Searched refs:reference_end (Results 1 – 15 of 15) sorted by relevance
| /dports/biology/py-deeptools/deepTools-3.5.1/deeptools/ |
| H A D | bamCoverage.py | 308 …foo = (read.reference_end, read.reference_end + abs(read.template_length) - read.infer_query_lengt…
321 …foo = (read.reference_end, read.reference_end + self.defaultFragmentLength - read.infer_query_leng…
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| H A D | correctGCBias.py | 137 fragEnd = read.reference_end
138 fragStart = read.reference_end + read.template_length
145 fragEnd = read.reference_end
146 fragStart = read.reference_end - fragmentLength
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| H A D | plotEnrichment.py | 216 fragmentEnd = read.reference_end
225 fragmentStart = read.reference_end - defaultFragmentLength
226 fragmentEnd = read.reference_end
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| H A D | countReadsPerBin.py | 881 fragmentEnd = read.reference_end
891 fragmentStart = read.reference_end - self.defaultFragmentLength
892 fragmentEnd = read.reference_end
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| /dports/biology/py-hits/hits-0.1/hits/ |
| H A D | sam.py | 1044 if alignment.reference_start > end or alignment.reference_end - 1 < start:
1048 if alignment.reference_start >= start and alignment.reference_end - 1 <= end:
1152 if left_cropped.reference_end > right_query.reference_start:
1161 if right_cropped.reference_end > left_query.reference_start:
1196 if left_ref.reference_end >= right_ref.reference_start:
1199 deletion_length = right_ref.reference_start - left_ref.reference_end
1583 3: alignment.reference_end - 1,
1587 5: alignment.reference_end - 1,
1594 return interval.Interval(alignment.reference_start, alignment.reference_end - 1)
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| H A D | paired_end.py | 37 max_end = max(R1_m.reference_end, R2_m.reference_end)
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| H A D | sw.py | 724 …gnment_start, initial_al.query_alignment_end, initial_al.reference_start, initial_al.reference_end)
774 …gnment_start, initial_al.query_alignment_end, initial_al.reference_start, initial_al.reference_end)
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| /dports/biology/py-crossmap/CrossMap-0.5.4/lib/cmmodule/ |
| H A D | mapbam.py | 289 read1_end = old_alignment.reference_end
517 read_end = old_alignment.reference_end
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/python/org/broadinstitute/hellbender/vqsr_cnn/vqsr_cnn/ |
| H A D | inference.py | 255 reference_end = variant.pos + index_offset + (window_size % 2)
256 return index_offset, reference_start, reference_end
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| /dports/security/vxquery/vxquery-0.2.1/ |
| H A D | handlers.cc | 426 BasicHandler::reference_end(const Element &element) in reference_end() function in BasicHandler
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/resources/org/broadinstitute/hellbender/tools/walkers/vqsr/ |
| H A D | training.py | 851 reference_end = variant.POS+index_offset
853 return index_offset, reference_start, reference_end
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| /dports/editors/jucipp/jucipp-b3b5182258b25835e7c5f683623ab774d8e34c75/src/ |
| H A D | tooltips.cpp | 838 auto reference_end = i; in insert_markdown() local
846 insert_text(reference_start, reference_end); in insert_markdown()
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| /dports/biology/py-pysam/pysam-0.18.0/pysam/ |
| H A D | libcalignedsegment.pyx | 1630 property reference_end:
1633 reference_end points to one past the last aligned residue.
2680 """deprecated, reference_end instead"""
2682 return self.reference_end
2684 self.reference_end = v
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| /dports/biology/py-pysam/pysam-0.18.0/ |
| H A D | NEWS | 553 * aend -> reference_end
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| /dports/biology/py-pysam/pysam-0.18.0/doc/ |
| H A D | release.rst | 652 * aend -> reference_end
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