| /dports/biology/checkm/CheckM-1.0.18/checkm/util/ |
| H A D | img.py | 432 contigStart = 0
447 contigStart += spacingBetweenContigs + seqLens[curSeqId]
456 genePosition[geneId] = [contigStart + start, contigStart + end]
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/ |
| H A D | ArtificialReadPileupTestProvider.java | 20 final int contigStart = 1; field in ArtificialReadPileupTestProvider
22 …eHeader header = ArtificialReadUtils.createArtificialSamHeader(1, 1, contigStop - contigStart + 1);
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| /dports/biology/velvet/velvet_1.2.10/src/ |
| H A D | graphStats.c | 1552 Graph * graph, Coordinate contigStart, in exportAMOSContig() argument
1562 char *string = expandNodeFragment(node, contigStart, contigFinish, in exportAMOSContig()
1564 Coordinate length = contigFinish - contigStart + wordShift; in exportAMOSContig()
1591 contigStart, contigFinish, wordShift); in exportAMOSContig()
1601 contigStart, contigFinish); in exportAMOSContig()
1613 contigStart, in exportAMOSContig()
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| H A D | graph.h | 135 char *expandNodeFragment(Node * node, Coordinate contigStart,
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| H A D | graph.c | 2691 char *expandNodeFragment(Node * node, Coordinate contigStart, in expandNodeFragment() argument
2697 Coordinate length = contigFinish - contigStart; in expandNodeFragment()
2707 twin->length - contigStart - in expandNodeFragment()
2733 contigStart + index); in expandNodeFragment()
2756 getNucleotideInDescriptor(node->descriptor, contigStart + index); in expandNodeFragment()
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| /dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Velvet-1.1.06/ |
| H A D | graphStats.c | 1563 Graph * graph, Coordinate contigStart, in exportAMOSContig() argument
1573 char *string = expandNodeFragment(node, contigStart, contigFinish, in exportAMOSContig()
1575 Coordinate length = contigFinish - contigStart + wordShift; in exportAMOSContig()
1602 contigStart, contigFinish, wordShift); in exportAMOSContig()
1612 contigStart, contigFinish); in exportAMOSContig()
1624 contigStart, in exportAMOSContig()
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| H A D | graph.h | 135 char *expandNodeFragment(Node * node, Coordinate contigStart,
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| H A D | graph.c | 2489 char *expandNodeFragment(Node * node, Coordinate contigStart, in expandNodeFragment() argument
2495 Coordinate length = contigFinish - contigStart; in expandNodeFragment()
2505 twin->length - contigStart - in expandNodeFragment()
2531 contigStart + index); in expandNodeFragment()
2554 getNucleotideInDescriptor(node->descriptor, contigStart + index); in expandNodeFragment()
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| /dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-v0.3.1/src/ |
| H A D | graph.h | 127 char *expandNodeFragment(Node * node, Coordinate contigStart,
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| H A D | graphStats.c | 2421 Graph * graph, Coordinate contigStart, in exportAMOSContig() argument
2431 char *string = expandNodeFragment(node, contigStart, contigFinish, in exportAMOSContig()
2433 Coordinate length = contigFinish - contigStart + wordShift; in exportAMOSContig()
2460 contigStart, contigFinish, wordShift); in exportAMOSContig()
2470 contigStart, contigFinish); in exportAMOSContig()
2482 contigStart, in exportAMOSContig()
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| H A D | graph.c | 2893 char *expandNodeFragment(Node * node, Coordinate contigStart, in expandNodeFragment() argument
2899 Coordinate length = contigFinish - contigStart; in expandNodeFragment()
2909 twin->length - contigStart - in expandNodeFragment()
2935 contigStart + index); in expandNodeFragment()
2958 getNucleotideInDescriptor(node->descriptor, contigStart + index); in expandNodeFragment()
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