Java : 什么是 BufferUnderflow Exceptio 使用 Samtools Java API 获取具有特定位置的外来字符串

Question

using Sam-tools Java API how i get seq. between start and end i am write following method it throws Exception . this method write to get Sequences from file .

方法在这里

private static List<SAMRecord> scan(String chromosome, int start, int end) throws IOException {
    List<SAMRecord> records = new ArrayList<SAMRecord>();
    CloseableIterator<SAMRecord> iter = null;
    try {
      iter = inputSam.query(chromosome, start, (start+70), containsbamRecord);
System.out.println("herer : Floe");
      SAMRecord s=iter.next();
      System.out.println("Value Of Start : "+start+"\t"+"VAlue of End : "+(start+70)+"Value Of iter : "+s.getSAMString());

      while (iter.hasNext()) {
        SAMRecord rec = iter.next();
           //System.out.println("Value Of Start : "+start+"\t"+"VAlue of End : "+end+"Value Of iter : "+rec.get);

        records.add(rec);
      }
      return records;
    } catch (Exception e) {
      throw new IOException(e);
    } finally {
      if (iter != null)
        iter.close();
    }
  }

This is Stack Trace Exception Occurred

java.io.IOException: java.nio.BufferUnderflowException
    at WrapperMain.scan(WrapperMain.java:99)
    at WrapperMain.getDataforPosition(WrapperMain.java:119)
    at TzurLookupVariant.main(TzurLookupVariant.java:145)
Caused by: java.nio.BufferUnderflowException
    at java.nio.Buffer.nextGetIndex(Buffer.java:506)
    at java.nio.DirectByteBuffer.getInt(DirectByteBuffer.java:677)
    at net.sf.samtools.AbstractBAMFileIndex$MemoryMappedFileBuffer.readInteger(AbstractBAMFileIndex.java:455)
    at net.sf.samtools.AbstractBAMFileIndex.readInteger(AbstractBAMFileIndex.java:406)
    at net.sf.samtools.AbstractBAMFileIndex.query(AbstractBAMFileIndex.java:266)
    at net.sf.samtools.DiskBasedBAMFileIndex.getSpanOverlapping(DiskBasedBAMFileIndex.java:60)
    at net.sf.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:719)
    at net.sf.samtools.BAMFileReader.query(BAMFileReader.java:369)
    at net.sf.samtools.SAMFileReader.query(SAMFileReader.java:381)
    at WrapperMain.scan(WrapperMain.java:86)
    ... 2 more
java.lang.NullPointerException
    at WrapperMain.getDataPoint(WrapperMain.java:199)
    at WrapperMain.getDataforPosition(WrapperMain.java:129)
    at TzurLookupVariant.main(TzurLookupVariant.java:145)

Answer 1

BufferUnderflowException 的 javadoc 说：

"Unchecked exception thrown when a relative get operation reaches the source buffer's limit."

所以一般的解决方案是避免在没有更多数据的缓冲区上调用 get。

在没有看到您代码的相关部分之前，我们不能比这更具体了。

你说：

... algorithm is correct ...

这可能不是真的，至少在某种程度上是这样。

... when i create new class and make some modification it fire me the exception and now i delete created class but still it throws same Exception ....Why ????

很可能是>>某事<<发生了变化。但也有可能您的问题的根本原因是从那里开始，并且您的应用程序的工作方式存在不确定性。

Java : 什么是 BufferUnderflow Exceptio 使用 Samtools Java API 获取具有特定位置的外来字符串

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