public void setValidationStringency(final ValidationStringency validationStringency) { codec.setValidationStringency(validationStringency); } }
public void setValidationStringency(final ValidationStringency validationStringency) { codec.setValidationStringency(validationStringency); } }
private void readHeader() { final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency); mFileHeader = headerCodec.decode(mReader, (mFile != null ? mFile.toString() : null)); advanceLine(); }
private void readHeader() { final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency); mFileHeader = headerCodec.decode(mReader, (mFile != null ? mFile.toString() : null)); advanceLine(); }
private void readHeader() { final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency); mFileHeader = headerCodec.decode(mReader, (mFile != null? mFile.toString(): null)); advanceLine(); }
public final SAMFileHeader clone() { final SAMTextHeaderCodec codec = new SAMTextHeaderCodec(); codec.setValidationStringency(ValidationStringency.SILENT); final StringWriter stringWriter = new StringWriter(); codec.encode(stringWriter, this); return codec.decode(new StringLineReader(stringWriter.toString()), "SAMFileHeader.clone"); } }
@Override public final SAMFileHeader clone() { final SAMTextHeaderCodec codec = new SAMTextHeaderCodec(); codec.setValidationStringency(ValidationStringency.SILENT); return codec.decode(BufferedLineReader.fromString(getSAMString()), "SAMFileHeader.clone"); }
@Override public final SAMFileHeader clone() { final SAMTextHeaderCodec codec = new SAMTextHeaderCodec(); codec.setValidationStringency(ValidationStringency.SILENT); return codec.decode(BufferedLineReader.fromString(getSAMString()), "SAMFileHeader.clone"); }
@Test(dataProvider = "DataForWrongTagTests", expectedExceptions = SAMFormatException.class) public void testValidationStringencyStrict(String stringHeader) { SAMTextHeaderCodec codec = new SAMTextHeaderCodec(); codec.setValidationStringency(ValidationStringency.STRICT); codec.decode(BufferedLineReader.fromString(stringHeader), null); }
@Test(dataProvider = "DataForWrongTagTests") public void testValidationStringencyLenientAndSilent(String stringHeader) { SAMTextHeaderCodec codec = new SAMTextHeaderCodec(); codec.setValidationStringency(ValidationStringency.LENIENT); SAMFileHeader headerLenient = codec.decode(BufferedLineReader.fromString(stringHeader), null); Assert.assertTrue(headerLenient.getSortOrder().equals(SAMFileHeader.SortOrder.unknown)); codec.setValidationStringency(ValidationStringency.SILENT); SAMFileHeader headerSilent = codec.decode(BufferedLineReader.fromString(stringHeader), null); Assert.assertTrue(headerSilent.getSortOrder().equals(SAMFileHeader.SortOrder.unknown)); } }
final String textHeader = stream.readString(headerTextLength); final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency); final SAMFileHeader samFileHeader = headerCodec.decode(new StringLineReader(textHeader), source);
final String textHeader = stream.readString(headerTextLength); final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency); final SAMFileHeader samFileHeader = headerCodec.decode(BufferedLineReader.fromString(textHeader), source);
final String textHeader = stream.readString(headerTextLength); final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency); final SAMFileHeader samFileHeader = headerCodec.decode(new StringLineReader(textHeader), source);
final String textHeader = stream.readString(headerTextLength); final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency); final SAMFileHeader samFileHeader = headerCodec.decode(BufferedLineReader.fromString(textHeader), source);
codec.setValidationStringency(ValidationStringency.STRICT); final SAMFileHeader parsedHeader = codec.decode( new StringLineReader(headerString), null);
final String textHeader = stream.readString(headerTextLength); final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency); final SAMFileHeader samFileHeader = headerCodec.decode(BufferedLineReader.fromString(textHeader), source);
codec.setValidationStringency(ValidationStringency.STRICT); final SAMFileHeader parsedHeader = codec.decode( new StringLineReader(headerString), null);