X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=faidx.c;h=055445f266cbdb429fe65c2aeb58c763af86d1d9;hb=c18ba0d59383e9bc2cf7d36c227617b03faeab25;hp=9302dfb4d6480bb94295d65e7fc7fcf4c4644332;hpb=635998cfe030da5f3dbec42a6daa3ca82fa5c871;p=samtools.git

diff --git a/faidx.c b/faidx.c
index 9302dfb..055445f 100644
--- a/faidx.c
+++ b/faidx.c
@@ -1,5 +1,4 @@
 #include <ctype.h>
-#include <assert.h>
 #include <string.h>
 #include <stdlib.h>
 #include <stdio.h>
@@ -15,8 +14,13 @@ KHASH_MAP_INIT_STR(s, faidx1_t)
 #ifndef _NO_RAZF
 #include "razf.h"
 #else
+#ifdef _WIN32
+#define ftello(fp) ftell(fp)
+#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
+#else
 extern off_t ftello(FILE *stream);
 extern int fseeko(FILE *stream, off_t offset, int whence);
+#endif
 #define RAZF FILE
 #define razf_read(fp, buf, size) fread(buf, 1, size, fp)
 #define razf_open(fn, mode) fopen(fn, mode)
@@ -66,6 +70,12 @@ faidx_t *fai_build_core(RAZF *rz)
 	name = 0; l_name = m_name = 0;
 	len = line_len = line_blen = -1; state = 0; l1 = l2 = -1; offset = 0;
 	while (razf_read(rz, &c, 1)) {
+		if (c == '\n') { // an empty line
+			if (state == 1) {
+				offset = razf_tell(rz);
+				continue;
+			} else if ((state == 0 && len < 0) || state == 2) continue;
+		}
 		if (c == '>') { // fasta header
 			if (len >= 0)
 				fai_insert_index(idx, name, len, line_len, line_blen, offset);
@@ -79,14 +89,19 @@ faidx_t *fai_build_core(RAZF *rz)
 				name[l_name++] = c;
 			}
 			name[l_name] = '\0';
-			assert(ret);
+			if (ret == 0) {
+				fprintf(stderr, "[fai_build_core] the last entry has no sequence\n");
+				free(name); fai_destroy(idx);
+				return 0;
+			}
 			if (c != '\n') while (razf_read(rz, &c, 1) && c != '\n');
 			state = 1; len = 0;
 			offset = razf_tell(rz);
 		} else {
 			if (state == 3) {
-				fprintf(stderr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'. Abort!\n", name);
-				exit(1);
+				fprintf(stderr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'.\n", name);
+				free(name); fai_destroy(idx);
+				return 0;
 			}
 			if (state == 2) state = 3;
 			l1 = l2 = 0;
@@ -95,13 +110,15 @@ faidx_t *fai_build_core(RAZF *rz)
 				if (isgraph(c)) ++l2;
 			} while ((ret = razf_read(rz, &c, 1)) && c != '\n');
 			if (state == 3 && l2) {
-				fprintf(stderr, "[fai_build_core] different line length in sequence '%s'. Abort!\n", name);
-				exit(1);
+				fprintf(stderr, "[fai_build_core] different line length in sequence '%s'.\n", name);
+				free(name); fai_destroy(idx);
+				return 0;
 			}
 			++l1; len += l2;
 			if (l2 >= 0x10000) {
-				fprintf(stderr, "[fai_build_core] line length exceeds 65535 in sequence '%s'. Abort!\n", name);
-				exit(1);
+				fprintf(stderr, "[fai_build_core] line length exceeds 65535 in sequence '%s'.\n", name);
+				free(name); fai_destroy(idx);
+				return 0;
 			}
 			if (state == 1) line_len = l1, line_blen = l2, state = 0;
 			else if (state == 0) {
@@ -122,7 +139,11 @@ void fai_save(const faidx_t *fai, FILE *fp)
 		faidx1_t x;
 		k = kh_get(s, fai->hash, fai->name[i]);
 		x = kh_value(fai->hash, k);
+#ifdef _WIN32
+		fprintf(fp, "%s\t%d\t%ld\t%d\t%d\n", fai->name[i], (int)x.len, (long)x.offset, (int)x.line_blen, (int)x.line_len);
+#else
 		fprintf(fp, "%s\t%d\t%lld\t%d\t%d\n", fai->name[i], (int)x.len, (long long)x.offset, (int)x.line_blen, (int)x.line_len);
+#endif
 	}
 }
 
