X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=razf.c;h=f67447c33bde6478787a5f95c9d60a14061bb6a3;hb=17d79b44a564aa4d5853bbc0b5f97ec2cefc927b;hp=e7499f9f61e6c2fae4ec71a5f4a500ed5b151fe8;hpb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351;p=samtools.git

diff --git a/razf.c b/razf.c
index e7499f9..f67447c 100644
--- a/razf.c
+++ b/razf.c
@@ -79,10 +79,17 @@ static inline int is_big_endian(){
 
 #ifndef _RZ_READONLY
 static void add_zindex(RAZF *rz, int64_t in, int64_t out){
+	uint32_t *cores;
+	int64_t *bores;
+
 	if(rz->index->size == rz->index->cap){
 		rz->index->cap = rz->index->cap * 1.5 + 2;
-		rz->index->cell_offsets = realloc(rz->index->cell_offsets, sizeof(int) * rz->index->cap);
-		rz->index->bin_offsets  = realloc(rz->index->bin_offsets, sizeof(int64_t) * (rz->index->cap/RZ_BIN_SIZE + 1));
+		cores = realloc(rz->index->cell_offsets, sizeof(int) * rz->index->cap);
+		bores = realloc(rz->index->bin_offsets, sizeof(int64_t) * (rz->index->cap/RZ_BIN_SIZE + 1));
+		if ((cores == NULL) || (bores == NULL)) {
+			fprintf(stderr, "[%s] failure to allocate space for new zindex.\n", __func__);
+			abort();
+		}
 	}
 	if(rz->index->size % RZ_BIN_SIZE == 0) rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE] = out;
 	rz->index->cell_offsets[rz->index->size] = out - rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE];
@@ -90,21 +97,39 @@ static void add_zindex(RAZF *rz, int64_t in, int64_t out){
 }
 
 static void save_zindex(RAZF *rz, int fd){
+	size_t count;
 	int32_t i, v32;
 	int is_be;
 	is_be = is_big_endian();
-	if(is_be) write(fd, &rz->index->size, sizeof(int));
+	if(is_be) {
+		if (write(fd, &rz->index->size, sizeof(int)) < 0) {
+			fprintf(stderr, "[%s] failure to write zindex size.\n", __func__);
+			abort();
+		}
+	}
 	else {
 		v32 = byte_swap_4((uint32_t)rz->index->size);
-		write(fd, &v32, sizeof(uint32_t));
+		if (write(fd, &v32, sizeof(uint32_t)) < 0) {
+			fprintf(stderr, "[%s] failure to write zindex size.\n", __func__);
+			abort();
+		}
 	}
 	v32 = rz->index->size / RZ_BIN_SIZE + 1;
 	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]);
 	}
-	write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
-	write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
+	count = sizeof(int64_t) * v32;
+	if (write(fd, rz->index->bin_offsets, count) < 0) {
+		fprintf(stderr, "[%s] failure to write zindex bin_offsets.\n", __func__);
+		abort();
+	}
+
+	count = sizeof(int32_t) * rz->index->size;
+	if (write(fd, rz->index->cell_offsets, count) < 0) {
+		fprintf(stderr, "[%s] failure to write zindex cell_offsets.\n", __func__);
+		abort();
+	}
 }
 #endif
 
