00001 #include "log.h"
00002 #include "format.h"
00003 #include "gfr.h"
00004
00005
00006
00007 static int sortGfrInterReads (GfrInterRead *a, GfrInterRead *b)
00008 {
00009 int diff;
00010
00011 diff = a->pairType - b->pairType;
00012 if (diff != 0) {
00013 return diff;
00014 }
00015 diff = a->number1 - b->number1;
00016 if (diff != 0) {
00017 return diff;
00018 }
00019 return a->number2 - b->number2;
00020 }
00021
00022
00023
00024 static void obtainPairCounts (GfrEntry *currGE)
00025 {
00026 GfrPairCount *currPC;
00027 GfrInterRead *currGIR,*nextGIR;
00028 int i,j;
00029
00030 currGE->pairCounts = arrayCreate (100,GfrPairCount);
00031 arraySort (currGE->interReads,(ARRAYORDERF)sortGfrInterReads);
00032 i = 0;
00033 while (i < arrayMax (currGE->interReads)) {
00034 currGIR = arrp (currGE->interReads,i,GfrInterRead);
00035 currPC = arrayp (currGE->pairCounts,arrayMax (currGE->pairCounts),GfrPairCount);
00036 currPC->number1 = currGIR->number1;
00037 currPC->number2 = currGIR->number2;
00038 currPC->pairType = currGIR->pairType;
00039 currPC->count = 1;
00040 j = i + 1;
00041 while (j < arrayMax (currGE->interReads)) {
00042 nextGIR = arrp (currGE->interReads,j,GfrInterRead);
00043 if (currGIR->pairType == nextGIR->pairType && currGIR->number1==nextGIR->number1 && currGIR->number2==nextGIR->number2) {
00044 currPC->count++;
00045 }
00046 else {
00047 break;
00048 }
00049 j++;
00050 }
00051 i = j;
00052 }
00053 }
00054
00055
00056
00057 int main (int argc, char *argv[])
00058 {
00059 GfrEntry *currGE;
00060 int count;
00061
00062 gfr_init ("-");
00063 gfr_addNewColumnType (GFR_COLUMN_NAME_PAIR_COUNT);
00064 puts (gfr_writeHeader ());
00065 count = 0;
00066 while (currGE = gfr_nextEntry ()){
00067 obtainPairCounts (currGE);
00068 puts (gfr_writeGfrEntry (currGE)); fflush (stdout);
00069 count++;
00070 }
00071 gfr_deInit ();
00072 warn ("%s_numGfrEntries: %d",argv[0],count);
00073 return 0;
00074 }
00075
00076
