int main(int argc, char** argv)
{
// input arguments are initial fragment file, variant file with variant information and alleles for each variant
// number of iterations total, when to output the solution, file to output solution .....
time_t ts; time(&ts); srand48((long int)ts);
if (MINCUTALGO ==2) RANDOM_START=0;
int i=0,j=0; int flag =0;
char fragfile[10000]; char varfile[10000]; char VCFfile[10000]; char hapfile[10000]; int maxiter =100;
strcpy(fragfile,"None"); strcpy(varfile,"None");strcpy(hapfile,"None");
for (i=1;i<argc;i+=2)
{
if (argc < 6) break;
if (strcmp(argv[i],"--fragments") ==0 || strcmp(argv[i],"--frags") ==0) { strcpy(fragfile,argv[i+1]); flag++; }
else if (strcmp(argv[i],"--variants") ==0)
{
j=strlen(argv[i+1]); // check if it is a VCF file ending with .vcf or .VCF
if (j > 3 && ((argv[i+1][j-1] == 'f' && argv[i+1][j-2] == 'c' && argv[i+1][j-3] == 'v') || (argv[i+1][j-1] == 'F' && argv[i+1][j-2] == 'C' && argv[i+1][j-3] == 'V')))
{
strcpy(VCFfile,argv[i+1]); VCFformat = 1; flag++;
}
else
{
fprintf(stderr,"please provide variant file in VCF format using --VCF option, old variant format is no longer supported\n\n");
return 1;
}
}
else if (strcmp(argv[i],"--VCF") ==0 || strcmp(argv[i],"--vcf")==0) { strcpy(VCFfile,argv[i+1]); VCFformat = 1; flag++; }
else if (strcmp(argv[i],"--output") ==0 || strcmp(argv[i],"--out") ==0) { strcpy(hapfile,argv[i+1]); flag++; }
else if (strcmp(argv[i],"--maxiter") ==0) maxiter = atoi(argv[i+1]);
else if (strcmp(argv[i],"--longreads") ==0 || strcmp(argv[i],"--lr") ==0) // long reads pacbio
{
FOSMIDS = atoi(argv[i+1]);
}
else if (strcmp(argv[i],"--fosmid") ==0 || strcmp(argv[i],"--fosmids") ==0)
{
FOSMIDS = atoi(argv[i+1]);
if (FOSMIDS ==1) SCORING_FUNCTION = 1; // unless explicitly specified, for fosmids use switch error based function...
}
else if (strcmp(argv[i],"--sf") ==0 || strcmp(argv[i],"--switches") ==0) SCORING_FUNCTION = atoi(argv[i+1]);
else if (strcmp(argv[i],"--printscores") ==0 || strcmp(argv[i],"--scores") ==0) PRINT_FRAGMENT_SCORES = atoi(argv[i+1]);
else if (strcmp(argv[i],"--maxcutiter") ==0)
{
MAXCUT_ITER = atoi(argv[i+1]);
fprintf(stderr,"max iterations for max-cut calculations is %d \n",MAXCUT_ITER);
}
else if (strcmp(argv[i],"--QVoffset") ==0 || strcmp(argv[i],"--qvoffset") ==0) QVoffset = atoi(argv[i+1]);
else if (strcmp(argv[i],"--maxmem") ==0 ) MAX_MEMORY = atoi(argv[i+1]);
else if (strcmp(argv[i],"--mbq") ==0 ) MINQ = atoi(argv[i+1]);
}
if (flag !=3) // three essential arguments are not supplied
{
print_hapcut_options(); return -1;
}
else
{
if (VCFformat ==1)
{
fprintf(stderr,"\n\nfragment file: %s\nvariantfile (VCF format):%s\nhaplotypes will be output to file: %s\niterations of maxcut algorithm: %d\nQVoffset: %d\n\n",fragfile,VCFfile,hapfile,maxiter,QVoffset);
maxcut_haplotyping(fragfile,VCFfile,0,hapfile,maxiter);
}
else
{
fprintf(stderr,"\n\nfragment file: %s\nvariantfile (variant format):%s\nhaplotypes will be output to file: %s\niterations of maxcut algorithm: %d\nQVoffset: %d\n\n",fragfile,varfile,hapfile,maxiter,QVoffset);
maxcut_haplotyping(fragfile,varfile,0,hapfile,maxiter);
}
}
return 0;
}
int main(int argc, char** argv) {
// input arguments are initial fragment file, variant file with variant information and alleles for each variant
// number of iterations total, when to output the solution, file to output solution .....
