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ForĪsBam asSam, and sortBam this is without theĪ GRanges() instance with destination. The sorted, filtered, or merged output file will be created. The character(1) file name of the location where The character(1) name of the index file of the 'BAM' fileīeing processed this is given without the '.bai' extension. For mergeBam, must satisfy length(files) >= The character() file names of the ‘BAM’ file to be The character(1) file name of the ‘BAM’ ('SAM' for , region = GRanges (), overwrite = FALSE, header = character (), byQname = FALSE, addRG = FALSE, compressLevel1 = FALSE, indexDestination = FALSE ) ) # S4 method for signature 'character' mergeBam ( files, destination. ) # S4 method for signature 'character' indexBam ( files. , byQname = FALSE, maxMemory = 512 ) indexBam ( files. ) # S4 method for signature 'character' sortBam ( file, destination. , filter = FilterRules (), indexDestination = TRUE, param = ScanBamParam ( what = scanBamWhat ())) sortBam ( file, destination. ) # S4 method for signature 'character' filterBam ( file, destination, index = file. , overwrite = FALSE ) filterBam ( file, destination, index = file. ) # S4 method for signature 'character' asSam ( file, destination = sub ( "\\.bam", "", file ). , overwrite = FALSE, indexDestination = TRUE ) asSam ( file, destination = sub ( "\\.bam", "", file ).

) # S4 method for signature 'character' asBam ( file, destination = sub ( "\\.sam(\\.gz)?", "", file ). ) # S4 method for signature 'character' scanBamHeader ( files. , param = ScanBamParam ()) idxstatsBam ( file, index = file. , param = ScanBamParam ( what = scanBamWhat ())) countBam ( file, index = file.