00001 #include "log.h"
00002 #include "format.h"
00003 #include "intervalFind.h"
00004 #include <stdlib.h>
00005 #include "util.h"
00006 #include "geneFusionsConfig.h"
00007 #include "gfr.h"
00008
00009 int main (int argc, char *argv[])
00010 {
00011 int i;
00012 GfrEntry* gfrE;
00013 Array intervals = arrayCreate( 50, Interval);
00014 Stringa buffer = stringCreate (100);
00015
00016 stringPrintf (buffer,"%s/%s",ANNOTATION_DIR,TRANSCRIPT_COMPOSITE_MODEL_FILENAME);
00017 intervalFind_addIntervalsToSearchSpace (string (buffer),0);
00018
00019 gfr_init("-");
00020 printf( "%s\n", gfr_writeHeader());
00021 while( gfrE = gfr_nextEntry() ) {
00022 if( strEqual( gfrE->fusionType, "cis" ) && (gfrE->strandTranscript1 == gfrE->strandTranscript2) ) {
00023 intervals = arrayCopy (intervalFind_getOverlappingIntervals (gfrE->chromosomeTranscript1, gfrE->endTranscript1+1, gfrE->startTranscript2-1 ));
00024 stringPrintf(buffer, "read-through");
00025 if( arrayMax(intervals)>0) {
00026 for( i=0; i<arrayMax(intervals); i++) {
00027 Interval *currInterval = arru( intervals, i, Interval*);
00028 if( (currInterval->strand == gfrE->strandTranscript1 ) ) {
00029 stringPrintf(buffer,"intra");
00030 i = arrayMax(intervals);
00031 }
00032 }
00033 }
00034 } else {
00035 if( strEqual( gfrE->fusionType, "trans" ) ) {
00036 stringPrintf( buffer, "inter");
00037 } else {
00038 stringPrintf( buffer, "cis");
00039 }
00040 }
00041 gfrE->fusionType = hlr_strdup(string(buffer));
00042 printf("%s\n", gfr_writeGfrEntry( gfrE ));
00043
00044 }
00045 gfr_deInit();
00046 arrayDestroy(intervals);
00047 stringDestroy (buffer);
00048
00049 return 0;
00050 }
