v2.1.2

bioinfo-biols · Sep 7, 2023 · 5da9bc0 · 5da9bc0
1 parent f1b818f
commit 5da9bc0
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Showing 22 changed files with 19 additions and 5 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1 @@
+.DS_Store
diff --git a/Makefile b/Makefile
@@ -0,0 +1,7 @@
+.PHONY: install test
+
+install:
+	javac -d bin src/*.java && cd bin && jar cvfm ../CIRI-Full_v2.1.2.jar MANIFEST.MF *.class
+
+test:
+	java -jar ./CIRI-Full_v2.1.2.jar 
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/bin/Exon_cov2.class b/bin/Exon_cov2.class
diff --git a/bin/Exon_gtf.class b/bin/Exon_gtf.class
diff --git a/bin/Exon_length.class b/bin/Exon_length.class
diff --git a/bin/MANIFEST.MF b/bin/MANIFEST.MF
@@ -0,0 +1,2 @@
+Manifest-Version: 1.0
+Main-Class: CIRI_Full2
diff --git a/bin/Merge3.class b/bin/Merge3.class
diff --git a/bin/RO1_single.class b/bin/RO1_single.class
diff --git a/bin/RO2.class b/bin/RO2.class
diff --git a/bin/Seq.class b/bin/Seq.class
diff --git a/bin/index_head_finder2.class b/bin/index_head_finder2.class
diff --git a/bin/index_head_finder_more.class b/bin/index_head_finder_more.class
diff --git a/bin/reversc.class b/bin/reversc.class
diff --git a/bin/sam5.class b/bin/sam5.class
diff --git a/src/CIRI_Full2.java b/src/CIRI_Full2.java
@@ -6,7 +6,7 @@ public class CIRI_Full2 {
 	public static void main(String[] args) throws InterruptedException, IOException {
 
 		long tstart = System.currentTimeMillis();
-		String v="Version: 2.0.1";
+		String v="Version: 2.1.2";
 		String dir=System.getProperty("user.dir");
 		int a=args.length;
 		int help=0;

diff --git a/src/Merge3.java b/src/Merge3.java
@@ -36,7 +36,7 @@ public int getmerge() throws IOException{
 		        Map<String,List<String>> mapchr=new HashMap<String,List<String>>();
 		        Map<String,List<int[]>> mapchr2=new HashMap<String,List<int[]>>();
 		        ArrayList<String> q1= new ArrayList<String>();
-
+		        int ifgtf=1;
 		        if(!gtf.equals("")){
 		        	FileReader in=new FileReader(gtf);
 		        	LineNumberReader reader=new LineNumberReader(in);
@@ -103,6 +103,7 @@ public int getmerge() throws IOException{
 		        System.out.println("Annotation Loaded");
 		        }
 		        else{
+		        	ifgtf=0;
 			        System.out.println("Annotation file not set");
 		        }
 		        //Load_CIRI_AS
@@ -236,7 +237,7 @@ public int getmerge() throws IOException{
 		    			if(in_c==i){
 						int n1=0;
 		    			while(n1<tmp2.length){
-		            		if(tmpa1[4].equals("")!=true){
+		            		if(tmpa1[4].equals("")!=true && tmpa1[4].equals("n/a")!=true){
 		            			String[] exon=tmpa1[4].split(",");
 		            			i=0;
 		    					while(i<exon.length){
@@ -785,8 +786,11 @@ else if(i==tmp2.length-1)
 		        String outline;
 		        while(i<total){
 		        	outline=chr[i]+":"+start[i]+"|"+end[i]+"	"+chr[i]+"	"+start[i]+"	"+end[i]+"	";
-		        	Exon_gtf test=new Exon_gtf(start[i],end[i],mapchr2.get(chr[i]));
-		        	List<int[]> gtf_exon=test.get_exon();
+		        	List<int[]> gtf_exon = new ArrayList<int[]>();
+		        	if(ifgtf==1) {
+		        		Exon_gtf test=new Exon_gtf(start[i],end[i],mapchr2.get(chr[i]));
+		        		gtf_exon=test.get_exon();
+		        	}
 		            Iterator<int[]> gtfexon=gtf_exon.iterator();
 		            int dd=0;