MarkDuplicates strategy of flow based reads that looks only at the qualities close to the end of the read #1942
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meganshand
reviewed
Feb 12, 2024
| public enum FLOW_DUPLICATE_SELECTION_STRATEGY { | ||
| FLOW_QUALITY_SUM_STRATEGY, | ||
| FLOW_END_QUALITY_STRATEGY | ||
| } | ||
| @Argument(doc = "enable parameters and behavior specific to flow based reads.", optional = true) | ||
| public boolean FLOW_MODE = false; | ||
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| @Argument(doc = "Use specific quality summing strategy for flow based reads. The strategy ensures that the same " + |
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Is this doc still up to date with the new enum?
src/main/java/picard/sam/markduplicates/MarkDuplicatesForFlowHelper.java
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| @@ -236,8 +273,8 @@ static protected int getFlowSumOfBaseQualities(final SAMRecord rec, final int th | |||
| final byte[] bases = rec.getReadBases(); | |||
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| // create iteration range and direction | |||
| final int startingOffset = !rec.getReadNegativeStrandFlag() ? 0 : bases.length; | |||
| final int endOffset = !rec.getReadNegativeStrandFlag() ? bases.length : 0; | |||
| final int startingOffset = !rec.getReadNegativeStrandFlag() ? 0 : bases.length - 1; | |||
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was this previously a bug? I don't see how this change is related to allowing a range in the start position or changing the quality score calculation.
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Was a bug indeed
| @@ -59,6 +60,7 @@ public class MarkDuplicatesForFlowHelper implements MarkDuplicatesHelper { | |||
| public static final char[] CLIPPING_TAG_CONTAINS_AQ = {'A', 'Q'}; | |||
| public static final char[] CLIPPING_TAG_CONTAINS_QZ = {'Q', 'Z'}; | |||
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| public static final int DIST_FROM_END = 10; | |||
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It's worth mentioning that the distance from the end is hard coded as 10 bases for the FLOW_END_QUALITY_STRATEGY
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Mentioned in the parameter description. Is this OK?
ilyasoifer
commented
Feb 14, 2024
meganshand
approved these changes
Feb 14, 2024
| @@ -59,6 +60,7 @@ public class MarkDuplicatesForFlowHelper implements MarkDuplicatesHelper { | |||
| public static final char[] CLIPPING_TAG_CONTAINS_AQ = {'A', 'Q'}; | |||
| public static final char[] CLIPPING_TAG_CONTAINS_QZ = {'Q', 'Z'}; | |||
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| public static final int DIST_FROM_END = 10; | |||
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Description
UNPAIRED_START_UNCERTAINTYin flow mode.FLOW_END_QUALITY_STRATEGY.Checklist (never delete this)
Never delete this, it is our record that procedure was followed. If you find that for whatever reason one of the checklist points doesn't apply to your PR, you can leave it unchecked but please add an explanation below.
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