v1.1.8

hartleys · Jul 13, 2016 · 3fa9585 · 3fa9585
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diff --git a/QoRTs-vignette.pdf b/QoRTs-vignette.pdf
diff --git a/QoRTs_1.1.6/QoRTs_1.1.6.tar.gz b/QoRTs_1.1.6/QoRTs_1.1.6.tar.gz
diff --git a/QoRTs_1.1.6.zip → QoRTs_1.1.8.zip b/QoRTs_1.1.6.zip → QoRTs_1.1.8.zip
diff --git a/QoRTs_1.1.6/QoRTs-reference-manual.pdf → QoRTs_1.1.8/QoRTs-reference-manual.pdf b/QoRTs_1.1.6/QoRTs-reference-manual.pdf → QoRTs_1.1.8/QoRTs-reference-manual.pdf
diff --git a/QoRTs_1.1.6/QoRTs-vignette.pdf → QoRTs_1.1.8/QoRTs-vignette.pdf b/QoRTs_1.1.6/QoRTs-vignette.pdf → QoRTs_1.1.8/QoRTs-vignette.pdf
diff --git a/QoRTs_1.1.6/QoRTs.jar → QoRTs_1.1.8/QoRTs.jar b/QoRTs_1.1.6/QoRTs.jar → QoRTs_1.1.8/QoRTs.jar
diff --git a/QoRTs_1.1.6/QoRTsExampleData_1.1.6.tar.gz → QoRTs_1.1.8/QoRTsExampleData_1.1.8.tar.gz b/QoRTs_1.1.6/QoRTsExampleData_1.1.6.tar.gz → QoRTs_1.1.8/QoRTsExampleData_1.1.8.tar.gz
diff --git a/QoRTs_1.1.8/QoRTs_1.1.8.tar.gz b/QoRTs_1.1.8/QoRTs_1.1.8.tar.gz
diff --git a/QoRTs_1.1.6/README.txt → QoRTs_1.1.8/README.txt b/QoRTs_1.1.6/README.txt → QoRTs_1.1.8/README.txt
@@ -1,5 +1,5 @@
-# QoRTs v1.1.6
-(Compiled Tue Jun 14 15:00:02 EDT 2016)
+# QoRTs v1.1.8
+(Compiled Wed Jul 13 13:35:00 EDT 2016)
 
 The [QoRTs software package](http://hartleys.github.io/QoRTs/) is a fast, efficient, and portable 
 multifunction toolkit designed to assist in

diff --git a/QoRTs_1.1.6/example-walkthrough.pdf → QoRTs_1.1.8/example-walkthrough.pdf b/QoRTs_1.1.6/example-walkthrough.pdf → QoRTs_1.1.8/example-walkthrough.pdf
diff --git a/QoRTs_1.1.6/scripts/QoRTs.sh → QoRTs_1.1.8/scripts/QoRTs.sh b/QoRTs_1.1.6/scripts/QoRTs.sh → QoRTs_1.1.8/scripts/QoRTs.sh
diff --git a/QoRTs_1.1.6/scripts/qortsGenMultiQC.R → QoRTs_1.1.8/scripts/qortsGenMultiQC.R b/QoRTs_1.1.6/scripts/qortsGenMultiQC.R → QoRTs_1.1.8/scripts/qortsGenMultiQC.R
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
-# QoRTs v1.1.6
-(Compiled Tue Jun 14 15:00:02 EDT 2016)
+# QoRTs v1.1.8
+(Compiled Wed Jul 13 13:35:00 EDT 2016)
 
