From 248fb57df36dba192fb42cc37dd4d89ec8328594 Mon Sep 17 00:00:00 2001
From: 5Aki1 <e.kirbizakis@gmail.com>
Date: Sun, 9 Feb 2025 19:28:25 -0500
Subject: [PATCH 1/2] Fixed issue with restriction fragment aware background
 correction

---
 hichipper/lambdaProcess.R | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/hichipper/lambdaProcess.R b/hichipper/lambdaProcess.R
index b67f661..fb4f3d4 100644
--- a/hichipper/lambdaProcess.R
+++ b/hichipper/lambdaProcess.R
@@ -8,10 +8,14 @@ suppressMessages(suppressWarnings(library(data.table)))
 suppressMessages(suppressWarnings(library(reshape2)))
 
 args <- commandArgs(trailingOnly = TRUE)
-resfile <- args[1]
-treatmentfile <- args[2]
-backgroundfile <- args[3]
-outdir <- args[4]
+# resfile <- args[1]
+# treatmentfile <- args[2]
+# backgroundfile <- args[3]
+# outdir <- args[4]
+resfile <- "hichipper/MboI_resfrag_hg38.bed"
+treatmentfile <- "hichipper/22RV1_REP1_temporary_treat_pileup.bdg"
+backgroundfile <- "hichipper/22RV1_REP1_temporary_control_lambda.bdg"
+outdir <- "hichipper"
 K <- 1000000 # Number of loci to sample from 
 
 # Import Restriction Fragments / Convert to GRanges
@@ -65,8 +69,12 @@ computeRatioEtc <- function(treatmentfile, backgroundfile){
   # Compute nearest neighbor for background
   mid <- (start(cont) + end(cont))/2
   backmid <- as(data.frame(chrom=seqnames(cont), start=mid, end=mid), "GRanges")
-  mcols(cont)$dist <- mcols(distanceToNearest(backmid, resSites))[,1]
-  
+  nearestHits <- distanceToNearest(backmid, resSites)
+  nearestDist <- rep(NA, length(cont))
+  nearestDist[queryHits(nearestHits)] <- mcols(nearestHits)$distance
+  nearestDist[is.na(nearestDist)] <- 0
+  mcols(cont)$dist <- nearestDist
+
   vals <- tapply(txtVals/contVals, nndist, mean)
   
   # Write adjusted treatment (only filters out regions where no restriction enzyme information is contained)

From ce7863b78ae6b9042beb66c27ecef7b22fdee479 Mon Sep 17 00:00:00 2001
From: 5Aki1 <e.kirbizakis@gmail.com>
Date: Sun, 9 Feb 2025 19:31:39 -0500
Subject: [PATCH 2/2] Update lambdaProcess.R

---
 hichipper/lambdaProcess.R | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/hichipper/lambdaProcess.R b/hichipper/lambdaProcess.R
index fb4f3d4..2154787 100644
--- a/hichipper/lambdaProcess.R
+++ b/hichipper/lambdaProcess.R
@@ -8,14 +8,10 @@ suppressMessages(suppressWarnings(library(data.table)))
 suppressMessages(suppressWarnings(library(reshape2)))
 
 args <- commandArgs(trailingOnly = TRUE)
-# resfile <- args[1]
-# treatmentfile <- args[2]
-# backgroundfile <- args[3]
-# outdir <- args[4]
-resfile <- "hichipper/MboI_resfrag_hg38.bed"
-treatmentfile <- "hichipper/22RV1_REP1_temporary_treat_pileup.bdg"
-backgroundfile <- "hichipper/22RV1_REP1_temporary_control_lambda.bdg"
-outdir <- "hichipper"
+resfile <- args[1]
+treatmentfile <- args[2]
+backgroundfile <- args[3]
+outdir <- args[4]
 K <- 1000000 # Number of loci to sample from 
 
 # Import Restriction Fragments / Convert to GRanges