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readInFragment value is not properly read from parquet file into RDD[AlignmentRecord] #942

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jpdna opened this Issue Feb 13, 2016 · 1 comment

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jpdna commented Feb 13, 2016

readInFragment field is not properly loaded from adam parquet file into an RDD when running adam flagstat due to a bug in defining the list of projected fields in FlagStat.scala here
There are no longer firstOfPair / secondOfPair fields as these are replaced by values 0,1 in the readInFragment field. Currently readInFragment field is ignored in input and assumes its default value of 0 in the RDD.

We should check if this same type of error is repeated outside of FlagStat, and for any other fields.

To prevent this problem in future @fnothaft suggests in #941 autogeneration for field names enum used in projections

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heuermh Feb 13, 2016

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Meanwhile we should also fix this issue by hand.

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heuermh commented Feb 13, 2016

Meanwhile we should also fix this issue by hand.

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