/** * Reads a boolean off the input stream, represented as a byte with value 1 or 0 * * @return boolean */ public boolean readBoolean() { return (((int)readByte()) == 1); }
/** * Reads a boolean off the input stream, represented as a byte with value 1 or 0 * * @return boolean */ public boolean readBoolean() { return (((int)readByte()) == 1); }
/** * Reads a boolean off the input stream, represented as a byte with value 1 or 0 * * @return boolean */ public boolean readBoolean() { return (((int)readByte()) == 1); }
/** * 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; }
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); }