private BAMFileSpan getSpanContained(int sequenceIndex, long start, long end) { if (recordRangeInfo.getTotalRecordRangeLength() <= 0) { throw new RuntimeException("Cannot create file span - SRA file is empty"); } long sequenceOffset = recordRangeInfo.getReferenceOffsets().get(sequenceIndex); long sequenceLength = recordRangeInfo.getReferenceLengthsAligned().get(sequenceIndex); if (end == -1) { end = sequenceLength; } if (start > sequenceLength) { throw new IllegalArgumentException("Sequence start position is larger than its length"); } if (end > sequenceLength) { throw new IllegalArgumentException("Sequence end position is larger than its length"); } return new BAMFileSpan(new Chunk(sequenceOffset + start, sequenceOffset + end)); } }
private BAMFileSpan getSpanContained(int sequenceIndex, long start, long end) { if (recordRangeInfo.getTotalRecordRangeLength() <= 0) { throw new RuntimeException("Cannot create file span - SRA file is empty"); } long sequenceOffset = recordRangeInfo.getReferenceOffsets().get(sequenceIndex); long sequenceLength = recordRangeInfo.getReferenceLengthsAligned().get(sequenceIndex); if (end == -1) { end = sequenceLength; } if (start > sequenceLength) { throw new IllegalArgumentException("Sequence start position is larger than its length"); } if (end > sequenceLength) { throw new IllegalArgumentException("Sequence end position is larger than its length"); } return new BAMFileSpan(new Chunk(sequenceOffset + start, sequenceOffset + end)); } }
@Override public SAMFileSpan getFilePointerSpanningReads() { if (recordRangeInfo.getTotalRecordRangeLength() <= 0) { throw new RuntimeException("Cannot create file span - SRA file is empty"); } return new BAMFileSpan(new Chunk(0, recordRangeInfo.getTotalRecordRangeLength())); }
@Override public CloseableIterator<SAMRecord> queryUnmapped() { if (recordRangeInfo.getTotalRecordRangeLength() <= 0) { throw new RuntimeException("Cannot create file span - SRA file is empty"); } SAMFileSpan span = new BAMFileSpan(new Chunk(recordRangeInfo.getTotalReferencesLength(), recordRangeInfo.getTotalRecordRangeLength())); return getIterator(span); }
@Override public SAMFileSpan getFilePointerSpanningReads() { if (recordRangeInfo.getTotalRecordRangeLength() <= 0) { throw new RuntimeException("Cannot create file span - SRA file is empty"); } return new BAMFileSpan(new Chunk(0, recordRangeInfo.getTotalRecordRangeLength())); }
@Override public CloseableIterator<SAMRecord> queryUnmapped() { if (recordRangeInfo.getTotalRecordRangeLength() <= 0) { throw new RuntimeException("Cannot create file span - SRA file is empty"); } SAMFileSpan span = new BAMFileSpan(new Chunk(recordRangeInfo.getTotalReferencesLength(), recordRangeInfo.getTotalRecordRangeLength())); return getIterator(span); }