X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam.h;h=eef2ea9853f25966c5a40c45a86272b78a507fb2;hp=4c8536fd33366883028ff9b77bb95049682c5f9f;hb=016b50ab60e879a0b8f81cb76ce11ea360a03d4a;hpb=62781a2daa24d74a3c590e2669fad1fa7cabf933

diff --git a/bam.h b/bam.h
index 4c8536f..eef2ea9 100644
--- a/bam.h
+++ b/bam.h
@@ -495,7 +495,7 @@ extern "C" {
 		bam1_t *b;
 		int32_t qpos;
 		int indel, level;
-		uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1;
+		uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1, aux:28;
 	} bam_pileup1_t;
 
 	typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);
@@ -508,6 +508,7 @@ extern "C" {
 	const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
 	const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
 	void bam_plp_set_mask(bam_plp_t iter, int mask);
+	void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt);
 	void bam_plp_reset(bam_plp_t iter);
 	void bam_plp_destroy(bam_plp_t iter);
 
@@ -516,6 +517,7 @@ extern "C" {
 
 	bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data);
 	void bam_mplp_destroy(bam_mplp_t iter);
+	void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt);
 	int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
 
 	/*! @typedef
@@ -708,8 +710,8 @@ static inline bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
 {
 	uint8_t *data = bdst->data;
 	int m_data = bdst->m_data;   // backup data and m_data
-	if (m_data < bsrc->m_data) { // double the capacity
-		m_data = bsrc->m_data; kroundup32(m_data);
+	if (m_data < bsrc->data_len) { // double the capacity
+		m_data = bsrc->data_len; kroundup32(m_data);
 		data = (uint8_t*)realloc(data, m_data);
 	}
 	memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data