X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=sam.c;h=f026bc80864dbc75557bf632c760978e54acc453;hp=e195b0f13e93d018d05f0784fc76c437e2eec8cd;hb=aa08abe5f0b84ee0dd3491f00fe357d661c08e0c;hpb=6828a9a9ef02c5634d488a3b3a52966a92d38088

diff --git a/sam.c b/sam.c
index e195b0f..f026bc8 100644
--- a/sam.c
+++ b/sam.c
@@ -59,9 +59,9 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 					append_header_text(fp->header, textheader->text, textheader->l_text);
 					bam_header_destroy(textheader);
 				}
-				if (fp->header->n_targets == 0)
+				if (fp->header->n_targets == 0 && bam_verbose >= 1)
 					fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
-			} else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
+			} else if (bam_verbose >= 2) fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
 		}
 	} else if (strchr(mode, 'w')) { // write
 		fp->header = bam_header_dup((const bam_header_t*)aux);
@@ -93,10 +93,10 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 				sam_header_parse(alt);
 				alt->l_text = 0; alt->text = 0;
 				// check if there are @SQ lines in the header
-				fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
+				fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw); // FIXME: better to skip the trailing NULL
 				if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
-					if (alt->n_targets != fp->header->n_targets)
-						fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
+					if (alt->n_targets != fp->header->n_targets && bam_verbose >= 1)
+						fprintf(stderr, "[samopen] inconsistent number of target sequences. Output the text header.\n");
 				} else { // then dump ->target_{name,len}
 					for (i = 0; i < fp->header->n_targets; ++i)
 						fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
@@ -168,7 +168,7 @@ char *samfaipath(const char *fn_ref)
 		if (access(fn_ref, R_OK) == -1) {
 			fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref);
 		} else {
-			fprintf(stderr, "[samfaipath] build FASTA index...\n");
+			if (bam_verbose >= 3) fprintf(stderr, "[samfaipath] build FASTA index...\n");
 			if (fai_build(fn_ref) == -1) {
 				fprintf(stderr, "[samfaipath] fail to build FASTA index.\n");
 				free(fn_list); fn_list = 0;