/**
* Returns the platform associated with the provided read's read group.
*
* @param read read whose platform information to retrieve
* @param header SAM header containing read groups
* @return the platform for the provided read's read group as a String, or null if the read has no
* read group.
*/
public static String getPlatform(final GATKRead read, final SAMFileHeader header) {
final SAMReadGroupRecord readGroup = getSAMReadGroupRecord(read, header);
return readGroup != null ? readGroup.getPlatform() : null;
}
@Override
public void onTraversalDone(Integer sum) {
final GATKReport report = new GATKReport();
report.addTable(TABLE_NAME, "Table of read group properties", 12);
GATKReportTable table = report.getTable(TABLE_NAME);
DateFormat dateFormatter = DateFormat.getDateInstance(DateFormat.SHORT);
table.addColumn("readgroup");
// * Emits a GATKReport containing read group, sample, library, platform, center, median insert
// size and
// * median read length for each read group in every BAM file.
table.addColumn("sample", "%s");
table.addColumn("library", "%s");
table.addColumn("platform", "%s");
table.addColumn("center", "%s");
table.addColumn("date", "%s");
table.addColumn("has.any.reads");
table.addColumn("is.paired.end");
table.addColumn("n.reads.analyzed", "%d");
table.addColumn("simple.read.type", "%s");
table.addColumn("median.read.length");
table.addColumn("median.insert.size");
for (final SAMReadGroupRecord rg : getToolkit().getSAMFileHeader().getReadGroups()) {
final String rgID = rg.getId();
table.addRowID(rgID, true);
PerReadGroupInfo info = readGroupInfo.get(rgID);
// we are paired if > 25% of reads are paired
final boolean isPaired = info.nReadsPaired / (1.0 * (info.nReadsSeen + 1)) > 0.25;
final boolean hasAnyReads = info.nReadsSeen > 0;
final int readLength = info.readLength.getMedian(0);
setTableValue(table, rgID, "sample", rg.getSample());
setTableValue(table, rgID, "library", rg.getLibrary());
setTableValue(table, rgID, "platform", rg.getPlatform());
setTableValue(table, rgID, "center", rg.getSequencingCenter());
try {
setTableValue(
table,
rgID,
"date",
rg.getRunDate() != null ? dateFormatter.format(rg.getRunDate()) : "NA");
} catch (NullPointerException e) {
// TODO: remove me when bug in Picard is fixed that causes NPE when date isn't present
setTableValue(table, rgID, "date", "NA");
}
setTableValue(table, rgID, "has.any.reads", hasAnyReads);
setTableValue(table, rgID, "is.paired.end", isPaired);
setTableValue(table, rgID, "n.reads.analyzed", info.nReadsSeen);
setTableValue(
table,
rgID,
"simple.read.type",
hasAnyReads ? String.format("%dx%d", isPaired ? 2 : 1, readLength) : "NA");
setTableValue(table, rgID, "median.read.length", hasAnyReads ? readLength : "NA");
setTableValue(
table,
rgID,
"median.insert.size",
hasAnyReads && isPaired ? info.insertSize.getMedian(0) : "NA");
}
report.print(out);
}