From: Heng Li <lh3@live.co.uk>
Date: Fri, 11 Jun 2010 17:23:53 +0000 (+0000)
Subject:  * samtools-0.1.7-9 (r586)
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=de48a5efc453a2fba80a1236b6bab37ecfd85260

 * samtools-0.1.7-9 (r586)
 * added "reheader" to replace the BAM header
---

diff --git a/Makefile b/Makefile
index 0ab4498..f9a406e 100644
--- a/Makefile
+++ b/Makefile
@@ -4,7 +4,7 @@ DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1
 KNETFILE_O=	knetfile.o
 LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
 			bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o \
-			$(KNETFILE_O) bam_sort.o sam_header.o
+			$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o
 AOBJS=		bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o	\
 			bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o	\
 			bamtk.o kaln.o
diff --git a/bam_reheader.c b/bam_reheader.c
new file mode 100644
index 0000000..bae97c7
--- /dev/null
+++ b/bam_reheader.c
@@ -0,0 +1,60 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include "bgzf.h"
+#include "bam.h"
+
+#define BUF_SIZE 0x10000
+
+int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
+{
+	BGZF *fp;
+	bam_header_t *old;
+	int len;
+	uint8_t *buf;
+	if (in->open_mode != 'r') return -1;
+	buf = malloc(BUF_SIZE);
+	old = bam_header_read(in);
+	fp = bgzf_fdopen(fd, "w");
+	bam_header_write(fp, h);
+	if (in->block_offset < in->block_length) {
+		bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
+		bgzf_flush(fp);
+	}
+#ifdef _USE_KNETFILE
+	while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0)
+#else
+	while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
+#endif
+		fwrite(buf, 1, len, fp->x.fpw);
+	free(buf);
+	fp->block_offset = in->block_offset = 0;
+	bgzf_close(fp);
+	return 0;
+}
+
+int main_reheader(int argc, char *argv[])
+{
+	bam_header_t *h;
+	BGZF *in;
+	if (argc != 3) {
+		fprintf(stderr, "Usage: samtools reheader <in.header.sam> <in.bam>\n");
+		return 1;
+	}
+	{ // read the header
+		tamFile fph = sam_open(argv[1]);
+		if (fph == 0) {
+			fprintf(stderr, "[%s] fail to read the header from %s.\n", __func__, argv[1]);
+			return 1;
+		}
+		h = sam_header_read(fph);
+		sam_close(fph);
+	}
+	in = strcmp(argv[2], "-")? bam_open(argv[2], "r") : bam_dopen(fileno(stdin), "r");
+	if (in == 0) {
+		fprintf(stderr, "[%s] fail to open file %s.\n", __func__, argv[2]);
+		return 1;
+	}
+	bam_reheader(in, h, fileno(stdout));
+	bgzf_close(in);
+	return 0;
+}
diff --git a/bamtk.c b/bamtk.c
index ec91abc..9edb6cb 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.7-8 (r585)"
+#define PACKAGE_VERSION "0.1.7-9 (r586)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -25,6 +25,7 @@ int bam_fillmd(int argc, char *argv[]);
 
 int main_samview(int argc, char *argv[]);
 int main_import(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
 
 int faidx_main(int argc, char *argv[]);
 int glf3_view_main(int argc, char *argv[]);
@@ -89,6 +90,7 @@ static int usage()
 	fprintf(stderr, "         calmd       recalculate MD/NM tags and '=' bases\n");
 	fprintf(stderr, "         merge       merge sorted alignments\n");
 	fprintf(stderr, "         rmdup       remove PCR duplicates\n");
+	fprintf(stderr, "         reheader    replace BAM header\n");
 	fprintf(stderr, "\n");
 	return 1;
 }
@@ -117,6 +119,7 @@ int main(int argc, char *argv[])
 	else if (strcmp(argv[1], "tagview") == 0) return bam_tagview(argc-1, argv+1);
 	else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
 	else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
+	else if (strcmp(argv[1], "reheader") == 0) return main_reheader(argc-1, argv+1);
 #if _CURSES_LIB != 0
 	else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif
diff --git a/bgzf.c b/bgzf.c
index 27dfe3d..a6923da 100644
--- a/bgzf.c
+++ b/bgzf.c
@@ -203,9 +203,7 @@ bgzf_open(const char* __restrict path, const char* __restrict mode)
 		if (fd == -1) return 0;
         fp = open_write(fd, strstr(mode, "u")? 1 : 0);
     }
-    if (fp != NULL) {
-        fp->owned_file = 1;
-    }
+    if (fp != NULL) fp->owned_file = 1;
     return fp;
 }
 
@@ -433,15 +431,15 @@ int
 bgzf_read_block(BGZF* fp)
 {
     bgzf_byte_t header[BLOCK_HEADER_LENGTH];
-	int size = 0;
+	int count, size = 0;
 #ifdef _USE_KNETFILE
     int64_t block_address = knet_tell(fp->x.fpr);
 	if (load_block_from_cache(fp, block_address)) return 0;
-    int count = knet_read(fp->x.fpr, header, sizeof(header));
+    count = knet_read(fp->x.fpr, header, sizeof(header));
 #else
     int64_t block_address = ftello(fp->file);
 	if (load_block_from_cache(fp, block_address)) return 0;
-    int count = fread(header, 1, sizeof(header), fp->file);
+    count = fread(header, 1, sizeof(header), fp->file);
 #endif
     if (count == 0) {
         fp->block_length = 0;
@@ -471,9 +469,7 @@ bgzf_read_block(BGZF* fp)
     }
 	size += count;
     count = inflate_block(fp, block_length);
-    if (count < 0) {
-        return -1;
-    }
+    if (count < 0) return -1;
     if (fp->block_length != 0) {
         // Do not reset offset if this read follows a seek.
         fp->block_offset = 0;
@@ -611,9 +607,7 @@ int bgzf_close(BGZF* fp)
 		else ret = knet_close(fp->x.fpr);
         if (ret != 0) return -1;
 #else
-        if (fclose(fp->file) != 0) {
-            return -1;
-        }
+        if (fclose(fp->file) != 0) return -1;
 #endif
     }
     free(fp->uncompressed_block);