void FileUtils::fileCounter(const QString& filePath, int* pCounter)
{
QFileInfo curFile(filePath);
if(!curFile.exists()) return;
if (curFile.isDir())
{
QString dir = curFile.filePath();
QDir curDir(dir);
int childCount = curDir.entryInfoList().count();
QFileInfoList newFileList = curDir.entryInfoList();
if(childCount > 2)
{
for(int i = 0;i< childCount; i++)
{
if(newFileList.at(i).fileName() == "." || newFileList.at(i).fileName() == "..")
continue;
fileCounter(newFileList.at(i).filePath(), pCounter);
}
}
}
else
{
if(pCounter) *pCounter += 1;
}
}
int FileUtils::fileCount(const QString& filePath)
{
int fCount = 0;
fileCounter(filePath, &fCount);
return fCount;
}
main(int argc, char *argv[]){
int tabSize = pow(4, atoi(argv[3])) ;
char hashSize = (char)tabSize;
pid_t parentpid;
pid_t pid[1];
int status;
char jfCountFile1[256];
char jfCountFile2[256];
char jfDumpFile1[256];
char jfDumpFile2[256];
char fileName1[256];
char fileName2[256];
sprintf(jfCountFile1,"time jellyfish count %s -m %s -s %i -o %s-%s-jfCount",argv[1],argv[3],tabSize, argv[1],argv[3]);
sprintf(jfCountFile2,"time jellyfish count %s -m %s -s %i -o %s-%s-jfCount",argv[2],argv[3],tabSize, argv[2],argv[3]);
sprintf(jfDumpFile1,"time jellyfish dump %s-%s-jfCount -c -o %s-%s-Kmers",argv[1],argv[3],argv[1],argv[3]);
sprintf(jfDumpFile2,"time jellyfish dump %s-%s-jfCount -c -o %s-%s-Kmers",argv[2],argv[3],argv[2],argv[3]);
sprintf(fileName1,"%s-%s-Kmers",argv[1],argv[3]);
sprintf(fileName2,"%s-%s-Kmers",argv[2],argv[3]);
printf("%s\n%s\n",jfCountFile1,jfCountFile2);
printf("%s\n%s\n%s\n%s\n",jfDumpFile1,jfDumpFile2,fileName1,fileName2);
if((pid[0] = fork())<0){
perror("fork");
abort();
}else if(pid[0]==0){
printf("Executing jellyfish functions on %s with %s-mers...\n",argv[1],argv[3]);
system(jfCountFile1);
printf("...Count file for %s completed\n",argv[1]);
system(jfDumpFile1);
printf("... jellyfish dump completed for %s with %s-mers.\n",argv[1],argv[3]);
exit(0);
}
if((pid[1] = fork())<0){
perror("fork");
abort();
}else if(pid[1]==0){
printf("Executing jellyfish functions on %s with %s-mers...\n",argv[2],argv[3]);
system(jfCountFile2);
printf("...Count file for %s completed\n",argv[2]);
system(jfDumpFile2);
printf("... jellyfish dump completed for %s with %s-mers.\n",argv[2],argv[3]);
exit(0);
}
while ((parentpid = wait(&status)) > 0);
puts("Both processes are completed.");
FILE *fp1 = fopen(fileName1,"r");
FILE *fp2 = fopen(fileName2,"r");
int lineCount = fileCounter(fp2);
fseek(fp2, 0, SEEK_SET);
struct hashtable_s *uniqueTable = createHashTable(1.5 * lineCount);
kmerKram(uniqueTable,fp2,1);
kmerKram(uniqueTable,fp1,-1);
char outFileName[256];
sprintf(outFileName,"%s-VS-%s-%sMERS.fasta",argv[1],argv[2],argv[3]);
FILE *outFile = fopen(outFileName,"w");
FILE *sequences = fopen(argv[2],"r");
fseek(fp2, 0, SEEK_SET);
skimThroughFasta(sequences, outFile, atoi(argv[3]),uniqueTable);
}
