00001 #include "log.h"
00002 #include "format.h"
00003 #include "bowtieParser.h"
00004 #include "bp.h"
00005 #include <stdio.h>
00006 #include <sys/types.h>
00007 #include <unistd.h>
00008 #include "geneFusionsConfig.h"
00009
00010
00011
00012 int main (int argc, char *argv[])
00013 {
00014 Array breakPoints;
00015 BreakPoint *currBP;
00016 BreakPointRead *currBPR;
00017 int i,j;
00018 Stringa buffer,cmd;
00019 FILE *fp;
00020 BowtieQuery *currBQ;
00021 Texta invalidJunctions;
00022 int index;
00023 char *str = NULL;
00024
00025 buffer = stringCreate (100);
00026 stringPrintf (buffer,"bpJunctionReads_%d.fa",getpid ());
00027 fp = fopen (string (buffer),"w");
00028 if (fp == NULL) {
00029 die ("Unable to open file: %s",string (buffer));
00030 }
00031 bp_init ("-");
00032 breakPoints = bp_getBreakPoints ();
00033 for (i = 0; i < arrayMax (breakPoints); i++) {
00034 currBP = arrp (breakPoints,i,BreakPoint);
00035 for (j = 0; j < arrayMax (currBP->breakPointReads); j++) {
00036 currBPR = arrp (currBP->breakPointReads,j,BreakPointRead);
00037 fprintf (fp,">%s|%s\n%s\n",currBP->tileCoordinate1,currBP->tileCoordinate2,currBPR->read);
00038 }
00039 }
00040 bp_deInit ();
00041 fclose (fp);
00042
00043 invalidJunctions = textCreate (1000);
00044 cmd = stringCreate (100);
00045 stringPrintf (cmd,"bowtie --quiet -p 4 -n 0 -f %s/%s/%s %s",BOWTIE_INDEXES,BOWTIE_GENOME, BOWTIE_GENOME, string (buffer));
00046 bowtieParser_initFromPipe (string (cmd));
00047 while (currBQ = bowtieParser_nextQuery ()) {
00048 textAdd (invalidJunctions,currBQ->sequenceName);
00049 }
00050 bowtieParser_deInit ();
00051 stringPrintf (cmd,"rm -f %s",string (buffer));
00052 hlr_system (string (cmd),0);
00053
00054 arraySort (invalidJunctions,(ARRAYORDERF)arrayStrcmp);
00055 arrayUniq (invalidJunctions,NULL,(ARRAYORDERF)arrayStrcmp);
00056 for (i = 0; i < arrayMax (breakPoints); i++) {
00057 currBP = arrp (breakPoints,i,BreakPoint);
00058 stringPrintf (buffer,"%s|%s",currBP->tileCoordinate1,currBP->tileCoordinate2);
00059 strReplace (&str,string (buffer));
00060 if (!arrayFind (invalidJunctions,&str,&index,(ARRAYORDERF)arrayStrcmp)) {
00061 puts (bp_writeBreakPoint (currBP));
00062 }
00063 }
00064 stringDestroy (buffer);
00065 stringDestroy (cmd);
00066 return 0;
00067 }
