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| import java.util.regex.Pattern;
/**
*
* @author bareri00
*/
public class brouillon {
// private static char[] cBases = new char[strCIGAR.length()];
// private static int[] basePOS = new int[strCIGAR.length()];
private static int startPOS = 7;
// private static int[] nucPOS = {};
// int[] basePOS = new int[strCIGAR.length()];
private static final String strCIGAR = "8M2I4M1D3M";
private static final String strSEQ = "TTAGATAAAGGATACTG";
// private static char[] charCIGAR = new char[(getCIGARoperations(strCIGAR)).length];
// private static int[] valCIGAR = new int[(getCIGARvalues(strCIGAR)).length];
public static void main(String[] args) throws Exception {
int[] basePOS = new int[strCIGAR.length()];
basePOS = getReadPOS(strCIGAR, strSEQ, startPOS);
System.out.println(basePOS.length);
/*
* char[] cg = getCIGARoperations(strCIGAR);
* //char[] cg = StringToCharArray(strCIGAR);
* for (char i:cg){
* System.out.println(i);
* }
*
*
* char[] out = new char[strCIGAR.length()];
* char[] inArray = StringToCharArray(strCIGAR);
* for(int i=0;i<inArray.length;i++){
* if(("M".charAt(0)== inArray[i]) || ("H".charAt(0)== inArray[i]) || ("S".charAt(0)== inArray[i])||("I".charAt(0)== inArray[i]) ||("D".charAt(0)== inArray[i])||("P".charAt(0)== inArray[i])||("N".charAt(0)== inArray[i]) ||("X".charAt(0)== inArray[i])||("=".charAt(0)== inArray[i])){
* out[i]=inArray[i];
* }
* }
* for (char i:out){
* System.out.println(i);
* }
*/
}
private static char[] StringToCharArray(String aString) {
char[] aCharArray;
aCharArray = aString.toCharArray();
return aCharArray;
}
private static int[] getReadPOS(String aCIGAR, String aSEQ, int POS_start) throws Exception {
int[] nucPOS = new int[aSEQ.length()];
int outBoundPOS = 100000000;
char[] aCharCIGAR = getCIGARoperations(aCIGAR);
int[] aValCIGAR = convertStringArraytoIntArray(getCIGARvalues(aCIGAR));
int[] intCIGAR = new int[aValCIGAR.length];
for (int i = 0; i < aCharCIGAR.length; i++) {
if ("M".charAt(0) == aCharCIGAR[i]) {
intCIGAR[i] = aValCIGAR[i];
for (int j = 0; j < intCIGAR[i]; j++) {
nucPOS[j] = POS_start + j;
POS_start = POS_start + intCIGAR[i];
}
}
if (("D".charAt(0) == aCharCIGAR[i]) || ("N".charAt(0) == aCharCIGAR[i])) {
intCIGAR[i] = aValCIGAR[i];
POS_start = POS_start + intCIGAR[i];
}
if (("I".charAt(0) == aCharCIGAR[i]) || ("S".charAt(0) == aCharCIGAR[i])) {
POS_start = POS_start + 1;
intCIGAR[i] = aValCIGAR[i];
for (int j = 0; j < intCIGAR[i]; j++) {
nucPOS[j] = outBoundPOS;
}
}
if ("P".charAt(0) == aCharCIGAR[i]) {
POS_start = POS_start + 1;
}
}
return nucPOS;
}
private static String[] getCIGARvalues(String CIGARstr) {
String[] outArray = new String[CIGARstr.length()];
String pattern = "[HMISDPN]";
Pattern splitter = Pattern.compile(pattern);
outArray = splitter.split(CIGARstr);
return outArray;
}
private static char[] getCIGARoperations(String CIGARstr) {
char[] outArray = new char[CIGARstr.length()];
char[] inArray = StringToCharArray(CIGARstr);
for (int i = 0; i < inArray.length; i++) {
if (("M".charAt(0) == inArray[i]) || ("H".charAt(0) == inArray[i]) || ("S".charAt(0) == inArray[i])
|| ("I".charAt(0) == inArray[i]) || ("D".charAt(0) == inArray[i]) || ("P".charAt(0) == inArray[i])
|| ("N".charAt(0) == inArray[i]) || ("X".charAt(0) == inArray[i])
|| ("=".charAt(0) == inArray[i])) {
outArray[i] = inArray[i];
}
}
return outArray;
}
public static int[] convertStringArraytoIntArray(String[] sarray) throws Exception {
if (sarray != null) {
int intarray[] = new int[sarray.length];
for (int i = 0; i < sarray.length; i++) {
intarray[i] = Integer.parseInt(sarray[i]);
}
return intarray;
}
return null;
}
} |
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