/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/clipping/ |
H A D | ReadClipper.java | 161 private GATKRead hardClipByReferenceCoordinatesLeftTail(final int refStop) { in hardClipByReferenceCoordinatesLeftTail() argument 328 return hardClipToRegion(read, refStart, refStop, start, stop); in hardClipToRegion() 333 if (alignmentStart <= refStop && alignmentStop >= refStart) { in hardClipToRegion() 334 if (alignmentStart < refStart && alignmentStop > refStop) { in hardClipToRegion() 338 } else if (alignmentStop > refStop) { in hardClipToRegion() 339 return hardClipByReferenceCoordinatesRightTail(read, refStop + 1); in hardClipToRegion() 420 if (refStop < 0) { in clipByReferenceCoordinates() 432 if (refStop >= 0) { in clipByReferenceCoordinates() 476 if (start <= refStop && stop >= refStart) { in softClipToRegionIncludingClippedBases() 477 if (start < refStart && stop > refStop) { in softClipToRegionIncludingClippedBases() [all …]
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/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | MultiStateAligner9PacBioAdapter.java | 995 final int refStop=refStart+read.length; 1004 if(refStop>ref.length){ 1005 int dif=(refStop-ref.length); 1061 final int refStop=refStart+read.length; 1069 if(refStop>ref.length){ 1070 int dif=(refStop-ref.length); 1128 final int refStop=refStart+read.length; 1133 if(refStop>ref.length){ 1134 int dif=(refStop-ref.length); 1208 if(refStop>ref.length){ [all …]
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H A D | MultiStateAligner9PacBioAdapter2.java | 1178 final int refStop=refStart+read.length; 1187 if(refStop>ref.length){ 1188 int dif=(refStop-ref.length); 1244 final int refStop=refStart+read.length; 1252 if(refStop>ref.length){ 1253 int dif=(refStop-ref.length); 1311 final int refStop=refStart+read.length; 1316 if(refStop>ref.length){ 1317 int dif=(refStop-ref.length); 1391 if(refStop>ref.length){ [all …]
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H A D | MultiStateAligner9PacBioAdapter3.java | 1001 final int refStop=refStart+read.length; in scoreNoIndels() local 1010 if(refStop>ref.length){ in scoreNoIndels() 1011 int dif=(refStop-ref.length); in scoreNoIndels() 1067 final int refStop=refStart+read.length; in scoreNoIndels() local 1075 if(refStop>ref.length){ in scoreNoIndels() 1076 int dif=(refStop-ref.length); in scoreNoIndels() 1134 final int refStop=refStart+read.length; in scoreNoIndelsAndMakeMatchString() local 1139 if(refStop>ref.length){ in scoreNoIndelsAndMakeMatchString() 1140 int dif=(refStop-ref.length); in scoreNoIndelsAndMakeMatchString() 1214 if(refStop>ref.length){ in scoreNoIndelsAndMakeMatchString() [all …]
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H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 1980 final int refStop=refStart+read.length; 1989 if(refStop>ref.length){ 1990 int dif=(refStop-ref.length); 2046 final int refStop=refStart+read.length; 2054 if(refStop>ref.length){ 2055 int dif=(refStop-ref.length); 2113 final int refStop=refStart+read.length; 2118 if(refStop>ref.length){ 2119 int dif=(refStop-ref.length); 2193 if(refStop>ref.length){ [all …]
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/dports/biology/bbmap/bbmap/current/align2/ |
H A D | MultiStateAligner11tsJNI.java | 1003 final int refStop=refStart+read.length; 1012 if(refStop>ref.length){ 1013 int dif=(refStop-ref.length); 1085 final int refStop=refStart+read.length; 1093 if(refStop>ref.length){ 1094 int dif=(refStop-ref.length); 1145 final int refStop=refStart+read.length; 1151 if(refStop>ref.length){ 1152 int dif=(refStop-ref.length); 1222 if(refStop>ref.length){ [all …]
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H A D | MultiStateAligner11ts.java | 1943 final int refStop=refStart+read.length; 1952 if(refStop>ref.length){ 1953 int dif=(refStop-ref.length); 2034 final int refStop=refStart+read.length; 2042 if(refStop>ref.length){ 2043 int dif=(refStop-ref.length); 2103 final int refStop=refStart+read.length; 2109 if(refStop>ref.length){ 2110 int dif=(refStop-ref.length); 2186 if(refStop>ref.length){ [all …]
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H A D | MultiStateAligner9XFlat.java | 1792 final int refStop=refStart+read.length; 1801 if(refStop>ref.length){ 1802 int dif=(refStop-ref.length); 1880 final int refStop=refStart+read.length; 1888 if(refStop>ref.length){ 1889 int dif=(refStop-ref.length); 1946 final int refStop=refStart+read.length; 1952 if(refStop>ref.length){ 1953 int dif=(refStop-ref.length); 2026 if(refStop>ref.length){ [all …]
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H A D | MultiStateAligner9ts.java | 1823 final int refStop=refStart+read.length; 1832 if(refStop>ref.length){ 1833 int dif=(refStop-ref.length); 1913 final int refStop=refStart+read.length; 1921 if(refStop>ref.length){ 1922 int dif=(refStop-ref.length); 1981 final int refStop=refStart+read.length; 1987 if(refStop>ref.length){ 1988 int dif=(refStop-ref.length); 2063 if(refStop>ref.length){ [all …]
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H A D | MultiStateAligner10ts.java | 2888 if(refStop>ref.length){ 2889 int dif=(refStop-ref.length); 2962 if(refStop>ref.length){ 2963 int dif=(refStop-ref.length); 3020 if(refStop>ref.length){ 3021 int dif=(refStop-ref.length); 3096 if(refStop>ref.length){ 3097 int dif=(refStop-ref.length); 3173 if(refStop>ref.length){ 3174 int dif=(refStop-ref.length); [all …]
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H A D | MultiStateAligner9Flat.java | 1868 final int refStop=refStart+read.length; 1877 if(refStop>ref.length){ 1878 int dif=(refStop-ref.length); 1958 final int refStop=refStart+read.length; 1966 if(refStop>ref.length){ 1967 int dif=(refStop-ref.length); 2026 final int refStop=refStart+read.length; 2032 if(refStop>ref.length){ 2033 int dif=(refStop-ref.length); 2108 if(refStop>ref.length){ [all …]
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H A D | MultiStateAligner9PacBio.java | 1868 final int refStop=refStart+read.length; 1877 if(refStop>ref.length){ 1878 int dif=(refStop-ref.length); 1958 final int refStop=refStart+read.length; 1966 if(refStop>ref.length){ 1967 int dif=(refStop-ref.length); 2026 final int refStop=refStart+read.length; 2032 if(refStop>ref.length){ 2033 int dif=(refStop-ref.length); 2108 if(refStop>ref.length){ [all …]
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/dports/math/mdal/MDAL-release-0.9.0/tests/ |
H A D | test_api.cpp | 298 std::vector<int> refStop; in TEST() local 302 refStop, in TEST() 318 EXPECT_TRUE( compareVectors( refStop, stop ) ); in TEST() 330 EXPECT_TRUE( compareVectors( refStop, stop ) ); in TEST()
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/dports/biology/bbmap/bbmap/current/stream/ |
H A D | SiteScore.java | 189 final int refStop=start+bases.length; in isSemiPerfect() local 195 if(refStop>ref.length){ in isSemiPerfect() 196 int dif=(refStop-ref.length); in isSemiPerfect()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/varrep/ |
H A D | varrep.asn | 129 refStop INTEGER,
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/varrep/ |
H A D | varrep.asn | 129 refStop INTEGER,
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