Eliminated the filtering by user transcripts and fixed locus level issue

[LeeTL1220]

• User defined transcripts were being used as a filter rather than a priority order. The filtering step has been eliminated. Closes Transcript list (userRequestedTranscripts) is acting as a filter, when it should be for prioritizing transcripts during selection. #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).

[codecov-io]

Codecov Report

Merging #4931 into master will increase coverage by 0.003%.
The diff coverage is 87.5%.

@@               Coverage Diff               @@
##              master     #4931       +/-   ##
===============================================
+ Coverage     80.471%   80.474%   +0.003%     
+ Complexity     17855     17854        -1     
===============================================
  Files           1093      1093               
  Lines          64295     64295               
  Branches       10378     10378               
===============================================
+ Hits           51739     51741        +2     
+ Misses          8501      8500        -1     
+ Partials        4055      4054        -1

Impacted Files	Coverage Δ	Complexity Δ
...dataSources/gencode/GencodeFuncotationFactory.java	83.308% <ø> (-0.325%)	160 <0> (-4)
...bender/utils/codecs/gencode/GencodeGtfFeature.java	78.453% <ø> (ø)	44 <0> (ø)	⬇️
...e/hellbender/tools/funcotator/FuncotatorUtils.java	80.357% <100%> (+0.027%)	169 <1> (+1)	⬆️
...nder/tools/funcotator/TranscriptSelectionMode.java	89.72% <83.333%> (ø)	1 <0> (ø)	⬇️
...utils/smithwaterman/SmithWatermanIntelAligner.java	90% <0%> (+40%)	3% <0%> (+2%)	⬆️

[jonn-smith]

Looks good to me.

[jonn-smith]

Once tests pass, feel free to merge.

[LeeTL1220]

Test failure is false alarm? @cmnbroad

[LeeTL1220]

@cmnbroad I am going to restart and see if it goes away. I am only bugging you about it since it is the python test. But my PR goes nowhere near that code.

[cmnbroad]

@LeeTL1220 Sorry - I didn't see the before it was restarted so I'm unsure which test failed. Looks like its nearly finished.

[LeeTL1220]

Only the python one...

…

On Fri, Jun 22, 2018 at 4:49 PM, Chris Norman ***@***.***> wrote: @LeeTL1220 <https://github.com/LeeTL1220> Sorry - I didn't see the before it was restarted so I'm unsure which test failed. Looks like its nearly finished. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4931 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACDXk7mrwN0gSPmXwZ7rs21ET7LGdoKJks5t_VhVgaJpZM4UynET> .

-- Lee Lichtenstein Broad Institute 75 Ames Street, Room 8011A Cambridge, MA 02142 617 714 8632

[LeeTL1220]

Assuming failed push test is transient, since this PR does not affect the python env.