v1.1.6

hartleys · Jun 14, 2016 · 7a81482 · 7a81482
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diff --git a/QoRTs-vignette.pdf b/QoRTs-vignette.pdf
diff --git a/QoRTs_1.1.2.zip b/QoRTs_1.1.2.zip
diff --git a/QoRTs_1.1.2/QoRTs_1.1.2.tar.gz b/QoRTs_1.1.2/QoRTs_1.1.2.tar.gz
diff --git a/QoRTs_1.1.2/QoRTs-reference-manual.pdf → QoRTs_1.1.6/QoRTs-reference-manual.pdf b/QoRTs_1.1.2/QoRTs-reference-manual.pdf → QoRTs_1.1.6/QoRTs-reference-manual.pdf
diff --git a/QoRTs_1.1.2/QoRTs-vignette.pdf → QoRTs_1.1.6/QoRTs-vignette.pdf b/QoRTs_1.1.2/QoRTs-vignette.pdf → QoRTs_1.1.6/QoRTs-vignette.pdf
diff --git a/QoRTs_1.1.2/QoRTs.jar → QoRTs_1.1.6/QoRTs.jar b/QoRTs_1.1.2/QoRTs.jar → QoRTs_1.1.6/QoRTs.jar
diff --git a/QoRTs_1.1.2/QoRTsExampleData_1.1.2.tar.gz → QoRTs_1.1.6/QoRTsExampleData_1.1.6.tar.gz b/QoRTs_1.1.2/QoRTsExampleData_1.1.2.tar.gz → QoRTs_1.1.6/QoRTsExampleData_1.1.6.tar.gz
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_1.1.2/README.txt → QoRTs_1.1.6/README.txt b/QoRTs_1.1.2/README.txt → QoRTs_1.1.6/README.txt
@@ -1,5 +1,5 @@
-# QoRTs v1.1.2
-(Compiled Mon Jun  6 15:18:28 EDT 2016)
+# QoRTs v1.1.6
+(Compiled Tue Jun 14 15:00:02 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_1.1.2/example-walkthrough.pdf → QoRTs_1.1.6/example-walkthrough.pdf b/QoRTs_1.1.2/example-walkthrough.pdf → QoRTs_1.1.6/example-walkthrough.pdf
diff --git a/QoRTs_1.1.2/scripts/QoRTs.sh → QoRTs_1.1.6/scripts/QoRTs.sh b/QoRTs_1.1.2/scripts/QoRTs.sh → QoRTs_1.1.6/scripts/QoRTs.sh
diff --git a/QoRTs_1.1.2/scripts/qortsGenMultiQC.R → QoRTs_1.1.6/scripts/qortsGenMultiQC.R b/QoRTs_1.1.2/scripts/qortsGenMultiQC.R → QoRTs_1.1.6/scripts/qortsGenMultiQC.R
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
-# QoRTs v1.1.2
-(Compiled Mon Jun  6 15:18:28 EDT 2016)
+# QoRTs v1.1.6
+(Compiled Tue Jun 14 15:00:02 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/bin/fileConversionUtils/gtfConverter$.class b/src/HartleyUtils/bin/fileConversionUtils/gtfConverter$.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/makeBedFromFlatGff$.class b/src/HartleyUtils/bin/fileConversionUtils/makeBedFromFlatGff$.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$1.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$10.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$10.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$2.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$2.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$3.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$3.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$4.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$4.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$5$$anonfun$6.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$5$$anonfun$6.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$5.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$5.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$7.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$7.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$8$$anonfun$9.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$8$$anonfun$9.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$8.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$8.class
diff --git a/.../bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildFeatures2$1$$anonfun$apply$6.class b/.../bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildFeatures2$1$$anonfun$apply$6.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildFeatures2$1.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildFeatures2$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildGeneSets$1.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildGeneSets$1.class
diff --git a/...s/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildGeneSets$2$$anonfun$apply$4.class b/...s/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildGeneSets$2$$anonfun$apply$4.class
diff --git a/...s/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildGeneSets$2$$anonfun$apply$5.class b/...s/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildGeneSets$2$$anonfun$apply$5.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildGeneSets$2.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildGeneSets$2.class
diff --git a/...n/fileConversionUtils/prepFlatGtfFile$$anonfun$buildGenomicArrayOfSets_Tx_and_Map$1.class b/...n/fileConversionUtils/prepFlatGtfFile$$anonfun$buildGenomicArrayOfSets_Tx_and_Map$1.class
diff --git a/...tleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildSpliceJunctionMap$1.class b/...tleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildSpliceJunctionMap$1.class
diff --git a/...eConversionUtils/prepFlatGtfFile$$anonfun$buildSpliceJunctionMap$2$$anonfun$apply$1.class b/...eConversionUtils/prepFlatGtfFile$$anonfun$buildSpliceJunctionMap$2$$anonfun$apply$1.class
diff --git a/...prepFlatGtfFile$$anonfun$buildSpliceJunctionMap$2$$anonfun$apply$2$$anonfun$apply$3.class b/...prepFlatGtfFile$$anonfun$buildSpliceJunctionMap$2$$anonfun$apply$2$$anonfun$apply$3.class
diff --git a/...eConversionUtils/prepFlatGtfFile$$anonfun$buildSpliceJunctionMap$2$$anonfun$apply$2.class b/...eConversionUtils/prepFlatGtfFile$$anonfun$buildSpliceJunctionMap$2$$anonfun$apply$2.class
diff --git a/...tleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildSpliceJunctionMap$2.class b/...tleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildSpliceJunctionMap$2.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildTxCdsSpanMap$1.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$buildTxCdsSpanMap$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$getFlatGtfIterator$1.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$getFlatGtfIterator$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$getFlatGtfIterator$2.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$getFlatGtfIterator$2.class
