00001 #include "log.h"
00002 #include "format.h"
00003 #include "gfr.h"
00004
00005
00006
00007 int main (int argc, char *argv[])
00008 {
00009 GfrEntry *currGE;
00010 int offset;
00011 int count;
00012 int countRemoved;
00013
00014 if (argc != 2) {
00015 usage ("%s <offset>",argv[0]);
00016 }
00017 count = 0;
00018 countRemoved = 0;
00019 offset = atoi (argv[1]);
00020 gfr_init ("-");
00021 puts (gfr_writeHeader ());
00022 while (currGE = gfr_nextEntry ()){
00023 if (strEqual (currGE->fusionType,"cis") &&
00024 currGE->strandTranscript1 != currGE->strandTranscript2 &&
00025 (currGE->startTranscript2 - currGE->endTranscript1) < offset) {
00026 countRemoved++;
00027 continue;
00028 }
00029 puts (gfr_writeGfrEntry (currGE));
00030 count++;
00031 }
00032 gfr_deInit ();
00033 warn ("%s_offset: %d",argv[0],offset);
00034 warn ("%s_numRemoved: %d",argv[0],countRemoved);
00035 warn ("%s_numGfrEntries: %d",argv[0],count);
00036 return 0;
00037 }
00038
