+++ /dev/null
-/*
- * RAZF : Random Access compressed(Z) File
- * Version: 1.0
- * Release Date: 2008-10-27
- *
- * Copyright 2008, Jue Ruan <ruanjue@gmail.com>, Heng Li <lh3@sanger.ac.uk>
- *
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- * 1. Redistributions of source code must retain the above copyright
- * notice, this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright
- * notice, this list of conditions and the following disclaimer in the
- * documentation and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
- * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
- * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
- * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- * SUCH DAMAGE.
- */
-
-#ifndef _NO_RAZF
-
-#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;
-};
-#warning "zlib < 1.2.2.1; RAZF writing is disabled."
-#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);
-}
-
-static inline uint64_t byte_swap_8(uint64_t v){
- v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
- v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
- return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
-}
-
-static inline int is_big_endian(){
- int x = 0x01;
- char *c = (char*)&x;
- 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;
- 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));
- }
- 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];
- rz->index->size ++;
-}
-
-static void save_zindex(RAZF *rz, int fd){
- int32_t i, v32;
- int is_be;
- is_be = is_big_endian();
- if(is_be) write(fd, &rz->index->size, sizeof(int));
- else {
- v32 = byte_swap_4((uint32_t)rz->index->size);
- write(fd, &v32, sizeof(uint32_t));
- }
- 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);
-}
-#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]);
- }
-}
-
-#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;
-#ifdef _WIN32
- setmode(fd, O_BINARY);
-#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);
- rz->index = calloc(sizeof(ZBlockIndex), 1);
- 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);
- rz->header->os = 0x03; //Unix
- rz->header->text = 0;
- rz->header->time = 0;
- rz->header->extra = malloc(7);
- strncpy((char*)rz->header->extra, "RAZF", 4);
- rz->header->extra[4] = 1; // obsolete field
- // block size = RZ_BLOCK_SIZE, Big-Endian
- rz->header->extra[5] = RZ_BLOCK_SIZE >> 8;
- rz->header->extra[6] = RZ_BLOCK_SIZE & 0xFF;
- rz->header->extra_len = 7;
- rz->header->name = rz->header->comment = 0;
- rz->header->hcrc = 0;
- deflateSetHeader(rz->stream, rz->header);
- rz->block_pos = rz->block_off = 0;
- return rz;
-}
-
-static void _razf_write(RAZF* rz, const void *data, int size){
- int tout;
- rz->stream->avail_in = size;
- rz->stream->next_in = (void*)data;
- while(1){
- tout = rz->stream->avail_out;
- 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;
- };
- rz->in += size - rz->stream->avail_in;
- rz->block_off += size - rz->stream->avail_in;
-}
-
-static void razf_flush(RAZF *rz){
- 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){
-#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;
- }
- while(1){
- tout = rz->stream->avail_out;
- 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;
- }
- rz->block_pos = rz->out;
- rz->block_off = 0;
-}
-
-static void razf_end_flush(RAZF *rz){
- uint32_t tout;
- if(rz->buf_len){
- _razf_write(rz, rz->inbuf, rz->buf_len);
- rz->buf_off = rz->buf_len = 0;
- }
- while(1){
- tout = rz->stream->avail_out;
- 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;
- }
-}
-
-static void _razf_buffered_write(RAZF *rz, const void *data, int size){
- int i, n;
- while(1){
- if(rz->buf_len == RZ_BUFFER_SIZE){
- _razf_write(rz, rz->inbuf, rz->buf_len);
- rz->buf_len = 0;
- }
- if(size + rz->buf_len < RZ_BUFFER_SIZE){
- for(i=0;i<size;i++) ((char*)rz->inbuf + rz->buf_len)[i] = ((char*)data)[i];
- rz->buf_len += size;
- return;
- } else {
- n = RZ_BUFFER_SIZE - rz->buf_len;
- for(i=0;i<n;i++) ((char*)rz->inbuf + rz->buf_len)[i] = ((char*)data)[i];
- size -= n;
- data += n;
- rz->buf_len += n;
- }
- }
-}
-
-int razf_write(RAZF* rz, const void *data, int size){
- int ori_size, n;
- int64_t next_block;
- ori_size = size;
- next_block = ((rz->in / RZ_BLOCK_SIZE) + 1) * RZ_BLOCK_SIZE;
- while(rz->in + rz->buf_len + size >= next_block){
- n = next_block - rz->in - rz->buf_len;
- _razf_buffered_write(rz, data, n);
