Searched refs:SW_PAD (Results 1 – 2 of 2) sorted by relevance
205 final String SW_PAD = "NNNNNNNNNN"; in testForIdenticalAlignmentsWithDifferingFlankLengths() local206 final String paddedsRef = SW_PAD + new String(paddedRef) + SW_PAD; in testForIdenticalAlignmentsWithDifferingFlankLengths()207 final String paddedsHap = SW_PAD + new String(paddedHap) + SW_PAD; in testForIdenticalAlignmentsWithDifferingFlankLengths()208 final String notPaddedsRef = SW_PAD + new String(notPaddedRef) + SW_PAD; in testForIdenticalAlignmentsWithDifferingFlankLengths()209 final String notpaddedsHap = SW_PAD + new String(notPaddedHap) + SW_PAD; in testForIdenticalAlignmentsWithDifferingFlankLengths()
32 private static final String SW_PAD = "NNNNNNNNNN"; field in CigarUtils195 final String paddedRef = SW_PAD + new String(refSeq) + SW_PAD; in calculateCigar()196 final String paddedPath = SW_PAD + new String(altSeq) + SW_PAD; in calculateCigar()204 final int baseStart = SW_PAD.length(); in calculateCigar()205 final int baseEnd = paddedPath.length() - SW_PAD.length() - 1; // -1 because it's inclusive in calculateCigar()