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Searched refs:refStop (Results 1 – 16 of 16) sorted by relevance

/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/clipping/
H A DReadClipper.java161 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 …]
/dports/biology/bbmap/bbmap/current/aligner/
H A DMultiStateAligner9PacBioAdapter.java995 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 …]
H A DMultiStateAligner9PacBioAdapter2.java1178 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 …]
H A DMultiStateAligner9PacBioAdapter3.java1001 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 …]
H A DMultiStateAligner9PacBioAdapter_WithBarriers.java1980 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 …]
/dports/biology/bbmap/bbmap/current/align2/
H A DMultiStateAligner11tsJNI.java1003 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 …]
H A DMultiStateAligner11ts.java1943 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 …]
H A DMultiStateAligner9XFlat.java1792 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 …]
H A DMultiStateAligner9ts.java1823 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 …]
H A DMultiStateAligner10ts.java2888 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 …]
H A DMultiStateAligner9Flat.java1868 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 …]
H A DMultiStateAligner9PacBio.java1868 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 …]
/dports/math/mdal/MDAL-release-0.9.0/tests/
H A Dtest_api.cpp298 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()
/dports/biology/bbmap/bbmap/current/stream/
H A DSiteScore.java189 final int refStop=start+bases.length; in isSemiPerfect() local
195 if(refStop>ref.length){ in isSemiPerfect()
196 int dif=(refStop-ref.length); in isSemiPerfect()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/varrep/
H A Dvarrep.asn129 refStop INTEGER,
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/varrep/
H A Dvarrep.asn129 refStop INTEGER,