Examples of picard.illumina.parser.IlluminaFileUtil

picard.illumina.parser.IlluminaFileUtil

General utils for dealing with IlluminaFiles as well as utils for specific, support formats. This class contains utils that span across multiple Illumina files but it's primary intent was to provide support for basic file types. Each supported file type can be accessed via a factory method (makeFt). When IlluminaFileUtil is created it is parameterized by basecallDir and lane and all IlluminaFileTypes created by IlluminaFileUtil will also be parameterized in this fashion. @author jburke@broadinstitute.org

        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) {
            IlluminaFileUtil fileUtil = new IlluminaFileUtil(BASECALLS_DIR, lane);
            final List<Integer> expectedTiles = fileUtil.getExpectedTiles();
            if (!TILE_NUMBERS.isEmpty()) {
                expectedTiles.retainAll(TILE_NUMBERS);
            }


            if (LINK_LOCS) {
                createLocFileSymlinks(fileUtil, lane);
                //we need to create a new file util because it stores a cache to the files it found on
                //construction and this doesn't inclue the recently created symlinks
                fileUtil = new IlluminaFileUtil(BASECALLS_DIR, lane);
            }


            log.info("Checking lane " + lane);
            log.info("Expected tiles: " + StringUtil.join(", ", expectedTiles));

Examples of picard.illumina.parser.IlluminaFileUtil

Related Classes of picard.illumina.parser.IlluminaFileUtil