本文整理了Java中htsjdk.samtools.util.Log.warn()方法的一些代码示例，展示了Log.warn()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。Log.warn()方法的具体详情如下：
包路径：htsjdk.samtools.util.Log
类名称：Log
方法名：warn
[英]Logs a Throwable and optional message parts at level warn.
[中]在警告级别记录可丢弃和可选消息部分。
代码示例来源：origin: com.github.samtools/htsjdk
/** Gets a string system property, prefixed with "samjdk." using the default
* if the property does not exist or if the java.security manager raises an exception for
* applications started with -Djava.security.manager . */
private static String getStringProperty(final String name, final String def) {
try {
return System.getProperty("samjdk." + name, def);
} catch (final java.security.AccessControlException error) {
log.warn(error,"java Security Manager forbids 'System.getProperty(\"" + name + "\")' , returning default value: " + def );
return def;
}
}代码示例来源：origin: samtools/htsjdk
/** Gets a string system property, prefixed with "samjdk." using the default
* if the property does not exist or if the java.security manager raises an exception for
* applications started with -Djava.security.manager . */
private static String getStringProperty(final String name, final String def) {
try {
return System.getProperty("samjdk." + name, def);
} catch (final java.security.AccessControlException error) {
log.warn(error,"java Security Manager forbids 'System.getProperty(\"" + name + "\")' , returning default value: " + def );
return def;
}
}代码示例来源：origin: samtools/htsjdk
/** Checks whether a string system property, prefixed with "samjdk.", exists.
* If the property does not exist or if the java.security manager raises an exception for
* applications started with -Djava.security.manager this method returns false. */
private static boolean hasProperty(final String name){
try {
return null != System.getProperty("samjdk." + name);
} catch (final java.security.AccessControlException error) {
log.warn(error,"java Security Manager forbids 'System.getProperty(\"" + name + "\")' , returning false");
return false;
}
}代码示例来源：origin: com.github.samtools/htsjdk
/** Checks whether a string system property, prefixed with "samjdk.", exists.
* If the property does not exist or if the java.security manager raises an exception for
* applications started with -Djava.security.manager this method returns false. */
private static boolean hasProperty(final String name){
try {
return null != System.getProperty("samjdk." + name);
} catch (final java.security.AccessControlException error) {
log.warn(error,"java Security Manager forbids 'System.getProperty(\"" + name + "\")' , returning false");
return false;
}
}代码示例来源：origin: samtools/htsjdk
ExperimentalCodec(final BitInputStream coreBlockInputStream,
final BitOutputStream coreBlockOutputStream) {
super(coreBlockInputStream, coreBlockOutputStream);
final String subclass = this.getClass().getName();
final String warning = String.format(
"Using the experimental codec %s which is untested and scheduled for removal from the CRAM spec",
subclass);
final Log log = Log.getInstance(ExperimentalCodec.class);
log.warn(warning);
}
}代码示例来源：origin: com.github.samtools/htsjdk
ExperimentalEncoding(final EncodingID encodingID) {
super(encodingID);
final String subclass = this.getClass().getName();
final String warning = String.format(
"Using the experimental encoding %s which is untested and scheduled for removal from the CRAM spec",
subclass);
final Log log = Log.getInstance(ExperimentalEncoding.class);
log.warn(warning);
}
}代码示例来源：origin: com.github.samtools/htsjdk
private File findIndexForFile(File indexFile, final File cramFile) {
indexFile = indexFile == null ? SamFiles.findIndex(cramFile) : indexFile;
if (indexFile != null && indexFile.lastModified() < cramFile.lastModified()) {
log.warn("CRAM index file " + indexFile.getAbsolutePath() +
" is older than CRAM " + cramFile.getAbsolutePath());
}
return indexFile;
}代码示例来源：origin: samtools/htsjdk
private File findIndexForFile(File indexFile, final File cramFile) {
indexFile = indexFile == null ? SamFiles.findIndex(cramFile) : indexFile;
if (indexFile != null && indexFile.lastModified() < cramFile.lastModified()) {
log.warn("CRAM index file " + indexFile.getAbsolutePath() +
" is older than CRAM " + cramFile.getAbsolutePath());
}
return indexFile;
}代码示例来源：origin: samtools/htsjdk
ExperimentalEncoding(final EncodingID encodingID) {
super(encodingID);
final String subclass = this.getClass().getName();
final String warning = String.format(
"Using the experimental encoding %s which is untested and scheduled for removal from the CRAM spec",
subclass);
final Log log = Log.getInstance(ExperimentalEncoding.class);
log.warn(warning);
}
}代码示例来源：origin: com.github.samtools/htsjdk
ExperimentalCodec(final BitInputStream coreBlockInputStream,
final BitOutputStream coreBlockOutputStream) {
super(coreBlockInputStream, coreBlockOutputStream);
final String subclass = this.getClass().getName();
final String warning = String.format(
"Using the experimental codec %s which is untested and scheduled for removal from the CRAM spec",
subclass);
final Log log = Log.getInstance(ExperimentalCodec.class);
log.warn(warning);
}
}代码示例来源：origin: enasequence/cramtools
private static void eofNotFound(htsjdk.samtools.cram.common.Version version) {
if (version.major >= 2 && version.minor >= 1) {
log.error("Incomplete data: EOF marker not found.");
if (quitOnMissingEOF)
System.exit(1);
} else {
log.warn("EOF marker not found, possibly incomplete file/stream.");
}
}代码示例来源：origin: com.github.samtools/htsjdk
/**
* @return true if we have surpassed the maximum accumulation threshold for the first locus in the accumulator, false otherwise
*/
private boolean surpassedAccumulationThreshold() {
final boolean surpassesThreshold = !accumulator.isEmpty() && accumulator.get(0).getRecordAndOffsets().size() >= maxReadsToAccumulatePerLocus;
if (surpassesThreshold && !enforcedAccumulationLimit) {
LOG.warn("We have encountered greater than " + maxReadsToAccumulatePerLocus + " reads at position " + accumulator.get(0).toString() + " and will ignore the remaining reads at this position. Note that further warnings will be suppressed.");
enforcedAccumulationLimit = true;
}
return surpassesThreshold;
}代码示例来源：origin: samtools/htsjdk
/**
* @return true if we have surpassed the maximum accumulation threshold for the first locus in the accumulator, false otherwise
*/
private boolean surpassedAccumulationThreshold() {
final boolean surpassesThreshold = !accumulator.isEmpty() && accumulator.get(0).getRecordAndOffsets().size() >= maxReadsToAccumulatePerLocus;
if (surpassesThreshold && !enforcedAccumulationLimit) {
LOG.warn("We have encountered greater than " + maxReadsToAccumulatePerLocus + " reads at position " + accumulator.get(0).toString() + " and will ignore the remaining reads at this position. Note that further warnings will be suppressed.");
enforcedAccumulationLimit = true;
}
return surpassesThreshold;
}代码示例来源：origin: broadinstitute/picard
/**
* Main method for the program. Checks that input file is present and
* readable, then iterates through the index printing meta data to stdout.