diff --git a/...yUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$writeFlatGtf_DEXSeqFormat$1.class b/...yUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$writeFlatGtf_DEXSeqFormat$1.class
diff --git a/...tleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$writeFlatGtf_stdFormat$1.class b/...tleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$writeFlatGtf_stdFormat$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/runFeatureComboCt$.class b/src/HartleyUtils/bin/fileConversionUtils/runFeatureComboCt$.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$.class b/src/HartleyUtils/bin/internalUtils/GtfTool$.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$FlatGtfLine$$anonfun$5.class b/src/HartleyUtils/bin/internalUtils/GtfTool$FlatGtfLine$$anonfun$5.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$FlatGtfLine$$anonfun$6.class b/src/HartleyUtils/bin/internalUtils/GtfTool$FlatGtfLine$$anonfun$6.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$FlatGtfLine$class.class b/src/HartleyUtils/bin/internalUtils/GtfTool$FlatGtfLine$class.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$FlatGtfLine.class b/src/HartleyUtils/bin/internalUtils/GtfTool$FlatGtfLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$FlatGtfReader$.class b/src/HartleyUtils/bin/internalUtils/GtfTool$FlatGtfReader$.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$FlatGtfReader.class b/src/HartleyUtils/bin/internalUtils/GtfTool$FlatGtfReader.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$FlatInputGtfLine$.class b/src/HartleyUtils/bin/internalUtils/GtfTool$FlatInputGtfLine$.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$FlatInputGtfLine.class b/src/HartleyUtils/bin/internalUtils/GtfTool$FlatInputGtfLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$FlatOutputGtfLine$$anonfun$1.class b/src/HartleyUtils/bin/internalUtils/GtfTool$FlatOutputGtfLine$$anonfun$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$FlatOutputGtfLine$$anonfun$2.class b/src/HartleyUtils/bin/internalUtils/GtfTool$FlatOutputGtfLine$$anonfun$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$FlatOutputGtfLine$.class b/src/HartleyUtils/bin/internalUtils/GtfTool$FlatOutputGtfLine$.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$FlatOutputGtfLine.class b/src/HartleyUtils/bin/internalUtils/GtfTool$FlatOutputGtfLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$GtfCodes$.class b/src/HartleyUtils/bin/internalUtils/GtfTool$GtfCodes$.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$GtfCodes.class b/src/HartleyUtils/bin/internalUtils/GtfTool$GtfCodes.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$GtfLine.class b/src/HartleyUtils/bin/internalUtils/GtfTool$GtfLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$GtfReader$.class b/src/HartleyUtils/bin/internalUtils/GtfTool$GtfReader$.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$GtfReader.class b/src/HartleyUtils/bin/internalUtils/GtfTool$GtfReader.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$InputGtfLine$$anonfun$lz_attributeArray$2.class b/src/HartleyUtils/bin/internalUtils/GtfTool$InputGtfLine$$anonfun$lz_attributeArray$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$InputGtfLine$$anonfun$lz_attributeMap$1.class b/src/HartleyUtils/bin/internalUtils/GtfTool$InputGtfLine$$anonfun$lz_attributeMap$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$InputGtfLine$.class b/src/HartleyUtils/bin/internalUtils/GtfTool$InputGtfLine$.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$InputGtfLine.class b/src/HartleyUtils/bin/internalUtils/GtfTool$InputGtfLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$3.class b/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$4.class b/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$4.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$lz_attr$1.class b/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$lz_attr$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$lz_attr$2.class b/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$lz_attr$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$lz_attr$3.class b/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$lz_attr$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$lz_attr$4.class b/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$lz_attr$4.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$lz_attributeArray$1.class b/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$$anonfun$lz_attributeArray$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$.class b/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine$.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine.class b/src/HartleyUtils/bin/internalUtils/GtfTool$OutputGtfLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$StdGtfLine$class.class b/src/HartleyUtils/bin/internalUtils/GtfTool$StdGtfLine$class.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$StdGtfReader$.class b/src/HartleyUtils/bin/internalUtils/GtfTool$StdGtfReader$.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$StdGtfReader.class b/src/HartleyUtils/bin/internalUtils/GtfTool$StdGtfReader.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$StdInputGtfLine$.class b/src/HartleyUtils/bin/internalUtils/GtfTool$StdInputGtfLine$.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$StdInputGtfLine.class b/src/HartleyUtils/bin/internalUtils/GtfTool$StdInputGtfLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$StdOutputGtfLine$.class b/src/HartleyUtils/bin/internalUtils/GtfTool$StdOutputGtfLine$.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$StdOutputGtfLine.class b/src/HartleyUtils/bin/internalUtils/GtfTool$StdOutputGtfLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool$defaultGtfCodes$.class b/src/HartleyUtils/bin/internalUtils/GtfTool$defaultGtfCodes$.class
