/**
* Read only header info
*
* @return
*/
public VcfHeader readHeader() {
// No more header to read?
if ((nextLine != null) && !nextLine.startsWith("#")) return header;
try {
while (ready()) {
line = readLine();
if (line == null) return null; // End of file?
if (!line.startsWith("#")) {
nextLine = line;
return header; // End of header?
}
header.addLine(line);
}
} catch (IOException e) {
throw new RuntimeException(
"Error reading file '"
+ fileName
+ "'. Line ignored:\n\tLine ("
+ lineNum
+ "):\t'"
+ line
+ "'");
}
return header;
}
/**
* Parse a line from a VCF file
*
* @param line
* @return
*/
protected VcfEntry parseVcfLine(String line) {
try {
if (line.startsWith("#")) {
header.addLine(line); // Header?
} else if ((line.length() > 0) && (!line.startsWith("#")))
return new VcfEntry(this, line, lineNum, parseNow); // Vcf entry?
} catch (Throwable t) {
Gpr.debug("Fatal error reading file '" + fileName + "' (line: " + lineNum + "):\n" + line);
throw new RuntimeException(t);
}
// Could not create a VcfEntry from this line (e.g. header line)
return null;
}
/**
* Get sample names
*
* @return
*/
public List<String> getSampleNames() {
return header.getSampleNames();
}