* no changes to samtools itself

[samtools.git] / razf.c

diff --git a/razf.c b/razf.c
index 80aef2c5b7faa4e9b1a785e416c470bad9355f1d..c782cad33f323ff8af511c805945e10c7f41a8cf 100644 (file)
--- a/razf.c
+++ b/razf.c
@@ -35,9 +35,31 @@
 
 #include <fcntl.h>
 #include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 #include <unistd.h>
 #include "razf.h"
 
+#if ZLIB_VERNUM < 0x1221
+struct _gz_header_s {
+    int     text;
+    uLong   time;
+    int     xflags;
+    int     os;
+    Bytef   *extra;
+    uInt    extra_len;
+    uInt    extra_max;
+    Bytef   *name;
+    uInt    name_max;
+    Bytef   *comment;
+    uInt    comm_max;
+    int     hcrc;
+    int     done;
+};
+#endif
+
+#define DEF_MEM_LEVEL 8
+
 static inline uint32_t byte_swap_4(uint32_t v){
        v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
        return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
@@ -55,6 +77,7 @@ static inline int is_big_endian(){
        return (c[0] != 0x01);
 }
 
+#ifndef _RZ_READONLY
 static void add_zindex(RAZF *rz, int64_t in, int64_t out){
        if(rz->index->size == rz->index->cap){
                rz->index->cap = rz->index->cap * 1.5 + 2;
@@ -83,6 +106,7 @@ static void save_zindex(RAZF *rz, int fd){
        write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
        write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
 }
+#endif
 
 static void load_zindex(RAZF *rz, int fd){
        int32_t i, v32;
@@ -104,6 +128,13 @@ static void load_zindex(RAZF *rz, int fd){
        }
 }
 
+#ifdef _RZ_READONLY
+static RAZF* razf_open_w(int fd)
+{
+       fprintf(stderr, "[razf_open_w] Writing is not available with zlib ver < 1.2.2.1\n");
+       return 0;
+}
+#else
 static RAZF* razf_open_w(int fd){
        RAZF *rz;
        rz = calloc(1, sizeof(RAZF));
@@ -233,6 +264,7 @@ int razf_write(RAZF* rz, const void *data, int size){
        _razf_buffered_write(rz, data, size);
        return ori_size;
 }
+#endif
 
 /* gzip flag byte */
 #define ASCII_FLAG   0x01 /* bit 0 set: file probably ascii text */
@@ -614,8 +646,8 @@ int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where)
 }
 
 void razf_close(RAZF *rz){
-       uint64_t v64;
        if(rz->mode == 'w'){
+#ifndef _RZ_READONLY
                razf_end_flush(rz);
                deflateEnd(rz->stream);
                save_zindex(rz, rz->filedes);
@@ -623,11 +655,12 @@ void razf_close(RAZF *rz){
                        write(rz->filedes, &rz->in, sizeof(int64_t));
                        write(rz->filedes, &rz->out, sizeof(int64_t));
                } else {
-                       v64 = byte_swap_8((uint64_t)rz->in);
+                       uint64_t v64 = byte_swap_8((uint64_t)rz->in);
                        write(rz->filedes, &v64, sizeof(int64_t));
                        v64 = byte_swap_8((uint64_t)rz->out);
                        write(rz->filedes, &v64, sizeof(int64_t));
                }
+#endif
        } else if(rz->mode == 'r'){
                if(rz->stream) inflateEnd(rz->stream);
        }