public FastaIndexedSequence(String path) throws IOException {
this.path = path;
contentLength = ParsingUtils.getContentLength(path);
String indexPath = path + ".fai";
// The check below is not useful in the files have been copied or moved, which is always the
// case for our hosted
// genomes. It causes lots of spurious warnings
// if(ParsingUtils.getLastModified(path) > ParsingUtils.getLastModified(indexPath)){
// log.warn("Index file for " + path + " is older than the file it indexes");
// }
index = new FastaIndex(indexPath);
chromoNamesList = new ArrayList<String>(index.getSequenceNames());
}
/**
* Return the sequence for the query interval as a byte array. Coordinates are "ucsc" style (0
* based)
*
* <p>Example: 5 bases per line, 6 bytes per line
*
* <p>Bases 0 1 2 3 4 * | 5 6 7 8 9 * | 10 11 12 13 14 * etc Offset 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4
* Bytes 0 1 2 3 4 5 | 6 7 8 9 10 | 11 12 13 14 15 16
*
* <p>query 9 - 13 start line = 1 base0 = 1*5 = 5 offset = (9 - 5) = 4 start byte = (1*6) + 3 = 10
* end line = 2
*
* @param chr
* @param qstart
* @param qend
* @return
*/
public byte[] getSequence(String chr, int qstart, int qend) {
FastaIndex.FastaSequenceIndexEntry idxEntry = index.getIndexEntry(chr);
if (idxEntry == null) {
return null;
}
try {
final int start = Math.max(0, qstart); // qstart should never be < 0
final int end = Math.min((int) idxEntry.getSize(), qend);
final int bytesPerLine = idxEntry.getBytesPerLine();
final int basesPerLine = idxEntry.getBasesPerLine();
int nEndBytes = bytesPerLine - basesPerLine;
int startLine = start / basesPerLine;
int endLine = end / basesPerLine;
int base0 = startLine * basesPerLine; // Base at beginning of start line
int offset = start - base0;
final long position = idxEntry.getPosition();
long startByte = position + startLine * bytesPerLine + offset;
int base1 = endLine * basesPerLine;
int offset1 = end - base1;
long endByte = Math.min(contentLength, position + endLine * bytesPerLine + offset1);
if (startByte >= endByte) {
return null;
}
// Read all the bytes in the range. This will include endline characters
byte[] allBytes = readBytes(startByte, endByte);
// Create the array for the sequence -- this will be "allBytes" without the endline
// characters.
ByteArrayOutputStream bos = new ByteArrayOutputStream(end - start);
int srcPos = 0;
int desPos = 0;
// Copy first line
final int allBytesLength = allBytes.length;
if (offset > 0) {
int nBases = Math.min(end - start, basesPerLine - offset);
bos.write(allBytes, srcPos, nBases);
srcPos += (nBases + nEndBytes);
desPos += nBases;
}
while (srcPos < allBytesLength) {
int nBases = Math.min(basesPerLine, allBytesLength - srcPos);
bos.write(allBytes, srcPos, nBases);
srcPos += (nBases + nEndBytes);
desPos += nBases;
}
return bos.toByteArray();
} catch (IOException e) {
e
.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
return null;
}
}
@Override
public int getChromosomeLength(String chrname) {
return index.getSequenceSize(chrname);
}
