* samtools-0.1.7-9 (r586)

 * added "reheader" to replace the BAM header

diff --git a/Makefile b/Makefile
index 0ab4498a10f81cfb4f0d677d393e354551b379b2..f9a406e5f3f7ffad175ce33e1017e805b0e9ed2b 100644 (file)
--- 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 (file)
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 ec91abc76c37e227da1d39064bdc163ed3bf59dd..9edb6cb8402032cfa1cdbc7a97ce6b8c853914f1 100644 (file)
--- 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 27dfe3dc2f1346c4ce9b176acd13beada972f996..a6923daa0cc1cfa8d0d0bc2269255326be8439e3 100644 (file)
--- 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);