Merge pull request #13 from daviesrob/master_fixes

Updates to master to add IO error checking

.gitignore

@@ -3,3 +3,5 @@ bwa
 test
 test64
 .*.swp
+Makefile.bak
+bwamem-lite

Makefile

@@ -1,12 +1,13 @@
 CC=			gcc
 CFLAGS=		-g -Wall -O2
+WRAP_MALLOC= -DUSE_MALLOC_WRAPPERS
 AR=			ar
-DFLAGS=		-DHAVE_PTHREAD
+DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
 LOBJS=		utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o
 AOBJS=		QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
 			is.o bwtindex.o bwape.o kopen.o pemerge.o \
 			bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
-			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
+			bwtsw2_chain.o fastmap.o bwtsw2_pair.o malloc_wrap.o
 PROG=		bwa
 INCLUDES=	
 LIBS=		-lm -lz -lpthread
@@ -28,26 +29,48 @@ bwamem-lite:libbwa.a example.o
 libbwa.a:$(LOBJS)
 		$(AR) -csru $@ $(LOBJS)
 
-ksw.o:ksw.h
-kstring.o:kstring.h
-utils.o:utils.h ksort.h kseq.h
-bntseq.o:bntseq.h
-bwt.o:bwt.h utils.h
-bwa.o:bwa.h bwt.h bntseq.h
-bwamem.o:ksw.h kbtree.h ksort.h kvec.h kstring.h utils.h bwamem.h
-bwamem_pair.o:ksw.h kvec.h kstring.h utils.h bwamem.h
-
-QSufSort.o:QSufSort.h
-bwt_gen.o:QSufSort.h
-
-fastmap.o:bwt.h bwamem.h
-
-bwtaln.o:bwt.h bwtaln.h kseq.h
-bwtgap.o:bwtgap.h bwtaln.h bwt.h
-
-bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h
-bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h
-bwtsw2_main.o:bwtsw2.h
-
 clean:
 		rm -f gmon.out *.o a.out $(PROG) *~ *.a
+
+depend:
+	( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c )
+
+# DO NOT DELETE THIS LINE -- make depend depends on it.
+
+QSufSort.o: QSufSort.h
+bamlite.o: bamlite.h malloc_wrap.h
+bntseq.o: bntseq.h utils.h kseq.h malloc_wrap.h
+bwa.o: bntseq.h bwa.h bwt.h ksw.h utils.h malloc_wrap.h kseq.h
+bwamem.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h ksw.h kvec.h
+bwamem.o: ksort.h utils.h kbtree.h
+bwamem_pair.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h kvec.h
+bwamem_pair.o: utils.h ksw.h
+bwape.o: bwtaln.h bwt.h kvec.h malloc_wrap.h bntseq.h utils.h bwase.h bwa.h
+bwape.o: ksw.h khash.h
+bwase.o: bwase.h bntseq.h bwt.h bwtaln.h utils.h kstring.h malloc_wrap.h
+bwase.o: bwa.h ksw.h
+bwaseqio.o: bwtaln.h bwt.h utils.h bamlite.h malloc_wrap.h kseq.h
+bwt.o: utils.h bwt.h kvec.h malloc_wrap.h
+bwt_gen.o: QSufSort.h malloc_wrap.h
+bwt_lite.o: bwt_lite.h malloc_wrap.h
+bwtaln.o: bwtaln.h bwt.h bwtgap.h utils.h bwa.h bntseq.h malloc_wrap.h
+bwtgap.o: bwtgap.h bwt.h bwtaln.h malloc_wrap.h
+bwtindex.o: bntseq.h bwt.h utils.h malloc_wrap.h
+bwtsw2_aux.o: bntseq.h bwt_lite.h utils.h bwtsw2.h bwt.h kstring.h
+bwtsw2_aux.o: malloc_wrap.h bwa.h ksw.h kseq.h ksort.h
+bwtsw2_chain.o: bwtsw2.h bntseq.h bwt_lite.h bwt.h malloc_wrap.h ksort.h
+bwtsw2_core.o: bwt_lite.h bwtsw2.h bntseq.h bwt.h kvec.h malloc_wrap.h
+bwtsw2_core.o: khash.h ksort.h
+bwtsw2_main.o: bwt.h bwtsw2.h bntseq.h bwt_lite.h utils.h bwa.h
+bwtsw2_pair.o: utils.h bwt.h bntseq.h bwtsw2.h bwt_lite.h kstring.h
+bwtsw2_pair.o: malloc_wrap.h ksw.h
+example.o: bwamem.h bwt.h bntseq.h bwa.h kseq.h malloc_wrap.h
+fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h malloc_wrap.h utils.h kseq.h
+is.o: malloc_wrap.h
+kopen.o: malloc_wrap.h
+kstring.o: kstring.h malloc_wrap.h
+ksw.o: ksw.h malloc_wrap.h
+main.o: utils.h
+malloc_wrap.o: malloc_wrap.h
+pemerge.o: ksw.h kseq.h malloc_wrap.h kstring.h bwa.h bntseq.h bwt.h utils.h
+utils.o: utils.h ksort.h malloc_wrap.h kseq.h

bamlite.c

@@ -2,8 +2,13 @@
 #include <ctype.h>
 #include <string.h>
 #include <stdio.h>
+#include <errno.h>
 #include "bamlite.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 /*********************
  * from bam_endian.c *
  *********************/
@@ -62,11 +67,11 @@ void bam_header_destroy(bam_header_t *header)
 	if (header == 0) return;
 	if (header->target_name) {
 		for (i = 0; i < header->n_targets; ++i)
-			free(header->target_name[i]);
+			if (header->target_name[i]) free(header->target_name[i]);
+		if (header->target_len) free(header->target_len);
 		free(header->target_name);
-		free(header->target_len);
 	}
-	free(header->text);
+	if (header->text) free(header->text);
 	free(header);
 }
 
@@ -80,28 +85,33 @@ bam_header_t *bam_header_read(bamFile fp)
 	magic_len = bam_read(fp, buf, 4);
 	if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
 		fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
-		return 0;
+		return NULL;
 	}
 	header = bam_header_init();
 	// read plain text and the number of reference sequences
-	bam_read(fp, &header->l_text, 4);
+	if (bam_read(fp, &header->l_text, 4) != 4) goto fail; 
 	if (bam_is_be) bam_swap_endian_4p(&header->l_text);
 	header->text = (char*)calloc(header->l_text + 1, 1);
-	bam_read(fp, header->text, header->l_text);
+	if (bam_read(fp, header->text, header->l_text) != header->l_text) goto fail;
-	bam_read(fp, &header->n_targets, 4);
+	if (bam_read(fp, &header->n_targets, 4) != 4) goto fail;
 	if (bam_is_be) bam_swap_endian_4p(&header->n_targets);
 	// read reference sequence names and lengths
 	header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
 	header->target_len = (uint32_t*)calloc(header->n_targets, 4);
 	for (i = 0; i != header->n_targets; ++i) {
-		bam_read(fp, &name_len, 4);
+		if (bam_read(fp, &name_len, 4) != 4) goto fail;
 		if (bam_is_be) bam_swap_endian_4p(&name_len);
 		header->target_name[i] = (char*)calloc(name_len, 1);
-		bam_read(fp, header->target_name[i], name_len);
+		if (bam_read(fp, header->target_name[i], name_len) != name_len) {
-		bam_read(fp, &header->target_len[i], 4);
+			goto fail;
+		}
+		if (bam_read(fp, &header->target_len[i], 4) != 4) goto fail;
 		if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
 	}
 	return header;
+ fail:
+	bam_header_destroy(header);
+	return NULL;
 }
 
 static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
@@ -153,3 +163,48 @@ int bam_read1(bamFile fp, bam1_t *b)
 	if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
 	return 4 + block_len;
 }
+
+
+#ifdef USE_VERBOSE_ZLIB_WRAPPERS
+// Versions of gzopen, gzread and gzclose that print up error messages
+
+gzFile bamlite_gzopen(const char *fn, const char *mode) {
+	gzFile fp;
+	if (strcmp(fn, "-") == 0) {
+		fp = gzdopen(fileno((strstr(mode, "r"))? stdin : stdout), mode);
+		if (!fp) {
+			fprintf(stderr, "Couldn't open %s : %s",
+					(strstr(mode, "r"))? "stdin" : "stdout",
+					strerror(errno));
+		}
+		return fp;
+	}
+	if ((fp = gzopen(fn, mode)) == 0) {
+		fprintf(stderr, "Couldn't open %s : %s\n", fn,
+				errno ? strerror(errno) : "Out of memory");
+	}
+	return fp;
+}
+
+int bamlite_gzread(gzFile file, void *ptr, unsigned int len) {
+	int ret = gzread(file, ptr, len);
+	
+	if (ret < 0) {
+		int errnum = 0;
+		const char *msg = gzerror(file, &errnum);
+		fprintf(stderr, "gzread error: %s\n",
+				Z_ERRNO == errnum ? strerror(errno) : msg);
+	}
+	return ret;
+}
+
+int bamlite_gzclose(gzFile file) {
+	int ret = gzclose(file);
+	if (Z_OK != ret) {
+		fprintf(stderr, "gzclose error: %s\n",
+						  Z_ERRNO == ret ? strerror(errno) : zError(ret));
+	}
+	
+	return ret;
+}
+#endif /* USE_VERBOSE_ZLIB_WRAPPERS */

bamlite.h

@@ -4,11 +4,25 @@
 #include <stdint.h>
 #include <zlib.h>
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+#define USE_VERBOSE_ZLIB_WRAPPERS
+
 typedef gzFile bamFile;
+#ifdef USE_VERBOSE_ZLIB_WRAPPERS
+/* These print error messages on failure */
+#  define bam_open(fn, mode)      bamlite_gzopen(fn, mode)
+#  define bam_dopen(fd, mode)     gzdopen(fd, mode)
+#  define bam_close(fp)           bamlite_gzclose(fp)
+#  define bam_read(fp, buf, size) bamlite_gzread(fp, buf, size)
+#else
 #  define bam_open(fn, mode)      gzopen(fn, mode)
 #  define bam_dopen(fd, mode)     gzdopen(fd, mode)
 #  define bam_close(fp)           gzclose(fp)
 #  define bam_read(fp, buf, size) gzread(fp, buf, size)
+#endif /* USE_VERBOSE_ZLIB_WRAPPERS */
 
 typedef struct {
 	int32_t n_targets;
@@ -87,6 +101,12 @@ extern "C" {
 	bam_header_t *bam_header_read(bamFile fp);
 	int bam_read1(bamFile fp, bam1_t *b);
 