- data += n;
- size -= n;
- razf_flush(rz);
- add_zindex(rz, rz->in, rz->out);
- next_block = ((rz->in / RZ_BLOCK_SIZE) + 1) * RZ_BLOCK_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 */
-#define HEAD_CRC 0x02 /* bit 1 set: header CRC present */
-#define EXTRA_FIELD 0x04 /* bit 2 set: extra field present */
-#define ORIG_NAME 0x08 /* bit 3 set: original file name present */
-#define COMMENT 0x10 /* bit 4 set: file comment present */
-#define RESERVED 0xE0 /* bits 5..7: reserved */
-
-static int _read_gz_header(unsigned char *data, int size, int *extra_off, int *extra_len){
- int method, flags, n, len;
- if(size < 2) return 0;
- if(data[0] != 0x1f || data[1] != 0x8b) return 0;
- if(size < 4) return 0;
- method = data[2];
- flags = data[3];
- if(method != Z_DEFLATED || (flags & RESERVED)) return 0;
- n = 4 + 6; // Skip 6 bytes
- *extra_off = n + 2;
- *extra_len = 0;
- if(flags & EXTRA_FIELD){
- if(size < n + 2) return 0;
- len = ((int)data[n + 1] << 8) | data[n];
- n += 2;
- *extra_off = n;
- while(len){
- if(n >= size) return 0;
- n ++;
- len --;
- }
- *extra_len = n - (*extra_off);
- }
- if(flags & ORIG_NAME) while(n < size && data[n++]);
- if(flags & COMMENT) while(n < size && data[n++]);
- if(flags & HEAD_CRC){
- if(n + 2 > size) return 0;
- n += 2;
- }
- 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->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:
- rz->in = n;
- rz->file_type = FILE_TYPE_PLAIN;
- memcpy(rz->outbuf, rz->inbuf, n);
- rz->buf_len = n;
- free(rz->stream);
- rz->stream = NULL;
- return rz;
- }
- rz->header_size = ret;
- ret = inflateInit2(rz->stream, -WINDOW_BITS);
- if(ret != Z_OK){ inflateEnd(rz->stream); goto PLAIN_FILE;}
- rz->stream->avail_in = n - rz->header_size;
- rz->stream->next_in = rz->inbuf + rz->header_size;
- rz->stream->avail_out = RZ_BUFFER_SIZE;
- rz->stream->next_out = rz->outbuf;
- rz->file_type = FILE_TYPE_GZ;
- rz->in = rz->header_size;
- rz->block_pos = rz->header_size;
- rz->next_block_pos = rz->header_size;
- rz->block_off = 0;
- if(ext_len < 7 || memcmp(rz->inbuf + ext_off, c, 4) != 0) return rz;
- if(((((unsigned char*)rz->inbuf)[ext_off + 5] << 8) | ((unsigned char*)rz->inbuf)[ext_off + 6]) != RZ_BLOCK_SIZE){
- fprintf(stderr, " -- WARNING: RZ_BLOCK_SIZE is not %d, treat source as gz file. in %s -- %s:%d --\n", RZ_BLOCK_SIZE, __FUNCTION__, __FILE__, __LINE__);
- return rz;
- }
- 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;
- rz->src_end = rz->end = 0x7FFFFFFFFFFFFFFFLL;
- } 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){
- rz->stream->avail_in -= n - rz->end;
- 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);
- else return NULL;
-}
-
-RAZF* razf_dopen2(int fd, const char *mode)
-{
- if(strstr(mode, "r")) return razf_open_r(fd, 0);
- 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, 0666);
-#else
- 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;
-}
-
-RAZF* razf_open(const char *filename, const char *mode){
- return _razf_open(filename, mode, 1);
-}
-
-RAZF* razf_open2(const char *filename, const char *mode){
- return _razf_open(filename, mode, 0);
-}
-
-int razf_get_data_size(RAZF *rz, int64_t *u_size, int64_t *c_size){
- int64_t n;
- if(rz->mode != 'r' && rz->mode != 'R') return 0;
- 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;
- case FILE_TYPE_GZ:
- return 0;
- case FILE_TYPE_RZ:
- if(rz->src_end == rz->end) return 0;
- *u_size = rz->src_end;
- *c_size = rz->end;
- return 1;
- default:
- return 0;
- }
-}
-
-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;
- }
- rz->stream->avail_out = size;
- rz->stream->next_out = data;
- while(rz->stream->avail_out){
- 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;
- break;
- }
- rz->stream->next_in = rz->inbuf;
- }
- tin = rz->stream->avail_in;
- 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 %s (at %s:%d)\n", ret, rz->stream->msg ? rz->stream->msg : "", __FILE__, __LINE__);
- rz->z_err = 1;
- break;
- }
- if(ret == Z_STREAM_END){
- rz->z_eof = 1;
- break;
- }
- if ((rz->stream->data_type&128) && !(rz->stream->data_type&64)){
- rz->buf_flush = 1;
- rz->next_block_pos = rz->in;
- break;
- }
- }
- return size - rz->stream->avail_out;
-}
-
-int razf_read(RAZF *rz, void *data, int size){
- int ori_size, i;
- ori_size = size;
- while(size > 0){
- if(rz->buf_len){
- if(size < rz->buf_len){
- for(i=0;i<size;i++) ((char*)data)[i] = ((char*)rz->outbuf + rz->buf_off)[i];
