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Transcript list (userRequestedTranscripts) is acting as a filter, when it should be for prioritizing transcripts during selection. #4918

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LeeTL1220 opened this issue Jun 20, 2018 · 3 comments
Closed
1 task

Transcript list (userRequestedTranscripts) is acting as a filter, when it should be for prioritizing transcripts during selection. #4918

LeeTL1220 opened this issue Jun 20, 2018 · 3 comments
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bug Funcotator PRIORITY_HIGH

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@LeeTL1220
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Bug Report

Affected tool(s) or class(es)

Funcotator

Affected version(s)

  • Latest master branch as of [June 19, 2018]

Expected behavior

The transcript list should define transcript priority. In other words, among transcripts that overlap a variant, any that appear on the transcript list should be given highest priority (above the EFFECT or CANONICAL selection)

Actual behavior

Currently, the transcript list is a filter -- i.e. if a transcript is not in the list, it will never be used.
@LeeTL1220
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@jonn-smith Hey, I think the fix for this is trivial. I believe that the sorting is already done and we just need to remove the filter line in Funcotator.java.

@LeeTL1220
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And need to add tests?

@LeeTL1220 LeeTL1220 self-assigned this Jun 20, 2018
@jonn-smith
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Yeah - I just looked. You're correct.

LeeTL1220 added a commit that referenced this issue Jun 21, 2018
@LeeTL1220
- User defined transcripts were being used as a filter rather than a …
1cf9fd7 
…priority order. The filtering step has been eliminated. Fixes #4918

- Fixed issue where locus level ranking was being reversed.  Updated tests.  This was identified thanks to the thousands of tests in Funcotator (only one failed).
@LeeTL1220 LeeTL1220 mentioned this issue Jun 21, 2018
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LeeTL1220 added a commit that referenced this issue Jun 22, 2018
@LeeTL1220
- User defined transcripts were being used as a filter rather than a …
8e00e3a 
…priority order. The filtering step has been eliminated. Fixes #4918

- Fixed issue where locus level ranking was being reversed.  Updated tests.  This was identified thanks to the thousands of tests in Funcotator (only one failed).
LeeTL1220 added a commit that referenced this issue Jun 22, 2018
@LeeTL1220
- User defined transcripts were being used as a filter rather than a …
ee7c717 
…priority order. The filtering step has been eliminated. Fixes #4918 (#4931)

- User defined transcripts were being used as a filter rather than a priority order.  The filtering step has been eliminated.  Closes #4918 
- Fixed previously unidentified issue where locus level ranking was being reversed.  Updated tests.  This was identified thanks to the thousands of tests in Funcotator (only one failed, but that was all it took).
danxmoran pushed a commit that referenced this issue Jun 26, 2018
@LeeTL1220 @danxmoran
- User defined transcripts were being used as a filter rather than a …
f783948 
…priority order. The filtering step has been eliminated. Fixes #4918 (#4931)

- User defined transcripts were being used as a filter rather than a priority order.  The filtering step has been eliminated.  Closes #4918 
- Fixed previously unidentified issue where locus level ranking was being reversed.  Updated tests.  This was identified thanks to the thousands of tests in Funcotator (only one failed, but that was all it took).
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