/** Inserts tag count values into the RandomAccessFile created by @link{createMergeOutfile}. */
public static final void fillMergeOutfile(String[] infiles, String outfile) {
TagsByTaxa tbtOut = newTBT(outfile);
tbtOut.setMethodByRows(true);
int count = 0;
int filesRead = 0;
for (String inName : infiles) {
filesRead++;
myLogger.info("Scanning " + inName + " (file " + filesRead + " of " + infiles.length + ").");
TagsByTaxa tbtFM = newTBT(inName);
if (combineSynonymousTaxa) {
tbtFM.truncateTaxonNames();
}
int[] theTR = taxaRedirect(tbtFM.getTaxaNames(), tbtOut.getTaxaNames());
for (int i = 0; i < tbtFM.getTagCount(); i++) {
int toTag = tbtOut.getTagIndex(tbtFM.getTag(i));
if (toTag < 0) {
continue;
}
for (int t = 0; t < tbtFM.getTaxaCount(); t++) {
if (theTR[t] < 0) {
continue;
}
int tagCount =
tbtOut.getReadCountForTagTaxon(toTag, theTR[t]) + tbtFM.getReadCountForTagTaxon(i, t);
if (tagCount > 0) {
tbtOut.setReadCountForTagTaxon(toTag, theTR[t], tagCount);
count++;
}
}
if (count % 100000 == 0) {
System.out.printf("Tag:%d BitSet:%d %n", i, count);
}
}
}
tbtOut.getFileReadyForClosing();
}
