本文整理汇总了Java中htsjdk.samtools.SAMRecord.getStart方法的典型用法代码示例。如果您正苦于以下问题：Java SAMRecord.getStart方法的具体用法？Java SAMRecord.getStart怎么用？Java SAMRecord.getStart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.getStart方法的3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: getReadsFromFile
import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
private Map<Sequence, List<SAMRecord>> getReadsFromFile(final Chromosome chromosome, final Track<Sequence> track,
final BamFile bamFile, final List<Sequence> blocks)
throws IOException {
final Map<Sequence, List<SAMRecord>> records = new HashMap<>();
try (SamReader reader = makeSamReader(bamFile, Collections.singletonList(chromosome),
chromosome.getReferenceId())) {
LOG.debug(getMessage(MessagesConstants.DEBUG_FILE_OPENING, bamFile.getPath()));
String chromosomeName = chromosome.getName();
final int startIndex = track.getStartIndex();
final int endIndex = track.getEndIndex();
if (reader.getFileHeader().getSequence(chromosomeName) == null) {
chromosomeName = Utils.changeChromosomeName(chromosomeName);
}
final SAMRecordIterator iterator = reader.queryOverlapping(chromosomeName, startIndex, endIndex);
LOG.debug(getMessage(MessagesConstants.DEBUG_GET_ITERATOR_QUERY, iterator.toString()));
while (iterator.hasNext()) {
final SAMRecord samRecord = iterator.next();
//if read unmapped
if (!samRecord.getSAMFlags().contains(SAMFlag.READ_UNMAPPED) && !samRecord.getCigar().isEmpty() &&
samRecord.getEnd() > samRecord.getStart()) {
addRecordToBlock(blocks, records, samRecord);
}
}
}
return records;
}
示例3: 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);
}
}