From 075eafd6b4069baa273556ec05506c69094ca0e6 Mon Sep 17 00:00:00 2001
From: nicola-calonaci <nicola.calonaci@gmail.com>
Date: Sat, 6 Apr 2024 22:10:44 +0200
Subject: [PATCH] bug fixed

---
 .DS_Store    | Bin 6148 -> 6148 bytes
 .Rhistory    |   4 ++--
 R/classify.R |   2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.DS_Store b/.DS_Store
index dcdf50a8727e1e87517c7ad9c8aea475f21cd663..89aa9d8d6d10158862ae25f311f8c4f7e7da237a 100644
GIT binary patch
delta 300
zcmZoMXfc=|#>B)qu~2NHo+2aL!~pA!9~u~ej2_kcr1Ii|q@4UD1_p*5Nd-BX#U%y?
z*BF_YSy<WFIoLV4Ibwq|^2>uu5=%;pof3<pLA;Rs{G22hJ25FNGqpTkK*TveuOu-u
zFSQ7)Au}Zvs3aylGcP5-+$p~_FQpi)Hy9$p!O6iHFCbCvT5W7-p`&1AVNt82P;F^s
zprc@7Y*t&#$sww&Zygk$os*lF-vx9W5HK=AXa-&=4Wqgz&X<#BXDDFEW=Lm9VaR7F
zXUHoHF3QWv&r1jC+qml{%Vu^Cehy$DY<&2gc{0C<p#aFR29PWmF)(Zn5ZS^E0688{
AX8-^I

delta 74
zcmZoMXfc=|#>CJ*u~2NHo+2a5!~knXmdQL!s+=js$vH{+`8f=m^_Xw6Y))V<VcN{j
e!OsCyyg88hJM(0I5kp3X$u>OFn`1;)FarPq(G)WP

diff --git a/.Rhistory b/.Rhistory
index 33e23da..51eb942 100644
--- a/.Rhistory
+++ b/.Rhistory
@@ -1,5 +1,3 @@
-any(!is.numeric(genomic_data$to))
-any(!is.integer(genomic_data$DP))
 any(!is.integer(genomic_data$DNV))
 any(!is.integer(genomic_data$NV))
 any(!is.numeric(genomic_data$VAF))
@@ -510,3 +508,5 @@ devtools::load_all()
 plot_classification(x = output, sample = sample,assembly = T)
 names(x)
 names(x$classification)
+setwd('~/Documents/GitHub/CNAqc/')
+CNAqc:::advanced_phasing
diff --git a/R/classify.R b/R/classify.R
index d4a8dde..24c3870 100644
--- a/R/classify.R
+++ b/R/classify.R
@@ -103,7 +103,7 @@ classify = function(x,
                                x = x,
                                mc.cores = num_cores)
 
-    tests = do.call(rbind, tests) %>% t()
+    tests = do.call(rbind, tests)
   } else {
 
     tests = lapply(ids(x), function(id) {