public boolean processString() {
String value = "";
SequenceReader r = new SequenceReader(true);
r.indexFASTAFile(hitFilename, null, true);
int l = (3 * querySeq.length()) / 2;
String hitSeq = r.getSubSequence(hitReference.getId(), hitStart, hitStart + l);
int hitPtr = 0;
int queryPtr = 0;
boolean displayResult = false;
boolean donePreClipping = false;
int tagCtr = 0;
int i = 0;
boolean continueParsing = true;
int totalCount = 0;
int delCount = 0;
int insCount = 0;
int matchCount = 0;
boolean processed = true;
// System.out.println(" Hit: "+hitSeq.length()+" "+hitSeq);
// System.out.println("Query: "+querySeq.length()+" "+querySeq);
hitAlnSize = 0;
queryAlnSize = 0;
hitAlnSize = 0;
while ((i < cigarString.length()) && (continueParsing)) {
// for (int i=0; i<cigarString.length(); i++) {
// System.out.println("hitPtr="+hitPtr+" queryPtr="+queryPtr);
// System.out.println("Query: " + queryString.toString());
// System.out.println(" Hit: " + hitString.toString());
char c = cigarString.charAt(i);
if (Character.isDigit(c)) {
value = value + c;
} else {
int n = Integer.parseInt(value);
totalCount += n;
// System.out.println(n + " " + c);
switch (c) {
case 'M':
case '=':
case 'X':
queryString.append(querySeq.substring(queryPtr, queryPtr + n));
hitString.append(hitSeq.substring(hitPtr, hitPtr + n));
queryPtr += n;
hitPtr += n;
queryAlnSize += n;
hitAlnSize += n;
donePreClipping = true;
matchCount += n;
break;
case 'I':
if (n > 100) {
System.out.println("");
System.out.println("Error: large I (" + n + ") - read " + queryID + " ignored");
processed = false;
continueParsing = false;
} else {
queryString.append(querySeq.substring(queryPtr, queryPtr + n));
for (int j = 0; j < n; j++) {
hitString.append('-');
}
queryPtr += n;
queryAlnSize += n;
}
donePreClipping = true;
insCount += n;
break;
case 'D':
if (n > 100) {
System.out.println("Error: large D (" + n + ") - read " + queryID + " ignored");
processed = false;
continueParsing = false;
} else {
hitString.append(hitSeq.substring(hitPtr, hitPtr + n));
for (int j = 0; j < n; j++) {
queryString.append('-');
}
hitPtr += n;
hitAlnSize += n;
}
donePreClipping = true;
delCount += n;
break;
case 'N':
System.out.println("Warning: encountered N in CIGAR format!");
System.out.println("");
displayResult = true;
hitString.append(hitSeq.substring(hitPtr, hitPtr + n));
for (int j = 0; j < n; j++) {
queryString.append('-');
}
queryPtr += n;
hitPtr += n;
donePreClipping = true;
break;
case 'S':
// System.out.println("Warnning: encountered S in CIGAR format!");
queryPtr += n;
if (!donePreClipping) {
queryStart += n;
}
displayResult = true;
break;
case 'H':
// System.out.println("Warning: encountered H in CIGAR format!");
if (!donePreClipping) {
queryStart += n;
} else {
// System.out.println("Warning: hard clipping at end");
}
displayResult = true;
break;
case 'P':
System.out.println("Warning: encountered P in CIGAR format!");
System.out.println("");
displayResult = true;
donePreClipping = true;
break;
default:
System.out.println("Unrecognised character in CIGAR string: " + c);
processed = false;
break;
}
value = "";
tagCtr++;
// System.out.println("qseq="+querySeq.length()+" matchCount="+matchCount+"
// insCount="+insCount+" delCount="+delCount+" totalCount="+totalCount);
// System.out.println("Query: "+queryString.toString());
// System.out.println(" Hit: "+hitString.toString());
}
i++;
// System.out.println("i="+i+" and length="+cigarString.length());
}
// if (displayResult) {
// System.out.println(queryFilename);
// System.out.println("Query: " + queryString.toString());
// System.out.println(" Hit: " + hitString.toString());
// System.exit(1);
// }
return processed;
}
