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It works on both read/query name and coordinate sorted SAM/BAM files.
It works on both read/query name and coordinate sorted SAM/BAM files.
If you want to convert a SAM/BAM that is read/query name sorted but the SO field of the header does not specify "queryname", then use the [[#BAM File Is Sorted By Read Name (<code>--readname</code>)|--readName]] option.
If you want to convert a SAM/BAM that is read/query name sorted but the SO field of the header does not specify "queryname", then use the [[#BAM File Is Sorted By Read Name (--readname)|--readName]] option.
When processing files sorted by read name, the only requirement is that matching read names are next to each other. It does not need to be in strict alphabetical order.
When processing files sorted by read name, the only requirement is that matching read names are next to each other. It does not need to be in strict alphabetical order.
