| /dports/audio/rezound/rezound-0.13.1beta/src/backend/Effects/ |
| H A D | CChangeRateEffect.cpp | 92 const sample_fpos_t readStart=(rateNode1.x*oldLength);
95 if(readStart==readStop)
101 const sample_fpos_t m=(s2-s1)/(readStop-readStart);
110 const sample_fpos_t b=m*readStart-s1;
135 const sample_fpos_t subReadLength=(readStop-readStart)+1;
138 const sample_fpos_t dReadPos=t*subReadLength/subWriteLength+readStart;
155 sample_pos_t copyLength=(sample_pos_t)((readStop-readStart)+1);
189 sample_fpos_t readStart=rateNode1.x*oldLength;
191 if(readStart==readStop) // vertical rate change
194 sample_fpos_t m=(s2-s1)/(readStop-readStart);
[all …]
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| /dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/SuperReadsR/src2/ |
| H A D | createFastaSuperReadSequences.cc | 306 int readStart=0, readOri='F'; in main() local
312 readStart = atoi(flds[2]); in main()
313 if (readStart < 0) in main()
314 readStart = 0; in main()
398 if (readStart < 0) in main()
399 readStart = 0; in main()
403 if (readStart < minReadLength) in main()
404 readStart = minReadLength; in main()
405 if (readStart > outputSeqLen) in main()
406 readStart = outputSeqLen; in main()
[all …]
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/transformers/ |
| H A D | PalindromeArtifactClipReadTransformerUnitTest.java | 61 final int readStart = readOffset + refStart; in test() local
77 …final GATKRead artifactRead = makeRead(header, contig, readStart, fragmentLength, readBasesWithArt… in test()
81 …final GATKRead notQuiteArtifactRead = makeRead(header, contig, readStart, fragmentLength + 1, read… in test()
85 …final GATKRead definitelyNotArtifactRead = makeRead(header, contig, readStart, fragmentLength, rea… in test()
89 …final GATKRead mateOffContigRead = makeRead(header, contig, readStart, contigLength, readBasesMatc… in test()
92 …final GATKRead mateOffContigRead2 = makeRead(header, contig, readStart, -contigLength, readBasesMa… in test()
97 …ead makeRead(final SAMFileHeader header, final String contig, final int readStart, final int fragm… in makeRead() argument
100 read.setAlignmentStart(readStart); in makeRead()
111 final int mateStart = readStart + fragmentLength - bases.length; in makeRead()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
| H A D | ReferenceConfidenceModel.java | 463 final int readStart, in calculateBaselineMMQualities() argument
474 final byte readBase = readBases[readStart + i]; in calculateBaselineMMQualities()
477 sum += readQuals[readStart + i]; in calculateBaselineMMQualities()
513 final int readStart, in readHasNoPlausibleIdealsOfSize() argument
520 Utils.validate(readStart >= 0, "readStart must >= 0"); in readHasNoPlausibleIdealsOfSize()
537 if (readBases.length - readStart > maxIndelSize) { in readHasNoPlausibleIdealsOfSize()
564 readStart, in readHasNoPlausibleIdealsOfSize()
577 readStart, in readHasNoPlausibleIdealsOfSize()
610 return cachedResult.get(readStart); in readHasNoPlausibleIdealsOfSize()
665 final byte readBase = readBases[readStart + readOffset]; in traverseEndOfReadForIndelMismatches()
[all …]
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| /dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.jdt.core/org.eclipse.jdt.core/search/org/eclipse/jdt/internal/core/nd/db/ |
| H A D | ModificationLog.java | 289 int readStart = (this.insertionPosition + oldBufferLength - newBufferSize) % oldBufferLength; in setBufferSize() local
290 if (readStart >= this.insertionPosition) { in setBufferSize()
291 int entriesFromEnd = oldBufferLength - readStart; in setBufferSize()
