X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraperseuscommand.h;h=0d907814e21b2ef48dbd3d1883fb3e8698533189;hp=4fa4cfff55e9582ffd699d5a66409717df8fbd36;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=037b7fccc64a5c7d5d5c23a949273a912160a400

diff --git a/chimeraperseuscommand.h b/chimeraperseuscommand.h
index 4fa4cff..0d90781 100644
--- a/chimeraperseuscommand.h
+++ b/chimeraperseuscommand.h
@@ -130,7 +130,7 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
         SequenceCountParser* cparser;
 		if (pDataArray->hasCount) {
             CountTable* ct = new CountTable();
-            ct->readTable(pDataArray->namefile);
+            ct->readTable(pDataArray->namefile, true, false);
             cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
             delete ct;
         }else {
@@ -343,10 +343,10 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
 					chimeraFile << j << '\t' << sequences[j].seqName << "\t0\t0\tNull\t0\t0\t0\tNull\tNull\t0.0\t0.0\t0.0\t0\t0\t0\t0.0\t0.0\tgood" << endl;
 				}
 				//report progress
-				if((j+1) % 100 == 0){ 	pDataArray->m->mothurOut("Processing sequence: " + toString(j+1) + "\n");		}
+				if((j+1) % 100 == 0){ 	pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(j+1) + "\n");		}
 			}
 			
-			if((numSeqs) % 100 != 0){ 	pDataArray->m->mothurOut("Processing sequence: " + toString(numSeqs) + "\n");		}
+			if((numSeqs) % 100 != 0){ 	pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(numSeqs) + "\n");		}
 			
 			chimeraFile.close();
 			accnosFile.close();