v1.2.42

README.md

@@ -1,5 +1,5 @@
-# QoRTs v1.2.37
-(Compiled Mon May  1 14:23:33 EDT 2017)
+# QoRTs v1.2.42
+(Compiled Fri Jun  2 12:23:55 EDT 2017)
 
 The [QoRTs software package](http://hartleys.github.io/QoRTs/) is a fast, efficient, and portable 
 multifunction toolkit designed to assist in

src/HartleyUtils/src/main/scala/internalUtils/genomicAnnoUtils.scala

@@ -154,24 +154,27 @@ object genomicAnnoUtils {
   }
 
   class EfficientGenomeSeqContainer_MFA(infile : String) extends EfficientGenomeSeqContainer {
+    //Implementation note: It is important that you never read from remainderIter without first emptying currentIter!
+    // Otherwise scala attempts to store the currentIter values.
+    // This even remains true if there are no external references to the attached currentIter.
     def switchToChrom(chrom : String){
-        var iterPair = remainderIter.span(line => line != (">"+chrom));
-        if(iterPair._2.hasNext){
-          iterPair = iterPair._2.drop(1).span(line => line.charAt(0) != '>');
-        } else {
-          iterPair = internalUtils.fileUtils.getLinesSmartUnzip(infile).span(line =>  line != (">"+chrom));
-          if(iterPair._2.hasNext){
+        report("Switching to Chromosome: " + chrom + " ["+getDateAndTimeString+"] ... ","debug");
+        while(currentIter.hasNext) currentIter.next;
+        var iter = remainderIter.dropWhile(line => line != (">"+chrom));
+        if(! iter.hasNext){
+          iter = internalUtils.fileUtils.getLinesSmartUnzip(infile).dropWhile(line => line != (">"+chrom));
+          if(iter.hasNext){
             reportln("Returning to start of genome FASTA file. NOTE: for optimal performance, sort the FASTA file so that the chromosomes appear in the same order as in the BAM files.","note");
-            iterPair = iterPair._2.drop(1).span(line => line.charAt(0) != '>');
           } else {
             error("FATAL ERROR: Cannot find chromosome \""+chrom+"\" in genome FASTA file!")
           }
         }
-        reportln("Switching to Chromosome: " + chrom,"debug");
+        val iterPair = iter.drop(1).span(line => line.charAt(0) != '>');
         currentIter = iterPair._1.map(_.toUpperCase());
         remainderIter = iterPair._2;
         clearBuffer();
         currChrom = chrom;
+        report("done ["+getDateAndTimeString+"]\n","debug");
     }
 
     var initialReader = internalUtils.fileUtils.getLinesSmartUnzip(infile);

src/HartleyUtils/src/main/scala/runner/runner.scala

@@ -9,9 +9,9 @@ import internalUtils.commandLineUI._;
 
 object runner {
 
-  final val QORTS_VERSION = "1.2.37"; // 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 May  1 14:23:33 EDT 2017"; // 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_COMPILE_TIME : Long = 1493663013; // REPLACE_THIS_QORTS_DATE_VARIABLE_WITH_TIME          (note this exact text is used in a search-and-replace. Do not change it.)
+  final val QORTS_VERSION = "1.2.42"; // 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 = "Fri Jun  2 12:23:55 EDT 2017"; // 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_COMPILE_TIME : Long = 1496420635; // REPLACE_THIS_QORTS_DATE_VARIABLE_WITH_TIME          (note this exact text is used in a search-and-replace. Do not change it.)
 
   final val QORTS_MAJOR_VERSION = QORTS_VERSION.split("\\.")(0);
   final val QORTS_MINOR_VERSION = QORTS_VERSION.split("\\.")(1);

src/QoRTs/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: QoRTs
-Version: 1.2.37
-Date: 2017-05-01
+Version: 1.2.42
+Date: 2017-06-02
 Title: Quality of RNA-seq Tool
 Authors@R: c(person("Stephen Hartley, PhD", "Developer", role = c("aut", "cre"),
                      email = "[email protected]"))

src/QoRTs/NAMESPACE

@@ -16,6 +16,7 @@ export(
  build.plotter.colorByLane,
  build.plotter.colorByGroup,
  build.plotter.basic,
+ build.plotter.advanced,
 
