Source:
<code>public CloseableIterator<SAMRecord> queryAlignmentStart(final String sequence, final int start) { long[] filePointers = null; final SAMFileHeader fileHeader = getFileHeader(); final int referenceIndex = fileHeader.getSequenceIndex(sequence); if (referenceIndex != -1) { final BAMIndex fileIndex = getIndex(); final BAMFileSpan fileSpan = fileIndex.getSpanOverlapping( referenceIndex, start, -1); filePointers = fileSpan != null ? fileSpan.toCoordinateArray() : null; } if (filePointers == null || filePointers.length == 0) return emptyIterator; <START> Container c; <END> final SeekableStream s = getSeekableStreamOrFailWithRTE(); for (int i = 0; i < filePointers.length; i += 2) { final long containerOffset = filePointers[i] >>> 16; try { if (s.position() != containerOffset || it.container == null) { s.seek(containerOffset); c = ContainerIO.readContainerHeader(it.getCramHeader().getVersion().major, s); if (c.alignmentStart + c.alignmentSpan > start) { s.seek(containerOffset); it.jumpWithinContainerToPos(fileHeader.getSequenceIndex(sequence), start); return new IntervalIterator(it, new QueryInterval(referenceIndex, start, -1)); } } else { c = it.container; if (c.alignmentStart + c.alignmentSpan > start) { it.jumpWithinContainerToPos(fileHeader.getSequenceIndex(sequence), start); return new IntervalIterator(it, new QueryInterval(referenceIndex, start, -1)); } } } catch (final IOException e) { throw new RuntimeException(e); } } return it; }</code><technical_language>Variable names c s extremely hard follow code, declaration are. please code change variable names reference objects more descriptive (ex. stream container)</technical_language>

Target:
public CloseableIterator<SAMRecord> queryAlignmentStart(final String sequence, final int start) { long[] filePointers = null; final SAMFileHeader fileHeader = getFileHeader(); final int referenceIndex = fileHeader.getSequenceIndex(sequence); if (referenceIndex != -1) { final BAMIndex fileIndex = getIndex(); final BAMFileSpan fileSpan = fileIndex.getSpanOverlapping( referenceIndex, start, -1); filePointers = fileSpan != null ? fileSpan.toCoordinateArray() : null; } if (filePointers == null || filePointers.length == 0) return emptyIterator; Container container; final SeekableStream seekableStream = getSeekableStreamOrFailWithRTE(); for (int i = 0; i < filePointers.length; i += 2) { final long containerOffset = filePointers[i] >>> 16; try { if (seekableStream.position() != containerOffset || iterator.container == null) { seekableStream.seek(containerOffset); container = ContainerIO.readContainerHeader(iterator.getCramHeader().getVersion().major, seekableStream); if (container.alignmentStart + container.alignmentSpan > start) { seekableStream.seek(containerOffset); iterator.jumpWithinContainerToPos(fileHeader.getSequenceIndex(sequence), start); return new IntervalIterator(iterator, new QueryInterval(referenceIndex, start, -1)); } } else { container = iterator.container; if (container.alignmentStart + container.alignmentSpan > start) { iterator.jumpWithinContainerToPos(fileHeader.getSequenceIndex(sequence), start); return new IntervalIterator(iterator, new QueryInterval(referenceIndex, start, -1)); } } } catch (final IOException e) { throw new RuntimeException(e); } } return iterator; }