turned all deletion longer than 9 bases in introns and filtered bam with -q 2

miniannotator.py

@@ -48,7 +48,7 @@ class Miniannotator:
         minimap = [self.conf["minimap2"], "-ax", "splice", "-t", str(self.conf["threads"]), self.reference,
                    self.assembly]
         samtools_sort = [self.conf["samtools"], "sort"]
-        samtools_bam = [self.conf["samtools"], "view", "-b", "-o", map_file]
+        samtools_bam = [self.conf["samtools"], "view", "-b", "-q", "2", "-o", map_file]
         p1 = subprocess.Popen(minimap, stdout=subprocess.PIPE)
         p2 = subprocess.Popen(samtools_sort, stdin=p1.stdout, stdout=subprocess.PIPE)
         p1.stdout.close()
@@ -128,8 +128,15 @@ class Miniannotator:
                                "exon": exon_nb})
                 qstart += length
             elif operation == 2:  # DELETION
-                indels.append({"type": "del", "start": exon_end + 1, "end": exon_end + length, "exon": exon_nb})  # 1-based coords
-                exon_end += length
+                if length < 10
+                    indels.append({"type": "del", "start": exon_end + 1, "end": exon_end + length, "exon": exon_nb})  # 1-based coords
+                    exon_end += length
+                else 
+                    exons.append({"start": exon_start + 1, "end": exon_end, "nb": exon_nb})  # 1-based coords
+                    complete = True
+                    exon_nb += 1
+                    exon_start = exon_end + length
+                    exon_end = exon_start
             elif operation == 3:  # SPLIT
                 exons.append({"start": exon_start + 1, "end": exon_end, "nb": exon_nb})  # 1-based coords
                 complete = True