Port of CallableLoci from GATK3
#9031
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@jonn-smith I have some comments. I noticed a few things that are minor bugs around the inputs, and then there are some style things I would probably change.
src/main/java/org/broadinstitute/hellbender/tools/walkers/coverage/CallableLoci.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/coverage/CallableLoci.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/coverage/CallableLoci.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/coverage/CallableLoci.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/coverage/CallableLoci.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/coverage/CallableLoci.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/coverage/CallableLoci.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/coverage/CallableLoci.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/coverage/CallableLoci.java
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...t/java/org/broadinstitute/hellbender/tools/walkers/coverage/CallableLociIntegrationTest.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/coverage/CallableLoci.java
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@lbergelson @cmnbroad Thanks for the comments. This was an interesting first experiment in using LLM-assisted coding. Looks like it doesn't understand our codebase quite as well as I would like, though it did produce working code. I'll see if I can tweak things in the future. In the meantime, back to you @lbergelson for another round if you like. |
| @@ -46,9 +49,9 @@ | |||
| * <dt>LOW_COVERAGE</dt> | |||
| * <dd>There were fewer than min. depth bases at the locus, after applying filters</dd> | |||
| * <dt>EXCESSIVE_COVERAGE</dt> | |||
| * <dd>More than -maxDepth read at the locus, indicating some sort of mapping problem</dd> | |||
| * <dd>More than --max-depth read at the locus, indicating some sort of mapping problem</dd> | |||
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good catch, I didn't see these.
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| private static class StateCounter { |
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👍 I know it's a few more lines but I think it's much clearer.
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@jonn-smith Thanks for making the changes. I know they were kind of nitpicky but I think its better this way.
Ported
CallableLocifrom GATK3 as an experimental tool.I have not included tests, but have verified on a test file that the statistics and regions are basically identical to the GATK3 results.