X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam.c;h=fa11df6c12b1abc589415d4d11fe269067ecd765;hb=0ccd9d36ebf35ce620a8248ecf4336c84065e6c0;hp=e195b0f13e93d018d05f0784fc76c437e2eec8cd;hpb=d382711a770f67a72b9af3bfd98a88fbced34f64;p=samtools.git

diff --git a/sam.c b/sam.c
index e195b0f..fa11df6 100644
--- a/sam.c
+++ b/sam.c
@@ -36,6 +36,13 @@ static void append_header_text(bam_header_t *header, char* text, int len)
 	header->text[header->l_text] = 0;
 }
 
+int samthreads(samfile_t *fp, int n_threads, int n_sub_blks)
+{
+	if (!(fp->type&1) || (fp->type&2)) return -1;
+	bgzf_mt(fp->x.bam, n_threads, n_sub_blks);
+	return 0;
+}
+
 samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 {
 	samfile_t *fp;
@@ -59,9 +66,9 @@ 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);
@@ -79,7 +86,7 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 		} else { // text
 			// open file
 			fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
-			if (fp->x.tamr == 0) goto open_err_ret;
+			if (fp->x.tamw == 0) goto open_err_ret;
 			if (strchr(mode, 'X')) fp->type |= BAM_OFSTR<<2;
 			else if (strchr(mode, 'x')) fp->type |= BAM_OFHEX<<2;
 			else fp->type |= BAM_OFDEC<<2;
@@ -93,10 +100,10 @@ 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 +175,7 @@ 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;