MapQ 0 on unanchored reads

ExpressionAnalysis · fdbe3b4bf796c322c6bb88eafd99e6d8c06c097b · earonesty committed Sep 5, 2014 · Sep 5, 2014 · fdbe3b4
1 parent d4567a1
commit fdbe3b4bf796c322c6bb88eafd99e6d8c06c097b
Unified Split

Showing with 1 addition and 1 deletion.

+1 −1 clipper/varcall.cpp
diff --git 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);
         }