hts-sys 2.2.0

/* bgzip.c -- Block compression/decompression utility.

   Copyright (C) 2008, 2009 Broad Institute / Massachusetts Institute of Technology
   Copyright (C) 2010, 2013-2019, 2021-2023 Genome Research Ltd.

   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
   in the Software without restriction, including without limitation the rights
   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   copies of the Software, and to permit persons to whom the Software is
   furnished to do so, subject to the following conditions:

   The above copyright notices and this permission notice shall be included in
   all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
   THE SOFTWARE.
*/

#include <config.h>

#include <stdlib.h>
#include <string.h>
#include <strings.h>
#include <stdio.h>
#include <fcntl.h>
#include <unistd.h>
#include <errno.h>
#include <stdarg.h>
#include <getopt.h>
#include <inttypes.h>
#include "htslib/bgzf.h"
#include "htslib/hts.h"
#include "htslib/hfile.h"

#ifdef _WIN32
#  define WIN32_LEAN_AND_MEAN
#  include <windows.h>
#endif

static const int WINDOW_SIZE = BGZF_BLOCK_SIZE;

static void error(const char *format, ...)
{
    va_list ap;
    va_start(ap, format);
    vfprintf(stderr, format, ap);
    va_end(ap);
    exit(EXIT_FAILURE);
}

static int ask_yn()
{
    char line[1024];
    if (fgets(line, sizeof line, stdin) == NULL)
        return 0;
    return line[0] == 'Y' || line[0] == 'y';
}

static int confirm_overwrite(const char *fn)
{
    int save_errno = errno;
    int ret = 0;

    if (isatty(STDIN_FILENO)) {
        fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn);
        if (ask_yn()) ret = 1;
    }

    errno = save_errno;
    return ret;
}

static int known_extension(const char *ext)
{
    static const char *known[] = {
        "gz", "bgz", "bgzf",
        NULL
    };

    const char **p;
    for (p = known; *p; p++)
        if (strcasecmp(ext, *p) == 0) return 1;
    return 0;
}

static int confirm_filename(int *is_forced, const char *name, const char *ext)
{
    if (*is_forced) {
        (*is_forced)--;
        return 1;
    }

    if (!isatty(STDIN_FILENO))
        return 0;

    fprintf(stderr, "[bgzip] .%s is not a known extension; do you wish to decompress to %s (y or n)? ", ext, name);
    return ask_yn();
}

static int bgzip_main_usage(FILE *fp, int status)
{
    fprintf(fp, "\n");
    fprintf(fp, "Version: %s\n", hts_version());
    fprintf(fp, "Usage:   bgzip [OPTIONS] [FILE] ...\n");
    fprintf(fp, "Options:\n");
    fprintf(fp, "   -b, --offset INT           decompress at virtual file pointer (0-based uncompressed offset)\n");
    fprintf(fp, "   -c, --stdout               write on standard output, keep original files unchanged\n");
    fprintf(fp, "   -d, --decompress           decompress\n");
    fprintf(fp, "   -f, --force                overwrite files without asking\n");
    fprintf(fp, "   -g, --rebgzip              use an index file to bgzip a file\n");
    fprintf(fp, "   -h, --help                 give this help\n");
    fprintf(fp, "   -i, --index                compress and create BGZF index\n");
    fprintf(fp, "   -I, --index-name FILE      name of BGZF index file [file.gz.gzi]\n");
    fprintf(fp, "   -k, --keep                 don't delete input files during operation\n");
    fprintf(fp, "   -l, --compress-level INT   Compression level to use when compressing; 0 to 9, or -1 for default [-1]\n");
    fprintf(fp, "   -r, --reindex              (re)index compressed file\n");
    fprintf(fp, "   -s, --size INT             decompress INT bytes (uncompressed size)\n");
    fprintf(fp, "   -t, --test                 test integrity of compressed file\n");
    fprintf(fp, "       --binary               Don't align blocks with text lines\n");
    fprintf(fp, "   -@, --threads INT          number of compression threads to use [1]\n");
    return status;
}

