Mercurial > repos > lsong10 > psiclass
view PsiCLASS-1.0.2/samtools-0.1.19/razip.c @ 0:903fc43d6227 draft default tip
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author | lsong10 |
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date | Fri, 26 Mar 2021 16:52:45 +0000 |
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#include <stdio.h> #include <fcntl.h> #include <unistd.h> #include <errno.h> #include <stdlib.h> #include <string.h> #include "razf.h" #define WINDOW_SIZE 4096 static int razf_main_usage() { printf("\n"); printf("Usage: razip [options] [file] ...\n\n"); printf("Options: -c write on standard output, keep original files unchanged\n"); printf(" -d decompress\n"); printf(" -l list compressed file contents\n"); printf(" -b INT decompress at INT position in the uncompressed file\n"); printf(" -s INT decompress INT bytes in the uncompressed file\n"); printf(" -h give this help\n"); printf("\n"); return 0; } static int write_open(const char *fn, int is_forced) { int fd = -1; char c; if (!is_forced) { if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) { printf("razip: %s already exists; do you wish to overwrite (y or n)? ", fn); scanf("%c", &c); if (c != 'Y' && c != 'y') { printf("razip: not overwritten\n"); exit(1); } } } if (fd < 0) { if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) { fprintf(stderr, "razip: %s: Fail to write\n", fn); exit(1); } } return fd; } int main(int argc, char **argv) { int c, compress, pstdout, is_forced; RAZF *rz; void *buffer; long start, end, size; compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0; while((c = getopt(argc, argv, "cdlhfb:s:")) >= 0){ switch(c){ case 'h': return razf_main_usage(); case 'd': compress = 0; break; case 'c': pstdout = 1; break; case 'l': compress = 2; break; case 'b': start = atol(optarg); break; case 's': size = atol(optarg); break; case 'f': is_forced = 1; break; } } if (size >= 0) end = start + size; if(end >= 0 && end < start){ fprintf(stderr, " -- Illegal region: [%ld, %ld] --\n", start, end); return 1; } if(compress == 1){ int f_src, f_dst = -1; if(argc > optind){ if((f_src = open(argv[optind], O_RDONLY)) < 0){ fprintf(stderr, " -- Cannot open file: %s --\n", argv[optind]); return 1; } if(pstdout){ f_dst = fileno(stdout); } else { char *name = malloc(sizeof(strlen(argv[optind]) + 5)); strcpy(name, argv[optind]); strcat(name, ".rz"); f_dst = write_open(name, is_forced); if (f_dst < 0) return 1; free(name); } } else if(pstdout){ f_src = fileno(stdin); f_dst = fileno(stdout); } else return razf_main_usage(); rz = razf_dopen(f_dst, "w"); buffer = malloc(WINDOW_SIZE); while((c = read(f_src, buffer, WINDOW_SIZE)) > 0) razf_write(rz, buffer, c); razf_close(rz); // f_dst will be closed here if (argc > optind && !pstdout) unlink(argv[optind]); free(buffer); close(f_src); return 0; } else { if(argc <= optind) return razf_main_usage(); if(compress == 2){ rz = razf_open(argv[optind], "r"); if(rz->file_type == FILE_TYPE_RZ) { printf("%20s%20s%7s %s\n", "compressed", "uncompressed", "ratio", "name"); printf("%20lld%20lld%6.1f%% %s\n", (long long)rz->end, (long long)rz->src_end, rz->end * 100.0f / rz->src_end, argv[optind]); } else fprintf(stdout, "%s is not a regular rz file\n", argv[optind]); } else { int f_dst; if (argc > optind && !pstdout) { char *name; if (strstr(argv[optind], ".rz") - argv[optind] != strlen(argv[optind]) - 3) { printf("razip: %s: unknown suffix -- ignored\n", argv[optind]); return 1; } name = strdup(argv[optind]); name[strlen(name) - 3] = '\0'; f_dst = write_open(name, is_forced); free(name); } else f_dst = fileno(stdout); rz = razf_open(argv[optind], "r"); buffer = malloc(WINDOW_SIZE); razf_seek(rz, start, SEEK_SET); while(1){ if(end < 0) c = razf_read(rz, buffer, WINDOW_SIZE); else c = razf_read(rz, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start)); if(c <= 0) break; start += c; write(f_dst, buffer, c); if(end >= 0 && start >= end) break; } free(buffer); if (!pstdout) unlink(argv[optind]); } razf_close(rz); return 0; } }