Home
last modified time | relevance | path

Searched refs:overlapLen (Results 1 – 25 of 53) sorted by relevance

123

/dports/emulators/qemu60/qemu-6.0.0/roms/edk2/MdeModulePkg/Library/BrotliCustomDecompressLib/brotli/research/
H A Ddictionary_generator.cc134 size_t overlapLen = 0; in main() local
247 overlapLen = readInt(arg2); in main()
248 if (overlapLen < 0 || overlapLen > INT_MAX) { in main()
275 } else if (chunkLen <= overlapLen) { in main()
282 chunkStart += chunkLen - overlapLen) { in main()
/dports/emulators/qemu60/qemu-6.0.0/roms/edk2/BaseTools/Source/C/BrotliCompress/brotli/research/
H A Ddictionary_generator.cc134 size_t overlapLen = 0; in main() local
247 overlapLen = readInt(arg2); in main()
248 if (overlapLen < 0 || overlapLen > INT_MAX) { in main()
275 } else if (chunkLen <= overlapLen) { in main()
282 chunkStart += chunkLen - overlapLen) { in main()
/dports/emulators/qemu/qemu-6.2.0/roms/edk2/BaseTools/Source/C/BrotliCompress/brotli/research/
H A Ddictionary_generator.cc134 size_t overlapLen = 0; in main() local
247 overlapLen = readInt(arg2); in main()
248 if (overlapLen < 0 || overlapLen > INT_MAX) { in main()
275 } else if (chunkLen <= overlapLen) { in main()
282 chunkStart += chunkLen - overlapLen) { in main()
/dports/emulators/qemu5/qemu-5.2.0/roms/edk2/MdeModulePkg/Library/BrotliCustomDecompressLib/brotli/research/
H A Ddictionary_generator.cc134 size_t overlapLen = 0; in main() local
247 overlapLen = readInt(arg2); in main()
248 if (overlapLen < 0 || overlapLen > INT_MAX) { in main()
275 } else if (chunkLen <= overlapLen) { in main()
282 chunkStart += chunkLen - overlapLen) { in main()
/dports/emulators/qemu5/qemu-5.2.0/roms/edk2/BaseTools/Source/C/BrotliCompress/brotli/research/
H A Ddictionary_generator.cc134 size_t overlapLen = 0; in main() local
247 overlapLen = readInt(arg2); in main()
248 if (overlapLen < 0 || overlapLen > INT_MAX) { in main()
275 } else if (chunkLen <= overlapLen) { in main()
282 chunkStart += chunkLen - overlapLen) { in main()
/dports/sysutils/uefi-edk2-bhyve/edk2-edk2-stable202102/BaseTools/Source/C/BrotliCompress/brotli/research/
H A Ddictionary_generator.cc134 size_t overlapLen = 0; in main() local
247 overlapLen = readInt(arg2); in main()
248 if (overlapLen < 0 || overlapLen > INT_MAX) { in main()
275 } else if (chunkLen <= overlapLen) { in main()
282 chunkStart += chunkLen - overlapLen) { in main()
/dports/sysutils/uefi-edk2-bhyve/edk2-edk2-stable202102/MdeModulePkg/Library/BrotliCustomDecompressLib/brotli/research/
H A Ddictionary_generator.cc134 size_t overlapLen = 0; in main() local
247 overlapLen = readInt(arg2); in main()
248 if (overlapLen < 0 || overlapLen > INT_MAX) { in main()
275 } else if (chunkLen <= overlapLen) { in main()
282 chunkStart += chunkLen - overlapLen) { in main()
/dports/emulators/qemu/qemu-6.2.0/roms/edk2/MdeModulePkg/Library/BrotliCustomDecompressLib/brotli/research/
H A Ddictionary_generator.cc134 size_t overlapLen = 0; in main() local
247 overlapLen = readInt(arg2); in main()
248 if (overlapLen < 0 || overlapLen > INT_MAX) { in main()
275 } else if (chunkLen <= overlapLen) { in main()
282 chunkStart += chunkLen - overlapLen) { in main()
/dports/sysutils/edk2/edk2-edk2-stable202102/MdeModulePkg/Library/BrotliCustomDecompressLib/brotli/research/
H A Ddictionary_generator.cc134 size_t overlapLen = 0; in poisonData()
247 overlapLen = readInt(arg2); in poisonData()
248 if (overlapLen < 0 || overlapLen > INT_MAX) { in poisonData()
275 } else if (chunkLen <= overlapLen) { in poisonData()
282 chunkStart += chunkLen - overlapLen) { in poisonData()
/dports/sysutils/edk2/edk2-edk2-stable202102/BaseTools/Source/C/BrotliCompress/brotli/research/
H A Ddictionary_generator.cc134 size_t overlapLen = 0;
247 overlapLen = readInt(arg2);
248 if (overlapLen < 0 || overlapLen > INT_MAX) {
275 } else if (chunkLen <= overlapLen) { in addPltSymbols()
282 chunkStart += chunkLen - overlapLen) {
/dports/biology/seqan1/seqan-1.3.1/seqan/consensus/
H A Dconsensus_library.h437 TSize overlapLen = 0; in appendSegmentMatches() local