int i = 0;
int flag = 0;
char fragfile[10000];
char varfile[10000];
char VCFfile[10000];
char hapfile[10000];
strcpy(fragfile, "None");
strcpy(varfile, "None");
strcpy(hapfile, "None");
strcpy(HTRANS_DATA_INFILE, "None");
strcpy(HTRANS_DATA_OUTFILE, "None");
if (argc % 2 != 1){
fprintf(stderr, "\nERROR: Invalid number of arguments specified.\n");
exit(1);
}
for (i = 1; i < argc; i += 2) {
if (argc < 6) break;
// BASIC OPTIONS
if (strcmp(argv[i], "--fragments") == 0 || strcmp(argv[i], "--f") == 0) {
strcpy(fragfile, argv[i + 1]);
flag++;
} else if (strcmp(argv[i], "--VCF") == 0 || strcmp(argv[i], "--vcf") == 0) {
strcpy(VCFfile, argv[i + 1]);
flag++;
} else if (strcmp(argv[i], "--output") == 0 || strcmp(argv[i], "--out") == 0|| strcmp(argv[i], "--o") == 0) {
strcpy(hapfile, argv[i + 1]);
flag++;
}else if ((strcmp(argv[i], "--converge") == 0) || (strcmp(argv[i], "--c") == 0)) {
CONVERGE = atoi(argv[i + 1]);
}else if ((strcmp(argv[i], "--rh") == 0) || (strcmp(argv[i], "--tags") == 0)) { // read-haplotype assignments
OUTPUT_RH_ASSIGNMENTS = atoi(argv[i + 1]);
}else if ((strcmp(argv[i], "--outvcf") == 0) ) { // output VCF or not, default is 1
OUTPUT_VCF = atoi(argv[i + 1]);
}else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "--v") == 0){
check_input_0_or_1(argv[i + 1]);
VERBOSE = atoi(argv[i + 1]);
}
// READ-TECHNOLOGY OPTIONS
else if (strcmp(argv[i], "--HiC") == 0 || strcmp(argv[i], "--hic") == 0){
check_input_0_or_1(argv[i + 1]);
if (atoi(argv[i + 1])){
MAX_HIC_EM_ITER = 100; //atoi(argv[i + 1]);
NEW_FRAGFILE_FORMAT = 1;
HIC = 1;
}
}else if (strcmp(argv[i], "--long_reads") == 0 || strcmp(argv[i], "--lr") == 0){
check_input_0_or_1(argv[i + 1]);
LONG_READS = atoi(argv[i + 1]);
AUTODETECT_LONGREADS = 0;
}else if (strcmp(argv[i], "--QV_offset") == 0 || strcmp(argv[i], "--qv_offset") == 0 || strcmp(argv[i], "--qo") == 0){
QVoffset = atoi(argv[i + 1]);
}else if (strcmp(argv[i], "--hic_htrans_file") == 0 || strcmp(argv[i], "--hf") == 0){
NEW_FRAGFILE_FORMAT = 1;
strcpy(HTRANS_DATA_INFILE, argv[i + 1]);
HIC = 1;
}
// HAPLOTYPE POST-PROCESSING OPTIONS
else if (strcmp(argv[i], "--threshold") == 0 || strcmp(argv[i], "--t") == 0){
THRESHOLD = 1.0 - unphred(atof(argv[i + 1]));
//}else if (strcmp(argv[i], "--split_blocks") == 0 || strcmp(argv[i], "--sb") == 0){
//SPLIT_BLOCKS = atoi(argv[i + 1]);
}else if (strcmp(argv[i], "--split_threshold") == 0 || strcmp(argv[i], "--st") == 0){
SPLIT_THRESHOLD = 1.0 - unphred(atof(argv[i + 1]));
}else if (strcmp(argv[i], "--call_homozygous") == 0 || strcmp(argv[i], "--ch") == 0){