int main(int argc, char **argv)
{
    int c, compress, compress_level = -1, pstdout, is_forced, test, index = 0, rebgzip = 0, reindex = 0, keep, binary;
    BGZF *fp;
    char *buffer;
    long start, end, size;
    char *index_fname = NULL;
    int threads = 1, isstdin = 0, usedstdout = 0, ret = 0;

    static const struct option loptions[] =
    {
        {"help", no_argument, NULL, 'h'},
        {"offset", required_argument, NULL, 'b'},
        {"stdout", no_argument, NULL, 'c'},
        {"decompress", no_argument, NULL, 'd'},
        {"force", no_argument, NULL, 'f'},
        {"index", no_argument, NULL, 'i'},
        {"index-name", required_argument, NULL, 'I'},
        {"compress-level", required_argument, NULL, 'l'},
        {"reindex", no_argument, NULL, 'r'},
        {"rebgzip",no_argument,NULL,'g'},
        {"size", required_argument, NULL, 's'},
        {"threads", required_argument, NULL, '@'},
        {"test", no_argument, NULL, 't'},
        {"version", no_argument, NULL, 1},
        {"keep", no_argument, NULL, 'k'},
        {"binary", no_argument, NULL, 2},
        {NULL, 0, NULL, 0}
    };

    compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0; test = 0; keep = 0; binary = 0;
    while((c  = getopt_long(argc, argv, "cdh?fb:@:s:iI:l:grtk",loptions,NULL)) >= 0){
        switch(c){
        case 'd': compress = 0; break;
        case 'c': pstdout = 1; break;
        case 'b': start = atol(optarg); compress = 0; pstdout = 1; break;
        case 's': size = atol(optarg); pstdout = 1; break;
        case 'f': is_forced++; break;
        case 'i': index = 1; break;
        case 'I': index_fname = optarg; break;
        case 'l': compress_level = atol(optarg); break;
        case 'g': rebgzip = 1; break;
        case 'r': reindex = 1; compress = 0; break;
        case '@': threads = atoi(optarg); break;
        case 't': test = 1; compress = 0; reindex = 0; break;
        case 'k': keep = 1; break;
        case 1:
            printf(
"bgzip (htslib) %s\n"
"Copyright (C) 2024 Genome Research Ltd.\n", hts_version());
            return EXIT_SUCCESS;
        case  2:  binary = 1; break;
        case 'h': return bgzip_main_usage(stdout, EXIT_SUCCESS);
        case '?': return bgzip_main_usage(stderr, EXIT_FAILURE);
        }
    }
    if (size >= 0) end = start + size;
    if (end >= 0 && end < start) {
        fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end);
        return 1;
    }

    if ( (index || reindex) && rebgzip )
    {
        fprintf(stderr, "[bgzip] Can't produce a index and rebgzip simultaneously\n");
        return 1;
    }
    if ( rebgzip && !index_fname )
    {
        fprintf(stderr, "[bgzip] Index file name expected with rebgzip.  See -I option.\n");
        return 1;
    }
    /* avoid -I / indexfile with multiple inputs while index/reindex. these wont be set during
    read/decompress and are not considered even if set */
    if ( (index || reindex) && index_fname && argc - optind > 1) {
        fprintf(stderr, "[bgzip] Cannot specify index filename with multiple data file on index, reindex.\n");
        return 1;
    }

    do {
        isstdin = optind >= argc ? 1 : !strcmp("-", argv[optind]);          //using stdin or not?
        /*stdout is in use when explicitly selected or when stdin in is in use, it need to be closed
        explicitly to get all io errors*/
        usedstdout |= isstdin || pstdout || test;

        if (compress == 1) {
            hFILE* f_src = NULL;
            char out_mode[3] = "w\0";
            char out_mode_exclusive[4] = "wx\0";

            if (compress_level < -1 || compress_level > 9) {
                fprintf(stderr, "[bgzip] Invalid compress-level: %d\n", compress_level);
                return 1;
            }
            if (compress_level >= 0) {
                out_mode[1] = compress_level + '0';
                out_mode_exclusive[2] = compress_level + '0';
            }
            if (!(f_src = hopen(!isstdin ? argv[optind] : "-", "r"))) {
                fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), isstdin ? "stdin" : argv[optind]);
                return 1;
            }

