Fix for incorrect output of dedup with --paired (#347)#363

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christianbioinf wants to merge 2 commits intoCGATOxford:masterfrom christianbioinf:{IS}_dedup_with_paired

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Commits on Jul 5, 2019

Fix for incorrect output of dedup with --paired (CGATOxford#347 )
christianbioinf
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Commits on Jul 8, 2019

Improvement of consistency in selection of read2 alignments for output with dedup and --paired as well as avoiding large memory footprint (CGATOxford#347 ).
christianbioinf
committed