+#ifdef USE_VERBOSE_ZLIB_WRAPPERS
+	gzFile bamlite_gzopen(const char *fn, const char *mode);
+	int bamlite_gzread(gzFile file, void *ptr, unsigned int len);
+	int bamlite_gzclose(gzFile file);
+#endif /* USE_VERBOSE_ZLIB_WRAPPERS */
+
 #ifdef __cplusplus
 }
 #endif

bntseq.c

@@ -30,12 +30,17 @@
 #include <string.h>
 #include <zlib.h>
 #include <unistd.h>
+#include <errno.h>
 #include "bntseq.h"
 #include "utils.h"
 
 #include "kseq.h"
 KSEQ_DECLARE(gzFile)
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 unsigned char nst_nt4_table[256] = {
 	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
 	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
@@ -63,25 +68,27 @@ void bns_dump(const bntseq_t *bns, const char *prefix)
 	{ // dump .ann
 		strcpy(str, prefix); strcat(str, ".ann");
 		fp = xopen(str, "w");
-		fprintf(fp, "%lld %d %u\n", (long long)bns->l_pac, bns->n_seqs, bns->seed);
+		err_fprintf(fp, "%lld %d %u\n", (long long)bns->l_pac, bns->n_seqs, bns->seed);
 		for (i = 0; i != bns->n_seqs; ++i) {
 			bntann1_t *p = bns->anns + i;
-			fprintf(fp, "%d %s", p->gi, p->name);
+			err_fprintf(fp, "%d %s", p->gi, p->name);
-			if (p->anno[0]) fprintf(fp, " %s\n", p->anno);
+			if (p->anno[0]) err_fprintf(fp, " %s\n", p->anno);
-			else fprintf(fp, "\n");
+			else err_fprintf(fp, "\n");
-			fprintf(fp, "%lld %d %d\n", (long long)p->offset, p->len, p->n_ambs);
+			err_fprintf(fp, "%lld %d %d\n", (long long)p->offset, p->len, p->n_ambs);
 		}
-		fclose(fp);
+		err_fflush(fp);
+		err_fclose(fp);
 	}
 	{ // dump .amb
 		strcpy(str, prefix); strcat(str, ".amb");
 		fp = xopen(str, "w");
-		fprintf(fp, "%lld %d %u\n", (long long)bns->l_pac, bns->n_seqs, bns->n_holes);
+		err_fprintf(fp, "%lld %d %u\n", (long long)bns->l_pac, bns->n_seqs, bns->n_holes);
 		for (i = 0; i != bns->n_holes; ++i) {
 			bntamb1_t *p = bns->ambs + i;
-			fprintf(fp, "%lld %d %c\n", (long long)p->offset, p->len, p->amb);
+			err_fprintf(fp, "%lld %d %c\n", (long long)p->offset, p->len, p->amb);
 		}
-		fclose(fp);
+		err_fflush(fp);
+		err_fclose(fp);
 	}
 }
 
@@ -89,13 +96,16 @@ bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, c
 {
 	char str[1024];
 	FILE *fp;
+	const char *fname;
 	bntseq_t *bns;
 	long long xx;
 	int i;
+	int scanres;
 	bns = (bntseq_t*)calloc(1, sizeof(bntseq_t));
 	{ // read .ann
-		fp = xopen(ann_filename, "r");
+		fp = xopen(fname = ann_filename, "r");
-		fscanf(fp, "%lld%d%u", &xx, &bns->n_seqs, &bns->seed);
+		scanres = fscanf(fp, "%lld%d%u", &xx, &bns->n_seqs, &bns->seed);
+		if (scanres != 3) goto badread;
 		bns->l_pac = xx;
 		bns->anns = (bntann1_t*)calloc(bns->n_seqs, sizeof(bntann1_t));
 		for (i = 0; i < bns->n_seqs; ++i) {
@@ -103,39 +113,54 @@ bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, c
 			char *q = str;
 			int c;
 			// read gi and sequence name
-			fscanf(fp, "%u%s", &p->gi, str);
+			scanres = fscanf(fp, "%u%s", &p->gi, str);
+			if (scanres != 2) goto badread;
 			p->name = strdup(str);
 			// read fasta comments 
-			while ((c = fgetc(fp)) != '\n' && c != EOF) *q++ = c;
+			while (str - q < sizeof(str) - 1 && (c = fgetc(fp)) != '\n' && c != EOF) *q++ = c;
+			while (c != '\n' && c != EOF) c = fgetc(fp);
+			if (c == EOF) {
+				scanres = EOF;
+				goto badread;
+			}
 			*q = 0;
 			if (q - str > 1) p->anno = strdup(str + 1); // skip leading space
 			else p->anno = strdup("");
 			// read the rest
-			fscanf(fp, "%lld%d%d", &xx, &p->len, &p->n_ambs);
+			scanres = fscanf(fp, "%lld%d%d", &xx, &p->len, &p->n_ambs);
+			if (scanres != 3) goto badread;
 			p->offset = xx;
 		}
-		fclose(fp);
+		err_fclose(fp);
 	}
 	{ // read .amb
 		int64_t l_pac;
 		int32_t n_seqs;
-		fp = xopen(amb_filename, "r");
+		fp = xopen(fname = amb_filename, "r");
-		fscanf(fp, "%lld%d%d", &xx, &n_seqs, &bns->n_holes);
+		scanres = fscanf(fp, "%lld%d%d", &xx, &n_seqs, &bns->n_holes);
+		if (scanres != 3) goto badread;
 		l_pac = xx;
 		xassert(l_pac == bns->l_pac && n_seqs == bns->n_seqs, "inconsistent .ann and .amb files.");
 		bns->ambs = bns->n_holes? (bntamb1_t*)calloc(bns->n_holes, sizeof(bntamb1_t)) : 0;
 		for (i = 0; i < bns->n_holes; ++i) {
 			bntamb1_t *p = bns->ambs + i;
-			fscanf(fp, "%lld%d%s", &xx, &p->len, str);
+			scanres = fscanf(fp, "%lld%d%s", &xx, &p->len, str);
+			if (scanres != 3) goto badread;
 			p->offset = xx;
 			p->amb = str[0];
 		}
-		fclose(fp);
+		err_fclose(fp);
 	}
 	{ // open .pac
 		bns->fp_pac = xopen(pac_filename, "rb");
 	}
 	return bns;
+
+ badread:
+	if (EOF == scanres) {
+		err_fatal(__func__, "Error reading %s : %s\n", fname, ferror(fp) ? strerror(errno) : "Unexpected end of file");
+	}
+	err_fatal(__func__, "Parse error reading %s\n", fname);
 }
 
 bntseq_t *bns_restore(const char *prefix)
@@ -152,7 +177,7 @@ void bns_destroy(bntseq_t *bns)
 	if (bns == 0) return;
 	else {
 		int i;
-		if (bns->fp_pac) fclose(bns->fp_pac);
+		if (bns->fp_pac) err_fclose(bns->fp_pac);
 		free(bns->ambs);
 		for (i = 0; i < bns->n_seqs; ++i) {
 			free(bns->anns[i].name);
@@ -250,16 +275,17 @@ int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix, int for_only)
 	ret = bns->l_pac;
 	{ // finalize .pac file
 		ubyte_t ct;
-		fwrite(pac, 1, (bns->l_pac>>2) + ((bns->l_pac&3) == 0? 0 : 1), fp);
+		err_fwrite(pac, 1, (bns->l_pac>>2) + ((bns->l_pac&3) == 0? 0 : 1), fp);
 		// the following codes make the pac file size always (l_pac/4+1+1)
 		if (bns->l_pac % 4 == 0) {
 			ct = 0;
-			fwrite(&ct, 1, 1, fp);
+			err_fwrite(&ct, 1, 1, fp);
 		}
 		ct = bns->l_pac % 4;
-		fwrite(&ct, 1, 1, fp);
+		err_fwrite(&ct, 1, 1, fp);
 		// close .pac file
-		fclose(fp);
+		err_fflush(fp);
+		err_fclose(fp);
 	}
 	bns_dump(bns, prefix);
 	bns_destroy(bns);
@@ -283,7 +309,7 @@ int bwa_fa2pac(int argc, char *argv[])
 	}
 	fp = xzopen(argv[optind], "r");
 	bns_fasta2bntseq(fp, (optind+1 < argc)? argv[optind+1] : argv[optind], for_only);
-	gzclose(fp);
+	err_gzclose(fp);
 	return 0;
 }
 

bwa.c

@@ -7,6 +7,10 @@
 #include "ksw.h"
 #include "utils.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 int bwa_verbose = 3;
 char bwa_rg_id[256];
 
@@ -258,8 +262,8 @@ bwaidx_t *bwa_idx_load(const char *hint, int which)
 		idx->bns = bns_restore(prefix);
 		if (which & BWA_IDX_PAC) {
 			idx->pac = calloc(idx->bns->l_pac/4+1, 1);
-			fread(idx->pac, 1, idx->bns->l_pac/4+1, idx->bns->fp_pac); // concatenated 2-bit encoded sequence
+			err_fread_noeof(idx->pac, 1, idx->bns->l_pac/4+1, idx->bns->fp_pac); // concatenated 2-bit encoded sequence
-			fclose(idx->bns->fp_pac);
+			err_fclose(idx->bns->fp_pac);
 			idx->bns->fp_pac = 0;
 		}
 	}

bwamem.c

@@ -15,6 +15,10 @@
 #include "ksort.h"
 #include "utils.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 /* Theory on probability and scoring *ungapped* alignment
  *
  * s'(a,b) = log[P(b|a)/P(b)] = log[4P(b|a)], assuming uniform base distribution
@@ -229,16 +233,16 @@ void mem_print_chain(const bntseq_t *bns, mem_chain_v *chn)
 	int i, j;
 	for (i = 0; i < chn->n; ++i) {
 		mem_chain_t *p = &chn->a[i];
-		printf("%d", p->n);
+		err_printf("%d", p->n);
 		for (j = 0; j < p->n; ++j) {
 			bwtint_t pos;
 			int is_rev, ref_id;
 			pos = bns_depos(bns, p->seeds[j].rbeg, &is_rev);
 			if (is_rev) pos -= p->seeds[j].len - 1;
 			bns_cnt_ambi(bns, pos, p->seeds[j].len, &ref_id);
-			printf("\t%d,%d,%ld(%s:%c%ld)", p->seeds[j].len, p->seeds[j].qbeg, (long)p->seeds[j].rbeg, bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - bns->anns[ref_id].offset) + 1);
+			err_printf("\t%d,%d,%ld(%s:%c%ld)", p->seeds[j].len, p->seeds[j].qbeg, (long)p->seeds[j].rbeg, bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - bns->anns[ref_id].offset) + 1);
 		}
-		putchar('\n');
+		err_putchar('\n');
 	}
 }
 

