From 392db369c0a56c182855acdc3ac932f8d9ac9181 Mon Sep 17 00:00:00 2001
From: Johan Zicola <johan.zicola@gmail.com>
Date: Fri, 19 Jul 2019 15:31:45 +0200
Subject: [PATCH 1/2] Fix the bug with function remove_temp(). Also made a pull
 request on Lister github

---
 tepid/tepid.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/tepid/tepid.py b/tepid/tepid.py
index dca9d7c..4b65ecb 100644
--- a/tepid/tepid.py
+++ b/tepid/tepid.py
@@ -1002,6 +1002,7 @@ def discover_pe(options):
     imput split reads bam file must be name sorted
     TE annotation can be gzipped
     """
+    
     print "Processing "+options.name
     print "Running paired-end mode"
     print 'Estimating mean insert size and coverage'
@@ -1123,10 +1124,12 @@ def discover_pe(options):
     remove_temp(options)
 
 
+# Fix bug by adding "./" in argument of x.startswith
+# otherwise the files in list temp are not matching
 def remove_temp(options):
     if options.keep is False:
         temp = glob('./*.temp')
-        mytempfiles = [x for x in temp if x.startswith(options.prefix)]
+        mytempfiles = [x for x in temp if x.startswith("./"+options.prefix)]
         for i in mytempfiles:
             os.remove(i)
         os.remove(options.prefix + 'disc_sorted.bam')
@@ -1155,6 +1158,7 @@ def discover_se(options):
     """
     Single-end mode
     """
+    
     print "Processing "+options.name
     print "Running single-end mode"
     cov = calc_cov(options.conc, 100000, 120000)
@@ -1227,4 +1231,4 @@ def discover_se(options):
     with open("tepid_discover_log_{}.txt".format(options.name), 'a') as logfile:
         logfile.write("tepid-discover finished normally at {}\n".format(ctime()))
 
-    remove_temp(options)
\ No newline at end of file
+    remove_temp(options)

From 236cd6d514d760c05cdc197dbe3de598bf05984c Mon Sep 17 00:00:00 2001
From: Johan Zicola <johan.zicola@gmail.com>
Date: Mon, 22 Jul 2019 10:08:21 +0200
Subject: [PATCH 2/2] Fix the bug for samtools sort due to old syntax usage

---
 Scripts/tepid-map | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Scripts/tepid-map b/Scripts/tepid-map
index a033fcb..15156e2 100644
--- a/Scripts/tepid-map
+++ b/Scripts/tepid-map
@@ -69,7 +69,7 @@ map () {
   rm "${fname}.split.sam"
 
   echo "Sorting alignment"
-  samtools sort -@ $proc "${fname}_unsort.bam" "${fname}"
+  samtools sort -@ $proc "${fname}_unsort.bam" -o "${fname}.bam"
   rm "${fname}_unsort.bam"
 
   echo "Indexing alignment"