292 System.arraycopy(oldBuffer0, readStart, this.buffer0, 0, entriesFromEnd); in setBufferSize()
293 System.arraycopy(oldBuffer1, readStart, this.buffer1, 0, entriesFromEnd); in setBufferSize()
294 System.arraycopy(oldOperation, readStart, this.operation, 0, entriesFromEnd); in setBufferSize()
300 int entriesToCopy = this.insertionPosition - readStart; in setBufferSize()
301 System.arraycopy(oldBuffer0, readStart, this.buffer0, 0, entriesToCopy); in setBufferSize()
302 System.arraycopy(oldBuffer1, readStart, this.buffer1, 0, entriesToCopy); in setBufferSize()
303 System.arraycopy(oldOperation, readStart, this.operation, 0, entriesToCopy); in setBufferSize()
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/loader/ |
| H A D | sequence-writer.c | 79 INSDC_coord_zero *readStart = (void *)readInfo; in SequenceWriteRecord() local
86 + sizeof(readStart[0]) + sizeof(readLen[0]) in SequenceWriteRecord()
100 readStart = h_readInfo; in SequenceWriteRecord()
102 readLen = (INSDC_coord_len *)&readStart[nreads]; in SequenceWriteRecord()
118 readStart[i] = rec->readStart[i]; in SequenceWriteRecord()
157 data.read_start.buffer = readStart; in SequenceWriteRecord()
249 sizeof(self->readStart[0]) + in SequenceRecordResize()
263 self->readStart = (uint32_t *)&self->ti[numreads]; in SequenceRecordResize()
264 self->readLen = (uint32_t *)&self->readStart[numreads]; in SequenceRecordResize()
297 self->readStart[i] = seqlen; in SequenceRecordInit()
[all …]
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/test/loader/ |
| H A D | sequence-writer.c | 79 INSDC_coord_zero *readStart = (void *)readInfo; in SequenceWriteRecord() local
86 + sizeof(readStart[0]) + sizeof(readLen[0]) in SequenceWriteRecord()
100 readStart = h_readInfo; in SequenceWriteRecord()
102 readLen = (INSDC_coord_len *)&readStart[nreads]; in SequenceWriteRecord()
118 readStart[i] = rec->readStart[i]; in SequenceWriteRecord()
157 data.read_start.buffer = readStart; in SequenceWriteRecord()
249 sizeof(self->readStart[0]) + in SequenceRecordResize()
263 self->readStart = (uint32_t *)&self->ti[numreads]; in SequenceRecordResize()
264 self->readLen = (uint32_t *)&self->readStart[numreads]; in SequenceRecordResize()
297 self->readStart[i] = seqlen; in SequenceRecordInit()
[all …]
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| /dports/biology/sra-tools/sra-tools-2.11.0/tools/fastq-loader/ |
| H A D | sequence-writer.c | 84 INSDC_coord_zero *readStart = (void *)readInfo; in SequenceWriteRecord() local
91 + sizeof(readStart[0]) + sizeof(readLen[0]) in SequenceWriteRecord()
105 readStart = h_readInfo; in SequenceWriteRecord()
107 readLen = (INSDC_coord_len *)&readStart[nreads]; in SequenceWriteRecord()
123 readStart[i] = rec->readStart[i]; in SequenceWriteRecord()
162 data.read_start.buffer = readStart; in SequenceWriteRecord()
255 sizeof(self->readStart[0]) + in SequenceRecordResize()
269 self->readStart = (uint32_t *)&self->ti[numreads]; in SequenceRecordResize()
270 self->readLen = (uint32_t *)&self->readStart[numreads]; in SequenceRecordResize()
303 self->readStart[i] = seqlen; in SequenceRecordInit()
[all …]
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/loader/ |
| H A D | sequence-writer.c | 79 INSDC_coord_zero *readStart = (void *)readInfo; in SequenceWriteRecord() local
86 + sizeof(readStart[0]) + sizeof(readLen[0]) in SequenceWriteRecord()
100 readStart = h_readInfo; in SequenceWriteRecord()
102 readLen = (INSDC_coord_len *)&readStart[nreads]; in SequenceWriteRecord()
118 readStart[i] = rec->readStart[i]; in SequenceWriteRecord()