diff --git a/src/HartleyUtils/bin/internalUtils/GtfTool.class b/src/HartleyUtils/bin/internalUtils/GtfTool.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$10.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$10.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$11.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$11.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$12.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$12.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$13.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$13.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$14.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$14.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$15.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$15.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$16.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$16.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$2.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$3.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$3.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$4.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$4.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$5.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$5.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$6.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$6.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$7.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$7.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$8.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$8.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$9.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$9.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$countExons$1.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$countExons$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$countSplices$1.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$countSplices$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$writeOutput$1.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$writeOutput$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$writeOutput$2.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$writeOutput$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$writeOutput$3.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$writeOutput$3.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$writeOutput$4.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$writeOutput$4.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$writeOutput$5.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$$anonfun$writeOutput$5.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts$.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcJunctionCounts.class b/src/HartleyUtils/bin/qcUtils/qcJunctionCounts.class
diff --git a/src/HartleyUtils/bin/qcUtils/runAllQC$.class b/src/HartleyUtils/bin/qcUtils/runAllQC$.class
diff --git a/src/HartleyUtils/src/main/scala/fileConversionUtils/prepFlatGtfFile.scala b/src/HartleyUtils/src/main/scala/fileConversionUtils/prepFlatGtfFile.scala
@@ -126,16 +126,52 @@ object prepFlatGtfFile {
          }
        }
    */
-
-  private def buildGenomicArrayOfSets_Tx_and_Map(stranded : Boolean, gtffile : String, codes : GtfCodes = new GtfCodes()) : (GenomicArrayOfSets[String], Map[String,String], Map[String,(Char,Map[String,Char])]) = {
+  private def buildTxCdsSpanMap(stranded: Boolean, gtffile : String, codes : GtfCodes = new GtfCodes()): Map[String,(Int,Int)] = {
+    var txCDS : Map[String,(Int,Int)] = Map[String,(Int,Int)]();
+    val gtfReader = GtfReader.getStdGtfReader(gtffile, stranded, true, "\\s+", codes);
+
+    for(gtfLine <- gtfReader){
+      if(gtfLine.isCDS){
+        val tx = gtfLine.getTxID;
+        txCDS.get(tx) match {
+          case Some((currStart : Int, currEnd : Int)) => {
+            txCDS += ((tx,(math.min(currStart,gtfLine.start),math.max(currEnd,gtfLine.end))))
+          }
+          case None => {
+            txCDS += ((tx,(gtfLine.start,gtfLine.end)))
+          }
+        }
+      }
+    }
+
+    return txCDS.withDefaultValue((0,0));
+  }
+  private def buildGenomicArrayOfSets_Tx_and_Map(stranded : Boolean, gtffile : String, codes : GtfCodes = new GtfCodes()) : (GenomicArrayOfSets[String], Map[String,String], Map[String,(Char,Map[String,Char])], Map[String,(Int,Int)]) = {
     val txArray : GenomicArrayOfSets[String] = GenomicArrayOfSets[String](stranded);
     val gtfReader = GtfReader.getStdGtfReader(gtffile, stranded, true, "\\s+", codes);
     var txMap : Map[String,String] = Map[String,String]();
     var geneInfoMap = Map[String,(Char,Map[String,Char])]();
-
+    var txCDS : Map[String,(Int,Int)] = Map[String,(Int,Int)]()
+    // returns txArray, txMap, geneInfoMap:
+    // txArray:
+    //     GenomicArrayOfSets -> geneID
+    // txMap:
+    //     Map[(geneID : String) -> (txID : String)]
+    // geneInfoMap:
+    //     Map [ (geneID : String) -> (strand : Char, Map[(txID : String) -> (strand : Char)] ) ]
 
