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/dports/science/elmerfem/elmerfem-release-9.0/fem/src/
H A DLinearForms.F9066 REAL(KIND=dp) CONTIG, INTENT(INOUT) :: G(:,:)
67 REAL(KIND=dp) CONTIG, INTENT(IN), OPTIONAL :: alpha(:)
146 REAL(KIND=dp) CONTIG, INTENT(INOUT) :: G(:,:)
269 REAL(KIND=dp) CONTIG, INTENT(INOUT) :: G(:,:)
270 REAL(KIND=dp) CONTIG, INTENT(IN), OPTIONAL :: alpha(:)
340 REAL(KIND=dp) CONTIG, INTENT(IN) :: U(:,:), weight(:) local
341 REAL(KIND=dp) CONTIG, INTENT(INOUT) :: G(:,:)
411 REAL(KIND=dp) CONTIG, INTENT(IN) :: U(:,:), F(:) local
412 REAL(KIND=dp) CONTIG, INTENT(INOUT) :: ProjectToU(:)
421 REAL(KIND=dp) CONTIG, INTENT(IN) :: U(:,:), F(:,:) local
[all …]
H A DSmoothers.F90325 REAL(KIND=dp) CONTIG :: x(:) local
342 REAL(KIND=dp) CONTIG :: x(:),y(:) local
359 COMPLEX(KIND=dp) CONTIG :: x(:),y(:) local
370 REAL(KIND=dp) CONTIG :: x(:), b(:) local
391 COMPLEX(KIND=dp) CONTIG :: x(:), b(:) local
406 REAL(KIND=dp) CONTIG :: x(:),b(:),r(:) local
428 REAL(KIND=dp) CONTIG :: x(:),b(:),r(:) local
565 REAL(KIND=dp) CONTIG :: x(:),b(:),r(:) local
606 REAL(KIND=dp) CONTIG :: x(:),b(:),r(:) local
1417 REAL(KIND=dp) CONTIG :: x(:),b(:) local
[all …]
H A DTypes.F90162 INTEGER, POINTER CONTIG :: ia(:) => NULL(), ja(:) => NULL()
163 REAL(kind=dp), POINTER CONTIG :: aa(:) => NULL(), rhs(:) => NULL(), &
165 INTEGER, POINTER CONTIG :: IParm(:) => NULL()
191 INTEGER, POINTER CONTIG :: Rows(:)=>NULL(),Cols(:)=>NULL(), Diag(:)=>NULL()
194 REAL(KIND=dp), POINTER CONTIG :: BulkResidual(:)=>NULL()
196 REAL(KIND=dp), POINTER CONTIG :: Values(:)=>NULL(), ILUValues(:)=>NULL(), &
323 REAL(KIND=dp), POINTER CONTIG :: &
666 INTEGER, DIMENSION(:), POINTER CONTIG :: &
702 REAL(KIND=dp), POINTER CONTIG :: x(:)=>NULL()
703 REAL(KIND=dp), POINTER CONTIG :: y(:)=>NULL()
[all …]
H A DParallelEigenSolve.F90114 REAL(KIND=dp), POINTER CONTIG :: x(:), b(:)
134 REAL(KIND=dp), POINTER CONTIG :: SaveRhs(:)
687 COMPLEX(KIND=dp), POINTER CONTIG :: x(:), b(:)
1260 REAL(KIND=dp) CONTIG :: x(:),b(:),r(:) local
1281 REAL(KIND=dp) CONTIG :: x(:),b(:),r(:) local
1339 REAL(KIND=dp) CONTIG :: x(:),b(:),r(:) local
1345 REAL(KIND=dp), POINTER CONTIG :: Mx(:),Mb(:),Mr(:)
1412 REAL(KIND=dp) CONTIG :: x(:) local
1425 REAL(KIND=dp) CONTIG :: x(:),y(:) local
1436 REAL(KIND=dp) CONTIG :: x(:), b(:) local
[all …]
H A DH1Basis.F9085 INTEGER, DIMENSION(:), POINTER CONTIG :: flatdir
203 INTEGER, DIMENSION(:), POINTER CONTIG :: flatdir
230 INTEGER, DIMENSION(:), POINTER CONTIG :: flatmap
289 INTEGER, DIMENSION(:), POINTER CONTIG :: flatmap
565 INTEGER, DIMENSION(:) CONTIG, INTENT(IN) :: pmax
597 INTEGER, DIMENSION(:) CONTIG, INTENT(IN) :: pmax
848 INTEGER, DIMENSION(:) CONTIG, INTENT(IN) :: pmax
880 INTEGER, DIMENSION(:) CONTIG, INTENT(IN) :: pmax