check_input_0_or_1(argv[i + 1]);
CALL_HOMOZYGOUS = atoi(argv[i + 1]);
}else if (strcmp(argv[i], "--discrete_pruning") == 0 || strcmp(argv[i], "--dp") == 0){
check_input_0_or_1(argv[i + 1]);
DISCRETE_PRUNING = atoi(argv[i + 1]);
}else if (strcmp(argv[i], "--error_analysis_mode") == 0 || strcmp(argv[i], "--ea") == 0){
check_input_0_or_1(argv[i + 1]);
ERROR_ANALYSIS_MODE = atoi(argv[i + 1]);
}else if (strcmp(argv[i], "--SNVs_before_indels") == 0 || strcmp(argv[i], "--si") == 0){
check_input_0_or_1(argv[i + 1]);
SNVS_BEFORE_INDELS = atoi(argv[i + 1]);
}
// ADVANCED OPTIONS
else if (strcmp(argv[i], "--nf") == 0 || strcmp(argv[i], "--new_format") == 0){
check_input_0_or_1(argv[i + 1]);
NEW_FRAGFILE_FORMAT = atoi(argv[i + 1]);
}else if (strcmp(argv[i], "--max_iter") == 0 || strcmp(argv[i], "--mi") == 0){
MAXITER = atoi(argv[i + 1]);
}else if (strcmp(argv[i], "--maxcut_iter") == 0 || strcmp(argv[i], "--mc") == 0) {
MAXCUT_ITER = atoi(argv[i + 1]);
}else if (strcmp(argv[i], "--htrans_read_lowbound") == 0 || strcmp(argv[i], "--hrl") == 0){
HTRANS_READ_LOWBOUND = atoi(argv[i + 1]);
}else if (strcmp(argv[i], "--htrans_max_window") == 0 || strcmp(argv[i], "--hmw") == 0){
HTRANS_MAX_WINDOW = atoi(argv[i + 1]);
}
// HIDDEN OPTIONS
else if (strcmp(argv[i], "--htrans_data_outfile") == 0 || strcmp(argv[i], "--ohf") == 0){
strcpy(HTRANS_DATA_OUTFILE, argv[i + 1]);
}else if (strcmp(argv[i], "--printscores") == 0 || strcmp(argv[i], "--scores") == 0){
PRINT_FRAGMENT_SCORES = atoi(argv[i + 1]);
}else if (strcmp(argv[i], "--mbq") == 0){
MINQ = atoi(argv[i + 1]);
}else if (strcmp(argv[i], "--skip_prune") == 0 || strcmp(argv[i], "--sp") == 0){
check_input_0_or_1(argv[i + 1]);
SKIP_PRUNE = atoi(argv[i + 1]);
}else if (strcmp(argv[i], "--max_IS") == 0 || strcmp(argv[i], "--mi") == 0){
MAX_IS = atoi(argv[i + 1]);
}else{
fprintf(stderr, "\nERROR: Invalid Option \"%s\" specified.\n",argv[i]);
exit(1);
}
}
if (ERROR_ANALYSIS_MODE && HIC){
fprintf_time(stderr,"WARNING: Switch error quality scores are not intended for use with Hi-C data. Scores will be left blank.\n");
}
if (flag != 3) // three essential arguments are not supplied
{
print_hapcut_options();
return 0;
}
fprintf(stderr, "\n\n");
fprintf_time(stderr, "fragment file: %s\n", fragfile);
fprintf_time(stderr, "variantfile (VCF format):%s\n", VCFfile);
fprintf_time(stderr, "haplotypes will be output to file: %s\n", hapfile);
fprintf_time(stderr, "solution convergence cutoff: %d\n", CONVERGE);
fprintf_time(stderr, "QVoffset: %d\n\n", QVoffset);
maxcut_haplotyping(fragfile, VCFfile, hapfile);
return 0;
}
