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

Example 1 with ReadNameReadFilter

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

the class ReadsContextUnitTest method getValidReadsContextData.

@DataProvider(name = "ReadsContextFilteringDataProvider")
public Object[][] getValidReadsContextData() {
    // Default-constructed ReadsContexts and ReadsContexts constructed from null ReadsDataSources/intervals
    // should behave as empty context objects.
    ReadNameReadFilter readNameFilter = new ReadNameReadFilter();
    readNameFilter.readName = "d";
    return new Object[][] { { new ReadsContext(new ReadsDataSource(IOUtils.getPath(publicTestDir + "org/broadinstitute/hellbender/engine/reads_data_source_test1.bam")), // query over small interval, with no read filter
    new SimpleInterval("1", 200, 210), ReadFilterLibrary.ALLOW_ALL_READS), new String[] { "a", "b", "c" } }, { new ReadsContext(new ReadsDataSource(IOUtils.getPath(publicTestDir + "org/broadinstitute/hellbender/engine/reads_data_source_test1.bam")), // query over larger interval with readNameFilter on "d"
    new SimpleInterval("1", 200, 1000), readNameFilter), new String[] { "d" } } };
}