     for(gtfLine <- gtfReader){
-      if(gtfLine.isExon){
+      if(gtfLine.isCDS){
+        val tx = gtfLine.getTxID;
+        txCDS.get(tx) match {
+          case Some((currStart : Int, currEnd : Int)) => {
+            txCDS += ((tx,(math.min(currStart,gtfLine.start),math.max(currEnd,gtfLine.end))))
+          }
+          case None => {
+            txCDS += ((tx,(gtfLine.start,gtfLine.end)))
+          }
+        }
+      } else if(gtfLine.isExon){
         val tx = gtfLine.getTxID;
         val gene = gtfLine.getGeneID;
         val strandedStrand : Char = gtfLine.strandedStrand;
@@ -158,7 +194,7 @@ object prepFlatGtfFile {
         }
       }
     }
-    return ((txArray.finalizeStepVectors, txMap, geneInfoMap));
+    return ((txArray.finalizeStepVectors, txMap, geneInfoMap, txCDS.withDefaultValue((0,0))));
   }
 
   private def buildSpliceJunctionMap(txArray : GenomicArrayOfSets[String]) : (Map[GenomicInterval, Set[String]]) = {
@@ -215,7 +251,9 @@ object prepFlatGtfFile {
                              txMap : Map[String,String], 
                              spliceJunctionMap : Map[GenomicInterval,Set[String]], 
                              aggregateGeneMap : Map[String,String], 
-                             aggregateSet : Set[String], gtfCodes : GtfCodes = new GtfCodes()) : Iterator[FlatGtfLine] = {
+                             aggregateSet : Set[String], 
+                             txCDS : Map[String,(Int,Int)],
+                             gtfCodes : GtfCodes = new GtfCodes()) : Iterator[FlatGtfLine] = {
     //var featureCountMap : Map[String,Int] = Map[String,Int]().withDefault(k => 0);
     //var featureList : Seq[GtfLine] = Seq[GtfLine]();
 
@@ -238,16 +276,15 @@ object prepFlatGtfFile {
         soFar;
       }
     });
-
 
     reportln("    FlatteningGtf: Adding the aggregate genes themselves...("+getDateAndTimeString+")","debug");
     val featureListMap2 = aggregateSet.foldLeft(featureListMap)((soFar, aggregateGene) =>{
       val features = soFar(aggregateGene);
       val iv = new GenomicInterval(features.head.chromName, features.head.strand, features.head.start - 1, features.last.end);
 
       val (geneStrand, geneCt, txInfoMap) = aggregateInfoMap(aggregateGene);
-        
-      val gtfLine = FlatOutputGtfLine.makeFlatGtfLine_aggregateGene(iv, stranded , aggregateGene , geneStrand, geneCt, txInfoMap, gtfCodes);
+
+      val gtfLine = FlatOutputGtfLine.makeFlatGtfLine_aggregateGene(iv, stranded , aggregateGene , geneStrand, geneCt, txInfoMap, txCDS, gtfCodes);
       soFar.updated(aggregateGene, gtfLine +: features);
     });
 