bwamem_pair.c

@@ -8,6 +8,11 @@
 #include "utils.h"
 #include "ksw.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+
 #define MIN_RATIO     0.8
 #define MIN_DIR_CNT   10
 #define MIN_DIR_RATIO 0.05

bwape.c

@@ -12,6 +12,10 @@
 #include "bwa.h"
 #include "ksw.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 typedef struct {
 	int n;
 	bwtint_t *a;
@@ -280,11 +284,11 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
 			p[j] = seqs[j] + i;
 			p[j]->n_multi = 0;
 			p[j]->extra_flag |= SAM_FPD | (j == 0? SAM_FR1 : SAM_FR2);
-			fread(&n_aln, 4, 1, fp_sa[j]);
+			err_fread_noeof(&n_aln, 4, 1, fp_sa[j]);
 			if (n_aln > kv_max(d->aln[j]))
 				kv_resize(bwt_aln1_t, d->aln[j], n_aln);
 			d->aln[j].n = n_aln;
-			fread(d->aln[j].a, sizeof(bwt_aln1_t), n_aln, fp_sa[j]);
+			err_fread_noeof(d->aln[j].a, sizeof(bwt_aln1_t), n_aln, fp_sa[j]);
 			kv_copy(bwt_aln1_t, buf[j][i].aln, d->aln[j]); // backup d->aln[j]
 			// generate SE alignment and mapping quality
 			bwa_aln2seq(n_aln, d->aln[j].a, p[j]);
@@ -498,8 +502,8 @@ ubyte_t *bwa_paired_sw(const bntseq_t *bns, const ubyte_t *_pacseq, int n_seqs,
 	// load reference sequence
 	if (_pacseq == 0) {
 		pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
-		rewind(bns->fp_pac);
+		err_rewind(bns->fp_pac);
-		fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
+		err_fread_noeof(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
 	} else pacseq = (ubyte_t*)_pacseq;
 	if (!popt->is_sw || ii->avg < 0.0) return pacseq;
 
@@ -644,18 +648,18 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
 	g_hash = kh_init(b128);
 	last_ii.avg = -1.0;
 
-	fread(&opt, sizeof(gap_opt_t), 1, fp_sa[0]);
+	err_fread_noeof(&opt, sizeof(gap_opt_t), 1, fp_sa[0]);
 	ks[0] = bwa_open_reads(opt.mode, fn_fa[0]);
 	opt0 = opt;
-	fread(&opt, sizeof(gap_opt_t), 1, fp_sa[1]); // overwritten!
+	err_fread_noeof(&opt, sizeof(gap_opt_t), 1, fp_sa[1]); // overwritten!
 	ks[1] = bwa_open_reads(opt.mode, fn_fa[1]);
 	{ // for Illumina alignment only
 		if (popt->is_preload) {
 			strcpy(str, prefix); strcat(str, ".bwt");  bwt = bwt_restore_bwt(str);
 			strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
 			pac = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
-			rewind(bns->fp_pac);
+			err_rewind(bns->fp_pac);
-			fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
+			err_fread_noeof(pac, 1, bns->l_pac/4+1, bns->fp_pac);
 		}
 	}
 
@@ -709,7 +713,7 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
 	bns_destroy(bns);
 	for (i = 0; i < 2; ++i) {
 		bwa_seq_close(ks[i]);
-		fclose(fp_sa[i]);
+		err_fclose(fp_sa[i]);
 	}
 	for (iter = kh_begin(g_hash); iter != kh_end(g_hash); ++iter)
 		if (kh_exist(g_hash, iter)) free(kh_val(g_hash, iter).a);
@@ -765,7 +769,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
 	}
 	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
 		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
-		return 0;
+		return 1;
 	}
 	bwa_sai2sam_pe_core(prefix, argv + optind + 1, argv + optind+3, popt, rg_line);
 	free(prefix); free(popt);

bwase.c

@@ -12,6 +12,10 @@
 #include "bwa.h"
 #include "ksw.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 int g_log_n[256];
 
 void bwa_print_sam_PG();
@@ -312,8 +316,8 @@ void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t
 
 	if (!_pacseq) {
 		pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
-		rewind(bns->fp_pac);
+		err_rewind(bns->fp_pac);
-		fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
+		err_fread_noeof(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
 	} else pacseq = _pacseq;
 	for (i = 0; i != n_seqs; ++i) {
 		bwa_seq_t *s = seqs + i;
@@ -381,6 +385,26 @@ static int64_t pos_5(const bwa_seq_t *p)
 	return -1;
 }
 
+void bwa_print_seq(FILE *stream, bwa_seq_t *seq) {
+	char buffer[4096];
+	const int bsz = sizeof(buffer);
+	int i, j, l;
+	
+	if (seq->strand == 0) {
+		for (i = 0; i < seq->full_len; i += bsz) {
+			l = seq->full_len - i > bsz ? bsz : seq->full_len - i;
+			for (j = 0; j < l; j++) buffer[j] = "ACGTN"[seq->seq[i + j]];
+			err_fwrite(buffer, 1, l, stream);
+		}
+	} else {
+		for (i = seq->full_len - 1; i >= 0; i -= bsz) {
+			l = i + 1 > bsz ? bsz : i + 1;
+			for (j = 0; j < l; j++) buffer[j] = "TGCAN"[seq->seq[i - j]];
+			err_fwrite(buffer, 1, l, stream);
+		}
+	}
+}
+
 void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2)
 {
 	int j;
@@ -432,10 +456,8 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 		else err_printf("\t*\t0\t0\t");
 
 		// print sequence and quality
-		if (p->strand == 0)
+		bwa_print_seq(stdout, p);
-			for (j = 0; j != p->full_len; ++j) putchar("ACGTN"[(int)p->seq[j]]);
+		err_putchar('\t');
-		else for (j = 0; j != p->full_len; ++j) putchar("TGCAN"[p->seq[p->full_len - 1 - j]]);
-		putchar('\t');
 		if (p->qual) {
 			if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
 			err_printf("%s", p->qual);
@@ -478,14 +500,16 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 				}
 			}
 		}
-		putchar('\n');
+		err_putchar('\n');
 	} else { // this read has no match
-		ubyte_t *s = p->strand? p->rseq : p->seq;
+		//ubyte_t *s = p->strand? p->rseq : p->seq;
 		int flag = p->extra_flag | SAM_FSU;
 		if (mate && mate->type == BWA_TYPE_NO_MATCH) flag |= SAM_FMU;
 		err_printf("%s\t%d\t*\t0\t0\t*\t*\t0\t0\t", p->name, flag);
-		for (j = 0; j != p->len; ++j) putchar("ACGTN"[(int)s[j]]);
+		//Why did this work differently to the version above??
-		putchar('\t');
+		//for (j = 0; j != p->len; ++j) putchar("ACGTN"[(int)s[j]]);
+		bwa_print_seq(stdout, p);
+		err_putchar('\t');
 		if (p->qual) {
 			if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
 			err_printf("%s", p->qual);
@@ -493,7 +517,7 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 		if (bwa_rg_id[0]) err_printf("\tRG:Z:%s", bwa_rg_id);
 		if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
 		if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
-		putchar('\n');
+		err_putchar('\n');
 	}
 }
 
@@ -522,7 +546,7 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
 	fp_sa = xopen(fn_sa, "r");
 
 	m_aln = 0;
-	fread(&opt, sizeof(gap_opt_t), 1, fp_sa);
+	err_fread_noeof(&opt, sizeof(gap_opt_t), 1, fp_sa);
 	bwa_print_sam_hdr(bns, rg_line);
 	//bwa_print_sam_PG();
 	// set ks
@@ -536,12 +560,12 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
 		for (i = 0; i < n_seqs; ++i) {
 			bwa_seq_t *p = seqs + i;
 			int n_aln;
-			fread(&n_aln, 4, 1, fp_sa);
+			err_fread_noeof(&n_aln, 4, 1, fp_sa);
 			if (n_aln > m_aln) {
 				m_aln = n_aln;
 				aln = (bwt_aln1_t*)realloc(aln, sizeof(bwt_aln1_t) * m_aln);
 			}
-			fread(aln, sizeof(bwt_aln1_t), n_aln, fp_sa);
+			err_fread_noeof(aln, sizeof(bwt_aln1_t), n_aln, fp_sa);
 			bwa_aln2seq_core(n_aln, aln, p, 1, n_occ);
 		}
 
@@ -565,7 +589,7 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
 	// destroy
 	bwa_seq_close(ks);
 	bns_destroy(bns);
-	fclose(fp_sa);
+	err_fclose(fp_sa);
 	free(aln);
 }
 
@@ -591,7 +615,7 @@ int bwa_sai2sam_se(int argc, char *argv[])
 	}
 	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
 		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
-		return 0;
+		return 1;
 	}
 	bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ, rg_line);
 	free(prefix);

bwaseqio.c

@@ -7,6 +7,10 @@
 #include "kseq.h"
 KSEQ_DECLARE(gzFile)
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 extern unsigned char nst_nt4_table[256];
 static char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
 
@@ -26,6 +30,7 @@ bwa_seqio_t *bwa_bam_open(const char *fn, int which)
 	bs->is_bam = 1;
 	bs->which = which;
 	bs->fp = bam_open(fn, "r");
+	if (0 == bs->fp) err_fatal_simple("Couldn't open bam file");
 	h = bam_header_read(bs->fp);
 	bam_header_destroy(h);
 	return bs;
@@ -44,9 +49,10 @@ bwa_seqio_t *bwa_seq_open(const char *fn)
 void bwa_seq_close(bwa_seqio_t *bs)
 {
 	if (bs == 0) return;
-	if (bs->is_bam) bam_close(bs->fp);
+	if (bs->is_bam) {
-	else {
+		if (0 != bam_close(bs->fp)) err_fatal_simple("Error closing bam file");
-		gzclose(bs->ks->f->f);
+	} else {
+		err_gzclose(bs->ks->f->f);
 		kseq_destroy(bs->ks);
 	}
 	free(bs);
@@ -90,11 +96,12 @@ static bwa_seq_t *bwa_read_bam(bwa_seqio_t *bs, int n_needed, int *n, int is_com
 	int n_seqs, l, i;
 	long n_trimmed = 0, n_tot = 0;
 	bam1_t *b;
+	int res;
 
