Examples with ReadFilter org.broadinstitute.hellbender.engine.filters.ReadFilter used on opensource projects

Example 1 with ReadFilter

use of org.broadinstitute.hellbender.engine.filters.ReadFilter in project gatk by broadinstitute.

the class GATKReadFilterPluginDescriptor method getAllInstances.

/**
     * Pass back the list of ReadFilter instances that were actually seen on the command line in the same
     * order they were specified. Its possible for this to return a filter that was originally included
     * in the list of tool defaults only in the case where the user also specifies it on the command line.
     *
     * NOTE: this method is somewhat misnamed in that it doesn't return ALL instances since it leaves out
     * default filters (Except as noted above). The refactored interface in Barclay renames this method and
     * changes it's contract. We'll change the implementation when we integrate the updated interface.
     */
@Override
public List<ReadFilter> getAllInstances() {
    final ArrayList<ReadFilter> filters = new ArrayList<>(userArgs.getUserEnabledReadFilterNames().size());
    userArgs.getUserEnabledReadFilterNames().forEach(s -> {
        ReadFilter rf = allDiscoveredReadFilters.get(s);
        filters.add(rf);
    });
    return filters;
}

Example 2 with ReadFilter

use of org.broadinstitute.hellbender.engine.filters.ReadFilter in project gatk by broadinstitute.

the class LocusWalker method getDefaultReadFilters.

/**
     * Returns the default list of CommandLineReadFilters that are used for this tool. The filters returned
     * by this method are subject to selective enabling/disabling by the user via the command line. The
     * default implementation uses the {@link WellformedReadFilter} and {@link ReadFilterLibrary.MappedReadFilter} filter
     * with all default options. Subclasses can override to provide alternative filters.
     *
     * Note: this method is called before command line parsing begins, and thus before a SAMFileHeader is
     * available through {link #getHeaderForReads}.
     *
     * @return List of individual filters to be applied for this tool.
     */
public List<ReadFilter> getDefaultReadFilters() {
    final List<ReadFilter> defaultFilters = new ArrayList<>(2);
    defaultFilters.add(new WellformedReadFilter());
    defaultFilters.add(new ReadFilterLibrary.MappedReadFilter());
    return defaultFilters;
}

Example 3 with ReadFilter

use of org.broadinstitute.hellbender.engine.filters.ReadFilter in project gatk by broadinstitute.

the class AssemblyRegionWalkerSpark method getDefaultReadFilters.

@Override
public List<ReadFilter> getDefaultReadFilters() {
    final List<ReadFilter> defaultFilters = new ArrayList<>(2);
    defaultFilters.add(new WellformedReadFilter());
    defaultFilters.add(new ReadFilterLibrary.MappedReadFilter());
    return defaultFilters;
}

Example 4 with ReadFilter

use of org.broadinstitute.hellbender.engine.filters.ReadFilter in project gatk by broadinstitute.

the class AssemblyRegionWalker method getDefaultReadFilters.

/**
     * Returns the default list of CommandLineReadFilters that are used for this tool. The filters
     * returned by this method are subject to selective enabling/disabling and customization by the
     * user via the command line. The default implementation uses the {@link WellformedReadFilter}
     * filter with all default options, as well as the {@link ReadFilterLibrary.MappedReadFilter}.
     * Subclasses can override to provide alternative filters.
     *
     * Note: this method is called before command line parsing begins, and thus before a SAMFileHeader is
     * available through {link #getHeaderForReads}.
     *
     * @return List of default filter instances to be applied for this tool.
     */
public List<ReadFilter> getDefaultReadFilters() {
    final List<ReadFilter> defaultFilters = new ArrayList<>(2);
    defaultFilters.add(new WellformedReadFilter());
    defaultFilters.add(new ReadFilterLibrary.MappedReadFilter());
    return defaultFilters;
}

Example 5 with ReadFilter

use of org.broadinstitute.hellbender.engine.filters.ReadFilter in project gatk by broadinstitute.

the class SparkGenomeReadCounts method collectReads.

