From a958954399757774ee26bfcf0b5b95e9ec9b62f4 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Sat, 12 Jun 2010 22:11:32 +0000
Subject: [PATCH] rename iterf as iter

---
 bam.h       |  8 ++++----
 bam_index.c | 22 +++++++++++-----------
 bam_plcmd.c |  8 ++++----
 samtools.1  |  2 ++
 4 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/bam.h b/bam.h
index f6d31a9..fb71a49 100644
--- a/bam.h
+++ b/bam.h
@@ -190,7 +190,7 @@ typedef struct {
 	uint8_t *data;
 } bam1_t;
 
-typedef struct __bam_iterf_t *bam_iterf_t;
+typedef struct __bam_iter_t *bam_iter_t;
 
 #define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
 #define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
@@ -594,9 +594,9 @@ extern "C" {
 	 */
 	int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);
 
-	bam_iterf_t bam_iterf_query(const bam_index_t *idx, int tid, int beg, int end);
-	int bam_iterf_read(bamFile fp, bam_iterf_t iter, bam1_t *b);
-	void bam_iterf_destroy(bam_iterf_t iter);
+	bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end);
+	int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b);
+	void bam_iter_destroy(bam_iter_t iter);
 
 	/*!
 	  @abstract       Parse a region in the format: "chr2:100,000-200,000".
diff --git a/bam_index.c b/bam_index.c
index 595ef04..6fffd75 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -494,7 +494,7 @@ static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
 	return (rend > beg && rbeg < end);
 }
 
-struct __bam_iterf_t {
+struct __bam_iter_t {
 	int from_first; // read from the first record; no random access
 	int tid, beg, end, n_off, i, finished;
 	uint64_t curr_off;
@@ -502,7 +502,7 @@ struct __bam_iterf_t {
 };
 
 // bam_fetch helper function retrieves 
-bam_iterf_t bam_iterf_query(const bam_index_t *idx, int tid, int beg, int end)
+bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end)
 {
 	uint16_t *bins;
 	int i, n_bins, n_off;
@@ -510,12 +510,12 @@ bam_iterf_t bam_iterf_query(const bam_index_t *idx, int tid, int beg, int end)
 	khint_t k;
 	khash_t(i) *index;
 	uint64_t min_off;
-	bam_iterf_t iter = 0;
+	bam_iter_t iter = 0;
 
 	if (beg < 0) beg = 0;
 	if (end < beg) return 0;
 	// initialize iter
-	iter = calloc(1, sizeof(struct __bam_iterf_t));
+	iter = calloc(1, sizeof(struct __bam_iter_t));
 	iter->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1;
 	//
 	bins = (uint16_t*)calloc(MAX_BIN, 2);
@@ -582,20 +582,20 @@ bam_iterf_t bam_iterf_query(const bam_index_t *idx, int tid, int beg, int end)
 
 pair64_t *get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int *cnt_off)
 { // for pysam compatibility
-	bam_iterf_t iter;
+	bam_iter_t iter;
 	pair64_t *off;
-	iter = bam_iterf_query(idx, tid, beg, end);
+	iter = bam_iter_query(idx, tid, beg, end);
 	off = iter->off; *cnt_off = iter->n_off;
 	free(iter);
 	return off;
 }
 
-void bam_iterf_destroy(bam_iterf_t iter)
+void bam_iter_destroy(bam_iter_t iter)
 {
 	if (iter) { free(iter->off); free(iter); }
 }
 
-int bam_iterf_read(bamFile fp, bam_iterf_t iter, bam1_t *b)
+int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b)
 {
 	if (iter->finished) return -1;
 	if (iter->from_first) {
@@ -627,11 +627,11 @@ int bam_iterf_read(bamFile fp, bam_iterf_t iter, bam1_t *b)
 
 int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
 {
-	bam_iterf_t iter;
+	bam_iter_t iter;
 	bam1_t *b;
 	b = bam_init1();
-	iter = bam_iterf_query(idx, tid, beg, end);
-	while (bam_iterf_read(fp, iter, b) >= 0) func(b, data);
+	iter = bam_iter_query(idx, tid, beg, end);
+	while (bam_iter_read(fp, iter, b) >= 0) func(b, data);
 	bam_destroy1(b);
 	return 0;
 }
diff --git a/bam_plcmd.c b/bam_plcmd.c
index d34cd26..d1ea03f 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -453,13 +453,13 @@ typedef struct {
 
 typedef struct {
 	bamFile fp;
-	bam_iterf_t iter;
+	bam_iter_t iter;
 } mplp_aux_t;
 
 static int mplp_func(void *data, bam1_t *b)
 {
 	mplp_aux_t *ma = (mplp_aux_t*)data;
-	if (ma->iter) return bam_iterf_read(ma->fp, ma->iter, b);
+	if (ma->iter) return bam_iter_read(ma->fp, ma->iter, b);
 	return bam_read1(ma->fp, b);
 }
 
@@ -494,7 +494,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 				exit(1);
 			}
 			if (i == 0) beg0 = beg, end0 = end;
-			data[i]->iter = bam_iterf_query(idx, tid, beg, end);
+			data[i]->iter = bam_iter_query(idx, tid, beg, end);
 			bam_index_destroy(idx);
 		}
 		if (i == 0) h = h_tmp;
@@ -536,7 +536,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 	bam_header_destroy(h);
 	for (i = 0; i < n; ++i) {
 		bam_close(data[i]->fp);
-		if (data[i]->iter) bam_iterf_destroy(data[i]->iter);
+		if (data[i]->iter) bam_iter_destroy(data[i]->iter);
 		free(data[i]);
 	}
 	free(data); free(plp); free(ref); free(n_plp);
diff --git a/samtools.1 b/samtools.1
index b028779..366a563 100644
--- a/samtools.1
+++ b/samtools.1
@@ -18,6 +18,8 @@ samtools faidx ref.fasta
 .PP
 samtools pileup -f ref.fasta aln.sorted.bam
 .PP
+samtools mpileup -f ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam
+.PP
 samtools tview aln.sorted.bam ref.fasta
 
 .SH DESCRIPTION
-- 
2.39.2