/** Parse fields */
void parseFields() {
if (fields != null) return;
try {
fields = new HashMap<String, String>();
if (values.isEmpty()) return; // Values are missing? Nothing to do
String fieldNames[] = vcfEntry.getFormat().split(":");
String fieldValues[] = values.split(":");
int min = Math.min(fieldValues.length, fieldNames.length);
for (int i = 0; i < min; i++) {
String name = fieldNames[i];
String value = fieldValues[i];
fields.put(name, value);
if (name.equals("GT")) parseGt(value);
else if (name.equals("PL")) parsePl(value);
else if (name.equals("GQ")) gQuality = Gpr.parseDoubleSafe(value);
}
} catch (Exception e) {
throw new RuntimeException(
"Error parsing fields on line:\n\tFormat: '"
+ vcfEntry.getFormat()
+ "'\n\tValues: '"
+ values
+ "'",
e);
}
}
/**
* Get genotype string by index
*
* <p>WARNING: If the genotype is missing, it returns an empty string. E.g.: './.' ->
* getGenotype(0) = ""
*
* @return
*/
public String getGenotype(int idx) {
parseFields(); // Lazy parse
if (genotype == null) return ""; // Missing genotype
int num = genotype[idx];
if (num < 0) return ""; // Missing genotype
return num == 0 ? vcfEntry.getRef() : vcfEntry.getAlts()[num - 1];
}
/**
* Is any genotype different than REF? Note: This is calculated for the most likely genotype (GT
* field)
*
* @return
*/
public boolean isVariant() {
if (values.isEmpty()) return false;
parseFields(); // Lazy parse
if (genotype != null) {
// Any genotype is different than REF? => This is a variant
for (int i = 0; i < genotype.length; i++) if (genotype[i] > 0) return true;
return false;
}
return vcfEntry.isVariant();
}
/**
* Is the most likely genotype homozygous?
*
* @return
*/
public boolean isHomozygous() {
parseFields(); // Lazy parse
if (genotype != null) {
// Any genotype is different? => not homozygous
for (int i = 1; i < genotype.length; i++) if (genotype[i] != genotype[i - 1]) return false;
return true; // Homozygous
}
return vcfEntry.isBiAllelic();
}
/**
* Parse GT field
*
* @param value
*/
void parseGt(String value) {
String gtStr[] = null;
if (value.indexOf('|') >= 0) {
gtStr = value.split("\\|");
phased = true; // Phased
} else {
gtStr = value.split("/");
phased = false; // Unphased
}
// Create fields
genotype = new int[gtStr.length];
for (int i = 0; i < genotype.length; i++)
if (gtStr[i].isEmpty() || gtStr[i].equals("."))
genotype[i] = -1; // Genotype '-1' means missing values
else {
genotype[i] = Gpr.parseIntSafe(gtStr[i]);
// Sanity check
if ((genotype[i] - 1) >= vcfEntry.getAlts().length) {
boolean plural = vcfEntry.getAlts().length > 1;
throw new RuntimeException(
"Error: Bad genotype field '"
+ value
+ "'. Genotype says '"
+ genotype[i]
+ "' but there "
+ (plural ? "are" : "is")
+ " only '"
+ vcfEntry.getAlts().length
+ "' allele"
+ (plural ? "s" : "")
+ " ('"
+ vcfEntry.getAltsStr()
+ "').");
}
}
}
/**
* Return genotypes as string (e.g. "A/C")
*
* @return
*/
public String getGenotypeStr() {
parseFields(); // Lazy parse
StringBuilder sb = new StringBuilder();
if (genotype != null) {
for (int i = 0; i < genotype.length; i++) {
int num = genotype[i];
String gen = ".";
if (num == 0) gen = vcfEntry.getRef();
else if (num > 0) gen = vcfEntry.getAlts()[num - 1];
sb.append(gen);
if (i < (genotype.length - 1)) {
if (isPhased()) sb.append("|");
else sb.append("/");
}
}
}
return sb.toString();
}
/**
* Add a name=value pair WARNING: This method does NOT change the FORMAT field. Use
* VcfEntry.addFormat() method
*
* @param name
* @param value
*/
public void add(String name, String value) {
// Sanity check value
if ((value.indexOf(' ') >= 0) //
|| (value.indexOf('\t') >= 0) //
|| (value.indexOf('=') >= 0) //
)
throw new RuntimeException(
"Error: Attempt to add a value containin illegal characters: no white-space, semi-colons, or equals-signs permitted\n\tname : '"
+ name
+ "'\n\tvalue : '"
+ value
+ "'");
// Sanity check format
if (vcfEntry.getFormat().indexOf(name) < 0)
throw new RuntimeException(
"Error Attempt to add a field (name="
+ name
+ ") that is not present in FORMAT field. Use VcfEntry.addFormat() method first!");
// Finally, add the values
values += (values.endsWith(":") ? "" : ":") + value; // Add to value string
if (fields != null) fields.put(name, value); // Add value to hash (if needed)
}
