Imported Upstream version 0.1.7~dfsg

[samtools.git] / razf.c

diff --git a/razf.c b/razf.c
index a5e8f5161a8d0780a820556e0e6640fd9762bb12..e7499f9f61e6c2fae4ec71a5f4a500ed5b151fe8 100644 (file)
--- a/razf.c
+++ b/razf.c
@@ -38,6 +38,7 @@
 #include <unistd.h>
 #include "razf.h"
 
+
 #if ZLIB_VERNUM < 0x1221
 struct _gz_header_s {
     int     text;
@@ -107,20 +108,36 @@ static void save_zindex(RAZF *rz, int fd){
 }
 #endif
 
+#ifdef _USE_KNETFILE
+static void load_zindex(RAZF *rz, knetFile *fp){
+#else
 static void load_zindex(RAZF *rz, int fd){
+#endif
        int32_t i, v32;
        int is_be;
        if(!rz->load_index) return;
        if(rz->index == NULL) rz->index = malloc(sizeof(ZBlockIndex));
        is_be = is_big_endian();
+#ifdef _USE_KNETFILE
+       knet_read(fp, &rz->index->size, sizeof(int));
+#else
        read(fd, &rz->index->size, sizeof(int));
+#endif
        if(!is_be) rz->index->size = byte_swap_4((uint32_t)rz->index->size);
        rz->index->cap = rz->index->size;
        v32 = rz->index->size / RZ_BIN_SIZE + 1;
        rz->index->bin_offsets  = malloc(sizeof(int64_t) * v32);
+#ifdef _USE_KNETFILE
+       knet_read(fp, rz->index->bin_offsets, sizeof(int64_t) * v32);
+#else
        read(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
+#endif
        rz->index->cell_offsets = malloc(sizeof(int) * rz->index->size);
+#ifdef _USE_KNETFILE
+       knet_read(fp, rz->index->cell_offsets, sizeof(int) * rz->index->size);
+#else
        read(fd, rz->index->cell_offsets, sizeof(int) * rz->index->size);
+#endif
        if(!is_be){
                for(i=0;i<v32;i++) rz->index->bin_offsets[i] = byte_swap_8((uint64_t)rz->index->bin_offsets[i]);
                for(i=0;i<rz->index->size;i++) rz->index->cell_offsets[i] = byte_swap_4((uint32_t)rz->index->cell_offsets[i]);
@@ -141,7 +158,11 @@ static RAZF* razf_open_w(int fd){
 #endif
        rz = calloc(1, sizeof(RAZF));
        rz->mode = 'w';
+#ifdef _USE_KNETFILE
+    rz->x.fpw = fd;
+#else
        rz->filedes = fd;
+#endif
        rz->stream = calloc(sizeof(z_stream), 1);
        rz->inbuf  = malloc(RZ_BUFFER_SIZE);
        rz->outbuf = malloc(RZ_BUFFER_SIZE);
@@ -176,7 +197,11 @@ static void _razf_write(RAZF* rz, const void *data, int size){
                deflate(rz->stream, Z_NO_FLUSH);
                rz->out += tout - rz->stream->avail_out;
                if(rz->stream->avail_out) break;
+#ifdef _USE_KNETFILE
+               write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#else
                write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#endif
                rz->stream->avail_out = RZ_BUFFER_SIZE;
                rz->stream->next_out  = rz->outbuf;
                if(rz->stream->avail_in == 0) break;
@@ -192,7 +217,11 @@ static void razf_flush(RAZF *rz){
                rz->buf_off = rz->buf_len = 0;
        }
        if(rz->stream->avail_out){
+#ifdef _USE_KNETFILE    
+               write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#else        
                write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#endif
                rz->stream->avail_out = RZ_BUFFER_SIZE;
                rz->stream->next_out  = rz->outbuf;
        }
@@ -201,7 +230,11 @@ static void razf_flush(RAZF *rz){
                deflate(rz->stream, Z_FULL_FLUSH);
                rz->out += tout - rz->stream->avail_out;
                if(rz->stream->avail_out == 0){
+#ifdef _USE_KNETFILE    
+                       write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#else            
                        write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#endif
                        rz->stream->avail_out = RZ_BUFFER_SIZE;
                        rz->stream->next_out  = rz->outbuf;
                } else break;
@@ -221,7 +254,11 @@ static void razf_end_flush(RAZF *rz){
                deflate(rz->stream, Z_FINISH);
                rz->out += tout - rz->stream->avail_out;
                if(rz->stream->avail_out < RZ_BUFFER_SIZE){
+#ifdef _USE_KNETFILE        
+                       write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#else            
                        write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#endif
                        rz->stream->avail_out = RZ_BUFFER_SIZE;
                        rz->stream->next_out  = rz->outbuf;
                } else break;
@@ -308,23 +345,35 @@ static int _read_gz_header(unsigned char *data, int size, int *extra_off, int *e
        return n;
 }
 
