本文整理汇总了Java中htsjdk.samtools.SAMRecord.getInferredInsertSize方法的典型用法代码示例。如果您正苦于以下问题：Java SAMRecord.getInferredInsertSize方法的具体用法？Java SAMRecord.getInferredInsertSize怎么用？Java SAMRecord.getInferredInsertSize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.getInferredInsertSize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: transfer
import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
/**
* Write the record.
*
* @param alignment SAMRecord.
*/
public BasicSamRecord transfer(final SAMRecord alignment) {
String readName = alignment.getReadName();
int flags = alignment.getFlags();
int contigId = alignment.getReferenceIndex();
if (contigId == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
contigId = FAKE_CONTIG_ID;
}
String contigName = alignment.getReferenceName();
int position = alignment.getAlignmentStart();
int mapQ = alignment.getMappingQuality();
String cigar = alignment.getCigarString();
int mateContigId = alignment.getMateReferenceIndex();
if (mateContigId == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
mateContigId = FAKE_CONTIG_ID;
}
String mateContigName = alignment.getMateReferenceName();
int matePosition = alignment.getMateAlignmentStart();
int inferredSize = alignment.getInferredInsertSize();
byte[] sequence = alignment.getReadString().getBytes();
byte[] quality = alignment.getBaseQualityString().getBytes();
List<SAMRecord.SAMTagAndValue> attributes = alignment.getAttributes();
List<String> encodedTags = new ArrayList<>(attributes.size());
for (SAMRecord.SAMTagAndValue attribute : attributes) {
encodedTags.add(tagCodec.encode(attribute.tag, attribute.value));
}
// 在这里统一不压缩，压缩操作是由scala代码中的执行引擎统一调配的。
return BasicSamRecord.apply(false, readName, flags, contigId, contigName, position, mapQ,
cigar, mateContigId, mateContigName, matePosition, inferredSize,
sequence, quality, encodedTags);
}
示例2: hasWellDefinedFragmentSize
import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
/**
* Can the adaptor sequence of read be reliably removed from the read based on the alignment of
* read and its mate?
*
* @param read the read to check
* @return true if it can, false otherwise
*/
public static boolean hasWellDefinedFragmentSize(final SAMRecord read) {
if ( read.getInferredInsertSize() == 0 )
// no adaptors in reads with mates in another chromosome or unmapped pairs
return false;
if ( ! read.getReadPairedFlag() )
// only reads that are paired can be adaptor trimmed
return false;
if ( read.getReadUnmappedFlag() || read.getMateUnmappedFlag() )
// only reads when both reads are mapped can be trimmed
return false;
// if ( ! read.getProperPairFlag() )
// // note this flag isn't always set properly in BAMs, can will stop us from eliminating some proper pairs
// // reads that aren't part of a proper pair (i.e., have strange alignments) can't be trimmed
// return false;
if ( read.getReadNegativeStrandFlag() == read.getMateNegativeStrandFlag() )
// sanity check on getProperPairFlag to ensure that read1 and read2 aren't on the same strand
return false;
if ( read.getReadNegativeStrandFlag() ) {
// we're on the negative strand, so our read runs right to left
return read.getAlignmentEnd() > read.getMateAlignmentStart();
} else {
// we're on the positive strand, so our mate should be to our right (his start + insert size should be past our start)
return read.getAlignmentStart() <= read.getMateAlignmentStart() + read.getInferredInsertSize();
}
}