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Searched refs:hardClip (Results 1 – 25 of 38) sorted by relevance

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/dports/biology/bamutil/bamUtil-1.0.15/src/
H A DFindCigars.cpp75 bool hardClip = false; in execute() local
91 LONG_PARAMETER("chardClip", &hardClip) in execute()
140 hardClip = true; in execute()
160 if(hardClip) in execute()
162 desiredOps[Cigar::hardClip] = true; in execute()
175 if(!insert && !del && !pad && !skip && !hardClip && !softClip) in execute()
/dports/www/qt5-webengine/qtwebengine-everywhere-src-5.15.2/src/3rdparty/chromium/third_party/skia/src/gpu/
H A DGrPipeline.cpp20 const GrAppliedHardClip& hardClip) in GrPipeline() argument
23 if (hardClip.hasStencilClip()) { in GrPipeline()
26 if (hardClip.scissorState().enabled()) { in GrPipeline()
30 fWindowRectsState = hardClip.windowRectsState(); in GrPipeline()
43 : GrPipeline(args, processors.refXferProcessor(), appliedClip.hardClip()) { in GrPipeline()
H A DGrAppliedClip.h102 const GrAppliedHardClip& hardClip() const { return fHardClip; } in hardClip() function
103 GrAppliedHardClip& hardClip() { return fHardClip; } in hardClip() function
H A DGrClipStackClip.cpp242 out->hardClip().addScissor(reducedClip.scissor(), bounds); in apply()
246 out->hardClip().addWindowRectangles(reducedClip.windowRectangles(), in apply()
321 out->hardClip().addStencilClip(reducedClip.maskGenID()); in applyClipMask()
/dports/www/chromium-legacy/chromium-88.0.4324.182/third_party/skia/src/gpu/
H A DGrPipeline.cpp20 const GrAppliedHardClip& hardClip) in GrPipeline() argument
23 if (hardClip.hasStencilClip()) { in GrPipeline()
26 if (hardClip.scissorState().enabled()) { in GrPipeline()
30 fWindowRectsState = hardClip.windowRectsState(); in GrPipeline()
45 : GrPipeline(args, processors.refXferProcessor(), appliedClip.hardClip()) { in GrPipeline()
H A DGrAppliedClip.h121 const GrAppliedHardClip& hardClip() const { return fHardClip; } in hardClip() function
122 GrAppliedHardClip& hardClip() { return fHardClip; } in hardClip() function
H A DGrClipStackClip.cpp231 out->hardClip().addScissor(reducedClip.scissor(), bounds); in apply()
236 out->hardClip().addWindowRectangles(reducedClip.windowRectangles(), in apply()
305 out->hardClip().addStencilClip(reducedClip.maskGenID()); in applyClipMask()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/
H A DClippingRankSumTestUnitTest.java40 private static GATKRead makeRead(final int hardClip) { in makeRead() argument
41 …Cigar cigar = hardClip == 0 ? TextCigarCodec.decode("10M") : TextCigarCodec.decode("10M" + hardCli… in makeRead()
/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/general/
H A DCigar.h95 …hardClip, ///< Hard clip on the read (clipped sequence not present in the query sequence or refer… enumerator
144 case hardClip: in getChar()
266 case hardClip: in isClip()
H A DCigar.cpp150 (cigarOperations[i].operation == hardClip)) in getNumBeginClips()
172 (cigarOperations[i].operation == hardClip)) in getNumEndClips()
493 case hardClip: in setQueryAndReferenceIndexes()
/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/
H A DCigarHelper.cpp133 if(op->operation == Cigar::hardClip) in softClipBeginByRefPos()
326 if(lastOp->operation == Cigar::hardClip) in softClipEndByRefPos()
H A DSamFilter.cpp239 case Cigar::hardClip: in softClip()
384 if(op->operation == Cigar::hardClip) in softClip()
/dports/www/chromium-legacy/chromium-88.0.4324.182/third_party/skia/src/gpu/tessellate/
