Remove reliance on MD tags #622

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fnothaft opened this Issue Mar 17, 2015 · 1 comment

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fnothaft commented Mar 17, 2015

MD tags are arcane and poorly spec'd. Even further, many aligners don't emit MD tags. We're currently relying on MD tags for BQSR, INDEL realignment, etc. We should eliminate them from the codebase (and eliminate their "promotion" into the schema upstream?) to both eliminate complexity and to improve robustness.

I've eliminated the use of MD tags downstream in avocado.

@fnothaft fnothaft added this to the 0.17.0 milestone Mar 17, 2015

@fnothaft fnothaft modified the milestones: 1.0.0, 0.17.0 May 31, 2015

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fnothaft Mar 3, 2017

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This issue only BQSR and INDEL realignment. #1412 resolves this for INDEL realignment, and #1358 will resolve this for BQSR. Closing this in favor of those more targeted tickets/PRs.

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fnothaft commented Mar 3, 2017

This issue only BQSR and INDEL realignment. #1412 resolves this for INDEL realignment, and #1358 will resolve this for BQSR. Closing this in favor of those more targeted tickets/PRs.

@fnothaft fnothaft closed this Mar 3, 2017

@heuermh heuermh added this to Completed in Release 1.0.0 Mar 8, 2017

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