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Searched refs:SW_PAD (Results 1 – 2 of 2) sorted by relevance

/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/smithwaterman/
H A DSmithWatermanAlignerAbstractUnitTest.java205 final String SW_PAD = "NNNNNNNNNN"; in testForIdenticalAlignmentsWithDifferingFlankLengths() local
206 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()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/
H A DCigarUtils.java32 private static final String SW_PAD = "NNNNNNNNNN"; field in CigarUtils
195 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()