 The [QoRTs software package](http://hartleys.github.io/QoRTs/) is a fast, efficient, and portable 
 multifunction toolkit designed to assist in

diff --git a/src/HartleyUtils/.cache b/src/HartleyUtils/.cache
diff --git a/src/HartleyUtils/.worksheet/bin/internalTests/testing$$anonfun$main$1$$anonfun$1.class b/src/HartleyUtils/.worksheet/bin/internalTests/testing$$anonfun$main$1$$anonfun$1.class
diff --git a/src/HartleyUtils/.worksheet/bin/internalTests/testing$$anonfun$main$1$$anonfun$2.class b/src/HartleyUtils/.worksheet/bin/internalTests/testing$$anonfun$main$1$$anonfun$2.class
diff --git a/src/HartleyUtils/.worksheet/bin/internalTests/testing$$anonfun$main$1$$anonfun$3.class b/src/HartleyUtils/.worksheet/bin/internalTests/testing$$anonfun$main$1$$anonfun$3.class
diff --git a/...yUtils/.worksheet/bin/internalTests/testing$$anonfun$main$1$$anonfun$apply$mcV$sp$1.class b/...yUtils/.worksheet/bin/internalTests/testing$$anonfun$main$1$$anonfun$apply$mcV$sp$1.class
diff --git a/...yUtils/.worksheet/bin/internalTests/testing$$anonfun$main$1$$anonfun$apply$mcV$sp$2.class b/...yUtils/.worksheet/bin/internalTests/testing$$anonfun$main$1$$anonfun$apply$mcV$sp$2.class
diff --git a/...ls/.worksheet/bin/internalTests/testing$$anonfun$main$1$$anonfun$escapifyString$1$1.class b/...ls/.worksheet/bin/internalTests/testing$$anonfun$main$1$$anonfun$escapifyString$1$1.class
diff --git a/src/HartleyUtils/.worksheet/bin/internalTests/testing$$anonfun$main$1.class b/src/HartleyUtils/.worksheet/bin/internalTests/testing$$anonfun$main$1.class
diff --git a/src/HartleyUtils/.worksheet/bin/internalTests/testing$.class b/src/HartleyUtils/.worksheet/bin/internalTests/testing$.class
diff --git a/src/HartleyUtils/.worksheet/src/internalTests.testing.scala b/src/HartleyUtils/.worksheet/src/internalTests.testing.scala
@@ -4,24 +4,21 @@ import net.sf.samtools._
 
 object testing {;import org.scalaide.worksheet.runtime.library.WorksheetSupport._; def main(args: Array[String])=$execute{;$skip(109); 
   println("Welcome to the Scala worksheet");$skip(25); val res$0 = 
-  "Hello".substring(0,2);System.out.println("""res0: String = """ + $show(res$0));$skip(26); val res$1 = 
+  "Hello".substring(0,2);System.out.println("""res0: String = """ + $show(res$0));$skip(23); val res$1 = 
+  "Hello".substring(1);System.out.println("""res1: String = """ + $show(res$1));$skip(27); val res$2 = 
 
-  scala.math.log(10.0);System.out.println("""res1: Double = """ + $show(res$1));$skip(235); val res$2 = 
+  scala.math.log(10.0);System.out.println("""res2: Double = """ + $show(res$2));$skip(235); val res$3 = 
 
   //val reader =  new SAMFileReader(new java.io.File("C:\\Users\\hartleys\\work\\nihwork\\home_copy\\projects\\ZZZ-ExampleDataset\\TestSets\\readLength50\\inputData\\fastq\\SAMP1_RG1.50bp.1.fq.gz"));
 
-  "Hello+World".split("\\+");System.out.println("""res2: Array[String] = """ + $show(res$2));$skip(26); val res$3 = 
+  "Hello+World".split("\\+");System.out.println("""res3: Array[String] = """ + $show(res$3));$skip(26); val res$4 = 
 
-  Range(0,10).toVector;System.out.println("""res3: Vector[Int] = """ + $show(res$3));$skip(23); val res$4 = 
+  Range(0,10).toVector;System.out.println("""res4: Vector[Int] = """ + $show(res$4));$skip(23); val res$5 = 
 
-  Vector("hi").tail;System.out.println("""res4: scala.collection.immutable.Vector[String] = """ + $show(res$4));$skip(32); val res$5 = 
+  Vector("hi").tail;System.out.println("""res5: scala.collection.immutable.Vector[String] = """ + $show(res$5));$skip(32); val res$6 = 
 
