int overlaplen = 25;
int verbosity = 3;
char verboseStr[verboseBufSize];
int inGraph;
long long n_ban;
long long n_solexa = 0;
long long prevNum = 0;
int ins_size_var = 20;
PE_INFO *pes = NULL;
MEM_MANAGER *rv_mem_manager = NULL;
MEM_MANAGER *cn_mem_manager = NULL;
MEM_MANAGER *arc_mem_manager = NULL;
unsigned int num_vt = 0;
unsigned int **found_routes = NULL;
unsigned int *so_far = NULL;
int max_n_routes = 10;
int num_trace;
Kmer WORDFILTER;
unsigned int num_ed = 0;
unsigned int num_ctg = 0;
unsigned int num_ed_limit;
unsigned int extraEdgeNum;
EDGE *edge_array = NULL;
VERTEX *vt_array = NULL;
unsigned int *index_array = NULL;
CONTIG *contig_array = NULL;
int lineLen;
int len_bar = 100;
int weakPE = 3;
int fillGap = 0;
boolean globalFlag;
long long arcCounter;
MEM_MANAGER *prearc_mem_manager = NULL;
MEM_MANAGER **preArc_mem_managers = NULL;
int maxReadLen = 0;
int maxReadLen4all = 0;
int minReadLen = 0;
int maxNameLen = 0;
ARC **arcLookupTable = NULL;
long long *markersArray = NULL;
boolean deLowKmer = 0;
boolean deLowEdge = 1;
long long newCntCounter;
boolean repsTie = 0;
CONNECT **cntLookupTable = NULL;
int num_libs = 0;
LIB_INFO *lib_array = NULL;
int libNo = 0;
long long readNumBack;
int gradsCounter;
unsigned int ctg_short = 0;
int thrd_num = 8;
int cvgAvg = 0;
KmerSet **KmerSets = NULL;
KmerSet **KmerSetsPatch = NULL;

spcKmerSet *spcSet = NULL;

DARRAY *readSeqInGap = NULL;
DARRAY *gapSeqDarray = NULL;
DARRAY **darrayBuf;
boolean orig2new;
int maxSteps;
boolean maskRep = 1;
int GLDiff = 50;
int initKmerSetSize = 0;
char *shortrdsfile;
char *graphfile;
double OverlapPercent = 0.05;
double ConflPercent = 0.05;
double close_threshold = 0.1;
int bund_threshold = 5;
char *ctg_file = NULL;
//boolean large_kmer=0;