FlowFeatureMapper speed improvements #8982
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…easing cache size
...adinstitute/hellbender/tools/walkers/featuremapping/FlowFeatureMapperArgumentCollection.java
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| /** | ||
| * do not emit edit distance at all | ||
| **/ | ||
| @Argument(fullName = "no-edit-distance", doc = "do not emit edit distance at all ?", optional = true) |
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Do we need this option?
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I imagine that these changes are going to raise some questions. Can you please add description in the PR?
| @@ -759,5 +886,35 @@ private FeatureMapper buildMapper() { | |||
| throw new GATKException("unsupported mappingFeature: " + fmArgs.mappingFeature); | |||
| } | |||
| } | |||
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| private FlowBasedRead buildTrimmedFlowBasedRead(final GATKRead read, final TrimInfo trimInfo, final FlowBasedReadUtils.ReadGroupInfo rgInfo) { | |||
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I think that this code might be duplicated.
HaplotypeCaller routinely trims reads. Could you check if there is a function like that?
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I have refactored this code to be closer in naming convention to its purpose
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Really sorry for being a pain, can you explain why functions from ReadClipper (e.g. SoftClipByReadCoordinates) etc. can't be used for this task?
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@ilyasoifer I have addressed your comments. Thank you |
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@ilyasoifer could you please take a look at the two failing CI/tests and see if there is something to be done - or it is a usual/environmental thing? Thanx |
@dror27 - looks like an environment thing (because I see that other PRs also fail), but let's wait for a bit with merging |
Additional changes include: