FlowFeatureMapper: added surrounding-median-quality-size feature #8222
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options, resulting VCF attr: X_SMQ_LEFT, X_SMQ_RIGHT
ilyasoifer
approved these changes
Mar 5, 2023
meganshand
approved these changes
Mar 6, 2023
| @@ -1,8 +1,11 @@ | |||
| package org.broadinstitute.hellbender.tools.walkers.featuremapping; | |||
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| import htsjdk.samtools.CigarElement; | |||
| import org.apache.commons.lang.ArrayUtils; | |||
| import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; | |||
| import org.apache.commons.text.similarity.LevenshteinDistance; | ||
| import org.broadinstitute.hellbender.engine.ReferenceContext; | ||
| import org.broadinstitute.hellbender.utils.MathUtils; |
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and this import as well can be removed.
| from = Math.max(0, Math.min(quals.length, from)); | ||
| to = Math.max(0, Math.min(quals.length, to - 1)); | ||
| if ( from > to ) { | ||
| return 0; |
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Should this be an error rather than returning 0?
| // calc median | ||
| byte[] range = Arrays.copyOfRange(quals, from, to + 1); | ||
| if ( range.length == 0 ) { | ||
| return 0; |
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same question about an error message here? 0 seems like a different value than missing.
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New feature: calculates the median quality over the N bases following or preceding the reported substitution.
For example, in the case where you have the following sequence and quality:
ATGACTGCA
II5II++5+
Where C is a substitution relative to the reference and the other bases match the reference.
The median of the qualities of the 4 bases after the substitution, ++5+, would be 20 (I = BQ40, 5 = BQ30, + = BQ20), and of the 4 bases before, II5I, 40.