- rz->buf_off += size;
- rz->buf_len -= size;
- data += size;
- rz->block_off += size;
- size = 0;
- break;
- } else {
- for(i=0;i<rz->buf_len;i++) ((char*)data)[i] = ((char*)rz->outbuf + rz->buf_off)[i];
- data += rz->buf_len;
- size -= rz->buf_len;
- rz->block_off += rz->buf_len;
- rz->buf_off = 0;
- rz->buf_len = 0;
- if(rz->buf_flush){
- rz->block_pos = rz->next_block_pos;
- rz->block_off = 0;
- rz->buf_flush = 0;
- }
- }
- } else if(rz->buf_flush){
- rz->block_pos = rz->next_block_pos;
- rz->block_off = 0;
- rz->buf_flush = 0;
- }
- if(rz->buf_flush) continue;
- rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE);
- if(rz->z_eof && rz->buf_len == 0) break;
- }
- rz->out += ori_size - size;
- return ori_size - size;
-}
-
-int razf_skip(RAZF* rz, int size){
- int ori_size;
- ori_size = size;
- while(size > 0){
- if(rz->buf_len){
- if(size < rz->buf_len){
- rz->buf_off += size;
- rz->buf_len -= size;
- rz->block_off += size;
- size = 0;
- break;
- } else {
- size -= rz->buf_len;
- rz->buf_off = 0;
- rz->buf_len = 0;
- rz->block_off += rz->buf_len;
- if(rz->buf_flush){
- rz->block_pos = rz->next_block_pos;
- rz->block_off = 0;
- rz->buf_flush = 0;
- }
- }
- } else if(rz->buf_flush){
- rz->block_pos = rz->next_block_pos;
- rz->block_off = 0;
- rz->buf_flush = 0;
- }
- if(rz->buf_flush) continue;
- rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE);
- 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;
- rz->next_block_pos = in;
- rz->block_off = 0;
- rz->buf_flush = 0;
- rz->z_eof = rz->z_err = 0;
- inflateReset(rz->stream);
- rz->stream->avail_in = 0;
- rz->buf_off = rz->buf_len = 0;
-}
-
-int64_t razf_jump(RAZF *rz, int64_t block_start, int block_offset){
- int64_t pos;
- rz->z_eof = 0;
- 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;
- }
- if(block_start == rz->block_pos && block_offset >= rz->block_off) {
- block_offset -= rz->block_off;
- goto SKIP; // Needn't reset inflate
- }
- if(block_start == 0) block_start = rz->header_size; // Automaticly revist wrong block_start
- _razf_reset_read(rz, block_start, 0);
- SKIP:
- if(block_offset) razf_skip(rz, block_offset);
- return rz->block_off;
-}
-
-int64_t razf_seek(RAZF* rz, int64_t pos, int where){
- int64_t idx;
- int64_t seek_pos, new_out;
- rz->z_eof = 0;
- 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;
- } else if(rz->file_type == FILE_TYPE_GZ){
- if(pos >= rz->out) goto SKIP;
- return rz->out;
- }
- if(pos == rz->out) return pos;
- if(pos > rz->src_end) return rz->out;
- if(!rz->seekable || !rz->load_index){
- if(pos >= rz->out) goto SKIP;
- }
- idx = pos / RZ_BLOCK_SIZE - 1;
- seek_pos = (idx < 0)? rz->header_size:(rz->index->cell_offsets[idx] + rz->index->bin_offsets[idx / RZ_BIN_SIZE]);
- new_out = (idx + 1) * RZ_BLOCK_SIZE;
- if(pos > rz->out && new_out <= rz->out) goto SKIP;
- _razf_reset_read(rz, seek_pos, new_out);
- SKIP:
- razf_skip(rz, (int)(pos - rz->out));
- return rz->out;
-}
-
-uint64_t razf_tell2(RAZF *rz)
-{
- /*
- if (rz->load_index) {
- int64_t idx, seek_pos;
- idx = rz->out / RZ_BLOCK_SIZE - 1;
- seek_pos = (idx < 0)? rz->header_size:(rz->index->cell_offsets[idx] + rz->index->bin_offsets[idx / RZ_BIN_SIZE]);
- if (seek_pos != rz->block_pos || rz->out%RZ_BLOCK_SIZE != rz->block_off)
- fprintf(stderr, "[razf_tell2] inconsistent block offset: (%lld, %lld) != (%lld, %lld)\n",
- (long long)seek_pos, (long long)rz->out%RZ_BLOCK_SIZE, (long long)rz->block_pos, (long long) rz->block_off);
- }
- */
- return (uint64_t)rz->block_pos<<16 | (rz->block_off&0xffff);
-}
-
-int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where)
-{
- if (where != SEEK_SET) return -1;
- return razf_jump(rz, voffset>>16, voffset&0xffff);
-}
-
-void razf_close(RAZF *rz){
- if(rz->mode == 'w'){
-#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));
- write(rz->filedes, &rz->out, sizeof(int64_t));
- } else {
- 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
-#endif
- } else if(rz->mode == 'r'){
- if(rz->stream) inflateEnd(rz->stream);
- }
- if(rz->inbuf) free(rz->inbuf);
- if(rz->outbuf) free(rz->outbuf);
- if(rz->header){
- free(rz->header->extra);
- free(rz->header->name);
- free(rz->header->comment);
- free(rz->header);
- }
- if(rz->index){
- free(rz->index->bin_offsets);
- free(rz->index->cell_offsets);
- 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);
-}
-
-#endif
projects / pysam.git / blobdiff