 	b = bam_init1();
 	n_seqs = 0;
 	seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
-	while (bam_read1(bs->fp, b) >= 0) {
+	while ((res = bam_read1(bs->fp, b)) >= 0) {
 		uint8_t *s, *q;
 		int go = 0;
 		if ((bs->which & 1) && (b->core.flag & BAM_FREAD1)) go = 1;
@@ -126,6 +133,7 @@ static bwa_seq_t *bwa_read_bam(bwa_seqio_t *bs, int n_needed, int *n, int is_com
 		p->name = strdup((const char*)bam1_qname(b));
 		if (n_seqs == n_needed) break;
 	}
+	if (res < 0 && res != -1) err_fatal_simple("Error reading bam file");
 	*n = n_seqs;
 	if (n_seqs && trim_qual >= 1)
 		fprintf(stderr, "[bwa_read_seq] %.1f%% bases are trimmed.\n", 100.0f * n_trimmed/n_tot);
@@ -184,7 +192,7 @@ bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int mode, int tri
 		p->qual = 0;
 		p->full_len = p->clip_len = p->len = l;
 		n_tot += p->full_len;
-		p->seq = (ubyte_t*)calloc(p->len, 1);
+		p->seq = (ubyte_t*)calloc(p->full_len, 1);
 		for (i = 0; i != p->full_len; ++i)
 			p->seq[i] = nst_nt4_table[(int)seq->seq.s[i]];
 		if (seq->qual.l) { // copy quality

bwt.c

@@ -34,6 +34,10 @@
 #include "bwt.h"
 #include "kvec.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 void bwt_gen_cnt_table(bwt_t *bwt)
 {
 	int i, j;
@@ -67,10 +71,6 @@ void bwt_cal_sa(bwt_t *bwt, int intv)
 	bwt->sa_intv = intv;
 	bwt->n_sa = (bwt->seq_len + intv) / intv;
 	bwt->sa = (bwtint_t*)calloc(bwt->n_sa, sizeof(bwtint_t));
-	if (bwt->sa == 0) {
-		fprintf(stderr, "[%s] Fail to allocate %.3fMB memory. Abort!\n", __func__, bwt->n_sa * sizeof(bwtint_t) / 1024.0/1024.0);
-		abort();
-	}
 	// calculate SA value
 	isa = 0; sa = bwt->seq_len;
 	for (i = 0; i < bwt->seq_len; ++i) {
@@ -354,22 +354,24 @@ void bwt_dump_bwt(const char *fn, const bwt_t *bwt)
 {
 	FILE *fp;
 	fp = xopen(fn, "wb");
-	fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
+	err_fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
-	fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
+	err_fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
-	fwrite(bwt->bwt, 4, bwt->bwt_size, fp);
+	err_fwrite(bwt->bwt, 4, bwt->bwt_size, fp);
-	fclose(fp);
+	err_fflush(fp);
+	err_fclose(fp);
 }
 
 void bwt_dump_sa(const char *fn, const bwt_t *bwt)
 {
 	FILE *fp;
 	fp = xopen(fn, "wb");
-	fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
+	err_fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
-	fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
+	err_fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
-	fwrite(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
+	err_fwrite(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
-	fwrite(&bwt->seq_len, sizeof(bwtint_t), 1, fp);
+	err_fwrite(&bwt->seq_len, sizeof(bwtint_t), 1, fp);
-	fwrite(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
+	err_fwrite(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
-	fclose(fp);
+	err_fflush(fp);
+	err_fclose(fp);
 }
 
 static bwtint_t fread_fix(FILE *fp, bwtint_t size, void *a)
@@ -378,7 +380,7 @@ static bwtint_t fread_fix(FILE *fp, bwtint_t size, void *a)
 	bwtint_t offset = 0;
 	while (size) {
 		int x = bufsize < size? bufsize : size;
-		if ((x = fread(a + offset, 1, x, fp)) == 0) break;
+		if ((x = err_fread_noeof(a + offset, 1, x, fp)) == 0) break;
 		size -= x; offset += x;
 	}
 	return offset;
@@ -391,11 +393,11 @@ void bwt_restore_sa(const char *fn, bwt_t *bwt)
 	bwtint_t primary;
 
 	fp = xopen(fn, "rb");
-	fread(&primary, sizeof(bwtint_t), 1, fp);
+	err_fread_noeof(&primary, sizeof(bwtint_t), 1, fp);
 	xassert(primary == bwt->primary, "SA-BWT inconsistency: primary is not the same.");
-	fread(skipped, sizeof(bwtint_t), 4, fp); // skip
+	err_fread_noeof(skipped, sizeof(bwtint_t), 4, fp); // skip
-	fread(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
+	err_fread_noeof(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
-	fread(&primary, sizeof(bwtint_t), 1, fp);
+	err_fread_noeof(&primary, sizeof(bwtint_t), 1, fp);
 	xassert(primary == bwt->seq_len, "SA-BWT inconsistency: seq_len is not the same.");
 
 	bwt->n_sa = (bwt->seq_len + bwt->sa_intv) / bwt->sa_intv;
@@ -403,7 +405,7 @@ void bwt_restore_sa(const char *fn, bwt_t *bwt)
 	bwt->sa[0] = -1;
 
 	fread_fix(fp, sizeof(bwtint_t) * (bwt->n_sa - 1), bwt->sa + 1);
-	fclose(fp);
+	err_fclose(fp);
 }
 
 bwt_t *bwt_restore_bwt(const char *fn)
@@ -413,15 +415,15 @@ bwt_t *bwt_restore_bwt(const char *fn)
 
 	bwt = (bwt_t*)calloc(1, sizeof(bwt_t));
 	fp = xopen(fn, "rb");
-	fseek(fp, 0, SEEK_END);
+	err_fseek(fp, 0, SEEK_END);
-	bwt->bwt_size = (ftell(fp) - sizeof(bwtint_t) * 5) >> 2;
+	bwt->bwt_size = (err_ftell(fp) - sizeof(bwtint_t) * 5) >> 2;
 	bwt->bwt = (uint32_t*)calloc(bwt->bwt_size, 4);
-	fseek(fp, 0, SEEK_SET);
+	err_fseek(fp, 0, SEEK_SET);
-	fread(&bwt->primary, sizeof(bwtint_t), 1, fp);
+	err_fread_noeof(&bwt->primary, sizeof(bwtint_t), 1, fp);
-	fread(bwt->L2+1, sizeof(bwtint_t), 4, fp);
+	err_fread_noeof(bwt->L2+1, sizeof(bwtint_t), 4, fp);
 	fread_fix(fp, bwt->bwt_size<<2, bwt->bwt);
 	bwt->seq_len = bwt->L2[4];
-	fclose(fp);
+	err_fclose(fp);
 	bwt_gen_cnt_table(bwt);
 
 	return bwt;

bwt_gen.c

@@ -27,8 +27,13 @@
 #include <string.h>
 #include <assert.h>
 #include <stdint.h>
+#include <errno.h>
 #include "QSufSort.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 typedef uint64_t bgint_t;
 typedef int64_t sbgint_t;
 
@@ -1443,13 +1448,29 @@ BWTInc *BWTIncConstructFromPacked(const char *inputFileName, bgint_t initialMaxB
 	packedFile = (FILE*)fopen(inputFileName, "rb");
 
 	if (packedFile == NULL) {
-		fprintf(stderr, "BWTIncConstructFromPacked() : Cannot open inputFileName!\n");
+		fprintf(stderr, "BWTIncConstructFromPacked() : Cannot open %s : %s\n",
+				inputFileName, strerror(errno));
 		exit(1);
 	}
 
-	fseek(packedFile, -1, SEEK_END);
+	if (fseek(packedFile, -1, SEEK_END) != 0) {
+		fprintf(stderr, "BWTIncConstructFromPacked() : Can't seek on %s : %s\n",
+				inputFileName, strerror(errno));
+		exit(1);
+	}
 	packedFileLen = ftell(packedFile);
-	fread(&lastByteLength, sizeof(unsigned char), 1, packedFile);
+	if (packedFileLen == -1) {
+		fprintf(stderr, "BWTIncConstructFromPacked() : Can't ftell on %s : %s\n",
+				inputFileName, strerror(errno));
+		exit(1);
+	}
+	if (fread(&lastByteLength, sizeof(unsigned char), 1, packedFile) != 1) {
+		fprintf(stderr,
+				"BWTIncConstructFromPacked() : Can't read from %s : %s\n",
+				inputFileName,
+				ferror(packedFile)? strerror(errno) : "Unexpected end of file");
+		exit(1);
+	}
 	totalTextLength = TextLengthFromBytePacked(packedFileLen, BIT_PER_CHAR, lastByteLength);
 
 	bwtInc = BWTIncCreate(totalTextLength, initialMaxBuildSize, incMaxBuildSize);
@@ -1463,10 +1484,23 @@ BWTInc *BWTIncConstructFromPacked(const char *inputFileName, bgint_t initialMaxB
 	}
 	textSizeInByte = textToLoad / CHAR_PER_BYTE;	// excluded the odd byte
 
-	fseek(packedFile, -2, SEEK_CUR);
+	if (fseek(packedFile, -((long)textSizeInByte + 2), SEEK_CUR) != 0) {
-	fseek(packedFile, -((long)textSizeInByte), SEEK_CUR);
+		fprintf(stderr, "BWTIncConstructFromPacked() : Can't seek on %s : %s\n",
-	fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte + 1, packedFile);
+				inputFileName, strerror(errno));
-	fseek(packedFile, -((long)textSizeInByte + 1), SEEK_CUR);
+		exit(1);
+	}
+	if (fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte + 1, packedFile) != textSizeInByte + 1) {
+		fprintf(stderr,
+				"BWTIncConstructFromPacked() : Can't read from %s : %s\n",
+				inputFileName,
+				ferror(packedFile)? strerror(errno) : "Unexpected end of file");
+		exit(1);
+	}
+	if (fseek(packedFile, -((long)textSizeInByte + 1), SEEK_CUR) != 0) {
+		fprintf(stderr, "BWTIncConstructFromPacked() : Can't seek on %s : %s\n",
+				inputFileName, strerror(errno));
+		exit(1);
+	}
 
