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scala.MatchError RegExp does not catch colons in value part properly #1061

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pauca opened this issue Jun 30, 2016 · 1 comment
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scala.MatchError RegExp does not catch colons in value part properly #1061

pauca opened this issue Jun 30, 2016 · 1 comment
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@fnothaft
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bug
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0.20.0

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@pauca
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pauca commented Jun 30, 2016

line

adam/adam-core/src/main/scala/org/bdgenomics/adam/util/AttributeUtils.scala

Line 31 in b29d204

val attrRegex = RegExp("([^:]{2,4}):([AifZHB]):([cCiIsSf]{1},)?(.*)")

with
val attrRegex = RegExp("([^:]{2,4}):([AifZHB]):([cCiIsSf]{1},)?(.*)")

does not handle properly alignmentrecords with attributes like
OQ:Z:C55/15D:::::::.7GFFAFDA442.40F=AGHHE
ie. have colons in the value part

some problematic reads are contained in gatk bundle file CEUTrio.HiSeq.WGS.b37.NA12878.bam

scala> BamWriter.adamSAMSave( "output.bam", bam.sequences, bam.recordGroups , true, true ,false)
2016-06-30 17:01:41 ERROR Utils:95 - Aborting task
scala.MatchError: Z:C, (of class java.lang.String)
    at org.bdgenomics.adam.util.AttributeUtils$.createAttribute(AttributeUtils.scala:92)
    at org.bdgenomics.adam.util.AttributeUtils$.parseAttribute(AttributeUtils.scala:74)
    at org.bdgenomics.adam.util.AttributeUtils$$anonfun$parseAttributes$2.apply(AttributeUtils.scala:61)
@fnothaft
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fnothaft commented Jul 1, 2016

Thanks for reporting this @pauca! We will look into this in the next week. We have some separate logic to extract the OQ field, and I think this isn't getting handled properly.

@fnothaft fnothaft added the bug label Jul 1, 2016
@fnothaft fnothaft added this to the 0.20.0 milestone Jul 1, 2016
@fnothaft fnothaft self-assigned this Jul 16, 2016
@fnothaft fnothaft mentioned this issue Jul 17, 2016
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fnothaft added a commit to fnothaft/adam that referenced this issue Jul 17, 2016
@fnothaft
[ADAM-1061] Fix attribute regex bug.
b49fe5e 
We had a bug in `org.bdgenomics.adam.util.AttributeUtils` where the regex for
splitting out the formatting string for array attributes was applied to all
attributes. In an array attribute (SAM "B" tags), the type of the array elements
is encoded before the attribute values, and is split off by commas. E.g.,
"B:i,1,2,3". If the attribute is a string (SAM "Z" tags), commas are allowed.
To resolve this, I split this regex into two regexes. We only apply the
regex for splitting out the array type if we are working on an array
attribute. This resolves bigdatagenomics#1061.
@fnothaft fnothaft mentioned this issue Jul 17, 2016
Merged
fnothaft added a commit to fnothaft/adam that referenced this issue Jul 18, 2016
@fnothaft
[ADAM-1061] Fix attribute regex bug.
1b482cb 
We had a bug in `org.bdgenomics.adam.util.AttributeUtils` where the regex for
splitting out the formatting string for array attributes was applied to all
attributes. In an array attribute (SAM "B" tags), the type of the array elements
is encoded before the attribute values, and is split off by commas. E.g.,
"B:i,1,2,3". If the attribute is a string (SAM "Z" tags), commas are allowed.
To resolve this, I split this regex into two regexes. We only apply the
regex for splitting out the array type if we are working on an array
attribute. This resolves bigdatagenomics#1061.
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