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Fixed debug log severity for read threading messages. #8419

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merged 3 commits into from
Aug 16, 2023
Merged

Fixed debug log severity for read threading messages. #8419

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24aebd6
Fixed debug log severity for read threading messages.
jonn-smith Jul 14, 2023
cc18791
Addressed review comments.
jonn-smith Aug 16, 2023
4713b87
Fixing one more spot with ternary log level.
jonn-smith Aug 16, 2023
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12 changes: 6 additions & 6 deletions ...titute/hellbender/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -396,7 +396,7 @@ List<Haplotype> findBestPaths(final Collection<T> graphs, final Map<T, AssemblyR
resultSet.add(h);
}

logger.log(debug ? Level.INFO : Level.OFF, () -> "Adding haplotype " + h.getCigar() + " from graph with kmer " + assemblyResult.getKmerSize());
logger.log(debug ? Level.INFO : Level.TRACE, () -> "Adding haplotype " + h.getCigar() + " from graph with kmer " + assemblyResult.getKmerSize());
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So the issue is that calling logger.log(Level.OFF, message) will print that message in every case if you turn the logger off? If thats true I actually want you to revert these to the way they were before they were recently refactored (which i reviewed and didn’t catch here)… replace them with the previous statements

if(debug) {
            logger.info( "Not using kmer size of " + kmerSize + " in read threading assembler because reference contains non-unique kmers");
}

}
}

Expand Down Expand Up @@ -623,7 +623,7 @@ private AssemblyResult createGraph(final Iterable<GATKRead> reads,
if ( !allowNonUniqueKmersInRef && !ReadThreadingGraph.determineNonUniqueKmers(
new ReadThreadingGraph.SequenceForKmers("ref", refHaplotype.getBases(), 0,
refHaplotype.getBases().length, 1, true), kmerSize).isEmpty() ) {
logger.log(debug ? Level.INFO : Level.OFF, () -> "Not using kmer size of " + kmerSize + " in read threading assembler because reference contains non-unique kmers");
logger.log(debug ? Level.INFO : Level.TRACE, () -> "Not using kmer size of " + kmerSize + " in read threading assembler because reference contains non-unique kmers");

return null;
}
Expand Down Expand Up @@ -655,13 +655,13 @@ private AssemblyResult createGraph(final Iterable<GATKRead> reads,

// sanity check: make sure there are no cycles in the graph, unless we are in experimental mode
if ( generateSeqGraph && rtgraph.hasCycles() ) {
logger.log(debug ? Level.INFO : Level.OFF, () -> "Not using kmer size of " + kmerSize + " in read threading assembler because it contains a cycle");
logger.log(debug ? Level.INFO : Level.TRACE, () -> "Not using kmer size of " + kmerSize + " in read threading assembler because it contains a cycle");
return null;
}

// sanity check: make sure the graph had enough complexity with the given kmer
if ( ! allowLowComplexityGraphs && rtgraph.isLowQualityGraph() ) {
logger.log(debug ? Level.INFO : Level.OFF, () -> "Not using kmer size of " + kmerSize + " in read threading assembler because it does not produce a graph with enough complexity");
logger.log(debug ? Level.INFO : Level.TRACE, () -> "Not using kmer size of " + kmerSize + " in read threading assembler because it does not produce a graph with enough complexity");
return null;
}

Expand Down Expand Up @@ -705,7 +705,7 @@ private AssemblyResult getAssemblyResult(final AbstractReadThreadingGraph rtgrap
return new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION, initialSeqGraph, null);
}

logger.log(debug ? Level.INFO : Level.OFF, () -> "Using kmer size of " + rtgraph.getKmerSize() + " in read threading assembler");
logger.log(debug ? Level.INFO : Level.TRACE, () -> "Using kmer size of " + rtgraph.getKmerSize() + " in read threading assembler");

initialSeqGraph.cleanNonRefPaths(); // TODO -- I don't this is possible by construction

Expand All @@ -719,7 +719,7 @@ private AssemblyResult getAssemblyResult(final AbstractReadThreadingGraph rtgrap
return new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION, null, rtgraph);
}

logger.log(debug ? Level.INFO : Level.OFF, () -> "Using kmer size of " + rtgraph.getKmerSize() + " in read threading assembler");
logger.log(debug ? Level.INFO : Level.TRACE, () -> "Using kmer size of " + rtgraph.getKmerSize() + " in read threading assembler");

final AssemblyResult cleaned = getResultSetForRTGraph(rtgraph);
final AssemblyResult.Status status = cleaned.getStatus();
Expand Down