| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ |
| H A D | ReblockGVCFUnitTest.java | 16 private final static Allele DELETION = Allele.create("A", false); field in ReblockGVCFUnitTest
28 …final Genotype g0 = makeG("sample1", LONG_REF, DELETION, 41, 0, 37, 200, 100, 200, 400, 600, 800, … in testCleanUpHighQualityVariant()
30 …ontext extraAlt0 = makeDeletionVC("lowQualVar", Arrays.asList(LONG_REF, DELETION, LONG_SNP, Allele… in testCleanUpHighQualityVariant()
38 Assert.assertTrue(cleaned1.getAlleles().contains(DELETION)); in testCleanUpHighQualityVariant()
47 …final Genotype hetNonRef = makeG("sample2", DELETION, LONG_SNP, 891,879,1128,84,0,30,891,879,84,89… in testCleanUpHighQualityVariant()
48 …ontext keepAlts = makeDeletionVC("keepAllAlts", Arrays.asList(LONG_REF, DELETION, LONG_SNP, Allele… in testCleanUpHighQualityVariant()
51 Assert.assertTrue(keepAlts.getAlleles().contains(DELETION)); in testCleanUpHighQualityVariant()
62 …ext toBeNoCalled = makeDeletionVC("lowQualVar", Arrays.asList(LONG_REF, DELETION, Allele.NON_REF_A… in testLowQualVariantToGQ0HomRef()
77 …final VariantContext noData = makeDeletionVC("noData", Arrays.asList(LONG_REF, DELETION, Allele.NO… in testLowQualVariantToGQ0HomRef()
87 …ext toBeNoCalled = makeDeletionVC("lowQualVar", Arrays.asList(LONG_REF, DELETION, Allele.NON_REF_A… in testChangeCallToGQ0HomRef()
[all …]
|
| /dports/devel/eric6/eric6-21.11/eric/eric6/Plugins/VcsPlugins/vcsGit/ |
| H A D | GitDiffParser.py | 171 DELETION = "-"
189 DELETION: 0,
203 (reverse and lineType == DELETION)
209 (not reverse and lineType == DELETION) or
222 if counts[ADDITION] == 0 and counts[DELETION] == 0:
225 oldCount = counts[CONTEXT] + counts[DELETION]
234 startOffset += counts[ADDITION] - counts[DELETION]
|
| /dports/textproc/py-three-merge/three-merge-0.1.1/three_merge/ |
| H A D | merge.py | 15 DELETION = -1 variable
45 if target_status == DELETION:
82 if source_status == DELETION:
124 elif source_status == DELETION and target_status == PRESERVED:
136 elif source_status == PRESERVED and target_status == DELETION:
147 elif source_status == DELETION and target_status == ADDITION:
159 elif source_status == ADDITION and target_status == DELETION:
191 elif source_status == DELETION and target_status == DELETION:
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | CigarBuilder.java | 62 if (removeDeletionsAtEnds && operator == CigarOperator.DELETION) { in add()
97 … } else if (operator == CigarOperator.DELETION && lastOperator == CigarOperator.INSERTION) { in add()
103 … if (size > 1 && cigarElements.get(size - 2).getOperator() == CigarOperator.DELETION) { in add()
104 …CigarElement(cigarElements.get(size-2).getLength() + element.getLength(), CigarOperator.DELETION)); in add()
118 ….size() > 1 && cigarElements.get(cigarElements.size() - 2).getOperator() == CigarOperator.DELETION; in lastTwoElementsWereDeletionAndInsertion()
131 if (removeDeletionsAtEnds && lastOperator == CigarOperator.DELETION) { in make()
|
| /dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.platform.team/bundles/org.eclipse.team.core/src/org/eclipse/team/core/synchronize/ |
| H A D | SyncInfo.java | 88 public static final int DELETION = 2; field in SyncInfo
380 …case DELETION: label = NLS.bind(Messages.concatStrings, new String[] { label, Messages.RemoteSyncE… in kindToString()
440 description = CONFLICTING | DELETION | PSEUDO_CONFLICT; in calculateKind()
443 description = OUTGOING | DELETION; in calculateKind()
450 description = INCOMING | DELETION; in calculateKind()
476 description= DELETION; in calculateKind()
|
| /dports/math/octave-forge-nan/nan-3.6.1/test/ |
| H A D | test_xval.m | 27 …arse', 'MDA/sparse', 'PLA', 'LMS', 'LDA/DELETION', 'MDA/DELETION', 'NBC/DELETION', 'RDA/DELETION',…
|
| H A D | test_fss.m | 37 …A/sparse','MDA/sparse', 'PLA', 'LMS','LDA/DELETION','MDA/DELETION','NBC/DELETION','RDA/DELETION','…
|
| H A D | test_train_sc.m | 26 …'LD6','NBC','aNBC','WienerHopf','PLA', 'LMS','LDA/DELETION','MDA/DELETION','NBC/DELETION','RDA/DEL…
