| /dports/biology/bbmap/bbmap/current/align2/ |
| H A D | MakeQualityHistogram.java | 83 processRead(r, mapped, paired); in processList()
90 private static void processRead(Read r, int[][] mapped, int[][] paired) { in processRead() method in MakeQualityHistogram
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| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | FuseSequence.java | 167 if(r1!=null && r1.length()>0){processRead(r1);} in processReadPair()
168 if(r2!=null && r2.length()>0){processRead(r2);} in processReadPair()
197 private void processRead(Read r) { in processRead() method in FuseSequence
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| H A D | MakeContaminatedGenomes.java | 205 processRead(r, bb, fracA, randy); in writeChimera()
212 processRead(r, bb, fracB, randy); in writeChimera()
243 public void processRead(Read r, ByteBuilder bb, double genomeFraction, Random randy){ in processRead() method in MakeContaminatedGenomes
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| H A D | AdjustHomopolymers.java | 398 processRead(r1); in processReadPair()
399 processRead(r2); in processReadPair()
403 void processRead(final Read r){ in processRead() method in AdjustHomopolymers
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| H A D | FungalRelease.java | 363 boolean keep = processRead(r1); in getReads()
403 boolean processRead(final Read r1) { in processRead() method in FungalRelease
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| /dports/biology/bbmap/bbmap/current/var/ |
| H A D | GenerateVarlets.java | 342 processRead(r); in processReads()
344 if(!TOSS_SOLO1 || r.paired()){processRead(r);} in processReads()
345 if(!TOSS_SOLO2 || r2.paired()){processRead(r2);} in processReads()
387 processRead(r); in multiprocessRead_old()
415 processRead(r); in multiprocessRead()
442 private void processRead(Read r){ in processRead() method in GenerateVarlets.ProcessThread
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| H A D | GenerateVarlets2.java | 287 processRead(r); in processReads()
289 if(!TOSS_SOLO1 || r.paired()){processRead(r);} in processReads()
290 if(!TOSS_SOLO2 || r2.paired()){processRead(r2);} in processReads()
332 processRead(r); in multiprocessRead_old()
361 processRead(r); in multiprocessRead()
388 private void processRead(Read r){ in processRead() method in GenerateVarlets2.ProcessThread
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| H A D | GenerateVarlets3.java | 491 processRead(r);
493 if(!TOSS_SOLO1 || r.paired()){processRead(r);}
494 if(!TOSS_SOLO2 || r2.paired()){processRead(r2);}
530 processRead(r);
554 private void processRead(Read r){
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| /dports/biology/bbmap/bbmap/current/jasper/ |
| H A D | KmerPosition.java | 125 processRead(r1, kr, counts1, totalEncounter1); in process()
127 processRead(r2, kr, counts2, totalEncounter2); in process()
208 private LongList processRead(Read r, HashSet<String> hs, LongList count, LongList readCount) { in processRead() method in KmerPosition
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| H A D | KmerPosition3.java | 206 processRead(r1, refKmerSet, matchCounts1, totalCounts1); in process()
208 processRead(r2, refKmerSet, matchCounts2, totalCounts2); in process()
414 private void processRead(Read r, LongHashSet hs, LongList matchCounts, LongList totalCounts) { in processRead() method in KmerPosition3
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| /dports/graphics/xournalpp/xournalpp-1.1.0/src/xoj-preview-extractor/ |
| H A D | xournalpp-thumbnailer.cpp | 152 cairo_read_func_t processRead = in main() local
165 cairo_surface_t* thumbnail = cairo_image_surface_create_from_png_stream(processRead, &closure); in main()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_assembly/ |
| H A D | CalculateCoveragePerBaseTask.cpp | 59 processRead(read); in run()
74 void CalculateCoveragePerBaseOnRegionTask::processRead(const U2AssemblyRead &read) { in processRead() function in U2::CalculateCoveragePerBaseOnRegionTask
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| H A D | CalculateCoveragePerBaseTask.h | 74 void processRead(const U2AssemblyRead &read);
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| /dports/biology/bbmap/bbmap/current/driver/ |
| H A D | ReduceSilva.java | 233 boolean keep=processRead(r1); in processInner()
265 boolean processRead(final Read r1){ in processRead() method in ReduceSilva
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| /dports/biology/bbmap/bbmap/current/prok/ |
| H A D | RiboMaker.java | 571 processRead(r1);
572 processRead(r2);
575 void processRead(final Read r){
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| H A D | MergeRibo_Fast.java | 404 boolean keep=processRead(r1);
412 boolean processRead(final Read r){
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/transforms/ |
| H A D | BaseRecalibratorSparkFn.java | 33 …Utils.stream(readsWithVariantsIterator).forEach(t -> bqsr.processRead(t._1, referenceDataSource, t… in apply()
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| /dports/biology/bbmap/bbmap/current/sketch/ |
| H A D | SketchMakerMini.java | 209 processRead(r1); in processReadPair()
210 if(r2!=null){processRead(r2);} in processReadPair()
237 public void processRead(final Read r){
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| H A D | CompareSSU.java | 367 processRead(r); in processInner()
371 void processRead(Read query){ in processRead() method in CompareSSU.ProcessThread
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| /dports/biology/bbmap/bbmap/current/template/ |
| H A D | A_SampleSamStreamer.java | 432 boolean keep=processRead(r);
452 boolean processRead(final Read r){
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| /dports/biology/bbmap/bbmap/current/pacbio/ |
| H A D | RemoveAdapters3.java | 288 processRead(r);
289 if(r.mate!=null){processRead(r.mate);}
371 private int processRead(Read r) {
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| /dports/biology/bbmap/bbmap/current/var2/ |
| H A D | Realign.java | 393 boolean keep=processRead(r1);
424 boolean processRead(final Read r){
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| H A D | FilterSam.java | 505 boolean keep=processRead(r1);
573 boolean keep=processRead(r1);
605 boolean processRead(final Read r1){
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/ |
| H A D | BaseRecalibrator.java | 189 … recalibrationEngine.processRead(read, referenceDataSource, featureContext.getValues(knownSites)); in apply()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/ |
| H A D | razers_paired_match_filter.h | 117 processRead(PairedMatchFilter<TOptionsSpec, TReadSeqSet, TCallback> & filter, unsigned pairId) in processRead() function
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