diff --git a/_modules/functions_PhageTerm.py b/_modules/functions_PhageTerm.py
index 63db8b31c46153491da95b91c6a9698b8e8c6536..5527a514a053df8012e50b4d4c4bb41b158d38c4 100644
--- a/_modules/functions_PhageTerm.py
+++ b/_modules/functions_PhageTerm.py
@@ -60,7 +60,7 @@ from reportlab.lib.units import inch
 from reportlab.lib import colors
 from reportlab.lib.utils import ImageReader
 
-from _modules.utilities import reverseComplement,hybridCoverage,applyCoverage,correctEdge
+from _modules.utilities import reverseComplement,hybridCoverage,applyCoverage,correctEdge,changeCase
 from _modules.common_readsCoverage_processing import picMax
 from _modules.readsCoverage_res import RCRes, RCCheckpoint_handler,RCWorkingS
 
@@ -114,13 +114,16 @@ def init_ws(p_res,refseq,hostseq):
 def readsCoverage(inRawDArgs,refseq,inDArgs,fParms,return_dict, core_id,line_start,line_end,tParms,\
                   chk_handler,idx_refseq,logger=None):
     """Calculate whole coverage and first base coverage. """
-
+    # initialize vars
     p_res=chk_handler.load(core_id,idx_refseq)
+    test_read_seq = False
+    match = 0
     gen_len,host_len,termini_coverage, whole_coverage, paired_whole_coverage, phage_hybrid_coverage, host_hybrid_coverage,\
     host_whole_coverage, list_hybrid, insert, paired_missmatch, k, count_line, read_match=init_ws(p_res, refseq, inDArgs.hostseq)
+
     if logger!=None:
         logger.add_rw(p_res)
-    test_read_seq = match = 0
+
     # Timer
     if core_id == (tParms.core-1):
         sys.stdout.write("  0.0 %")
@@ -139,19 +142,19 @@ def readsCoverage(inRawDArgs,refseq,inDArgs,fParms,return_dict, core_id,line_sta
         line = filin.readline()
     while line:
         count_line+=1
-        if count_line//4 <= line_start:
-            test_read_seq = 0
+        if count_line//4 < line_start:
+            test_read_seq = False
         if count_line//4 > line_end:
             break
 
         if test_read_seq:
             k += 1
             # Read sequence
-            read = line.split("\n")[0].split("\r")[0]
+            read = changeCase(line.split("\n")[0].split("\r")[0])
             line = filin.readline()
             
             if inRawDArgs.paired != "":
-                read_paired = line_paired.split("\n")[0].split("\r")[0]
+                read_paired = changeCase(line_paired.split("\n")[0].split("\r")[0])
                 line_paired = filin_paired.readline()
             
             readlen = len(read)
@@ -301,7 +304,6 @@ def readsCoverage(inRawDArgs,refseq,inDArgs,fParms,return_dict, core_id,line_sta
             # TEST limit_coverage
             read_match += match*readlen
 
-            match = test_read_seq = 0
             # Timer
             if core_id == (tParms.core-1):
                 if k%1000 == 0:
@@ -312,9 +314,14 @@ def readsCoverage(inRawDArgs,refseq,inDArgs,fParms,return_dict, core_id,line_sta
                  phage_hybrid_coverage, host_hybrid_coverage, \
                  host_whole_coverage,list_hybrid,insert,paired_missmatch,k,read_match) # maybe time to create checkpoint
 
+            # reset variables
+            test_read_seq = False
+            match = 0
+
+
         else:
-            if line[0] == "@":
-                test_read_seq = 1
+            if line.startswith("@"):
+                test_read_seq = True
             
             line = filin.readline()
             if inRawDArgs.paired != "":