26   Work_Area_t  *WA = (Work_Area_t *)ptr;  in Process_Overlaps()  local
33   while (WA->bgnID < G.endRefID) {  in Process_Overlaps()
34     WA->overlapsLen                = 0;  in Process_Overlaps()
36     WA->Total_Overlaps             = 0;  in Process_Overlaps()
37     WA->Contained_Overlap_Ct       = 0;  in Process_Overlaps()
38     WA->Dovetail_Overlap_Ct        = 0;  in Process_Overlaps()
40     WA->Kmer_Hits_Without_Olap_Ct  = 0;  in Process_Overlaps()
41     WA->Kmer_Hits_With_Olap_Ct     = 0;  in Process_Overlaps()
42     WA->Kmer_Hits_Skipped_Ct       = 0;  in Process_Overlaps()
43     WA->Multi_Overlap_Ct           = 0;  in Process_Overlaps()
46             WA->thread_id, WA->bgnID, WA->endID);  in Process_Overlaps()
48     for (uint32 fi=WA->bgnID; fi<=WA->endID; fi++) {  in Process_Overlaps()
49       uint32  libID   = WA->readStore->sqStore_getLibraryIDForRead(fi);  in Process_Overlaps()
50       uint32  readLen = WA->readCache->sqCache_getLength(fi);  in Process_Overlaps()
62       WA->readCache->sqCache_getSequence(fi, seqptr, seqptrLen, seqptrMax);  in Process_Overlaps()
74       Find_Overlaps(bases, readLen, fi, FORWARD, WA);  in Process_Overlaps()
79       Find_Overlaps(bases, readLen, fi, REVERSE, WA);  in Process_Overlaps()
86             WA->thread_id, WA->bgnID, WA->endID,  in Process_Overlaps()
87             WA->overlapsLen,  in Process_Overlaps()
88             WA->Kmer_Hits_With_Olap_Ct, WA->Kmer_Hits_Without_Olap_Ct, WA->Kmer_Hits_Skipped_Ct);  in Process_Overlaps()
94       for (int zz=0; zz<WA->overlapsLen; zz++)  in Process_Overlaps()
95         Out_BOF->writeOverlap(WA->overlaps + zz);  in Process_Overlaps()
97       WA->overlapsLen = 0;  in Process_Overlaps()
99       Total_Overlaps            += WA->Total_Overlaps;  in Process_Overlaps()
100       Contained_Overlap_Ct      += WA->Contained_Overlap_Ct;  in Process_Overlaps()
101       Dovetail_Overlap_Ct       += WA->Dovetail_Overlap_Ct;  in Process_Overlaps()
103       Kmer_Hits_Without_Olap_Ct += WA->Kmer_Hits_Without_Olap_Ct;  in Process_Overlaps()
104       Kmer_Hits_With_Olap_Ct    += WA->Kmer_Hits_With_Olap_Ct;  in Process_Overlaps()
105       Kmer_Hits_Skipped_Ct      += WA->Kmer_Hits_Skipped_Ct;  in Process_Overlaps()
106       Multi_Overlap_Ct          += WA->Multi_Overlap_Ct;  in Process_Overlaps()
108       WA->bgnID = G.curRefID;  in Process_Overlaps()
109       WA->endID = G.curRefID + G.perThread - 1;  in Process_Overlaps()
111       if (WA->endID > G.endRefID)  in Process_Overlaps()
112         WA->endID = G.endRefID;  in Process_Overlaps()
114       G.curRefID = WA->endID + 1;  in Process_Overlaps()