- set the buffer on stdin

- fflush stdout in bwtaln after writing the header and set of
alignments.

bwtaln.c

@@ -194,6 +194,7 @@ void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
 		strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
 		free(str);
 		bwa_print_sam_hdr(bns, opt->rg_line);
+		fflush(stdout);
 	}
 
 	// core loop
@@ -252,6 +253,7 @@ void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
 			fprintf(stderr, "[bwa_aln_core] print alignments... ");
 			for (i = 0; i < n_seqs; ++i)
 				bwa_print_sam1(bns, seqs + i, 0, opt->mode, opt->max_top2);
+			fflush(stdout);
 			fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
 		}
 		else {

utils.c

@@ -84,9 +84,8 @@ gzFile err_xzopen_core2(const char *func, const char *fn, const char *mode, int
 		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) {
+	else if ((fp = gzopen(fn, mode)) == 0) {
 		err_fatal(func, "fail to open file '%s' : %s", fn, errno ? strerror(errno) : "Out of memory");
 	}
 	if (0 < bufsize && gzbuffer(fp, bufsize) != 0) {