From 94069c4270bbe3dec2dfe767e8f5b41cad60325b Mon Sep 17 00:00:00 2001
From: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: Thu, 18 Apr 2024 13:21:03 -0400
Subject: [PATCH 1/4] Update strand information in read.modkit.R

---
 R/read.modkit.R | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/R/read.modkit.R b/R/read.modkit.R
index d4f6af2..ba77f49 100644
--- a/R/read.modkit.R
+++ b/R/read.modkit.R
@@ -15,7 +15,8 @@ read.modkit <- function(files,
         if (length(unique(data$V4)) == 2){
             gr <- GRanges(seqnames = data[data$V4 == "m", ]$V1,
                     ranges = IRanges(start = data[data$V4 == "m", ]$V2+1,
-                                     end = data[data$V4 == "m", ]$V3))
+                                     end = data[data$V4 == "m", ]$V3),
+                    strand = data[data$V4 == "m", ]$V6)
 
             mcols(gr)$m <- data[data$V4 == "m", ]$V12
             mcols(gr)$h <- data[data$V4 != "m", ]$V12
@@ -23,7 +24,8 @@ read.modkit <- function(files,
             mcols(gr)$filter <- data[data$V4 == "m", ]$V16
         }else{
             gr <- GRanges(seqnames = data$V1,
-                          ranges = IRanges(start = data$V2+1, end = data$V3))
+                          ranges = IRanges(start = data$V2+1, end = data$V3),
+                          strand = data$V6)
 
             mcols(gr)$m <- data$V12
             mcols(gr)$u <- data$V13
@@ -61,7 +63,9 @@ read.modkit <- function(files,
                              parameters = NULL, pData = colData, gr = NULL,
                              chr = as.vector(seqnames(overlap_gr)),
                              sampleNames = sampleNames, rmZeroCov = rmZeroCov)
-          if (strandCollapse) {strandCollapse(bsseq_obj)}
+          if (strandCollapse) {
+            bsseq_obj <- strandCollapse(bsseq_obj)
+          }
     }else{
       bsseq_obj <- BSseq(M = as.matrix(m), Cov = as.matrix(u + m),
                          Filtered = as.matrix(filter),
@@ -70,7 +74,9 @@ read.modkit <- function(files,
                          parameters = NULL, pData = colData, gr = NULL,
                          chr = as.vector(seqnames(overlap_gr)),
                          sampleNames = sampleNames, rmZeroCov = rmZeroCov)
-      if (strandCollapse) {strandCollapse(bsseq_obj)}
+      if (strandCollapse) {
+        bsseq_obj <- strandCollapse(bsseq_obj)
+      }
     }
 
     return(bsseq_obj)

From 39ac79f179b07d80bdd4766165fc2e5a0bb6917f Mon Sep 17 00:00:00 2001
From: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: Thu, 18 Apr 2024 14:36:20 -0400
Subject: [PATCH 2/4] Update strand information in read.modkit.R

---
 R/read.modkit.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/read.modkit.R b/R/read.modkit.R
index ba77f49..20ea8f9 100644
--- a/R/read.modkit.R
+++ b/R/read.modkit.R
@@ -11,6 +11,7 @@ read.modkit <- function(files,
     for (i in seq_along(files)){
         data <- read.table(files[i], header = FALSE, sep="\t",
                     stringsAsFactors=FALSE, quote="")
+        data$V6[data$V6 == "."] <- "*"
 
         if (length(unique(data$V4)) == 2){
             gr <- GRanges(seqnames = data[data$V4 == "m", ]$V1,

From f4bb6e8a43a5ba44c56a778ce545c71dad914ea8 Mon Sep 17 00:00:00 2001
From: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: Fri, 19 Apr 2024 14:56:40 -0400
Subject: [PATCH 3/4] Update strand information for read.modkit.R

---
 R/read.modkit.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/read.modkit.R b/R/read.modkit.R
index 20ea8f9..01fe208 100644
--- a/R/read.modkit.R
+++ b/R/read.modkit.R
@@ -61,7 +61,7 @@ read.modkit <- function(files,
                              Filtered = as.matrix(filter),
                              coef = NULL, se.coef = NULL,
                              pos = start(overlap_gr), trans = NULL,
-                             parameters = NULL, pData = colData, gr = NULL,
+                             parameters = NULL, pData = colData, gr = overlap_gr,
                              chr = as.vector(seqnames(overlap_gr)),
                              sampleNames = sampleNames, rmZeroCov = rmZeroCov)
           if (strandCollapse) {
@@ -72,7 +72,7 @@ read.modkit <- function(files,
                          Filtered = as.matrix(filter),
                          coef = NULL, se.coef = NULL,
                          pos = start(overlap_gr), trans = NULL,
-                         parameters = NULL, pData = colData, gr = NULL,
+                         parameters = NULL, pData = colData, gr = overlap_gr,
                          chr = as.vector(seqnames(overlap_gr)),
                          sampleNames = sampleNames, rmZeroCov = rmZeroCov)
       if (strandCollapse) {

From b8886bc930c5858c200b68149790f3b38b4d8f42 Mon Sep 17 00:00:00 2001
From: yixuanchen <116841407+yixuan-chen-elisa@users.noreply.github.com>
Date: Mon, 29 Apr 2024 17:10:07 -0400
Subject: [PATCH 4/4] Update read.modkit.R - change read.table to fread

---
 R/read.modkit.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/read.modkit.R b/R/read.modkit.R
index 01fe208..b79158d 100644
--- a/R/read.modkit.R
+++ b/R/read.modkit.R
@@ -9,7 +9,7 @@ read.modkit <- function(files,
         }
 
     for (i in seq_along(files)){
-        data <- read.table(files[i], header = FALSE, sep="\t",
+        data <- fread(files[i], header = FALSE, sep="\t",
                     stringsAsFactors=FALSE, quote="")
         data$V6[data$V6 == "."] <- "*"