From: Heng Li <lh3@live.co.uk>
Date: Tue, 30 Jun 2009 13:04:30 +0000 (+0000)
Subject:  * samtools-0.1.4-20 (r365)
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=3b5a80b412333883de8da5b449d2ff097e82afd1;p=samtools.git

 * samtools-0.1.4-20 (r365)
 * download the BAM index file if it is not found in the current working directory.
---

diff --git a/bam_index.c b/bam_index.c
index 1c0b29b..329df32 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -3,6 +3,7 @@
 #include "khash.h"
 #include "ksort.h"
 #include "bam_endian.h"
+#include "knetfile.h"
 
 /*!
   @header
@@ -321,16 +322,7 @@ static bam_index_t *bam_index_load_core(FILE *fp)
 	return idx;
 }
 
-bam_index_t *bam_index_load2(const char *fnidx)
-{
-	bam_index_t *idx;
-	FILE *fp = fopen(fnidx, "r");
-	idx = bam_index_load_core(fp);
-	fclose(fp);
-	return idx;
-}
-
-bam_index_t *bam_index_load(const char *_fn)
+bam_index_t *bam_index_load_local(const char *_fn)
 {
 	bam_index_t *idx;
 	FILE *fp;
@@ -360,6 +352,51 @@ bam_index_t *bam_index_load(const char *_fn)
 	return idx;
 }
 
+static void download_from_remote(const char *url)
+{
+	const int buf_size = 1 * 1024 * 1024;
+	char *fn;
+	FILE *fp;
+	uint8_t *buf;
+	knetFile *fp_remote;
+	int l;
+	if (strstr(url, "ftp://") != url) return;
+	l = strlen(url);
+	for (fn = (char*)url + l - 1; fn >= url; --fn)
+		if (*fn == '/') break;
+	++fn; // fn now points to the file name
+	fp_remote = knet_open(url, "r");
+	if (fp_remote == 0) {
+		fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
+		return;
+	}
+	if ((fp = fopen(fn, "w")) == 0) {
+		fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
+		knet_close(fp_remote);
+		return;
+	}
+	buf = (uint8_t*)calloc(buf_size, 1);
+	while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
+		fwrite(buf, 1, l, fp);
+	free(buf);
+	fclose(fp);
+	knet_close(fp_remote);
+}
+
+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) {
+		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");
+		download_from_remote(fnidx);
+		idx = bam_index_load_local(fn);
+	}
+	return idx;
+}
+
 int bam_index_build2(const char *fn, const char *_fnidx)
 {
 	char *fnidx;
diff --git a/bamtk.c b/bamtk.c
index db42873..61ead10 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.4-19 (r364)"
+#define PACKAGE_VERSION "0.1.4-20 (r365)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
diff --git a/knetfile.c b/knetfile.c
index 45c921f..8dd7e86 100644
--- a/knetfile.c
+++ b/knetfile.c
@@ -116,7 +116,7 @@ int kftp_reconnect(knetFile *ftp)
 }
 
 // initialize ->type, ->host and ->retr
-knetFile *kftp_prep(const char *fn, const char *mode)
+knetFile *kftp_parse_url(const char *fn, const char *mode)
 {
 	knetFile *fp;
 	char *p;
@@ -156,6 +156,7 @@ int kftp_connect_file(knetFile *fp)
 		fprintf(stderr, "[kftp_connect_file] %s\n", fp->response);
 		close(fp->fd);
 		fp->fd = -1;
+		return -1;
 	}
 	fp->is_ready = 1;
 	return 0;
@@ -169,7 +170,7 @@ knetFile *knet_open(const char *fn, const char *mode)
 		return 0;
 	}
 	if (strstr(fn, "ftp://") == fn) {
-		fp = kftp_prep(fn, mode);
+		fp = kftp_parse_url(fn, mode);
 		if (fp == 0) return 0;
 		if (kftp_connect(fp) == -1) {
 			knet_close(fp);
diff --git a/knetfile.h b/knetfile.h
index 85f348c..bf45f3d 100644
--- a/knetfile.h
+++ b/knetfile.h
@@ -29,8 +29,22 @@ extern "C" {
 #endif
 
 	knetFile *knet_open(const char *fn, const char *mode);
+
+	/* 
+	   This only works with local files.
+	 */
 	knetFile *knet_dopen(int fd, const char *mode);
+
+	/*
+	  If ->is_ready==0, this routine updates ->fd; otherwise, it simply
+	  reads from ->fd.
+	 */
 	off_t knet_read(knetFile *fp, void *buf, off_t len);
+
+	/*
+	  This routine only sets ->offset and ->is_ready=0. It does not
+	  communicate with the FTP server.
+	 */
 	int knet_seek(knetFile *fp, off_t off, int whence);
 	int knet_close(knetFile *fp);