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Genotype.getAnyAttribute incorrectly handles converting int[] to List<Integer> #274

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dfsurdyk opened this issue Jul 1, 2015 · 4 comments
Open

Genotype.getAnyAttribute incorrectly handles converting int[] to List<Integer> #274

dfsurdyk opened this issue Jul 1, 2015 · 4 comments

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@dfsurdyk
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dfsurdyk commented Jul 1, 2015

Both getAD() and getPL() return an int[], and doing Arrays.asList(int[]) will return a List<int[]> instead of List<Integer>.

https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/variant/variantcontext/Genotype.java#L544
dfsurdyk pushed a commit to dfsurdyk/htsjdk that referenced this issue Jul 2, 2015
Fix for incorrect return value.
0fe815a 
See: samtools#274
@dfsurdyk dfsurdyk changed the title Geotype.getAnyAttribute incorrectly handles converting int[] to List<Integer> Genotype.getAnyAttribute incorrectly handles converting int[] to List<Integer> Jul 2, 2015
dfsurdyk pushed a commit to dfsurdyk/htsjdk that referenced this issue Jul 2, 2015
Fix for incorrect return value in Genotype.getAnyAttribute()
d2966fa 
* The Genotype.getAnyAttribute() incorrectly handles converting int[] to
  List<Integer>.  Both getAD() and getPL() return an int[], and doing
  Arrays.asList(int[]) will return a List<int[]> instead of List<Integer>.

See: samtools#274
@dfsurdyk dfsurdyk mentioned this issue Jul 2, 2015
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@nh13
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nh13 commented Jul 2, 2015

Arrays.asList(int[]) will return `List``, so I am closing this issue.

@nh13 nh13 closed this as completed Jul 2, 2015
@nh13
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nh13 commented Jul 2, 2015

Wow, I am so wrong. Let us take a look at this.

@lbergelson lbergelson reopened this Jul 2, 2015
nh13 pushed a commit that referenced this issue Jul 23, 2015
Fix for incorrect return value in Genotype.getAnyAttribute()
b2638e0 
* The Genotype.getAnyAttribute() incorrectly handles converting int[] to
  List<Integer>.  Both getAD() and getPL() return an int[], and doing
  Arrays.asList(int[]) will return a List<int[]> instead of List<Integer>.

See: #274
@dfsurdyk
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@lbergelson - I think this can be closed:
#275

@yfarjoun
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yfarjoun commented Apr 1, 2019

My 2ct: I think we shoudl get rid of GetAnyAttribute and implement (as for the info field) getAttributeAsArray{String,Int,Float}

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@dfsurdyk @nh13 @yfarjoun @lbergelson