-  scala.math.log(0).isInfinite;System.out.println("""res5: Boolean = """ + $show(res$5));$skip(82); 
+  scala.math.log(0).isInfinite;System.out.println("""res6: Boolean = """ + $show(res$6));$skip(54); 
 
-  val splitstr = "Gene = \"HRG10;2\"; TX = \"Blah\"; exon = 1; variant = \"3\";";System.out.println("""splitstr  : String = """ + $show(splitstr ));$skip(58); val res$6 = 
-
-
-  splitstr.split(";(?=([^\"]*\"[^\"]*\")*[^\"]*$)");System.out.println("""res6: Array[String] = """ + $show(res$6));$skip(53); 
 
   print(Vector("Hello","World","How","Are","You"));$skip(20); ;
   print(Some("Hi"));$skip(123); 
@@ -117,7 +114,21 @@ System.getProperty("sun.arch.data.model");System.out.println("""res17: String =
   X.toDouble / Y.toDouble;System.out.println("""res24: Double = """ + $show(res$24));$skip(38); val res$25 = 
 
 
-   Seq(1,2,3,4,5).filter(_ < 3);System.out.println("""res25: Seq[Int] = """ + $show(res$25))}
+   Seq(1,2,3,4,5).filter(_ < 3);System.out.println("""res25: Seq[Int] = """ + $show(res$25));$skip(117); 
+
+
+  val splitstr = "Gene = \"HRG10;2\"; TX = \"Blah\"; exon = 1; variant = \"3\"; Gene = \"Say \\\"Hello\\\"\";";System.out.println("""splitstr  : String = """ + $show(splitstr ));$skip(60); val res$26 = 
+
+  internalUtils.stdUtils.splitRespectQuote(splitstr,";");System.out.println("""res26: Array[String] = """ + $show(res$26));$skip(107); 
+
+
+  internalUtils.stdUtils.parseTokens(splitstr,';').toList.foreach((s : String) => println("'"+s+"'"));$skip(109); 
+
+
+  splitstr.split(";(?=([^\"]*\"[^\"]*\")*[^\"]*$)").toList.foreach((s : String) => println("'"+s+"'"))}
+
+
+
 
 
 }
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$1.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$10.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$10.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$11.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$11.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$12$$anonfun$13.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$12$$anonfun$13.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$12.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$12.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$14.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$14.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$16.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$16.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$17.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$17.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$18.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$18.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$19.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$19.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$2.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$2.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$3.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$3.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$4.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$4.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$5.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$5.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$6$$anonfun$apply$1.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$6$$anonfun$apply$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$6$$anonfun$apply$2.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$6$$anonfun$apply$2.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$6$$anonfun$apply$3.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$6$$anonfun$apply$3.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$6$$anonfun$apply$4.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$6$$anonfun$apply$4.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$6.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$6.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$7.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$7.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$8.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$8.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$9.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$9.class
diff --git a/.../bin/fileConversionUtils/addNovelSplices$$anonfun$buildGenomicArrayOfSets_fromGtf$1.class b/.../bin/fileConversionUtils/addNovelSplices$$anonfun$buildGenomicArrayOfSets_fromGtf$1.class
diff --git a/...tils/bin/fileConversionUtils/addNovelSplices$$anonfun$makeJunctionCountsWithNovel$1.class b/...tils/bin/fileConversionUtils/addNovelSplices$$anonfun$makeJunctionCountsWithNovel$1.class
diff --git a/...tils/bin/fileConversionUtils/addNovelSplices$$anonfun$makeJunctionCountsWithNovel$2.class b/...tils/bin/fileConversionUtils/addNovelSplices$$anonfun$makeJunctionCountsWithNovel$2.class
diff --git a/...tils/bin/fileConversionUtils/addNovelSplices$$anonfun$makeJunctionCountsWithNovel$3.class b/...tils/bin/fileConversionUtils/addNovelSplices$$anonfun$makeJunctionCountsWithNovel$3.class
diff --git a/...tils/bin/fileConversionUtils/addNovelSplices$$anonfun$makeJunctionCountsWithNovel$4.class b/...tils/bin/fileConversionUtils/addNovelSplices$$anonfun$makeJunctionCountsWithNovel$4.class
diff --git a/...eyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$makeOrphanJunctionCounts$1.class b/...eyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$makeOrphanJunctionCounts$1.class
diff --git a/...eyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$makeOrphanJunctionCounts$2.class b/...eyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$makeOrphanJunctionCounts$2.class
diff --git a/...onversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$1$$anonfun$apply$mcVI$sp$1.class b/...onversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$1$$anonfun$apply$mcVI$sp$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$1.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$1.class
diff --git a/...n/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$10$$anonfun$apply$6.class b/...n/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$10$$anonfun$apply$6.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$10.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$10.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$11.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$11.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$2.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$2.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$3.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$3.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$4.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$4.class
diff --git a/...ils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$5$$anonfun$15.class b/...ils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$5$$anonfun$15.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$5.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$5.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$6.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$6.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$7.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$7.class
diff --git a/...in/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$8$$anonfun$apply$5.class b/...in/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$8$$anonfun$apply$5.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$8.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$8.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$9.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$$anonfun$mergeNovelHelper$9.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$.class b/src/HartleyUtils/bin/fileConversionUtils/addNovelSplices$.class
diff --git a/src/HartleyUtils/bin/internalTests/testing.sc b/src/HartleyUtils/bin/internalTests/testing.sc
@@ -5,27 +5,20 @@ import net.sf.samtools._
 object testing {
   println("Welcome to the Scala worksheet")       //> Welcome to the Scala worksheet
   "Hello".substring(0,2)                          //> res0: String = He
+  "Hello".substring(1)                            //> res1: String = ello
 