@@ -131,14 +152,22 @@ faidx_t *fai_read(FILE *fp)
 	faidx_t *fai;
 	char *buf, *p;
 	int len, line_len, line_blen;
+#ifdef _WIN32
+	long offset;
+#else
 	long long offset;
+#endif
 	fai = (faidx_t*)calloc(1, sizeof(faidx_t));
 	fai->hash = kh_init(s);
 	buf = (char*)calloc(0x10000, 1);
 	while (!feof(fp) && fgets(buf, 0x10000, fp)) {
 		for (p = buf; *p && isgraph(*p); ++p);
 		*p = 0; ++p;
+#ifdef _WIN32
+		sscanf(p, "%d%ld%d%d", &len, &offset, &line_blen, &line_len);
+#else
 		sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
+#endif
 		fai_insert_index(fai, buf, len, line_len, line_blen, offset);
 	}
 	free(buf);
@@ -155,7 +184,7 @@ void fai_destroy(faidx_t *fai)
 	free(fai);
 }
 
-void fai_build(const char *fn)
+int fai_build(const char *fn)
 {
 	char *str;
 	RAZF *rz;
@@ -164,15 +193,24 @@ void fai_build(const char *fn)
 	str = (char*)calloc(strlen(fn) + 5, 1);
 	sprintf(str, "%s.fai", fn);
 	rz = razf_open(fn, "r");
-	assert(rz);
+	if (rz == 0) {
+		fprintf(stderr, "[fai_build] fail to open the FASTA file.\n");
+		free(str);
+		return -1;
+	}
 	fai = fai_build_core(rz);
 	razf_close(rz);
-	fp = fopen(str, "w");
-	assert(fp);
+	fp = fopen(str, "wb");
+	if (fp == 0) {
+		fprintf(stderr, "[fai_build] fail to write FASTA index.\n");
+		fai_destroy(fai); free(str);
+		return -1;
+	}
 	fai_save(fai, fp);
 	fclose(fp);
 	free(str);
 	fai_destroy(fai);
+	return 0;
 }
 
 faidx_t *fai_load(const char *fn)
@@ -182,22 +220,25 @@ faidx_t *fai_load(const char *fn)
 	faidx_t *fai;
 	str = (char*)calloc(strlen(fn) + 5, 1);
 	sprintf(str, "%s.fai", fn);
-	fp = fopen(str, "r");
+	fp = fopen(str, "rb");
 	if (fp == 0) {
 		fprintf(stderr, "[fai_load] build FASTA index.\n");
 		fai_build(fn);
 		fp = fopen(str, "r");
 		if (fp == 0) {
+			fprintf(stderr, "[fai_load] fail to open FASTA index.\n");
 			free(str);
 			return 0;
 		}
 	}
 	fai = fai_read(fp);
 	fclose(fp);
-	fai->rz = razf_open(fn, "r");
-	if (fai->rz == 0) return 0;
-	assert(fai->rz);
+	fai->rz = razf_open(fn, "rb");
 	free(str);
+	if (fai->rz == 0) {
+		fprintf(stderr, "[fai_load] fail to open FASTA file.\n");
+		return 0;
+	}
 	return fai;
 }
 
@@ -265,7 +306,7 @@ int faidx_main(int argc, char *argv[])
 			char *s;
 			faidx_t *fai;
 			fai = fai_load(argv[1]);
-			assert(fai);
+			if (fai == 0) return 1;
 			for (i = 2; i != argc; ++i) {
 				printf(">%s\n", argv[i]);
 				s = fai_fetch(fai, argv[i], &l);