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ReferenceRegion.apply(AlignmentRecord) should not NPE on unmapped reads #1099

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fnothaft opened this issue Aug 1, 2016 · 3 comments
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ReferenceRegion.apply(AlignmentRecord) should not NPE on unmapped reads #1099

fnothaft opened this issue Aug 1, 2016 · 3 comments
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bug
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0.20.0

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@fnothaft
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fnothaft commented Aug 1, 2016

This is a little one that's bugged me for a long time. We should have a require that checks whether the read is mapped and throws a more informative error message.
@fnothaft fnothaft added the bug label Aug 1, 2016
@fnothaft fnothaft added this to the 0.20.0 milestone Aug 1, 2016
@fnothaft fnothaft self-assigned this Aug 1, 2016
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heuermh commented Aug 1, 2016

Dupe of #821?

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fnothaft commented Aug 1, 2016

Nah, I would categorize #821 differently, since #821 is the join operation.

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fnothaft commented Aug 1, 2016

Also, #821 won't be resolved by the resolution to this. You'll still get an exception from calling ReferenceRegion.apply on an unmapped read, it'll just be a clearer exception.

fnothaft added a commit to fnothaft/adam that referenced this issue Aug 13, 2016
@fnothaft
[ADAM-1099] Make reference region not throw NPE.
7dd3022 
Resolves bigdatagenomics#1099.
@fnothaft fnothaft mentioned this issue Aug 13, 2016
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fnothaft added a commit to fnothaft/adam that referenced this issue Aug 14, 2016
@fnothaft
[ADAM-1099] Make reference region not throw NPE.
fd1b6b4 
Resolves bigdatagenomics#1099.
heuermh pushed a commit to heuermh/adam that referenced this issue Sep 27, 2016
@fnothaft @heuermh
[ADAM-1099] Make reference region not throw NPE.
9733c76 
Resolves bigdatagenomics#1099.
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