@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;
}
public void fill(Read r, long[] kmers) {
final byte[] bases = r.bases;
long kmer = 0;
long rkmer = 0;
int len = 0;
if (bases == null || bases.length < k) {
return;
}
long[] mods = local2.get();
if (mods == null) {
mods = new long[comparisons];
local2.set(mods);
}
Arrays.fill(mods, -1);
for (int i = 0; i < bases.length; i++) {
byte b = bases[i];
long x = Dedupe.baseToNumber[b];
long x2 = Dedupe.baseToComplementNumber[b];
kmer = ((kmer << 2) | x) & mask;
rkmer = (rkmer >>> 2) | (x2 << shift2);
if (b == 'N') {
len = 0;
} else {
len++;
}
if (len >= k) {
final long kmax = Tools.max(kmer, rkmer);
for (int j = 0; j < comparisons; j++) {
final long div = divisors[j];
final long mod = kmax % div;
if (mod > mods[j]) {
mods[j] = mod;
kmers[j] = kmax;
}
}
}
}
}