private long[] getTagsInBits(TagsByTaxaByte aTBT, int tagIndex, int[] reDirect, int anchorTaxa) {
int lgPerSite = (anchorTaxa / 64) + 1;
long[] seq = new long[lgPerSite];
for (int j = 0; j < aTBT.getTaxaCount(); j++) {
if (reDirect[j] < 0) continue;
int index = reDirect[j] / 64;
int offset = reDirect[j] % 64;
if (aTBT.getReadCountForTagTaxon(tagIndex, j) > 0) { // reference alleles
seq[index] = seq[index] | (1L << offset);
}
}
return seq;
}
public long[] getTagDistInBits(int[] newTestFamilies) {
int lgPerSite = (refAlignment.getSequenceCount() / 64) + 1;
long[] seq = new long[lgPerSite];
for (int i = 0; i < newTestFamilies.length; i++) {
for (int j = 0; j < family2TBTIndex[newTestFamilies[i]].length; j++) {
int index =
tbt2anchorRedirect[newTestFamilies[i]][family2TBTIndex[newTestFamilies[i]][j]] / 64;
int offset =
tbt2anchorRedirect[newTestFamilies[i]][family2TBTIndex[newTestFamilies[i]][j]] % 64;
if (tbt.getReadCountForTagTaxon(tagIndex, family2TBTIndex[newTestFamilies[i]][j])
> 0) { // reference alleles
seq[index] = seq[index] | (1L << offset);
}
}
}
return seq;
}
private int[] getMinPresentFamily(int tagIndex, float minPresentInFamily) {
ArrayList<Integer> overMinPresentFamilyList = new ArrayList();
for (int i = 0; i < family2TBTIndex.length; i++) {
int cnt = 0;
for (int j = 0; j < family2TBTIndex[i].length; j++) {
if (tbt.getReadCountForTagTaxon(tagIndex, family2TBTIndex[i][j]) != 0) cnt++;
}
float rate = (float) cnt / family2TBTIndex[i].length;
if (rate > minPresentInFamily) overMinPresentFamilyList.add(i);
}
if (overMinPresentFamilyList.isEmpty()) return null;
int[] overMinPresentFamily = new int[overMinPresentFamilyList.size()];
for (int i = 0; i < overMinPresentFamily.length; i++) {
overMinPresentFamily[i] = overMinPresentFamilyList.get(i);
}
return overMinPresentFamily;
}