            if ( argc>optind && !isstdin )                  //named input file that isn't an explicit "-"
            {
                if (pstdout)
                    fp = bgzf_open("-", out_mode);
                else
                {
                    char *name = malloc(strlen(argv[optind]) + 5);
                    strcpy(name, argv[optind]);
                    strcat(name, ".gz");
                    fp = bgzf_open(name, is_forced? out_mode : out_mode_exclusive);
                    if (fp == NULL && errno == EEXIST) {
                        if (confirm_overwrite(name)) {
                            fp = bgzf_open(name, out_mode);
                        }
                        else {
                            ret = 2;                        //explicit N - no overwrite, continue and return 2
                            if (hclose(f_src) < 0)
                                ;                           //ignoring return value
                            free(name);
                            continue;
                        }
                    }
                    if (fp == NULL) {
                        fprintf(stderr, "[bgzip] can't create %s: %s\n", name, strerror(errno));
                        free(name);
                        return 1;
                    }
                    free(name);
                }
            }
            else if (!pstdout && isatty(fileno((FILE *)stdout)) )
                return bgzip_main_usage(stderr, EXIT_FAILURE);
            else if ( index && !index_fname )
            {
                fprintf(stderr, "[bgzip] Index file name expected when writing to stdout\n");
                return 1;
            }
            else
                fp = bgzf_open("-", out_mode);

            if ( index ) bgzf_index_build_init(fp);
            if (threads > 1)
                bgzf_mt(fp, threads, 256);

            buffer = malloc(WINDOW_SIZE);
            if (!buffer)
                return 1;
            if (rebgzip){
                if ( bgzf_index_load(fp, index_fname, NULL) < 0 ) error("Could not load index: %s.%s\n", !isstdin ? argv[optind] : index_fname, !isstdin ? "gzi" : "");

                while ((c = hread(f_src, buffer, WINDOW_SIZE)) > 0)
                    if (bgzf_block_write(fp, buffer, c) < 0) error("Could not write %d bytes: Error %d\n", c, fp->errcode);
            }
            else {
                htsFormat fmt;
                int textual = 0;
                if (!binary
                    && hts_detect_format(f_src, &fmt) == 0
                    && fmt.compression == no_compression) {
                    switch(fmt.format) {
                    case text_format:
                    case sam:
                    case vcf:
                    case bed:
                    case fasta_format:
                    case fastq_format:
                    case fai_format:
                    case fqi_format:
                        textual = 1;
                        break;
                    default: break; // silence clang warnings
                    }
                }

                if (binary || !textual) {
                    // Binary data, either detected or explicit
                    while ((c = hread(f_src, buffer, WINDOW_SIZE)) > 0)
                        if (bgzf_write(fp, buffer, c) < 0)
                            error("Could not write %d bytes: Error %d\n",
                                c, fp->errcode);
                } else {
                    /* Text mode, try a flush after a newline */
                    int in_header = 1, n = 0, long_line = 0;
                    while ((c = hread(f_src, buffer+n, WINDOW_SIZE-n)) > 0) {
                        int c2 = c+n;
                        int flush = 0;
                        if (in_header &&
                            (long_line || buffer[0] == '@' || buffer[0] == '#')) {
                            // Scan forward to find the last header line.
                            int last_start = 0;
                            n = 0;
                            while (n < c2) {
                                if (buffer[n++] != '\n')
                                    continue;

                                last_start = n;
                                if (n < c2 &&
                                    !(buffer[n] == '@' || buffer[n] == '#')) {
                                    in_header = 0;
                                    break;
                                }
                            }
                            if (!last_start) {
                                n = c2;
                                long_line = 1;
                            } else {
                                n = last_start;
                                flush = 1;
                                long_line = 0;
                            }
                        } else {
                            // Scan backwards to find the last newline.
                            n += c; // c read plus previous n overflow
                            while (--n >= 0 && ((char *)buffer)[n] != '\n')
                                ;

