071411060cc1a45ba936194d5bb3f541be93e6b4
kent
  Thu Aug 8 00:04:37 2013 -0700
Starting to add test cases.
diff --git src/utils/raToStructGen/test.as src/utils/raToStructGen/test.as
new file mode 100644
index 0000000..7b8b404
--- /dev/null
+++ src/utils/raToStructGen/test.as
@@ -0,0 +1,33 @@
+table edwFastqFile
+"info on a file in fastq short read format beyond what's in edwValidFile"
+    (
+    uint id primary auto;  "ID in this table"
+    uint fileId;	"ID in edwFile table"
+    bigint sampleCount; "# of items in sample if we are just subsampling as we do for reads." 
+    string sampleFileName; "Name of file containing sampleCount randomly selected items from file."
+    bigint readCount; "# of reads in file"
+    bigint baseCount; "# of bases in all reads added up"
+    double readSizeMean; "Average read size"
+    double readSizeStd;  "Standard deviation of read size"
+    double readSizeMin;  "Minimum read size"
+    double readSizeMax; "Maximum read size"
+    double qualMean;  "Mean quality scored as 10*-log10(errorProbability) or close to it.  >25 is good"
+    double qualStd;   "Standard deviation of quality"
+    double qualMin;   "Minimum observed quality"
+    double qualMax;   "Maximum observed quality"
+    string qualType;  "For fastq files either 'sanger' or 'illumina'
+    int qualZero;  "For fastq files offset to get to zero value in ascii encoding"
+    double atRatio;  "Ratio of A+T to total sequence (not including Ns)"
+    double aRatio; "Ratio of A to total sequence (including Ns)"
+    double cRatio; "Ratio of C to total sequence (including Ns)"
+    double gRatio; "Ratio of G to total sequence (including Ns)"
+    double tRatio; "Ratio of T to total sequence (including Ns)"
+    double nRatio; "Ratio of N or . to total sequence"
+    double[readSizeMax] qualPos;  "Mean value for each position in a read up to some max."
+    double[readSizeMax] aAtPos;   "% of As at each pos"
+    double[readSizeMax] cAtPos;   "% of Cs at each pos"
+    double[readSizeMax] gAtPos;   "% of Gs at each pos"
+    double[readSizeMax] tAtPos;   "% of Ts at each pos"
+    double[readSizeMax] nAtPos;   "% of '.' or 'N' at each pos"
+    )
+