本文整理了Java中org.broadinstitute.gatk.utils.sam.GATKSAMRecord.getHeader()
方法的一些代码示例,展示了GATKSAMRecord.getHeader()
的具体用法。这些代码示例主要来源于Github
/Stackoverflow
/Maven
等平台,是从一些精选项目中提取出来的代码,具有较强的参考意义,能在一定程度帮忙到你。GATKSAMRecord.getHeader()
方法的具体详情如下:
包路径:org.broadinstitute.gatk.utils.sam.GATKSAMRecord
类名称:GATKSAMRecord
方法名:getHeader
暂无
代码示例来源:origin: broadgsa/gatk
private void createBAM(final List<GATKSAMRecord> reads) throws IOException {
testBAM = createTempFile("TraverseActiveRegionsUnitTest", ".bam");
SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(reads.get(0).getHeader(), true, testBAM);
for (GATKSAMRecord read : reads ) {
out.addAlignment(read);
}
out.close();
new File(testBAM.getAbsolutePath().replace(".bam", ".bai")).deleteOnExit();
new File(testBAM.getAbsolutePath() + ".bai").deleteOnExit();
}
代码示例来源:origin: broadgsa/gatk
private void createBAM(List<GATKSAMRecord> reads) throws IOException {
testBAM = createTempFile("TraverseActiveRegionsUnitTest", ".bam");
SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(reads.get(0).getHeader(), true, testBAM);
for (GATKSAMRecord read : ReadUtils.sortReadsByCoordinate(reads)) {
out.addAlignment(read);
}
out.close();
new File(testBAM.getAbsolutePath().replace(".bam", ".bai")).deleteOnExit();
new File(testBAM.getAbsolutePath() + ".bai").deleteOnExit();
}
代码示例来源:origin: broadgsa/gatk-protected
/**
* Creates a hard-clipped view on a existing read record.
* @param read the underlying unclipped read.
* @param start inclusive first position in {@code read} included in the clipped view.
* @param end inclusive last position in {@code read} included in the clipped view.
*/
public ClippedGATKSAMRecord(final GATKSAMRecord read, int start, int end) {
super(read.getHeader());
this.setReferenceIndex(read.getReferenceIndex());
this.setAlignmentStart(read.getAlignmentStart() + start);
this.setMappingQuality(100);
// setting read indexing bin below
this.setFlags(read.getFlags());
this.setMateReferenceIndex(read.getMateReferenceIndex());
this.setMateAlignmentStart(read.getMateAlignmentStart());
this.setInferredInsertSize(read.getInferredInsertSize());
this.setReadBases(Arrays.copyOfRange(read.getReadBases(), start, end));
this.setBaseQualities(Arrays.copyOfRange(read.getBaseQualities(),start,end));
this.setReadName(read.getReadName());
insertionQuals = Arrays.copyOfRange(read.getBaseInsertionQualities(),start,end);
deletionQuals = Arrays.copyOfRange(read.getBaseDeletionQualities(),start,end);
// Set these to null in order to mark them as being candidates for lazy initialization.
// If this is not done, they will have non-null defaults.
super.setReadName(null);
super.setCigarString(null);
super.setReadBases(null);
super.setBaseQualities(null);
// Do this after the above because setCigarString will clear it.
GATKBin.setReadIndexingBin(this, -1);
}
代码示例来源:origin: broadgsa/gatk
final GATKSAMRecord returnRead = new GATKSAMRecord( firstRead.getHeader() );
returnRead.setIsStrandless(true);
returnRead.setAlignmentStart( firstRead.getAlignmentStart() );
代码示例来源:origin: broadgsa/gatk
final GATKSAMRecord emptyRead = new GATKSAMRecord(read.getHeader());
emptyRead.setReferenceIndex(read.getReferenceIndex());
emptyRead.setAlignmentStart(0);
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