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add JoinedFastqManifestPhred33 as a format for joined reads #162

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gregcaporaso opened this issue Nov 30, 2017 · 4 comments
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add JoinedFastqManifestPhred33 as a format for joined reads #162

gregcaporaso opened this issue Nov 30, 2017 · 4 comments

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@gregcaporaso
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@ebolyen
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ebolyen commented Nov 30, 2017

This seems like it kind of counteracts the distinction between semantic type and format, since there isn't really a difference here between single and joined from a data-structure perspective.

In my mind we would want to share the formats between SingleEnd and JoinedEnd as it means less code, testing, and transformers.

Granted the current naming is probably confusing.

@gregcaporaso
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gregcaporaso commented Dec 1, 2017

@ebolyen, that makes sense. It's really just the confusing naming that I'm trying to get around so I'm open to solutions that would help with that.

@thermokarst
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What about SingleOrJoinedFastqManifestPhred33 (coupled with deprecating SingleEnd...)?

@lizgehret
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This is handled here, closing as completed.

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