added revised MAQ error model

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 0cf081d046a0614303957723a94061069545cc86..aef10d38e37797bd24e728e3dd13955e92dc7b64 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -343,12 +343,12 @@ 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->c->errmod = BAM_ERRMOD_MAQ2; // 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:PA")) >= 0) {
                switch (c) {
-               case 'a': d->c->is_soap = 1; break;
-               case 'A': d->c->is_soap = 0; break;
+               case 'a': d->c->errmod = BAM_ERRMOD_SOAP; break;
+               case 'A': d->c->errmod = BAM_ERRMOD_MAQ; break;
                case 's': d->format |= BAM_PLF_SIMPLE; break;
                case 't': fn_list = strdup(optarg); break;
                case 'l': fn_pos = strdup(optarg); break;