@@ -345,10 +382,11 @@ object prepFlatGtfFile {
         //OutputGtfLine(iv : .GenomicInterval, featureType : String, attributeMap : Map[String,String], stranded : Boolean)
 
 
+  //txCDS:Map[String,(Int,Int)]
 
   private def getFlatGtfIterator(infile : String, stranded : Boolean) : Iterator[FlatGtfLine] = {
     reportln("FlatteningGtf: starting...("+getDateAndTimeString+")","debug");
-    val (txArray, txMap, geneInfoMap) : (GenomicArrayOfSets[String], Map[String,String], Map[String, (Char, Map[String,Char])]) = buildGenomicArrayOfSets_Tx_and_Map(stranded,infile);
+    val (txArray, txMap, geneInfoMap, txCDS) : (GenomicArrayOfSets[String], Map[String,String], Map[String, (Char, Map[String,Char])],  Map[String,(Int,Int)]) = buildGenomicArrayOfSets_Tx_and_Map(stranded,infile);
 
     //val txStrandMap = scala.collection.mutable.AnyRefMap[String,Char]();
 
@@ -383,7 +421,7 @@ object prepFlatGtfFile {
     reportln("    FlatteningGtf: Finished Compiling Aggregate Info. ("+getDateAndTimeString+")","debug");
 
     //val sortedFeatureList = buildFeatures(stranded, txArray, txMap , spliceJunctionMap , aggregateGeneMap , aggregateSet );
-    val sortedFeatureIterator : Iterator[internalUtils.GtfTool.FlatGtfLine] = buildFeatures2(stranded,  aggregateInfoMap, txArray, txMap , spliceJunctionMap , aggregateGeneMap , aggregateSet);
+    val sortedFeatureIterator : Iterator[internalUtils.GtfTool.FlatGtfLine] = buildFeatures2(stranded,  aggregateInfoMap, txArray, txMap , spliceJunctionMap , aggregateGeneMap , aggregateSet, txCDS);
     reportln("    FlatteningGtf: Features Built.("+getDateAndTimeString+")","debug");
     return(sortedFeatureIterator);
   }

diff --git a/src/HartleyUtils/src/main/scala/internalUtils/GtfTool.scala b/src/HartleyUtils/src/main/scala/internalUtils/GtfTool.scala
@@ -69,6 +69,8 @@ object GtfTool {
      val JS_AGGREGATEGENE_TXCT = "tx_ct";
      val JS_AGGREGATEGENE_TXSTRANDS = "tx_strands";
 
+     val JS_TRANSCRIPT_CDS_SPANS = "tx_cds_spans";
+
      val JS_FEATURETYPE_CODEMAP = Map(JS_FEATURETYPE_GENE -> "A", JS_FEATURETYPE_EXON -> "E", JS_FEATURETYPE_KNOWNSPLICE -> "J", JS_FEATURETYPE_NOVELSPLICE -> "N");
 
      def getJSFeatureName(gtfLine : GtfLine) : String = {
@@ -100,7 +102,8 @@ object GtfTool {
                        JS_AGGREGATEGENE_CT : String = defaultGtfCodes.JS_AGGREGATEGENE_CT,
                        JS_AGGREGATEGENE_TXCT : String = defaultGtfCodes.JS_AGGREGATEGENE_TXCT,
                        JS_AGGREGATEGENE_TXSTRANDS : String = defaultGtfCodes.JS_AGGREGATEGENE_TXSTRANDS,
-                       BIOTYPE_ATTRIBUTE_KEY : String = defaultGtfCodes.BIOTYPE_ATTRIBUTE_KEY
+                       BIOTYPE_ATTRIBUTE_KEY : String = defaultGtfCodes.BIOTYPE_ATTRIBUTE_KEY,
+                       JS_TRANSCRIPT_CDS_SPANS : String = defaultGtfCodes.JS_TRANSCRIPT_CDS_SPANS
                        ) {
 
      val KEY_SORTING : List[String] = List[String](  GENE_ID_ATTRIBUTE_KEY, 
@@ -112,6 +115,7 @@ object GtfTool {
                                                      JS_AGGREGATEGENE_CT,
                                                      JS_AGGREGATEGENE_TXCT,
                                                      JS_AGGREGATEGENE_TXSTRANDS,
+                                                     JS_TRANSCRIPT_CDS_SPANS,
                                                      BIOTYPE_ATTRIBUTE_KEY
                                                      );
    }
@@ -167,15 +171,19 @@ object GtfTool {
        new FlatOutputGtfLine(iv.chromName, DEF_FEATURESOURCE, featureType, iv.start + 1, iv.end, DEF_SCORE, iv.strand, attributeMap, DEF_ATTRBREAK, stranded, Some(codes.KEY_SORTING), codes);
      }
 
