Examples of UnmappedReadFilter

Examples of org.broadinstitute.gatk.engine.filters.UnmappedReadFilter

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            argCollection.samFiles = Collections.singletonList(inputFile.getAbsolutePath());

            engine.setArguments(argCollection);
            // Bugs in the engine mean that this has to be set twice.
            engine.setSAMFileIDs(Collections.singletonList(new SAMReaderID(inputFile,new Tags())));
            engine.setFilters(Collections.<ReadFilter>singletonList(new UnmappedReadFilter()));
            engine.setReferenceMetaDataFiles(Collections.<RMDTriplet>emptyList());

            // Create the walker
            engine.setWalker(walkerType.create());
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