--- /dev/null
+#include "pysam.h"
+
+#include <math.h>
+#include "sam.h"
+#include "khash.h"
+#include "klist.h"
+
+#define QUEUE_CLEAR_SIZE 0x100000
+#define MAX_POS 0x7fffffff
+
+typedef struct {
+ int endpos;
+ uint32_t score:31, discarded:1;
+ bam1_t *b;
+} elem_t, *elem_p;
+#define __free_elem(p) bam_destroy1((p)->data.b)
+KLIST_INIT(q, elem_t, __free_elem)
+typedef klist_t(q) queue_t;
+
+KHASH_MAP_INIT_INT(best, elem_p)
+typedef khash_t(best) besthash_t;
+
+typedef struct {
+ uint64_t n_checked, n_removed;
+ besthash_t *left, *rght;
+} lib_aux_t;
+KHASH_MAP_INIT_STR(lib, lib_aux_t)
+
+static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
+{
+ khint_t k = kh_get(lib, aux, lib);
+ if (k == kh_end(aux)) {
+ int ret;
+ char *p = strdup(lib);
+ lib_aux_t *q;
+ k = kh_put(lib, aux, p, &ret);
+ q = &kh_val(aux, k);
+ q->left = kh_init(best);
+ q->rght = kh_init(best);
+ q->n_checked = q->n_removed = 0;
+ return q;
+ } else return &kh_val(aux, k);
+}
+
+static inline int sum_qual(const bam1_t *b)
+{
+ int i, q;
+ uint8_t *qual = bam1_qual(b);
+ for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
+ return q;
+}
+
+static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score)
+{
+ elem_t *p = kl_pushp(q, queue);
+ p->discarded = 0;
+ p->endpos = endpos; p->score = score;
+ if (p->b == 0) p->b = bam_init1();
+ bam_copy1(p->b, b);
+ return p;
+}
+
+static void clear_besthash(besthash_t *h, int32_t pos)
+{
+ khint_t k;
+ for (k = kh_begin(h); k != kh_end(h); ++k)
+ if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos)
+ kh_del(best, h, k);
+}
+
+static void dump_alignment(samfile_t *out, queue_t *queue, int32_t pos, khash_t(lib) *h)
+{
+ if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) {
+ khint_t k;
+ while (1) {
+ elem_t *q;
+ if (queue->head == queue->tail) break;
+ q = &kl_val(queue->head);
+ if (q->discarded) {
+ q->b->data_len = 0;
+ kl_shift(q, queue, 0);
+ continue;
+ }
+ if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break;
+ samwrite(out, q->b);
+ q->b->data_len = 0;
+ kl_shift(q, queue, 0);
+ }
+ for (k = kh_begin(h); k != kh_end(h); ++k) {
+ if (kh_exist(h, k)) {
+ clear_besthash(kh_val(h, k).left, pos);
+ clear_besthash(kh_val(h, k).rght, pos);
+ }
+ }
+ }
+}
+
+void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se)
+{
+ bam1_t *b;
+ queue_t *queue;
+ khint_t k;
+ int last_tid = -2;
+ khash_t(lib) *aux;
+
+ aux = kh_init(lib);
+ b = bam_init1();
+ queue = kl_init(q);
+ while (samread(in, b) >= 0) {
+ bam1_core_t *c = &b->core;
+ int endpos = bam_calend(c, bam1_cigar(b));
+ int score = sum_qual(b);
+
+ if (last_tid != c->tid) {
+ if (last_tid >= 0) dump_alignment(out, queue, MAX_POS, aux);
+ last_tid = c->tid;
+ } else dump_alignment(out, queue, c->pos, aux);
+ if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) {
+ push_queue(queue, b, endpos, score);
+ } else {
+ const char *lib;
+ lib_aux_t *q;
+ besthash_t *h;
+ uint32_t key;
+ int ret;
+ lib = bam_get_library(in->header, b);
+ q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
+ ++q->n_checked;
+ h = (c->flag&BAM_FREVERSE)? q->rght : q->left;
+ key = (c->flag&BAM_FREVERSE)? endpos : c->pos;
+ k = kh_put(best, h, key, &ret);
+ if (ret == 0) { // in the hash table
+ elem_t *p = kh_val(h, k);
+ ++q->n_removed;
+ if (p->score < score) {
+ if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue
+ p->discarded = 1;
+ kh_val(h, k) = push_queue(queue, b, endpos, score);
+ } else { // replace
+ p->score = score; p->endpos = endpos;
+ bam_copy1(p->b, b);
+ }
+ } // otherwise, discard the alignment
+ } else kh_val(h, k) = push_queue(queue, b, endpos, score);
+ }
+ }
+ dump_alignment(out, queue, MAX_POS, aux);
+
+ for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+ if (kh_exist(aux, k)) {
+ lib_aux_t *q = &kh_val(aux, k);
+ fprintf(pysamerr, "[bam_rmdupse_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
+ (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
+ kh_destroy(best, q->left); kh_destroy(best, q->rght);
+ free((char*)kh_key(aux, k));
+ }
+ }
+ kh_destroy(lib, aux);
+ bam_destroy1(b);
+ kl_destroy(q, queue);
+}