private void readCramRecord() { final CramCompressionRecord cramRecord = new CramCompressionRecord(); super.read(cramRecord); if (APDelta) { currentAlignmentStart += cramRecord.alignmentDelta; } else { currentAlignmentStart = cramRecord.alignmentStart; } if (!spans.containsKey(cramRecord.sequenceId)) { spans.put(cramRecord.sequenceId, new AlignmentSpan(currentAlignmentStart, cramRecord.readLength)); } else { spans.get(cramRecord.sequenceId).addSingle(currentAlignmentStart, cramRecord.readLength); } } }
private void readCramRecord() { final CramCompressionRecord cramRecord = new CramCompressionRecord(); super.read(cramRecord); if (APDelta) { currentAlignmentStart += cramRecord.alignmentDelta; } else { currentAlignmentStart = cramRecord.alignmentStart; } if (!spans.containsKey(cramRecord.sequenceId)) { spans.put(cramRecord.sequenceId, new AlignmentSpan(currentAlignmentStart, cramRecord.readLength)); } else { spans.get(cramRecord.sequenceId).addSingle(currentAlignmentStart, cramRecord.readLength); } } }
reader.read(record); if (record.isSegmentUnmapped() || record.readFeatures == null || record.readFeatures.isEmpty()) continue;
private CramCompressionRecord read(final byte[] dataBytes, final CompressionHeader header, final int refId, final Map<Integer, ByteArrayInputStream> inputMap) throws IOException { try (final ByteArrayInputStream is = new ByteArrayInputStream(dataBytes); final BitInputStream bis = new DefaultBitInputStream(is)) { final CramRecordReader reader = new CramRecordReader(bis, inputMap, header, refId, ValidationStringency.DEFAULT_STRINGENCY); final CramCompressionRecord recordToRead = new CramCompressionRecord(); reader.read(recordToRead); return recordToRead; } }
record.index = i; reader.read(record);
record.index = i; reader.read(record);