439 …if (from != to) getAlignmentStatistics(matches, pairSet, from, to, matchLen, overlapLen, alignLen); in appendSegmentMatches()
443 …if ((overlapLen) && ((matchLen * 100) / overlapLen >= thresholdQuality) && (matchLen >= thresholdM… in appendSegmentMatches()
456 …eq1<seq2) _getAlignmentStatistics(dist, seq1, seq2, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
457 else _getAlignmentStatistics(dist, seq2, seq1, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
550 TSize overlapLen = 0; in appendSegmentMatches() local
552 getAlignmentStatistics(matches, pairSet, from, to, matchLen, overlapLen, alignLen); in appendSegmentMatches()
554 if (((matchLen * 100) / overlapLen >= 80) && (matchLen >= 5)) { in appendSegmentMatches()
556 …eq1<seq2) _getAlignmentStatistics(dist, seq1, seq2, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
557 else _getAlignmentStatistics(dist, seq2, seq1, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/consensus/
H A Dconsensus_library.h431 TSize overlapLen = 0; in appendSegmentMatches() local
433 …if (from != to) getAlignmentStatistics(matches, pairSet, from, to, matchLen, overlapLen, alignLen); in appendSegmentMatches()
437 …if ((overlapLen) && ((matchLen * 100) / overlapLen >= thresholdQuality) && (matchLen >= thresholdM… in appendSegmentMatches()
450 …eq1<seq2) _getAlignmentStatistics(dist, seq1, seq2, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
451 … else _getAlignmentStatistics(dist, seq2, seq1, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
544 TSize overlapLen = 0; in appendSegmentMatches() local
546 getAlignmentStatistics(matches, pairSet, from, to, matchLen, overlapLen, alignLen); in appendSegmentMatches()
548 if (((matchLen * 100) / overlapLen >= 80) && (matchLen >= 5)) { in appendSegmentMatches()
550 …eq1<seq2) _getAlignmentStatistics(dist, seq1, seq2, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
551 … else _getAlignmentStatistics(dist, seq2, seq1, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/consensus/
H A Dconsensus_library.h431 TSize overlapLen = 0; in appendSegmentMatches() local
433 …if (from != to) getAlignmentStatistics(matches, pairSet, from, to, matchLen, overlapLen, alignLen); in appendSegmentMatches()
437 …if ((overlapLen) && ((matchLen * 100) / overlapLen >= thresholdQuality) && (matchLen >= thresholdM… in appendSegmentMatches()
450 …eq1<seq2) _getAlignmentStatistics(dist, seq1, seq2, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
451 … else _getAlignmentStatistics(dist, seq2, seq1, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
544 TSize overlapLen = 0; in appendSegmentMatches() local
546 getAlignmentStatistics(matches, pairSet, from, to, matchLen, overlapLen, alignLen); in appendSegmentMatches()
548 if (((matchLen * 100) / overlapLen >= 80) && (matchLen >= 5)) { in appendSegmentMatches()
550 …eq1<seq2) _getAlignmentStatistics(dist, seq1, seq2, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
551 … else _getAlignmentStatistics(dist, seq2, seq1, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/consensus/
H A Dconsensus_library.h434 TSize overlapLen = 0; in appendSegmentMatches() local
436 …if (from != to) getAlignmentStatistics(matches, pairSet, from, to, matchLen, overlapLen, alignLen); in appendSegmentMatches()
440 …if ((overlapLen) && ((matchLen * 100) / overlapLen >= thresholdQuality) && (matchLen >= thresholdM… in appendSegmentMatches()
453 …eq1<seq2) _getAlignmentStatistics(dist, seq1, seq2, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
454 … else _getAlignmentStatistics(dist, seq2, seq1, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
547 TSize overlapLen = 0; in appendSegmentMatches() local
549 getAlignmentStatistics(matches, pairSet, from, to, matchLen, overlapLen, alignLen); in appendSegmentMatches()
551 if (((matchLen * 100) / overlapLen >= 80) && (matchLen >= 5)) { in appendSegmentMatches()
553 …eq1<seq2) _getAlignmentStatistics(dist, seq1, seq2, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
