本文整理了Java中org.broadinstitute.gatk.utils.sam.GATKSAMRecord.getExistingBaseDeletionQualities()
方法的一些代码示例,展示了GATKSAMRecord.getExistingBaseDeletionQualities()
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.getExistingBaseDeletionQualities()
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:getExistingBaseDeletionQualities
暂无
代码示例来源:origin: broadgsa/gatk
/**
* Default utility to query the base deletion quality of a read. If the read doesn't have one, it creates an array of default qualities (currently Q45)
* and assigns it to the read.
*
* @return the base deletion quality array
*/
public byte[] getBaseDeletionQualities() {
byte[] quals = getExistingBaseDeletionQualities();
if( quals == null ) {
quals = new byte[getBaseQualities().length];
Arrays.fill(quals, DEFAULT_INSERTION_DELETION_QUAL); // Some day in the future when base insertion and base deletion quals exist the samtools API will
// be updated and the original quals will be pulled here, but for now we assume the original quality is a flat Q45
}
return quals;
}
代码示例来源:origin: broadgsa/gatk-protected
public ReadRecalibrationInfo(final GATKSAMRecord read,
final ReadCovariates covariates,
final boolean[] skips,
final double[] snpErrors,
final double[] insertionErrors,
final double[] deletionErrors) {
if ( read == null ) throw new IllegalArgumentException("read cannot be null");
if ( covariates == null ) throw new IllegalArgumentException("covariates cannot be null");
if ( skips == null ) throw new IllegalArgumentException("skips cannot be null");
if ( snpErrors == null ) throw new IllegalArgumentException("snpErrors cannot be null");
if ( insertionErrors == null ) throw new IllegalArgumentException("insertionErrors cannot be null");
if ( deletionErrors == null ) throw new IllegalArgumentException("deletionErrors cannot be null");
this.read = read;
this.baseQuals = read.getBaseQualities();
this.length = baseQuals.length;
this.covariates = covariates;
this.skips = skips;
this.insertionQuals = read.getExistingBaseInsertionQualities();
this.deletionQuals = read.getExistingBaseDeletionQualities();
this.snpErrors = snpErrors;
this.insertionErrors = insertionErrors;
this.deletionErrors = deletionErrors;
if ( skips.length != length ) throw new IllegalArgumentException("skips.length " + snpErrors.length + " != length " + length);
if ( snpErrors.length != length ) throw new IllegalArgumentException("snpErrors.length " + snpErrors.length + " != length " + length);
if ( insertionErrors.length != length ) throw new IllegalArgumentException("insertionErrors.length " + snpErrors.length + " != length " + length);
if ( deletionErrors.length != length ) throw new IllegalArgumentException("deletionErrors.length " + snpErrors.length + " != length " + length);
}
内容来源于网络,如有侵权,请联系作者删除!