diff --git a/R/Data.Processing.Report.r b/R/Data.Processing.Report.r index fff22d2be..788353527 100644 --- a/R/Data.Processing.Report.r +++ b/R/Data.Processing.Report.r @@ -25,6 +25,7 @@ if(is.na(sample_sets)){ read.delim(file=lanes, header= TRUE)->bylane; }else{ lanes->bylane + colnames(bylane)<-c(Initiative,Project,GSSR.ID,External.ID,WR.ID,Flowcell,Lane,Lane.Type,Library,AL_TOTAL_READS,AL_PF_READS,AL_PCT_PF_READS,AL_PF_NOISE_READS,AL_PF_READS_ALIGNED,AL_PCT_PF_READS_ALIGNED,AL_PF_HQ_ALIGNED_READS,AL_PF_HQ_ALIGNED_BASES,AL_PF_HQ_ALIGNED_Q20_BASES,AL_PF_HQ_MEDIAN_MISMATCHES,AL_MEAN_READ_LENGTH,AL_READS_ALIGNED_IN_PAIRS,AL_PCT_READS_ALIGNED_IN_PAIRS,AL_BAD_CYCLES,AL_PCT_STRAND_BALANCE,DUP_UNPAIRED_READS_EXAMINED,DUP_READ_PAIRS_EXAMINED,DUP_UNMAPPED_READS,DUP_UNPAIRED_READ_DUPLICATES,DUP_READ_PAIR_DUPLICATES,DUP_PERCENT_DUPLICATION,DUP_ESTIMATED_LIBRARY_SIZE,HS_BAIT_SET,HS_GENOME_SIZE,HS_LIBRARY_SIZE,HS_BAIT_TERRITORY,HS_TARGET_TERRITORY,HS_BAIT_DESIGN_EFFICIENCY,HS_TOTAL_READS,HS_PF_READS,HS_PF_UNIQUE_READS,HS_PCT_PF_READS,HS_PCT_PF_UQ_READS,HS_PCT_PF_UQ_READS_ALIGNED,HS_PF_UQ_READS_ALIGNED,HS_PF_UQ_BASES_ALIGNED,HS_ON_BAIT_BASES,HS_NEAR_BAIT_BASES,HS_OFF_BAIT_BASES,HS_ON_TARGET_BASES,HS_PCT_SELECTED_BASES,HS_PCT_OFF_BAIT,HS_ON_BAIT_VS_SELECTED,HS_MEAN_BAIT_COVERAGE,HS_MEAN_TARGET_COVERAGE,HS_FOLD_ENRICHMENT,HS_ZERO_CVG_TARGETS_PCT,HS_FOLD_80_BASE_PENALTY,HS_PCT_TARGET_BASES_2X,HS_PCT_TARGET_BASES_10X,HS_PCT_TARGET_BASES_20X,HS_PCT_TARGET_BASES_30X,HS_PENALTY_10X,HS_PENALTY_20X,HS_PENALTY_30X,SNP_TOTAL_SNPS,SNP_PCT_DBSNP,SNP_NUM_IN_DBSNP,Lane.IC.Matches,Lane.IC.PCT.Mean.RD1.Err.Rate,Lane.IC.PCT.Mean.RD2.Err.Rate,FP_PANEL_NAME,FP_PANEL_SNPS,FP_CONFIDENT_CALLS,FP_CONFIDENT_MATCHING_SNPS,FP_CONFIDENT_CALLED_PCT,FP_CONFIDENT_MATCHING_SNPS_PCT,LPCNCRD_REFERENCE,LPCNCRD_NON_REFERENCE,LPCNCRD_PCT_CONCORDANCE) } if(typeof(samples)=="character"){ read.delim(file=samples, header= TRUE)->bysample; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java index 4c7d25a7e..6716a4f35 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java @@ -15,13 +15,13 @@ public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEv long nTi = 0; @DataPoint(name = "tv_count", description = "number of transversion loci") long nTv = 0; - @DataPoint(name = "ti/tv ratio", description = "the transition to transversion ratio") + @DataPoint(name = "ti/tv_ratio", description = "the transition to transversion ratio") double tiTvRatio = 0.0; @DataPoint(name = "ti_count_comp", description = "number of comp transition sites") long nTiInComp = 0; @DataPoint(name = "tv_count_comp", description = "number of comp transversion sites") long nTvInComp = 0; - @DataPoint(name = "ti/tv ratio standard", description = "the transition to transversion ratio for comp sites") + @DataPoint(name = "ti/tv_ratio_standard", description = "the transition to transversion ratio for comp sites") double TiTvRatioStandard = 0.0; public TiTvVariantEvaluator(VariantEvalWalker parent) { @@ -65,4 +65,4 @@ public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEv this.tiTvRatio = rate(nTi,nTv); this.TiTvRatioStandard = rate(nTiInComp, nTvInComp); } -} \ No newline at end of file +}