From fdbe3b4bf796c322c6bb88eafd99e6d8c06c097b Mon Sep 17 00:00:00 2001
From: earonesty <earonesty@f1db881f-09c6-4a82-8334-ae7ceabc6398>
Date: Fri, 5 Sep 2014 19:42:15 +0000
Subject: [PATCH] MapQ 0 on unanchored reads

---
 clipper/varcall.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/clipper/varcall.cpp b/clipper/varcall.cpp
index e43bbad..21192df 100644
--- a/clipper/varcall.cpp
+++ b/clipper/varcall.cpp
@@ -1039,7 +1039,7 @@ void PileupSummary::Parse(char *line, PileupReads &rds, tidx *adex, char atype)
         if (read_i == rds.ReadList.end()) {
             warn("warning\tread start without '^', partial pileup: '%s'\n", cur_p);
             Read x;
-            x.MapQ = -1;
+            x.MapQ = 0;
             x.Pos = -1;
             read_i=rds.ReadList.insert(read_i,x);
         }