protected void advanceSubIterator() {
try {
if (mCurrentOffset < mOffsets.size()) {
if (mOffsets.start(mCurrentOffset) != mPreviousVirtualOffsetStart) {
// Diagnostic.developerLog("After region " + mCurrentOffset + " " + mCurrentRegion + ",
// opening new reader at offset " +
// VirtualOffsets.offsetToString(mOffsets.start(mCurrentOffset)) + " for region " +
// mOffsets.region(mCurrentOffset));
mReader.seek(mOffsets.start(mCurrentOffset));
mBuffered = false;
// } else {
// Diagnostic.developerLog("After region " + mCurrentOffset + " " + mCurrentRegion + ",
// re-using existing reader for region " + mOffsets.region(mCurrentOffset));
}
mCurrentRegion = mOffsets.region(mCurrentOffset);
final int newTemplate = mSequenceLookup.get(mCurrentRegion.getSequenceName());
if (newTemplate != mCurrentTemplate) {
mPreviousAlignmentStart = Integer.MIN_VALUE;
}
mPreviousVirtualOffsetStart = mOffsets.start(mCurrentOffset);
mCurrentTemplate = newTemplate;
}
mCurrentOffset++;
} catch (IOException e) {
throw new RuntimeIOException(e.getMessage(), e);
}
}
public SingleRestrictionLineReader(File input, TabixIndexReader tir, RegionRestriction region)
throws IOException {
if (region == null) {
throw new NullPointerException();
}
mSequence = region.getSequenceName();
mBeg = region.getStart();
mEnd = region.getEnd();
final BlockCompressedLineReader bclr =
new BlockCompressedLineReader(new BlockCompressedInputStream(input));
mBCPositionReader =
tir.getOptions().mFormat == TabixIndexer.TabixOptions.FORMAT_VCF
? new VcfPositionReader(bclr, tir.getOptions().mSkip)
: new GenericPositionReader(bclr, tir.getOptions());
mRange = tir.getFilePointers(region);
if (mRange != null) {
mBCPositionReader.seek(mRange.start(0));
}
}