-  scala.math.log(10.0)                            //> res1: Double = 2.302585092994046
+  scala.math.log(10.0)                            //> res2: Double = 2.302585092994046
 
   //val reader =  new SAMFileReader(new java.io.File("C:\\Users\\hartleys\\work\\nihwork\\home_copy\\projects\\ZZZ-ExampleDataset\\TestSets\\readLength50\\inputData\\fastq\\SAMP1_RG1.50bp.1.fq.gz"));
 
-  "Hello+World".split("\\+")                      //> res2: Array[String] = Array(Hello, World)
+  "Hello+World".split("\\+")                      //> res3: Array[String] = Array(Hello, World)
 
-  Range(0,10).toVector                            //> res3: Vector[Int] = Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9)
+  Range(0,10).toVector                            //> res4: Vector[Int] = Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9)
 
-  Vector("hi").tail                               //> res4: scala.collection.immutable.Vector[String] = Vector()
+  Vector("hi").tail                               //> res5: scala.collection.immutable.Vector[String] = Vector()
 
-  scala.math.log(0).isInfinite                    //> res5: Boolean = true
+  scala.math.log(0).isInfinite                    //> res6: Boolean = true
 
-  val splitstr = "Gene = \"HRG10;2\"; TX = \"Blah\"; exon = 1; variant = \"3\";"
-                                                  //> splitstr  : String = Gene = "HRG10;2"; TX = "Blah"; exon = 1; variant = "3";
-                                                  //| 
-
-
-  splitstr.split(";(?=([^\"]*\"[^\"]*\")*[^\"]*$)")
-                                                  //> res6: Array[String] = Array(Gene = "HRG10;2", " TX = "Blah"", " exon = 1", "
-                                                  //|  variant = "3"")
 
   print(Vector("Hello","World","How","Are","You"));
                                                   //> Vector(Hello, World, How, Are, You)
@@ -134,4 +127,32 @@ System.getProperty("sun.arch.data.model")         //> res17: String = 64
    Seq(1,2,3,4,5).filter(_ < 3)                   //> res25: Seq[Int] = List(1, 2)
 
