From f8941aebcb194dbe1ff32c161d3cd51d80805d5d Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Mon, 13 Jul 2009 09:12:57 +0000
Subject: [PATCH]  * samtools-0.1.5-5 (r395)  * added bam_pileup_file() and
 removed bam_lpileup_file()

---
 bam.h         |  5 ++---
 bam_lite.c    | 16 ++++++++++++++++
 bam_lpileup.c | 16 ----------------
 bam_pileup.c  | 16 ++++++++++++++++
 bamtk.c       |  2 +-
 5 files changed, 35 insertions(+), 20 deletions(-)

diff --git a/bam.h b/bam.h
index 124817e..64867f1 100644
--- a/bam.h
+++ b/bam.h
@@ -509,6 +509,8 @@ extern "C" {
 	 */
 	int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
 
+	int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
+
 	struct __bam_lplbuf_t;
 	typedef struct __bam_lplbuf_t bam_lplbuf_t;
 
@@ -523,9 +525,6 @@ extern "C" {
 	/*! @abstract  bam_plbuf_push() equivalent with level calculated. */
 	int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf);
 
-	/*! @abstract  bam_plbuf_file() equivalent with level calculated. */
-	int bam_lpileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
-
 	struct __bam_index_t;
 	typedef struct __bam_index_t bam_index_t;
 
diff --git a/bam_lite.c b/bam_lite.c
index 12c719c..93af6c4 100644
--- a/bam_lite.c
+++ b/bam_lite.c
@@ -552,6 +552,22 @@ int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
 	return 0;
 }
 
+int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
+{
+	bam_plbuf_t *buf;
+	int ret;
+	bam1_t *b;
+	b = bam_init1();
+	buf = bam_plbuf_init(func, func_data);
+	bam_plbuf_set_mask(buf, mask);
+	while ((ret = bam_read1(fp, b)) >= 0)
+		bam_plbuf_push(b, buf);
+	bam_plbuf_push(0, buf);
+	bam_plbuf_destroy(buf);
+	bam_destroy1(b);
+	return 0;
+}
+
 /**********************
  *** from bam_aux.c ***
  **********************/
diff --git a/bam_lpileup.c b/bam_lpileup.c
index 425290e..d4dd63b 100644
--- a/bam_lpileup.c
+++ b/bam_lpileup.c
@@ -196,19 +196,3 @@ int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *tv)
 {
 	return bam_plbuf_push(b, tv->plbuf);
 }
-
-int bam_lpileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
-{
-	bam_lplbuf_t *buf;
-	int ret;
-	bam1_t *b;
-	b = (bam1_t*)calloc(1, sizeof(bam1_t));
-	buf = bam_lplbuf_init(func, func_data);
-	bam_plbuf_set_mask(buf->plbuf, mask);
-	while ((ret = bam_read1(fp, b)) >= 0)
-		bam_lplbuf_push(b, buf);
-	bam_lplbuf_push(0, buf);
-	bam_lplbuf_destroy(buf);
-	free(b->data); free(b);
-	return 0;
-}
diff --git a/bam_pileup.c b/bam_pileup.c
index 3ffd528..d2d2aa6 100644
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -212,3 +212,19 @@ int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
 	}
 	return 0;
 }
+
+int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
+{
+	bam_plbuf_t *buf;
+	int ret;
+	bam1_t *b;
+	b = bam_init1();
+	buf = bam_plbuf_init(func, func_data);
+	bam_plbuf_set_mask(buf, mask);
+	while ((ret = bam_read1(fp, b)) >= 0)
+		bam_plbuf_push(b, buf);
+	bam_plbuf_push(0, buf);
+	bam_plbuf_destroy(buf);
+	bam_destroy1(b);
+	return 0;
+}
diff --git a/bamtk.c b/bamtk.c
index 0846a70..e071d31 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -4,7 +4,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-4 (r394)"
+#define PACKAGE_VERSION "0.1.5-5 (r395)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
-- 
2.39.2