124 lines
2.7 KiB
C
124 lines
2.7 KiB
C
# include <stdio.h>
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# include <stdlib.h>
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# include <zlib.h>
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#include <string.h>
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#include <stdbool.h>
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bool StartsWith(const char *a, const char *b)
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{
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if(strncmp(a, b, strlen(b)) == 0) return 1;
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return 0;
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}
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void slice_str(const char * str, char * buffer, size_t start, size_t end)
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{
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size_t j = 0;
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for ( size_t i = start; i <= end; ++i ) {
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buffer[j++] = str[i];
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}
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buffer[j] = 0;
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}
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int min(int * array, int size){
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//Consider first element as smallest
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int smallest = array[0];
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int i;
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for (i = 0; i < num; i++) {
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if (a[i] < smallest) {
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smallest = a[i];
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}
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}
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}
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int countDistinct(int a[], int n) //Function Definition
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{
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int i, j, count = 0;
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//Traverse the array
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for (i = 1; i < n; i++) //hold an array element
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{
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for (j = 0; j < i; j++)
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{
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if (a[i] == a[j]) //Check for duplicate elements
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{
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break; //If duplicate elements found then break
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}
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}
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if (i == j)
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{
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count++; //increment the number of distinct elements
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}
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}
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return count; //Return the number of distinct elements
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}
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# define LL 8192 /* line length maximum */
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# define DIPLOID true
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# define FOLDED true
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# define IGNORED_FIELDS 9
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int main ( int argc, char *argv[] ){
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if ( argc < 3) {
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printf("Need 2 args!\n");
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return 1;
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}
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gzFile fp;
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char line[LL];
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int N;
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char delim[] = "\t";
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fp = gzopen( argv[1], "r" );
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// pop of size 2N when diploid
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if (DIPLOID == true && FOLDED == false) {
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N = 2 * atoi(argv[2]);
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} else {
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N = atoi(argv[2]);
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}
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int snp_genotypes[N];
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int SFS_values[N];
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gzgets( fp, line, LL );
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while ( ! gzeof( fp ) ){
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int k = 0;
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if ( StartsWith(line, "##") || ( StartsWith(line, "#") ) || (strstr(line, "./.:.") != NULL)){
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gzgets( fp, line, LL );
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continue;
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}
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char *vcf_field = strtok(line, delim);
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while(vcf_field != NULL){
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k++;
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if (k > IGNORED_FIELDS) {
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const size_t len = strlen(vcf_field);
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char buffer[len + 1];
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//printf("'%s'\n", ptr);
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slice_str(vcf_field, buffer, 0, 0);
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//printf("%d %s ", N, buffer);
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snp_genotypes[k-IGNORED_FIELDS] = atoi(buffer);
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//printf("%d ", smpl_genotype[k-9]);
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}
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vcf_field = strtok(NULL, delim);
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int c= countDistinct(snp_genotypes, N);
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// skip if all individuals have the same genotype
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if (c == 1) {
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continue;
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gzgets( fp, line, LL );
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}
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/* int i; */
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/* for (i = 1; i < N; ++i) */
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/* { */
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/* printf("%d ", snp_genotypes[i]); */
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/* } */
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int allele_counts[c];
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min(allele_counts, N);
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}
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// printf("%s", line );
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// loads the next line
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gzgets( fp, line, LL );
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}
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gzclose( fp );
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return 0;
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}
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