modify edlib realignment

Genomon-Project · Mar 18, 2021 · 88dd0ee · 88dd0ee
1 parent 392120d
commit 88dd0ee
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/genomon_mutation_filter/realignment_filter.py b/genomon_mutation_filter/realignment_filter.py
@@ -50,7 +50,7 @@ def math_log_fisher_pvalue(self,fisher_pvalue):
 
 
     ############################################################
-    def extractRead(self, bamfile, chr,start,end, output):
+    def extractRead(self, bamfile, chr,start,end, output, flag_blat):
 
         with open(output, 'w') as hOUT:
             for read in bamfile.fetch(chr,start,end):
@@ -63,7 +63,7 @@ def extractRead(self, bamfile, chr,start,end, output):
                 flags = format(read_flag, "#014b")[:1:-1]
 
                 tempSeq = ""
-                if flags[4] == "1":
+                if flags[4] == "1" and flag_blat:
                     tempSeq = "".join(self.complement.get(base) for base in reversed(str(read.seq)))
                 else:
                     tempSeq = read.seq
@@ -235,7 +235,7 @@ def edlib_read_count(self, samfile, chr, start, end, output):
     ############################################################
     def count_reads(self, samfile, chr, start, end, output, thread_idx):
         # extract short reads from tumor sequence data around the candidate
-        self.extractRead(samfile,chr,start,end,output + ".tmp.fa")
+        self.extractRead(samfile,chr,start,end,output + ".tmp.fa", self.uses_blat)
 
         if self.uses_blat:
             return self.blat_read_count(samfile, chr, start, end, output, thread_idx)

diff --git a/genomon_mutation_filter/version.py b/genomon_mutation_filter/version.py
@@ -1,3 +1,3 @@
 #! /usr/bin/env python
 
-__version__ = '0.3.0'
+__version__ = '0.3.1'