-     def makeFlatGtfLine_aggregateGene(iv : internalUtils.commonSeqUtils.GenomicInterval, stranded : Boolean, aggregateGene : String, geneStrand : Char, geneCt : Int, txInfoMap : Map[String,Char], codes : GtfCodes = new GtfCodes()) : FlatOutputGtfLine = {
+     def makeFlatGtfLine_aggregateGene(iv : internalUtils.commonSeqUtils.GenomicInterval, stranded : Boolean, aggregateGene : String, geneStrand : Char, geneCt : Int, txInfoMap : Map[String,Char], txCDS : Map[String,(Int,Int)], codes : GtfCodes = new GtfCodes()) : FlatOutputGtfLine = {
        val attributeMap = Map[String,String](codes.GENE_ID_ATTRIBUTE_KEY -> aggregateGene, 
                                              codes.JS_EXONIC_PART_NUMBER_ATTRIBUTE_KEY -> "000", 
                                              codes.JS_AGGREGATEGENE_STRAND -> geneStrand.toString,
                                              codes.JS_AGGREGATEGENE_CT -> geneCt.toString,
                                              codes.JS_AGGREGATEGENE_TXCT -> txInfoMap.keySet.size.toString,
                                              codes.JS_TX_ID_ATTRIBUTE_KEY -> txInfoMap.keySet.toVector.sorted.mkString("+"),
-                                             codes.JS_AGGREGATEGENE_TXSTRANDS -> txInfoMap.keySet.toVector.sorted.map(txInfoMap(_).toString).mkString(",")
-                                             );
+                                             codes.JS_AGGREGATEGENE_TXSTRANDS -> txInfoMap.keySet.toVector.sorted.map(txInfoMap(_).toString).mkString(","),
+                                             codes.JS_TRANSCRIPT_CDS_SPANS -> txInfoMap.keySet.toVector.sorted.map((txID : String) => {
+                                                                                 val (s,e) = txCDS(txID);
+                                                                                 s + "_" + e;
+                                                                              }).mkString(",")
+                                             )
        return makeFlatGtfLine(iv,codes.JS_FEATURETYPE_GENE, attributeMap, stranded, codes);
      }
 
@@ -188,7 +196,9 @@ object GtfTool {
 
        return makeFlatGtfLine(iv, featureType, attributeMap, stranded, codes);
      }
-
+
+
+
    }
 
    var ERROR_COUNT_SORTING = 0;

diff --git a/src/HartleyUtils/src/main/scala/qcUtils/qcJunctionCounts.scala b/src/HartleyUtils/src/main/scala/qcUtils/qcJunctionCounts.scala
@@ -78,8 +78,7 @@ object qcJunctionCounts {
       })
     })
   }
-
-} 
+}
 //runFunc.contains("writeDEXSeq"), runFunc.contains("writeSpliceExon"), runFunc.contains("writeKnownSplices"), runFunc.contains("writeNovelSplices")
 class qcJunctionCounts(anno_holder : qcGtfAnnotationBuilder, stranded : Boolean, fr_secondStrand : Boolean, 
                        writeDEXSeq : Boolean, writeSpliceExon : Boolean, writeKnownSplices : Boolean, writeNovelSplices : Boolean, annotatedSpliceExonCounts : Boolean,

diff --git a/src/HartleyUtils/src/main/scala/qcUtils/runAllQC.scala b/src/HartleyUtils/src/main/scala/qcUtils/runAllQC.scala
@@ -1131,7 +1131,7 @@ object runAllQC {
 
     summaryWriter.write("KEPT_NOT_UNIQUE_ALIGNMENT	"+keptMultiMappedCt+"\n");
     summaryWriter.write("minObservedReadLength\t"+minObsReadLength + "\n");
-    summaryWriter.write("maxObservedReadLength\t"+minObsReadLength + "\n");
+    summaryWriter.write("maxObservedReadLength\t"+maxObsReadLength + "\n");
     summaryWriter.write("maxLegalPhredScore\t"+maxPhredScore + "\n");
 
