93cedf42855df36983da1f3d08ffd5e010c31690,java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/AnalyzePowerWalker.java,AnalyzePowerWalker,map,#RefMetaDataTracker#ReferenceContext#AlignmentContext#,63

Before Change


                throw new StingException("Input file reader was not ready before an attempt to read from it, but there was no IOException");
            } else if(!outOfLinesInSyzyFile) {
                Pair<Double,String> syzyPow = getSyzyPowFromFile();
                out.printf("%s: %d %d %d %d %d %d %f %f %f %f |%s%n", context.getLocation(), splitReads.getFirst().getFirst().size(), splitReads.getFirst().getSecond().size(),
                        context.getReads().size(), powPair.getSecond()[0], powPair.getSecond()[1], powPair.getSecond()[2],
                        powPair.getFirst()[0], powPair.getFirst()[1], powPair.getFirst()[2], syzyPow.getFirst(), syzyPow.getSecond());
            } else {

After Change





            int tabIndexChrom = getTableChromIndex(context.getLocation().toString());
            int tabIndexLoc = getTablePosIndex(context.getLocation().toString());
            double syzyPow = 0;
            String syzySanity = "NoLoc";
            if(tabIndexChrom >= 0 && tabIndexLoc >= 0) {