@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;
}
