
81 }
82 if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break;
83 samwrite(out, q->b);
84 q->b->data_len = 0;
85 kl_shift(q, queue, 0);
86 }
87 for (k = kh_begin(h); k != kh_end(h); ++k) {
88 if (kh_exist(h, k)) {
89 clear_besthash(kh_val(h, k).left, pos);
90 clear_besthash(kh_val(h, k).rght, pos);
91 }
92 }
93 }
94 }
95
96 void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se)
97 {
98 bam1_t *b;
99 queue_t *queue;
100 khint_t k;
101 int last_tid = -2;
102 khash_t(lib) *aux;
103
104 aux = kh_init(lib);
105 b = bam_init1();
106 queue = kl_init(q);
107 while (samread(in, b) >= 0) {
108 bam1_core_t *c = &b->core;
109 int endpos = bam_calend(c, bam1_cigar(b));
110 int score = sum_qual(b);
111
112 if (last_tid != c->tid) {
113 if (last_tid >= 0) dump_alignment(out, queue, MAX_POS, aux);
114 last_tid = c->tid;
115 } else dump_alignment(out, queue, c->pos, aux);
116 if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) {
117 push_queue(queue, b, endpos, score);
118 } else {
119 const char *lib;
120 lib_aux_t *q;
121 besthash_t *h;
122 uint32_t key;
123 int ret;
124 lib = bam_get_library(in->header, b);
125 q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
126 ++q->n_checked;
127 h = (c->flag&BAM_FREVERSE)? q->rght : q->left;
128 key = (c->flag&BAM_FREVERSE)? endpos : c->pos;
129 k = kh_put(best, h, key, &ret);
130 if (ret == 0) { // in the hash table
131 elem_t *p = kh_val(h, k);
132 ++q->n_removed;
133 if (p->score < score) {
134 if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue
135 p->discarded = 1;
136 kh_val(h, k) = push_queue(queue, b, endpos, score);
137 } else { // replace
138 p->score = score; p->endpos = endpos;
139 bam_copy1(p->b, b);
140 }
141 } // otherwise, discard the alignment
142 } else kh_val(h, k) = push_queue(queue, b, endpos, score);
143 }
144 }
145 dump_alignment(out, queue, MAX_POS, aux);
146
147 for (k = kh_begin(aux); k != kh_end(aux); ++k) {
148 if (kh_exist(aux, k)) {
149 lib_aux_t *q = &kh_val(aux, k);
150 fprintf(stderr, "[bam_rmdupse_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
151 (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
152 kh_destroy(best, q->left); kh_destroy(best, q->rght);
153 free((char*)kh_key(aux, k));
154 }
155 }
156 kh_destroy(lib, aux);
157 bam_destroy1(b);
158 kl_destroy(q, queue);
159 }