本文整理汇总了Java中htsjdk.samtools.SAMRecord.getReadString方法的典型用法代码示例。如果您正苦于以下问题：Java SAMRecord.getReadString方法的具体用法？Java SAMRecord.getReadString怎么用？Java SAMRecord.getReadString使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类htsjdk.samtools.SAMRecord的用法示例。
在下文中一共展示了SAMRecord.getReadString方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: computeDifferentBase
import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
public List<BasePosition> computeDifferentBase(final SAMRecord record)
throws IOException {
if (record.getStart() < min) {
refreshHeadReferenceBuffer(record.getStart());
}
if (record.getEnd() > max) {
refreshTailReferenceBuffer(record.getEnd());
}
ReadBaseProcessor
baseCounter = new ReadBaseProcessor(record.getReadString(), referenceBuffer.getBuffer(), record.getStart(),
min, record.getCigar().getCigarElements(), showClipping, record);
return baseCounter.getMismatchBasePositions();
}
示例2: add
import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
/**
* @param record for processing
* @throws IOException
*/
@Override
public void add(final SAMRecord record) throws IOException {
int start = record.getStart();
int end = record.getEnd();
final List<CigarElement> cigarList = record.getCigar().getCigarElements();
final int flags = record.getFlags();
String head = null;
String tail = null;
if (BamUtil.validateReadParams(flags, cigarList, end, start)) {
coverageAdd(start, end, coverageArray, true);
final String readString = record.getReadString();
if (showClipping) {
final CigarElement first = cigarList.get(0);
final CigarElement last = cigarList.get(cigarList.size() - 1);
if (first.getOperator().equals(CigarOperator.S)) {
start -= first.getLength();
head = readString.substring(0, first.getLength());
}
if (last.getOperator().equals(CigarOperator.S)) {
end += last.getLength();
tail = readString.substring(readString.length() - last.getLength(), readString.length());
}
}
if (start < min) {
refreshHeadReferenceBuffer(start);
}
if (end > max) {
refreshTailReferenceBuffer(end);
}
List<BasePosition> differentBase = computeDifferentBase(readString,
referenceBuffer != null ? referenceBuffer.getBuffer() : null, start, min, cigarList, showClipping,
record);
filter.add(record, start, end, mode == BamTrackMode.FULL ? differentBase : null, head, tail);
}
}