applied patches from Alec Wysoker

bwase.c

@@ -437,15 +437,15 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 				if (mate->strand) flag |= SAM_FMR;
 			} else flag |= SAM_FMU;
 		}
-		printf("%s\t%d\t%s\t", p->name, flag, bns->anns[seqid].name);
+		err_printf("%s\t%d\t%s\t", p->name, flag, bns->anns[seqid].name);
-		printf("%d\t%d\t", (int)(p->pos - bns->anns[seqid].offset + 1), p->mapQ);
+		err_printf("%d\t%d\t", (int)(p->pos - bns->anns[seqid].offset + 1), p->mapQ);
 
 		// print CIGAR
 		if (p->cigar) {
 			for (j = 0; j != p->n_cigar; ++j)
-				printf("%d%c", __cigar_len(p->cigar[j]), "MIDS"[__cigar_op(p->cigar[j])]);
+				err_printf("%d%c", __cigar_len(p->cigar[j]), "MIDS"[__cigar_op(p->cigar[j])]);
-		} else if (p->type == BWA_TYPE_NO_MATCH) printf("*");
+		} else if (p->type == BWA_TYPE_NO_MATCH) err_printf("*");
-		else printf("%dM", p->len);
+		else err_printf("%dM", p->len);
 
 		// print mate coordinate
 		if (mate && mate->type != BWA_TYPE_NO_MATCH) {
@@ -454,12 +454,12 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 			am = mate->seQ < p->seQ? mate->seQ : p->seQ; // smaller single-end mapping quality
 			// redundant calculation here, but should not matter too much
 			m_is_N = bns_coor_pac2real(bns, mate->pos, mate->len, &m_seqid);
-			printf("\t%s\t", (seqid == m_seqid)? "=" : bns->anns[m_seqid].name);
+			err_printf("\t%s\t", (seqid == m_seqid)? "=" : bns->anns[m_seqid].name);
 			isize = (seqid == m_seqid)? pos_5(mate) - pos_5(p) : 0;
 			if (p->type == BWA_TYPE_NO_MATCH) isize = 0;
-			printf("%d\t%lld\t", (int)(mate->pos - bns->anns[m_seqid].offset + 1), isize);
+			err_printf("%d\t%lld\t", (int)(mate->pos - bns->anns[m_seqid].offset + 1), isize);
-		} else if (mate) printf("\t=\t%d\t0\t", (int)(p->pos - bns->anns[seqid].offset + 1));
+		} else if (mate) err_printf("\t=\t%d\t0\t", (int)(p->pos - bns->anns[seqid].offset + 1));
-		else printf("\t*\t0\t0\t");
+		else err_printf("\t*\t0\t0\t");
 
 		// print sequence and quality
 		if (p->strand == 0)
@@ -468,42 +468,42 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 		putchar('\t');
 		if (p->qual) {
 			if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
-			printf("%s", p->qual);
+			err_printf("%s", p->qual);
-		} else printf("*");
+		} else err_printf("*");
 
-		if (bwa_rg_id) printf("\tRG:Z:%s", bwa_rg_id);
+		if (bwa_rg_id) err_printf("\tRG:Z:%s", bwa_rg_id);
-		if (p->bc[0]) printf("\tBC:Z:%s", p->bc);
+		if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
-		if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
+		if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
 		if (p->type != BWA_TYPE_NO_MATCH) {
 			int i;
 			// calculate XT tag
 			XT = "NURM"[p->type];
 			if (nn > 10) XT = 'N';
 			// print tags
-			printf("\tXT:A:%c\t%s:i:%d", XT, (mode & BWA_MODE_COMPREAD)? "NM" : "CM", p->nm);
+			err_printf("\tXT:A:%c\t%s:i:%d", XT, (mode & BWA_MODE_COMPREAD)? "NM" : "CM", p->nm);
-			if (nn) printf("\tXN:i:%d", nn);
+			if (nn) err_printf("\tXN:i:%d", nn);
-			if (mate) printf("\tSM:i:%d\tAM:i:%d", p->seQ, am);
+			if (mate) err_printf("\tSM:i:%d\tAM:i:%d", p->seQ, am);
 			if (p->type != BWA_TYPE_MATESW) { // X0 and X1 are not available for this type of alignment
-				printf("\tX0:i:%d", p->c1);
+				err_printf("\tX0:i:%d", p->c1);
-				if (p->c1 <= max_top2) printf("\tX1:i:%d", p->c2);
+				if (p->c1 <= max_top2) err_printf("\tX1:i:%d", p->c2);
 			}
-			printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
+			err_printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
-			if (p->md) printf("\tMD:Z:%s", p->md);
+			if (p->md) err_printf("\tMD:Z:%s", p->md);
 			// print multiple hits
 			if (p->n_multi) {
-				printf("\tXA:Z:");
+				err_printf("\tXA:Z:");
 				for (i = 0; i < p->n_multi; ++i) {
 					bwt_multi1_t *q = p->multi + i;
 					int k;
 					j = pos_end_multi(q, p->len) - q->pos;
 					nn = bns_coor_pac2real(bns, q->pos, j, &seqid);
-					printf("%s,%c%d,", bns->anns[seqid].name, q->strand? '-' : '+',
+					err_printf("%s,%c%d,", bns->anns[seqid].name, q->strand? '-' : '+',
 						   (int)(q->pos - bns->anns[seqid].offset + 1));
 					if (q->cigar) {
 						for (k = 0; k < q->n_cigar; ++k)
-							printf("%d%c", __cigar_len(q->cigar[k]), "MIDS"[__cigar_op(q->cigar[k])]);
+							err_printf("%d%c", __cigar_len(q->cigar[k]), "MIDS"[__cigar_op(q->cigar[k])]);
-					} else printf("%dM", p->len);
+					} else err_printf("%dM", p->len);
-					printf(",%d;", q->gap + q->mm);
+					err_printf(",%d;", q->gap + q->mm);
 				}
 			}
 		}
@@ -512,16 +512,16 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 		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;
-		printf("%s\t%d\t*\t0\t0\t*\t*\t0\t0\t", p->name, flag);
+		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]]);
 		putchar('\t');
 		if (p->qual) {
 			if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
-			printf("%s", p->qual);
+			err_printf("%s", p->qual);
-		} else printf("*");
+		} else err_printf("*");
-		if (bwa_rg_id) printf("\tRG:Z:%s", bwa_rg_id);
+		if (bwa_rg_id) err_printf("\tRG:Z:%s", bwa_rg_id);
-		if (p->bc[0]) printf("\tBC:Z:%s", p->bc);
+		if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
-		if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
+		if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
 		putchar('\n');
 	}
 }
@@ -541,8 +541,8 @@ void bwa_print_sam_SQ(const bntseq_t *bns)
 {
 	int i;
 	for (i = 0; i < bns->n_seqs; ++i)
-		printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
+		err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
-	if (bwa_rg_line) printf("%s\n", bwa_rg_line);
+	if (bwa_rg_line) err_printf("%s\n", bwa_rg_line);
 }
 
