Remove hardcoded limit on max homopolymer call#8088
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ilyasoifer merged 9 commits intobroadinstitute:masterfrom Dec 7, 2022
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Remove hardcoded limit on max homopolymer call#8088ilyasoifer merged 9 commits intobroadinstitute:masterfrom
ilyasoifer merged 9 commits intobroadinstitute:masterfrom
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meganshand
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Nov 16, 2022
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This looks good. Do we have test cases that include this max class value in the header? If not it would be good to add at least one test file with the new header.
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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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Just a few minor questions about expected test output and default argument values.
| 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
| 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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| collapseHmerSize = AssemblyBasedCallerUtils.determineFlowAssemblyColapseHmer(header); | |
| collapseHmerSize = AssemblyBasedCallerUtils.determineFlowAssemblyCollapseHmer(header); |
| } | ||
| } | ||
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| private static int determineFlowAssemblyColapseHmer(SAMFileHeader readsHeader) { |
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| private static int determineFlowAssemblyColapseHmer(SAMFileHeader readsHeader) { | |
| private static int determineFlowAssemblyCollapseHmer(SAMFileHeader readsHeader) { |
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