chimera.uchime skipgap,skipgap2 param conversion

chimera.uchime skipgap=false should generate a uchime param --noskipgap


$ diff -c chimerauchimecommand.cpp.orig chimerauchimecommand.cpp *** chimerauchimecommand.cpp.orig Tue Jun 21 10:01:49 2011 --- chimerauchimecommand.cpp Wed Jun 22 09:54:34 2011 *************** *** 673,688 **** }

if (!skipgaps) {
! char* tempskipgaps = new char[15];
//strcpy(tempskipgaps, “–[no]skipgaps”);
! *tempskipgaps = ‘\0’; strncat(tempskipgaps, “–[no]skipgaps”, 14);
cPara.push_back(tempskipgaps);
}

if (!skipgaps2) {
! char* tempskipgaps2 = new char[16];
//strcpy(tempskipgaps2, “–[no]skipgaps2”);
! *tempskipgaps2 = ‘\0’; strncat(tempskipgaps2, “–[no]skipgaps2”, 15);
cPara.push_back(tempskipgaps2);
}

— 673,688 ----
}

if (!skipgaps) {
! char* tempskipgaps = new char[13];
//strcpy(tempskipgaps, “–[no]skipgaps”);
! *tempskipgaps = ‘\0’; strncat(tempskipgaps, “–noskipgaps”, 12);
cPara.push_back(tempskipgaps);
}

if (!skipgaps2) {
! char* tempskipgaps2 = new char[14];
//strcpy(tempskipgaps2, “–[no]skipgaps2”);
! *tempskipgaps2 = ‘\0’; strncat(tempskipgaps2, “–noskipgaps2”, 13);
cPara.push_back(tempskipgaps2);
}