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;
}
/**
* For each line in the MULTIPLEX_PARAMS file create a FastqRecordsWriter and put it in the
* sampleBarcodeFastqWriterMap map, where the key to the map is the concatenation of all
* sampleBarcodes in order for the given line.
*/
private void populateWritersFromMultiplexParams() {
final TabbedTextFileWithHeaderParser libraryParamsParser =
new TabbedTextFileWithHeaderParser(MULTIPLEX_PARAMS);
final Set<String> expectedColumnLabels = CollectionUtil.makeSet("OUTPUT_PREFIX");
final List<String> sampleBarcodeColumnLabels = new ArrayList<String>();
for (int i = 1; i <= readStructure.sampleBarcodes.length(); i++) {
sampleBarcodeColumnLabels.add("BARCODE_" + i);
}
expectedColumnLabels.addAll(sampleBarcodeColumnLabels);
assertExpectedColumns(libraryParamsParser.columnLabels(), expectedColumnLabels);
for (final TabbedTextFileWithHeaderParser.Row row : libraryParamsParser) {
List<String> sampleBarcodeValues = null;
if (sampleBarcodeColumnLabels.size() > 0) {
sampleBarcodeValues = new ArrayList<String>();
for (final String sampleBarcodeLabel : sampleBarcodeColumnLabels) {
sampleBarcodeValues.add(row.getField(sampleBarcodeLabel));
}
}
final String key =
(sampleBarcodeValues == null || sampleBarcodeValues.contains("N"))
? null
: StringUtil.join("", sampleBarcodeValues);
if (sampleBarcodeFastqWriterMap.containsKey(
key)) { // This will catch the case of having more than 1 line in a non-barcoded
// MULTIPLEX_PARAMS file
throw new PicardException(
"Row for barcode "
+ key
+ " appears more than once in MULTIPLEX_PARAMS file "
+ MULTIPLEX_PARAMS);
}
final FastqRecordsWriter writer = buildWriter(new File(row.getField("OUTPUT_PREFIX")));
sampleBarcodeFastqWriterMap.put(key, writer);
}
if (sampleBarcodeFastqWriterMap.isEmpty()) {
throw new PicardException(
"MULTIPLEX_PARAMS file " + MULTIPLEX_PARAMS + " does have any data rows.");
}
libraryParamsParser.close();
}