 	ConvertBytePackedToWordPacked(bwtInc->textBuffer, bwtInc->packedText, ALPHABET_SIZE, textToLoad);
 	BWTIncConstruct(bwtInc, textToLoad);
@@ -1479,9 +1513,23 @@ BWTInc *BWTIncConstructFromPacked(const char *inputFileName, bgint_t initialMaxB
 			textToLoad = totalTextLength - processedTextLength;
 		}
 		textSizeInByte = textToLoad / CHAR_PER_BYTE;
-		fseek(packedFile, -((long)textSizeInByte), SEEK_CUR);
+		if (fseek(packedFile, -((long)textSizeInByte), SEEK_CUR) != 0) {
-		fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte, packedFile);
+			fprintf(stderr, "BWTIncConstructFromPacked() : Can't seek on %s : %s\n",
-		fseek(packedFile, -((long)textSizeInByte), SEEK_CUR);
+					inputFileName, strerror(errno));
+			exit(1);
+		}
+		if (fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte, packedFile) != textSizeInByte) {
+			fprintf(stderr,
+				"BWTIncConstructFromPacked() : Can't read from %s : %s\n",
+				inputFileName,
+				ferror(packedFile)? strerror(errno) : "Unexpected end of file");
+			exit(1);
+		}
+		if (fseek(packedFile, -((long)textSizeInByte), SEEK_CUR) != 0) {
+			fprintf(stderr, "BWTIncConstructFromPacked() : Can't seek on %s : %s\n",
+					inputFileName, strerror(errno));
+			exit(1);
+		}
 		ConvertBytePackedToWordPacked(bwtInc->textBuffer, bwtInc->packedText, ALPHABET_SIZE, textToLoad);
 		BWTIncConstruct(bwtInc, textToLoad);
 		processedTextLength += textToLoad;
@@ -1526,15 +1574,28 @@ void BWTSaveBwtCodeAndOcc(const BWT *bwt, const char *bwtFileName, const char *o
 
 	bwtFile = (FILE*)fopen(bwtFileName, "wb");
 	if (bwtFile == NULL) {
-		fprintf(stderr, "BWTSaveBwtCodeAndOcc(): Cannot open BWT code file!\n");
+		fprintf(stderr,
+				"BWTSaveBwtCodeAndOcc(): Cannot open %s for writing: %s\n",
+				bwtFileName, strerror(errno));
 		exit(1);
 	}
 
-	fwrite(&bwt->inverseSa0, sizeof(bgint_t), 1, bwtFile);
-	fwrite(bwt->cumulativeFreq + 1, sizeof(bgint_t), ALPHABET_SIZE, bwtFile);
 	bwtLength = BWTFileSizeInWord(bwt->textLength);
-	fwrite(bwt->bwtCode, sizeof(unsigned int), bwtLength, bwtFile);
+
-	fclose(bwtFile);
+	if (fwrite(&bwt->inverseSa0, sizeof(bgint_t), 1, bwtFile) != 1
+		|| fwrite(bwt->cumulativeFreq + 1,
+				  sizeof(bgint_t), ALPHABET_SIZE, bwtFile) != ALPHABET_SIZE
+		|| fwrite(bwt->bwtCode,
+				  sizeof(unsigned int), bwtLength, bwtFile) != bwtLength) {
+		fprintf(stderr, "BWTSaveBwtCodeAndOcc(): Error writing to %s : %s\n",
+				bwtFileName, strerror(errno));
+		exit(1);
+	}
+	if (fclose(bwtFile) != 0) {
+		fprintf(stderr, "BWTSaveBwtCodeAndOcc(): Error on closing %s : %s\n",
+				bwtFileName, strerror(errno));
+		exit(1);
+	}
 }
 
 void bwt_bwtgen(const char *fn_pac, const char *fn_bwt)

bwt_lite.c

@@ -3,6 +3,10 @@
 #include <stdio.h>
 #include "bwt_lite.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 int is_sa(const uint8_t *T, uint32_t *SA, int n);
 int is_bwt(uint8_t *T, int n);
 

bwtaln.c

@@ -17,6 +17,10 @@
 #include <pthread.h>
 #endif
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 gap_opt_t *gap_init_opt()
 {
 	gap_opt_t *o;
@@ -306,7 +310,7 @@ int bwa_aln(int argc, char *argv[])
 	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
 		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
 		free(opt);
-		return 0;
+		return 1;
 	}
 	bwa_aln_core(prefix, argv[optind+1], opt);
 	free(opt); free(prefix);

bwtgap.c

@@ -4,6 +4,10 @@
 #include "bwtgap.h"
 #include "bwtaln.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 #define STATE_M 0
 #define STATE_I 1
 #define STATE_D 2

bwtindex.c

@@ -39,6 +39,11 @@
 #include "divsufsort.h"
 #endif
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+
 int is_bwt(ubyte_t *T, int n);
 
 int64_t bwa_seq_len(const char *fn_pac)
@@ -47,10 +52,10 @@ int64_t bwa_seq_len(const char *fn_pac)
 	int64_t pac_len;
 	ubyte_t c;
 	fp = xopen(fn_pac, "rb");
-	fseek(fp, -1, SEEK_END);
+	err_fseek(fp, -1, SEEK_END);
-	pac_len = ftell(fp);
+	pac_len = err_ftell(fp);
-	fread(&c, 1, 1, fp);
+	err_fread_noeof(&c, 1, 1, fp);
-	fclose(fp);
+	err_fclose(fp);
 	return (pac_len - 1) * 4 + (int)c;
 }
 
@@ -70,8 +75,8 @@ bwt_t *bwt_pac2bwt(const char *fn_pac, int use_is)
 	// prepare sequence
 	pac_size = (bwt->seq_len>>2) + ((bwt->seq_len&3) == 0? 0 : 1);
 	buf2 = (ubyte_t*)calloc(pac_size, 1);
-	fread(buf2, 1, pac_size, fp);
+	err_fread_noeof(buf2, 1, pac_size, fp);
-	fclose(fp);
+	err_fclose(fp);
 	memset(bwt->L2, 0, 5 * 4);
 	buf = (ubyte_t*)calloc(bwt->seq_len + 1, 1);
 	for (i = 0; i < bwt->seq_len; ++i) {
@@ -229,7 +234,7 @@ int bwa_index(int argc, char *argv[]) // the "index" command
 		fprintf(stderr, "[bwa_index] Pack FASTA... ");
 		l_pac = bns_fasta2bntseq(fp, prefix, 0);
 		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
-		gzclose(fp);
+		err_gzclose(fp);
 	}
 	if (algo_type == 0) algo_type = l_pac > 50000000? 2 : 3; // set the algorithm for generating BWT
 	{
@@ -263,7 +268,7 @@ int bwa_index(int argc, char *argv[]) // the "index" command
 		fprintf(stderr, "[bwa_index] Pack forward-only FASTA... ");
 		l_pac = bns_fasta2bntseq(fp, prefix, 1);
 		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
-		gzclose(fp);
+		err_gzclose(fp);
 	}
 	{
 		bwt_t *bwt;

bwtsw2_aux.c

@@ -22,6 +22,11 @@ KSEQ_DECLARE(gzFile)
 #define __left_lt(a, b) ((a).end > (b).end)
 KSORT_INIT(hit, bsw2hit_t, __left_lt)
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+
 extern unsigned char nst_nt4_table[256];
 
 unsigned char nt_comp_table[256] = {
@@ -710,12 +715,12 @@ static void process_seqs(bsw2seq_t *_seq, const bsw2opt_t *opt, const bntseq_t *
 	// print and reset
 	for (i = 0; i < _seq->n; ++i) {
 		bsw2seq1_t *p = _seq->seq + i;
-		if (p->sam) printf("%s", p->sam);
+		if (p->sam) err_printf("%s", p->sam);
 		free(p->name); free(p->seq); free(p->qual); free(p->sam);
 		p->tid = -1; p->l = 0;
 		p->name = p->seq = p->qual = p->sam = 0;
 	}
-	fflush(stdout);
+	err_fflush(stdout);
 	_seq->n = 0;
 }
 
@@ -729,13 +734,9 @@ void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target, c
 	bseq1_t *bseq;
 
 	pac = calloc(bns->l_pac/4+1, 1);
-	if (pac == 0) {
-		fprintf(stderr, "[bsw2_aln] insufficient memory!\n");
-		return;
-	}
 	for (l = 0; l < bns->n_seqs; ++l)
-		printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[l].name, bns->anns[l].len);
+		err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[l].name, bns->anns[l].len);
-	fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
+	err_fread_noeof(pac, 1, bns->l_pac/4+1, bns->fp_pac);
 	fp = xzopen(fn, "r");
 	ks = kseq_init(fp);
 	_seq = calloc(1, sizeof(bsw2seq_t));
@@ -767,9 +768,9 @@ void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target, c
 	free(pac);
 	free(_seq->seq); free(_seq);
 	kseq_destroy(ks);
-	gzclose(fp);
+	err_gzclose(fp);
 	if (fn2) {
 		kseq_destroy(ks2);
-		gzclose(fp2);
+		err_gzclose(fp2);
 	}
 }

bwtsw2_chain.c

@@ -1,6 +1,10 @@
 #include <stdio.h>
 #include "bwtsw2.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 typedef struct {
 	uint32_t tbeg, tend;
 	int qbeg, qend;

bwtsw2_core.c

@@ -8,6 +8,10 @@
 #include "bwt.h"
 #include "kvec.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 typedef struct {
 	bwtint_t k, l;
 } qintv_t;

bwtsw2_main.c

@@ -37,6 +37,7 @@ int bwa_bwtsw2(int argc, char *argv[])
 		case 'S': opt->skip_sw = 1; break;
 		case 'C': opt->cpy_cmt = 1; break;
 		case 'G': opt->max_chain_gap = atoi(optarg); break;
+		default: return 1;
 		}
 	}
 	opt->qr = opt->q + opt->r;
@@ -79,7 +80,7 @@ int bwa_bwtsw2(int argc, char *argv[])
 	opt->t *= opt->a;
 	opt->coef *= opt->a;
 
-	if ((idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS)) == 0) return 0;
+	if ((idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS)) == 0) return 1;
 	bsw2_aln(opt, idx->bns, idx->bwt, argv[optind+1], optind+2 < argc? argv[optind+2] : 0);
 	bwa_idx_destroy(idx);
 	free(opt);

bwtsw2_pair.c

@@ -2,13 +2,17 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
+#include "utils.h"
 #include "bwt.h"
 #include "bntseq.h"
 #include "bwtsw2.h"
 #include "kstring.h"
-#include "utils.h"
 #include "ksw.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 #define MIN_RATIO     0.8
 #define OUTLIER_BOUND 2.0
 #define MAX_STDDEV    4.0

example.c

@@ -1,11 +1,16 @@
 #include <stdio.h>
 #include <zlib.h>
 #include <string.h>
+#include <errno.h>
 #include <assert.h>
 #include "bwamem.h"
 #include "kseq.h" // for the FASTA/Q parser
 KSEQ_DECLARE(gzFile)
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 int main(int argc, char *argv[])
 {
 	bwaidx_t *idx;
@@ -19,9 +24,17 @@ int main(int argc, char *argv[])
 	}
 
 	idx = bwa_idx_load(argv[1], BWA_IDX_ALL); // load the BWA index
-	assert(idx);
+	if (NULL == idx) {
+		fprintf(stderr, "Index load failed.\n");
+		exit(EXIT_FAILURE);
+	}
 	fp = strcmp(argv[2], "-")? gzopen(argv[2], "r") : gzdopen(fileno(stdin), "r");
-	assert(fp);
+	if (NULL == fp) {
+		fprintf(stderr, "Couldn't open %s : %s\n",
+				strcmp(argv[2], "-") ? argv[2] : "stdin",
+				errno ? strerror(errno) : "Out of memory");
+		exit(EXIT_FAILURE);
+	}
 	ks = kseq_init(fp); // initialize the FASTA/Q parser
 	opt = mem_opt_init(); // initialize the BWA-MEM parameters to the default values
 
