bcftools.1 and samtools.1 were merged in upstream release 0.1.17.

[samtools.git] / bgzf.c

diff --git a/bgzf.c b/bgzf.c
index a6923daa0cc1cfa8d0d0bc2269255326be8439e3..216cd04527f1ad187420cf1fab781e1d72e485b8 100644 (file)
--- a/bgzf.c
+++ b/bgzf.c
@@ -111,6 +111,32 @@ report_error(BGZF* fp, const char* message) {
     fp->error = message;
 }
 
+int bgzf_check_bgzf(const char *fn)
+{
+    BGZF *fp;
+    uint8_t buf[10],magic[10]="\037\213\010\4\0\0\0\0\0\377";
+    int n;
+
+    if ((fp = bgzf_open(fn, "r")) == 0) 
+    {
+        fprintf(stderr, "[bgzf_check_bgzf] failed to open the file: %s\n",fn);
+        return -1;
+    }
+
+#ifdef _USE_KNETFILE
+    n = knet_read(fp->x.fpr, buf, 10);
+#else
+    n = fread(buf, 1, 10, fp->file);
+#endif
+    bgzf_close(fp);
+
+    if ( n!=10 ) 
+        return -1;
+
+    if ( !memcmp(magic, buf, 10) ) return 1;
+    return 0;
+}
+
 static BGZF *bgzf_read_init()
 {
        BGZF *fp;
@@ -148,7 +174,7 @@ open_read(int fd)
 
 static
 BGZF*
-open_write(int fd, bool is_uncompressed)
+open_write(int fd, int compress_level) // compress_level==-1 for the default level
 {
     FILE* file = fdopen(fd, "w");
     BGZF* fp;
@@ -156,7 +182,9 @@ open_write(int fd, bool is_uncompressed)
        fp = malloc(sizeof(BGZF));
     fp->file_descriptor = fd;
     fp->open_mode = 'w';
-    fp->owned_file = 0; fp->is_uncompressed = is_uncompressed;
+    fp->owned_file = 0;
+       fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1
+       if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION;
 #ifdef _USE_KNETFILE
     fp->x.fpw = file;
 #else
@@ -177,7 +205,7 @@ BGZF*
 bgzf_open(const char* __restrict path, const char* __restrict mode)
 {
     BGZF* fp = NULL;
-    if (mode[0] == 'r' || mode[0] == 'R') { /* The reading mode is preferred. */
+    if (strchr(mode, 'r') || strchr(mode, 'R')) { /* The reading mode is preferred. */
 #ifdef _USE_KNETFILE
                knetFile *file = knet_open(path, mode);
                if (file == 0) return 0;
@@ -194,14 +222,21 @@ bgzf_open(const char* __restrict path, const char* __restrict mode)
                if (fd == -1) return 0;
         fp = open_read(fd);
 #endif
-    } else if (mode[0] == 'w' || mode[0] == 'W') {
-               int fd, oflag = O_WRONLY | O_CREAT | O_TRUNC;
+    } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
+               int fd, compress_level = -1, oflag = O_WRONLY | O_CREAT | O_TRUNC;
 #ifdef _WIN32
                oflag |= O_BINARY;
 #endif
                fd = open(path, oflag, 0666);
                if (fd == -1) return 0;
-        fp = open_write(fd, strstr(mode, "u")? 1 : 0);
+               { // set compress_level
+                       int i;
+                       for (i = 0; mode[i]; ++i)
+                               if (mode[i] >= '0' && mode[i] <= '9') break;
+                       if (mode[i]) compress_level = (int)mode[i] - '0';
+                       if (strchr(mode, 'u')) compress_level = 0;
+               }
+        fp = open_write(fd, compress_level);
     }
     if (fp != NULL) fp->owned_file = 1;
     return fp;
@@ -214,7 +249,12 @@ bgzf_fdopen(int fd, const char * __restrict mode)
     if (mode[0] == 'r' || mode[0] == 'R') {
         return open_read(fd);
     } else if (mode[0] == 'w' || mode[0] == 'W') {
-        return open_write(fd, strstr(mode, "u")? 1 : 0);
+               int i, compress_level = -1;
+               for (i = 0; mode[i]; ++i)
+                       if (mode[i] >= '0' && mode[i] <= '9') break;
+               if (mode[i]) compress_level = (int)mode[i] - '0';
+               if (strchr(mode, 'u')) compress_level = 0;
+        return open_write(fd, compress_level);
     } else {
         return NULL;
     }
@@ -254,7 +294,6 @@ deflate_block(BGZF* fp, int block_length)
     int input_length = block_length;
     int compressed_length = 0;
     while (1) {
-               int compress_level = fp->is_uncompressed? 0 : Z_DEFAULT_COMPRESSION;
         z_stream zs;
         zs.zalloc = NULL;
         zs.zfree = NULL;
@@ -263,7 +302,7 @@ deflate_block(BGZF* fp, int block_length)
         zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH];
         zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
 
