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, 17:48, 16 May 2012
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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. |
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− | 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. |
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| 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. |