forward port new picard functionality--query-sorted mark duplicates

[yfarjoun]

see: broadinstitute/picard#491

[akiezun]

This is blocked by #1210
(note though that MarkDuplicatesSpark already defaults to query-sorted input because it improves speed by 2x by doing only 1 shuffle).

[yfarjoun]

interesting, but the functionality should change then to mark the secondary
and supplementaries and unmapped mates..

On Sat, Mar 26, 2016 at 12:29 AM, Adam Kiezun [email protected]
wrote:

This is blocked by #1210
#1210
(note though that MarkDuplicatesSpark already defaults to query-sorted
input because it improves speed by 2x by doing only 1 shuffle).

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#1636 (comment)

[magicDGS]

This can be closed as Picard is pull-out as a dependency, no @droazen?

[droazen]

Closing as duplicate of #3705