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 }