1214 INTEGER, DIMENSION(:) CONTIG, INTENT(IN) :: pmax
1245 INTEGER, DIMENSION(:) CONTIG, INTENT(IN) :: pmax
[all …]
/dports/biology/gatk/gatk-4.2.0.0/scripts/funcotator/testing/
H A DgetGencodeGenesForVcfVariants.sh154 CONTIG=$( echo "${line}" | awk '{print $1}' )
155 if [[ $CONTIG != chr* ]] && [[ "${REF}" == "hg19" ]] ; then
156 CONTIG="chr${CONTIG}"
159 ${SCRIPTDIR}/getGeneFromGenomicCoordinates.sh ${REF} ${CONTIG} ${START} ${START}
H A DgetGencodeSequencesForVcfVariants.sh160 CONTIG=$( echo "${line}" | awk '{print $1}' )
161 if [[ $CONTIG != chr* ]] && [[ "${REF}" == "hg19" ]] ; then
162 CONTIG="chr${CONTIG}"
165 ${SCRIPTDIR}/getGeneFromGenomicCoordinates.sh ${REF} ${CONTIG} ${START} ${START}
H A DcreateSimpleGencodeDataSourceFromVariants.sh212 CONTIG=$( echo ${variant} | awk '{print $1}' )
214 …wk "{ if (((\$1 == \"${CONTIG}\") || (\"chr\"\$1 == \"${CONTIG}\" ) || (\$1 == \"chr${CONTIG}\" ) …
H A DgetGeneFromGenomicCoordinates.sh107 CONTIG=$2
121 awk "{ if (\$1 == \"${CONTIG}\" && \$4 <= ${START} && \$5 >= ${END}) {print} }" ${geneList}
/dports/math/py-numpy/numpy-1.20.3/numpy/core/src/umath/
H A Dloops_unary_fp.dispatch.c.src78 #define CONTIG 0
92 * #STYPE = CONTIG, NCONTIG, CONTIG, NCONTIG#
93 * #DTYPE = CONTIG, CONTIG, NCONTIG, NCONTIG#
109 #if @STYPE@ == CONTIG
121 #if @DTYPE@ == CONTIG
130 #if @STYPE@ == CONTIG
144 #if @DTYPE@ == CONTIG
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/contamination/
H A DMinorAlleleFractionRecord.java77 dataLine.set(MinorAlleleFractionTableColumn.CONTIG.toString(), segment.getContig()) in composeLine()
91 final String contig = dataLine.get(MinorAlleleFractionTableColumn.CONTIG); in createRecord()
100 CONTIG("contig"), enumConstant
116 …public static final TableColumnCollection COLUMNS = new TableColumnCollection(CONTIG, START, END, …
/dports/biology/emboss/EMBOSS-6.6.0/doc/programs/master/emboss/apps/inc/
H A Dinfoassembly.usage23 CONTIG LENGTH Mean_QUAL #READS Max DEPTH Mean_DEPTH %GC
53 CONTIG LENGTH Mean_QUAL #READS Max DEPTH Mean_DEPTH %GC
82 CONTIG LENGTH Mean_QUAL #READS Max DEPTH Mean_DEPTH %GC
111 CONTIG LENGTH Mean_QUAL #READS Max DEPTH Mean_DEPTH %GC
/dports/devel/plan9port/plan9port-1f098efb7370a0b28306d10681e21883fb1c1507/src/cmd/eqn/
H A Deqn.y1 %term CONTIG QTEXT SPACE THIN TAB
48 | CONTIG { text(CONTIG, (char *)$1); }
136 text : CONTIG
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/datatype/
H A DDNAInfo.cpp64 const QString DNAInfo::CONTIG = "CONTIG"; member in U2::DNAInfo
91 if (vm.contains(CONTIG)) { in getContig()
92 QVariant v = vm.value(CONTIG); in getContig()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/
H A DReadPosRankSumTestUnitTest.java27 private static final String CONTIG = "1"; field in ReadPosRankSumTestUnitTest