 
+  val splitstr = "Gene = \"HRG10;2\"; TX = \"Blah\"; exon = 1; variant = \"3\"; Gene = \"Say \\\"Hello\\\"\";"
+                                                  //> splitstr  : String = Gene = "HRG10;2"; TX = "Blah"; exon = 1; variant = "3"
+                                                  //| ; Gene = "Say \"Hello\"";
+
+  internalUtils.stdUtils.splitRespectQuote(splitstr,";")
+                                                  //> res26: Array[String] = Array(Gene = "HRG10;2", " TX = "Blah"", " exon = 1",
+                                                  //|  " variant = "3"", " Gene = "Say \"Hello\""")
+
+
+  internalUtils.stdUtils.parseTokens(splitstr,';').toList.foreach((s : String) => println("'"+s+"'"))
+                                                  //> 'Gene = "HRG10;2"'
+                                                  //| ' TX = "Blah"'
+                                                  //| ' exon = 1'
+                                                  //| ' variant = "3"'
+                                                  //| ' Gene = "Say \"Hello\""'
+
+
+  splitstr.split(";(?=([^\"]*\"[^\"]*\")*[^\"]*$)").toList.foreach((s : String) => println("'"+s+"'"))
+                                                  //> 'Gene = "HRG10;2"'
+                                                  //| ' TX = "Blah"'
+                                                  //| ' exon = 1'
+                                                  //| ' variant = "3"'
+                                                  //| ' Gene = "Say \"Hello\""'
+
+
+
+
+
 }
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$$anonfun$1.class b/src/HartleyUtils/bin/internalUtils/VcfTool$$anonfun$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$$anonfun$2.class b/src/HartleyUtils/bin/internalUtils/VcfTool$$anonfun$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$$anonfun$3.class b/src/HartleyUtils/bin/internalUtils/VcfTool$$anonfun$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$$anonfun$4.class b/src/HartleyUtils/bin/internalUtils/VcfTool$$anonfun$4.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$$anonfun$5.class b/src/HartleyUtils/bin/internalUtils/VcfTool$$anonfun$5.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$InputVcfLine$$anonfun$genoTableBySample$1.class b/src/HartleyUtils/bin/internalUtils/VcfTool$InputVcfLine$$anonfun$genoTableBySample$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$InputVcfLine$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$InputVcfLine$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$InputVcfLine.class b/src/HartleyUtils/bin/internalUtils/VcfTool$InputVcfLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfAnnoLine$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfAnnoLine$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfAnnoLine.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfAnnoLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfChar$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfChar$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfChar.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfChar.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfFilterLine$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfFilterLine$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfFilterLine.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfFilterLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfFloat$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfFloat$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfFloat.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfFloat.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfFormatLine$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfFormatLine$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfFormatLine.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfFormatLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfInfoLine$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfInfoLine$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfInfoLine.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfInfoLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfInt$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfInt$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfInt.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfInt.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfLine$$anonfun$fmtInfo$1.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfLine$$anonfun$fmtInfo$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfLine$$anonfun$fmtMeta$1.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfLine$$anonfun$fmtMeta$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfLine.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfMetaLine.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfMetaLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfMetadata$$anonfun$filterMap$1.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfMetadata$$anonfun$filterMap$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfMetadata$$anonfun$formatMap$1.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfMetadata$$anonfun$formatMap$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfMetadata$$anonfun$infoMap$1.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfMetadata$$anonfun$infoMap$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfMetadata$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfMetadata$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfMetadata.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfMetadata.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberField.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberField.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldA$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldA$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldA.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldA.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldDot$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldDot$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldDot.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldDot.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldG$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldG$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldG.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldG.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldInt$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldInt$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldInt.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldInt.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldKnown.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldKnown.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldR$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldR$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldR.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfNumberFieldR.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfString$.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfString$.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfString.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfString.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool$VcfVal.class b/src/HartleyUtils/bin/internalUtils/VcfTool$VcfVal.class
