fixed bug in CIRI-full Pipeline

bioinfo-biols · Sep 8, 2023 · 6f18e3c · 6f18e3c
1 parent 5da9bc0
commit 6f18e3c
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Showing 6 changed files with 22 additions and 8 deletions.
diff --git a/bin/CIRI_Full2$1.class b/bin/CIRI_Full2$1.class
diff --git a/bin/CIRI_Full2$2.class b/bin/CIRI_Full2$2.class
diff --git a/bin/CIRI_Full2$3.class b/bin/CIRI_Full2$3.class
diff --git a/bin/CIRI_Full2$4.class b/bin/CIRI_Full2$4.class
diff --git a/bin/CIRI_Full2.class b/bin/CIRI_Full2.class
diff --git a/src/CIRI_Full2.java b/src/CIRI_Full2.java
@@ -149,15 +149,29 @@ public static void main(String[] args) throws InterruptedException, IOException
 		        writeStream1.newLine();
 		        	writeStream1.write("bwa mem -T 19 -t "+t+" "+ref+" "+read1+" "+read2+" > "+workdir+"/sam/"+prefix+"_ciri.sam");
 		        	writeStream1.newLine();
-		        if(z.indexOf("-0")!=-1){
-			        writeStream1.write("perl "+cdir+ciri+" -I "+workdir+"/sam/"+prefix+"_ciri.sam -O "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -A "+anno+" -T "+t+" -0");
-		        }
-		        else{
-			        writeStream1.write("perl "+cdir+ciri+" -I "+workdir+"/sam/"+prefix+"_ciri.sam -O "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -A "+anno+" -T "+t);
-
-		        }
+
+                if (!anno.equals("")) {
+                    if(z.indexOf("-0")!=-1){
+			            writeStream1.write("perl "+cdir+ciri+" -I "+workdir+"/sam/"+prefix+"_ciri.sam -O "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -A "+anno+" -T "+t+" -0");
+    		        }
+		            else {
+    			        writeStream1.write("perl "+cdir+ciri+" -I "+workdir+"/sam/"+prefix+"_ciri.sam -O "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -A "+anno+" -T "+t);
+       		        }
+                } else {
+                    if(z.indexOf("-0")!=-1){
+                        writeStream1.write("perl "+cdir+ciri+" -I "+workdir+"/sam/"+prefix+"_ciri.sam -O "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -T "+t+" -0");
+                    }
+                    else {
+                        writeStream1.write("perl "+cdir+ciri+" -I "+workdir+"/sam/"+prefix+"_ciri.sam -O "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -T "+t);
+                    }
+                }
+
 		        writeStream1.newLine();
-		        writeStream1.write("perl "+cdir+as+" -S "+workdir+"/sam/"+prefix+"_ciri.sam -C "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -A "+anno+" -O "+workdir+"/CIRI-AS_output/"+prefix+" -D yes");
+                if (!anno.equals("")) {
+		            writeStream1.write("perl "+cdir+as+" -S "+workdir+"/sam/"+prefix+"_ciri.sam -C "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -A "+anno+" -O "+workdir+"/CIRI-AS_output/"+prefix+" -D yes");
+                } else {
+                    writeStream1.write("perl "+cdir+as+" -S "+workdir+"/sam/"+prefix+"_ciri.sam -C "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -O "+workdir+"/CIRI-AS_output/"+prefix+" -D yes");
+                }
 		        writeStream1.close();
 		        String[] ciri_c={"sh",workdir+"/tmp1.sh"};
 		        Process cirip= Runtime.getRuntime().exec(ciri_c);