From 998b354209b48256a4ffa6fa2be118ec7e021081 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Mon, 23 Aug 2010 21:36:17 +0000
Subject: [PATCH] change the default correlation coefficient

---
 bam_maqcns.c | 2 +-
 bam_plcmd.c  | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/bam_maqcns.c b/bam_maqcns.c
index 9caa5d7..dfc83e9 100644
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -110,7 +110,7 @@ bam_maqcns_t *bam_maqcns_init()
 	bm = (bam_maqcns_t*)calloc(1, sizeof(bam_maqcns_t));
 	bm->aux = (bmc_aux_t*)calloc(1, sizeof(bmc_aux_t));
 	bm->het_rate = 0.001;
-	bm->theta = 0.85;
+	bm->theta = 0.83f;
 	bm->n_hap = 2;
 	bm->eta = 0.03;
 	bm->cap_mapQ = 60;
diff --git a/bam_plcmd.c b/bam_plcmd.c
index a23477f..53972de 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -375,6 +375,8 @@ int bam_pileup(int argc, char *argv[])
 		default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1;
 		}
 	}
+	if (d->c->errmod != BAM_ERRMOD_MAQ2) d->c->theta += 0.02;
+	if (d->c->theta > 1.0) d->c->theta = 1.0;
 	if (fn_list) is_SAM = 1;
 	if (optind == argc) {
 		fprintf(stderr, "\n");
-- 
2.39.2