main.c

#include <string.h>
#include <unistd.h>
#include <stdlib.h>
#include <stdio.h>
#include <sys/stat.h>
#include <errno.h>
#include "bgzf.h"
#include "tabix.h"
#include "knetfile.h"

#define PACKAGE_VERSION "0.2.5 (r1005)"

#define error(...) { fprintf(stderr,__VA_ARGS__); return -1; }

int reheader_file(const char *header, const char *file, int meta)
{
    BGZF *fp = bgzf_open(file,"r");
    if (bgzf_read_block(fp) != 0 || !fp->block_length)
        return -1;
    
    char *buffer = fp->uncompressed_block;
    int skip_until = 0;

    if ( buffer[0]==meta )
    {
        skip_until = 1;

        // Skip the header
        while (1)
        {
            if ( buffer[skip_until]=='\n' )
            {
                skip_until++;
                if ( skip_until>=fp->block_length )
                {
                    if (bgzf_read_block(fp) != 0 || !fp->block_length)
                        error("no body?\n");
                    skip_until = 0;
                }
                // The header has finished
                if ( buffer[skip_until]!=meta ) break;
            }
            skip_until++;
            if ( skip_until>=fp->block_length )
            {
                if (bgzf_read_block(fp) != 0 || !fp->block_length)
                    error("no body?\n");
                skip_until = 0;
            }
        }
    }

    FILE *fh = fopen(header,"r");
    if ( !fh )
        error("%s: %s", header,strerror(errno));
    int page_size = getpagesize();
    char *buf = valloc(page_size);
    BGZF *bgzf_out = bgzf_dopen(fileno(stdout), "w");
    ssize_t nread;
    while ( (nread=fread(buf,1,page_size-1,fh))>0 )
    {
        if ( nread<page_size-1 && buf[nread-1]!='\n' )
            buf[nread++] = '\n';
        if (bgzf_write(bgzf_out, buf, nread) < 0) error("Error: %d\n",bgzf_out->errcode);
    }
    fclose(fh);

    if ( fp->block_length - skip_until > 0 )
    {
        if (bgzf_write(bgzf_out, buffer+skip_until, fp->block_length-skip_until) < 0) 
            error("Error: %d\n",fp->errcode);
    }
    if (bgzf_flush(bgzf_out) < 0) 
        error("Error: %d\n",bgzf_out->errcode);

    while (1)
    {
#ifdef _USE_KNETFILE
        nread = knet_read(fp->fp, buf, page_size);
#else
        nread = fread(buf, 1, page_size, fp->fp);
#endif
        if ( nread<=0 ) 
            break;

        int count = fwrite(buf, 1, nread, bgzf_out->fp);
        if (count != nread)
            error("Write failed, wrote %d instead of %d bytes.\n", count,(int)nread);
    }

    if (bgzf_close(bgzf_out) < 0) 
        error("Error: %d\n",bgzf_out->errcode);
   
