\n <\/td>\n | /**<\/span><\/td>\n <\/tr>\n \n <\/td>\n | * Author: Pierre Lindenbaum PhD. @yokofakun<\/span><\/td>\n <\/tr>\n \n <\/td>\n | * http://www.biostars.org/p/63016/<\/span><\/td>\n <\/tr>\n \n <\/td>\n | * Compare two BAM files<\/span><\/td>\n <\/tr>\n \n <\/td>\n | * tested with picard.1-62 and berkeleydb java edition 4.1.10<\/span><\/td>\n <\/tr>\n \n <\/td>\n | * <\/span><\/td>\n <\/tr>\n \n <\/td>\n | * compilation & exec:<\/span><\/td>\n <\/tr>\n \n <\/td>\n | * javac -cp path/to/picard.jar:path/to/sam.jar:path/to/je-4.1.10.jar Biostar63016.java<\/span><\/td>\n <\/tr>\n \n <\/td>\n | * mkdir TMP<\/span><\/td>\n <\/tr>\n \n <\/td>\n | * java -cp path/to/picard.jar:path/to/sam.jar:path/to/je-4.1.10.jar:. Biostar63016 -d TMP file1.bam file2.bam<\/span><\/td>\n <\/tr>\n \n <\/td>\n | */<\/span><\/td>\n <\/tr>\n \n <\/td>\n | \n<\/td>\n <\/tr>\n | \n <\/td>\n | import<\/span> java<\/span>.io<\/span>.File<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> java<\/span>.io<\/span>.IOException<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> java<\/span>.util<\/span>.ArrayList<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> java<\/span>.util<\/span>.HashMap<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> java<\/span>.util<\/span>.HashSet<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> java<\/span>.util<\/span>.Iterator<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> java<\/span>.util<\/span>.List<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> java<\/span>.util<\/span>.Map<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> java<\/span>.util<\/span>.Set<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> java<\/span>.util<\/span>.logging<\/span>.Logger<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | \n<\/td>\n <\/tr>\n | \n <\/td>\n | import<\/span> net<\/span>.sf<\/span>.samtools<\/span>.SAMFileReader<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> net<\/span>.sf<\/span>.samtools<\/span>.SAMFileReader<\/span>.ValidationStringency<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> net<\/span>.sf<\/span>.samtools<\/span>.SAMRecord<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> net<\/span>.sf<\/span>.samtools<\/span>.SAMSequenceRecord<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | \n<\/td>\n <\/tr>\n | \n <\/td>\n | import<\/span> com<\/span>.sleepycat<\/span>.bind<\/span>.tuple<\/span>.StringBinding<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> com<\/span>.sleepycat<\/span>.bind<\/span>.tuple<\/span>.TupleInput<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> com<\/span>.sleepycat<\/span>.bind<\/span>.tuple<\/span>.TupleOutput<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> com<\/span>.sleepycat<\/span>.je<\/span>.Cursor<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> com<\/span>.sleepycat<\/span>.je<\/span>.Database<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> com<\/span>.sleepycat<\/span>.je<\/span>.DatabaseConfig<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> com<\/span>.sleepycat<\/span>.je<\/span>.DatabaseEntry<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> com<\/span>.sleepycat<\/span>.je<\/span>.Environment<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> com<\/span>.sleepycat<\/span>.je<\/span>.EnvironmentConfig<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> com<\/span>.sleepycat<\/span>.je<\/span>.LockMode<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> com<\/span>.sleepycat<\/span>.je<\/span>.OperationStatus<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | import<\/span> com<\/span>.sleepycat<\/span>.je<\/span>.Transaction<\/span>;<\/td>\n <\/tr>\n \n <\/td>\n | \n<\/td>\n <\/tr>\n | \n <\/td>\n | \n<\/td>\n <\/tr>\n | \n <\/td>\n | public<\/span> class<\/span> Biostar63016<\/span><\/td>\n <\/tr>\n \n <\/td>\n | {<\/td>\n <\/tr>\n | \n <\/td>\n | private<\/span> static<\/span> final<\/span> Logger<\/span> LOG<\/span>=Logger<\/span>.getLogger<\/span>(Biostar63016<\/span>.class<\/span>.getName<\/span>());<\/td>\n <\/tr>\n \n <\/td>\n | private<\/span> static<\/span> final<\/span> String<\/span> DATABASENAME<\/span>="read2pos"<\/span>;<\/td>\n <\/tr>\n | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |