X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=84838dd98e1d56c7270ae78225a8023e9c96ca57;hb=efa4a1055d7691e3cd1368dcafa210c2691a5fd2;hp=d34cd267a9edd363a32605c083fefe5ba512e8bb;hpb=4967051aa734ece6ce44f0fb891a936e849c2fe2;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index d34cd26..84838dd 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -341,10 +341,11 @@ int bam_pileup(int argc, char *argv[])
     d->max_depth = 0;
 	d->tid = -1; d->mask = BAM_DEF_MASK;
 	d->c = bam_maqcns_init();
+	d->c->is_soap = 1; // change the default model
 	d->ido = bam_maqindel_opt_init();
 	while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:P")) >= 0) {
 		switch (c) {
-		case 'a': d->c->is_soap = 1; break;
+		case 'a': d->c->is_soap = 0; break;
 		case 's': d->format |= BAM_PLF_SIMPLE; break;
 		case 't': fn_list = strdup(optarg); break;
 		case 'l': fn_pos = strdup(optarg); break;
@@ -379,7 +380,7 @@ int bam_pileup(int argc, char *argv[])
 		fprintf(stderr, "Usage:  samtools pileup [options] <in.bam>|<in.sam>\n\n");
 		fprintf(stderr, "Option: -s        simple (yet incomplete) pileup format\n");
 		fprintf(stderr, "        -S        the input is in SAM\n");
-		fprintf(stderr, "        -a        use the SOAPsnp model for SNP calling\n");
+		fprintf(stderr, "        -a        use the MAQ model for SNP calling\n");
 		fprintf(stderr, "        -2        output the 2nd best call and quality\n");
 		fprintf(stderr, "        -i        only show lines/consensus with indels\n");
 		fprintf(stderr, "        -m INT    filtering reads with bits in INT [%d]\n", d->mask);
@@ -453,13 +454,13 @@ typedef struct {
 
 typedef struct {
 	bamFile fp;
-	bam_iterf_t iter;
+	bam_iter_t iter;
 } mplp_aux_t;
 
 static int mplp_func(void *data, bam1_t *b)
 {
 	mplp_aux_t *ma = (mplp_aux_t*)data;
-	if (ma->iter) return bam_iterf_read(ma->fp, ma->iter, b);
+	if (ma->iter) return bam_iter_read(ma->fp, ma->iter, b);
 	return bam_read1(ma->fp, b);
 }
 
@@ -494,7 +495,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 				exit(1);
 			}
 			if (i == 0) beg0 = beg, end0 = end;
-			data[i]->iter = bam_iterf_query(idx, tid, beg, end);
+			data[i]->iter = bam_iter_query(idx, tid, beg, end);
 			bam_index_destroy(idx);
 		}
 		if (i == 0) h = h_tmp;
@@ -536,7 +537,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 	bam_header_destroy(h);
 	for (i = 0; i < n; ++i) {
 		bam_close(data[i]->fp);
-		if (data[i]->iter) bam_iterf_destroy(data[i]->iter);
+		if (data[i]->iter) bam_iter_destroy(data[i]->iter);
 		free(data[i]);
 	}
 	free(data); free(plp); free(ref); free(n_plp);