Examples of picard.illumina.parser.OutputMapping

picard.illumina.parser.OutputMapping
In multiple locations we need to know what cycles are output, as of now we output all non-skip cycles, but rather than sprinkle this knowledge throughout the parser code, instead OutputMapping provides all the data a client might want about the cycles to be output including what ReadType they are. @author jburke@broadinstitute.org

        }


        final List<Integer> failingLanes = new ArrayList<Integer>();
        int totalFailures = 0;


        final int[] expectedCycles = new OutputMapping(readStructure).getOutputCycles();
        log.info("Checking lanes(" + StringUtil.join(",", LANES) + " in basecalls directory (" + BASECALLS_DIR
                .getAbsolutePath() + ")\n");
        log.info("Expected cycles: " + StringUtil.intValuesToString(expectedCycles));


        for (final Integer lane : LANES) {

View Full Code Here

TOP

Related Classes of picard.illumina.parser.OutputMapping

picard.illumina.CheckIlluminaDirectory

picard.PicardException

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.