 void bwase_initialize() 

bwtaln.c

@@ -176,7 +176,7 @@ void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
 	}
 
 	// core loop
-	fwrite(opt, sizeof(gap_opt_t), 1, stdout);
+	err_fwrite(opt, sizeof(gap_opt_t), 1, stdout);
 	while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt->mode, opt->trim_qual)) != 0) {
 		tot_seqs += n_seqs;
 		t = clock();
@@ -213,8 +213,8 @@ void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
 		fprintf(stderr, "[bwa_aln_core] write to the disk... ");
 		for (i = 0; i < n_seqs; ++i) {
 			bwa_seq_t *p = seqs + i;
-			fwrite(&p->n_aln, 4, 1, stdout);
+			err_fwrite(&p->n_aln, 4, 1, stdout);
-			if (p->n_aln) fwrite(p->aln, sizeof(bwt_aln1_t), p->n_aln, stdout);
+			if (p->n_aln) err_fwrite(p->aln, sizeof(bwt_aln1_t), p->n_aln, stdout);
 		}
 		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
 

main.c

@@ -1,9 +1,10 @@
 #include <stdio.h>
 #include <string.h>
 #include "main.h"
+#include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.5.9-r16"
+#define PACKAGE_VERSION "0.5.9-r18-dev"
 #endif
 
 static int usage()
@@ -59,5 +60,7 @@ int main(int argc, char *argv[])
 		fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
 		return 1;
 	}
+        err_fflush(stdout);
+        err_fclose(stdout);
 	return 0;
 }

utils.c

@@ -30,6 +30,7 @@
 #include <stdlib.h>
 #include <string.h>
 #include <zlib.h>
+#include <errno.h>
 #include "utils.h"
 
 FILE *err_xopen_core(const char *func, const char *fn, const char *mode)
@@ -80,3 +81,68 @@ void err_fatal_simple_core(const char *func, const char *msg)
 	fprintf(stderr, "[%s] %s Abort!\n", func, msg);
 	abort();
 }
+
+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));
+    }
+    return ret;
+}
+
+int err_printf(const char *format, ...) 
+{
+    va_list arg;
+    int done;
+
+    va_start(arg, format);
+    done = vfprintf(stdout, format, arg);
+    int saveErrno = errno;
+    va_end(arg);
+
+    if (done < 0) 
+    {
+        err_fatal_simple_core("vfprintf(stdout)", strerror(saveErrno));
+    }
+    return done;
+}
+
+int err_fprintf(FILE *stream, const char *format, ...) 
+{
+    va_list arg;
+    int done;
+
+    va_start(arg, format);
+    done = vfprintf(stream, format, arg);
+    int saveErrno = errno;
+    va_end(arg);
+
+    if (done < 0) 
+    {
+        err_fatal_simple_core("vfprintf", strerror(saveErrno));
+    }
+    return done;
+}
+
+int err_fflush(FILE *stream) 
+{
+    int ret = fflush(stream);
+    if (ret != 0) 
+    {
+        err_fatal_simple_core("fflush", strerror(errno));
+    }
+    return ret;
+}
+
+int err_fclose(FILE *stream) 
+{
+    int ret = fclose(stream);
+    if (ret != 0) 
+    {
+        err_fatal_simple_core("fclose", strerror(errno));
+    }
+    return ret;
+}
+

utils.h

@@ -31,6 +31,15 @@
 #include <stdio.h>
 #include <zlib.h>
 
+#ifdef __GNUC__
+// Tell GCC to validate printf format string and args
+#define ATTRIBUTE(list) __attribute__ (list)
+#else
+#define ATTRIBUTE(list)
+#endif
+
+
+
 #define err_fatal_simple(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)
@@ -46,6 +55,13 @@ extern "C" {
 	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);
+	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_fflush(FILE *stream);
+	int err_fclose(FILE *stream);
 
 #ifdef __cplusplus
 }