Changes

--in : the SAM/BAM file to be read --out : the SAM/BAM file to be written

--noeof : do not expect an EOF block on a bam file. --params : print the parameter settings

./bam convert --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--noeof][--params] 

--in : the SAM/BAM file to be split --out : the base filename for the SAM/BAM files to write into. Does not include the extension. _N will be appended to the basename where N indicates the Chromosome.

--noeof : do not expect an EOF block on a bam file. --bamIndex : the path/name of the bam index file (if not specified, uses the --in value + ".bai") --bamout : write the output files in BAM format (default). --samout : write the output files in SAM format. --params : print the parameter settings

./bam splitChromosome --in <inputFilename> --out <outputFileBaseName> [--bamIndex <bamIndexFile>] [--noeof] [--bamout|--samout] [--params]

Required Parameters: --in : the BAM file to be read --out : the SAM/BAM file to write to Optional Parameters: --noeof : do not expect an EOF block on a bam file. --bamIndex : the path/name of the bam index file (if not specified, uses the --in value + ".bai") --refName : the BAM reference Name to read (either this or refID can be specified) --refID : the BAM reference ID to read (defaults to -1: unmapped) --start : the inclusive 0-based start position (defaults to -1) --end : the exclusive 0-based end position (defaults to -1: meaning til the end of the reference) --params : print the parameter settings

./bam writeRegion --in <inputFilename> --out <outputFilename> [--bamIndex <bamIndexFile>] [--noeof] [--refName <reference Name> | --refID <reference ID>] [--start <0-based start pos>] [--end <0-based end psoition>] [--params]

Required Parameters: --in : the SAM/BAM file to be read Optional Parameters: --noeof : do not expect an EOF block on a bam file. --printRecordRefs : print the reference information for the records in the file (grouped by reference). --params : print the parameter settings

./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]

Required Parameters: --bamIndex : the path/name of the bam index file to display Optional Parameters: --refID : the reference ID to read, defaults to print all --summary : only print a summary - 1 line per reference. --params : print the parameter settings

./bam dumpIndex --bamIndex <bamIndexFile> [--refID <ref#>] [--summary] [--params]

--refName : the SAM/BAM reference Name to read (either this or refID can be specified)

./bam readReference --refFile <referenceFilename> --refName <reference Name>--start <0 based start> --end <0 based end>|--numBases <number of bases>[--params]