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Adding require for Coverage Conversion and related tests #1472

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@devin-petersohn
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@devin-petersohn devin-petersohn commented Apr 4, 2017

Resolves #1471

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@coveralls coveralls commented Apr 4, 2017

Coverage Status

Coverage increased (+0.002%) to 81.535% when pulling f6e726f on devin-petersohn:issue#1471nullpointer into b26b851 on bigdatagenomics:master.

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@AmplabJenkins AmplabJenkins commented Apr 4, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1927/
Test PASSed.

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@fnothaft fnothaft left a comment

LGTM, but please switch try/catch to intercept. Thanks @devin-petersohn!

.setEnd(2)
.setScore(100)
.build()
try {

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fnothaft Apr 4, 2017
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Use intercept[IllegalArgumentException] instead of try/catch.

.setEnd(2)
.setScore(100)
.build()
try {

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fnothaft Apr 4, 2017
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Ditto

.setEnd(2)
.setScore(100)
.build()
try {

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fnothaft Apr 4, 2017
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Ditto.

.setStart(1)
.setScore(100)
.build()
try {

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fnothaft Apr 4, 2017
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Ditto.

.setStart(1)
.setEnd(2)
.build()
try {

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fnothaft Apr 4, 2017
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Ditto.

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@coveralls coveralls commented Apr 4, 2017

Coverage Status

Coverage increased (+0.002%) to 81.535% when pulling 7a6d8d9 on devin-petersohn:issue#1471nullpointer into b26b851 on bigdatagenomics:master.

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@AmplabJenkins AmplabJenkins commented Apr 4, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1928/
Test PASSed.

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@fnothaft fnothaft left a comment

One small nit! Thanks @devin-petersohn!

.build()

val caughtWithEmptyContigName =
intercept[java.lang.IllegalArgumentException](Coverage(featureWithEmptyContigName))

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fnothaft Apr 4, 2017
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Small nit, but you shouldn't need java.lang. in front of IllegalArgumentException. Would you mind making the change throughout the file?

Addressing reviewer comments

Addressing reviewer comments
@devin-petersohn devin-petersohn force-pushed the devin-petersohn:issue#1471nullpointer branch from 7a6d8d9 to 690f948 Apr 4, 2017
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@coveralls coveralls commented Apr 4, 2017

Coverage Status

Coverage increased (+0.002%) to 81.535% when pulling 690f948 on devin-petersohn:issue#1471nullpointer into b26b851 on bigdatagenomics:master.

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@AmplabJenkins AmplabJenkins commented Apr 4, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1929/
Test PASSed.

@fnothaft fnothaft merged commit 98d2c92 into bigdatagenomics:master Apr 4, 2017
2 of 3 checks passed
2 of 3 checks passed
codacy/pr Not so good... This pull request quality could be better.
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coverage/coveralls Coverage increased (+0.002%) to 81.535%
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default Merged build finished.
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@fnothaft fnothaft commented Apr 4, 2017

Merged! Thanks @devin-petersohn!

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017
@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018
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