X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=blobdiff_plain;f=main.c;h=ab2e1743b2225689f09993fed8fd3c6423ac5b50;hp=e0417b9d8b3fd2f5d293e4094de799561f8b83c8;hb=HEAD;hpb=7f5c10e58cb433a02137112209d408ecb9e65751

diff --git a/main.c b/main.c
index e0417b9..ab2e174 100644
--- a/main.c
+++ b/main.c
@@ -2,32 +2,116 @@
 #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 "0.1.2 (r543)"
+#define PACKAGE_VERSION "0.2.5 (r1005)"
 
-static int fetch_func(int l, const char *s, void *data)
+#define error(...) { fprintf(stderr,__VA_ARGS__); return -1; }
+
+int reheader_file(const char *header, const char *file, int meta)
 {
-	printf("%s\n", s);
-	return 0;
+    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;
-	ti_conf_t conf = ti_conf_gff;
-	while ((c = getopt(argc, argv, "p:s:b:e:0S:c:")) >= 0) {
+	int c, skip = -1, meta = -1, list_chrms = 0, force = 0, print_header = 0, print_only_header = 0, bed_reg = 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:lhHfBr:")) >= 0) {
 		switch (c) {
+		case 'B': 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 = ti_conf_gff;
-			else if (strcmp(optarg, "bed") == 0) conf = ti_conf_bed;
-			else if (strcmp(optarg, "sam") == 0) conf = ti_conf_sam;
-			else if (strcmp(optarg, "vcf") == 0) conf = ti_conf_vcf;
-			else if (strcmp(optarg, "psltbl") == 0) conf = ti_conf_psltbl;
+			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;
@@ -36,10 +120,13 @@ int main(int argc, char *argv[])
 		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 (skip >= 0) conf.line_skip = skip;
-	if (meta >= 0) conf.meta_char = meta;
 	if (optind == argc) {
 		fprintf(stderr, "\n");
 		fprintf(stderr, "Program: tabix (TAB-delimited file InderXer)\n");
@@ -48,46 +135,204 @@ int main(int argc, char *argv[])
 		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 [5]\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 (optind + 1 == argc)
+    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
-		BGZF *fp;
-		fp = bgzf_open(argv[optind], "r");
-		if (fp == 0) {
+		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
-			kstring_t *str = calloc(1, sizeof(kstring_t));
-			while (ti_readline(fp, str) >= 0) { // FIXME: check return code for error
-				fputs(str->s, stdout); fputc('\n', stdout);
+			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);
 			}
-			free(str->s); free(str);
+			ti_iter_destroy(iter);
 		} else { // retrieve from specified regions
-			ti_index_t *idx;
-			int i;
-			idx = ti_index_load(argv[optind]);
-			if (idx == 0) {
-				bgzf_close(fp);
-				fprintf(stderr, "[main] fail to load the index.\n");
-				return 1;
-			}
-			for (i = optind + 1; i < argc; ++i) {
-				int tid, beg, end;
-				if (ti_parse_region(idx, argv[i], &tid, &beg, &end) == 0) {
-					ti_fetch(fp, idx, tid, beg, end, 0, fetch_func);
-				} else fprintf(stderr, "[main] invalid region: unknown target name or minus interval.\n");
+			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);
+            }
+			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;
+					ti_get_intv(conf_, len, (char*)s, &intv);
+					c = *intv.se; *intv.se = '\0';
+					if (bed_overlap(bed, intv.ss, intv.beg, intv.end)) {
+						*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_index_destroy(idx);
 		}
-		bgzf_close(fp);
+		ti_close(t);
 	}
 	return 0;
 }