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DoC of overlapping genes #16

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commented Jan 29, 2016

I have discovered that coverage stats generated for an interval are attributed only to the first gene on the list that overlaps the interval. Subsequent genes overlapping the interval are ignored. Here is a simple fix.

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commented Feb 17, 2016

@ronlevine Would you be able to look at this PR please? This sounds like something that would be useful for a lot of users but someone needs to check that it passes tests and also add a test for the new functionality. May need to ask the user for a test case.

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commented Feb 29, 2016

@vdauwera Will do.

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commented Mar 1, 2016

@seru71 Please add integration tests.

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commented Mar 1, 2016

@ronlevine External users don't have access to our testing infrastructure
so we need to add the tests ourselves. We can however request a test case.

On Tue, Mar 1, 2016 at 10:03 AM Ron Levine notifications@github.com wrote:

@seru71 https://github.com/seru71 Please add integration tests.


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#16 (comment).

Geraldine A. Van der Auwera, PhD
Manager of Outreach and Communications
Data Sciences and Data Engineering
Broad Institute

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commented Mar 1, 2016

@seru71 Do you have a test case that exercises this fix?

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commented Mar 1, 2016

Yes, I will post it in a moment. Need to recap a bit first.

On Tue, Mar 1, 2016 at 4:16 PM, Ron Levine notifications@github.com wrote:

@seru71 https://github.com/seru71 Do you have a test case that
exercises this fix?


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#16 (comment).

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commented Mar 1, 2016

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commented Mar 1, 2016

@seru71 Thanks for the files. What bam and reference did you use?

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commented Mar 1, 2016

I used bams from exome-seq, but any will do. In case of no coverage the
stats would just show 0. Reference genome was b37 from GATK's bundle.
On Mar 1, 2016 6:38 PM, "Ron Levine" notifications@github.com wrote:

@seru71 https://github.com/seru71 Thanks for the files. What bam and
reference did you use?


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#16 (comment).

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commented Sep 7, 2016

This was merged in and is available in version 3.6. Thanks @seru71 for your contribution!

@vdauwera vdauwera closed this Sep 7, 2016

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