Ultima, New/Updated Features #8579
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the number of reads in the locus that pass the FeatureMap filters, regardless of whether the considered base matches the reference or not
format <name>[,<type>[,<desc>]]. types: Integer, Float, String, Character, Fl Defaults to type String Defaults to desc: copy-attr: <name>
added deviation to reports report to use true base instead of aligned Fixed hardcoded 12-mer (partial fix) --add-mean-call parameter added ReadProbs and ReadMeanCall added merge changes
- range extended - clipping implemented
Adding option to omit lines with zero count from report. Note that some initial lines w/ 0 are kept to make sure a table will be output even if empty. Also better handling of unmapped reads.
meganshand
reviewed
Nov 27, 2023
src/main/java/org/broadinstitute/hellbender/tools/walkers/featuremapping/FlowFeatureMapper.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/featuremapping/FlowFeatureMapper.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/featuremapping/FlowFeatureMapper.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/featuremapping/SNVMapper.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/groundtruth/GroundTruthScorer.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/groundtruth/GroundTruthScorer.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/groundtruth/GroundTruthScorer.java
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New: GroundTruthScorer
Update: FlowFeatureMapper