|
| /dports/devel/git-cola/git-cola-3.10.1/cola/ |
| H A D | diffparse.py | 265 DELETION = '-'
294 line_type = DELETION
295 elif line_type == DELETION:
303 if line_type == DELETION:
317 if not counts[ADDITION] and not counts[DELETION]:
320 old_count = counts[CONTEXT] + counts[DELETION]
333 start_offset += counts[ADDITION] - counts[DELETION]
|
| /dports/biology/pbbam/pbbam-0.18.0/tests/src/ |
| H A D | test_Cigar.cpp | 18 EXPECT_EQ('D', CigarOperation::TypeToChar(CigarOperationType::DELETION) ); in TEST()
31 EXPECT_EQ(CigarOperationType::DELETION, CigarOperation::CharToType('D')); in TEST()
44 CigarOperation c3; c3.Type(CigarOperationType::DELETION); in TEST()
77 EXPECT_EQ(CigarOperationType::DELETION, c3.Type()); in TEST()
156 cigar.push_back(CigarOperation(CigarOperationType::DELETION, 2)); in TEST()
|
| /dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.platform.team/bundles/org.eclipse.compare/compare/org/eclipse/compare/ |
| H A D | CompareConfiguration.java | 90 …fgImages[Differencer.DELETION]= CompareUIPlugin.getImageDescriptor("ovr16/del_ov.png"); //$NON-NLS…
91 …fgImages[Differencer.LEFT + Differencer.DELETION]= CompareUIPlugin.getImageDescriptor("ovr16/r_ind…
92 …fgImages[Differencer.RIGHT + Differencer.DELETION]= CompareUIPlugin.getImageDescriptor("ovr16/r_ou…
98 …fgImages[Differencer.CONFLICTING + Differencer.DELETION]= CompareUIPlugin.getImageDescriptor("ovr1…
106 …fgImages[16 + Differencer.DELETION]= CompareUIPlugin.getImageDescriptor("ovr16/del_ov.png"); //$NO…
107 …fgImages[16 + Differencer.LEFT + Differencer.DELETION]= CompareUIPlugin.getImageDescriptor("ovr16/…
108 …fgImages[16 + Differencer.RIGHT + Differencer.DELETION]= CompareUIPlugin.getImageDescriptor("ovr16…
114 …fgImages[16 + Differencer.CONFLICTING + Differencer.DELETION]= CompareUIPlugin.getImageDescriptor(…
|
| /dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.platform.team/tests/org.eclipse.team.tests.cvs.core/src/org/eclipse/team/tests/ccvs/core/subscriber/ |
| H A D | CVSCompareSubscriberTest.java | 100 SyncInfo.DELETION, in testStandardChanges()
102 SyncInfo.DELETION, in testStandardChanges()
124 SyncInfo.DELETION, in testInvalidTag()
125 SyncInfo.DELETION}); in testInvalidTag()
|
| H A D | CVSMergeSubscriberTest.java | 120 SyncInfo.INCOMING | SyncInfo.DELETION, in testIncomingChanges()
136 SyncInfo.OUTGOING | SyncInfo.DELETION, in testIncomingChanges()
309 SyncInfo.OUTGOING | SyncInfo.DELETION, in testUnmergableConflicts()
346 SyncInfo.INCOMING | SyncInfo.DELETION, in testLocalScrub()
350 SyncInfo.INCOMING | SyncInfo.DELETION, in testLocalScrub()
448 SyncInfo.INCOMING | SyncInfo.DELETION, in testOutgoingDeletionAfterMergeBug53129()
449 SyncInfo.INCOMING | SyncInfo.DELETION}); in testOutgoingDeletionAfterMergeBug53129()
457 SyncInfo.OUTGOING | SyncInfo.DELETION, in testOutgoingDeletionAfterMergeBug53129()
458 SyncInfo.OUTGOING | SyncInfo.DELETION}); in testOutgoingDeletionAfterMergeBug53129()
468 SyncInfo.OUTGOING | SyncInfo.DELETION, in testOutgoingDeletionAfterMergeBug53129()
[all …]
|
| H A D | CVSWorkspaceSubscriberTest.java | 382 SyncInfo.INCOMING | SyncInfo.DELETION, in testIncomingChanges()
434 SyncInfo.OUTGOING | SyncInfo.DELETION, in testOutgoingChanges()
472 SyncInfo.OUTGOING | SyncInfo.DELETION, in testOverideAndUpdateSimple()
544 SyncInfo.OUTGOING | SyncInfo.DELETION, in testOverrideOutgoingChanges()
597 SyncInfo.OUTGOING | SyncInfo.DELETION, in testOutgoingQuestionables()
772 SyncInfo.OUTGOING | SyncInfo.DELETION, in testDeletionConflicts()
773 SyncInfo.OUTGOING | SyncInfo.DELETION, in testDeletionConflicts()
775 SyncInfo.OUTGOING | SyncInfo.DELETION, in testDeletionConflicts()
1018 SyncInfo.INCOMING | SyncInfo.DELETION, in testSyncOnBranch()
1056 SyncInfo.OUTGOING | SyncInfo.DELETION, in testDeleteProject()
[all …]
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/utils/ |
| H A D | TagGermlineEventsIntegrationTest.java | 49 …lue(TagGermlineEvents.GERMLINE_TAG_HEADER), CalledCopyRatioSegment.Call.DELETION.getOutputString()… in testBasic()
