Changes

Required Parameters: --in : the SAM/BAM file to convert to FastQ Optional Parameters: --readname : Process the BAM as readName sorted instead of coordinate if the header does not indicate a sort order. --splitRG : Split into RG specific fastqs. --qualField : Use the base quality from the specified tag rather than from the Quality field (default) --merge : Generate 1 interleaved (merged) FASTQ for paired-ends (unpaired in a separate file) use firstOut to override the filename of the interleaved file. --refFile : Reference file for converting '=' in the sequence to the actual base if '=' are found and the refFile is not specified, 'N' is written to the FASTQ --firstRNExt : read name extension to use for first read in a pair default is "/1" --secondRNExt : read name extension to use for second read in a pair default is "/2" --rnPlus : Add the Read Name/extension to the '+' line of the fastq records --noReverseComp : Do not reverse complement reads marked as reverse --region : Only convert reads containing the specified region/nucleotide. Position formatted as: chr:pos:base pos (0-based) & base are optional. --gzip : Compress the output FASTQ files using gzip --noeof : Do not expect an EOF block on a bam file. --params : Print the parameter settings to stderr Optional OutputFile Names: --outBase : Base output name for generated output files --firstOut : Output name for the first in pair file over-rides setting of outBase --secondOut : Output name for the second in pair file over-rides setting of outBase --unpairedOut : Output name for unpaired reads over-rides setting of outBase