added summary outputs for align.check

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index c0f91969eda2277e4c8b02c3a78db2a7390716fe..8c13e7fbbd76895b751ae982b8df9a093e1c1ca9 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -328,13 +328,14 @@ int SeqSummaryCommand::execute(){
                sort(seqLength.begin(), seqLength.end());
                sort(ambigBases.begin(), ambigBases.end());
                sort(longHomoPolymer.begin(), longHomoPolymer.end());
-               
-               int ptile0_25   = int(numSeqs * 0.025);
-               int ptile25             = int(numSeqs * 0.250);
-               int ptile50             = int(numSeqs * 0.500);
-               int ptile75             = int(numSeqs * 0.750);
-               int ptile97_5   = int(numSeqs * 0.975);
-               int ptile100    = numSeqs - 1;
+               int size = startPosition.size();
+                               
+               int ptile0_25   = int(size * 0.025);
+               int ptile25             = int(size * 0.250);
+               int ptile50             = int(size * 0.500);
+               int ptile75             = int(size * 0.750);
+               int ptile97_5   = int(size * 0.975);
+               int ptile100    = size - 1;
                
                //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
                if (startPosition[0] == -1) {  startPosition[0] = 0;    }