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Changing a name of a column for variantevals output for easier reading by R--let me know if this needs to be updated elsewhere; it's just a space to an underscore. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4062 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2010-08-19 19:18:16 +00:00
parent 4b94f8c21b
commit 8054b6b295
2 changed files with 4 additions and 3 deletions
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1
R/Data.Processing.Report.r
View File

@ -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;

6
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java
View File

@ -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);
}
}
}