Add C version start

compile.sh

@@ -0,0 +1,2 @@
+#!/bin/sh
+gcc -Wall -pthread vcf_to_sfs.c -lm -lz -std=c99 -Wextra -o vcf_to_sfs

vcf_to_sfs.c

@@ -0,0 +1,62 @@
+# include <stdio.h>
+# include <stdlib.h>
+# include <zlib.h>
+#include <string.h>
+#include <stdbool.h>
+
+bool StartsWith(const char *a, const char *b)
+{
+   if(strncmp(a, b, strlen(b)) == 0) return 1;
+   return 0;
+}
+
+void slice_str(const char * str, char * buffer, size_t start, size_t end)
+{
+    size_t j = 0;
+    for ( size_t i = start; i <= end; ++i ) {
+        buffer[j++] = str[i];
+    }
+    buffer[j] = 0;
+}
+
+
+# define LL 8192   /* line length maximum */
+
+int main ( int argc, char *argv[] ){
+    if ( argc < 3) {
+	printf("Need 2 args!\n");
+	return 1;
+    }
+    gzFile fp;
+    char line[LL];
+    char delim[] = "\t";
+    fp = gzopen( argv[1], "r" );
+
+    gzgets( fp, line, LL );
+    while ( ! gzeof( fp ) ){
+	int k = 0;
+	if ( StartsWith(line, "##") || ( StartsWith(line, "#") ) || (strstr(line, "./.:.") != NULL)){
+	    gzgets( fp, line, LL );
+	    continue;
+	}
+	
+	char *vcf_field = strtok(line, delim);
+	while(vcf_field != NULL){
+	    k++;
+	    if (k > 9) {
+		const size_t len = strlen(vcf_field);
+		char buffer[len + 1];
+		//printf("'%s'\n", ptr);
+		slice_str(vcf_field, buffer, 0, 0);
+		printf("%s      ", buffer);
+	    }
+	    vcf_field = strtok(NULL, delim);
+	}
+	// printf("%s", line );
+	// loads the next line
+	gzgets( fp, line, LL );
+    }
+
+    gzclose( fp );
+    return 0;
+}

vcf_to_sfs.py

@@ -71,10 +71,11 @@ with gzip.open(sys.argv[1], "rb") as inputgz:
             for k in set(snp_genotypes):
                 allele_counts[snp_genotypes.count(k)] = k
                 allele_counts_list.append(snp_genotypes.count(k))
-            if folded :
+            if folded and len(ALT) >= 2:
-                for al in range(polyallelic-1):
+                for al in range(len(ALT)-1):
                     SFS_values[min(allele_counts_list)-1] += 1/len(ALT)
                     allele_counts_list.remove(min(allele_counts_list))
+            else:
+                SFS_values[min(allele_counts_list)-1] += 1
         line = inputgz.readline()
         print(SFS_values)
-print(polycount)