X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_index.c;h=a6278843583c605799360affb0b9c3c21fbd02c4;hp=72ef270f9c7afd143759e1f98d681ce69147bb13;hb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906

diff --git a/bam_index.c b/bam_index.c
index 72ef270..a627884 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -4,7 +4,9 @@
 #include "khash.h"
 #include "ksort.h"
 #include "bam_endian.h"
+#ifdef _USE_KNETFILE
 #include "knetfile.h"
+#endif
 
 /*!
   @header
@@ -328,7 +330,7 @@ bam_index_t *bam_index_load_local(const char *_fn)
 	FILE *fp;
 	char *fnidx, *fn;
 
-	if (strstr(_fn, "ftp://") == _fn) {
+	if (strstr(_fn, "ftp://") == _fn || strstr(_fn, "http://") == _fn) {
 		const char *p;
 		int l = strlen(_fn);
 		for (p = _fn + l - 1; p >= _fn; --p)
@@ -354,6 +356,7 @@ bam_index_t *bam_index_load_local(const char *_fn)
 	} else return 0;
 }
 
+#ifdef _USE_KNETFILE
 static void download_from_remote(const char *url)
 {
 	const int buf_size = 1 * 1024 * 1024;
@@ -362,7 +365,7 @@ static void download_from_remote(const char *url)
 	uint8_t *buf;
 	knetFile *fp_remote;
 	int l;
-	if (strstr(url, "ftp://") != url) return;
+	if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
 	l = strlen(url);
 	for (fn = (char*)url + l - 1; fn >= url; --fn)
 		if (*fn == '/') break;
@@ -384,12 +387,18 @@ static void download_from_remote(const char *url)
 	fclose(fp);
 	knet_close(fp_remote);
 }
+#else
+static void download_from_remote(const char *url)
+{
+	return;
+}
+#endif
 
 bam_index_t *bam_index_load(const char *fn)
 {
 	bam_index_t *idx;
 	idx = bam_index_load_local(fn);
-	if (idx == 0 && strstr(fn, "ftp://") == fn) {
+	if (idx == 0 && (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)) {
 		char *fnidx = calloc(strlen(fn) + 5, 1);
 		strcat(strcpy(fnidx, fn), ".bai");
 		fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n");
@@ -467,7 +476,8 @@ static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
 	return (rend > beg && rbeg < end);
 }
 
-int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
+// bam_fetch helper function retrieves 
+pair64_t * get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int* cnt_off)
 {
 	uint16_t *bins;
 	int i, n_bins, n_off;
@@ -498,10 +508,8 @@ int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, voi
 	}
 	free(bins);
 	{
-		bam1_t *b;
-		int l, ret, n_seeks;
-		uint64_t curr_off;
-		b = (bam1_t*)calloc(1, sizeof(bam1_t));
+		bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
+		int l;
 		ks_introsort(off, n_off, off);
 		// resolve completely contained adjacent blocks
 		for (i = 1, l = 0; i < n_off; ++i)
@@ -524,8 +532,23 @@ int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, voi
 			n_off = l + 1;
 #endif
 		}
+		bam_destroy1(b);
+	}
+	*cnt_off = n_off;
+	return off;
+}
+
+int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
+{
+	int n_off;
+	pair64_t *off = get_chunk_coordinates(idx, tid, beg, end, &n_off);
+	if (off == 0) return 0;
+	{
 		// retrive alignments
+		uint64_t curr_off;
+		int i, ret, n_seeks;
 		n_seeks = 0; i = -1; curr_off = 0;
+		bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
 		for (;;) {
 			if (curr_off == 0 || curr_off >= off[i].v) { // then jump to the next chunk
 				if (i == n_off - 1) break; // no more chunks