does it make any sense to (Unix) pipe input into Picard SortSam, or will SortSam wait for all the input before starting?
For example, if I have the command
samtools view -Shu in.sam | \ java -Xmx4g SortSam.jar I=/dev/stdin O=sorted.bam SO=coordinate VALIDATION_STRINGENCY=SILENT
Will SortSam already do some work on the reads it gets from samtools view (e.g. by putting new reads in place) or will it wait for ALL reads from samtools until it starts sorting? In the latter case I would have SortSam running and blocking memory without doing something for the execution time of samtools view. Does anybody know?