Remove hardcoded limit on max homopolymer call #8088
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meganshand
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Nov 16, 2022
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…in results between JAVA8 and JAVA11
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@meganshand can you take a look again please?
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meganshand
reviewed
Dec 5, 2022
| @@ -264,7 +264,7 @@ public enum FlowMode { | |||
| MIN_BASE_QUALITY_SCORE_SHORT_NAME, "0", | |||
| FILTER_ALLELES, "true", | |||
| FILTER_ALLELES_SOR_THRESHOLD, "3", | |||
| FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME, "12", | |||
| FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME, String.valueOf(AssemblyBasedCallerUtils.DETERMINE_COLLAPSE_THRESHOLD), | |||
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Does this change the default for STANDARD/ADVANCED flow mode for older samples that don't have the mc tag?
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It should not, if there is no mc - then it will be 12
| @@ -3879,7 +3879,7 @@ chr9 81153765 . G <NON_REF> . . END=81153766 GT:DP:GQ:MIN_DP:PL 0/0:27:69:25:0,6 | |||
| chr9 81153767 . A <NON_REF> . . END=81153783 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,802 | |||
| chr9 81153784 . A <NON_REF> . . END=81153785 GT:DP:GQ:MIN_DP:PL 0/0:28:22:27:0,22,996 | |||
| chr9 81153786 . G <NON_REF> . . END=81153800 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1175 | |||
| chr9 81153801 . C CA,<NON_REF> 0 . ASSEMBLED_HAPS=10;AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=90000.00|10800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=8,17|3,0|0,0;BaseQRankSum=0.000;DP=29;ExcessHet=0.0000;FILTERED_HAPS=6;HAPCOMP=4,0;HAPDOM=0.500,0.00;HEC=55,3,2,1,0,0;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=104400,29;ReadPosRankSum=0.929;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/0:25,3,0:28:18:0,18,58,75,692,115:8,17,3,0 | |||
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The change in HAPCOMP annotations is expected?
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Yes, I fixed a small bug in assemblycomplexity annotation that caused a different result between two different java versions, it subtly changed the output, but it should be fine
| ? new LongHomopolymerHaplotypeCollapsingEngine(argumentCollection.flowAssemblyCollapseHKerSize, argumentCollection.flowAssemblyCollapsePartialMode, fullReferenceWithPadding, | ||
| int collapseHmerSize = argumentCollection.flowAssemblyCollapseHKerSize; | ||
| if (collapseHmerSize == DETERMINE_COLLAPSE_THRESHOLD){ | ||
| collapseHmerSize = AssemblyBasedCallerUtils.determineFlowAssemblyColapseHmer(header); |
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Suggested change
| collapseHmerSize = AssemblyBasedCallerUtils.determineFlowAssemblyColapseHmer(header); | |
| collapseHmerSize = AssemblyBasedCallerUtils.determineFlowAssemblyCollapseHmer(header); |
| @@ -411,6 +417,18 @@ public static AssemblyResultSet assembleReads(final AssemblyRegion region, | |||
| } | |||
| } | |||
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| private static int determineFlowAssemblyColapseHmer(SAMFileHeader readsHeader) { | |||
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Suggested change
| private static int determineFlowAssemblyColapseHmer(SAMFileHeader readsHeader) { | |
| private static int determineFlowAssemblyCollapseHmer(SAMFileHeader readsHeader) { |
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