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();
}
/** Conversion from 0-based half-open to 1-based inclusive intervals is done here. */
private Gene.Transcript makeTranscriptFromRefFlatLine(
final Gene gene, final TabbedTextFileWithHeaderParser.Row row) {
final String geneName = row.getField(RefFlatColumns.GENE_NAME.name());
final String transcriptName = row.getField(RefFlatColumns.TRANSCRIPT_NAME.name());
final String transcriptDescription = geneName + ":" + transcriptName;
final int exonCount = Integer.parseInt(row.getField(RefFlatColumns.EXON_COUNT.name()));
final String[] exonStarts = row.getField(RefFlatColumns.EXON_STARTS.name()).split(",");
final String[] exonEnds = row.getField(RefFlatColumns.EXON_ENDS.name()).split(",");
if (exonCount != exonStarts.length) {
throw new AnnotationException(
"Number of exon starts does not agree with number of exons for " + transcriptDescription);
}
if (exonCount != exonEnds.length) {
throw new AnnotationException(
"Number of exon ends does not agree with number of exons for " + transcriptDescription);
}
final int transcriptionStart = row.getIntegerField(RefFlatColumns.TX_START.name()) + 1;
final int transcriptionEnd = row.getIntegerField(RefFlatColumns.TX_END.name());
final int codingStart = row.getIntegerField(RefFlatColumns.CDS_START.name()) + 1;
final int codingEnd = row.getIntegerField(RefFlatColumns.CDS_END.name());
final Transcript tx =
gene.addTranscript(
transcriptName,
transcriptionStart,
transcriptionEnd,
codingStart,
codingEnd,
exonCount);
for (int i = 0; i < exonCount; ++i) {
final Exon e = tx.addExon(Integer.parseInt(exonStarts[i]) + 1, Integer.parseInt(exonEnds[i]));
if (e.start > e.end) {
throw new AnnotationException("Exon has 0 or negative extent for " + transcriptDescription);
}
if (i > 0 && tx.exons[i - 1].end >= tx.exons[i].start) {
throw new AnnotationException("Exons overlap for " + transcriptDescription);
}
}
return tx;
}
private Gene makeGeneFromRefFlatLines(
final List<TabbedTextFileWithHeaderParser.Row> transcriptLines) {
final String geneName = transcriptLines.get(0).getField(RefFlatColumns.GENE_NAME.name());
final String strandStr = transcriptLines.get(0).getField(RefFlatColumns.STRAND.name());
final boolean negative = strandStr.equals("-");
final String chromosome = transcriptLines.get(0).getField(RefFlatColumns.CHROMOSOME.name());
// Figure out the extend of the gene
int start = Integer.MAX_VALUE;
int end = Integer.MIN_VALUE;
for (final TabbedTextFileWithHeaderParser.Row row : transcriptLines) {
start = Math.min(start, row.getIntegerField(RefFlatColumns.TX_START.name()) + 1);
end = Math.max(end, row.getIntegerField(RefFlatColumns.TX_END.name()));
}
final Gene gene = new Gene(chromosome, start, end, negative, geneName);
for (final TabbedTextFileWithHeaderParser.Row row : transcriptLines) {
if (!strandStr.equals(row.getField(RefFlatColumns.STRAND.name()))) {
throw new AnnotationException("Strand disagreement in refFlat file for gene " + geneName);
}
if (!chromosome.equals(row.getField(RefFlatColumns.CHROMOSOME.name()))) {
throw new AnnotationException(
"Chromosome disagreement("
+ chromosome
+ " != "
+ row.getField(RefFlatColumns.CHROMOSOME.name())
+ ") in refFlat file for gene "
+ geneName);
}
// This adds it to the Gene also
final Transcript tx = makeTranscriptFromRefFlatLine(gene, row);
}
return gene;
}