0.2.2.1

src/MAP2FASTA.java

@@ -35,7 +35,7 @@ import java.util.*;
 public class MAP2FASTA {
 
     //### constants  ################################################################
-    final static String VERSION = "0.1.200711c";
+    final static String VERSION = "0.2.200712ac";
     final static String NOTHING = "N.o./.T.h.I.n.G";
     final static String STDIN = "-";
     final static int MIN_COV = 10;          // default minimum coverage
@@ -216,7 +216,8 @@ public class MAP2FASTA {
 	basename = mapFile.getName();
 	if ( (x=basename.lastIndexOf(".")) <= 0 )                       { System.err.println("incorrect MAP file name (option -i)");            System.exit(1); }
 	if ( ! basename.substring(x).equals(".map") )                   { System.err.println("MAP file does not end with .map (option -i)");    System.exit(1); }
-	basename = mapFile.getParent() + File.separatorChar + basename.substring(0, x);
+	basename = basename.substring(0, x);
+	if ( mapFile.getParent() != null ) basename = mapFile.getParent() + File.separatorChar + basename;
 	//### testing numerical options
 	if ( bfreq <= 0 || bfreq >= 1 )                                 { System.err.println("incorrect proportion value: " + bfreq + " (option -f)");    System.exit(1); }
 	if ( minS < 1 )                                                 { System.err.println("incorrect positive value: " + minS + " (option -s)");       System.exit(1); }
@@ -1003,7 +1004,7 @@ public class MAP2FASTA {
 	    out.newLine();
 	}
 	z = 0; u=(--x); while ( ++x < distrib.length ) z += distrib[x];
-	out.write((">" + u + BLANK).substring(0,5) + "    ");
+	out.write((">" + u + BLANK).substring(0,5) + "      ");
 	y = -1; while ( ++y <= z*scale/sumy ) out.write("=");
 	y -= 2; while ( ++y <= depth ) out.write(" "); out.write("" + z); out.newLine();
 	out.close();

src/SAM2MAP.java

@@ -35,7 +35,7 @@ import java.util.*;
 public class SAM2MAP {
 
     //### constants  ################################################################
-    final static String VERSION = "0.1.200711c";
+    final static String VERSION = "0.2.200712c";
     final static String NOTHING = "N.o./.T.h.I.n.G";
     final static String STDIN = "-";
     final static int MIN_COV = 10;          // default minimum coverage
@@ -403,9 +403,11 @@ public class SAM2MAP {
 		}
 	    }
 	}
+	/*
 	pos = -1;
 	while ( ++pos < lref )
-	    if ( oi[pos] > 0 ) System.out.println("WARNING: " + oi[pos] + " aligned reads with insertion to the reference at position " + (pos+1));
+	    if ( oi[pos] > 5 ) System.out.println("WARNING: " + oi[pos] + " aligned reads with insertion to the reference at position " + (pos+1));
+	*/
 	    
 	
 	//##########################################################################################################
@@ -1092,7 +1094,7 @@ public class SAM2MAP {
 	    out.newLine();
 	}
 	z = 0; u=(--x); while ( ++x < distrib.length ) z += distrib[x];
-	out.write((">" + u + BLANK).substring(0,5) + "    ");
+	out.write((">" + u + BLANK).substring(0,5) + "      ");
 	y = -1; while ( ++y <= z*scale/sumy ) out.write("=");
 	y -= 2; while ( ++y <= depth ) out.write(" "); out.write("" + z); out.newLine();
 	out.close();