    return 0;
}


int main(int argc, char *argv[])
{
	int c, skip = -1, meta = -1, list_chrms = 0, force = 0, print_header = 0, print_only_header = 0, bed_reg = 0, bed_comp = 0;
	ti_conf_t conf = ti_conf_gff, *conf_ptr = NULL;
    const char *reheader = NULL;
	while ((c = getopt(argc, argv, "p:s:b:e:0S:c:lhHfCBr:")) >= 0) {
		switch (c) {
		case 'B': bed_reg = 1; break;
		case 'C': bed_comp = bed_reg = 1; break;
		case '0': conf.preset |= TI_FLAG_UCSC; break;
		case 'S': skip = atoi(optarg); break;
		case 'c': meta = optarg[0]; break;
		case 'p':
			if (strcmp(optarg, "gff") == 0) conf_ptr = &ti_conf_gff;
			else if (strcmp(optarg, "bed") == 0) conf_ptr = &ti_conf_bed;
			else if (strcmp(optarg, "sam") == 0) conf_ptr = &ti_conf_sam;
			else if (strcmp(optarg, "vcf") == 0 || strcmp(optarg, "vcf4") == 0) conf_ptr = &ti_conf_vcf;
			else if (strcmp(optarg, "psltbl") == 0) conf_ptr = &ti_conf_psltbl;
			else {
				fprintf(stderr, "[main] unrecognized preset '%s'\n", optarg);
				return 1;
			}
			break;
		case 's': conf.sc = atoi(optarg); break;
		case 'b': conf.bc = atoi(optarg); break;
		case 'e': conf.ec = atoi(optarg); break;
        case 'l': list_chrms = 1; break;
        case 'h': print_header = 1; break;
        case 'H': print_only_header = 1; break;
		case 'f': force = 1; break;
        case 'r': reheader = optarg; break;
		}
	}
	if (optind == argc) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Program: tabix (TAB-delimited file InderXer)\n");
		fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
		fprintf(stderr, "Usage:   tabix <in.tab.bgz> [region1 [region2 [...]]]\n\n");
		fprintf(stderr, "Options: -p STR     preset: gff, bed, sam, vcf, psltbl [gff]\n");
		fprintf(stderr, "         -s INT     sequence name column [1]\n");
		fprintf(stderr, "         -b INT     start column [4]\n");
		fprintf(stderr, "         -e INT     end column; can be identical to '-b' [5]\n");
		fprintf(stderr, "         -S INT     skip first INT lines [0]\n");
		fprintf(stderr, "         -c CHAR    symbol for comment/meta lines [#]\n");
	    fprintf(stderr, "         -r FILE    replace the header with the content of FILE [null]\n");
		fprintf(stderr, "         -B         region1 is a BED file (entire file will be read)\n");
		fprintf(stderr, "         -0         zero-based coordinate\n");
		fprintf(stderr, "         -h         print also the header lines\n");
		fprintf(stderr, "         -H         print only the header lines\n");
		fprintf(stderr, "         -l         list chromosome names\n");
		fprintf(stderr, "         -f         force to overwrite the index\n");
		fprintf(stderr, "\n");
		return 1;
	}
    if ( !conf_ptr )
    {
        int l = strlen(argv[optind]);
        int strcasecmp(const char *s1, const char *s2);
    	if (l>=7 && strcasecmp(argv[optind]+l-7, ".gff.gz") == 0) conf_ptr = &ti_conf_gff;
        else if (l>=7 && strcasecmp(argv[optind]+l-7, ".bed.gz") == 0) conf_ptr = &ti_conf_bed;
        else if (l>=7 && strcasecmp(argv[optind]+l-7, ".sam.gz") == 0) conf_ptr = &ti_conf_sam;
        else if (l>=7 && strcasecmp(argv[optind]+l-7, ".vcf.gz") == 0) conf_ptr = &ti_conf_vcf;
        else if (l>=10 && strcasecmp(argv[optind]+l-10, ".psltbl.gz") == 0) conf_ptr = &ti_conf_psltbl;
    }
    if ( conf_ptr )
        conf = *conf_ptr;

	if (skip >= 0) conf.line_skip = skip;
	if (meta >= 0) conf.meta_char = meta;
    if (list_chrms) {
		ti_index_t *idx;
		int i, n;
		const char **names;
		idx = ti_index_load(argv[optind]);
		if (idx == 0) {
			fprintf(stderr, "[main] fail to load the index file.\n");
			return 1;
		}
		names = ti_seqname(idx, &n);
		for (i = 0; i < n; ++i) printf("%s\n", names[i]);
		free(names);
		ti_index_destroy(idx);
		return 0;
	}
    if (reheader)
        return reheader_file(reheader,argv[optind],conf.meta_char);

	struct stat stat_tbi,stat_vcf;
    char *fnidx = calloc(strlen(argv[optind]) + 5, 1);
   	strcat(strcpy(fnidx, argv[optind]), ".tbi");

	if (optind + 1 == argc && !print_only_header) {
		if (force == 0) {
			if (stat(fnidx, &stat_tbi) == 0) 
            {
                // Before complaining, check if the VCF file isn't newer. This is a common source of errors,
                //  people tend not to notice that tabix failed
                stat(argv[optind], &stat_vcf);
                if ( stat_vcf.st_mtime <= stat_tbi.st_mtime )
                {
                    fprintf(stderr, "[tabix] the index file exists. Please use '-f' to overwrite.\n");
                    free(fnidx);
                    return 1;
                }
			}
		}
        if ( bgzf_is_bgzf(argv[optind])!=1 )
        {
            fprintf(stderr,"[tabix] was bgzip used to compress this file? %s\n", argv[optind]);
            free(fnidx);
            return 1;
        }
        if ( !conf_ptr )
        {
            // Building the index but the file type was neither recognised nor given. If no custom change
            //  has been made, warn the user that GFF is used 
            if ( conf.preset==ti_conf_gff.preset 
                && conf.sc==ti_conf_gff.sc 
                && conf.bc==ti_conf_gff.bc 
                && conf.ec==ti_conf_gff.ec 
                && conf.meta_char==ti_conf_gff.meta_char 
                && conf.line_skip==ti_conf_gff.line_skip )
                fprintf(stderr,"[tabix] The file type not recognised and -p not given, using the preset [gff].\n");
        }
		return ti_index_build(argv[optind], &conf);
	}
	{ // retrieve
		tabix_t *t;
        // On some systems, stat on non-existent files returns undefined value for sm_mtime, the user had to use -f
        int is_remote = (strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx) ? 1 : 0;
        if ( !is_remote )
        {
            // Common source of errors: new VCF is used with an old index
            stat(fnidx, &stat_tbi);
            stat(argv[optind], &stat_vcf);
            if ( force==0 && stat_vcf.st_mtime > stat_tbi.st_mtime )
            {
                fprintf(stderr, "[tabix] the index file either does not exist or is older than the vcf file. Please reindex.\n");
                free(fnidx);
                return 1;
            }
        }
        free(fnidx);

