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FastqRecordConverter needs cleanup and tests #1172

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fnothaft opened this Issue Sep 15, 2016 · 5 comments

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fnothaft commented Sep 15, 2016

We need to refactor org.bdgenomics.adam.converters.FastqRecordConverter as there's a lot of code duplication between the AlignmentRecord and Fragment code paths. Also, there apparently are no tests for this class, which is surprising!

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zyxue Sep 27, 2016

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I would like to try to fix this issue, how do I get started?

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zyxue commented Sep 27, 2016

I would like to try to fix this issue, how do I get started?

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heuermh Sep 27, 2016

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@zyxue unit tests would be a good place to start. Once there is some test coverage, then start cleaning things up!

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heuermh commented Sep 27, 2016

@zyxue unit tests would be a good place to start. Once there is some test coverage, then start cleaning things up!

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Do I need spark to start the development? I just run another test suite, FastaConverter.scala, on IntelliJ, and seems the tests passed successfully.

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zyxue commented Sep 27, 2016

Do I need spark to start the development? I just run another test suite, FastaConverter.scala, on IntelliJ, and seems the tests passed successfully.

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The maven build (and by extension, the build in IntelliJ) is self contained.

You will need Spark to run the adam-submit and adam-shell commands in the bin directory though.

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heuermh commented Sep 27, 2016

The maven build (and by extension, the build in IntelliJ) is self contained.

You will need Spark to run the adam-submit and adam-shell commands in the bin directory though.

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Do you know why would the input be of type (Void, Text), see this line? Where is Void from, why not just Text?

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zyxue commented Sep 27, 2016

Do you know why would the input be of type (Void, Text), see this line? Where is Void from, why not just Text?

zyxue added a commit to zyxue/adam that referenced this issue Sep 28, 2016

@heuermh heuermh modified the milestone: 0.20.0 Oct 13, 2016

@fnothaft fnothaft closed this in df00eff Oct 13, 2016

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