@@ -34,10 +47,10 @@ int main(int argc, char *argv[])
 			if (ar.a[i].secondary >= 0) continue; // skip secondary alignments
 			a = mem_reg2aln(opt, idx->bns, idx->pac, ks->seq.l, ks->seq.s, &ar.a[i]); // get forward-strand position and CIGAR
 			// print alignment
-			printf("%s\t%c\t%s\t%ld\t%d\t", ks->name.s, "+-"[a.is_rev], idx->bns->anns[a.rid].name, (long)a.pos, a.mapq);
+			err_printf("%s\t%c\t%s\t%ld\t%d\t", ks->name.s, "+-"[a.is_rev], idx->bns->anns[a.rid].name, (long)a.pos, a.mapq);
 			for (k = 0; k < a.n_cigar; ++k) // print CIGAR
-				printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]);
+				err_printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]);
-			printf("\t%d\n", a.NM); // print edit distance
+			err_printf("\t%d\n", a.NM); // print edit distance
 			free(a.cigar); // don't forget to deallocate CIGAR
 		}
 		free(ar.a); // and deallocate the hit list
@@ -45,7 +58,7 @@ int main(int argc, char *argv[])
 
 	free(opt);
 	kseq_destroy(ks);
-	gzclose(fp);
+	err_gzclose(fp);
 	bwa_idx_destroy(idx);
 	return 0;
 }

fastmap.c

@@ -7,6 +7,7 @@
 #include "kvec.h"
 #include "utils.h"
 #include "kseq.h"
+#include "utils.h"
 KSEQ_DECLARE(gzFile)
 
 extern unsigned char nst_nt4_table[256];
@@ -51,6 +52,7 @@ int main_mem(int argc, char *argv[])
 		else if (c == 'R') {
 			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1; // FIXME: memory leak
 		} else if (c == 's') opt->split_width = atoi(optarg);
+		else return 1;
 	}
 	if (opt->n_threads < 1) opt->n_threads = 1;
 	if (optind + 1 >= argc) {
@@ -130,7 +132,7 @@ int main_mem(int argc, char *argv[])
 			fprintf(stderr, "[M::%s] read %d sequences (%ld bp)...\n", __func__, n, (long)size);
 		mem_process_seqs(opt, idx->bwt, idx->bns, idx->pac, n, seqs, 0);
 		for (i = 0; i < n; ++i) {
-			fputs(seqs[i].sam, stdout);
+			err_fputs(seqs[i].sam, stdout);
 			free(seqs[i].name); free(seqs[i].comment); free(seqs[i].seq); free(seqs[i].qual); free(seqs[i].sam);
 		}
 		free(seqs);
@@ -139,10 +141,10 @@ int main_mem(int argc, char *argv[])
 	free(opt);
 	bwa_idx_destroy(idx);
 	kseq_destroy(ks);
-	gzclose(fp); kclose(ko);
+	err_gzclose(fp); kclose(ko);
 	if (ks2) {
 		kseq_destroy(ks2);
-		gzclose(fp2); kclose(ko2);
+		err_gzclose(fp2); kclose(ko2);
 	}
 	return 0;
 }
@@ -163,6 +165,7 @@ int main_fastmap(int argc, char *argv[])
 			case 'p': print_seq = 1; break;
 			case 'w': min_iwidth = atoi(optarg); break;
 			case 'l': min_len = atoi(optarg); break;
+		    default: return 1;
 		}
 	}
 	if (optind + 1 >= argc) {
@@ -170,16 +173,16 @@ int main_fastmap(int argc, char *argv[])
 		return 1;
 	}
 
-	fp = gzopen(argv[optind + 1], "r");
+	fp = xzopen(argv[optind + 1], "r");
 	seq = kseq_init(fp);
-	idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS);
+	if ((idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS)) == 0) return 1;
 	itr = smem_itr_init(idx->bwt);
 	while (kseq_read(seq) >= 0) {
-		printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l);
+		err_printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l);
 		if (print_seq) {
-			putchar('\t');
+			err_putchar('\t');
-			puts(seq->seq.s);
+			err_puts(seq->seq.s);
-		} else putchar('\n');
+		} else err_putchar('\n');
 		for (i = 0; i < seq->seq.l; ++i)
 			seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
 		smem_set_query(itr, seq->seq.l, (uint8_t*)seq->seq.s);
@@ -187,7 +190,7 @@ int main_fastmap(int argc, char *argv[])
 			for (i = 0; i < a->n; ++i) {
 				bwtintv_t *p = &a->a[i];
 				if ((uint32_t)p->info - (p->info>>32) < min_len) continue;
-				printf("EM\t%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
+				err_printf("EM\t%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
 				if (p->x[2] <= min_iwidth) {
 					for (k = 0; k < p->x[2]; ++k) {
 						bwtint_t pos;
@@ -196,18 +199,18 @@ int main_fastmap(int argc, char *argv[])
 						pos = bns_depos(idx->bns, bwt_sa(idx->bwt, p->x[0] + k), &is_rev);
 						if (is_rev) pos -= len - 1;
 						bns_cnt_ambi(idx->bns, pos, len, &ref_id);
-						printf("\t%s:%c%ld", idx->bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - idx->bns->anns[ref_id].offset) + 1);
+						err_printf("\t%s:%c%ld", idx->bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - idx->bns->anns[ref_id].offset) + 1);
 					}
-				} else fputs("\t*", stdout);
+				} else err_puts("\t*");
-				putchar('\n');
+				err_putchar('\n');
 			}
 		}
-		puts("//");
+		err_puts("//");
 	}
 
 	smem_itr_destroy(itr);
 	bwa_idx_destroy(idx);
 	kseq_destroy(seq);
-	gzclose(fp);
+	err_gzclose(fp);
 	return 0;
 }

is.c

@@ -26,6 +26,10 @@
 
 #include <stdlib.h>
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 typedef unsigned char ubyte_t;
 #define chr(i) (cs == sizeof(int) ? ((const int *)T)[i]:((const unsigned char *)T)[i])
 
@@ -205,7 +209,8 @@ int is_bwt(ubyte_t *T, int n)
 {
 	int *SA, i, primary = 0;
 	SA = (int*)calloc(n+1, sizeof(int));
-	is_sa(T, SA, n);
+
+	if (is_sa(T, SA, n)) return -1;
 
 	for (i = 0; i <= n; ++i) {
 		if (SA[i] == 0) primary = i;

kbtree.h

@@ -32,6 +32,10 @@
 #include <string.h>
 #include <stdint.h>
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 typedef struct {
 	int32_t is_internal:1, n:31;
 } kbnode_t;

khash.h

@@ -116,6 +116,10 @@ int main() {
 #include <string.h>
 #include <limits.h>
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 /* compipler specific configuration */
 
 #if UINT_MAX == 0xffffffffu

kopen.c

@@ -14,6 +14,10 @@
 #include <sys/socket.h>
 #endif
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 #ifdef _WIN32
 #define _KO_NO_NET
 #endif
@@ -54,10 +58,26 @@ static int socket_connect(const char *host, const char *port)
 #undef __err_connect
 }
 
+static int write_bytes(int fd, const char *buf, size_t len)
+{
+	ssize_t bytes;
+	do {
+		bytes = write(fd, buf, len);
+		if (bytes >= 0) {
+			len -= bytes;
+		} else if (errno != EAGAIN && errno != EWOULDBLOCK && errno != EINTR) {
+			return -1;
+		}
+	} while (len > 0);
+
+	return 0;
+}
+
 static int http_open(const char *fn)
 {
 	char *p, *proxy, *q, *http_host, *host, *port, *path, *buf;
 	int fd, ret, l;
+	ssize_t bytes = 0, bufsz = 0x10000;
 
 	/* parse URL; adapted from khttp_parse_url() in knetfile.c */
 	if (strstr(fn, "http://") != fn) return 0;
@@ -87,26 +107,35 @@ static int http_open(const char *fn)
 	/* connect; adapted from khttp_connect() in knetfile.c */
 	l = 0;
 	fd = socket_connect(host, port);
-	buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
+	buf = calloc(bufsz, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
-	l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", path, http_host);
+	l += snprintf(buf + l, bufsz, "GET %s HTTP/1.0\r\nHost: %s\r\n\r\n",
-	l += sprintf(buf + l, "\r\n");
+				 path, http_host);
-	write(fd, buf, l);
+	if (write_bytes(fd, buf, l) != 0) {
+		close(fd);
+		fd = -1;
+		goto out;
+	}
 	l = 0;
-	while (read(fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency
+ retry:
+	while (l < bufsz && (bytes = read(fd, buf + l, 1)) > 0) { // read HTTP header; FIXME: bad efficiency
 		if (buf[l] == '\n' && l >= 3)
 			if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break;
 		++l;
 	}
+	if (bytes < 0 && (errno == EAGAIN || errno == EWOULDBLOCK || errno == EINTR)) goto retry;
+
 	buf[l] = 0;
-	if (l < 14) { // prematured header
+	if (bytes < 0 || l < 14) { // prematured header
 		close(fd);
 		fd = -1;
+		goto out;
 	}
 	ret = strtol(buf + 8, &p, 0); // HTTP return code
 	if (ret != 200) {
 		close(fd);
 		fd = -1;
 	}
+ out:
 	free(buf); free(http_host); free(host); free(port); free(path);
 	return fd;
 }
@@ -143,7 +172,7 @@ static int kftp_get_response(ftpaux_t *aux)
 static int kftp_send_cmd(ftpaux_t *aux, const char *cmd, int is_get)
 {
 	if (socket_wait(aux->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing
-	write(aux->ctrl_fd, cmd, strlen(cmd));
+	if (write_bytes(aux->ctrl_fd, cmd, strlen(cmd)) != 0) return -1;
 	return is_get? kftp_get_response(aux) : 0;
 }
 