+#ifdef _USE_KNETFILE
+static RAZF* razf_open_r(knetFile *fp, int _load_index){
+#else
 static RAZF* razf_open_r(int fd, int _load_index){
+#endif
        RAZF *rz;
        int ext_off, ext_len;
        int n, is_be, ret;
        int64_t end;
        unsigned char c[] = "RAZF";
+       rz = calloc(1, sizeof(RAZF));
+       rz->mode = 'r';
+#ifdef _USE_KNETFILE
+    rz->x.fpr = fp;
+#else
 #ifdef _WIN32
        setmode(fd, O_BINARY);
 #endif
-       rz = calloc(1, sizeof(RAZF));
-       rz->mode = 'r';
        rz->filedes = fd;
+#endif
        rz->stream = calloc(sizeof(z_stream), 1);
        rz->inbuf  = malloc(RZ_BUFFER_SIZE);
        rz->outbuf = malloc(RZ_BUFFER_SIZE);
        rz->end = rz->src_end = 0x7FFFFFFFFFFFFFFFLL;
+#ifdef _USE_KNETFILE
+    n = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
+#else
        n = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE);
+#endif
        ret = _read_gz_header(rz->inbuf, n, &ext_off, &ext_len);
        if(ret == 0){
                PLAIN_FILE:
@@ -355,7 +404,11 @@ static RAZF* razf_open_r(int fd, int _load_index){
        }
        rz->load_index = _load_index;
        rz->file_type = FILE_TYPE_RZ;
+#ifdef _USE_KNETFILE
+       if(knet_seek(fp, -16, SEEK_END) == -1){
+#else
        if(lseek(fd, -16, SEEK_END) == -1){
+#endif
                UNSEEKABLE:
                rz->seekable = 0;
                rz->index = NULL;
@@ -363,10 +416,19 @@ static RAZF* razf_open_r(int fd, int _load_index){
        } else {
                is_be = is_big_endian();
                rz->seekable = 1;
+#ifdef _USE_KNETFILE
+        knet_read(fp, &end, sizeof(int64_t));
+#else
                read(fd, &end, sizeof(int64_t));
+#endif        
                if(!is_be) rz->src_end = (int64_t)byte_swap_8((uint64_t)end);
                else rz->src_end = end;
+
+#ifdef _USE_KNETFILE
+               knet_read(fp, &end, sizeof(int64_t));
+#else
                read(fd, &end, sizeof(int64_t));
+#endif        
                if(!is_be) rz->end = (int64_t)byte_swap_8((uint64_t)end);
                else rz->end = end;
                if(n > rz->end){
@@ -374,19 +436,47 @@ static RAZF* razf_open_r(int fd, int _load_index){
                        n = rz->end;
                }
                if(rz->end > rz->src_end){
+#ifdef _USE_KNETFILE
+            knet_seek(fp, rz->in, SEEK_SET);
+#else
                        lseek(fd, rz->in, SEEK_SET);
+#endif
                        goto UNSEEKABLE;
                }
+#ifdef _USE_KNETFILE
+        knet_seek(fp, rz->end, SEEK_SET);
+               if(knet_tell(fp) != rz->end){
+                       knet_seek(fp, rz->in, SEEK_SET);
+#else
                if(lseek(fd, rz->end, SEEK_SET) != rz->end){
                        lseek(fd, rz->in, SEEK_SET);
+#endif
                        goto UNSEEKABLE;
                }
+#ifdef _USE_KNETFILE
+               load_zindex(rz, fp);
+               knet_seek(fp, n, SEEK_SET);
+#else
                load_zindex(rz, fd);
                lseek(fd, n, SEEK_SET);
+#endif
        }
        return rz;
 }
 