private void collectReads() {
    if (readArguments.getReadFilesNames().size() != 1) {
        throw new UserException("This tool only accepts a single bam/sam/cram as input");
    }
    final SampleCollection sampleCollection = new SampleCollection(getHeaderForReads());
    if (sampleCollection.sampleCount() > 1) {
        throw new UserException.BadInput("We do not support bams with more than one sample.");
    }
    final String sampleName = sampleCollection.sampleIds().get(0);
    final String[] commentsForRawCoverage = { "##fileFormat  = tsv", "##commandLine = " + getCommandLine(), String.format("##title = Coverage counts in %d base bins for WGS", binsize) };
    final ReadFilter filter = makeGenomeReadFilter();
    final SAMSequenceDictionary sequenceDictionary = getReferenceSequenceDictionary();
    logger.info("Starting Spark coverage collection...");
    final long coverageCollectionStartTime = System.currentTimeMillis();
    final JavaRDD<GATKRead> rawReads = getReads();
    final JavaRDD<GATKRead> reads = rawReads.filter(read -> filter.test(read));
    //Note: using a field inside a closure will pull in the whole enclosing object to serialization
    // (which leads to bad performance and can blow up if some objects in the fields are not
    // Serializable - closures always use java Serializable and not Kryo)
    //Solution here is to use a temp variable for binsize because it's just an int.
    final int binsize_tmp = binsize;
    final JavaRDD<SimpleInterval> readIntervals = reads.filter(read -> sequenceDictionary.getSequence(read.getContig()) != null).map(read -> SparkGenomeReadCounts.createKey(read, sequenceDictionary, binsize_tmp));
    final Map<SimpleInterval, Long> byKey = readIntervals.countByValue();
    final Set<SimpleInterval> readIntervalKeySet = byKey.keySet();
    final long totalReads = byKey.values().stream().mapToLong(v -> v).sum();
    final long coverageCollectionEndTime = System.currentTimeMillis();
    logger.info(String.format("Finished the spark coverage collection with %d targets and %d reads. Elapse of %d seconds", readIntervalKeySet.size(), totalReads, (coverageCollectionEndTime - coverageCollectionStartTime) / 1000));
    final String[] commentsForProportionalCoverage = { commentsForRawCoverage[0], commentsForRawCoverage[1], String.format("##title = Proportional coverage counts in %d base bins for WGS (total reads: %d)", binsize, totalReads) };
    logger.info("Creating full genome bins...");
    final long createGenomeBinsStartTime = System.currentTimeMillis();
    final List<SimpleInterval> fullGenomeBins = createFullGenomeBins(binsize);
    List<Target> fullGenomeTargetCollection = createTargetListFromSimpleInterval(fullGenomeBins);
    TargetWriter.writeTargetsToFile(new File(outputFile.getAbsolutePath() + ".targets.tsv"), fullGenomeTargetCollection);
    final long createGenomeBinsEndTime = System.currentTimeMillis();
    logger.info(String.format("Finished creating genome bins. Elapse of %d seconds", (createGenomeBinsEndTime - createGenomeBinsStartTime) / 1000));
    logger.info("Creating missing genome bins...");
    final long createMissingGenomeBinsStartTime = System.currentTimeMillis();
    logger.info("Creating missing genome bins: Creating a mutable mapping...");
    final Map<SimpleInterval, Long> byKeyMutable = new HashMap<>();
    byKeyMutable.putAll(byKey);
    logger.info("Creating missing genome bins: Populating mutable mapping with zero counts for empty regions...");
    fullGenomeBins.stream().forEach(b -> byKeyMutable.putIfAbsent(b, 0l));
    final long createMissingGenomeBinsEndTime = System.currentTimeMillis();
    logger.info(String.format("Finished creating missing genome bins. Elapse of %d seconds", (createMissingGenomeBinsEndTime - createMissingGenomeBinsStartTime) / 1000));
    logger.info("Creating final map...");
    final long createFinalMapStartTime = System.currentTimeMillis();
    final SortedMap<SimpleInterval, Long> byKeySorted = new TreeMap<>(IntervalUtils.LEXICOGRAPHICAL_ORDER_COMPARATOR);
    byKeySorted.putAll(byKeyMutable);
    final long createFinalMapEndTime = System.currentTimeMillis();
    logger.info(String.format("Finished creating final map. Elapse of %d seconds", (createFinalMapEndTime - createFinalMapStartTime) / 1000));
    logger.info("Creating proportional coverage... ");
    final long pCovFileStartTime = System.currentTimeMillis();
    final SortedMap<SimpleInterval, Double> byKeyProportionalSorted = new TreeMap<>(IntervalUtils.LEXICOGRAPHICAL_ORDER_COMPARATOR);
    byKeySorted.entrySet().stream().forEach(e -> byKeyProportionalSorted.put(e.getKey(), (double) e.getValue() / totalReads));
    final long pCovFileEndTime = System.currentTimeMillis();
    logger.info(String.format("Finished creating proportional coverage map. Elapse of %d seconds", (pCovFileEndTime - pCovFileStartTime) / 1000));
    logger.info("Writing raw coverage file ...");
    final long writingCovFileStartTime = System.currentTimeMillis();
    ReadCountCollectionUtils.writeReadCountsFromSimpleInterval(new File(outputFile.getAbsolutePath() + RAW_COV_OUTPUT_EXTENSION), sampleName, byKeySorted, commentsForRawCoverage);
    final long writingCovFileEndTime = System.currentTimeMillis();
    logger.info(String.format("Finished writing coverage file. Elapse of %d seconds", (writingCovFileEndTime - writingCovFileStartTime) / 1000));
    logger.info("Writing proportional coverage file ...");
    final long writingPCovFileStartTime = System.currentTimeMillis();
    ReadCountCollectionUtils.writeReadCountsFromSimpleInterval(outputFile, sampleName, byKeyProportionalSorted, commentsForProportionalCoverage);
    final long writingPCovFileEndTime = System.currentTimeMillis();
    logger.info(String.format("Finished writing proportional coverage file. Elapse of %d seconds", (writingPCovFileEndTime - writingPCovFileStartTime) / 1000));
}