@@ -115,29 +140,52 @@ static void load_zindex(RAZF *rz, int fd){
 #endif
 	int32_t i, v32;
 	int is_be;
+	size_t count;
 	if(!rz->load_index) return;
-	if(rz->index == NULL) rz->index = malloc(sizeof(ZBlockIndex));
+	if(rz->index == NULL) {
+		if ((rz->index = malloc(sizeof(ZBlockIndex))) == NULL) {
+			fprintf(stderr, "[%s] failure to allocate index.\n", __func__);
+			abort();
+		}
+	}
 	is_be = is_big_endian();
 #ifdef _USE_KNETFILE
-	knet_read(fp, &rz->index->size, sizeof(int));
+	if (knet_read(fp, &rz->index->size, sizeof(int)) < 0) {
 #else
-	read(fd, &rz->index->size, sizeof(int));
+	if (read(fd, &rz->index->size, sizeof(int)) < 0) {
 #endif
+		fprintf(stderr, "[%s] failure to read zindex size.\n", __func__);
+		abort();
+	}
 	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);
+	count = sizeof(int64_t) * v32;
+	if ((rz->index->bin_offsets = malloc(count)) == NULL) {
+		fprintf(stderr, "[%s] failure to allocate bin_offsets array.\n", __func__);
+		abort();
+	}
 #ifdef _USE_KNETFILE
-	knet_read(fp, rz->index->bin_offsets, sizeof(int64_t) * v32);
+	if (knet_read(fp, rz->index->bin_offsets, count) < 0) {
 #else
-	read(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
+	if (read(fd, rz->index->bin_offsets, count) < 0) {
 #endif
-	rz->index->cell_offsets = malloc(sizeof(int) * rz->index->size);
+		fprintf(stderr, "[%s] failure to read bin_offsets.\n", __func__);
+		abort();
+	}
+	count = sizeof(int) * rz->index->size;
+	if ((rz->index->cell_offsets = malloc(count)) == NULL) {
+		fprintf(stderr, "[%s] failure to allocate cell_offsets array.\n", __func__);
+		abort();
+	}
 #ifdef _USE_KNETFILE
-	knet_read(fp, rz->index->cell_offsets, sizeof(int) * rz->index->size);
+	if (knet_read(fp, rz->index->cell_offsets, count) < count) {
 #else
-	read(fd, rz->index->cell_offsets, sizeof(int) * rz->index->size);
+	if (read(fd, rz->index->cell_offsets, count) < count) {
 #endif
+		fprintf(stderr, "[%s] failure to read cell_offsets.\n", __func__);
+		abort();
+	}
 	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]);
@@ -156,25 +204,68 @@ static RAZF* razf_open_w(int fd){
 #ifdef _WIN32
 	setmode(fd, O_BINARY);
 #endif
-	rz = calloc(1, sizeof(RAZF));
+	if ((rz = calloc(1, sizeof(RAZF))) == NULL) {
+		fprintf(stderr, "[%s] failure to allocate RAZF structure.\n", __func__);
+		return NULL;
+	}
 	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);
-	rz->index = calloc(sizeof(ZBlockIndex), 1);
+	if ((rz->stream = calloc(sizeof(z_stream), 1)) == NULL) {
+		fprintf(stderr, "[%s] failure to allocate stream buffer.\n", __func__);
+		free(rz);
+		return NULL;
+	}
+	if ((rz->inbuf  = malloc(RZ_BUFFER_SIZE)) == NULL) {
+		fprintf(stderr, "[%s] failure to allocate input buffer.\n", __func__);
+		free(rz->stream);
+		free(rz);
+		return NULL;
+	}
+	if ((rz->outbuf = malloc(RZ_BUFFER_SIZE)) == NULL) {
+		fprintf(stderr, "[%s] failure to allocate output buffer.\n", __func__);
+		free(rz->stream);
+		free(rz->inbuf);
+		free(rz);
+		return NULL;
+	}
+	if ((rz->index = calloc(sizeof(ZBlockIndex), 1)) == NULL) {
+		fprintf(stderr, "[%s] failure to allocate index.\n", __func__);
+		free(rz->stream);
+		free(rz->inbuf);
+		free(rz->outbuf);
+		free(rz);
+		return NULL;
+	}
+
 	deflateInit2(rz->stream, RZ_COMPRESS_LEVEL, Z_DEFLATED, WINDOW_BITS + 16, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY);
 	rz->stream->avail_out = RZ_BUFFER_SIZE;
 	rz->stream->next_out  = rz->outbuf;
-	rz->header = calloc(sizeof(gz_header), 1);
+	if ((rz->header = calloc(sizeof(gz_header), 1)) == NULL) {
+		fprintf(stderr, "[%s] failure to allocate header buffer.\n", __func__);
+		free(rz->stream);
+		free(rz->inbuf);
+		free(rz->outbuf);
+		free(rz->index);
+		free(rz);
+		return NULL;
+	}
 	rz->header->os    = 0x03; //Unix
 	rz->header->text  = 0;
 	rz->header->time  = 0;
-	rz->header->extra = malloc(7);
+	if ((rz->header->extra = malloc(7)) == NULL) {
+		fprintf(stderr, "[%s] failure to allocate header buffer.\n", __func__);
+		free(rz->stream);
+		free(rz->inbuf);
+		free(rz->outbuf);
+		free(rz->index);
+		free(rz->header);
+		free(rz);
+		return NULL;
+	}
 	strncpy((char*)rz->header->extra, "RAZF", 4);
 	rz->header->extra[4] = 1; // obsolete field
 	// block size = RZ_BLOCK_SIZE, Big-Endian
@@ -190,6 +281,7 @@ static RAZF* razf_open_w(int fd){
 
