Placeholder commit. Implements a loader for a new multi-part GATK reporting format. See what it looks like at /home/radon01/kiran/scr1/projects/NewVariantEvalOutput/results/v1/tableexample.txt . Still need to address the issue where numeric columns are being interpreted as a vector of strings, not numbers.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4115 348d0f76-0448-11de-a6fe-93d51630548a

R/GATKReport.R

@@ -0,0 +1,47 @@
+read.gatkreport <- function(filename) {
+    con = file(filename, "r", blocking = TRUE);
+    lines = readLines(con);
+    close(con);
+
+    tableEnv = new.env();
+
+    tableName = NA;
+    tableHeader = c();
+    tableRows = c();
+
+    for (line in lines) {
+        if (length(grep("^#:table[[:space:]]+", line, ignore.case=TRUE)) > 0) {
+            headerFields = unlist(strsplit(line, "[[:space:]]+"));
+
+            if (!is.na(tableName)) {
+                d = data.frame(tableRows, row.names=NULL, stringsAsFactors=FALSE);
+                colnames(d) = tableHeader;
+
+                assign(tableName, d, envir=tableEnv);
+            }
+
+            tableName = headerFields[2];
+            tableHeader = c();
+            tableRows = c();
+        } else if (length(grep("^[[:space:]]*$", line)) > 0 | length(grep("^[[:space:]]*#", line)) > 0) {
+            # do nothing
+        } else if (!is.na(tableName)) {
+            row = unlist(strsplit(line, "[[:space:]]+"));
+
+            if (length(tableHeader) == 0) {
+                tableHeader = row;
+            } else {
+                tableRows = rbind(tableRows, row);
+            }
+        }
+    }
+
+    if (!is.na(tableName)) {
+        d = data.frame(tableRows, row.names=NULL);
+        colnames(d) = tableHeader;
+
+        assign(tableName, d, envir=tableEnv);
+    }
+
+    gatkreport = as.list(tableEnv);
+}