@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;
}
private final void pair(ArrayList<Read> buffer1, ArrayList<Read> buffer2) {
final int len1 = buffer1.size(), len2 = buffer2.size();
assert (ALLOW_UNEQUAL_LENGTHS || len1 == len2)
: "\nThere appear to be different numbers of reads in the paired input files."
+ "\nThe pairing may have been corrupted by an upstream process. It may be fixable by running repair.sh.";
final int lim = Tools.min(len1, len2);
for (int i = 0; i < lim; i++) {
Read a = buffer1.get(i);
Read b = buffer2.get(i);
assert (a.numericID == b.numericID)
: "\n"
+ a.numericID
+ ", "
+ b.numericID
+ "\n"
+ a.toText(false)
+ "\n"
+ b.toText(false)
+ "\n";
assert (a.mate == null)
: "Please set interleaved=false when using dual input files.\n"
+ a.id
+ "\n"
+ a.mate.id
+ "\n"
+ b.id
+ "\n"
+ producer1
+ "\n"
+ producer2;
assert (b.mate == null) : "Please set interleaved=false when using dual input files.";
a.mate = b;
b.mate = a;
assert (a.pairnum() == 0);
b.setPairnum(1);
// assert(a.pairnum()!=b.pairnum());
}
if (len1 > len2) {
// do nothing;
} else if (len2 > len1) {
for (int i = lim; i < len2; i++) {
Read b = buffer2.get(i);
b.setPairnum(0);
buffer1.add(b);
}
}
}