+#ifdef _USE_KNETFILE
+RAZF* razf_dopen(int fd, const char *mode){
+    if (strstr(mode, "r")) fprintf(stderr,"[razf_dopen] implement me\n");
+    else if(strstr(mode, "w")) return razf_open_w(fd);
+       return NULL;
+}
+
+RAZF* razf_dopen2(int fd, const char *mode)
+{
+    fprintf(stderr,"[razf_dopen2] implement me\n");
+    return NULL;
+}
+#else
 RAZF* razf_dopen(int fd, const char *mode){
        if(strstr(mode, "r")) return razf_open_r(fd, 1);
        else if(strstr(mode, "w")) return razf_open_w(fd);
@@ -399,23 +489,34 @@ RAZF* razf_dopen2(int fd, const char *mode)
        else if(strstr(mode, "w")) return razf_open_w(fd);
        else return NULL;
 }
+#endif
 
 static inline RAZF* _razf_open(const char *filename, const char *mode, int _load_index){
        int fd;
        RAZF *rz;
        if(strstr(mode, "r")){
+#ifdef _USE_KNETFILE
+        knetFile *fd = knet_open(filename, "r");
+        if (fd == 0) {
+            fprintf(stderr, "[_razf_open] fail to open %s\n", filename);
+            return NULL;
+        }
+#else
 #ifdef _WIN32
                fd = open(filename, O_RDONLY | O_BINARY);
 #else
                fd = open(filename, O_RDONLY);
 #endif
+#endif
+               if(fd < 0) return NULL;
                rz = razf_open_r(fd, _load_index);
        } else if(strstr(mode, "w")){
 #ifdef _WIN32
-               fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC | O_BINARY, 0644);
+               fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC | O_BINARY, 0666);
 #else
-               fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC, 0644);
+               fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC, 0666);
 #endif
+               if(fd < 0) return NULL;
                rz = razf_open_w(fd);
        } else return NULL;
        return rz;
@@ -435,9 +536,17 @@ int razf_get_data_size(RAZF *rz, int64_t *u_size, int64_t *c_size){
        switch(rz->file_type){
                case FILE_TYPE_PLAIN:
                        if(rz->end == 0x7fffffffffffffffLL){
+#ifdef _USE_KNETFILE
+                               if(knet_seek(rz->x.fpr, 0, SEEK_CUR) == -1) return 0;
+                n = knet_tell(rz->x.fpr);
+                               knet_seek(rz->x.fpr, 0, SEEK_END);
+                rz->end = knet_tell(rz->x.fpr);
+                               knet_seek(rz->x.fpr, n, SEEK_SET);
+#else
                                if((n = lseek(rz->filedes, 0, SEEK_CUR)) == -1) return 0;
                                rz->end = lseek(rz->filedes, 0, SEEK_END);
                                lseek(rz->filedes, n, SEEK_SET);
+#endif                
                        }
                        *u_size = *c_size = rz->end;
                        return 1;
@@ -457,7 +566,11 @@ static int _razf_read(RAZF* rz, void *data, int size){
        int ret, tin;
        if(rz->z_eof || rz->z_err) return 0;
        if (rz->file_type == FILE_TYPE_PLAIN) {
+#ifdef _USE_KNETFILE
+               ret = knet_read(rz->x.fpr, data, size);
+#else
                ret = read(rz->filedes, data, size);
+#endif        
                if (ret == 0) rz->z_eof = 1;
                return ret;
        }
@@ -467,9 +580,17 @@ static int _razf_read(RAZF* rz, void *data, int size){
                if(rz->stream->avail_in == 0){
                        if(rz->in >= rz->end){ rz->z_eof = 1; break; }
                        if(rz->end - rz->in < RZ_BUFFER_SIZE){
+#ifdef _USE_KNETFILE
+                               rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, rz->end -rz->in);
+#else
                                rz->stream->avail_in = read(rz->filedes, rz->inbuf, rz->end -rz->in);
+#endif        
                        } else {
+#ifdef _USE_KNETFILE
+                               rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
+#else
                                rz->stream->avail_in = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE);
+#endif        
                        }
                        if(rz->stream->avail_in == 0){
                                rz->z_eof = 1;
@@ -481,7 +602,7 @@ static int _razf_read(RAZF* rz, void *data, int size){
                ret = inflate(rz->stream, Z_BLOCK);
                rz->in += tin - rz->stream->avail_in;
                if(ret == Z_NEED_DICT || ret == Z_MEM_ERROR || ret == Z_DATA_ERROR){
-                       fprintf(stderr, "[_razf_read] inflate error: %d (at %s:%d)\n", ret, __FILE__, __LINE__);
+                       fprintf(stderr, "[_razf_read] inflate error: %d %s (at %s:%d)\n", ret, rz->stream->msg ? rz->stream->msg : "", __FILE__, __LINE__);
                        rz->z_err = 1;
                        break;
                }
@@ -566,14 +687,18 @@ int razf_skip(RAZF* rz, int size){
                }
                if(rz->buf_flush) continue;
                rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE);
-               if(rz->z_eof) break;
+               if(rz->z_eof || rz->z_err) break;
        }
        rz->out += ori_size - size;
        return ori_size - size;
 }
 