  #Specific Plots:
  makePlot.qual.pair,

src/QoRTs/R/external.plotting.func.R

@@ -4413,7 +4413,9 @@ makePlot.legend.box <- function(plotter,debugMode = DEFAULTDEBUGMODE, singleEndM
   plotter.error.wrapper(plot.name, plotterFcn = function(){
     plotter.NVC <- plotter;
     plot(0,0,col="transparent",xlim=c(0,1),ylim=c(0,1), axes=F,xlab="",ylab="");
-
+
+    diff.text <- "Colored/Marked";
+
     #internal.plot.legend(plotter,"lines","bottomleft");
     #internal.plot.legend(plotter,"points","bottomright");
     if(is.null(plotter$title.annotations[["main.subtitle"]])){
@@ -4459,6 +4461,12 @@ makePlot.legend.box <- function(plotter,debugMode = DEFAULTDEBUGMODE, singleEndM
     } else if(plotter$plot.type == "colorByX"){
       title.text <- paste0("Summary Plots, By ",plotter$title.highlight.name)
       title.cex <- fit.character.vector(title.text);
+    } else if(plotter$plot.type == "highlightByX"){
+      title.text <- paste0("Summary Plots\n",plotter$title.annotations[["highlight.by.title.name"]],"=",plotter$title.annotations[["highlight"]]," Highlighted")
+      title.cex <- fit.character.vector(title.text);
+    } else if(plotter$plot.type == "colorByXhighlightByY"){
+      title.text <- paste0("Summary Plots\n",plotter$title.annotations[["highlight.by.title.name"]],"=",plotter$title.annotations[["highlight"]]," Highlighted\n",diff.text," by ",plotter$title.annotations[["color.by.title.name"]])
+      title.cex <- fit.character.vector(title.text);
     } else {
       title.text <- paste0("Summary Plots, Custom");
       title.cex <- fit.character.vector(title.text);

src/QoRTs/R/internal.plotting.func.R

@@ -2416,14 +2416,16 @@ internal.plot.legend <- function(plotter, legend.type, legend.pos,
   } else if(plotter$plot.type == "colorByLane"){
   } else if(plotter$plot.type == "colorBySample"){ 
   } else if(plotter$plot.type == "colorByX"){ 
+  } else if(plotter$plot.type == "highlightByX"){ 
+
   } else if(plotter$plot.type == "colorByXhighlightByY"){ 
 
   } else if(plotter$plot.type == "summary"){
     #Do nothing. plot nothing.
     return("");
   } else {
-    #Do nothing. Plot nothing.
-    return("");
+    #???
+    #return("");
   }
 
 
@@ -2578,6 +2580,9 @@ internal.get.main.title.fragment <- function(plotter, plot.type){
   if(plotter$plot.type == "colorByGroup") return(paste0("\n",diff.text," by Group"));
   if(plotter$plot.type == "colorBySample") return(paste0("\n",diff.text," by Sample"));
   if(plotter$plot.type == "colorByX") return(paste0("\n",diff.text," by ",plotter$title.highlight.name));
+  if(plotter$plot.type == "highlightByX"){
+    return(paste0("\n",plotter$title.annotations[["highlight.by.title.name"]],"=",plotter$title.annotations[["highlight"]]," Highlighted"));
+  }
   if(plotter$plot.type == "colorByXhighlightByY"){
     #return(paste0("\n",plotter$title.annotations[["highlight"]]," Highlighted, ",diff.text," by ",plotter$title.annotations[["color.by.title.name"]]));
     return(paste0("\n",plotter$title.annotations[["highlight.by.title.name"]],"=",plotter$title.annotations[["highlight"]]," Highlighted, ",diff.text," by ",plotter$title.annotations[["color.by.title.name"]]));