/* (non-Javadoc)
* @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
*/
@Override
public int compare(Read a, Read b) {
final long[] alist, blist;
if (useCache) {
if (a.obj == null) {
alist = new long[comparisons];
a.obj = alist;
fill(a, alist);
} else {
alist = (long[]) a.obj;
}
if (b.obj == null) {
blist = new long[comparisons];
b.obj = alist;
fill(b, blist);
} else {
blist = (long[]) b.obj;
}
} else {
long[][] matrix = local1.get();
if (matrix == null) {
matrix = new long[2][comparisons];
local1.set(matrix);
}
alist = matrix[0];
blist = matrix[1];
fill(a, alist);
fill(b, blist);
}
return compare(alist, blist);
}
@Override
boolean processReadPair(Read r1, Read r2) {
assert (r2 == null);
final byte[] quals = r1.quality, bases = r1.bases;
final byte[] match =
(r1.match == null ? null : !r1.shortmatch() ? r1.match : Read.toLongMatchString(r1.match));
if (match == null || quals == null || bases == null) {
return false;
}
int subs = 0;
int indels = 0;
for (int qpos = 0, mpos = 0, last = quals.length - 1; mpos < match.length; mpos++) {
final byte m = match[mpos];
final byte mprev = match[Tools.max(mpos - 1, 0)];
final byte mnext = match[Tools.min(mpos + 1, match.length - 1)];
final byte q1 = quals[qpos];
final byte b2 = bases[qpos];
int sub = 0, indel = 0;
if (m == 'S') {
sub = 1;
} else if (m == 'I') {
indel = 1;
} else if (m == 'm') {
if (mprev == 'D' || mnext == 'D') {
indel = 1;
}
} else if (m == 'D') {
// do nothing
} else if (m == 'C') {
// do nothing
} else {
throw new RuntimeException(
"Bad symbol m='"
+ ((char) m)
+ "'\n"
+ new String(match)
+ "\n"
+ new String(bases)
+ "\n");
}
subs += sub;
indels += indel;
if (q1 >= minq && q1 <= maxq) {
if (sub > 0 || (indel > 0 && countIndels)) {
return true;
}
}
if (m != 'D') {
qpos++;
}
}
return keepPerfect && subs == 0 && indels == 0;
}
/** This will create a count consensus of the bases at each position in the cluster. */
public int[][] baseCounts() {
int maxLeft = -1, maxRight = -1;
for (Read r : this) {
long[] obj = (long[]) r.obj;
int pos = (int) obj[1];
maxLeft = Tools.max(maxLeft, pos);
maxRight = Tools.max(maxRight, r.length() - pos);
}
final int width = maxLeft + maxRight;
// assert(size()==1) : "\nleft="+maxLeft+", right="+maxRight+", width="+width+",
// "+k+"\n"+get(0).toFastq()+"\n"+get(size()-1).toFastq();
// System.err.println("\n\n");
final int[][] counts = new int[4][width];
for (Read r : this) {
long[] obj = (long[]) r.obj;
int pos = (int) obj[1];
byte[] bases = r.bases, quals = r.quality;
// System.err.println("pos="+pos+", maxLeft="+maxLeft);
for (int cloc = 0, rloc = maxLeft - pos; cloc < bases.length; cloc++, rloc++) {
// System.err.println("cloc="+cloc+"/"+bases.length+", rloc="+rloc+"/"+width);
int x = AminoAcid.baseToNumber[bases[cloc]];
if (x > -1) {
int q = (quals == null ? 20 : quals[cloc]);
counts[x][rloc] += q;
}
}
}
// if(size()>0){//Looks correct.
// System.err.println(Arrays.toString(counts[0]));
// System.err.println(Arrays.toString(counts[1]));
// System.err.println(Arrays.toString(counts[2]));
// System.err.println(Arrays.toString(counts[3]));
// }
return counts;
}