getNotPrimaryAlignmentFlag deprecated; tests for bamstats04

src/main/java/com/github/lindenb/jvarkit/tools/bam2graphics/PaintContext.java

@@ -161,7 +161,7 @@ private void writeBamSection(
 					{
 					SAMRecord rec=iter.next();
 					if(rec.getReadUnmappedFlag()) continue;
-					if(rec.getNotPrimaryAlignmentFlag()) continue;
+					if(rec.isSecondaryAlignment()) continue;
 					if(rec.getDuplicateReadFlag()) continue;
 					if(rec.getReadFailsVendorQualityCheckFlag()) continue;
 					for(int i1= Math.max(interval.start+1,rec.getAlignmentStart());

src/main/java/com/github/lindenb/jvarkit/tools/bamstats01/BamStats01.java

@@ -245,7 +245,7 @@ void watch(SAMRecord rec)
 				}
 
 
-			if(!rec.getNotPrimaryAlignmentFlag())
+			if(!rec.isSecondaryAlignment())
 				{
 				this.increment(Category.PRIMARY_ALIGNMENT);
 				}

src/main/java/com/github/lindenb/jvarkit/tools/tests/TestNg01.java

@@ -46,6 +46,7 @@ of this software and associated documentation files (the "Software"), to deal
 import com.github.lindenb.jvarkit.tools.bam2graphics.Bam2Raster;
 import com.github.lindenb.jvarkit.tools.bam2graphics.LowResBam2Raster;
 import com.github.lindenb.jvarkit.tools.bam2wig.Bam2Wig;
+import com.github.lindenb.jvarkit.tools.bamstats04.BamStats04;
 import com.github.lindenb.jvarkit.tools.bioalcidae.BioAlcidaeJdk;
 import com.github.lindenb.jvarkit.tools.biostar.Biostar59647;
 import com.github.lindenb.jvarkit.tools.biostar.Biostar86480;
@@ -121,6 +122,7 @@ class TestNg01 {
 	static final File TEST_RESULTS_DIR= new File("test-results");
 	static final File JETER_VCF = new File(TEST_RESULTS_DIR,"jeter.vcf");
 	static final String TOY_FA="src/test/resources/toy.fa";
+	static final String TOY_BED_GZ="src/test/resources/toy.bed.gz";
 	static final String TOY_VCF_GZ="src/test/resources/toy.vcf.gz";
 	static final String TOY_BAM="src/test/resources/toy.bam";
 	static final String TOY_DICT="src/test/resources/toy.dict";
@@ -1060,4 +1062,17 @@ public void testVcfToSql(final String path) throws IOException {
         		}));
     	Assert.assertTrue(outvcf.delete());
 		}
+
+    @Test
+    public void testBamStats04() throws IOException {
+    	final File output =new File(TEST_RESULTS_DIR,"jeter.tsv");
+    	Assert.assertEquals(0,new BamStats04().instanceMain(new String[]{
+        		"-o",output.getPath(),
+        		"-R",TOY_FA,
+        		"-B",TOY_BED_GZ,
+        		TOY_BAM
+        		}));
+    	Assert.assertTrue(output.delete());
+		}
+
 }

src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/ParseException.java

@@ -1,5 +1,5 @@
-/* Generated By:JavaCC: Do not edit this line. ParseException.java Version 7.0 */
-/* JavaCCOptions:KEEP_LINE_COLUMN=true */
+/* Generated By:JavaCC: Do not edit this line. ParseException.java Version 5.0 */
+/* JavaCCOptions:KEEP_LINE_COL=null */
 /*
 The MIT License (MIT)
 
@@ -44,11 +44,6 @@ public class ParseException extends Exception {
    */
   private static final long serialVersionUID = 1L;
 
-  /**
-   * The end of line string for this machine.
-   */
-  protected static String EOL = System.getProperty("line.separator", "\n");
-
   /**
    * This constructor is used by the method "generateParseException"
    * in the generated parser.  Calling this constructor generates
@@ -117,7 +112,7 @@ public ParseException(String message) {
   private static String initialise(Token currentToken,
                            int[][] expectedTokenSequences,
                            String[] tokenImage) {
-
+    String eol = System.getProperty("line.separator", "\n");
     StringBuffer expected = new StringBuffer();
     int maxSize = 0;
     for (int i = 0; i < expectedTokenSequences.length; i++) {
@@ -130,7 +125,7 @@ private static String initialise(Token currentToken,
       if (expectedTokenSequences[i][expectedTokenSequences[i].length - 1] != 0) {
         expected.append("...");
       }
-      expected.append(EOL).append("    ");
+      expected.append(eol).append("    ");
     }
     String retval = "Encountered \"";
     Token tok = currentToken.next;
@@ -147,23 +142,20 @@ private static String initialise(Token currentToken,
       tok = tok.next;
     }
     retval += "\" at line " + currentToken.next.beginLine + ", column " + currentToken.next.beginColumn;
-    retval += "." + EOL;
-
-
-    if (expectedTokenSequences.length == 0) {
-        // Nothing to add here
+    retval += "." + eol;
+    if (expectedTokenSequences.length == 1) {
+      retval += "Was expecting:" + eol + "    ";
     } else {
-	    if (expectedTokenSequences.length == 1) {
-	      retval += "Was expecting:" + EOL + "    ";
-	    } else {
-	      retval += "Was expecting one of:" + EOL + "    ";
-	    }
-	    retval += expected.toString();
+      retval += "Was expecting one of:" + eol + "    ";
     }
-
+    retval += expected.toString();
     return retval;
   }
 
+  /**
+   * The end of line string for this machine.
+   */
+  protected String eol = System.getProperty("line.separator", "\n");
 
   /**
    * Used to convert raw characters to their escaped version
@@ -176,6 +168,8 @@ static String add_escapes(String str) {
       for (int i = 0; i < str.length(); i++) {
         switch (str.charAt(i))
         {
+           case 0 :
+              continue;
            case '\b':
               retval.append("\\b");
               continue;
@@ -214,4 +208,4 @@ static String add_escapes(String str) {
    }
 
 }
-/* JavaCC - OriginalChecksum=8f1e51aa4b916bc256163d0c1bebb8ed (do not edit this line) */
+/* JavaCC - OriginalChecksum=2478e7e15dfcd9937c47bf4e1260ae77 (do not edit this line) */