ReadContextFactory { @NotNull public ReadContext createSNVContext(int refPosition, int readIndex, @NotNull final SAMRecord record, final IndexedBases refBases) { return createMNVContext(refPosition, readIndex, 1, record, refBases); } ReadContextFactory(final int flankSize); @NotNull ReadContext createDelContext(@NotNull final String ref, int refPosition, int readIndex, @NotNull final SAMRecord record,
            final IndexedBases refBases); @NotNull ReadContext createInsertContext(@NotNull final String alt, int refPosition, int readIndex,
            @NotNull final SAMRecord record, final IndexedBases refBases); @NotNull ReadContext createSNVContext(int refPosition, int readIndex, @NotNull final SAMRecord record, final IndexedBases refBases); @NotNull ReadContext createMNVContext(int refPosition, int readIndex, int length, @NotNull final SAMRecord record,
            final IndexedBases refBases);  }
@Test public void testSimpleSnvHas5BaseCore() { String refSequence = "GATCATCTAGG"; String readSequence = "GATCACCTAGG"; IndexedBases refBases = new IndexedBases(1000, 0, refSequence.getBytes()); SAMRecord record = buildSamRecord("11M", readSequence); ReadContext victim = this.victim.createSNVContext(1005, 5, record, refBases); assertEquals("CACCT", victim.centerBases()); }