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MDTagging fails on GRCh38 #1192

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fnothaft opened this Issue Oct 3, 2016 · 8 comments

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fnothaft commented Oct 3, 2016

I was running the transform -add_md_tags code on GRCh38, and was getting contig name mismatches that caused failures. It looked like a header parsing problem. TBD. I need to look back in the logs for the stack trace.

@fnothaft fnothaft added the bug label Oct 3, 2016

@fnothaft fnothaft self-assigned this Oct 3, 2016

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heuermh Oct 6, 2016

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@fnothaft thinking about cutting a 0.20.0 release sooner rather than later, would this need to go?

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heuermh commented Oct 6, 2016

@fnothaft thinking about cutting a 0.20.0 release sooner rather than later, would this need to go?

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Yeah, from inspection, I've found that this isn't "MD tagging is borked", but rather it is "loading the GRCh38 FASTA is borked", which is IMO a showstopper.

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fnothaft commented Oct 6, 2016

Yeah, from inspection, I've found that this isn't "MD tagging is borked", but rather it is "loading the GRCh38 FASTA is borked", which is IMO a showstopper.

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I'm hoping to have a PR today or tomorrow.

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fnothaft commented Oct 6, 2016

I'm hoping to have a PR today or tomorrow.

@heuermh heuermh added this to the 0.20.0 milestone Oct 6, 2016

@heuermh heuermh referenced this issue Oct 6, 2016

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Release ADAM version 0.20.0 #1048

47 of 61 tasks complete
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Mind if I add a new 0.22 milestone, rework the 0.20 and 0.21 milestones, and prepare for a 0.20.0 release on Monday Oct 10th?

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heuermh commented Oct 6, 2016

Mind if I add a new 0.22 milestone, rework the 0.20 and 0.21 milestones, and prepare for a 0.20.0 release on Monday Oct 10th?

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@heuermh What would get kicked from 0.20.0 to 0.21.0? The variant refactoring? Otherwise, I'd reallllly like to get the pipe stuff in to 0.20.0, as well as this.

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fnothaft commented Oct 6, 2016

@heuermh What would get kicked from 0.20.0 to 0.21.0? The variant refactoring? Otherwise, I'd reallllly like to get the pipe stuff in to 0.20.0, as well as this.

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What would the timing be for 0.20.0, 0.21.0, etc?

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fnothaft commented Oct 6, 2016

What would the timing be for 0.20.0, 0.21.0, etc?

fnothaft added a commit to fnothaft/adam that referenced this issue Oct 6, 2016

[ADAM-1192] Correctly handle other whitespace in FASTA description.
Resolves #1192. More broadly handles whitespace in the FASTA description, and
also disregards FASTA metadata which is inlined.

fnothaft added a commit to fnothaft/adam that referenced this issue Oct 6, 2016

[ADAM-1192] Correctly handle other whitespace in FASTA description.
Resolves #1192. More broadly handles whitespace in the FASTA description, and
also disregards FASTA metadata which is inlined.
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I'd bump everything but this to 0.21. I'm not sure I have bandwidth to fully test the pipe API stuff by Monday, since SnpEff is perhaps not the best first thing to try, given the variant annotation refactor is still incomplete. Have other uses for the pipe API in mind?

For dates I'd propose Oct 10th for 0.20.0, Dec 10th for 0.21, and sometime in 2017 for 0.22.

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heuermh commented Oct 6, 2016

I'd bump everything but this to 0.21. I'm not sure I have bandwidth to fully test the pipe API stuff by Monday, since SnpEff is perhaps not the best first thing to try, given the variant annotation refactor is still incomplete. Have other uses for the pipe API in mind?

For dates I'd propose Oct 10th for 0.20.0, Dec 10th for 0.21, and sometime in 2017 for 0.22.

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Have other uses for the pipe API in mind?

Yes, I'm rewriting https://github.com/bigdatagenomics/snappea using the pipe API and need a stable release with the pipe API before December.

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fnothaft commented Oct 6, 2016

Have other uses for the pipe API in mind?

Yes, I'm rewriting https://github.com/bigdatagenomics/snappea using the pipe API and need a stable release with the pipe API before December.

fnothaft added a commit to fnothaft/adam that referenced this issue Oct 6, 2016

[ADAM-1194] Correctly handle other whitespace in FASTA description.
Resolves #1192. More broadly handles whitespace in the FASTA description, and
also disregards FASTA metadata which is inlined.

@heuermh heuermh closed this in #1198 Oct 8, 2016

heuermh added a commit that referenced this issue Oct 8, 2016

[ADAM-1194] Correctly handle other whitespace in FASTA description.
Resolves #1192. More broadly handles whitespace in the FASTA description, and
also disregards FASTA metadata which is inlined.
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