     if(isSingleEnd){

diff --git a/src/HartleyUtils/src/main/scala/runner/runner.scala b/src/HartleyUtils/src/main/scala/runner/runner.scala
@@ -9,8 +9,8 @@ import internalUtils.commandLineUI._;
 
 object runner {
 
-  final val QORTS_VERSION = "1.1.2"; // REPLACE_THIS_QORTS_VERSION_VARIABLE_WITH_VERSION_NUMBER          (note this exact text is used in a search-and-replace. Do not change it.)
-  final val QORTS_COMPILE_DATE = "Mon Jun  6 15:18:28 EDT 2016"; // REPLACE_THIS_QORTS_DATE_VARIABLE_WITH_DATE          (note this exact text is used in a search-and-replace. Do not change it.)
+  final val QORTS_VERSION = "1.1.6"; // REPLACE_THIS_QORTS_VERSION_VARIABLE_WITH_VERSION_NUMBER          (note this exact text is used in a search-and-replace. Do not change it.)
+  final val QORTS_COMPILE_DATE = "Tue Jun 14 15:00:02 EDT 2016"; // REPLACE_THIS_QORTS_DATE_VARIABLE_WITH_DATE          (note this exact text is used in a search-and-replace. Do not change it.)
 
   //final val FOR_HELP_STRING = "For help, use command: "
 

diff --git a/src/QoRTs/DESCRIPTION b/src/QoRTs/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: QoRTs
-Version: 1.1.2
-Date: 2016-06-06
+Version: 1.1.6
+Date: 2016-06-14
 Title: Quality of RNA-seq Tool
 Authors@R: c(person("Stephen Hartley, PhD", "Developer", role = c("aut", "cre"),
                      email = "[email protected]"))

diff --git a/src/QoRTs/NEWS b/src/QoRTs/NEWS
@@ -1,4 +1,11 @@
-## v1.1.0:
+## v1.1.6:
+Minor additions and tweaks:
+* Added new optional tag to "flattened" GFF file, containing transcript coding region information. This is intended for use by a future update to JunctionSeq.
+* Fixed x-axis label autofitting to not produce oversized x-axis labels when there is only one column to label.
+* Legend plot now autofits and autoselects the number of columns. Added cex.legend and ncol parameters to these functions to allow users to override this behavior.
+* Fixed bug with maxObsReadLength field.
+
+## v1.1.2:
 New features, updates, and bug-fixes.
 * Major bugfix: Fixed the geneCounts file so that UTR/CDS counts are no longer switched. Thanks to Roy Francis!
 * Added "rasterize.medium.plots" parameter to all makeMultiPlot functions. This option will 

diff --git a/src/QoRTs/R/external.plotting.func.R b/src/QoRTs/R/external.plotting.func.R
@@ -2532,7 +2532,7 @@ makePlot.splicing.mismatch <- function(plotter, debugMode = DEFAULTDEBUGMODE,  s
 ####################################################################################
 
 
-makePlot.legend.box <- function(plotter,debugMode = DEFAULTDEBUGMODE, singleEndMode = plotter$res@singleEnd, ...){
+makePlot.legend.box <- function(plotter,debugMode = DEFAULTDEBUGMODE, singleEndMode = plotter$res@singleEnd, cex.legend = NULL, ncol = NULL, ...){
   plot.name <- "legend box";
   plotter.error.wrapper(plot.name, plotterFcn = function(){
     plotter.NVC <- plotter;
@@ -2546,45 +2546,55 @@ makePlot.legend.box <- function(plotter,debugMode = DEFAULTDEBUGMODE, singleEndM
       title.text <- paste0("Sample Highlight:\n",plotter$title.highlight.name,"\nColored by Lane")
       title.cex <- fit.character.vector(title.text);
 
-      text(0.5,1,title.text,adj=c(0.5,1),cex=title.cex, ...);
-      internal.plot.legend(plotter,"lnpt","bottom", ...);
+      #text(0.5,1,title.text,adj=c(0.5,1),cex=title.cex, ...);
+      #internal.plot.legend(plotter,"lnpt","bottom", ...);
       #internal.plot.legend(plotter.NVC,"NVC.both","center");
     } else if(plotter$plot.type == "highlightSample") {
       #internal.plot.legend(plotter.NVC,"NVC.both","center");
       title.text <- paste0("Sample Highlight:\n",plotter$title.highlight.name)
       title.cex <- fit.character.vector(title.text);
 