42 ….alleles(Arrays.asList(REF, ALT)).chr(CONTIG).start(position).stop(position).genotypes(testGC).mak… in makeVC()
49 read.setPosition(CONTIG, start); in makeRead()
119 read.setPosition(CONTIG, start); in testIsUsableRead()
192 …w VariantContextBuilder().alleles(Arrays.asList(REF, ALT_INSERTION)).chr(CONTIG).start(start-1).st… in testLeadingInsertion()
H A DLikelihoodRankSumTestUnitTest.java27 private static final String CONTIG = "chr1"; field in LikelihoodRankSumTestUnitTest
44 read.setPosition(CONTIG, 1); in makeRead()
77 final VariantContext vc= makeVC(CONTIG, position, REF, ALT); in testReadPos()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/
H A DStrandBiasUtilsUnitTest.java13 private static final String CONTIG = "1"; field in StrandBiasUtilsUnitTest
24 ….alleles(Arrays.asList(REF, ALT)).chr(CONTIG).start(position).stop(position).genotypes(testGC).mak… in makeVC()
/dports/textproc/heirloom-doctools/heirloom-doctools-160308/eqn/
H A De.y51 %token <str> CONTIG QTEXT SPACE THIN TAB
201 | CONTIG { text(CONTIG, (char *) $1); }
211 text : CONTIG
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/collections/
H A DSimpleIntervalCollection.java25 CONTIG, enumConstant
33 final String contig = dataLine.get(SimpleIntervalTableColumn.CONTIG);
H A DAlleleFractionSegmentCollection.java25 CONTIG, enumConstant
34 final String contig = dataLine.get(AlleleFractionSegmentTableColumn.CONTIG);
H A DLinearCopyRatioCollection.java25 CONTIG, enumConstant
53 final String contig = dataLine.get(DenoisedLocatableCopyRatioTableColumn.CONTIG); in getLinearCopyRatioRecordFromDataLineDecoder()
H A DMultidimensionalSegmentCollection.java23 CONTIG, enumConstant
34 final String contig = dataLine.get(MultidimensionalSegmentTableColumn.CONTIG);
H A DCopyRatioSegmentCollection.java23 CONTIG, enumConstant
33 final String contig = dataLine.get(CopyRatioSegmentTableColumn.CONTIG);
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/
H A DBasicValidationResult.java146 dataLine.set(BasicValidationResultTableColumn.CONTIG.toString(), record.getContig()); in composeLine()
171 final String contig = dataLine.get(BasicValidationResultTableColumn.CONTIG); in createRecord()
196 CONTIG("CONTIG"), enumConstant
223 …public static final TableColumnCollection COLUMNS = new TableColumnCollection(CONTIG, START, END, …
/dports/biology/gatk/gatk-4.2.0.0/src/main/resources/org/broadinstitute/hellbender/tools/funcotator/
H A Dsimple_funcotator_seg_file.config6 # constants in LocatableFuncotationCreator. As of this writing: CONTIG, START, and END.
18 chr:CONTIG,contig,Chromosome,chrom,chromosome,Chrom,seqname,seqnames,CHROM,target_contig,segment_co…

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