 static void _razf_write(RAZF* rz, const void *data, int size){
 	int tout;
+	size_t count;
 	rz->stream->avail_in = size;
 	rz->stream->next_in  = (void*)data;
 	while(1){
@@ -197,11 +289,15 @@ 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;
+		count = RZ_BUFFER_SIZE - rz->stream->avail_out;
 #ifdef _USE_KNETFILE
-		write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+		if (write(rz->x.fpw, rz->outbuf, count) < 0) {
 #else
-		write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+		if (write(rz->filedes, rz->outbuf, count) < 0) {
 #endif
+			fprintf(stderr, "[%s] failed to write output buffer.\n", __func__);
+			abort();
+		}
 		rz->stream->avail_out = RZ_BUFFER_SIZE;
 		rz->stream->next_out  = rz->outbuf;
 		if(rz->stream->avail_in == 0) break;
@@ -211,17 +307,22 @@ static void _razf_write(RAZF* rz, const void *data, int size){
 }
 
 static void razf_flush(RAZF *rz){
+	size_t count;
 	uint32_t tout;
 	if(rz->buf_len){
 		_razf_write(rz, rz->inbuf, rz->buf_len);
 		rz->buf_off = rz->buf_len = 0;
 	}
 	if(rz->stream->avail_out){
+		count = RZ_BUFFER_SIZE - rz->stream->avail_out;
 #ifdef _USE_KNETFILE    
-		write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+		if (write(rz->x.fpw, rz->outbuf, count) < 0) {
 #else        
-		write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+		if (write(rz->filedes, rz->outbuf, count) < 0) {
 #endif
+			fprintf(stderr, "[%s] failed to flush output buffer.\n", __func__);
+			abort();
+		}
 		rz->stream->avail_out = RZ_BUFFER_SIZE;
 		rz->stream->next_out  = rz->outbuf;
 	}
@@ -230,11 +331,15 @@ 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){
+			count = RZ_BUFFER_SIZE - rz->stream->avail_out;
 #ifdef _USE_KNETFILE    
-			write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+			if (write(rz->x.fpw, rz->outbuf, count) < 0) {
 #else            
-			write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+			if (write(rz->filedes, rz->outbuf, count) < 0) {
 #endif
+				fprintf(stderr, "[%s] failed to flush output buffer.\n", __func__);
+				abort();
+			}
 			rz->stream->avail_out = RZ_BUFFER_SIZE;
 			rz->stream->next_out  = rz->outbuf;
 		} else break;
@@ -244,6 +349,7 @@ static void razf_flush(RAZF *rz){
 }
 