-        int status = deflateInit2(&zs, compress_level, Z_DEFLATED,
+        int status = deflateInit2(&zs, fp->compress_level, Z_DEFLATED,
                                   GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
         if (status != Z_OK) {
             report_error(fp, "deflate init failed");
@@ -330,6 +369,7 @@ inflate_block(BGZF* fp, int block_length)
     // Inflate the block in fp->compressed_block into fp->uncompressed_block
 
     z_stream zs;
+       int status;
     zs.zalloc = NULL;
     zs.zfree = NULL;
     zs.next_in = fp->compressed_block + 18;
@@ -337,7 +377,7 @@ inflate_block(BGZF* fp, int block_length)
     zs.next_out = fp->uncompressed_block;
     zs.avail_out = fp->uncompressed_block_size;
 
-    int status = inflateInit2(&zs, GZIP_WINDOW_BITS);
+    status = inflateInit2(&zs, GZIP_WINDOW_BITS);
     if (status != Z_OK) {
         report_error(fp, "inflate init failed");
         return -1;
@@ -431,7 +471,7 @@ int
 bgzf_read_block(BGZF* fp)
 {
     bgzf_byte_t header[BLOCK_HEADER_LENGTH];
-       int count, size = 0;
+       int count, size = 0, block_length, remaining;
 #ifdef _USE_KNETFILE
     int64_t block_address = knet_tell(fp->x.fpr);
        if (load_block_from_cache(fp, block_address)) return 0;
@@ -454,10 +494,10 @@ bgzf_read_block(BGZF* fp)
         report_error(fp, "invalid block header");
         return -1;
     }
-    int block_length = unpackInt16((uint8_t*)&header[16]) + 1;
+    block_length = unpackInt16((uint8_t*)&header[16]) + 1;
     bgzf_byte_t* compressed_block = (bgzf_byte_t*) fp->compressed_block;
     memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
-    int remaining = block_length - BLOCK_HEADER_LENGTH;
+    remaining = block_length - BLOCK_HEADER_LENGTH;
 #ifdef _USE_KNETFILE
     count = knet_read(fp->x.fpr, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
 #else
@@ -494,7 +534,8 @@ bgzf_read(BGZF* fp, void* data, int length)
     int bytes_read = 0;
     bgzf_byte_t* output = data;
     while (bytes_read < length) {
-        int available = fp->block_length - fp->block_offset;
+        int copy_length, available = fp->block_length - fp->block_offset;
+               bgzf_byte_t *buffer;
         if (available <= 0) {
             if (bgzf_read_block(fp) != 0) {
                 return -1;
@@ -504,8 +545,8 @@ bgzf_read(BGZF* fp, void* data, int length)
                 break;
             }
         }
-        int copy_length = bgzf_min(length-bytes_read, available);
-        bgzf_byte_t* buffer = fp->uncompressed_block;
+        copy_length = bgzf_min(length-bytes_read, available);
+        buffer = fp->uncompressed_block;
         memcpy(output, buffer + fp->block_offset, copy_length);
         fp->block_offset += copy_length;
         output += copy_length;
@@ -552,6 +593,8 @@ int bgzf_flush_try(BGZF *fp, int size)
 
 int bgzf_write(BGZF* fp, const void* data, int length)
 {
+       const bgzf_byte_t *input = data;
+       int block_length, bytes_written;
     if (fp->open_mode != 'w') {
         report_error(fp, "file not open for writing");
         return -1;
@@ -560,9 +603,9 @@ int bgzf_write(BGZF* fp, const void* data, int length)
     if (fp->uncompressed_block == NULL)
         fp->uncompressed_block = malloc(fp->uncompressed_block_size);
 
-    const bgzf_byte_t* input = data;
-    int block_length = fp->uncompressed_block_size;
-    int bytes_written = 0;
+    input = data;
+    block_length = fp->uncompressed_block_size;
+    bytes_written = 0;
     while (bytes_written < length) {
         int copy_length = bgzf_min(block_length - fp->block_offset, length - bytes_written);
         bgzf_byte_t* buffer = fp->uncompressed_block;