                            if (n >= 0) {
                                flush = 1;
                                n++;
                            } else {
                                n = c2;
                            }
                        }

                        // Pos n is either at the end of the buffer with flush==0,
                        // or the first byte after a newline and a flush point.
                        if (bgzf_write(fp, buffer, n) < 0)
                            error("Could not write %d bytes: Error %d\n",
                                n, fp->errcode);
                        if (flush)
                            if (bgzf_flush_try(fp, 65536) < 0) // force
                                return -1;

                        memmove(buffer, buffer+n, c2-n);
                        n = c2-n;
                    }

                    // Trailing data.
                    if (bgzf_write(fp, buffer, n) < 0)
                        error("Could not write %d bytes: Error %d\n",
                            n, fp->errcode);
                }
            }
            if ( index )
            {
                if (index_fname) {
                    if (bgzf_index_dump(fp, index_fname, NULL) < 0)
                        error("Could not write index to '%s'\n", index_fname);
                } else if (!isstdin) {
                    if (bgzf_index_dump(fp, argv[optind], ".gz.gzi") < 0)
                        error("Could not write index to '%s.gz.gzi'\n", argv[optind]);
                }
                else {
                    //stdin, cant create index file as name is not present "-.gz.gzi" not a valid one!
                    error("Can not write index for stdin data without index filename, use -I option to set index file.\n");
                }
            }
            if (bgzf_close(fp) < 0)
                error("Output close failed: Error %d\n", fp->errcode);
            if (hclose(f_src) < 0)
                error("Input close failed\n");
            if (argc > optind && !pstdout && !keep && !isstdin) unlink(argv[optind]);
            free(buffer);
        }
        else if ( reindex )
        {
            if ( argc>optind && !isstdin )
            {
                fp = bgzf_open(argv[optind], "r");
                if ( !fp ) error("[bgzip] Could not open file: %s\n", argv[optind]);
            }
            else
            {
                if ( !index_fname ) error("[bgzip] Index file name expected when reading from stdin\n");
                fp = bgzf_open("-", "r");
                if ( !fp ) error("[bgzip] Could not read from stdin: %s\n", strerror(errno));
            }

            buffer = malloc(BGZF_BLOCK_SIZE);
            bgzf_index_build_init(fp);
            int ret;
            while ( (ret=bgzf_read(fp, buffer, BGZF_BLOCK_SIZE))>0 ) ;
            free(buffer);
            if ( ret<0 ) error("Is the file gzipped or bgzipped? The latter is required for indexing.\n");

            if ( index_fname ) {
                if (bgzf_index_dump(fp, index_fname, NULL) < 0)
                    error("Could not write index to '%s'\n", index_fname);
            } else if (!isstdin) {
                if (bgzf_index_dump(fp, argv[optind], ".gzi") < 0)
                    error("Could not write index to '%s.gzi'\n", argv[optind]);
            }
            else {
                //stdin, cant create index file as name is not present "-.gzi" not a valid one!
                error("Can not write index for stdin data without index filename, use -I option to set index file.\n");
            }

            if ( bgzf_close(fp)<0 ) error("Close failed: Error %d\n",fp->errcode);
        }
        else
        {
            int f_dst, is_forced_tmp = is_forced;

            if ( argc>optind && !isstdin )
            {
                fp = bgzf_open(argv[optind], "r");
                if (fp == NULL) {
                    fprintf(stderr, "[bgzip] Could not open %s: %s\n", argv[optind], strerror(errno));
                    return 1;
                }
                if (bgzf_compression(fp) == no_compression) {
                    fprintf(stderr, "[bgzip] %s: not a compressed file -- ignored\n", argv[optind]);
                    bgzf_close(fp);
                    return 1;
                }

