Add some checking of REF and ALT during initial parsing - makes things not so lenient

Author: Lenbok

test/com/rtg/variant/bayes/multisample/population/PopulationHwHypothesesCreatorTest.java

@@ -59,7 +59,6 @@ public class PopulationHwHypothesesCreatorTest extends TestCase {
       + "#CHROM" + TAB + "POS" + TAB + "ID" + TAB + "REF" + TAB + "ALT" + TAB + "QUAL" + TAB + "FILTER" + TAB + "INFO" + TAB + "FORMAT" + TAB + "HG00096" + TAB + "HG00097" + TAB + "HG00099" + TAB + "HG00100" + TAB + "HG00101" + "\n"
       + "1" + TAB + "10" + TAB + "rs117577454" + TAB + "C" + TAB + "G" + TAB + "100" + TAB + "PASS" + TAB + "." + TAB + "GT:AP" + TAB + "0|0:0.075,0.060" + TAB + "1|0:0.640,0.000" + TAB + "0|0:0.115,0.015" + TAB + "0|0:0.020,0.000" + TAB + "0|0:0.060,0.000" + "\n"
       + "1" + TAB + "12" + TAB + "rs117577454" + TAB + "CT" + TAB + "GT" + TAB + "100" + TAB + "PASS" + TAB + "." + TAB + "GT:AP" + TAB + "0|0:0.075,0.060" + TAB + "1|0:0.640,0.000" + TAB + "0|0:0.115,0.015" + TAB + "0|0:0.020,0.000" + TAB + "0|0:0.060,0.000" + "\n"
-      + "1" + TAB + "15" + TAB + "rs117577454" + TAB + "." + TAB + "GT" + TAB + "100" + TAB + "PASS" + TAB + "." + TAB + "GT:AP" + TAB + "0|0:0.075,0.060" + TAB + "1|0:0.640,0.000" + TAB + "0|0:0.115,0.015" + TAB + "0|0:0.020,0.000" + TAB + "0|0:0.060,0.000" + "\n"
       + "1" + TAB + "18" + TAB + "rs117577454" + TAB + "C" + TAB + "G" + TAB + "100" + TAB + "BLAH" + TAB + "." + TAB + "GT:AP" + TAB + "0|1:0.075,0.060" + TAB + "1|0:0.640,0.000" + TAB + "0|0:0.115,0.015" + TAB + "0|0:0.020,0.000" + TAB + "0|0:0.060,0.000" + "\n"
       + "1" + TAB + "19" + TAB + "rs117577454" + TAB + "CTGAGG" + TAB + "C,CTGAAG" + TAB + "100" + TAB + "PASS" + TAB + "XRX" + TAB + "GT:AP" + TAB + "0|0:0.075,0.060" + TAB + "1|2:0.640,0.000" + TAB + "0|0:0.115,0.015" + TAB + "0|0:0.020,0.000" + TAB + "0|0:0.060,0.000" + "\n";