UPDATE: Remove the old checkstyle.xml and rename checkstyle_google.xml to checkstyle.xml. Update the checkstyle.xml to check header of java file with content of checkstyle-license.txt.
FIX: Fix findbugs warning in DistCp, replace Integer.valueOf() by Integer.parseInt().
FIX: Fix findbugs warning in UniqueIdentifierTranslator.
FIX: Fix findbugs warning by setting Serializable SAMComparator class.
FIX: Fix findbugs warning by removing unnecessary null check in HTSeqCounter.java
FIX: Fix findbugs warning by checking the return value of File.delete() in BWAReadsMapper.
FIX: Fix findbugs warning by removing unnecessary null check in GSNAPReadsMapper.
FIX: Fix findbugs warning by checking the return value of File.delete() in SOAPReadsMapper.
FIX: Fix findbugs warning by checking the return value of File.delete() and File.mkdir() in STARReadsMapper.