554 … else _getAlignmentStatistics(dist, seq2, seq1, nseq, matchLen, (matchLen * 100) / overlapLen); in appendSegmentMatches()
/dports/biology/seqan1/seqan-1.3.1/seqan/graph_msa/
H A Dgraph_align_tcoffee_library.h418 TValue overlapLen = 0; in _setDistanceValue() local
420 …Statistics(matches, pairSet, (TPos) from, (TPos) length(matches), matchLen, overlapLen, alignLen); in _setDistanceValue()
446 TCargo overlapLen = 0; in _setDistanceValue() local
448 …atistics(matches, pairSet, (TSize) from, (TSize) length(matches), matchLen, overlapLen, alignLen); in _setDistanceValue()
451 …N_DISTANCE_UNITY - (TCargo) (((double) matchLen / (double) overlapLen) * ((double) overlapLen / (d… in _setDistanceValue()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/graph_msa/
H A Dgraph_align_tcoffee_library.h780 TValue overlapLen = 0; in _setDistanceValue() local
782 …Statistics(matches, pairSet, (TPos) from, (TPos) length(matches), matchLen, overlapLen, alignLen); in _setDistanceValue()
808 TCargo overlapLen = 0; in _setDistanceValue() local
810 …atistics(matches, pairSet, (TSize) from, (TSize) length(matches), matchLen, overlapLen, alignLen); in _setDistanceValue()
813 …N_DISTANCE_UNITY - (TCargo) (((double) matchLen / (double) overlapLen) * ((double) overlapLen / (d… in _setDistanceValue()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_msa/
H A Dgraph_align_tcoffee_library.h898 TValue overlapLen = 0; in _setDistanceValue() local
900 …Statistics(matches, pairSet, (TPos) from, (TPos) length(matches), matchLen, overlapLen, alignLen); in _setDistanceValue()
925 TCargo overlapLen = 0; in _setDistanceValue() local
927 …atistics(matches, pairSet, (TSize) from, (TSize) length(matches), matchLen, overlapLen, alignLen); in _setDistanceValue()
930 …N_DISTANCE_UNITY - (TCargo) (((double) matchLen / (double) overlapLen) * ((double) overlapLen / (d… in _setDistanceValue()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_msa/
H A Dgraph_align_tcoffee_library.h898 TValue overlapLen = 0; in _setDistanceValue() local
900 …Statistics(matches, pairSet, (TPos) from, (TPos) length(matches), matchLen, overlapLen, alignLen); in _setDistanceValue()
925 TCargo overlapLen = 0; in _setDistanceValue() local
927 …atistics(matches, pairSet, (TSize) from, (TSize) length(matches), matchLen, overlapLen, alignLen); in _setDistanceValue()
930 …N_DISTANCE_UNITY - (TCargo) (((double) matchLen / (double) overlapLen) * ((double) overlapLen / (d… in _setDistanceValue()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/
H A DSVIntervalUnitTest.java17 Assert.assertTrue(container.overlapLen(containee) == containee.getLength()); in testOverlapLen()
/dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/src/
H A DGBase.h318 int overlapLen(GSeg* r) { in overlapLen() function
328 int overlapLen(uint rstart, uint rend) { in overlapLen() function
H A Dgff_utils.cpp113 ovlen=a.exons[0]->overlapLen(b.exons[0]); in tMatch()
152 if (ti.exons[0]->overlapLen(tj.exons[j])>=minovl) in unsplContained()
237 return (ti.exons[0]->overlapLen(tj.exons[0])>=minlen*0.8) ? bigger : NULL; in redundantTranscripts()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/
H A DSVReadFilter.java72 if (depthFilteredInterval.getInterval().overlapLen(interval) == interval.getLength()) { in containedInRegionToIgnore()
H A DAlignedAssemblyOrExcuse.java160 final int overlapLen = input.readInt(); in readConnection() local
163 return new Connection(target, overlapLen, isRC, isTargetRC); in readConnection()
/dports/biology/bbmap/bbmap/current/jgi/
H A DBBMergeOverlapper.java590 final int overlapLen=(imax-istart); in mateByOverlapJava_unrolled() local
591 …System.err.println("overlapLen="+overlapLen+"; coordinates ("+jstart+"-"+(jstart+overlapLen)+"), (… in mateByOverlapJava_unrolled()
592 System.err.println(new String(abases, jstart, overlapLen)); in mateByOverlapJava_unrolled()
593 System.err.println(new String(bbases, istart, overlapLen)); in mateByOverlapJava_unrolled()
/dports/biology/canu/canu-2.2/src/stores/
H A DovStoreFile.H210 void writeOverlaps(ovOverlap *overlaps, uint64 overlapLen);

123