-      internal.plot.legend(plotter,"lnpt","bottom", ...);
-      text(0.5,1,title.text,adj=c(0.5,1),cex=title.cex, ...);
+      #internal.plot.legend(plotter,"lnpt","bottom", ...);
+      #text(0.5,1,title.text,adj=c(0.5,1),cex=title.cex, ...);
     } else if(plotter$plot.type == "colorBySample") {
       title.text <- paste0("Summary Plots, By Sample")
       title.cex <- fit.character.vector(title.text);
-      text(0.5,1,title.text,adj=c(0.5,1),cex=title.cex, ...);
-      internal.plot.legend(plotter,"lnpt","bottom", ...);
+      #text(0.5,1,title.text,adj=c(0.5,1),cex=title.cex, ...);
+      #internal.plot.legend(plotter,"lnpt","bottom", ...);
     } else if(plotter$plot.type == "summary"){
       title.text <- paste0("All\nQuality Control\nSummary Plots")
       title.cex <- fit.character.vector(title.text);
       text(0.5,0.5,title.text,adj=c(0.5,0.5),cex=title.cex, ...);
+      return("");
     } else if(plotter$plot.type == "colorByLane"){
       title.text <- paste0("Summary Plots, By Lane")
       title.cex <- fit.character.vector(title.text);
-      text(0.5,1,title.text,adj=c(0.5,1),cex=title.cex, ...);
-      internal.plot.legend(plotter,"lnpt","bottom", ...);
+      #text(0.5,1,title.text,adj=c(0.5,1),cex=title.cex, ...);
+      #internal.plot.legend(plotter,"lnpt","bottom", ...);
     } else if(plotter$plot.type == "colorByGroup"){
       title.text <- paste0("Summary Plots, By Group")
       title.cex <- fit.character.vector(title.text);
-      text(0.5,1,title.text,adj=c(0.5,1),cex=title.cex, ...);
-      internal.plot.legend(plotter,"lnpt","bottom", ...);
-    } else {
+      #text(0.5,1,title.text,adj=c(0.5,1),cex=title.cex, ...);
+      #internal.plot.legend(plotter,"lnpt","bottom", ...);
+    } #else {
       #Do nothing.
-      return("");
+    #  return("");
+    #}
+    text(0.5,1,title.text,adj=c(0.5,1),cex=title.cex, ...);
+
+    if(is.null(cex.legend)){
+      autofit.limits <- device.limits();
+      autofit.limits[4] <- par("usr")[4] - strheight(paste0(title.text,"\n"),cex = title.cex);
+      internal.plot.legend(plotter,"lnpt","bottom",autofit.limits=autofit.limits, ncol=ncol, ...);
+    } else {
+      internal.plot.legend(plotter,"lnpt","bottom", cex = cex.legend, ncol=ncol, ...);
     }
   })
 }
 
-makePlot.legend.over <- function(position, plotter, debugMode = DEFAULTDEBUGMODE, singleEndMode = plotter$res@singleEnd, ...) {
+makePlot.legend.over <- function(position, plotter, debugMode = DEFAULTDEBUGMODE, singleEndMode = plotter$res@singleEnd,ncol = NULL, ...) {
   plotter.NVC <- plotter;
-  internal.plot.legend(plotter, "lnpt", position, ...);
+  internal.plot.legend(plotter, "lnpt", position,ncol=ncol, ...);
 }
 
 get.summary.table <- function(res, outfile = NULL, debugMode = DEFAULTDEBUGMODE){
-Original file line number
+Diff line change
@@ Expand Up / @@ -78,8 +78,7 @@ object qcJunctionCounts { @@
           })
         })
       }
-    }
+    }
     //runFunc.contains("writeDEXSeq"), runFunc.contains("writeSpliceExon"), runFunc.contains("writeKnownSplices"), runFunc.contains("writeNovelSplices")
     class qcJunctionCounts(anno_holder : qcGtfAnnotationBuilder, stranded : Boolean, fr_secondStrand : Boolean,
                            writeDEXSeq : Boolean, writeSpliceExon : Boolean, writeKnownSplices : Boolean, writeNovelSplices : Boolean, annotatedSpliceExonCounts : Boolean,
@@ Expand Down @@