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));