		if ((t = ti_open(argv[optind], 0)) == 0) {
			fprintf(stderr, "[main] fail to open the data file.\n");
			return 1;
		}
        if ( print_only_header )
        {
            ti_iter_t iter;
            const char *s;
            int len;
            if (ti_lazy_index_load(t) < 0 && bed_reg == 0) {
                fprintf(stderr,"[tabix] failed to load the index file.\n");
                return 1;
            }
            const ti_conf_t *idxconf = ti_get_conf(t->idx);
            iter = ti_query(t, 0, 0, 0);
            while ((s = ti_read(t, iter, &len)) != 0) {
                if ((int)(*s) != idxconf->meta_char) break;
                fputs(s, stdout); fputc('\n', stdout);
            }
            ti_iter_destroy(iter);
            return 0;
        }

		if (strcmp(argv[optind+1], ".") == 0) { // retrieve all
			ti_iter_t iter;
			const char *s;
			int len;
			iter = ti_query(t, 0, 0, 0);
			while ((s = ti_read(t, iter, &len)) != 0) {
				fputs(s, stdout); fputc('\n', stdout);
			}
			ti_iter_destroy(iter);
		} else { // retrieve from specified regions
			int i, len;
            ti_iter_t iter;
            const char *s;
			const ti_conf_t *idxconf;

			if (ti_lazy_index_load(t) < 0 && bed_reg == 0) {
                fprintf(stderr,"[tabix] failed to load the index file.\n");
                return 1;
            }
			idxconf = ti_get_conf(t->idx);

            if ( print_header )
            {
                // If requested, print the header lines here
                iter = ti_query(t, 0, 0, 0);
                while ((s = ti_read(t, iter, &len)) != 0) {
                    if ((int)(*s) != idxconf->meta_char) break;
                    fputs(s, stdout); fputc('\n', stdout);
                }
                ti_iter_destroy(iter);
                bgzf_seek(t->fp, 0, SEEK_SET);
            }
			if (bed_reg) {
				extern int bed_overlap(const void *_h, const char *chr, int beg, int end);
				extern void *bed_read(const char *fn);
				extern void bed_destroy(void *_h);

				const ti_conf_t *conf_ = idxconf? idxconf : &conf; // use the index file if available
				void *bed = bed_read(argv[optind+1]); // load the BED file
				ti_interval_t intv;

				if (bed == 0) {
					fprintf(stderr, "[main] fail to read the BED file.\n");
					return 1;
				}
				iter = ti_query(t, 0, 0, 0);
				while ((s = ti_read(t, iter, &len)) != 0) {
					int c, is_ovlp;
					ti_get_intv(conf_, len, (char*)s, &intv);
					c = *intv.se; *intv.se = '\0';
					is_ovlp = bed_overlap(bed, intv.ss, intv.beg, intv.end);
					if ((!bed_comp && is_ovlp) || (bed_comp && !is_ovlp)) { // or (bed_comp ^ is_ovlp)
						*intv.se = c;
						puts(s);
					}
					*intv.se = c;
				}
                ti_iter_destroy(iter);
				bed_destroy(bed);
			} else {
				for (i = optind + 1; i < argc; ++i) {
					int tid, beg, end;
					if (ti_parse_region(t->idx, argv[i], &tid, &beg, &end) == 0) {
						iter = ti_queryi(t, tid, beg, end);
							while ((s = ti_read(t, iter, &len)) != 0) {
							fputs(s, stdout); fputc('\n', stdout);
						}
						ti_iter_destroy(iter);
					} 
            	    // else fprintf(stderr, "[main] invalid region: unknown target name or minus interval.\n");
				}
			}
		}
		ti_close(t);
	}
	return 0;
}