/** * Read an int length, and then a String of that length * @param devourNull if true, the length include a null terminator, which is read and discarded */ public String readLengthAndString(final boolean devourNull) { int length = readInt(); if (devourNull) { --length; } final String ret = readString(length); if (devourNull) { readByte(); } return ret; }
/** * Read an int length, and then a String of that length * @param devourNull if true, the length include a null terminator, which is read and discarded */ public String readLengthAndString(final boolean devourNull) { int length = readInt(); if (devourNull) { --length; } final String ret = readString(length); if (devourNull) { readByte(); } return ret; }
/** * Read an int length, and then a String of that length * @param devourNull if true, the length include a null terminator, which is read and discarded */ public String readLengthAndString(final boolean devourNull) { int length = readInt(); if (devourNull) { --length; } final String ret = readString(length); if (devourNull) { readByte(); } return ret; }
@Test public void testReadAndWriteString() throws IOException { final String value = "Test String to Write"; //Writing to file final File outputFile = File.createTempFile(TEST_BASENAME, ".bin"); outputFile.deleteOnExit(); final OutputStream stream = new FileOutputStream(outputFile); final BinaryCodec codec = new BinaryCodec(stream); codec.writeString(value, true, false); codec.close(); //Reading from file final InputStream instream = new FileInputStream(outputFile); final BinaryCodec readCodec = new BinaryCodec(instream); final int stringLength = readCodec.readInt(); Assert.assertEquals(value.length(), stringLength); final String s = readCodec.readString(stringLength); Assert.assertEquals(value, s); readCodec.close(); }
private static SAMSequenceRecord readSequenceRecord(final BinaryCodec stream, final String source) { final int nameLength = stream.readInt(); if (nameLength <= 1) { throw new SAMFormatException("Invalid BAM file header: missing sequence name in file " + source); } final String sequenceName = stream.readString(nameLength - 1); // Skip the null terminator stream.readByte(); final int sequenceLength = stream.readInt(); return new SAMSequenceRecord(SAMSequenceRecord.truncateSequenceName(sequenceName), sequenceLength); }
/** * Reads a single binary sequence record from the file or stream * @param source Note that this is used only for reporting errors. */ private static SAMSequenceRecord readSequenceRecord(final BinaryCodec stream, final String source) { final int nameLength = stream.readInt(); if (nameLength <= 1) { throw new SAMFormatException("Invalid BAM file header: missing sequence name in file " + source); } final String sequenceName = stream.readString(nameLength - 1); // Skip the null terminator stream.readByte(); final int sequenceLength = stream.readInt(); return new SAMSequenceRecord(SAMSequenceRecord.truncateSequenceName(sequenceName), sequenceLength); }
/** * Reads a single binary sequence record from the file or stream * @param source Note that this is used only for reporting errors. */ private static SAMSequenceRecord readSequenceRecord(final BinaryCodec stream, final String source) { final int nameLength = stream.readInt(); if (nameLength <= 1) { throw new SAMFormatException("Invalid BAM file header: missing sequence name in file " + source); } final String sequenceName = stream.readString(nameLength - 1); // Skip the null terminator stream.readByte(); final int sequenceLength = stream.readInt(); return new SAMSequenceRecord(SAMSequenceRecord.truncateSequenceName(sequenceName), sequenceLength); }
/** * Reads a single binary sequence record from the file or stream * @param source Note that this is used only for reporting errors. */ private static SAMSequenceRecord readSequenceRecord(final BinaryCodec stream, final String source) { final int nameLength = stream.readInt(); if (nameLength <= 1) { throw new SAMFormatException("Invalid BAM file header: missing sequence name in file " + source); } final String sequenceName = stream.readString(nameLength - 1); // Skip the null terminator stream.readByte(); final int sequenceLength = stream.readInt(); return new SAMSequenceRecord(SAMSequenceRecord.truncateSequenceName(sequenceName), sequenceLength); }
/** * Reads a single binary sequence record from the file or stream * @param source Note that this is used only for reporting errors. */ private static SAMSequenceRecord readSequenceRecord(final BinaryCodec stream, final String source) { final int nameLength = stream.readInt(); if (nameLength <= 1) { throw new SAMFormatException("Invalid BAM file header: missing sequence name in file " + source); } final String sequenceName = stream.readString(nameLength - 1); // Skip the null terminator stream.readByte(); final int sequenceLength = stream.readInt(); return new SAMSequenceRecord(SAMSequenceRecord.truncateSequenceName(sequenceName), sequenceLength); }
@Test public void testReadAndWriteMutlitpleData() throws IOException{ final float fValue = 42.5F; final String sValue = "TestString"; final File outputFile = File.createTempFile(TEST_BASENAME, ".bin"); outputFile.deleteOnExit(); final OutputStream stream = new FileOutputStream(outputFile); final BinaryCodec codec = new BinaryCodec(stream); codec.writeFloat(fValue); codec.writeString(sValue, true, false); codec.close(); //Reading from file final InputStream instream = new FileInputStream(outputFile); final BinaryCodec readCodec = new BinaryCodec(instream); Assert.assertEquals(fValue, readCodec.readFloat()); final int stringLength = readCodec.readInt(); Assert.assertEquals(sValue, readCodec.readString(stringLength)); readCodec.close(); }
final String textHeader = stream.readString(headerTextLength); final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency);
final String textHeader = stream.readString(headerTextLength); final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency);
final String textHeader = stream.readString(headerTextLength); final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency);
final String textHeader = stream.readString(headerTextLength); final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency);
final String textHeader = stream.readString(headerTextLength); final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency);