Package picard.illumina.parser

Examples of picard.illumina.parser.IlluminaFileUtil


        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));
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Related Classes of picard.illumina.parser.IlluminaFileUtil

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