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/*
* The MIT License
*
* Copyright (c) 2010 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools.util;
/**
* Static for manipulating virtual file pointers in BGZF files.
*/
public class BlockCompressedFilePointerUtil {
private static final int SHIFT_AMOUNT = 16;
private static final int OFFSET_MASK = 0xffff;
private static final long ADDRESS_MASK = 0xFFFFFFFFFFFFL;
public static final long MAX_BLOCK_ADDRESS = ADDRESS_MASK;
public static final int MAX_OFFSET = OFFSET_MASK;
/**
* @param vfp1
* @param vfp2
* @return negative if vfp1 is earlier in file than vfp2, positive if it is later, 0 if equal.
*/
public static int compare(final long vfp1, final long vfp2) {
if (vfp1 == vfp2) return 0;
// When treating as unsigned, negative number is > positive.
if (vfp1 < 0 && vfp2 >= 0) return 1;
if (vfp1 >= 0 && vfp2 < 0) return -1;
// Either both negative or both non-negative, so regular comparison works.
if (vfp1 < vfp2) return -1;
return 1; // vfp1 > vfp2
}
/**
* @return true if vfp2 points to somewhere in the same BGZF block, or the one immediately following vfp1's BGZF block.
*/
public static boolean areInSameOrAdjacentBlocks(final long vfp1, final long vfp2) {
final long block1 = getBlockAddress(vfp1);
final long block2 = getBlockAddress(vfp2);
return (block1 == block2 || block1 + 1 == block2);
}
/**
* @param blockAddress File offset of start of BGZF block.
* @return Virtual file pointer that points to the start of a BGZF block.
*/
public static long makeFilePointer(final long blockAddress) {
return makeFilePointer(blockAddress, 0);
}
/**
* @param blockAddress File offset of start of BGZF block.
* @param blockOffset Offset into uncompressed block.
* @return Virtual file pointer that embodies the input parameters.
*/
public static long makeFilePointer(final long blockAddress, final int blockOffset) {
if (blockOffset < 0) {
throw new IllegalArgumentException("Negative blockOffset " + blockOffset + " not allowed.");
}
if (blockAddress < 0) {
throw new IllegalArgumentException("Negative blockAddress " + blockAddress + " not allowed.");
}
if (blockOffset > MAX_OFFSET) {
throw new IllegalArgumentException("blockOffset " + blockOffset + " too large.");
}
if (blockAddress > MAX_BLOCK_ADDRESS) {
throw new IllegalArgumentException("blockAddress " + blockAddress + " too large.");
}
return blockAddress << SHIFT_AMOUNT | blockOffset;
}
/**
* @param virtualFilePointer
* @return File offset of start of BGZF block for this virtual file pointer.
*/
public static long getBlockAddress(final long virtualFilePointer) {
return (virtualFilePointer >> SHIFT_AMOUNT) & ADDRESS_MASK;
}
/**
* @param virtualFilePointer
* @return Offset into uncompressed block for this virtual file pointer.
*/
public static int getBlockOffset(final long virtualFilePointer) {
return (int) (virtualFilePointer & OFFSET_MASK);
}
public static String asString(final long vfp) {
return String.format("%d(0x%x): (block address: %d, offset: %d)", vfp, vfp, getBlockAddress(vfp), getBlockOffset(vfp));
}
}
