本文整理汇总了Java中htsjdk.samtools.SAMRecord.getUnclippedStart方法的典型用法代码示例。如果您正苦于以下问题：Java SAMRecord.getUnclippedStart方法的具体用法？Java SAMRecord.getUnclippedStart怎么用？Java SAMRecord.getUnclippedStart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.getUnclippedStart方法的1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: calcBAQFromHMM
import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
public BAQCalculationResult calcBAQFromHMM(SAMRecord read, RefContentProvider refContentProvider) {
// start is alignment start - band width / 2 - size of first I element, if there is one. Stop is similar
int offset = getBandWidth() / 2;
long readStart = includeClippedBases ? read.getUnclippedStart() : read.getAlignmentStart();
long start = Math.max(readStart - offset - ReadUtils.getFirstInsertionOffset(read), 0);
long stop = (includeClippedBases ? read.getUnclippedEnd() : read.getAlignmentEnd()) + offset + ReadUtils.getLastInsertionOffset(read);
if ( stop > refContentProvider.getSamSequenceDictionary().getSequence(read.getReferenceName()).getSequenceLength() ) {
return null;
} else {
// now that we have the start and stop, get the reference sequence covering it
GenomeLoc locus = new GenomeLoc(read.getReferenceName(), read.getReferenceIndex(), (int)start, (int)stop);
byte[] refSeq = refContentProvider.getReferenceContext(locus).getBases();
return calcBAQFromHMM(read, refSeq, (int)(start - readStart));
}
}