 static void _razf_reset_read(RAZF *rz, int64_t in, int64_t out){
+#ifdef _USE_KNETFILE
+       knet_seek(rz->x.fpr, in, SEEK_SET);
+#else
        lseek(rz->filedes, in, SEEK_SET);
+#endif
        rz->in  = in;
        rz->out = out;
        rz->block_pos = in;
@@ -592,7 +717,12 @@ int64_t razf_jump(RAZF *rz, int64_t block_start, int block_offset){
        if(rz->file_type == FILE_TYPE_PLAIN){
                rz->buf_off = rz->buf_len = 0;
                pos = block_start + block_offset;
+#ifdef _USE_KNETFILE
+               knet_seek(rz->x.fpr, pos, SEEK_SET);
+        pos = knet_tell(rz->x.fpr);
+#else
                pos = lseek(rz->filedes, pos, SEEK_SET);
+#endif
                rz->out = rz->in = pos;
                return pos;
        }
@@ -614,7 +744,12 @@ int64_t razf_seek(RAZF* rz, int64_t pos, int where){
        if (where == SEEK_CUR) pos += rz->out;
        else if (where == SEEK_END) pos += rz->src_end;
        if(rz->file_type == FILE_TYPE_PLAIN){
+#ifdef _USE_KNETFILE
+               knet_seek(rz->x.fpr, pos, SEEK_SET);
+        seek_pos = knet_tell(rz->x.fpr);
+#else
                seek_pos = lseek(rz->filedes, pos, SEEK_SET);
+#endif
                rz->buf_off = rz->buf_len = 0;
                rz->out = rz->in = seek_pos;
                return seek_pos;
@@ -663,6 +798,18 @@ void razf_close(RAZF *rz){
 #ifndef _RZ_READONLY
                razf_end_flush(rz);
                deflateEnd(rz->stream);
+#ifdef _USE_KNETFILE
+               save_zindex(rz, rz->x.fpw);
+               if(is_big_endian()){
+                       write(rz->x.fpw, &rz->in, sizeof(int64_t));
+                       write(rz->x.fpw, &rz->out, sizeof(int64_t));
+               } else {
+                       uint64_t v64 = byte_swap_8((uint64_t)rz->in);
+                       write(rz->x.fpw, &v64, sizeof(int64_t));
+                       v64 = byte_swap_8((uint64_t)rz->out);
+                       write(rz->x.fpw, &v64, sizeof(int64_t));
+               }
+#else
                save_zindex(rz, rz->filedes);
                if(is_big_endian()){
                        write(rz->filedes, &rz->in, sizeof(int64_t));
@@ -673,6 +820,7 @@ void razf_close(RAZF *rz){
                        v64 = byte_swap_8((uint64_t)rz->out);
                        write(rz->filedes, &v64, sizeof(int64_t));
                }
+#endif
 #endif
        } else if(rz->mode == 'r'){
                if(rz->stream) inflateEnd(rz->stream);
@@ -691,7 +839,14 @@ void razf_close(RAZF *rz){
                free(rz->index);
        }
        free(rz->stream);
+#ifdef _USE_KNETFILE
+    if (rz->mode == 'r')
+        knet_close(rz->x.fpr);
+    if (rz->mode == 'w')
+        close(rz->x.fpw);
+#else
        close(rz->filedes);
+#endif
        free(rz);
 }