--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/bam_rmdup.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,206 @@
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <zlib.h>
+#include <unistd.h>
+#include "sam.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 {
+	uint64_t n_checked, n_removed;
+	khash_t(pos) *best_hash;
+} lib_aux_t;
+KHASH_MAP_INIT_STR(lib, lib_aux_t)
+
+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, samfile_t *out)
+{
+	int i;
+	for (i = 0; i != stack->n; ++i) {
+		samwrite(out, stack->a[i]);
+		bam_destroy1(stack->a[i]);
+	}
+	stack->n = 0;
+}
+
+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);
+}
+
+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->n_checked = q->n_removed = 0;
+		q->best_hash = kh_init(pos);
+		return q;
+	} else return &kh_val(aux, k);
+}
+
+static void clear_best(khash_t(lib) *aux, int max)
+{
+	khint_t k;
+	for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+		if (kh_exist(aux, k)) {
+			lib_aux_t *q = &kh_val(aux, k);
+			if (kh_size(q->best_hash) >= max)
+				kh_clear(pos, q->best_hash);
+		}
+	}
+}
+
+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;
+}
+
+void bam_rmdup_core(samfile_t *in, samfile_t *out)
+{
+	bam1_t *b;
+	int last_tid = -1, last_pos = -1;
+	tmp_stack_t stack;
+	khint_t k;
+	khash_t(lib) *aux;
+	khash_t(name) *del_set;
+	
+	aux = kh_init(lib);
+	del_set = kh_init(name);
+	b = bam_init1();
+	memset(&stack, 0, sizeof(tmp_stack_t));
+
+	kh_resize(name, del_set, 4 * BUFFER_SIZE);
+	while (samread(in, b) >= 0) {
+		bam1_core_t *c = &b->core;
+		if (c->tid != last_tid || last_pos != c->pos) {
+			dump_best(&stack, out); // write the result
+			clear_best(aux, BUFFER_SIZE);
+			if (c->tid != last_tid) {
+				clear_best(aux, 0);
+				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);
+				}
+				if ((int)c->tid == -1) { // append unmapped reads
+					samwrite(out, b);
+					while (samread(in, b) >= 0) samwrite(out, b);
+					break;
+				}
+				last_tid = c->tid;
+				fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", in->header->target_name[c->tid]);
+			}
+		}
+		if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) {
+			samwrite(out, b);
+		} else if (c->isize > 0) { // paired, head
+			uint64_t key = (uint64_t)c->pos<<32 | c->isize;
+			const char *lib;
+			lib_aux_t *q;
+			int ret;
+			lib = bam_get_library(in->header, b);
+			q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
+			++q->n_checked;
+			k = kh_put(pos, q->best_hash, key, &ret);
+			if (ret == 0) { // found in best_hash
+				bam1_t *p = kh_val(q->best_hash, k);
+				++q->n_removed;
+				if (sum_qual(p) < sum_qual(b)) { // the current alignment is better; this can be accelerated in principle
+					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(q->best_hash, k) = bam_dup1(b);
+				stack_insert(&stack, kh_val(q->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 samwrite(out, b);
+		}
+		last_pos = c->pos;
+	}
+
+	for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+		if (kh_exist(aux, k)) {
+			lib_aux_t *q = &kh_val(aux, k);			
+			dump_best(&stack, out);
+			fprintf(stderr, "[bam_rmdup_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(pos, q->best_hash);
+			free((char*)kh_key(aux, k));
+		}
+	}
+	kh_destroy(lib, aux);
+
+	clear_del_set(del_set);
+	kh_destroy(name, del_set);
+	free(stack.a);
+	bam_destroy1(b);
+}
+
+void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se);
+
+int bam_rmdup(int argc, char *argv[])
+{
+	int c, is_se = 0, force_se = 0;
+	samfile_t *in, *out;
+	while ((c = getopt(argc, argv, "sS")) >= 0) {
+		switch (c) {
+		case 's': is_se = 1; break;
+		case 'S': force_se = is_se = 1; break;
+		}
+	}
+	if (optind + 2 > argc) {
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:  samtools rmdup [-sS] <input.srt.bam> <output.bam>\n\n");
+		fprintf(stderr, "Option: -s    rmdup for SE reads\n");
+		fprintf(stderr, "        -S    treat PE reads as SE in rmdup (force -s)\n\n");
+		return 1;
+	}
+	in = samopen(argv[optind], "rb", 0);
+	out = samopen(argv[optind+1], "wb", in->header);
+	if (in == 0 || out == 0) {
+		fprintf(stderr, "[bam_rmdup] fail to read/write input files\n");
+		return 1;
+	}
+	if (is_se) bam_rmdupse_core(in, out, force_se);
+	else bam_rmdup_core(in, out);
+	samclose(in); samclose(out);
+	return 0;
+}