| /dports/biology/bbmap/bbmap/current/var2/ |
| H A D | VarFilter.java | 16 maxCov=Integer.parseInt(b); in parse()
100 maxCov=Integer.MAX_VALUE; in clear()
131 maxCov=filter.maxCov; in setFrom()
173 if(cov<minCov || cov>maxCov){return false;} in passesFilter()
246 sb.append("maxCov=").append(maxCov).append("\n"); in toString()
267 public int maxCov=Integer.MAX_VALUE; field in VarFilter
|
| /dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Peak/ |
| H A D | PeakDetectorParameters.hh | 11 PeakDetectorParameters( double minCov, double maxCov, double width, double ratio ) in PeakDetectorParameters() argument
12 : minCoverage(minCov), maxCoverage(maxCov), binWidth(width), snRatio(ratio){} in PeakDetectorParameters()
|
| H A D | EMPeakDetector.cc | 52 int maxCov = 0; in detectCoveragePeaks() local
56 if (covlist[index]> maxCov){ in detectCoveragePeaks()
57 subMaxCov = maxCov; in detectCoveragePeaks()
58 maxCov = covlist[index]; in detectCoveragePeaks()
|
| /dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-v0.3.1/ |
| H A D | scriptEstimatedCovMulti.py | 87 maxCov = 0
92 if listShort1Cov[i] > maxCov:
93 subMaxCov = maxCov
94 maxCov = listShort1Cov[i]
|
| /dports/biology/bbmap/bbmap/current/assemble/ |
| H A D | BubblePopper.java | 365 left.maxCov=Tools.max(left.maxCov, right.maxCov, mid.maxCov); in pop()
366 left.minCov=Tools.min(left.maxCov, right.maxCov); in pop()
473 left.maxCov=Tools.max(left.maxCov, right.maxCov); in merge()
474 left.minCov=Tools.min(left.maxCov, right.maxCov); in merge()
|
| H A D | Contig.java | 73 bb.append(",max=").append(maxCov); in toHeader()
453 public int maxCov;
|
| /dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-v0.3.1/src/ |
| H A D | splay.c | 406 int maxCov) in filterAndExportSplayTree() argument
411 filterAndExportSplayTree(file, T->left, minCov, maxCov); in filterAndExportSplayTree()
412 filterAndExportSplayTree(file, T->right, minCov, maxCov); in filterAndExportSplayTree()
414 && (maxCov == -1 || T->position <= maxCov)) in filterAndExportSplayTree()
|
| H A D | splay.h | 48 int maxCov);
|
| H A D | graphStats.h | 153 void removeHighCoverageNodes(Graph * graph, double maxCov);
|
| H A D | graphStats.c | 2258 void removeHighCoverageNodes(Graph * graph, double maxCov) in removeHighCoverageNodes() argument
2264 if (maxCov < 0) in removeHighCoverageNodes()
2267 printf("Applying an upper coverage cutoff of %f...\n", maxCov); in removeHighCoverageNodes()
2274 maxCov) { in removeHighCoverageNodes()
|
| /dports/biology/bbmap/bbmap/current/var/ |
| H A D | GenerateConsensusVariations.java | 181 int maxCov=midCov, minCov=midCov; in passesFilter() local
203 maxCov=Tools.max(maxCov, cov); in passesFilter()
204 if(verbose){System.err.println("minCov = "+minCov+", maxCov = "+maxCov);} in passesFilter()
|
| /dports/biology/canu/canu-2.2/src/stores/ |
| H A D | tgTig.H | 287 void stashContains(double maxCov, tgTigStashed &S);
290 void dropExcessCoverage(double maxCov) { in dropExcessCoverage() argument
293 stashContains(maxCov, S); in dropExcessCoverage()
|
| /dports/biology/canu/canu-2.2/src/utgcns/ |
| H A D | stashContains.C | 40 tgTig::stashContains(double maxCov, tgTigStashed &S) { in stashContains() argument
106 uint64 bLimit = (uint64)floor(maxCov * hiEnd); in stashContains()
|
| H A D | utgcns.C | 82 double maxCov = 0.0; variable
390 tig->stashContains(params.maxCov, S); in processImportedTigs()
593 tig->stashContains(params.maxCov, S); in processTigs()
772 params.maxCov = strtodouble(argv[++arg]); in main()
|
| /dports/lang/gcc6-aux/gcc-6-20180516/libjava/classpath/gnu/java/awt/java2d/ |
| H A D | ScanlineCoverage.java | 459 void setMaxCoverage(int maxCov) in setMaxCoverage() argument
461 maxCoverage = maxCov; in setMaxCoverage()
|
| /dports/lang/gcc48/gcc-4.8.5/libjava/classpath/gnu/java/awt/java2d/ |
| H A D | ScanlineCoverage.java | 459 void setMaxCoverage(int maxCov) in setMaxCoverage() argument
461 maxCoverage = maxCov; in setMaxCoverage()
|
| /dports/devel/arm-none-eabi-gcc492/gcc-4.9.2/libjava/classpath/gnu/java/awt/java2d/ |
| H A D | ScanlineCoverage.java | 459 void setMaxCoverage(int maxCov) in setMaxCoverage() argument
461 maxCoverage = maxCov; in setMaxCoverage()
|
| /dports/lang/gnat_util/gcc-6-20180516/libjava/classpath/gnu/java/awt/java2d/ |
| H A D | ScanlineCoverage.java | 459 void setMaxCoverage(int maxCov) in setMaxCoverage() argument
461 maxCoverage = maxCov; in setMaxCoverage()
|
| /dports/devel/mingw32-gcc/gcc-4.8.1/libjava/classpath/gnu/java/awt/java2d/ |
| H A D | ScanlineCoverage.java | 459 void setMaxCoverage(int maxCov) in setMaxCoverage() argument
461 maxCoverage = maxCov; in setMaxCoverage()
|
| /dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Velvet-1.1.06/ |
| H A D | graphStats.h | 69 void removeHighCoverageNodes(Graph * graph, double maxCov, boolean _export, Coordinate minLength, c…
|
| H A D | graphStats.c | 1408 void removeHighCoverageNodes(Graph * graph, double maxCov, boolean _export, Coordinate minLength, c… in removeHighCoverageNodes() argument
1414 if (maxCov < 0) in removeHighCoverageNodes()
1417 velvetLog("Applying an upper coverage cutoff of %f...\n", maxCov); in removeHighCoverageNodes()
1434 && getTotalCoverage(node) / getNodeLength(node) > maxCov) { in removeHighCoverageNodes()
|
| /dports/biology/velvet/velvet_1.2.10/src/ |
| H A D | graphStats.h | 69 void removeHighCoverageNodes(Graph * graph, double maxCov, boolean export, Coordinate minLength, ch…
|
| H A D | graphStats.c | 1397 void removeHighCoverageNodes(Graph * graph, double maxCov, boolean export, Coordinate minLength, ch… in removeHighCoverageNodes() argument
1403 if (maxCov < 0) in removeHighCoverageNodes()
1406 velvetLog("Applying an upper coverage cutoff of %f...\n", maxCov); in removeHighCoverageNodes()
1423 && getTotalCoverage(node) / getNodeLength(node) > maxCov) { in removeHighCoverageNodes()
|
| /dports/security/afl++/AFLplusplus-3.14c/custom_mutators/honggfuzz/ |
| H A D | honggfuzz.h | 288 uint64_t maxCov[4]; member
|
| /dports/biology/bbmap/bbmap/current/ukmer/ |
| H A D | KmerTableSetU.java | 1003 contig.maxCov=max; in calcCoverage()
|