BAM files can have either 'coordinate' sort order, or 'qname' one. The first one means to sort the file by (integer) reference ID, and for each reference sort corresponding reads by start coordinate. 'qname' sorting order is when reads are sorted lexicographically by their names. sambamba sort does an external sort on input file. That means it reads the source BAM file in chunks that fit into memory, sorts them and writes to a temporary directory, and then merges them. After merging temporary files are removed automatically. The sort is stable, and efforts have been done to make it multithreaded. Both sorting orders are supported. Default one is 'coordinate' because this is the one used for building index later. In order to switch to 'qname' sorting order, use -n|--sort-by-name flag.
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