diff --git a/src/HartleyUtils/bin/internalUtils/VcfTool.class b/src/HartleyUtils/bin/internalUtils/VcfTool.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anon$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anon$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anon$2.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anon$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anon$3.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anon$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anon$5.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anon$5.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$1$$anonfun$apply$mcDI$sp$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$1$$anonfun$apply$mcDI$sp$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$2$$anonfun$3.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$2$$anonfun$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$2$$anonfun$4.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$2$$anonfun$4.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$2.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$5.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$5.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$6.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$6.class
diff --git a/...yUtils/bin/internalUtils/stdUtils$$anonfun$calculateGeometricSizeFactorsForMatrix$1.class b/...yUtils/bin/internalUtils/stdUtils$$anonfun$calculateGeometricSizeFactorsForMatrix$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$escapifyString$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$escapifyString$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$leftRightJustifySeq$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$leftRightJustifySeq$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$parseTokens$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$parseTokens$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$peekIterator$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$peekIterator$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$peekIterator$2.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$peekIterator$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$peekIterator$3.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$peekIterator$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$repToSeq$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$repToSeq$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$repToVector$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$repToVector$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$seqIsSortedBy$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$seqIsSortedBy$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$splitIterator$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$splitIterator$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$standardStatusReport_threeLine$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$standardStatusReport_threeLine$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$transposeMatrix$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$transposeMatrix$1.class
diff --git a/...HartleyUtils/bin/internalUtils/stdUtils$$anonfun$transposeMatrix$2$$anonfun$apply$1.class b/...HartleyUtils/bin/internalUtils/stdUtils$$anonfun$transposeMatrix$2$$anonfun$apply$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$transposeMatrix$2.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$transposeMatrix$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$wrapLinesWithIndent_helper$1.class b/src/HartleyUtils/bin/internalUtils/stdUtils$$anonfun$wrapLinesWithIndent_helper$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$.class b/src/HartleyUtils/bin/internalUtils/stdUtils$.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$IteratorProgressReporter$$anon$4.class b/src/HartleyUtils/bin/internalUtils/stdUtils$IteratorProgressReporter$$anon$4.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$IteratorProgressReporter.class b/src/HartleyUtils/bin/internalUtils/stdUtils$IteratorProgressReporter.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$IteratorProgressReporter_ThreeLevel$.class b/src/HartleyUtils/bin/internalUtils/stdUtils$IteratorProgressReporter_ThreeLevel$.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$IteratorProgressReporter_ThreeLevel.class b/src/HartleyUtils/bin/internalUtils/stdUtils$IteratorProgressReporter_ThreeLevel.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$MemoryUtil$.class b/src/HartleyUtils/bin/internalUtils/stdUtils$MemoryUtil$.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$TimeStampUtil$.class b/src/HartleyUtils/bin/internalUtils/stdUtils$TimeStampUtil$.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$TimeStampUtil.class b/src/HartleyUtils/bin/internalUtils/stdUtils$TimeStampUtil.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$filterWithCount.class b/src/HartleyUtils/bin/internalUtils/stdUtils$filterWithCount.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils$presetProgressReporters$.class b/src/HartleyUtils/bin/internalUtils/stdUtils$presetProgressReporters$.class
diff --git a/src/HartleyUtils/bin/internalUtils/stdUtils.class b/src/HartleyUtils/bin/internalUtils/stdUtils.class
diff --git a/src/HartleyUtils/src/main/scala/fileConversionUtils/addNovelSplices.scala b/src/HartleyUtils/src/main/scala/fileConversionUtils/addNovelSplices.scala
@@ -122,6 +122,10 @@ object addNovelSplices {
      val idCol = decoderTitleLine.indexOf("sample.ID");
      val sfCol = decoderTitleLine.indexOf("size.factor");
 
