| /dports/biology/py-crossmap/CrossMap-0.5.4/lib/cmmodule/ |
| H A D | annoGene.py | 18 cdsEnd = int(f[7])
30 if base > cdsEnd: continue
32 exon_end = min( base+offset, cdsEnd )
53 cdsEnd=int(fields[7])
69 if end > cdsEnd:
70 utr_st = max(st, cdsEnd)
153 cdsEnd=int(fields[7])
169 if end > cdsEnd:
170 utr_st = max(st, cdsEnd)
191 cdsEnd = int(f[7])
[all …]
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| H A D | BED.py | 433 cdsEnd=int(fields[7])
449 if end > cdsEnd:
462 if end > cdsEnd:
481 cdsEnd = int(f[7])
523 cdsEnd = int(f[7])
533 if base > cdsEnd: continue
1113 cdsEnd_float=cdsEnd
1184 cdsEnd_float=cdsEnd
1422 cdsEnd= fields[7] #
2368 cdsEnd = fields[7]
[all …]
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/ucsc_io/ |
| H A D | ucsc_record.h | 92 int32_t cdsEnd; variable
124 UcscRecord() : cdsBegin(0), cdsEnd(0), annotationBeginPos(0), annotationEndPos(0) in UcscRecord()
152 record.cdsEnd = -1; in clear()
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| H A D | ucsc_io.h | 285 record.cdsEnd = lexicalCast<uint32_t>(buffer);
333 std::swap(record.cdsBegin, record.cdsEnd);
387 cdsEndPos = record.cdsEnd;
395 cdsBeginPos = record.cdsEnd;
|
| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/ucsc_io/ |
| H A D | ucsc_record.h | 92 int32_t cdsEnd; variable
124 UcscRecord() : cdsBegin(0), cdsEnd(0), annotationBeginPos(0), annotationEndPos(0) in UcscRecord()
152 record.cdsEnd = -1; in clear()
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| H A D | ucsc_io.h | 285 record.cdsEnd = lexicalCast<uint32_t>(buffer);
333 std::swap(record.cdsBegin, record.cdsEnd);
387 cdsEndPos = record.cdsEnd;
395 cdsBeginPos = record.cdsEnd;
|
| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/ucsc_io/ |
| H A D | ucsc_record.h | 92 __int32 cdsEnd; variable
124 UcscRecord() : cdsBegin(0), cdsEnd(0), annotationBeginPos(0), annotationEndPos(0) in UcscRecord()
152 record.cdsEnd = -1; in clear()
|
| H A D | ucsc_io.h | 285 record.cdsEnd = lexicalCast<__uint32>(buffer);
333 std::swap(record.cdsBegin, record.cdsEnd);
387 cdsEndPos = record.cdsEnd;
395 cdsBeginPos = record.cdsEnd;
|
| /dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/ |
| H A D | gene_reader.py | 102 cdsEnd = int(f[7])
112 if base > cdsEnd:
115 exon_end = min(base+offset, cdsEnd)
188 cdsEnd = int(f[7])
200 if base > cdsEnd:
208 exon_end = min(base+offset, cdsEnd)
|
| /dports/biology/seqan1/seqan-1.3.1/seqan/store/ |
| H A D | store_io_ucsc.h | 103 __int64 cdsEnd; member
209 ctx.cdsEnd = _parseReadNumber(file, c); in _readOneAnnotation()
212 ctx.cdsEnd = TAnnotation::INVALID_POS; in _readOneAnnotation()
257 ctx.cdsBegin = ctx.cdsEnd; in _readOneAnnotation()
258 ctx.cdsEnd = tmp; in _readOneAnnotation()
315 cds.endPos = ctx.cdsEnd; in _storeOneAnnotationKnownGene()
452 ctx.cdsEnd = anno.endPos; in _retrieveOneAnnotation()
517 cdsEndPos = ctx.cdsEnd; in _writeOneAnnotation()
525 cdsBeginPos = ctx.cdsEnd; in _writeOneAnnotation()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/ |
| H A D | EnsemblGtfCodecUnitTest.java | 30 … final String exonId, final int cdsStart, final int cdsEnd) { in createEcoliEnsemblGene() argument
67 …cdsStart, cdsEnd, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, geneId, transcriptId, Genc… in createEcoliEnsemblGene()
85 …cdsEnd+1, cdsEnd+3, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, geneId, transcriptId, Ge… in createEcoliEnsemblGene()
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/ucsc_io/ |
| H A D | test_ucsc_io.cpp | 64 SEQAN_ASSERT_EQ(record.cdsEnd, 33026870); in SEQAN_DEFINE_TEST()
79 SEQAN_ASSERT_EQ(record.cdsEnd, 33040891); in SEQAN_DEFINE_TEST()
188 SEQAN_ASSERT_EQ(record.cdsEnd, 33026870); in SEQAN_DEFINE_TEST()
203 SEQAN_ASSERT_EQ(record.cdsEnd, 33040891); in SEQAN_DEFINE_TEST()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/coverage/DepthOfCoverage/ |
| H A D | refGene_CDK11B.refseq | 1 #bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsS…
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/store/ |
| H A D | store_io_ucsc.h | 85 cds.endPos = record.cdsEnd; in _storeAnnotationRecord()
238 record.cdsEnd = anno.endPos; in _fillAnnotationRecord()
|
| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/store/ |
| H A D | store_io_ucsc.h | 85 cds.endPos = record.cdsEnd; in _storeAnnotationRecord()
238 record.cdsEnd = anno.endPos; in _fillAnnotationRecord()
|
| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/store/ |
| H A D | store_io_ucsc.h | 85 cds.endPos = record.cdsEnd; in _storeAnnotationRecord()
238 record.cdsEnd = anno.endPos; in _fillAnnotationRecord()
|
| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/bedFile/ |
| H A D | bedFile.h | 593 CHRPOS cdsEnd = stoll(fields[7].c_str()); in parseLine() local
596 if (cdsStart > 0 && cdsEnd > 0&& numExons > 0 && in parseLine()
|
| /dports/textproc/datamash/datamash-1.7/examples/ |
| H A D | readme.md | 127 8. cdsEnd - coding end site
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/ |
| H A D | DataProviderForExampleGencodeGtfGene.java | 540 …final int cdsEnd = codingDirection == Strand.POSITIVE ? exon.getGenomicEndLocation() - length3pUt… in createStopCodonExon() local
543 …cdsStart, cdsEnd, codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCR… in createStopCodonExon()
|