Examples with MetricsFile htsjdk.samtools.metrics.MetricsFile used on opensource projects

Example 31 with MetricsFile

use of htsjdk.samtools.metrics.MetricsFile in project gridss by PapenfussLab.

the class TestHelper method IDSV.

public IdsvMetrics IDSV(Collection<SAMRecord> input) {
    IdsvSamFileMetricsCollector c = new IdsvSamFileMetricsCollector(null);
    for (SAMRecord r : input) {
        c.acceptRecord(r, null);
    }
    MetricsFile<IdsvMetrics, Integer> idsv = new MetricsFile<IdsvMetrics, Integer>();
    MetricsFile<InsertSizeMetrics, Integer> is = new MetricsFile<InsertSizeMetrics, Integer>();
    MetricsFile<CigarDetailMetrics, Integer> sc = new MetricsFile<CigarDetailMetrics, Integer>();
    MetricsFile<MapqMetrics, Integer> mqm = new MetricsFile<MapqMetrics, Integer>();
    c.finish(is, idsv, mqm, sc);
    IdsvMetrics metrics = idsv.getMetrics().get(0);
    return metrics;
}

Example 32 with MetricsFile

use of htsjdk.samtools.metrics.MetricsFile in project gridss by PapenfussLab.

the class InsertSizeDistribution method create.

public static InsertSizeDistribution create(File insertSizeMetricsFile) {
    InsertSizeDistribution result = null;
    if (insertSizeMetricsFile != null && insertSizeMetricsFile.exists()) {
        FileReader reader = null;
        try {
            reader = new FileReader(insertSizeMetricsFile);
            MetricsFile<InsertSizeMetrics, Integer> file = new MetricsFile<InsertSizeMetrics, Integer>();
            file.read(reader);
            result = InsertSizeDistribution.create(file.getHistogram());
        } catch (FileNotFoundException e) {
            log.error("Missing insert size distribution for ", insertSizeMetricsFile);
        } finally {
            CloserUtil.close(reader);
        }
        if (result == null) {
            log.debug("Unable to extract insert size distribution from ", insertSizeMetricsFile);
        }
    }
    return result;
}