OverlapDetector<Gene> load() {
final OverlapDetector<Gene> overlapDetector = new OverlapDetector<Gene>(0, 0);
final int expectedColumns = RefFlatColumns.values().length;
final TabbedTextFileWithHeaderParser parser =
new TabbedTextFileWithHeaderParser(refFlatFile, RefFlatColumnLabels);
final Map<String, List<TabbedTextFileWithHeaderParser.Row>> refFlatLinesByGene =
new HashMap<String, List<TabbedTextFileWithHeaderParser.Row>>();
for (final TabbedTextFileWithHeaderParser.Row row : parser) {
final int lineNumber =
parser.getCurrentLineNumber(); // getCurrentLineNumber returns the number of the next line
if (row.getFields().length != expectedColumns) {
throw new AnnotationException(
"Wrong number of fields in refFlat file " + refFlatFile + " at line " + lineNumber);
}
final String geneName = row.getField(RefFlatColumns.GENE_NAME.name());
final String transcriptName = row.getField(RefFlatColumns.TRANSCRIPT_NAME.name());
final String transcriptDescription = geneName + ":" + transcriptName;
final String chromosome = row.getField(RefFlatColumns.CHROMOSOME.name());
if (!isSequenceRecognized(chromosome)) {
LOG.debug(
"Skipping " + transcriptDescription + " due to unrecognized sequence " + chromosome);
} else {
List<TabbedTextFileWithHeaderParser.Row> transcriptLines = refFlatLinesByGene.get(geneName);
if (transcriptLines == null) {
transcriptLines = new ArrayList<TabbedTextFileWithHeaderParser.Row>();
refFlatLinesByGene.put(geneName, transcriptLines);
}
transcriptLines.add(row);
}
}
int longestInterval = 0;
int numIntervalsOver1MB = 0;
for (final List<TabbedTextFileWithHeaderParser.Row> transcriptLines :
refFlatLinesByGene.values()) {
try {
final Gene gene = makeGeneFromRefFlatLines(transcriptLines);
overlapDetector.addLhs(gene, gene);
if (gene.length() > longestInterval) longestInterval = gene.length();
if (gene.length() > 1000000) ++numIntervalsOver1MB;
} catch (AnnotationException e) {
LOG.debug(e.getMessage() + " -- skipping");
}
}
LOG.debug(
"Longest gene: " + longestInterval + "; number of genes > 1MB: " + numIntervalsOver1MB);
return overlapDetector;
}