 static void razf_end_flush(RAZF *rz){
+	size_t count;
 	uint32_t tout;
 	if(rz->buf_len){
 		_razf_write(rz, rz->inbuf, rz->buf_len);
@@ -254,11 +360,15 @@ 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){
+			count = RZ_BUFFER_SIZE - rz->stream->avail_out;
 #ifdef _USE_KNETFILE        
-			write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+			if (write(rz->x.fpw, rz->outbuf, count) < 0) {
 #else            
-			write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+			if (write(rz->filedes, rz->outbuf, count) < 0) {
 #endif
+				fprintf(stderr, "[%s] failed to flush output buffer.\n", __func__);
+				abort();
+			}
 			rz->stream->avail_out = RZ_BUFFER_SIZE;
 			rz->stream->next_out  = rz->outbuf;
 		} else break;
@@ -355,7 +465,10 @@ static RAZF* razf_open_r(int fd, int _load_index){
 	int n, is_be, ret;
 	int64_t end;
 	unsigned char c[] = "RAZF";
-	rz = calloc(1, sizeof(RAZF));
+	if ((rz = calloc(1, sizeof(RAZF))) == NULL) {
+		fprintf(stderr, "[%s] failure to allocate RAZF structure.\n", __func__);
+		return NULL;
+	}
 	rz->mode = 'r';
 #ifdef _USE_KNETFILE
     rz->x.fpr = fp;
@@ -365,9 +478,24 @@ static RAZF* razf_open_r(int fd, int _load_index){
 #endif
 	rz->filedes = fd;
 #endif
-	rz->stream = calloc(sizeof(z_stream), 1);
-	rz->inbuf  = malloc(RZ_BUFFER_SIZE);
-	rz->outbuf = malloc(RZ_BUFFER_SIZE);
+	if ((rz->stream = calloc(sizeof(z_stream), 1)) == NULL) {
+		fprintf(stderr, "[%s] failure to allocate z_stream.\n", __func__);
+		free(rz);
+		return NULL;
+	}
+	if ((rz->inbuf = malloc(RZ_BUFFER_SIZE)) == NULL) {
+		fprintf(stderr, "[%s] failure to allocate input buffer.\n", __func__);
+		free(rz->stream);
+		free(rz);
+		return NULL;
+	}
+	if ((rz->outbuf = malloc(RZ_BUFFER_SIZE)) == NULL) {
+		fprintf(stderr, "[%s] failure to allocate output buffer.\n", __func__);
+		free(rz->inbuf);
+		free(rz->stream);
+		free(rz);
+		return NULL;
+	}
 	rz->end = rz->src_end = 0x7FFFFFFFFFFFFFFFLL;
 #ifdef _USE_KNETFILE
     n = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
@@ -801,24 +929,48 @@ void razf_close(RAZF *rz){
 #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));
+			if (write(rz->x.fpw, &rz->in, sizeof(int64_t)) < 0) {
+				fprintf(stderr, "[%s] failed to write rz.in.\n", __func__);
+				abort();
+			}
+			if (write(rz->x.fpw, &rz->out, sizeof(int64_t)) < 0) {
+				fprintf(stderr, "[%s] failed to write rz.out.\n", __func__);
+				abort();
+			}
 		} else {
 			uint64_t v64 = byte_swap_8((uint64_t)rz->in);
-			write(rz->x.fpw, &v64, sizeof(int64_t));
+			if (write(rz->x.fpw, &v64, sizeof(int64_t)) < 0) {
+				fprintf(stderr, "[%s] failed to write rz.in.\n", __func__);
+				abort();
+			}
 			v64 = byte_swap_8((uint64_t)rz->out);
-			write(rz->x.fpw, &v64, sizeof(int64_t));
+			if (write(rz->x.fpw, &v64, sizeof(int64_t)) < 0) {
+				fprintf(stderr, "[%s] failed to write rz.out.\n", __func__);
+				abort();
+			}
 		}
 #else
 		save_zindex(rz, rz->filedes);
 		if(is_big_endian()){
-			write(rz->filedes, &rz->in, sizeof(int64_t));
-			write(rz->filedes, &rz->out, sizeof(int64_t));
+			if (write(rz->filedes, &rz->in, sizeof(int64_t)) < 0) {
+				fprintf(stderr, "[%s] failed to write rz.in.\n", __func__);
+				abort();
+			}
+			if (write(rz->filedes, &rz->out, sizeof(int64_t)) < 0) {
+				fprintf(stderr, "[%s] failed to write rz.out.\n", __func__);
+				abort();
+			}
 		} else {
 			uint64_t v64 = byte_swap_8((uint64_t)rz->in);
-			write(rz->filedes, &v64, sizeof(int64_t));
+			if (write(rz->filedes, &v64, sizeof(int64_t)) < 0) {
+				fprintf(stderr, "[%s] failed to write rz.in.\n", __func__);
+				abort();
+			}
 			v64 = byte_swap_8((uint64_t)rz->out);
-			write(rz->filedes, &v64, sizeof(int64_t));
+			if (write(rz->filedes, &v64, sizeof(int64_t)) < 0) {
+				fprintf(stderr, "[%s] failed to write rz.out.\n", __func__);
+				abort();
+			}
 		}
 #endif
 #endif