51 …lue(TagGermlineEvents.GERMLINE_TAG_HEADER), CalledCopyRatioSegment.Call.DELETION.getOutputString()… in testBasic()
79 …lue(TagGermlineEvents.GERMLINE_TAG_HEADER), CalledCopyRatioSegment.Call.DELETION.getOutputString()… in testSlightlyDifferent()
107 …lue(TagGermlineEvents.GERMLINE_TAG_HEADER), CalledCopyRatioSegment.Call.DELETION.getOutputString()… in testSlightlyDifferentAndSplit()
108 …lue(TagGermlineEvents.GERMLINE_TAG_HEADER), CalledCopyRatioSegment.Call.DELETION.getOutputString()… in testSlightlyDifferentAndSplit()
177 …lue(TagGermlineEvents.GERMLINE_TAG_HEADER), CalledCopyRatioSegment.Call.DELETION.getOutputString()… in testSplit()
|
| /dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.platform.team/bundles/org.eclipse.compare/compare/org/eclipse/compare/structuremergeviewer/ |
| H A D | Differencer.java | 74 public static final int DELETION= 2; field in Differencer
365 description= CONFLICTING | DELETION | PSEUDO_CONFLICT; in compare()
368 description= LEFT | DELETION; in compare()
375 description= RIGHT | DELETION; in compare()
406 description= DELETION; in compare()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/smithwaterman/ |
| H A D | SmithWatermanJavaAligner.java | 43 DELETION, enumConstant
320 new_state = State.DELETION; in calculateCigar()
331 case DELETION: p1 -= step_length; break; // move up in calculateCigar()
370 lce.add(makeElement(State.DELETION, p1)); in calculateCigar()
386 case DELETION: op = CigarOperator.D; break; in makeElement()
|
| /dports/math/cvc4/CVC4-1.7/src/proof/drat/ |
| H A D | drat_proof.cpp | 150 case DratInstructionKind::DELETION: in outputAsText()
210 proof.d_instructions.emplace_back(DELETION, in fromBinary()
265 case DELETION: in outputAsLfsc()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/caller/ |
| H A D | SimpleCopyRatioCallerUnitTest.java | 51 …PLIFICATION, AMPLIFICATION, NEUTRAL, NEUTRAL, DELETION, NEUTRAL, AMPLIFICATION, NEUTRAL, DELETION,… in testMakeCalls()
|
| /dports/devel/kdevelop/kdevelop-21.12.3/plugins/projectmanagerview/ |
| H A D | cutcopypastehelpers.cpp | 58 TaskType::DELETION, src, dest); in createDeletion()
83 case TaskType::DELETION: in createPasteStatsWidget()
98 case TaskType::DELETION: in createPasteStatsWidget()
252 … tasks.append(TaskInfo(TaskStatus::SKIPPED, TaskType::DELETION, pathsList, destPath)); in copyMoveItems()
275 … tasks.append(TaskInfo(TaskStatus::SKIPPED, TaskType::DELETION, cl.alienSrcPaths, destPath)); in copyMoveItems()
|
| /dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.platform.team/bundles/org.eclipse.compare.core/src/org/eclipse/compare/internal/core/patch/ |
| H A D | FilePatch2.java | 41 public static final int DELETION= 2; field in FilePatch2
158 } else if (type == DELETION ){ in getDiffType()
165 return DELETION; in getDiffType()
|
| /dports/devel/lazygit/lazygit-0.31.4/pkg/commands/patch/ |
| H A D | patch_parser.go | 21 DELETION const
107 case DELETION:
164 lineKind = DELETION
|
| /dports/devel/doctorj/doctorj-5.1.2/org/incava/text/ |
| H A D | SpellChecker.java | 175 final int DELETION = 1; in compare() local
182 distance[j][0] = distance[j - 1][0] + DELETION; in compare()
189 distance[i - 1][j] + DELETION); in compare()
|
| /dports/deskutils/egroupware/egroupware/vendor/egroupware/z-push-dev/src/lib/core/ |
| H A D | changesmemorywrapper.php | 28 const DELETION = 2; define in ChangesMemoryWrapper
204 $this->changes[] = array(self::DELETION, $id);
230 …return !((array_search(array(self::DELETION, $id), $this->changes) === false) && (array_search(arr…
371 $this->changes[] = array(self::DELETION, $folder);
|
| /dports/www/groupoffice/groupoffice-6.4.231-php-71/modules/z-push/vendor/z-push/lib/core/ |
| H A D | changesmemorywrapper.php | 28 const DELETION = 2; define in ChangesMemoryWrapper
204 $this->changes[] = array(self::DELETION, $id);
230 …return !((array_search(array(self::DELETION, $id), $this->changes) === false) && (array_search(arr…
371 $this->changes[] = array(self::DELETION, $folder);
|