From cd512bf8572765d303b3da7480e255d361f85a7f Mon Sep 17 00:00:00 2001
From: Lesky47 <slai4@mdanderson.org>
Date: Wed, 11 Feb 2026 15:51:13 -0600
Subject: [PATCH] Fix data.table subsetting compatability bug with ASCAT v3.2

ASCAT expects data frames; convert SNPpos to data.frame. Deep copy of SNPpos to avoid modifying the original object by reference.
---
 .DS_Store       | Bin 0 -> 6148 bytes
 R/.DS_Store     | Bin 0 -> 6148 bytes
 R/run_ASCAT.m.R |   7 ++++---
 3 files changed, 4 insertions(+), 3 deletions(-)
 create mode 100644 .DS_Store
 create mode 100644 R/.DS_Store

diff --git a/.DS_Store b/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..f7076326e83f87f16e5e4cb0621caf1c2e4d7ae9
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diff --git a/R/.DS_Store b/R/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
GIT binary patch
literal 6148
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diff --git a/R/run_ASCAT.m.R b/R/run_ASCAT.m.R
index 863243a..e507c6f 100755
--- a/R/run_ASCAT.m.R
+++ b/R/run_ASCAT.m.R
@@ -286,7 +286,7 @@ run_ASCAT.m <- function (patient_id,sample_id,sex,
                     Germline_BAF=data.frame(rBAF_n=dt_sample_SNPs$rBAF_n),
                     Tumor_LogR_segmented=NULL, Tumor_BAF_segmented=NULL,
                     Tumor_counts=NULL, Germline_counts=NULL,
-                    SNPpos=SNPpos[,c("chrom","POS")], chr=chr,
+                    SNPpos = as.data.frame(SNPpos[, .(chrom, POS)]), chr=chr,
                     samples=paste(patient_id, sample_id, sep="."), 
                     chrs=chr_names, ch=ch, 
                     gender=sex, sexchromosomes=c("X", "Y"),
@@ -307,7 +307,7 @@ run_ASCAT.m <- function (patient_id,sample_id,sex,
     ascat.frag <- ascat.aspcf(ascat.bc, ascat.gg=gg, penalty=200)
     # penalty = 200 recommended for sequencing data
 
-    # fix issue with ascat.ascpcf renaming samples 
+    # fix issue with ascat.aspcf renaming samples 
     ascat.frag$samples <- paste(patient_id, sample_id, sep=".")
     rm(ascat.bc)
     
@@ -409,7 +409,8 @@ run_ASCAT.m <- function (patient_id,sample_id,sex,
 
 split_genome_RRBS = function(SNPpos) {
   # look for gaps of more than 1Mb and chromosome borders
-  SNPposnum <- SNPpos
+  # hard copy for data table to avoid modifying SNPpos
+  SNPposnum <- data.table::copy(SNPpos)
   SNPposnum[, chrom := ifelse(chrom == "X", 23, chrom)]
   SNPposnum <- SNPposnum[, lapply(.SD, as.numeric)]