Merge commit 'upstream/0.1.10'

[samtools.git] / bgzf.c

diff --git a/bgzf.c b/bgzf.c
index 646b2b4a142e2c35f4ab039b515e68fcd9126d66..66d6b024f5441f694faf1d875febe9fe8e3c248c 100644 (file)
--- a/bgzf.c
+++ b/bgzf.c
@@ -177,7 +177,7 @@ 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;
@@ -194,18 +194,16 @@ 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') {
+    } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
                int fd, oflag = O_WRONLY | O_CREAT | O_TRUNC;
 #ifdef _WIN32
                oflag |= O_BINARY;
 #endif
-               fd = open(path, oflag, 0644);
+               fd = open(path, oflag, 0666);
                if (fd == -1) return 0;
-        fp = open_write(fd, strstr(mode, "u")? 1 : 0);
-    }
-    if (fp != NULL) {
-        fp->owned_file = 1;
+        fp = open_write(fd, strchr(mode, 'u')? 1 : 0);
     }
+    if (fp != NULL) fp->owned_file = 1;
     return fp;
 }
 
@@ -429,20 +427,19 @@ static void cache_block(BGZF *fp, int size)
        memcpy(kh_val(h, k).block, fp->uncompressed_block, MAX_BLOCK_SIZE);
 }
 
-static
 int
-read_block(BGZF* fp)
+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;
@@ -472,9 +469,7 @@ 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;
@@ -501,7 +496,7 @@ bgzf_read(BGZF* fp, void* data, int length)
     while (bytes_read < length) {
         int available = fp->block_length - fp->block_offset;
         if (available <= 0) {
-            if (read_block(fp) != 0) {
+            if (bgzf_read_block(fp) != 0) {
                 return -1;
             }
             available = fp->block_length - fp->block_offset;
@@ -528,19 +523,16 @@ bgzf_read(BGZF* fp, void* data, int length)
     return bytes_read;
 }
 
-static
-int
-flush_block(BGZF* fp)
+int bgzf_flush(BGZF* fp)
 {
     while (fp->block_offset > 0) {
-        int block_length = deflate_block(fp, fp->block_offset);
-        if (block_length < 0) {
-            return -1;
-        }
+        int count, block_length;
+               block_length = deflate_block(fp, fp->block_offset);
+        if (block_length < 0) return -1;
 #ifdef _USE_KNETFILE
-        int count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
+        count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
 #else
-        int count = fwrite(fp->compressed_block, 1, block_length, fp->file);
+        count = fwrite(fp->compressed_block, 1, block_length, fp->file);
 #endif
         if (count != block_length) {
             report_error(fp, "write failed");
@@ -551,17 +543,22 @@ flush_block(BGZF* fp)
     return 0;
 }
 
-int
-bgzf_write(BGZF* fp, const void* data, int length)
+int bgzf_flush_try(BGZF *fp, int size)
+{
+       if (fp->block_offset + size > fp->uncompressed_block_size)
+               return bgzf_flush(fp);
+       return -1;
+}
+
+int bgzf_write(BGZF* fp, const void* data, int length)
 {
     if (fp->open_mode != 'w') {
         report_error(fp, "file not open for writing");
         return -1;
     }
 
-    if (fp->uncompressed_block == NULL) {
+    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;
@@ -574,7 +571,7 @@ bgzf_write(BGZF* fp, const void* data, int length)
         input += copy_length;
         bytes_written += copy_length;
         if (fp->block_offset == block_length) {
-            if (flush_block(fp) != 0) {
+            if (bgzf_flush(fp) != 0) {
                 break;
             }
         }
@@ -582,13 +579,10 @@ bgzf_write(BGZF* fp, const void* data, int length)
     return bytes_written;
 }
 
-int
-bgzf_close(BGZF* fp)
+int bgzf_close(BGZF* fp)
 {
     if (fp->open_mode == 'w') {
-        if (flush_block(fp) != 0) {
-            return -1;
-        }
+        if (bgzf_flush(fp) != 0) return -1;
                { // add an empty block
                        int count, block_length = deflate_block(fp, 0);
 #ifdef _USE_KNETFILE
@@ -613,9 +607,7 @@ 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);
@@ -625,12 +617,6 @@ bgzf_close(BGZF* fp)
     return 0;
 }
 
-int64_t
-bgzf_tell(BGZF* fp)
-{
-    return ((fp->block_address << 16) | (fp->block_offset & 0xFFFF));
-}
-
 void bgzf_set_cache_size(BGZF *fp, int cache_size)
 {
        if (fp) fp->cache_size = cache_size;
@@ -655,9 +641,11 @@ int bgzf_check_EOF(BGZF *fp)
        return (memcmp(magic, buf, 28) == 0)? 1 : 0;
 }
 
-int64_t
-bgzf_seek(BGZF* fp, int64_t pos, int where)
+int64_t bgzf_seek(BGZF* fp, int64_t pos, int where)
 {
+       int block_offset;
+       int64_t block_address;
+
     if (fp->open_mode != 'r') {
         report_error(fp, "file not open for read");
         return -1;
@@ -666,8 +654,8 @@ bgzf_seek(BGZF* fp, int64_t pos, int where)
         report_error(fp, "unimplemented seek option");
         return -1;
     }
-    int block_offset = pos & 0xFFFF;
-    int64_t block_address = (pos >> 16) & 0xFFFFFFFFFFFFLL;
+    block_offset = pos & 0xFFFF;
+    block_address = (pos >> 16) & 0xFFFFFFFFFFFFLL;
 #ifdef _USE_KNETFILE
     if (knet_seek(fp->x.fpr, block_address, SEEK_SET) != 0) {
 #else