                if (pstdout || test) {
                    f_dst = fileno(stdout);
                }
                else {
                    const int wrflags = O_WRONLY | O_CREAT | O_TRUNC;
                    char *name = argv[optind], *ext;
                    size_t pos;
                    for (pos = strlen(name); pos > 0; --pos)
                        if (name[pos] == '.' || name[pos] == '/') break;
                    if (pos == 0 || name[pos] != '.') {
                        fprintf(stderr, "[bgzip] can't remove an extension from %s -- please rename\n", argv[optind]);
                        bgzf_close(fp);
                        return 1;
                    }
                    name = strdup(argv[optind]);
                    name[pos] = '\0';
                    ext = &name[pos+1];
                    if (! (known_extension(ext) || confirm_filename(&is_forced_tmp, name, ext))) {
                        fprintf(stderr, "[bgzip] unknown extension .%s -- declining to decompress to %s\n", ext, name);
                        bgzf_close(fp);
                        free(name);
                        ret = 2;                            //explicit N, continue and return 2
                        continue;
                    }
                    f_dst = open(name, is_forced_tmp? wrflags : wrflags|O_EXCL, 0666);
                    if (f_dst < 0 && errno == EEXIST) {
                        if (confirm_overwrite(name)) {
                            f_dst = open(name, wrflags, 0666);
                        }
                        else {
                            ret = 2;                        //explicit N - no overwrite, continue and return 2
                            free(name);
                            bgzf_close(fp);
                            continue;
                        }
                    }
                    if (f_dst < 0) {
                        fprintf(stderr, "[bgzip] can't create %s: %s\n", name, strerror(errno));
                        free(name);
                        return 1;
                    }
                    free(name);
                }
            }
            else if (!pstdout && isatty(fileno((FILE *)stdin)) )
                return bgzip_main_usage(stderr, EXIT_FAILURE);
            else
            {
                f_dst = fileno(stdout);
                fp = bgzf_open("-", "r");
                if (fp == NULL) {
                    fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));
                    return 1;
                }
                if (bgzf_compression(fp) == no_compression) {
                    fprintf(stderr, "[bgzip] stdin is not compressed -- ignored\n");
                    bgzf_close(fp);
                    return 1;
                }
            }

            buffer = malloc(WINDOW_SIZE);
            if ( start>0 )
            {
                if (index_fname) {
                    if ( bgzf_index_load(fp, index_fname, NULL) < 0 )
                        error("Could not load index: %s\n", index_fname);
                } else {
                    if (optind >= argc || isstdin) {
                        error("The -b option requires -I when reading from stdin "
                            "(and stdin must be seekable)\n");
                    }
                    if ( bgzf_index_load(fp, argv[optind], ".gzi") < 0 )
                        error("Could not load index: %s.gzi\n", argv[optind]);
                }
                if ( bgzf_useek(fp, start, SEEK_SET) < 0 ) error("Could not seek to %d-th (uncompressd) byte\n", start);
            }

            if (threads > 1)
                bgzf_mt(fp, threads, 256);

    #ifdef _WIN32
            _setmode(f_dst, O_BINARY);
    #endif
            long start_reg = start, end_reg = end;
            while (1) {
                if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE);
                else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
                if (c == 0) break;
                if (c < 0) error("Error %d in block starting at offset %" PRId64 "(%" PRIX64 ")\n", fp->errcode, fp->block_address, fp->block_address);
                start += c;
                if ( !test && write(f_dst, buffer, c) != c ) {
    #ifdef _WIN32
                    if (GetLastError() != ERROR_NO_DATA)
    #endif
                    error("Could not write %d bytes\n", c);
                }
                if (end >= 0 && start >= end) break;
            }
            start = start_reg;
            end = end_reg;
            free(buffer);
            if (bgzf_close(fp) < 0) error("Close failed: Error %d\n",fp->errcode);
            if (argc > optind && !pstdout && !test && !keep && !isstdin) unlink(argv[optind]);
            if (!isstdin && !pstdout && !test) {
                close(f_dst);                               //close output file when it is not stdout
            }
        }
    } while (++optind < argc);

    if (usedstdout && !reindex) {
        //stdout in use, have to close explicitly to get any pending write errors
        if (fclose(stdout) != 0 && errno != EBADF) {
            fprintf(stderr, "[bgzip] Failed to close stdout, errno %d", errno);
            ret = 1;
        }
    }
    return ret;
}