+     if(idCol == -1){
+       reportln("WARNING WARNING WARNING: no column found with title 'sample.ID' in the size factor / decoder file. The size factor / decoder file must contain a column titled 'sample.ID'. Fatal errors will almost certainly follow.","warn");
+     }
+
      val sampleSF : Seq[(String,Double)] = if(sfCol == -1){
        reportln("decoderTitleLine: "+decoderTitleLine,"debug");
        reportln("idCol: "+idCol,"debug");

diff --git a/src/HartleyUtils/src/main/scala/internalTests/testing.sc b/src/HartleyUtils/src/main/scala/internalTests/testing.sc
@@ -5,27 +5,20 @@ import net.sf.samtools._
 object testing {
   println("Welcome to the Scala worksheet")       //> Welcome to the Scala worksheet
   "Hello".substring(0,2)                          //> res0: String = He
+  "Hello".substring(1)                            //> res1: String = ello
 
-  scala.math.log(10.0)                            //> res1: Double = 2.302585092994046
+  scala.math.log(10.0)                            //> res2: Double = 2.302585092994046
 
   //val reader =  new SAMFileReader(new java.io.File("C:\\Users\\hartleys\\work\\nihwork\\home_copy\\projects\\ZZZ-ExampleDataset\\TestSets\\readLength50\\inputData\\fastq\\SAMP1_RG1.50bp.1.fq.gz"));
 
-  "Hello+World".split("\\+")                      //> res2: Array[String] = Array(Hello, World)
+  "Hello+World".split("\\+")                      //> res3: Array[String] = Array(Hello, World)
 
-  Range(0,10).toVector                            //> res3: Vector[Int] = Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9)
+  Range(0,10).toVector                            //> res4: Vector[Int] = Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9)
 
-  Vector("hi").tail                               //> res4: scala.collection.immutable.Vector[String] = Vector()
+  Vector("hi").tail                               //> res5: scala.collection.immutable.Vector[String] = Vector()
 
-  scala.math.log(0).isInfinite                    //> res5: Boolean = true
+  scala.math.log(0).isInfinite                    //> res6: Boolean = true
 
-  val splitstr = "Gene = \"HRG10;2\"; TX = \"Blah\"; exon = 1; variant = \"3\";"
-                                                  //> splitstr  : String = Gene = "HRG10;2"; TX = "Blah"; exon = 1; variant = "3";
-                                                  //| 
-
-
-  splitstr.split(";(?=([^\"]*\"[^\"]*\")*[^\"]*$)")
-                                                  //> res6: Array[String] = Array(Gene = "HRG10;2", " TX = "Blah"", " exon = 1", "
-                                                  //|  variant = "3"")
 
   print(Vector("Hello","World","How","Are","You"));
                                                   //> Vector(Hello, World, How, Are, You)
@@ -134,4 +127,32 @@ System.getProperty("sun.arch.data.model")         //> res17: String = 64
    Seq(1,2,3,4,5).filter(_ < 3)                   //> res25: Seq[Int] = List(1, 2)
 
 
+  val splitstr = "Gene = \"HRG10;2\"; TX = \"Blah\"; exon = 1; variant = \"3\"; Gene = \"Say \\\"Hello\\\"\";"
+                                                  //> splitstr  : String = Gene = "HRG10;2"; TX = "Blah"; exon = 1; variant = "3"
+                                                  //| ; Gene = "Say \"Hello\"";
+
+  internalUtils.stdUtils.splitRespectQuote(splitstr,";")
+                                                  //> res26: Array[String] = Array(Gene = "HRG10;2", " TX = "Blah"", " exon = 1",
+                                                  //|  " variant = "3"", " Gene = "Say \"Hello\""")
+
+
+  internalUtils.stdUtils.parseTokens(splitstr,';').toList.foreach((s : String) => println("'"+s+"'"))
+                                                  //> 'Gene = "HRG10;2"'
+                                                  //| ' TX = "Blah"'
+                                                  //| ' exon = 1'
+                                                  //| ' variant = "3"'
+                                                  //| ' Gene = "Say \"Hello\""'
+
+
+  splitstr.split(";(?=([^\"]*\"[^\"]*\")*[^\"]*$)").toList.foreach((s : String) => println("'"+s+"'"))
+                                                  //> 'Gene = "HRG10;2"'
+                                                  //| ' TX = "Blah"'
+                                                  //| ' exon = 1'
+                                                  //| ' variant = "3"'
+                                                  //| ' Gene = "Say \"Hello\""'
+
+
+
+
+
 }