00001 #include "log.h"
00002 #include "format.h"
00003 #include "intervalFind.h"
00004 #include "geneFusionsConfig.h"
00005 #include "gfr.h"
00006
00007
00008
00009 int main (int argc, char *argv[])
00010 {
00011 GfrEntry *currGE;
00012 int count,countRemoved;
00013 int i;
00014 Array intervals;
00015 GfrInterRead *currGIR;
00016 int totalOverlaps;
00017 int minNumInterReads;
00018
00019 if (argc != 3) {
00020 usage ("%s <repeatMasker.interval> <minNumInterReads>",argv[0]);
00021 }
00022 intervalFind_addIntervalsToSearchSpace (argv[1],0);
00023 minNumInterReads = atoi (argv[2]);
00024 count = 0;
00025 countRemoved = 0;
00026 gfr_init ("-");
00027 puts (gfr_writeHeader ());
00028 while (currGE = gfr_nextEntry ()){
00029 for (i = 0; i < arrayMax (currGE->interReads); i++) {
00030 currGIR = arrp (currGE->interReads,i,GfrInterRead);
00031 if (currGIR->pairType == GFR_PAIR_TYPE_EXONIC_EXONIC) {
00032 continue;
00033 }
00034 totalOverlaps = 0;
00035 intervals = intervalFind_getOverlappingIntervals (currGE->chromosomeTranscript1,currGIR->readStart1,currGIR->readEnd1);
00036 totalOverlaps += arrayMax (intervals);
00037 intervals = intervalFind_getOverlappingIntervals (currGE->chromosomeTranscript2,currGIR->readStart2,currGIR->readEnd2);
00038 totalOverlaps += arrayMax (intervals);
00039 if (totalOverlaps > 0) {
00040 currGE->numInter--;
00041 currGIR->flag = 1;
00042 }
00043 }
00044 if (currGE->numInter < minNumInterReads) {
00045 countRemoved++;
00046 continue;
00047 }
00048 puts (gfr_writeGfrEntry (currGE));
00049 count++;
00050 }
00051 gfr_deInit ();
00052 warn ("%s_numRemoved: %d",argv[0],countRemoved);
00053 warn ("%s_numGfrEntries: %d",argv[0],count);
00054 return 0;
00055 }
00056
