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package jgi;
import fileIO.TextFile;
/**
* @author Brian Bushnell
* @date Oct 10, 2012
*
*/
public class KmerSample {
public static int[] makeKmerSet(int K, String filename){
//Number of bits in a kmer
int kbits=2*K;
//Number of possible kmers
long kmerSpace=(1L<<kbits);
//Make an array of the correct size, remembering that int is 32 bits
int[] array=new int[(int)(kmerSpace/32)];
//Current kmer
long kmer=0;
//Length of current kmer
int len=0;
//This will create a bitmask of 00000...0000111111...11111, where the number if 1's is equal to kbits.
long mask=(kbits>63 ? -1L : ~((-1L)<<kbits));
//Initialize an input stream for the fasta file
TextFile tf=new TextFile(filename, false);
//Grab the first line of the fasta file
String line=tf.nextLine();
while(line!=null){
if(line.length()<1){
//The line is empty, so ignore it (should never happen in a proper fasta file)
}else if(line.charAt(0)=='>'){
//The line is name of a new contig/scaffold, so reset the kmer
kmer=0;
len=0;
}else{
//Otherwise, generate kmers
for(int i=0; i<line.length(); i++){
//The base at location "i" in the string
char letter=line.charAt(i);
//The 2-bit numeric code for the base
int code;
if(letter=='A'){code=0;}
else if(letter=='C'){code=1;}
else if(letter=='G'){code=2;}
else if(letter=='T'){code=3;}
else{code=-1;}
if(code<0){
//The base was an N or degenerate letter, so reset the kmer
kmer=0;
len=0;
}else{
//insert the code into the current kmer
kmer=(kmer<<2); //left shift by 2
kmer=(kmer|code); //or with the code
kmer=(kmer&mask); //and with the mask to prevent going past the intended kmer length
len++; //Increment the length of the kmer
if(len>=K){
//If the kmer is long enough, then add it to the array
//The index in the array is the upper bits of the kmer. Each location in the array is 32 bits.
int index=(int)(kmer/32);
//The bit within the word of the array is the lower 5 bits of the kmer
int bit=(int)(kmer%32);
//A bitmask to set the correct bit in the array to 1.
int x=(1<<bit);
//OR the array location with the new mask.
array[index]=(array[index] | x);
}
}
}
}
//Grab the next line
line=tf.nextLine();
}
//Close your input stream
tf.close();
return array;
}
public static boolean containsKmer(long kmer, int[] array){
//The index in the array is the upper bits of the kmer. Each location in the array is 32 bits.
int index=(int)(kmer/32);
//The bit within the word of the array is the lower 5 bits of the kmer
int bit=(int)(kmer%32);
//A bitmask to test the correct bit in the array to 1.
int x=(1<<bit);
if((array[index]&x)==0){//Check to see if the bit is set in the array
return false;
}else{
return true;
}
}
}
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