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In align_and_count, change default to count only properly-paired reads#534
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tomkinsc wants to merge 2 commits intomasterbroadinstitute/viral-pipelines:masterfrom ct-align_and_count-filter-to-proper-by-defaultbroadinstitute/viral-pipelines:ct-align_and_count-filter-to-proper-by-defaultCopy head branch name to clipboard
