From bac2742e237ffddfc414bb5d3b7d0268e6ce81f3 Mon Sep 17 00:00:00 2001
From: William Gasper <wkg@williamgasper.com>
Date: Sat, 2 Mar 2024 06:58:25 -0600
Subject: [PATCH 1/2] resolve paths for working directory

---
 bin/xtea      | 2 ++
 bin/xtea_hg19 | 5 +++++
 bin/xtea_long | 2 ++
 3 files changed, 9 insertions(+)

diff --git a/bin/xtea b/bin/xtea
index ec1103b..d67984c 100755
--- a/bin/xtea
+++ b/bin/xtea
@@ -1269,6 +1269,8 @@ if __name__ == '__main__':
         b_denovo=options.denovo
     ####
 
+        s_wfolder = os.path.abspath(s_wfolder)
+
         if s_wfolder[-1]!="/":
             s_wfolder+="/"
         if os.path.exists(s_wfolder) == False:
diff --git a/bin/xtea_hg19 b/bin/xtea_hg19
index a87b5f5..81be52b 100755
--- a/bin/xtea_hg19
+++ b/bin/xtea_hg19
@@ -4,6 +4,9 @@ import os
 from subprocess import *
 from optparse import OptionParser
 import ntpath
+
+from xtea import utils
+
 #import global_values
 ILLUMINA="illumina"
 X10="10X"
@@ -1173,6 +1176,8 @@ if __name__ == '__main__':
         b_resume=options.resume
         b_denovo = options.denovo
 
+        s_wfolder = os.path.abspath(s_wfolder)
+
         if s_wfolder[-1]!="/":
             s_wfolder+="/"
         if os.path.exists(s_wfolder) == False:
diff --git a/bin/xtea_long b/bin/xtea_long
index c69157a..2fbca23 100755
--- a/bin/xtea_long
+++ b/bin/xtea_long
@@ -484,6 +484,8 @@ if __name__ == '__main__':
         b_clean=options.clean
         i_peak_win = options.win #maximum window size when try to cluster the breakpoints
 
+        s_wfolder = os.path.abspath(s_wfolder)
+
         if s_wfolder[-1]!="/":
             s_wfolder+="/"
         if os.path.exists(s_wfolder) == False:

From cf2efa589274ce5dfad02156b652d16939b07375 Mon Sep 17 00:00:00 2001
From: William Gasper <wkg@williamgasper.com>
Date: Sat, 2 Mar 2024 07:17:08 -0600
Subject: [PATCH 2/2] cleanup

---
 bin/xtea_hg19 | 2 --
 1 file changed, 2 deletions(-)

diff --git a/bin/xtea_hg19 b/bin/xtea_hg19
index 81be52b..1b2738f 100755
--- a/bin/xtea_hg19
+++ b/bin/xtea_hg19
@@ -5,8 +5,6 @@ from subprocess import *
 from optparse import OptionParser
 import ntpath
 
-from xtea import utils
-
 #import global_values
 ILLUMINA="illumina"
 X10="10X"