Merge remote-tracking branch 'unstable/master'

build.xml

@@ -955,8 +955,8 @@
                 <jvmarg value="-Dpipeline.run=${pipeline.run}" />
                 <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
                 <jvmarg line="${cofoja.jvm.args}"/>
-<!--                 <jvmarg value="-Xdebug"/> -->
-<!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
+<!--                 <jvmarg value="-Xdebug"/>  -->
+<!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/>   -->
 
                 <classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/>
                 <classfileset dir="${java.private.test.classes}" erroronmissingdir="false">

LICENSE → licensing/GATK1_LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2011 The Broad Institute
+Copyright (c) 2012 The Broad Institute
 
 Permission is hereby granted, free of charge, to any person
 obtaining a copy of this software and associated documentation

public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R

@@ -2,19 +2,19 @@
 .gsa.assignGATKTableToEnvironment <- function(tableName, tableHeader, tableRows, tableEnv) {
     d = data.frame(tableRows, row.names=NULL, stringsAsFactors=FALSE);
     colnames(d) = tableHeader;
-
+    
     for (i in 1:ncol(d)) {
         # use the general type.convert infrastructure of read.table to convert column data to R types 
         v = type.convert(d[,i])
         d[,i] = v;
     }
-
+    
     usedNames = ls(envir=tableEnv, pattern=tableName);
-
+    
     if (length(usedNames) > 0) {
         tableName = paste(tableName, ".", length(usedNames), sep="");
     }
-
+    
     assign(tableName, d, envir=tableEnv);
 }
 
@@ -28,74 +28,163 @@
 
     starts = c(1, columnStarts);
     stops = c(columnStarts - 1, nchar(line));
-
+    
     sapply(line, splitStartStop)[,1];
 }
 
-# Load all GATKReport tables from a file
-gsa.read.gatkreport <- function(filename) {
-    con = file(filename, "r", blocking = TRUE);
-    lines = readLines(con);
-    close(con);
-
+# Old implementaton for v0.*
+gsa.read.gatkreportv0 <- function(lines) {
+
     tableEnv = new.env();
-
+    
     tableName = NA;
     tableHeader = c();
     tableRows = c();
     version = NA;
-
+    
     for (line in lines) {
         if (length(grep("^##:GATKReport.v", line, ignore.case=TRUE)) > 0) {
             headerFields = unlist(strsplit(line, "[[:space:]]+"));
-
+            
             if (!is.na(tableName)) {
                 .gsa.assignGATKTableToEnvironment(tableName, tableHeader, tableRows, tableEnv);
             }
-
+            
             tableName = headerFields[2];
             tableHeader = c();
             tableRows = c();
-
+            
             # For differences in versions see
             #   $STING_HOME/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java
             if (length(grep("^##:GATKReport.v0.1[[:space:]]+", line, ignore.case=TRUE)) > 0) {
                 version = "v0.1";
-
+                
             } else if (length(grep("^##:GATKReport.v0.2[[:space:]]+", line, ignore.case=TRUE)) > 0) {
                 version = "v0.2";
                 columnStarts = c();
-
+                
             }
-
+            
         } else if (length(grep("^[[:space:]]*$", line)) > 0 | length(grep("^[[:space:]]*#", line)) > 0) {
             # do nothing
         } else if (!is.na(tableName)) {
-
+            
             if (version == "v0.1") {
                 row = unlist(strsplit(line, "[[:space:]]+"));
-
+                
             } else if (version == "v0.2") {
                 if (length(tableHeader) == 0) {
                     headerChars = unlist(strsplit(line, ""));
                     # Find the first position of non space characters, excluding the first character
                     columnStarts = intersect(grep("[[:space:]]", headerChars, invert=TRUE), grep("[[:space:]]", headerChars) + 1);
                 }
-
+                
                 row = .gsa.splitFixedWidth(line, columnStarts);
             }
-
+            
             if (length(tableHeader) == 0) {
-              tableHeader = row;
+                tableHeader = row;
             } else {
                 tableRows = rbind(tableRows, row);
             }
         }
     }
-
+    
     if (!is.na(tableName)) {
         .gsa.assignGATKTableToEnvironment(tableName, tableHeader, tableRows, tableEnv);
     }
-
+    
     gatkreport = as.list(tableEnv, all.names=TRUE);
 }
+
+# Load all GATKReport v1 tables from file
+gsa.read.gatkreportv1 <- function(lines) {
+  #print("loading with optimized v1 reader")
+  nLines = length(lines)
+  tableEnv = new.env();
+
+  tableName = NA;
+  tableHeader = c();
+  tableRows = NULL;
+  version = "";
+  rowCount = 0
+  headerRowCount = -1;
+
+  finishTable <- function() {
+    .gsa.assignGATKTableToEnvironment(tableName, tableHeader, tableRows[1:rowCount,], tableEnv);
+  }
+
+  for (line in lines) {
+
+    if (length(grep("^#:GATKReport.v1", line, ignore.case=TRUE)) > 0) {
+      version = "v1.0";
+      headerRowCount = 0;
+    }
+
+    if ( (headerRowCount %% 2 == 1) && (version == "v1.0") ) {
+      #print("Trying to start a table with line:");
+      #print(line);
+
+      #Get table header
+      headerFields = unlist(strsplit(line, ":"));
+
+      if (!is.na(tableName)) {
+        finishTable()
+      }
+
+      tableName = headerFields[3];
+      tableHeader = c();
+      tableRows = NULL
+      rowCount = 0
+
+      columnStarts = c();
+    }
+
+    if (length(grep("^#:GATKTable", line, ignore.case=TRUE)) > 0) {
+      headerRowCount = headerRowCount+1;
+      #print("Header Row count is at:")
+      #print(headerRowCount);
+    } else if (!is.na(tableName)) {
+      if ( version == "v1.0") {
+        if (length(tableHeader) == 0) {
+          headerChars = unlist(strsplit(line, ""));
+          # Find the first position of non space characters, excluding the first character
+          columnStarts = intersect(grep("[[:space:]]", headerChars, invert=TRUE), grep("[[:space:]]", headerChars) + 1);
+          tableRows = matrix(nrow=nLines, ncol=length(columnStarts)+1);
+        }
+
+        row = .gsa.splitFixedWidth(line, columnStarts);
+      }
+
+      if (length(tableHeader) == 0) {
+        tableHeader = row;
+      } else if ( nchar(line) > 0 ) {
+        rowCount = rowCount + 1
+        tableRows[rowCount,] <- row
+      }
+    }
+  }
+
+  if (!is.na(tableName)) {
+    finishTable()
+  }
+
+  gatkreport = as.list(tableEnv, all.names=TRUE);
+}
+
+# Load all GATKReport tables from a file
+gsa.read.gatkreport <- function(filename) {
+    con = file(filename, "r", blocking = TRUE);
+    lines = readLines(con);
+    close(con);
+
+    # get first line
+    line = lines[1];
+
+    if (length(grep("^#:GATKReport.v1", line, ignore.case=TRUE)) > 0) {
+        gsa.read.gatkreportv1(lines)
+    }
+    else if (length(grep("^##:GATKReport.v0", line, ignore.case=TRUE)) > 0) {
+        gsa.read.gatkreportv0(lines)
+    }
+}