X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam_lpileup.c;fp=samtools%2Fbam_lpileup.c;h=0000000000000000000000000000000000000000;hp=d4dd63b99b85dd4c5811758153a56757c908a52c;hb=bd0c3067c187d1f718004fb38acc093af8810a02;hpb=1b740fc70684c92a5e2293013217d5a2fd661d8a

diff --git a/samtools/bam_lpileup.c b/samtools/bam_lpileup.c
deleted file mode 100644
index d4dd63b..0000000
--- a/samtools/bam_lpileup.c
+++ /dev/null
@@ -1,198 +0,0 @@
-#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);
-}