*/
protected int doWork() {
if (INPUT.getName().endsWith(BAMIndex.BAMIndexSuffix))
log.warn("INPUT should be the BAM file name, not its index file");
IOUtil.assertFileIsReadable(INPUT);
BAMIndexMetaData.printIndexStats(INPUT);
return 0;
}
}代码示例来源：origin: com.github.broadinstitute/picard
/**
* Main method for the program. Checks that input file is present and
* readable, then iterates through the index printing meta data to stdout.
*/
protected int doWork() {
if (INPUT.getName().endsWith(BAMIndex.BAMIndexSuffix))
log.warn("INPUT should be the BAM file name, not its index file");
IOUtil.assertFileIsReadable(INPUT);
BAMIndexMetaData.printIndexStats(INPUT);
return 0;
}
}代码示例来源：origin: PapenfussLab/gridss
@Override
public void close() {
log.debug("Closing UntemplatedSequenceAnnotator");
// TODO: close feeding thread more cleanly than just shutting down the process
vcfStream.close();
try {
aligner.close();
} catch (IOException e) {
log.warn(e);
}
}
}代码示例来源：origin: broadinstitute/picard
@Override protected void setup(final SAMFileHeader header, final File samFile) {
IOUtil.assertFileIsWritable(OUTPUT);
if (header.getSequenceDictionary().isEmpty()) {
log.warn(INPUT.getAbsoluteFile() + " has no sequence dictionary. If any reads " +
"in the file are aligned, then alignment summary metrics collection will fail.");
}
final boolean doRefMetrics = REFERENCE_SEQUENCE != null;
collector = new AlignmentSummaryMetricsCollector(METRIC_ACCUMULATION_LEVEL, header.getReadGroups(), doRefMetrics,
ADAPTER_SEQUENCE, MAX_INSERT_SIZE, EXPECTED_PAIR_ORIENTATIONS, IS_BISULFITE_SEQUENCED);
}代码示例来源：origin: com.github.broadinstitute/picard
@Override protected void setup(final SAMFileHeader header, final File samFile) {
IOUtil.assertFileIsWritable(OUTPUT);
if (header.getSequenceDictionary().isEmpty()) {
log.warn(INPUT.getAbsoluteFile() + " has no sequence dictionary. If any reads " +
"in the file are aligned, then alignment summary metrics collection will fail.");
}
final boolean doRefMetrics = REFERENCE_SEQUENCE != null;
collector = new AlignmentSummaryMetricsCollector(METRIC_ACCUMULATION_LEVEL, header.getReadGroups(), doRefMetrics,
ADAPTER_SEQUENCE, MAX_INSERT_SIZE, EXPECTED_PAIR_ORIENTATIONS, IS_BISULFITE_SEQUENCED);
}代码示例来源：origin: com.github.samtools/htsjdk
private void warnIfReferenceIsTooLargeForBinField(final SAMRecord rec) {
final SAMSequenceRecord sequence = rec.getHeader() != null ? rec.getHeader().getSequence(rec.getReferenceName()) : null;
if (!isReferenceSizeWarningShowed
&& sequence != null
&& SAMUtils.isReferenceSequenceCompatibleWithBAI(sequence)
&& rec.getValidationStringency() != ValidationStringency.SILENT) {
LOG.warn("Reference length is too large for BAM bin field. Values in the bin field could be incorrect.");
isReferenceSizeWarningShowed = true;
}
}代码示例来源：origin: PapenfussLab/gridss
private void warnIfReferenceIsTooLargeForBinField(final SAMRecord rec) {
final SAMSequenceRecord sequence = rec.getHeader() != null ? rec.getHeader().getSequence(rec.getReferenceName()) : null;
if (!isReferenceSizeWarningShowed
&& sequence != null
&& SAMUtils.isReferenceSequenceCompatibleWithBAI(sequence)
&& rec.getValidationStringency() != ValidationStringency.SILENT) {
LOG.warn("Reference length is too large for BAM bin field. Values in the bin field could be incorrect.");
isReferenceSizeWarningShowed = true;
}
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