157 data.read_start.buffer = readStart; in SequenceWriteRecord()
249 sizeof(self->readStart[0]) + in SequenceRecordResize()
263 self->readStart = (uint32_t *)&self->ti[numreads]; in SequenceRecordResize()
264 self->readLen = (uint32_t *)&self->readStart[numreads]; in SequenceRecordResize()
297 self->readStart[i] = seqlen; in SequenceRecordInit()
[all …]
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/test/loader/ |
| H A D | sequence-writer.c | 79 INSDC_coord_zero *readStart = (void *)readInfo; in SequenceWriteRecord() local
86 + sizeof(readStart[0]) + sizeof(readLen[0]) in SequenceWriteRecord()
100 readStart = h_readInfo; in SequenceWriteRecord()
102 readLen = (INSDC_coord_len *)&readStart[nreads]; in SequenceWriteRecord()
118 readStart[i] = rec->readStart[i]; in SequenceWriteRecord()
157 data.read_start.buffer = readStart; in SequenceWriteRecord()
249 sizeof(self->readStart[0]) + in SequenceRecordResize()
263 self->readStart = (uint32_t *)&self->ti[numreads]; in SequenceRecordResize()
264 self->readLen = (uint32_t *)&self->readStart[numreads]; in SequenceRecordResize()
297 self->readStart[i] = seqlen; in SequenceRecordInit()
[all …]
|
| /dports/www/gitea/gitea-1.16.5/modules/charset/ |
| H A D | escape.go | 65 readStart := 0
76 n, err = text.Read(buf[readStart:])
77 bs := buf[:n+readStart]
99 readStart = n - i
205 readStart = 0
209 if readStart > 0 {
213 if err = writeBroken(output, buf[:readStart]); err != nil {
|
| /dports/sysutils/k3b/k3b-21.12.3/plugins/decoder/mp3/ |
| H A D | k3bmad.cpp | 87 unsigned char* readStart; in fillStreamBuffer() local
92 readStart = m_inputBuffer + remaining; in fillStreamBuffer()
97 readStart = m_inputBuffer; in fillStreamBuffer()
102 qint64 result = m_inputFile.read( (char*)readStart, readSize ); in fillStreamBuffer()
113 readStart += result; in fillStreamBuffer()
117 memset( readStart, 0, MAD_BUFFER_GUARD ); in fillStreamBuffer()
|
| /dports/biology/bamutil/bamUtil-1.0.15/src/ |
| H A D | OverlapHandler.cpp | 61 int32_t readStart = record.get0BasedPosition(); in getOverlapInfo() local
67 if((readStart == -1) || (mateStart == -1)) in getOverlapInfo()
72 if(readStart > mateStart) in getOverlapInfo()
82 else if(readStart == mateStart) in getOverlapInfo()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
| H A D | PileupReadErrorCorrectorUnitTest.java | 38 final int readStart = Utils.getRandomGenerator().nextInt(ref.length - readLength); in TestErrorCorrection() local
39 final byte[] bases = Arrays.copyOfRange(ref, readStart,readStart + readLength); in TestErrorCorrection()
49 read.setPosition(read.getContig(), refOffset + readStart); in TestErrorCorrection() local
|
| /dports/math/R-cran-raster/raster/man/ |
| H A D | programming.Rd | 3 \alias{readStart}
5 \alias{readStart,Raster-method}
6 \alias{readStart,RasterStack-method}
24 readStart opens file connection(s) for reading, readStop removes it.
34 readStart(x, ...)
48 …\item{...}{additional arguments (None implemented, except for 'silent=TRUE' for readStart for file…
|
| /dports/biology/bbmap/bbmap/current/var/ |
| H A D | Varlet.java | 36 readStart=readStart_; in Varlet()
62 assert(readStart<readStop) : this; in Varlet()
115 sb.append(readStart).append('\t');
171 int readStart=Integer.parseInt(split[2]);
208 mapScore, errors, expectedErrors, paired, readID, readLen, readStart, readStop, numReads,
259 if(readStart!=other.readStart){return readStart-other.readStart;}
328 public int readStart;
|
| /dports/math/R-cran-raster/raster/R/ |
| H A D | mean.R | 15 x <- readStart(x, ...)
