option.cpp

#include "option.h"

void PrintSynopsis() {
  printf(
      "The input command is incorrect.\nFor more info, please check: http://code.google.com/p/perm/\n");
}

int GetIntVal(int argc, const char** argv, const char * str, SIZE_T & nVal) {
  for (int i = 1; i < argc; i++) {
    if (strcmp(argv[i], str) == 0 && i + 1 <= argc - 1) {
      if (argv[i + 1][0] != '-') {
        nVal = (SIZE_T) atoi(argv[i + 1]);
        return 1;
      }
    }
  }
  return 0;
}

int GetStrVal(int argc, const char** argv, const char* str, string & strVal) {
  for (int i = 1; i < argc; i++) {
    if (strcmp(argv[i], str) == 0 && i + 1 <= argc - 1) {
      if (argv[i + 1][0] != '-') {
        strVal = argv[i + 1];
        return 1;
      }
    }
  }
  return 0;
}

int ChkStrExist(int argc, const char** argv, const char* str) {
  for (int i = 1; i < argc; i++) {
    if (strcmp(argv[i], str) == 0) {
      return 1;
    }
  }
  return 0;
}

void GetNameBeforeDot(const string & strFile, string & fileName) {
  int pos = strFile.find_last_of('.');
  fileName = strFile.substr(0, pos);
}

void GetReadLength(Option & opt) {
  ifstream fin(opt.readsFile.c_str());
  if (!fin.good()) {
    printf("--ERROR INFO-- reads file open error. %s\n", opt.readsFile.c_str());
    exit (EXIT_FAILURE);
  }
  opt.nNumOfreads = 0;
  string strLine;
  while (getline(fin, strLine)) {
    if (strLine[0] == '>') {
      opt.nNumOfreads++;
      continue;
    }
    opt.readLen = strLine.size();
    cout << "--INFO-- Full sensitivity for " << opt.mapOpt.nMaxMismatch
        << " errors." << endl;
    cout << "--INFO-- The length of the reads is " << opt.readLen << endl;
    if (opt.readLen / HASHSEEDLEN <= opt.mapOpt.nMaxMismatch) {
      //printf("--ERROR INFO-- seed length is not proper. please set shorter seed length.\n");
      //exit (EXIT_FAILURE);
    }
    opt.mapOpt.ems = opt.readLen / HASHSEEDLEN - opt.mapOpt.nMaxMismatch;
    opt.nSeed = (opt.readLen - 1) / HASHSEEDLEN + 1;
    if (opt.nSeed < 1) {
      //printf("--ERROR INFO-- seed length is not proper. please set shorter seed length.\n");
      //exit (EXIT_FAILURE);
    }
    MEMORY_ALLOCATE_CHECK(
        opt.seedStartPos = (SIZE_T *) malloc(sizeof(SIZE_T) * opt.nSeed));
    for (SIZE_T i = 0; i < opt.nSeed - 1; i++) {
      opt.seedStartPos[i] = HASHSEEDLEN * i;
    }
    opt.seedStartPos[opt.nSeed - 1] = opt.readLen - HASHSEEDLEN;
    cout << "--INFO-- Seeds start positions are ";
    for (SIZE_T i = 0; i < opt.nSeed; i++) {
      cout << opt.seedStartPos[i] << ", ";
    }
    cout << "respectively" << endl;
    cout << "--INFO-- The matched positions should have at least "
        << opt.mapOpt.ems << " exact seeds for each read." << endl;
    break;
  }

  while (getline(fin, strLine)) {
    if (strLine[0] == '>') {
      opt.nNumOfreads++;
      continue;
    }
  }
  fin.close();
  INFO("There are", opt.nNumOfreads, "reads in the reads file");
}

void PrintOutVersion() {
  printf("####################################################\n");
  printf("#                                                  #\n");
  printf("#  seed-extension-aligner                          #\n");
  printf("#  Haifeng Chen (haifengc at usc dot edu)          #\n");
  printf("#  University of Southern California               #\n");
  printf("#  Feb 5, 2014                                     #\n");
  printf("#                                                  #\n");
  printf("####################################################\n");
  printf("\n");
}

void GetParameter(int argc, const char* argv[], Option & opt) {
  if (argc <= 2 || argv == NULL)
    PrintSynopsis();
  else {
    PrintOutVersion();
    cout << "--INFO-- Input command:";
    for (int i = 0; i < argc; i++) {
      cout << " " << argv[i];
    }
    cout << endl;

    opt.refFile = argv[1];
    cout << "--INFO-- The reference file is " << opt.refFile << endl;

    opt.bIndexExist = 0;
    string indexsf = ".sdindex";
    if (opt.refFile.size() > indexsf.size()
        && opt.refFile.substr(opt.refFile.size() - indexsf.size()) == indexsf) {
      opt.bIndexExist = 1;
    }
    opt.readsFile = argv[2];
    cout << "--INFO-- The reads file is " << opt.readsFile << "." << endl;

    if (GetIntVal(argc, argv, "-v", opt.mapOpt.nMaxMismatch) == 0)
      opt.mapOpt.nMaxMismatch = 2;

    if (GetStrVal(argc, argv, "-o", opt.outputFile) == 0) {
      string fileName;
      GetNameBeforeDot(opt.readsFile, fileName);
      opt.outputFile = fileName;
      opt.outputFile += ".sam";
    }
    opt.bSaveIndex = 0;
    if (ChkStrExist(argc, argv, "-s")) {
      opt.bSaveIndex = 1;
    }
    if (GetStrVal(argc, argv, "-s", opt.indexFile) == 0
        && opt.bSaveIndex == 1) {
      string fileName;
      GetNameBeforeDot(opt.refFile, fileName);
      opt.indexFile = fileName;
      opt.indexFile += indexsf;
    }
    GetReadLength(opt);
  }
}