private void parse(Map<String, Integer> names, final Reader reference, final Sex sex)
throws IOException {
final BufferedReader in = new BufferedReader(reference);
final ReferenceParse parse = new ReferenceParse(names, in, sex);
try {
parse.parse();
} catch (final IOException e) {
throw new IOException("I/O error while reading reference file. ", e);
}
postProcessing(names, parse);
if (parse.mError) {
throw new NoTalkbackSlimException("Invalid reference file (see earlier warning messages).");
}
}
/**
* Finish constructing the references and link in duplicates.
*
* @param names the ordered set of reference sequence names
* @param parse results from parsing.
*/
private void postProcessing(Map<String, Integer> names, final ReferenceParse parse) {
mReferences = new LinkedHashMap<>();
// deal with sequences in genome but explicitly described.
for (final Map.Entry<String, Integer> entry : names.entrySet()) {
final String name = entry.getKey();
if (parse.mReferences.containsKey(
name)) { // have seen explicitly declared seq line, so copy from parse
mReferences.put(name, parse.mReferences.get(name));
continue;
}
if (parse.mPloidyDefault == null) {
parse.error("No default specified but required for sequence:" + name);
return;
}
try {
mReferences.put(
name,
new ReferenceSequence(
false, parse.mLinearDefault, parse.mPloidyDefault, name, null, entry.getValue()));
} catch (final IllegalArgumentException e) {
throw new NoTalkbackSlimException("Invalid reference file. " + e.getMessage());
}
}
// add duplicate information into sequence entries
for (final Pair<RegionRestriction, RegionRestriction> duplicate : parse.mDuplicates) {
final RegionRestriction r1 = duplicate.getA();
if (!mReferences.containsKey(r1.getSequenceName())) {
continue;
}
final RegionRestriction r2 = duplicate.getB();
if (!mReferences.containsKey(r2.getSequenceName())) {
continue;
}
try {
mReferences.get(r1.getSequenceName()).addDuplicate(duplicate);
mReferences.get(r2.getSequenceName()).addDuplicate(duplicate);
} catch (final IllegalArgumentException e) {
throw new NoTalkbackSlimException("Invalid reference file. " + e.getMessage());
}
}
}
