From 8fbcab53dd4ade836c2229cd47e9c2968742ad49 Mon Sep 17 00:00:00 2001
From: Gavin Ha <gavinha@broadinstitute.org>
Date: Wed, 6 Feb 2019 19:42:57 -0500
Subject: [PATCH 1/2] ploidy2 path fix Typo in ploidyRun2 path corrected. Fixes
 #65 Thanks to @aleighgreen for finding this typo

---
 scripts/snakemake/TitanCNA.snakefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/snakemake/TitanCNA.snakefile b/scripts/snakemake/TitanCNA.snakefile
index 098b582..fa56281 100644
--- a/scripts/snakemake/TitanCNA.snakefile
+++ b/scripts/snakemake/TitanCNA.snakefile
@@ -71,7 +71,7 @@ rule selectSolution:
 		"logs/titan/selectSolution.log"
 	shell:
 		"""
-		ploidyRun2=results/titan/titanCNA_ploidy2/
+		ploidyRun2=results/titan/hmm/titanCNA_ploidy2/
 		if [ -d results/titan/hmm/titanCNA_ploidy3/ ]; then
 			ploidyRun3=results/titan/hmm/titanCNA_ploidy3/
 		else
@@ -84,4 +84,4 @@ rule selectSolution:
 		fi
 		Rscript {params.solutionRscript} --ploidyRun2 $ploidyRun2 --ploidyRun3 $ploidyRun3 --ploidyRun4 $ploidyRun4 --threshold {params.threshold} --outFile {output} > {log} 2> {log}
 		"""
-	
\ No newline at end of file
+	

From 88a51c0a327c8a590563894b829539b538a95fa5 Mon Sep 17 00:00:00 2001
From: Gavin Ha <gavinha@broadinstitute.org>
Date: Fri, 8 Feb 2019 14:30:59 -0500
Subject: [PATCH 2/2] fix Corrected_Ratio column in output segs file
 Corrected_Ratio contained all NAs because correctIntegerCN() was looking at
 the Median_HaplotypeRatio column.  Median_HaplotypeRatio should only be
 present in the segs and results objects/files for 10X Genomics WGS data. Now,
 Median_HaplotypeRatio will not be included in the output files if not using
 TitanCNA_10X_snakemake pipeline. Fixes #67. Thanks to @aleighgreen for
 catching this bug.

---
 R/utils.R | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 164169a..dc62c75 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1080,8 +1080,12 @@ outputTitanSegments <- function(results, id, convergeParams, filename = NULL, ig
 	  results$HaplotypeRatio <- pmax(results$HaplotypeRatio, 1-results$HaplotypeRatio)
 	}
   segs <- data.table(Sample = character(), Chromosome = character(), Start_Position.bp. = integer(), 
-                     End_Position.bp. = integer(), Length.snp. = integer(), Median_Ratio = numeric(),
-                     Median_HaplotypeRatio = numeric(), Median_logR = numeric(), TITAN_state = integer(),
+                     End_Position.bp. = integer(), Length.snp. = integer(), Median_Ratio = numeric())
+  # add HaplotypeRatio column if also present in results object
+  if (!is.null(results$HaplotypeRatio)){
+  	segs <- cbind(segs, Median_HaplotypeRatio = numeric())
+  }
+  segs <- cbind(segs, Median_logR = numeric(), TITAN_state = integer(),
                      TITAN_call = character(), Copy_Number = integer(), MinorCN = integer(), MajorCN = integer(),
                      Clonal_Cluster = integer(), Cellular_Prevalence = numeric())[1:numSegs]
 	segs[, Sample := id]
@@ -1106,8 +1110,6 @@ outputTitanSegments <- function(results, id, convergeParams, filename = NULL, ig
 		segs[j, "Cellular_Prevalence"] <- segDF[1, "CellularPrevalence"]
 		if (!is.null(segDF$HaplotypeRatio)){
 		  segs[j, "Median_HaplotypeRatio"] <- round(median(segDF$HaplotypeRatio, na.rm = TRUE), digits = 6)
-		}else{
-		  segs[j, "Median_HaplotypeRatio"] <- NA
 		}
 		if (segDF[1, "Chr"] == segDF[numR, "Chr"]){
 			segs[j, "End_Position.bp."] <- segDF[numR, "Position"]
@@ -1180,7 +1182,9 @@ correctIntegerCN <- function(cn, segs, purity, ploidy, maxCNtoCorrect.autosomes
 	## determine if Median_HaplotypeRatio (segs) and HaplotypeRatio (cn) columns exists (i.e. 10X analysis)
 	segs.allelicRatioColName <- "Median_Ratio"
 	if ("Median_HaplotypeRatio" %in% names(segs)){
-		segs.allelicRatioColName <- "Median_HaplotypeRatio"
+		if (segs[, Median_HaplotypeRatio]){
+			segs.allelicRatioColName <- "Median_HaplotypeRatio"
+		}
 	}
 	cn.allelicRatioColName <- "AllelicRatio"
 	if ("HaplotypeRatio" %in% names(cn)){