58 x <- readStart(x, ...)
84 x <- readStart(x, ...)
116 x <- readStart(x)
141 x <- readStart(x)
193 x <- readStart(x)
223 x <- readStart(x)
245 x <- readStart(x)
|
| H A D | math.R | 31 x <- readStart(x)
58 x <- readStart(x)
84 x <- readStart(x)
126 x <- readStart(x)
164 x <- readStart(x)
|
| H A D | arith.R | 57 e1 <- readStart(e1)
58 e2 <- readStart(e2)
106 e1 <- readStart(e1)
148 e2 <- readStart(e2)
211 e1 <- readStart(e1)
235 e1 <- readStart(e1)
273 e2 <- readStart(e2)
299 e2 <- readStart(e2)
|
| /dports/biology/bbmap/bbmap/current/aligner/ |
| H A D | MultiStateAligner9PacBioAdapter.java | 993 int readStart=0;
1000 readStart=0-refStart;
1001 score+=POINTS_NOREF*readStart;
1002 norefs+=readStart;
1059 int readStart=0;
1065 readStart=0-refStart;
1067 norefs+=readStart;
1126 int readStart=0;
1130 readStart=0-refStart;
1201 int readStart=0;
[all …]
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| H A D | MultiStateAligner9PacBioAdapter2.java | 1176 int readStart=0;
1183 readStart=0-refStart;
1184 score+=POINTS_NOREF*readStart;
1185 norefs+=readStart;
1242 int readStart=0;
1248 readStart=0-refStart;
1250 norefs+=readStart;
1309 int readStart=0;
1313 readStart=0-refStart;
1384 int readStart=0;
[all …]
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| H A D | MultiStateAligner9PacBioAdapter3.java | 999 int readStart=0; in scoreNoIndels() local
1006 readStart=0-refStart; in scoreNoIndels()
1007 score+=POINTS_NOREF*readStart; in scoreNoIndels()
1008 norefs+=readStart; in scoreNoIndels()
1065 int readStart=0; in scoreNoIndels() local
1071 readStart=0-refStart; in scoreNoIndels()
1073 norefs+=readStart; in scoreNoIndels()
1132 int readStart=0; in scoreNoIndelsAndMakeMatchString() local
1136 readStart=0-refStart; in scoreNoIndelsAndMakeMatchString()
1207 int readStart=0; in scoreNoIndelsAndMakeMatchString() local
[all …]
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| /dports/biology/sra-tools/sra-tools-2.11.0/tools/bam-loader/ |
| H A D | sequence-writer.c | 88 INSDC_coord_zero *readStart = (void *)readInfo; in writeRecordX() local
95 + sizeof(readStart[0]) + sizeof(readLen[0]) in writeRecordX()
111 readStart = h_readInfo; in writeRecordX()
113 readLen = (INSDC_coord_len *)&readStart[nreads]; in writeRecordX()
129 int const start = rec->readStart[i]; in writeRecordX()
136 readStart[i] = start; in writeRecordX()
162 data.read_start.buffer = readStart; in writeRecordX()
261 data.read_start.buffer = rec->readStart; in writeRecord2()
|
| /dports/math/R-cran-terra/terra/R/ |
| H A D | read.R | 14 success <- x@ptr$readStart()
23 success <- x@ptr$readStart()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/ |
| H A D | ArtificialReadPileupTestProvider.java | 35 private final int readStart = locStart - readOffset; field in ArtificialReadPileupTestProvider
128 …dAll(createPileupElements(refAllele, loc, numReadsPerAllele[0], sample, readStart, altBases, addEr… in generateRBPForVariant()
129 …dAll(createPileupElements(altAllele, loc, numReadsPerAllele[1], sample, readStart, altBases, addEr… in generateRBPForVariant()
133 …String allele, GenomeLoc loc, int numReadsPerAllele, String sample, int readStart, String altBases… in createPileupElements() argument
167 read.setPosition(loc.getContig(), readStart); in createPileupElements() local
|