H A DGrPathTessellateOp.cpp67 GrAppliedHardClip hardClip = GrAppliedHardClip( in onPrePrepare() local
68 (clip) ? clip->hardClip() : GrAppliedHardClip::Disabled()); in onPrePrepare()
70 PrePrepareArgs args{recordTimeAllocator, writeView, &hardClip, clip, &dstProxyView, in onPrePrepare()
394 GrAppliedHardClip hardClip = GrAppliedHardClip(flushState->appliedHardClip()); in onPrepare() local
396 PrePrepareArgs args{flushState->allocator(), flushState->writeView(), &hardClip, in onPrepare()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/
H A DAlignmentInterval.java502 … final byte[] unclippedBases, final boolean hardClip, final int otherFlags, in toSAMRecord() argument
506 …if (hardClip && SAMFlag.SECONDARY_ALIGNMENT.isUnset(otherFlags) && SAMFlag.SUPPLEMENTARY_ALIGNMENT… in toSAMRecord()
517 … : hardClip ? Arrays.copyOfRange(unclippedBases, startInAssembledContig - 1, endInAssembledContig) in toSAMRecord()
528 result.setCigar(softOrHardReclip(cigar, hardClip ? CigarOperator.H : CigarOperator.S)); in toSAMRecord()
/dports/lang/spidermonkey60/firefox-60.9.0/gfx/skia/skia/src/gpu/
H A DGrClipStackClip.cpp215 out->hardClip().addScissor(reducedClip.scissor(), bounds); in apply()
219 out->hardClip().addWindowRectangles(reducedClip.windowRectangles(), in apply()
294 out->hardClip().addStencilClip(reducedClip.maskGenID()); in applyClipMask()
H A DGrAppliedClip.h97 GrAppliedHardClip& hardClip() { return fHardClip; } in hardClip() function
/dports/www/firefox-esr/firefox-91.8.0/gfx/skia/skia/src/gpu/
H A DGrClipStackClip.cpp233 out->hardClip().addScissor(reducedClip.scissor(), bounds); in apply()
237 out->hardClip().addWindowRectangles(reducedClip.windowRectangles(), in apply()
311 out->hardClip().addStencilClip(reducedClip.maskGenID()); in applyClipMask()
H A DGrAppliedClip.h97 GrAppliedHardClip& hardClip() { return fHardClip; } in hardClip() function
/dports/www/firefox/firefox-99.0/gfx/skia/skia/src/gpu/
H A DGrClipStackClip.cpp233 out->hardClip().addScissor(reducedClip.scissor(), bounds); in apply()
237 out->hardClip().addWindowRectangles(reducedClip.windowRectangles(), in apply()
311 out->hardClip().addStencilClip(reducedClip.maskGenID()); in applyClipMask()
H A DGrAppliedClip.h97 GrAppliedHardClip& hardClip() { return fHardClip; } in hardClip() function
/dports/mail/thunderbird/thunderbird-91.8.0/gfx/skia/skia/src/gpu/
H A DGrClipStackClip.cpp233 out->hardClip().addScissor(reducedClip.scissor(), bounds); in apply()
237 out->hardClip().addWindowRectangles(reducedClip.windowRectangles(), in apply()
311 out->hardClip().addStencilClip(reducedClip.maskGenID()); in applyClipMask()
H A DGrAppliedClip.h97 GrAppliedHardClip& hardClip() { return fHardClip; } in hardClip() function
/dports/lang/spidermonkey78/firefox-78.9.0/gfx/skia/skia/src/gpu/
H A DGrClipStackClip.cpp233 out->hardClip().addScissor(reducedClip.scissor(), bounds); in apply()
237 out->hardClip().addWindowRectangles(reducedClip.windowRectangles(), in apply()
311 out->hardClip().addStencilClip(reducedClip.maskGenID()); in applyClipMask()
H A DGrAppliedClip.h97 GrAppliedHardClip& hardClip() { return fHardClip; } in hardClip() function
/dports/biology/sra-tools/sra-tools-2.11.0/tools/util/
H A Dpseudo-aligner.cpp342 …dNo, bool reversed, bool secondary, int pos, int lclip, int rclip, bool hardClip, int mpos, Sequen… in printSAM() argument
347 out << lclip << (hardClip ? 'H' : 'S'); in printSAM()
350 out << rclip << (hardClip ? 'H' : 'S'); in printSAM()

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