* Merge from branches/dev/

[samtools.git] / bam_rmdup.c

diff --git a/bam_rmdup.c b/bam_rmdup.c
new file mode 100644 (file)
index 0000000..321938f
--- /dev/null
+++ b/bam_rmdup.c
@@ -0,0 +1,140 @@
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <assert.h>
+#include <zlib.h>
+#include "bam.h"
+
+typedef bam1_t *bam1_p;
+#include "khash.h"
+KHASH_SET_INIT_STR(name)
+KHASH_MAP_INIT_INT64(pos, bam1_p)
+
+#define BUFFER_SIZE 0x40000
+
+typedef struct {
+       int n, max;
+       bam1_t **a;
+} tmp_stack_t;
+
+static inline void stack_insert(tmp_stack_t *stack, bam1_t *b)
+{
+       if (stack->n == stack->max) {
+               stack->max = stack->max? stack->max<<1 : 0x10000;
+               stack->a = (bam1_t**)realloc(stack->a, sizeof(bam1_t*) * stack->max);
+       }
+       stack->a[stack->n++] = b;
+}
+
+static inline void dump_best(tmp_stack_t *stack, khash_t(pos) *best_hash, bamFile out)
+{
+       int i;
+       for (i = 0; i != stack->n; ++i) {
+               bam_write1(out, stack->a[i]);
+               bam_destroy1(stack->a[i]);
+       }
+       stack->n = 0;
+       if (kh_size(best_hash) > BUFFER_SIZE) kh_clear(pos, best_hash);
+}
+
+static void clear_del_set(khash_t(name) *del_set)
+{
+       khint_t k;
+       for (k = kh_begin(del_set); k < kh_end(del_set); ++k)
+               if (kh_exist(del_set, k))
+                       free((char*)kh_key(del_set, k));
+       kh_clear(name, del_set);
+}
+
+void bam_rmdup_core(bamFile in, bamFile out)
+{
+       bam_header_t *header;
+       bam1_t *b;
+       int last_tid = -1, last_pos = -1;
+       uint64_t n_checked = 0, n_removed = 0;
+       tmp_stack_t stack;
+       khint_t k;
+       khash_t(pos) *best_hash;
+       khash_t(name) *del_set;
+
+       best_hash = kh_init(pos);
+       del_set = kh_init(name);
+       b = bam_init1();
+       memset(&stack, 0, sizeof(tmp_stack_t));
+       header = bam_header_read(in);
+       bam_header_write(out, header);
+
+       kh_resize(name, del_set, 4 * BUFFER_SIZE);
+       kh_resize(pos, best_hash, 3 * BUFFER_SIZE);
+       while (bam_read1(in, b) >= 0) {
+               bam1_core_t *c = &b->core;
+               if (c->tid != last_tid || last_pos != c->pos) {
+                       dump_best(&stack, best_hash, out); // write the result
+                       if (c->tid != last_tid) {
+                               kh_clear(pos, best_hash);
+                               if (kh_size(del_set)) { // check
+                                       fprintf(stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set));
+                                       clear_del_set(del_set);
+                               }
+                               last_tid = c->tid;
+                               fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", header->target_name[c->tid]);
+                       }
+               }
+               if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) {
+                       bam_write1(out, b);
+               } else if (c->isize > 0) { // paired, head
+                       uint64_t key = (uint64_t)c->pos<<32 | c->isize;
+                       int ret;
+                       ++n_checked;
+                       k = kh_put(pos, best_hash, key, &ret);
+                       if (ret == 0) { // found in best_hash
+                               bam1_t *p = kh_val(best_hash, k);
+                               ++n_removed;
+                               if (p->core.qual < c->qual) { // the current alignment is better
+                                       kh_put(name, del_set, strdup(bam1_qname(p)), &ret); // p will be removed
+                                       bam_copy1(p, b); // replaced as b
+                               } else kh_put(name, del_set, strdup(bam1_qname(b)), &ret); // b will be removed
+                               if (ret == 0)
+                                       fprintf(stderr, "[bam_rmdup_core] inconsistent BAM file for pair '%s'. Continue anyway.\n", bam1_qname(b));
+                       } else { // not found in best_hash
+                               kh_val(best_hash, k) = bam_dup1(b);
+                               stack_insert(&stack, kh_val(best_hash, k));
+                       }
+               } else { // paired, tail
+                       k = kh_get(name, del_set, bam1_qname(b));
+                       if (k != kh_end(del_set)) {
+                               free((char*)kh_key(del_set, k));
+                               kh_del(name, del_set, k);
+                       } else bam_write1(out, b);
+               }
+               last_pos = c->pos;
+       }
+       dump_best(&stack, best_hash, out);
+
+       bam_header_destroy(header);
+       clear_del_set(del_set);
+       kh_destroy(name, del_set);
+       kh_destroy(pos, best_hash);
+       free(stack.a);
+       bam_destroy1(b);
+       fprintf(stderr, "[bam_rmdup_core] %lld / %lld = %.4lf\n", (long long)n_removed, (long long)n_checked,
+                       (double)n_removed/n_checked);
+}
+int bam_rmdup(int argc, char *argv[])
+{
+       bamFile in, out;
+       if (argc < 3) {
+               fprintf(stderr, "Usage: samtools rmdup <input.srt.bam> <output.bam>\n");
+               return 1;
+       }
+       in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
+       out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
+       if (in == 0 || out == 0) {
+               fprintf(stderr, "[bam_rmdup] fail to read/write input files\n");
+               return 1;
+       }
+       bam_rmdup_core(in, out);
+       bam_close(in);
+       bam_close(out);
+       return 0;
+}