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Wrong filtering in Alignment metrics#943

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Ksenomorfa wants to merge 2 commits intobroadinstitute:masterbroadinstitute/picard:masterfrom EpamLifeSciencesTeam:epam-ls_WrongFilteringInAlignmentMetricsEpamLifeSciencesTeam/picard:epam-ls_WrongFilteringInAlignmentMetricsCopy head branch name to clipboard

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Commits on Sep 29, 2017

• Wrong filtering in Alignment metrics

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Commits on Oct 23, 2017

• * Add check for secondary reads

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  PolinaBevad

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