--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/bam_lpileup.c	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,198 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <assert.h>
+#include "bam.h"
+#include "ksort.h"
+
+#define TV_GAP 2
+
+typedef struct __freenode_t {
+	uint32_t level:28, cnt:4;
+	struct __freenode_t *next;
+} freenode_t, *freenode_p;
+
+#define freenode_lt(a,b) ((a)->cnt < (b)->cnt || ((a)->cnt == (b)->cnt && (a)->level < (b)->level))
+KSORT_INIT(node, freenode_p, freenode_lt)
+
+/* Memory pool, similar to the one in bam_pileup.c */
+typedef struct {
+	int cnt, n, max;
+	freenode_t **buf;
+} mempool_t;
+
+static mempool_t *mp_init()
+{
+	return (mempool_t*)calloc(1, sizeof(mempool_t));
+}
+static void mp_destroy(mempool_t *mp)
+{
+	int k;
+	for (k = 0; k < mp->n; ++k) free(mp->buf[k]);
+	free(mp->buf); free(mp);
+}
+static inline freenode_t *mp_alloc(mempool_t *mp)
+{
+	++mp->cnt;
+	if (mp->n == 0) return (freenode_t*)calloc(1, sizeof(freenode_t));
+	else return mp->buf[--mp->n];
+}
+static inline void mp_free(mempool_t *mp, freenode_t *p)
+{
+	--mp->cnt; p->next = 0; p->cnt = TV_GAP;
+	if (mp->n == mp->max) {
+		mp->max = mp->max? mp->max<<1 : 256;
+		mp->buf = (freenode_t**)realloc(mp->buf, sizeof(freenode_t*) * mp->max);
+	}
+	mp->buf[mp->n++] = p;
+}
+
+/* core part */
+struct __bam_lplbuf_t {
+	int max, n_cur, n_pre;
+	int max_level, *cur_level, *pre_level;
+	mempool_t *mp;
+	freenode_t **aux, *head, *tail;
+	int n_nodes, m_aux;
+	bam_pileup_f func;
+	void *user_data;
+	bam_plbuf_t *plbuf;
+};
+
+void bam_lplbuf_reset(bam_lplbuf_t *buf)
+{
+	freenode_t *p, *q;
+	bam_plbuf_reset(buf->plbuf);
+	for (p = buf->head; p->next;) {
+		q = p->next;
+		mp_free(buf->mp, p);
+		p = q;
+	}
+	buf->head = buf->tail;
+	buf->max_level = 0;
+	buf->n_cur = buf->n_pre = 0;
+	buf->n_nodes = 0;
+}
+
+static int tview_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
+{
+	bam_lplbuf_t *tv = (bam_lplbuf_t*)data;
+	freenode_t *p;
+	int i, l, max_level;
+	// allocate memory if necessary
+	if (tv->max < n) { // enlarge
+		tv->max = n;
+		kroundup32(tv->max);
+		tv->cur_level = (int*)realloc(tv->cur_level, sizeof(int) * tv->max);
+		tv->pre_level = (int*)realloc(tv->pre_level, sizeof(int) * tv->max);
+	}
+	tv->n_cur = n;
+	// update cnt
+	for (p = tv->head; p->next; p = p->next)
+		if (p->cnt > 0) --p->cnt;
+	// calculate cur_level[]
+	max_level = 0;
+	for (i = l = 0; i < n; ++i) {
+		const bam_pileup1_t *p = pl + i;
+		if (p->is_head) {
+			if (tv->head->next && tv->head->cnt == 0) { // then take a free slot
+				freenode_t *p = tv->head->next;
+				tv->cur_level[i] = tv->head->level;
+				mp_free(tv->mp, tv->head);
+				tv->head = p;
+				--tv->n_nodes;
+			} else tv->cur_level[i] = ++tv->max_level;
+		} else {
+			tv->cur_level[i] = tv->pre_level[l++];
+			if (p->is_tail) { // then return a free slot
+				tv->tail->level = tv->cur_level[i];
+				tv->tail->next = mp_alloc(tv->mp);
+				tv->tail = tv->tail->next;
+				++tv->n_nodes;
+			}
+		}
+		if (tv->cur_level[i] > max_level) max_level = tv->cur_level[i];
+		((bam_pileup1_t*)p)->level = tv->cur_level[i];
+	}
+	assert(l == tv->n_pre);
+	tv->func(tid, pos, n, pl, tv->user_data);
+	// sort the linked list
+	if (tv->n_nodes) {
+		freenode_t *q;
+		if (tv->n_nodes + 1 > tv->m_aux) { // enlarge
+			tv->m_aux = tv->n_nodes + 1;
+			kroundup32(tv->m_aux);
+			tv->aux = (freenode_t**)realloc(tv->aux, sizeof(void*) * tv->m_aux);
+		}
+		for (p = tv->head, i = l = 0; p->next;) {
+			if (p->level > max_level) { // then discard this entry
+				q = p->next;
+				mp_free(tv->mp, p);
+				p = q;
+			} else {
+				tv->aux[i++] = p;
+				p = p->next;
+			}
+		}
+		tv->aux[i] = tv->tail; // add a proper tail for the loop below
+		tv->n_nodes = i;
+		if (tv->n_nodes) {
+			ks_introsort(node, tv->n_nodes, tv->aux);
+			for (i = 0; i < tv->n_nodes; ++i) tv->aux[i]->next = tv->aux[i+1];
+			tv->head = tv->aux[0];
+		} else tv->head = tv->tail;
+	}
+	// clean up
+	tv->max_level = max_level;
+	memcpy(tv->pre_level, tv->cur_level, tv->n_cur * 4);
+	// squeeze out terminated levels
+	for (i = l = 0; i < n; ++i) {
+		const bam_pileup1_t *p = pl + i;
+		if (!p->is_tail)
+			tv->pre_level[l++] = tv->pre_level[i];
+	}
+	tv->n_pre = l;
+/*
+	fprintf(stderr, "%d\t", pos+1);
+	for (i = 0; i < n; ++i) {
+		const bam_pileup1_t *p = pl + i;
+		if (p->is_head) fprintf(stderr, "^");
+		if (p->is_tail) fprintf(stderr, "$");
+		fprintf(stderr, "%d,", p->level);
+	}
+	fprintf(stderr, "\n");
+*/
+	return 0;
+}
+
+bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data)
+{
+	bam_lplbuf_t *tv;
+	tv = (bam_lplbuf_t*)calloc(1, sizeof(bam_lplbuf_t));
+	tv->mp = mp_init();
+	tv->head = tv->tail = mp_alloc(tv->mp);
+	tv->func = func;
+	tv->user_data = data;
+	tv->plbuf = bam_plbuf_init(tview_func, tv);
+	return (bam_lplbuf_t*)tv;
+}
+
+void bam_lplbuf_destroy(bam_lplbuf_t *tv)
+{
+	freenode_t *p, *q;
+	free(tv->cur_level); free(tv->pre_level);
+	bam_plbuf_destroy(tv->plbuf);
+	free(tv->aux);
+	for (p = tv->head; p->next;) {
+		q = p->next;
+		mp_free(tv->mp, p); p = q;
+	}
+	mp_free(tv->mp, p);
+	assert(tv->mp->cnt == 0);
+	mp_destroy(tv->mp);
+	free(tv);
+}
+
+int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *tv)
+{
+	return bam_plbuf_push(b, tv->plbuf);
+}