void
mappedLengths(atacFile &AF, atacMatchList &matches, seqCache *A, seqCache *B, char *prefix) {
histogram h1(100, 1000000);
histogram h2(100, 1000000);
// For the coverage to work correctly, we need to either have one
// intervalList per input sequence, or build a table of the chained
// sequence positions.
//
uint64 *offset1 = buildOffset(AF.fastaA());
uint64 *offset2 = buildOffset(AF.fastaB());
intervalList<uint64> intervalA;
intervalList<uint64> intervalB;
for (uint32 m=0; m<matches.numberOfMatches(); m++) {
intervalA.add(offset1[matches[m]->iid1] + (uint64)matches[m]->pos1, (uint64)matches[m]->len1);
intervalB.add(offset2[matches[m]->iid2] + (uint64)matches[m]->pos2, (uint64)matches[m]->len2);
h1.add(matches[m]->len1);
h2.add(matches[m]->len2);
}
fprintf(stdout, "numberOfItems "uint64FMT"\n", (uint64)matches.numberOfMatches());
fprintf(stdout, "matchLength %s "uint64FMT" %s "uint64FMT" # Sum of lengths of sequence in matches\n",
AF.labelA(), (uint64)intervalA.sumOfLengths(),
AF.labelB(), (uint64)intervalB.sumOfLengths());
h1.show("AmatchLength");
h2.show("BmatchLength");
h1.dump(prefix, "AmatchLength"); h1.plot(prefix, "AmatchLength");
h2.dump(prefix, "BmatchLength"); h2.plot(prefix, "BmatchLength");
intervalA.merge();
intervalB.merge();
fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, including N\n",
AF.labelA(), (uint64)intervalA.sumOfLengths(),
AF.labelB(), (uint64)intervalB.sumOfLengths());
fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, ACGT only (new)\n",
AF.labelA(), tandemRepeatACGTLength(intervalA, offset1, A),
AF.labelB(), tandemRepeatACGTLength(intervalB, offset2, B));
delete [] offset1;
delete [] offset2;
}
// ******************
template <class Type> void MyVector<Type>::scatter() {
buildOffset();
scatter(_offset);
}
void
tandemRepeatStats(atacFileStream &featuresA,
atacFileStream &featuresB,
atacFile &AF,
seqCache *A,
seqCache *B) {
intervalList<uint64> ifa, ifb;
intervalList<uint64> ima, imb;
intervalList<uint64> mma, mmb;
atacMatchList &matches = *AF.matches();
uint64 *offset1 = buildOffset(A);
uint64 *offset2 = buildOffset(B);
// ifa, ifb are intervalLists, storing the intervals labeled as
// tandem repeats. They are using the offset[] to encode the
// entire sequence as one consecutive string.
//
atacFeature *f = 0L;
while ((f = featuresA.nextFeature("tr")) != 0L)
ifa.add(offset1[f->iid] + f->pos, f->len);
while ((f = featuresB.nextFeature("tr")) != 0L)
ifb.add(offset2[f->iid] + f->pos, f->len);
// ima, imb, like if?, encode the matches in one string.
//
for (uint32 m=0; m<matches.numberOfMatches(); m++)
ima.add(offset1[matches[m]->iid1] + (uint64)matches[m]->pos1, (uint64)matches[m]->len1);
for (uint32 m=0; m<matches.numberOfMatches(); m++)
imb.add(offset2[matches[m]->iid2] + (uint64)matches[m]->pos2, (uint64)matches[m]->len2);
fprintf(stdout, "\nTANDEM REPEATS in %s\n", AF.labelA());
fprintf(stdout, "numberOfItems "uint64FMT"\n", (uint64)ifa.numberOfIntervals());
fprintf(stdout, "totalLength "uint64FMT" # sum of lengths of all features\n", ifa.sumOfLengths());
ifa.merge();
fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions\n", (uint64)ifa.numberOfIntervals());
fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, including N\n", ifa.sumOfLengths());
fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, ACGT only\n", tandemRepeatACGTLength(ifa, offset1, A));
mma.intersect(ifa, ima);
fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions, only in matches\n", (uint64)mma.numberOfIntervals());
fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, including N\n", mma.sumOfLengths());
fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, ACGT only\n", tandemRepeatACGTLength(mma, offset1, A));
fprintf(stdout, "\nTANDEM REPEATS in %s\n", AF.labelB());
fprintf(stdout, "numberOfItems "uint64FMT"\n", (uint64)ifb.numberOfIntervals());
fprintf(stdout, "totalLength "uint64FMT" # sum of lengths of all features\n", ifb.sumOfLengths());
ifb.merge();
fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions\n", (uint64)ifb.numberOfIntervals());
fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, including N\n", ifb.sumOfLengths());
fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, ACGT only\n", tandemRepeatACGTLength(ifb, offset2, B));
mmb.intersect(ifb, imb);
fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions, only in matches\n", (uint64)mmb.numberOfIntervals());
fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, including N\n", mmb.sumOfLengths());
fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, ACGT only\n", tandemRepeatACGTLength(mmb, offset2, B));
delete [] offset1;
delete [] offset2;
}
