本文整理了Java中org.broadinstitute.gatk.utils.Utils.warnUser()方法的一些代码示例，展示了Utils.warnUser()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。Utils.warnUser()方法的具体详情如下：
包路径：org.broadinstitute.gatk.utils.Utils
类名称：Utils
方法名：warnUser

Utils.warnUser介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

public static void warnUser(final String msg) {
  warnUser(logger, msg);
}

代码示例来源：origin: broadgsa/gatk-protected

/**
 * Checks whether the last-modification-time of the inputs is consistent with their relative roles.
 *
 * This routine does not thrown an exception but may output a warning message if inconsistencies are spotted.
 *
 * @param beforeFile the before report file.
 * @param afterFile  the after report file.
 */
private void checkInputReportFileLMT(final File beforeFile, final File afterFile) {
  if (ignoreLastModificationTime  || beforeFile == null || afterFile == null) {
    return; // nothing to do here
  } else if (beforeFile.lastModified() > afterFile.lastModified()) {
    Utils.warnUser("Last modification timestamp for 'Before' and 'After'"
        + "recalibration reports are in the wrong order. Perhaps, have they been swapped?");
  }
}

代码示例来源：origin: broadgsa/gatk

@Override
public Feature decodeLoc(final LineIterator lineIterator) {
  final String line = lineIterator.next();
  if (line.startsWith("#")) return null;
  String fields[] = line.split("\t");
  if (fields.length < 3) throw new TribbleException("RefSeq (decodeLoc) : Unable to parse line -> " + line + ", we expected at least 3 columns, we saw " + fields.length);
  String contig_name = fields[2];
  try {
    return new RefSeqFeature(genomeLocParser.createGenomeLoc(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5])));
  } catch ( UserException.MalformedGenomeLoc e ) {
    Utils.warnUser("RefSeq file is potentially incorrect, as some transcripts or exons have a negative length ("+fields[2]+")");
    return null;
  } catch ( NumberFormatException e ) {
    throw new UserException.MalformedFile("Could not parse location from line: " + line);
  }
}

代码示例来源：origin: broadgsa/gatk

Utils.warnUser("RefSeq file contains transcripts with zero coding length. "+
    "Such transcripts will be ignored (this warning is printed only once)");
zero_coding_length_user_warned = true;

代码示例来源：origin: broadgsa/gatk-protected

Utils.warnUser(logger, String.format(
    "Rscript not found in environment path. %s will be generated but PDF plots will not.",
    RSCRIPT_FILE));

代码示例来源：origin: broadgsa/gatk-protected

Utils.warnUser(logger, "cycle caused at merging haplotypes with different kmerSizes: active region " + assemblyResultSet.getRegionForGenotyping() + " will be skipped");

代码示例来源：origin: broadgsa/gatk-protected

/**
 * Construct a haplotype graph given the haplotype list and the elected kmerSize.
 *
 * @param haplotypes whose path to add to the graph.
 * @param kmerSize   the kmerSize use to compose the graph.
 */
public HaplotypeGraph(final int kmerSize, final List<Haplotype> haplotypes) {
  super(kmerSize);
  referenceHaplotype = findReferenceHaplotypeOrFail(haplotypes);
  this.haplotypes = new LinkedHashSet<>(haplotypes);
  addSequence("anonymous", referenceHaplotype.getBases(), true);
  for (final Haplotype h : haplotypes) {
    if (h.isReference())
      continue;
    if (h.length() < kmerSize) {
      Utils.warnUser(logger, "haplotype shorter than kmerSize " + h.length() + " < " + kmerSize + " will be dropped");
    } else
      addSequence("anonymous", h.getBases(), false);
  }
  buildGraphIfNecessary();
}

代码示例来源：origin: broadgsa/gatk

/**
 * Section of code shared between the two recalibration walkers which uses the command line arguments to adjust attributes of the read such as quals or platform string
 *
 * @param read The read to adjust
 * @param RAC  The list of shared command line arguments
 */
public static void parsePlatformForRead(final GATKSAMRecord read, final RecalibrationArgumentCollection RAC) {
  GATKSAMReadGroupRecord readGroup = read.getReadGroup();
  if (RAC.FORCE_PLATFORM != null && (readGroup.getPlatform() == null || !readGroup.getPlatform().equals(RAC.FORCE_PLATFORM))) {
    readGroup.setPlatform(RAC.FORCE_PLATFORM);
  }
  if (readGroup.getPlatform() == null) {
    if (RAC.DEFAULT_PLATFORM != null) {
      if (!warnUserNullPlatform) {
        Utils.warnUser("The input .bam file contains reads with no platform information. " +
            "Defaulting to platform = " + RAC.DEFAULT_PLATFORM + ". " +
            "First observed at read with name = " + read.getReadName());
        warnUserNullPlatform = true;
      }
      readGroup.setPlatform(RAC.DEFAULT_PLATFORM);
    }
    else {
      throw new UserException.MalformedBAM(read, "The input .bam file contains reads with no platform information. First observed at read with name = " + read.getReadName());
    }
  }
}