@@ -262,7 +291,7 @@ void *kopen(const char *fn, int *_fd)
 				if (ispunct(*q) && *q != '.' && *q != '_' && *q != '-' && *q != ':')
 					break;
 			need_shell = (*q != 0);
-			pipe(pfd);
+			if (pipe(pfd) != 0) return 0;
 			pid = vfork();
 			if (pid == -1) { /* vfork() error */
 				close(pfd[0]); close(pfd[1]);

kseq.h

@@ -32,6 +32,10 @@
 #include <string.h>
 #include <stdlib.h>
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
 #define KS_SEP_TAB   1 // isspace() && !' '
 #define KS_SEP_LINE  2 // line separator: "\n" (Unix) or "\r\n" (Windows)

ksort.h

@@ -58,6 +58,10 @@
 #include <stdlib.h>
 #include <string.h>
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 typedef struct {
 	void *left, *right;
 	int depth;

kstring.c

@@ -2,6 +2,10 @@
 #include <stdio.h>
 #include "kstring.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 int ksprintf(kstring_t *s, const char *fmt, ...)
 {
 	va_list ap;

kstring.h

@@ -4,6 +4,10 @@
 #include <stdlib.h>
 #include <string.h>
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 #ifndef kroundup32
 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
 #endif

ksw.c

@@ -28,6 +28,10 @@
 #include <emmintrin.h>
 #include "ksw.h"
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 #ifdef __GNUC__
 #define LIKELY(x) __builtin_expect((x),1)
 #define UNLIKELY(x) __builtin_expect((x),0)
@@ -553,7 +557,7 @@ int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
 #include <stdio.h>
 #include <zlib.h>
 #include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
+KSEQ_INIT(gzFile, err_gzread)
 
 unsigned char seq_nt4_table[256] = {
 	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
@@ -609,8 +613,8 @@ int main(int argc, char *argv[])
 	}
 	for (j = 0; j < 5; ++j) mat[k++] = 0;
 	// open file
-	fpt = gzopen(argv[optind],   "r"); kst = kseq_init(fpt);
+	fpt = xzopen(argv[optind],   "r"); kst = kseq_init(fpt);
-	fpq = gzopen(argv[optind+1], "r"); ksq = kseq_init(fpq);
+	fpq = xzopen(argv[optind+1], "r"); ksq = kseq_init(fpq);
 	// all-pair alignment
 	while (kseq_read(ksq) > 0) {
 		kswq_t *q[2] = {0, 0};
@@ -629,18 +633,18 @@ int main(int argc, char *argv[])
 			for (i = 0; i < (int)kst->seq.l; ++i) kst->seq.s[i] = seq_nt4_table[(int)kst->seq.s[i]];
 			r = ksw_align(ksq->seq.l, (uint8_t*)ksq->seq.s, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[0]);
 			if (r.score >= minsc)
-				printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, r.qb, r.qe+1, r.score, r.score2, r.te2);
+				err_printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, r.qb, r.qe+1, r.score, r.score2, r.te2);
 			if (rseq) {
 				r = ksw_align(ksq->seq.l, rseq, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[1]);
 				if (r.score >= minsc)
-					printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, (int)ksq->seq.l - r.qb, (int)ksq->seq.l - 1 - r.qe, r.score, r.score2, r.te2);
+					err_printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, (int)ksq->seq.l - r.qb, (int)ksq->seq.l - 1 - r.qe, r.score, r.score2, r.te2);
 			}
 		}
 		free(q[0]); free(q[1]);
 	}
 	free(rseq);
-	kseq_destroy(kst); gzclose(fpt);
+	kseq_destroy(kst); err_gzclose(fpt);
-	kseq_destroy(ksq); gzclose(fpq);
+	kseq_destroy(ksq); err_gzclose(fpq);
 	return 0;
 }
 #endif

kvec.h

@@ -50,6 +50,10 @@ int main() {
 
 #include <stdlib.h>
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 #define kv_roundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
 
 #define kvec_t(type) struct { size_t n, m; type *a; }

main.c

@@ -55,7 +55,7 @@ static int usage()
 
 void bwa_print_sam_PG()
 {
-	printf("@PG\tID:bwa\tPN:bwa\tVN:%s\n", PACKAGE_VERSION);
+	err_printf("@PG\tID:bwa\tPN:bwa\tVN:%s\n", PACKAGE_VERSION);
 }
 
 int main(int argc, char *argv[])

malloc_wrap.c

@@ -0,0 +1,57 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <errno.h>
+#ifdef USE_MALLOC_WRAPPERS
+/* Don't wrap ourselves */
+#  undef USE_MALLOC_WRAPPERS
+#endif
+#include "malloc_wrap.h"
+
+void *wrap_calloc(size_t nmemb, size_t size,
+				  const char *file, unsigned int line, const char *func) {
+	void *p = calloc(nmemb, size);
+	if (NULL == p) {
+		fprintf(stderr,
+				"[%s] Failed to allocate %zd bytes at %s line %u: %s\n",
+				func, nmemb * size, file, line, strerror(errno));
+		exit(EXIT_FAILURE);
+	}
+	return p;
+}
+
+void *wrap_malloc(size_t size,
+				  const char *file, unsigned int line, const char *func) {
+	void *p = malloc(size);
+	if (NULL == p) {
+		fprintf(stderr,
+				"[%s] Failed to allocate %zd bytes at %s line %u: %s\n",
+				func, size, file, line, strerror(errno));
+		exit(EXIT_FAILURE);
+	}
+	return p;
+}
+
+void *wrap_realloc(void *ptr, size_t size,
+				   const char *file, unsigned int line, const char *func) {
+	void *p = realloc(ptr, size);
+	if (NULL == p) {
+		fprintf(stderr,
+				"[%s] Failed to allocate %zd bytes at %s line %u: %s\n",
+				func, size, file, line, strerror(errno));
+		exit(EXIT_FAILURE);
+	}
+	return p;
+}
+
+char *wrap_strdup(const char *s,
+				  const char *file, unsigned int line, const char *func) {
+	char *p = strdup(s);
+	if (NULL == p) {
+		fprintf(stderr,
+				"[%s] Failed to allocate %zd bytes at %s line %u: %s\n",
+				func, strlen(s), file, line, strerror(errno));
+		exit(EXIT_FAILURE);
+	}
+	return p;
+}

malloc_wrap.h

@@ -0,0 +1,47 @@
+#ifndef MALLOC_WRAP_H
+#define MALLOC_WRAP_H
+
+#include <stdlib.h>  /* Avoid breaking the usual definitions */
+#include <string.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	void *wrap_calloc(size_t nmemb, size_t size,
+					  const char *file, unsigned int line, const char *func);
+	void *wrap_malloc(size_t size,
+					  const char *file, unsigned int line, const char *func);
+	void *wrap_realloc(void *ptr, size_t size,
+					   const char *file, unsigned int line, const char *func);
+	char *wrap_strdup(const char *s,
+					  const char *file, unsigned int line, const char *func);
+
+#ifdef __cplusplus
+}
+#endif
+
+#ifdef USE_MALLOC_WRAPPERS
+#  ifdef calloc
+#    undef calloc
+#  endif
+#  define calloc(n, s)  wrap_calloc( (n), (s), __FILE__, __LINE__, __func__)
+
+#  ifdef malloc
+#    undef malloc
+#  endif
+#  define malloc(s)     wrap_malloc( (s),      __FILE__, __LINE__, __func__)
+
+#  ifdef realloc
+#    undef realloc
+#  endif
+#  define realloc(p, s) wrap_realloc((p), (s), __FILE__, __LINE__, __func__)
+
+#  ifdef strdup
+#    undef strdup
+#  endif
+#  define strdup(s)     wrap_strdup( (s),      __FILE__, __LINE__, __func__)
+
+#endif /* USE_MALLOC_WRAPPERS */
+
+#endif /* MALLOC_WRAP_H */

pemerge.c

@@ -4,12 +4,18 @@
 #include <string.h>
 #include <zlib.h>
 #include <pthread.h>
+#include <errno.h>
 #include "ksw.h"
 #include "kseq.h"
 #include "kstring.h"
 #include "bwa.h"
+#include "utils.h"
 KSEQ_DECLARE(gzFile)
 
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
 #define MAX_SCORE_RATIO 0.9f
 #define MAX_ERR 8
 
@@ -140,14 +146,14 @@ pem_ret:
 
 static inline void print_bseq(const bseq1_t *s, int rn)
 {
-	putchar(s->qual? '@' : '>');
+	err_putchar(s->qual? '@' : '>');
-	fputs(s->name, stdout);
+	err_fputs(s->name, stdout);
 	if (rn == 1 || rn == 2) {
-		putchar('/'); putchar('0' + rn); putchar('\n');
+		err_putchar('/'); err_putchar('0' + rn); err_putchar('\n');
-	} else puts(" merged");
+	} else err_puts(" merged");
-	puts(s->seq);
+	err_puts(s->seq);
 	if (s->qual) {
-		puts("+"); puts(s->qual);
+		err_puts("+"); err_puts(s->qual);
 	}
 }
 
@@ -224,6 +230,7 @@ int main_pemerge(int argc, char *argv[])
 		else if (c == 'Q') opt->q_thres = atoi(optarg);
 		else if (c == 't') opt->n_threads = atoi(optarg);
 		else if (c == 'T') min_ovlp = atoi(optarg);
+		else return 1;
 	}
 	if (flag == 0) flag = 3;
 	opt->flag = flag;
@@ -243,9 +250,21 @@ int main_pemerge(int argc, char *argv[])
 	}
 
 	fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
+	if (NULL == fp) {
+		fprintf(stderr, "Couldn't open %s : %s\n",
+				strcmp(argv[optind], "-") ? argv[optind] : "stdin",
+				errno ? strerror(errno) : "Out of memory");
+		exit(EXIT_FAILURE);
+	}
 	ks = kseq_init(fp);
 	if (optind + 1 < argc) {
 		fp2 = strcmp(argv[optind+1], "-")? gzopen(argv[optind+1], "r") : gzdopen(fileno(stdin), "r");
+		if (NULL == fp) {
+			fprintf(stderr, "Couldn't open %s : %s\n",
+					strcmp(argv[optind+1], "-") ? argv[optind+1] : "stdin",
+					errno ? strerror(errno) : "Out of memory");
+			exit(EXIT_FAILURE);
+		}
 		ks2 = kseq_init(fp2);
 	}
 
@@ -259,11 +278,14 @@ int main_pemerge(int argc, char *argv[])
 	for (i = 1; i <= MAX_ERR; ++i)
 		fprintf(stderr, "%12ld %s\n", (long)cnt[i], err_msg[i]);
 	kseq_destroy(ks);
-	gzclose(fp);
+	err_gzclose(fp);
 	if (ks2) {
 		kseq_destroy(ks2);
-		gzclose(fp2);
+		err_gzclose(fp2);
 	}
 	free(opt);
+
+	err_fflush(stdout);
+
 	return 0;
 }

utils.c

@@ -24,6 +24,7 @@
 */
 
 /* Contact: Heng Li <lh3@sanger.ac.uk> */
+#define FSYNC_ON_FLUSH
 
 #include <stdio.h>
 #include <stdarg.h>
@@ -31,6 +32,11 @@
 #include <string.h>
 #include <zlib.h>
 #include <errno.h>
+#ifdef FSYNC_ON_FLUSH
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <unistd.h>
+#endif
 #include <sys/resource.h>
 #include <sys/time.h>
 #include "utils.h"
@@ -41,7 +47,7 @@ KSORT_INIT(128, pair64_t, pair64_lt)
 KSORT_INIT(64,  uint64_t, ks_lt_generic)
 
