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Replaced a useless getInt with a skipInt to remove 1/4 of the initial seek time in the BAM Index.

This commit is contained in:
Yossi Farjoun 2012-12-12 15:26:38 -05:00
parent 62eaffdf0a
commit 5e66109268
1 changed files with 5 additions and 1 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
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@ -282,7 +282,7 @@ public class GATKBAMIndex {
final int nBins = readInteger(); final int nBins = readInteger();
// System.out.println("# nBins: " + nBins); // System.out.println("# nBins: " + nBins);
for (int j = 0; j < nBins; j++) { for (int j = 0; j < nBins; j++) {
final int bin = readInteger(); skipInteger();
final int nChunks = readInteger(); final int nChunks = readInteger();
// System.out.println("# bin[" + j + "] = " + bin + ", nChunks = " + nChunks); // System.out.println("# bin[" + j + "] = " + bin + ", nChunks = " + nChunks);
skipBytes(16 * nChunks); skipBytes(16 * nChunks);
@ -334,6 +334,10 @@ public class GATKBAMIndex {
return buffer.getInt(); return buffer.getInt();
} }
private void skipInteger() {
skipBytes(INT_SIZE_IN_BYTES);
}
/** /**
* Reads an array of <count> longs from the file channel, returning the results as an array. * Reads an array of <count> longs from the file channel, returning the results as an array.
* @param count Number of longs to read. * @param count Number of longs to read.