 #include "kseq.h"
-KSEQ_INIT2(, gzFile, gzread)
+KSEQ_INIT2(, gzFile, err_gzread)
 
 /********************
  * System utilities *
@@ -53,8 +59,7 @@ FILE *err_xopen_core(const char *func, const char *fn, const char *mode)
 	if (strcmp(fn, "-") == 0)
 		return (strstr(mode, "r"))? stdin : stdout;
 	if ((fp = fopen(fn, mode)) == 0) {
-		fprintf(stderr, "[%s] fail to open file '%s'. Abort!\n", func, fn);
+		err_fatal(func, "fail to open file '%s' : %s", fn, strerror(errno));
-		abort();
 	}
 	return fp;
 }
@@ -62,10 +67,7 @@ FILE *err_xopen_core(const char *func, const char *fn, const char *mode)
 FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp)
 {
 	if (freopen(fn, mode, fp) == 0) {
-		fprintf(stderr, "[%s] fail to open file '%s': ", func, fn);
+		err_fatal(func, "fail to open file '%s' : %s", fn, strerror(errno));
-		perror(NULL);
-		fprintf(stderr, "Abort!\n");
-		abort();
 	}
 	return fp;
 }
@@ -73,16 +75,30 @@ FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE
 gzFile err_xzopen_core(const char *func, const char *fn, const char *mode)
 {
 	gzFile fp;
-	if (strcmp(fn, "-") == 0)
+	if (strcmp(fn, "-") == 0) {
-		return gzdopen(fileno((strstr(mode, "r"))? stdin : stdout), mode);
+		fp = gzdopen(fileno((strstr(mode, "r"))? stdin : stdout), mode);
+		/* According to zlib.h, this is the only reason gzdopen can fail */
+		if (!fp) err_fatal(func, "Out of memory");
+		return fp;
+	}
 	if ((fp = gzopen(fn, mode)) == 0) {
-		fprintf(stderr, "[%s] fail to open file '%s'. Abort!\n", func, fn);
+		err_fatal(func, "fail to open file '%s' : %s", fn, errno ? strerror(errno) : "Out of memory");
-		abort();
 	}
 	return fp;
 }
 
 void err_fatal(const char *header, const char *fmt, ...)
+{
+	va_list args;
+	va_start(args, fmt);
+	fprintf(stderr, "[%s] ", header);
+	vfprintf(stderr, fmt, args);
+	fprintf(stderr, "\n");
+	va_end(args);
+	exit(EXIT_FAILURE);
+}
+
+void err_fatal_core(const char *header, const char *fmt, ...)
 {
 	va_list args;
 	va_start(args, fmt);
@@ -93,7 +109,13 @@ void err_fatal(const char *header, const char *fmt, ...)
 	abort();
 }
 
-void err_fatal_simple_core(const char *func, const char *msg)
+void _err_fatal_simple(const char *func, const char *msg)
+{
+	fprintf(stderr, "[%s] %s\n", func, msg);
+	exit(EXIT_FAILURE);
+}
+
+void _err_fatal_simple_core(const char *func, const char *msg)
 {
 	fprintf(stderr, "[%s] %s Abort!\n", func, msg);
 	abort();
@@ -103,7 +125,51 @@ size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream)
 {
 	size_t ret = fwrite(ptr, size, nmemb, stream);
 	if (ret != nmemb) 
-		err_fatal_simple_core("fwrite", strerror(errno));
+		_err_fatal_simple("fwrite", strerror(errno));
+	return ret;
+}
+
+size_t err_fread_noeof(void *ptr, size_t size, size_t nmemb, FILE *stream)
+{
+	size_t ret = fread(ptr, size, nmemb, stream);
+	if (ret != nmemb)
+	{
+		_err_fatal_simple("fread", ferror(stream) ? strerror(errno) : "Unexpected end of file");
+	}
+	return ret;
+}
+
+int err_gzread(gzFile file, void *ptr, unsigned int len)
+{
+	int ret = gzread(file, ptr, len);
+
+	if (ret < 0)
+	{
+		int errnum = 0;
+		const char *msg = gzerror(file, &errnum);
+		_err_fatal_simple("gzread", Z_ERRNO == errnum ? strerror(errno) : msg);
+	}
+
+	return ret;
+}
+
+int err_fseek(FILE *stream, long offset, int whence)
+{
+	int ret = fseek(stream, offset, whence);
+	if (0 != ret)
+	{
+		_err_fatal_simple("fseek", strerror(errno));
+	}
+	return ret;
+}
+
+long err_ftell(FILE *stream)
+{
+	long ret = ftell(stream);
+	if (-1 == ret)
+	{
+		_err_fatal_simple("ftell", strerror(errno));
+	}
 	return ret;
 }
 
@@ -115,7 +181,7 @@ int err_printf(const char *format, ...)
 	done = vfprintf(stdout, format, arg);
 	int saveErrno = errno;
 	va_end(arg);
-	if (done < 0) err_fatal_simple_core("vfprintf(stdout)", strerror(saveErrno));
+	if (done < 0) _err_fatal_simple("vfprintf(stdout)", strerror(saveErrno));
 	return done;
 }
 
@@ -127,21 +193,74 @@ int err_fprintf(FILE *stream, const char *format, ...)
 	done = vfprintf(stream, format, arg);
 	int saveErrno = errno;
 	va_end(arg);
-	if (done < 0) err_fatal_simple_core("vfprintf", strerror(saveErrno));
+	if (done < 0) _err_fatal_simple("vfprintf", strerror(saveErrno));
 	return done;
 }
 
+int err_fputc(int c, FILE *stream)
+{
+	int ret = putc(c, stream);
+	if (EOF == ret)
+	{
+		_err_fatal_simple("fputc", strerror(errno));
+	}
+
+	return ret;
+}
+
+int err_fputs(const char *s, FILE *stream)
+{
+	int ret = fputs(s, stream);
+	if (EOF == ret)
+	{
+		_err_fatal_simple("fputs", strerror(errno));
+	}
+
+	return ret;
+}
+
 int err_fflush(FILE *stream) 
 {
     int ret = fflush(stream);
-	if (ret != 0) err_fatal_simple_core("fflush", strerror(errno));
+    if (ret != 0) _err_fatal_simple("fflush", strerror(errno));
+
+#ifdef FSYNC_ON_FLUSH
+	/* Calling fflush() ensures that all the data has made it to the
+	   kernel buffers, but this may not be sufficient for remote filesystems
+	   (e.g. NFS, lustre) as an error may still occur while the kernel
+	   is copying the buffered data to the file server.  To be sure of
+	   catching these errors, we need to call fsync() on the file
+	   descriptor, but only if it is a regular file.  */
+	{
+		struct stat sbuf;
+		if (0 != fstat(fileno(stream), &sbuf))
+			_err_fatal_simple("fstat", strerror(errno));
+		
+		if (S_ISREG(sbuf.st_mode))
+		{
+			if (0 != fsync(fileno(stream)))
+				_err_fatal_simple("fsync", strerror(errno));
+		}
+	}
+#endif
     return ret;
 }
 
 int err_fclose(FILE *stream) 
 {
 	int ret = fclose(stream);
-	if (ret != 0) err_fatal_simple_core("fclose", strerror(errno));
+	if (ret != 0) _err_fatal_simple("fclose", strerror(errno));
+	return ret;
+}
+
+int err_gzclose(gzFile file)
+{
+	int ret = gzclose(file);
+	if (Z_OK != ret)
+	{
+		_err_fatal_simple("gzclose", Z_ERRNO == ret ? strerror(errno) : zError(ret));
+	}
+
 	return ret;
 }
 

utils.h

@@ -39,11 +39,14 @@
 #define ATTRIBUTE(list)
 #endif
 
-#define err_fatal_simple(msg) err_fatal_simple_core(__func__, msg)
+#define err_fatal_simple(msg) _err_fatal_simple(__func__, msg)
+#define err_fatal_simple_core(msg) _err_fatal_simple_core(__func__, msg)
+
 #define xopen(fn, mode) err_xopen_core(__func__, fn, mode)
 #define xreopen(fn, mode, fp) err_xreopen_core(__func__, fn, mode, fp)
 #define xzopen(fn, mode) err_xzopen_core(__func__, fn, mode)
-#define xassert(cond, msg) if ((cond) == 0) err_fatal_simple_core(__func__, msg)
+
+#define xassert(cond, msg) if ((cond) == 0) _err_fatal_simple_core(__func__, msg)
 
 typedef struct {
 	uint64_t x, y;
@@ -56,18 +59,31 @@ typedef struct { size_t n, m; pair64_t *a; } pair64_v;
 extern "C" {
 #endif
 
-	void err_fatal(const char *header, const char *fmt, ...);
+	void err_fatal(const char *header, const char *fmt, ...) ATTRIBUTE((noreturn));
-	void err_fatal_simple_core(const char *func, const char *msg);
+	void err_fatal_core(const char *header, const char *fmt, ...) ATTRIBUTE((noreturn));
+	void _err_fatal_simple(const char *func, const char *msg) ATTRIBUTE((noreturn));
+	void _err_fatal_simple_core(const char *func, const char *msg) ATTRIBUTE((noreturn));
 	FILE *err_xopen_core(const char *func, const char *fn, const char *mode);
 	FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp);
 	gzFile err_xzopen_core(const char *func, const char *fn, const char *mode);
     size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream);
+	size_t err_fread_noeof(void *ptr, size_t size, size_t nmemb, FILE *stream);
+
+	int err_gzread(gzFile file, void *ptr, unsigned int len);
+	int err_fseek(FILE *stream, long offset, int whence);
+#define err_rewind(FP) err_fseek((FP), 0, SEEK_SET)
+	long err_ftell(FILE *stream);
 	int err_fprintf(FILE *stream, const char *format, ...)
         ATTRIBUTE((format(printf, 2, 3)));
 	int err_printf(const char *format, ...)
         ATTRIBUTE((format(printf, 1, 2)));
+	int err_fputc(int c, FILE *stream);
+#define err_putchar(C) err_fputc((C), stdout)
+	int err_fputs(const char *s, FILE *stream);
+#define err_puts(S) err_fputs((S), stdout)
 	int err_fflush(FILE *stream);
 	int err_fclose(FILE *stream);
+	int err_gzclose(gzFile file);
 
 	double cputime();
 	double realtime();